Query psy17007
Match_columns 165
No_of_seqs 166 out of 1889
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 19:22:30 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy17007.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/17007hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG2251|consensus 99.8 3.7E-18 8E-23 125.8 8.5 68 39-106 31-98 (228)
2 KOG0488|consensus 99.8 1E-18 2.3E-23 137.6 5.5 70 37-106 164-233 (309)
3 KOG0484|consensus 99.7 6.9E-19 1.5E-23 114.9 1.5 62 41-102 13-74 (125)
4 KOG0487|consensus 99.7 1.3E-18 2.9E-23 135.3 2.9 65 41-105 231-295 (308)
5 KOG0843|consensus 99.7 1.2E-17 2.6E-22 119.4 6.4 63 44-106 101-163 (197)
6 KOG0842|consensus 99.7 1.4E-17 3E-22 129.7 6.9 67 42-108 150-216 (307)
7 KOG0850|consensus 99.7 1.8E-17 3.9E-22 122.7 5.9 69 37-105 114-182 (245)
8 KOG0489|consensus 99.7 4.5E-18 9.7E-23 131.7 2.4 67 42-108 156-222 (261)
9 PF00046 Homeobox: Homeobox do 99.7 2.8E-17 6.1E-22 98.9 2.8 56 46-101 1-56 (57)
10 KOG0490|consensus 99.7 1.2E-16 2.6E-21 121.6 5.9 122 42-163 57-199 (235)
11 KOG0492|consensus 99.7 4.6E-17 9.9E-22 118.8 3.4 64 41-104 140-203 (246)
12 KOG0494|consensus 99.7 1.5E-16 3.3E-21 119.6 6.2 65 44-108 140-204 (332)
13 KOG0848|consensus 99.7 8.8E-17 1.9E-21 121.3 4.2 58 47-104 201-258 (317)
14 KOG0485|consensus 99.6 2.5E-16 5.4E-21 115.7 4.4 63 43-105 102-164 (268)
15 TIGR01565 homeo_ZF_HD homeobox 99.6 8.6E-16 1.9E-20 91.8 5.8 52 46-97 2-57 (58)
16 KOG3802|consensus 99.6 5.9E-16 1.3E-20 123.1 4.9 64 42-105 291-354 (398)
17 smart00389 HOX Homeodomain. DN 99.6 3.1E-15 6.6E-20 89.5 5.3 54 47-100 2-55 (56)
18 KOG0493|consensus 99.6 5E-15 1.1E-19 111.6 6.2 64 45-108 246-309 (342)
19 cd00086 homeodomain Homeodomai 99.5 7.5E-15 1.6E-19 88.6 4.7 56 47-102 2-57 (59)
20 KOG0844|consensus 99.5 1.8E-14 3.9E-19 110.8 3.6 64 40-103 176-239 (408)
21 KOG0491|consensus 99.5 7.7E-15 1.7E-19 103.6 0.6 65 44-108 99-163 (194)
22 KOG0483|consensus 99.5 1.1E-13 2.4E-18 102.3 6.4 62 45-106 50-111 (198)
23 KOG4577|consensus 99.5 1.4E-14 3.1E-19 110.6 1.4 99 11-109 129-231 (383)
24 KOG0486|consensus 99.4 5.4E-14 1.2E-18 108.5 3.9 65 44-108 111-175 (351)
25 COG5576 Homeodomain-containing 99.4 9.3E-14 2E-18 99.3 3.5 65 42-106 48-112 (156)
26 KOG0847|consensus 99.4 9.3E-13 2E-17 97.2 5.9 67 39-105 161-227 (288)
27 KOG1168|consensus 99.2 6E-12 1.3E-16 96.4 0.4 65 43-107 307-371 (385)
28 KOG0849|consensus 99.1 1.2E-10 2.6E-15 93.9 5.9 67 38-104 169-235 (354)
29 TIGR01565 homeo_ZF_HD homeobox 99.0 4.1E-10 8.8E-15 67.3 2.9 46 118-163 2-51 (58)
30 KOG0488|consensus 98.9 7.6E-10 1.7E-14 87.6 3.4 49 114-162 169-217 (309)
31 KOG0775|consensus 98.9 1.4E-09 2.9E-14 83.0 4.0 47 55-101 186-232 (304)
32 KOG0484|consensus 98.8 1.1E-09 2.3E-14 72.0 0.9 51 113-163 13-63 (125)
33 KOG0489|consensus 98.8 4.1E-09 8.9E-14 81.8 3.3 68 88-163 138-205 (261)
34 PF00046 Homeobox: Homeobox do 98.7 6.1E-09 1.3E-13 62.3 2.4 45 119-163 2-46 (57)
35 KOG0843|consensus 98.7 6.5E-09 1.4E-13 74.8 2.6 48 116-163 101-148 (197)
36 KOG2251|consensus 98.7 6.7E-09 1.5E-13 77.1 2.7 52 112-163 32-83 (228)
37 KOG0487|consensus 98.7 4.7E-09 1E-13 82.3 1.8 53 110-162 228-280 (308)
38 KOG0848|consensus 98.7 8.5E-09 1.9E-13 78.5 2.6 52 112-163 194-245 (317)
39 KOG0842|consensus 98.7 9.7E-09 2.1E-13 80.5 2.8 49 114-162 150-198 (307)
40 KOG0850|consensus 98.7 1E-08 2.2E-13 76.5 2.6 53 111-163 116-168 (245)
41 PF05920 Homeobox_KN: Homeobox 98.6 1.1E-08 2.4E-13 56.7 0.5 33 66-98 7-39 (40)
42 KOG0774|consensus 98.6 4E-08 8.7E-13 74.6 3.6 57 45-101 188-247 (334)
43 smart00389 HOX Homeodomain. DN 98.6 5.5E-08 1.2E-12 57.7 3.2 45 119-163 2-46 (56)
44 cd00086 homeodomain Homeodomai 98.5 9.8E-08 2.1E-12 57.1 3.2 45 119-163 2-46 (59)
45 KOG2252|consensus 98.5 2.2E-07 4.8E-12 77.2 5.0 58 43-100 418-475 (558)
46 KOG0492|consensus 98.4 7.7E-08 1.7E-12 70.8 1.8 50 114-163 141-190 (246)
47 KOG0493|consensus 98.4 1.7E-07 3.6E-12 71.3 3.2 76 88-163 213-292 (342)
48 KOG0491|consensus 98.4 1.5E-07 3.3E-12 66.9 1.4 50 114-163 97-146 (194)
49 KOG0485|consensus 98.3 1.6E-07 3.4E-12 69.7 1.2 48 116-163 103-150 (268)
50 KOG0494|consensus 98.3 6.7E-07 1.4E-11 68.0 2.9 50 114-163 137-187 (332)
51 KOG0490|consensus 98.0 5.3E-06 1.1E-10 63.0 2.7 67 39-105 147-213 (235)
52 KOG1146|consensus 97.8 5.3E-05 1.1E-09 68.9 7.1 60 44-103 902-961 (1406)
53 KOG0849|consensus 97.7 3.1E-05 6.8E-10 62.7 3.8 50 114-163 173-222 (354)
54 KOG0486|consensus 97.7 1E-05 2.2E-10 63.2 0.9 47 116-162 111-157 (351)
55 PF11569 Homez: Homeodomain le 97.7 3E-05 6.5E-10 45.7 2.2 43 56-98 9-51 (56)
56 KOG0844|consensus 97.6 9.3E-06 2E-10 63.2 -0.3 48 116-163 180-227 (408)
57 COG5576 Homeodomain-containing 97.5 0.00011 2.4E-09 52.8 3.5 48 116-163 50-97 (156)
58 KOG0483|consensus 97.5 0.00011 2.3E-09 54.7 3.1 45 118-162 51-95 (198)
59 KOG3623|consensus 97.0 0.0015 3.3E-08 56.7 5.4 52 57-108 568-619 (1007)
60 PF05920 Homeobox_KN: Homeobox 97.0 0.00074 1.6E-08 37.3 2.3 26 138-163 7-32 (40)
61 KOG3802|consensus 96.8 0.0023 4.9E-08 51.9 4.9 47 116-162 293-339 (398)
62 KOG0847|consensus 96.7 0.0008 1.7E-08 50.3 1.6 44 120-163 170-213 (288)
63 KOG0773|consensus 96.7 0.0019 4.1E-08 52.1 3.8 57 45-101 239-298 (342)
64 KOG4577|consensus 96.2 0.0028 6E-08 49.4 2.0 48 116-163 166-213 (383)
65 KOG2252|consensus 96.1 0.0088 1.9E-07 50.4 4.5 50 115-164 418-467 (558)
66 KOG0774|consensus 96.0 0.0049 1.1E-07 47.4 2.4 46 117-162 188-236 (334)
67 KOG0775|consensus 95.1 0.018 3.9E-07 44.7 2.6 37 126-162 185-221 (304)
68 KOG1146|consensus 95.0 0.11 2.4E-06 48.2 7.6 119 43-162 703-948 (1406)
69 PF04218 CENP-B_N: CENP-B N-te 94.6 0.077 1.7E-06 31.0 3.9 46 46-96 1-46 (53)
70 PF04967 HTH_10: HTH DNA bindi 92.4 0.064 1.4E-06 31.4 1.0 39 124-162 1-41 (53)
71 COG3413 Predicted DNA binding 85.2 0.4 8.8E-06 36.1 1.0 41 123-163 155-197 (215)
72 KOG1168|consensus 85.0 0.42 9E-06 37.6 1.0 47 116-162 308-354 (385)
73 PF01527 HTH_Tnp_1: Transposas 84.8 1.8 3.9E-05 26.5 3.7 47 47-97 2-48 (76)
74 PF04218 CENP-B_N: CENP-B N-te 84.3 0.49 1.1E-05 27.5 0.9 41 119-164 2-42 (53)
75 PF04967 HTH_10: HTH DNA bindi 84.2 1.9 4.1E-05 25.1 3.3 39 52-90 1-41 (53)
76 cd04764 HTH_MlrA-like_sg1 Heli 83.3 4.1 8.8E-05 24.4 4.8 64 75-165 3-66 (67)
77 PF01710 HTH_Tnp_IS630: Transp 81.2 11 0.00023 25.6 6.7 87 53-163 4-90 (119)
78 cd01104 HTH_MlrA-CarA Helix-Tu 80.9 5.6 0.00012 23.7 4.8 64 75-164 3-66 (68)
79 cd04763 HTH_MlrA-like Helix-Tu 80.8 6 0.00013 23.7 4.9 63 75-164 3-66 (68)
80 PF09607 BrkDBD: Brinker DNA-b 79.5 5.5 0.00012 23.7 4.1 46 49-95 3-48 (58)
81 PRK09413 IS2 repressor TnpA; R 76.8 8.8 0.00019 26.1 5.3 44 48-95 9-52 (121)
82 PF11569 Homez: Homeodomain le 76.2 1.6 3.4E-05 25.8 1.2 34 130-163 11-44 (56)
83 PF10668 Phage_terminase: Phag 75.7 2.2 4.8E-05 25.6 1.7 24 74-97 24-47 (60)
84 PF13551 HTH_29: Winged helix- 75.7 3.7 8E-05 26.9 3.1 85 74-164 14-107 (112)
85 KOG0773|consensus 73.5 3.4 7.3E-05 33.3 2.9 33 65-97 117-149 (342)
86 PF04545 Sigma70_r4: Sigma-70, 73.0 7.3 0.00016 21.8 3.5 39 51-94 4-42 (50)
87 cd01106 HTH_TipAL-Mta Helix-Tu 71.6 11 0.00024 24.7 4.6 21 75-95 3-23 (103)
88 PF13443 HTH_26: Cro/C1-type H 69.5 10 0.00022 22.1 3.7 23 74-96 12-34 (63)
89 cd00131 PAX Paired Box domain 67.3 32 0.00068 23.7 6.3 93 50-156 16-108 (128)
90 PF13936 HTH_38: Helix-turn-he 67.0 4 8.6E-05 22.6 1.4 37 122-163 3-39 (44)
91 PF13411 MerR_1: MerR HTH fami 66.4 12 0.00027 22.2 3.7 63 75-164 3-65 (69)
92 cd04767 HTH_HspR-like_MBC Heli 65.7 16 0.00034 25.1 4.4 45 75-134 4-48 (120)
93 COG3415 Transposase and inacti 65.5 13 0.00028 26.2 4.0 75 74-157 23-97 (138)
94 smart00351 PAX Paired Box doma 64.1 43 0.00094 22.8 6.8 91 51-156 17-108 (125)
95 cd00569 HTH_Hin_like Helix-tur 64.0 16 0.00034 17.7 4.3 38 51-93 5-42 (42)
96 cd06171 Sigma70_r4 Sigma70, re 61.8 9.6 0.00021 20.7 2.5 41 51-96 10-50 (55)
97 PF02796 HTH_7: Helix-turn-hel 60.0 12 0.00026 20.6 2.6 37 122-163 4-40 (45)
98 cd04774 HTH_YfmP Helix-Turn-He 59.8 29 0.00063 22.5 4.8 21 75-95 3-23 (96)
99 COG3413 Predicted DNA binding 58.8 13 0.00029 27.8 3.4 39 51-89 155-195 (215)
100 PF08671 SinI: Anti-repressor 58.6 4.2 9.1E-05 20.8 0.4 17 148-164 9-25 (30)
101 PF08280 HTH_Mga: M protein tr 57.5 6.2 0.00014 23.2 1.1 33 128-164 7-39 (59)
102 PF06056 Terminase_5: Putative 57.4 9.3 0.0002 22.6 1.9 21 74-94 15-35 (58)
103 smart00422 HTH_MERR helix_turn 56.8 39 0.00084 19.9 4.8 64 75-164 3-66 (70)
104 TIGR03879 near_KaiC_dom probab 56.3 5.4 0.00012 24.9 0.7 34 63-96 23-56 (73)
105 cd01109 HTH_YyaN Helix-Turn-He 55.1 42 0.0009 22.3 5.1 21 75-95 3-23 (113)
106 cd01105 HTH_GlnR-like Helix-Tu 55.1 32 0.0007 21.8 4.3 47 75-135 4-51 (88)
107 cd04765 HTH_MlrA-like_sg2 Heli 54.5 35 0.00077 22.3 4.5 47 75-135 3-50 (99)
108 cd04761 HTH_MerR-SF Helix-Turn 54.5 11 0.00024 20.6 1.8 21 75-95 3-23 (49)
109 TIGR02047 CadR-PbrR Cd(II)/Pb( 54.1 37 0.0008 23.2 4.7 21 75-95 3-23 (127)
110 PF08281 Sigma70_r4_2: Sigma-7 53.9 27 0.00058 19.6 3.5 39 52-95 11-49 (54)
111 COG4367 Uncharacterized protei 53.3 26 0.00056 22.7 3.5 39 52-90 3-41 (97)
112 PRK10072 putative transcriptio 51.9 15 0.00032 24.1 2.3 41 51-98 32-72 (96)
113 PF13518 HTH_28: Helix-turn-he 51.9 12 0.00027 20.7 1.8 22 75-96 15-36 (52)
114 cd04768 HTH_BmrR-like Helix-Tu 51.6 48 0.001 21.4 4.8 21 75-95 3-23 (96)
115 cd01110 HTH_SoxR Helix-Turn-He 51.4 37 0.00081 23.7 4.5 21 75-95 4-24 (139)
116 cd04773 HTH_TioE_rpt2 Second H 51.4 46 0.001 22.0 4.8 21 75-95 3-23 (108)
117 PHA02955 hypothetical protein; 51.3 26 0.00057 26.5 3.8 43 54-96 60-103 (213)
118 PF13384 HTH_23: Homeodomain-l 51.0 14 0.0003 20.4 1.9 22 74-95 19-40 (50)
119 PF00196 GerE: Bacterial regul 50.6 29 0.00062 20.0 3.3 43 51-99 3-45 (58)
120 TIGR02044 CueR Cu(I)-responsiv 49.3 47 0.001 22.6 4.7 21 75-95 3-23 (127)
121 TIGR02054 MerD mercuric resist 48.7 50 0.0011 22.6 4.6 22 74-95 5-26 (120)
122 cd04779 HTH_MerR-like_sg4 Heli 48.5 47 0.001 23.1 4.6 21 75-95 3-23 (134)
123 TIGR01950 SoxR redox-sensitive 48.1 45 0.00097 23.4 4.5 21 75-95 4-24 (142)
124 cd00592 HTH_MerR-like Helix-Tu 47.5 44 0.00096 21.4 4.2 48 75-136 3-50 (100)
125 cd04788 HTH_NolA-AlbR Helix-Tu 47.0 61 0.0013 20.9 4.7 21 75-95 3-23 (96)
126 cd04775 HTH_Cfa-like Helix-Tur 46.9 63 0.0014 21.1 4.8 21 75-95 4-24 (102)
127 cd01282 HTH_MerR-like_sg3 Heli 46.9 57 0.0012 21.7 4.7 21 75-95 3-23 (112)
128 cd04782 HTH_BltR Helix-Turn-He 46.8 67 0.0015 20.7 4.9 21 75-95 3-23 (97)
129 COG4367 Uncharacterized protei 46.7 9.1 0.0002 24.7 0.7 40 125-164 4-43 (97)
130 PF11212 DUF2999: Protein of u 46.1 13 0.00029 23.1 1.3 39 123-165 12-50 (82)
131 PF01257 2Fe-2S_thioredx: Thio 46.1 13 0.00028 26.2 1.5 36 130-165 17-52 (145)
132 TIGR02043 ZntR Zn(II)-responsi 44.9 59 0.0013 22.3 4.6 21 75-95 4-24 (131)
133 TIGR01958 nuoE_fam NADH-quinon 44.5 24 0.00052 24.9 2.6 29 137-165 27-55 (148)
134 cd04785 HTH_CadR-PbrR-like Hel 44.4 63 0.0014 22.0 4.7 21 75-95 3-23 (126)
135 PRK05988 formate dehydrogenase 44.1 23 0.00049 25.4 2.5 29 137-165 34-62 (156)
136 COG2963 Transposase and inacti 44.1 58 0.0013 21.6 4.4 43 49-95 5-48 (116)
137 cd04766 HTH_HspR Helix-Turn-He 44.0 72 0.0016 20.2 4.7 21 75-95 4-24 (91)
138 cd04781 HTH_MerR-like_sg6 Heli 43.0 70 0.0015 21.5 4.7 21 75-95 3-23 (120)
139 PRK09514 zntR zinc-responsive 42.8 64 0.0014 22.5 4.6 21 75-95 4-24 (140)
140 cd04789 HTH_Cfa Helix-Turn-Hel 42.7 81 0.0018 20.6 4.8 21 75-95 4-24 (102)
141 PF01381 HTH_3: Helix-turn-hel 42.0 30 0.00064 19.4 2.4 23 75-97 12-34 (55)
142 cd01111 HTH_MerD Helix-Turn-He 41.8 75 0.0016 21.0 4.6 21 75-95 3-23 (107)
143 cd04762 HTH_MerR-trunc Helix-T 41.5 23 0.0005 18.9 1.8 22 75-96 3-24 (49)
144 PRK07539 NADH dehydrogenase su 40.9 28 0.00061 24.8 2.5 29 137-165 33-61 (154)
145 cd08318 Death_NMPP84 Death dom 40.6 21 0.00046 22.7 1.7 34 124-164 5-38 (86)
146 PF00376 MerR: MerR family reg 40.6 27 0.00058 18.6 1.8 21 75-95 2-22 (38)
147 PRK07571 bidirectional hydroge 40.5 27 0.00059 25.4 2.5 29 137-165 47-75 (169)
148 PF03672 UPF0154: Uncharacteri 40.1 34 0.00074 20.7 2.4 35 130-164 20-56 (64)
149 cd01108 HTH_CueR Helix-Turn-He 40.1 78 0.0017 21.5 4.6 21 75-95 3-23 (127)
150 cd04770 HTH_HMRTR Helix-Turn-H 40.0 84 0.0018 21.1 4.7 21 75-95 3-23 (123)
151 cd01392 HTH_LacI Helix-turn-he 39.5 22 0.00047 19.7 1.5 20 77-96 2-21 (52)
152 TIGR03643 conserved hypothetic 39.2 18 0.00038 22.5 1.1 20 146-165 15-34 (72)
153 TIGR02051 MerR Hg(II)-responsi 39.1 67 0.0014 21.8 4.1 19 75-93 2-20 (124)
154 PRK09480 slmA division inhibit 39.0 35 0.00076 24.4 2.9 38 59-97 18-55 (194)
155 PF06971 Put_DNA-bind_N: Putat 38.9 22 0.00048 20.4 1.4 16 147-162 31-46 (50)
156 COG1905 NuoE NADH:ubiquinone o 38.8 64 0.0014 23.3 4.1 37 54-90 25-61 (160)
157 cd01279 HTH_HspR-like Helix-Tu 38.0 1E+02 0.0022 19.9 4.8 47 75-135 4-50 (98)
158 PRK13558 bacterio-opsin activa 37.9 18 0.00039 31.6 1.4 41 122-162 606-648 (665)
159 TIGR03070 couple_hipB transcri 37.2 36 0.00078 18.9 2.2 22 75-96 18-39 (58)
160 smart00027 EH Eps15 homology d 36.8 1.1E+02 0.0023 19.5 4.6 44 51-94 3-51 (96)
161 PRK15002 redox-sensitivie tran 36.6 89 0.0019 22.3 4.6 23 74-96 13-35 (154)
162 PF15063 TC1: Thyroid cancer p 36.6 83 0.0018 19.8 3.8 37 49-85 31-67 (79)
163 PF13404 HTH_AsnC-type: AsnC-t 36.6 26 0.00056 19.1 1.4 17 146-162 19-35 (42)
164 PF08765 Mor: Mor transcriptio 36.5 16 0.00034 24.3 0.6 20 146-165 74-93 (108)
165 PRK13890 conjugal transfer pro 36.4 1.1E+02 0.0023 20.8 4.8 22 75-96 21-42 (120)
166 PF12244 DUF3606: Protein of u 35.7 32 0.00069 20.2 1.8 20 145-164 21-40 (57)
167 PF10078 DUF2316: Uncharacteri 35.6 7.8 0.00017 25.1 -0.9 32 130-165 13-44 (89)
168 cd08313 Death_TNFR1 Death doma 35.3 43 0.00094 21.2 2.5 21 144-164 11-31 (80)
169 cd04783 HTH_MerR1 Helix-Turn-H 35.1 1.1E+02 0.0024 20.6 4.8 20 75-94 3-22 (126)
170 cd04784 HTH_CadR-PbrR Helix-Tu 35.1 1.1E+02 0.0023 20.8 4.6 21 75-95 3-23 (127)
171 cd08306 Death_FADD Fas-associa 35.0 29 0.00063 22.1 1.7 19 146-164 15-33 (86)
172 cd08319 Death_RAIDD Death doma 35.0 30 0.00065 22.0 1.7 19 146-164 15-33 (83)
173 PF08667 BetR: BetR domain; I 33.6 1.3E+02 0.0029 21.4 5.0 58 56-138 6-63 (147)
174 PF10985 DUF2805: Protein of u 33.2 25 0.00054 21.9 1.1 19 147-165 15-33 (73)
175 smart00421 HTH_LUXR helix_turn 32.9 87 0.0019 17.0 3.7 39 51-95 3-41 (58)
176 cd04787 HTH_HMRTR_unk Helix-Tu 32.7 1.2E+02 0.0027 20.7 4.7 20 75-94 3-22 (133)
177 PF04539 Sigma70_r3: Sigma-70 32.4 21 0.00046 21.8 0.7 19 146-164 22-40 (78)
178 PRK03975 tfx putative transcri 32.2 48 0.001 23.4 2.5 45 49-99 4-48 (141)
179 cd08315 Death_TRAILR_DR4_DR5 D 32.2 43 0.00093 21.9 2.2 35 130-164 4-39 (96)
180 PRK04217 hypothetical protein; 31.9 34 0.00073 23.1 1.7 45 115-164 34-78 (110)
181 cd01670 Death Death Domain: a 31.8 35 0.00076 20.7 1.7 19 146-164 12-30 (79)
182 COG1905 NuoE NADH:ubiquinone o 31.6 49 0.0011 23.9 2.5 37 128-164 27-63 (160)
183 PF08880 QLQ: QLQ; InterPro: 31.0 52 0.0011 17.5 2.0 15 50-64 1-15 (37)
184 PRK05988 formate dehydrogenase 30.6 1.1E+02 0.0024 21.8 4.3 36 55-90 24-59 (156)
185 cd06170 LuxR_C_like C-terminal 30.3 72 0.0016 17.4 2.8 37 53-95 2-38 (57)
186 TIGR01764 excise DNA binding d 29.9 53 0.0012 17.4 2.1 22 75-96 4-25 (49)
187 PHA01976 helix-turn-helix prot 29.7 55 0.0012 19.1 2.2 22 75-96 18-39 (67)
188 COG2944 Predicted transcriptio 28.7 57 0.0012 21.8 2.3 43 51-100 43-85 (104)
189 PF12824 MRP-L20: Mitochondria 28.6 2.3E+02 0.005 20.5 5.8 41 49-91 83-123 (164)
190 cd00131 PAX Paired Box domain 28.4 2E+02 0.0043 19.7 6.1 46 51-96 75-127 (128)
191 PRK10227 DNA-binding transcrip 28.3 1.6E+02 0.0035 20.4 4.7 21 75-95 3-23 (135)
192 PF12728 HTH_17: Helix-turn-he 28.3 53 0.0012 18.1 1.9 22 75-96 4-25 (51)
193 PRK07539 NADH dehydrogenase su 28.2 1.3E+02 0.0028 21.3 4.2 35 56-90 24-58 (154)
194 PF00440 TetR_N: Bacterial reg 28.1 53 0.0012 17.9 1.8 35 61-96 6-40 (47)
195 PF00531 Death: Death domain; 28.1 43 0.00094 20.4 1.6 17 148-164 16-32 (83)
196 cd00093 HTH_XRE Helix-turn-hel 27.8 65 0.0014 16.9 2.2 22 75-96 15-36 (58)
197 cd04790 HTH_Cfa-like_unk Helix 27.6 1.9E+02 0.0042 20.8 5.2 21 75-95 4-24 (172)
198 TIGR00270 conserved hypothetic 27.4 1.8E+02 0.004 20.7 4.9 22 75-96 85-106 (154)
199 cd08777 Death_RIP1 Death Domai 27.3 48 0.001 21.2 1.7 19 146-164 15-33 (86)
200 PRK06759 RNA polymerase factor 27.3 1.1E+02 0.0023 21.0 3.7 22 74-95 124-145 (154)
201 PF12824 MRP-L20: Mitochondria 27.0 61 0.0013 23.5 2.4 41 121-163 83-123 (164)
202 PF08279 HTH_11: HTH domain; 26.5 55 0.0012 18.3 1.8 18 146-163 17-34 (55)
203 TIGR01958 nuoE_fam NADH-quinon 26.5 1.4E+02 0.0031 20.9 4.2 36 55-90 17-52 (148)
204 PF13730 HTH_36: Helix-turn-he 26.2 42 0.00092 18.8 1.2 19 146-164 27-45 (55)
205 PF04936 DUF658: Protein of un 26.1 64 0.0014 23.5 2.3 28 74-101 16-43 (186)
206 TIGR02607 antidote_HigA addict 25.6 69 0.0015 19.3 2.2 22 75-96 21-42 (78)
207 PRK13182 racA polar chromosome 25.6 2.1E+02 0.0045 20.9 5.0 21 75-95 3-23 (175)
208 cd04777 HTH_MerR-like_sg1 Heli 25.3 1.9E+02 0.0041 18.9 4.4 21 75-95 3-23 (107)
209 PF01257 2Fe-2S_thioredx: Thio 25.3 1.3E+02 0.0028 21.0 3.8 35 56-90 15-49 (145)
210 PF08452 DNAP_B_exo_N: DNA pol 25.2 24 0.00053 16.4 0.0 9 90-98 6-14 (22)
211 cd08317 Death_ank Death domain 25.1 55 0.0012 20.5 1.7 19 146-164 17-35 (84)
212 PRK07571 bidirectional hydroge 24.9 1.6E+02 0.0035 21.4 4.3 34 57-90 39-72 (169)
213 PF00325 Crp: Bacterial regula 24.8 62 0.0013 16.7 1.5 16 146-161 4-19 (32)
214 PRK09975 DNA-binding transcrip 24.7 82 0.0018 22.9 2.8 39 58-97 18-56 (213)
215 TIGR03629 arch_S13P archaeal r 24.7 83 0.0018 22.3 2.7 16 51-66 51-66 (144)
216 COG0789 SoxR Predicted transcr 24.5 2E+02 0.0043 18.9 4.6 21 75-95 3-23 (124)
217 PF12844 HTH_19: Helix-turn-he 24.1 81 0.0018 18.2 2.2 24 74-97 14-37 (64)
218 PRK11511 DNA-binding transcrip 23.9 72 0.0016 21.6 2.2 24 72-95 25-48 (127)
219 PRK06424 transcription factor; 23.8 1.5E+02 0.0032 21.0 3.8 24 75-98 100-123 (144)
220 PF13565 HTH_32: Homeodomain-l 23.7 1.7E+02 0.0037 17.4 6.0 32 53-84 32-64 (77)
221 PRK14996 TetR family transcrip 23.6 94 0.002 22.2 3.0 40 58-98 15-54 (192)
222 cd08804 Death_ank2 Death domai 23.2 64 0.0014 20.4 1.7 18 147-164 18-35 (84)
223 PF13412 HTH_24: Winged helix- 22.9 46 0.00099 18.2 0.9 19 146-164 19-37 (48)
224 COG5484 Uncharacterized conser 22.8 54 0.0012 25.6 1.5 30 69-98 16-45 (279)
225 cd01107 HTH_BmrR Helix-Turn-He 22.7 2.3E+02 0.005 18.5 5.1 21 75-95 3-23 (108)
226 cd08311 Death_p75NR Death doma 22.5 62 0.0014 20.2 1.6 19 146-164 17-35 (77)
227 smart00530 HTH_XRE Helix-turn- 22.4 96 0.0021 16.0 2.3 22 75-96 13-34 (56)
228 smart00005 DEATH DEATH domain, 22.4 67 0.0015 19.9 1.7 20 145-164 18-37 (88)
229 PRK11552 putative DNA-binding 22.4 96 0.0021 23.2 2.8 39 58-98 20-58 (225)
230 cd08784 Death_DRs Death Domain 22.2 1E+02 0.0022 19.1 2.5 20 145-164 12-31 (79)
231 cd08779 Death_PIDD Death Domai 22.2 68 0.0015 20.4 1.7 19 146-164 15-33 (86)
232 PF05263 DUF722: Protein of un 22.0 1.4E+02 0.003 20.8 3.3 21 74-94 101-121 (130)
233 cd04776 HTH_GnyR Helix-Turn-He 21.4 2.5E+02 0.0054 18.8 4.5 20 75-94 3-22 (118)
234 PRK09652 RNA polymerase sigma 21.1 1.5E+02 0.0033 20.6 3.6 40 51-95 128-167 (182)
235 PRK00118 putative DNA-binding 20.9 2.1E+02 0.0045 19.0 3.9 44 51-99 17-60 (104)
236 PF13560 HTH_31: Helix-turn-he 20.7 1E+02 0.0023 17.8 2.2 25 74-98 16-40 (64)
237 cd04769 HTH_MerR2 Helix-Turn-H 20.7 2.7E+02 0.0058 18.5 4.7 21 75-95 3-23 (116)
238 TIGR03826 YvyF flagellar opero 20.5 1.5E+02 0.0033 20.8 3.3 27 74-100 48-74 (137)
239 PRK09706 transcriptional repre 20.2 94 0.002 21.2 2.2 25 75-99 21-45 (135)
No 1
>KOG2251|consensus
Probab=99.75 E-value=3.7e-18 Score=125.75 Aligned_cols=68 Identities=34% Similarity=0.459 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS 106 (165)
Q Consensus 39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~ 106 (165)
....+|.||.||+|+..|+++||.+|.++.||++..+++||.+|+|.+.+|+|||.|||+|+++....
T Consensus 31 ~~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 31 SSGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred CccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 36778999999999999999999999999999999999999999999999999999999999876543
No 2
>KOG0488|consensus
Probab=99.75 E-value=1e-18 Score=137.64 Aligned_cols=70 Identities=53% Similarity=0.725 Sum_probs=64.0
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007 37 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS 106 (165)
Q Consensus 37 ~~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~ 106 (165)
......+|.|+.||.||..|+..||+.|+..+|++..+|.+||..|||+..||++||||||+|+|+....
T Consensus 164 ~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 164 YQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3455668889999999999999999999999999999999999999999999999999999999875544
No 3
>KOG0484|consensus
Probab=99.73 E-value=6.9e-19 Score=114.90 Aligned_cols=62 Identities=34% Similarity=0.535 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007 41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL 102 (165)
Q Consensus 41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~ 102 (165)
..+|+||-||+||..||.+||..|.+..||++-.|++||.++.|++..|++||||||+|.+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 45788999999999999999999999999999999999999999999999999999999764
No 4
>KOG0487|consensus
Probab=99.73 E-value=1.3e-18 Score=135.32 Aligned_cols=65 Identities=38% Similarity=0.557 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
..++.|++|+.||+.|+.+||+.|.-|.|++.+.|.+|+..|+|+++||+|||||||.|+|++..
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 34788999999999999999999999999999999999999999999999999999999987663
No 5
>KOG0843|consensus
Probab=99.72 E-value=1.2e-17 Score=119.39 Aligned_cols=63 Identities=44% Similarity=0.656 Sum_probs=59.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS 106 (165)
Q Consensus 44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~ 106 (165)
+.+|.||.|+.+|+..||..|+.+.|....+|+.||..|+|++.||+|||||||.|.|+....
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 778999999999999999999999999999999999999999999999999999999876544
No 6
>KOG0842|consensus
Probab=99.71 E-value=1.4e-17 Score=129.67 Aligned_cols=67 Identities=46% Similarity=0.674 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
..++||.|..||..|+-+||..|....|++..||+.||..|+||..||||||||||.|.||......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 4566777888999999999999999999999999999999999999999999999999998665543
No 7
>KOG0850|consensus
Probab=99.70 E-value=1.8e-17 Score=122.70 Aligned_cols=69 Identities=43% Similarity=0.655 Sum_probs=64.3
Q ss_pred CCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 37 ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 37 ~~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
..+++.+|.|+.||.|+.-||..|...|++++|+-..||.+||..|||+..||+|||||||.|.|....
T Consensus 114 ~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 114 RPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred ccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 358889999999999999999999999999999999999999999999999999999999999876443
No 8
>KOG0489|consensus
Probab=99.70 E-value=4.5e-18 Score=131.72 Aligned_cols=67 Identities=37% Similarity=0.558 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
.++.||.||.||..|+.+||+.|.-|.|+++..|.+||..|+|+++||+|||||||+|+|+......
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3567999999999999999999999999999999999999999999999999999999987554443
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.67 E-value=2.8e-17 Score=98.93 Aligned_cols=56 Identities=46% Similarity=0.652 Sum_probs=53.4
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS 101 (165)
Q Consensus 46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~ 101 (165)
|+.|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|.+.+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 57789999999999999999999999999999999999999999999999998764
No 10
>KOG0490|consensus
Probab=99.66 E-value=1.2e-16 Score=121.61 Aligned_cols=122 Identities=32% Similarity=0.357 Sum_probs=104.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC--CCCcc---------
Q psy17007 42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST--SPHEL--------- 110 (165)
Q Consensus 42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~--~~~~~--------- 110 (165)
..++++.|+.|+..|+++|+..|+.++||+...++.||..+++++..|++||||+|++.+.... .....
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~ 136 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAP 136 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCC
Confidence 5678899999999999999999999999999999999999999999999999999999875441 11100
Q ss_pred ----------CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 111 ----------GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 111 ----------~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.....+.++.++.+...|+..+...|..+.+|+...+..|+..+|+++..|+-
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~ 199 (235)
T KOG0490|consen 137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQV 199 (235)
T ss_pred ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhh
Confidence 11123556678899999999999999999999999999999999999987763
No 11
>KOG0492|consensus
Probab=99.66 E-value=4.6e-17 Score=118.78 Aligned_cols=64 Identities=47% Similarity=0.748 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007 41 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS 104 (165)
Q Consensus 41 ~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~ 104 (165)
+.+-+|+.|+.||..||..||..|.+.+|+++.+|.+++..|.|++.||+|||||||+|.|+.+
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 4455678899999999999999999999999999999999999999999999999999998754
No 12
>KOG0494|consensus
Probab=99.66 E-value=1.5e-16 Score=119.58 Aligned_cols=65 Identities=34% Similarity=0.456 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
++|+.||.||..|++.||+.|++..||+..-|+.||.++.|.+++|+|||||||+|+++......
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 34445999999999999999999999999999999999999999999999999999987655443
No 13
>KOG0848|consensus
Probab=99.65 E-value=8.8e-17 Score=121.35 Aligned_cols=58 Identities=47% Similarity=0.659 Sum_probs=54.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS 104 (165)
Q Consensus 47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~ 104 (165)
+.|.+||+.|..+||+.|..+.|+++..+.+||..|||+++||+|||||||+|+++..
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 5688999999999999999999999999999999999999999999999999997543
No 14
>KOG0485|consensus
Probab=99.63 E-value=2.5e-16 Score=115.71 Aligned_cols=63 Identities=52% Similarity=0.679 Sum_probs=59.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
.++|+.||+|+..|+..||..|+...|++..+|..||..|.|++.||+|||||||.|+|+...
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 477888999999999999999999999999999999999999999999999999999987543
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=99.63 E-value=8.6e-16 Score=91.80 Aligned_cols=52 Identities=19% Similarity=0.323 Sum_probs=50.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007 46 RKARTVFSDHQLTGLEKRFEAQRY----LSTPERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 46 rr~R~~~s~~q~~~Le~~f~~~~~----p~~~~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
+|.||.||.+|++.|+..|..+.| |+..++++||..+||++.+|++||+|.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 788999999999999999999999 9999999999999999999999999964
No 16
>KOG3802|consensus
Probab=99.61 E-value=5.9e-16 Score=123.07 Aligned_cols=64 Identities=30% Similarity=0.401 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
..|+||+||.|....+..||.+|.+|+.|+.+++..||.+|+|..++|+|||||||.|+||...
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3478899999999999999999999999999999999999999999999999999999999877
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.58 E-value=3.1e-15 Score=89.53 Aligned_cols=54 Identities=52% Similarity=0.682 Sum_probs=51.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG 100 (165)
Q Consensus 47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~ 100 (165)
+.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|+.||+|+|++.
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 567789999999999999999999999999999999999999999999999875
No 18
>KOG0493|consensus
Probab=99.56 E-value=5e-15 Score=111.61 Aligned_cols=64 Identities=38% Similarity=0.595 Sum_probs=58.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
-+|.||.||.+||..|...|+.+.|++...|..||.+|+|.+.||+|||||+|+|-|....+..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn 309 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKN 309 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCC
Confidence 3577999999999999999999999999999999999999999999999999999987555443
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.55 E-value=7.5e-15 Score=88.61 Aligned_cols=56 Identities=50% Similarity=0.640 Sum_probs=52.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccc
Q psy17007 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSL 102 (165)
Q Consensus 47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~ 102 (165)
+.+..|+.+++..|+.+|..++||+..++..||..+||+..+|++||+|+|.+.+.
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 46789999999999999999999999999999999999999999999999988754
No 20
>KOG0844|consensus
Probab=99.48 E-value=1.8e-14 Score=110.79 Aligned_cols=64 Identities=44% Similarity=0.629 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007 40 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF 103 (165)
Q Consensus 40 ~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~ 103 (165)
+.+..-||.||.||.+|+..||+.|-+.+|-+...|.+||..|+|.+..|++||||||.|+|+.
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 4455678999999999999999999999999999999999999999999999999999999874
No 21
>KOG0491|consensus
Probab=99.47 E-value=7.7e-15 Score=103.58 Aligned_cols=65 Identities=72% Similarity=0.936 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
+.++.|++|+..|+..|++.|+...|.+-.++.+||..|+|++.||+.||||||.|.|+......
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 45677999999999999999999999999999999999999999999999999999987654443
No 22
>KOG0483|consensus
Probab=99.47 E-value=1.1e-13 Score=102.30 Aligned_cols=62 Identities=29% Similarity=0.389 Sum_probs=56.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007 45 RRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS 106 (165)
Q Consensus 45 ~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~ 106 (165)
..+++.+|+.+|+..||..|....+.....+..||..|||..+||.+|||||||++|..+..
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE 111 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLE 111 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhh
Confidence 44556689999999999999999999999999999999999999999999999999875543
No 23
>KOG4577|consensus
Probab=99.46 E-value=1.4e-14 Score=110.61 Aligned_cols=99 Identities=18% Similarity=0.258 Sum_probs=81.3
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccch
Q psy17007 11 YLHKSDSFYITPQGLPFGSLFSTSPHELG----SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSE 86 (165)
Q Consensus 11 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~ 86 (165)
.+.+.+.||++.....+.-.+..+..... ..+...+|.||++|..||+-|...|...+.|-...|+.|+.++||.-
T Consensus 129 ~L~TGdEFYLmeD~rLvCK~DYE~Ak~k~~~~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDM 208 (383)
T KOG4577|consen 129 QLATGDEFYLMEDARLVCKDDYETAKQKHCNELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDM 208 (383)
T ss_pred ccccCCeeEEeccceeehhhhHHHHHhccccccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcce
Confidence 45677888888877776655544433221 23445688999999999999999999999999999999999999999
Q ss_pred hhhhhhhccCCCCccccCCCCCc
Q psy17007 87 TQVKTWFQNRLPFGSLFSTSPHE 109 (165)
Q Consensus 87 ~~V~~WF~nrr~~~~~~~~~~~~ 109 (165)
+.||+||||||+|+|+..+..+.
T Consensus 209 RVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 209 RVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred eehhhhhhhhhHHHHhhhhhcch
Confidence 99999999999999987766653
No 24
>KOG0486|consensus
Probab=99.45 E-value=5.4e-14 Score=108.54 Aligned_cols=65 Identities=32% Similarity=0.524 Sum_probs=60.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
|+||.|+.|+.+|+.+||..|..+.||+...|++||.-++|++..|++||.|||+|++..+....
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 78899999999999999999999999999999999999999999999999999999976554443
No 25
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.43 E-value=9.3e-14 Score=99.35 Aligned_cols=65 Identities=28% Similarity=0.419 Sum_probs=58.3
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCC
Q psy17007 42 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTS 106 (165)
Q Consensus 42 ~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~ 106 (165)
.+..+++|.+-+.+|+.+|+..|..++||+...+..|+..++|+++-|++||||+|++.+.....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34556777888999999999999999999999999999999999999999999999999765444
No 26
>KOG0847|consensus
Probab=99.37 E-value=9.3e-13 Score=97.16 Aligned_cols=67 Identities=36% Similarity=0.622 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
..++++++..|.+|+..|+..|+..|+..+|+-..++.+||..+|+++.+|+|||||||.|++....
T Consensus 161 ~~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 161 PNLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 4466778888999999999999999999999999999999999999999999999999999976543
No 27
>KOG1168|consensus
Probab=99.16 E-value=6e-12 Score=96.42 Aligned_cols=65 Identities=23% Similarity=0.318 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCC
Q psy17007 43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSP 107 (165)
Q Consensus 43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~ 107 (165)
..++|+||.+..-+...||++|...+.|+.+.+..||++|+|..+.|++||||+|.|.|++..+.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 34678899999999999999999999999999999999999999999999999999998865443
No 28
>KOG0849|consensus
Probab=99.11 E-value=1.2e-10 Score=93.86 Aligned_cols=67 Identities=33% Similarity=0.361 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccC
Q psy17007 38 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFS 104 (165)
Q Consensus 38 ~~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~ 104 (165)
.+..+++.+|.|++|+..|+..|++.|..++||++..|+.||.++++++..|++||+|+|++.++..
T Consensus 169 ~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 169 GYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3556677888899999999999999999999999999999999999999999999999999887654
No 29
>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=98.97 E-value=4.1e-10 Score=67.33 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=43.9
Q ss_pred ccccccccccchhhhhhhccccCC----CCHHHHHHHHHHcCCChhhhhh
Q psy17007 118 RKARTVFSDHQLTGLEKRFEAQRY----LSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 118 rr~rt~ft~~Q~~~Le~~F~~~~y----p~~~~r~~La~~lgl~~~qVq~ 163 (165)
++.||.||.+|+..|+..|+.+.| |+..++++||..|||++.+||-
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKV 51 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKV 51 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeee
Confidence 567999999999999999999999 9999999999999999999985
No 30
>KOG0488|consensus
Probab=98.92 E-value=7.6e-10 Score=87.58 Aligned_cols=49 Identities=57% Similarity=0.843 Sum_probs=46.9
Q ss_pred ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
+.+.++.||.||+.|+.+||+.|++-+|++..+|.+||..||||.+|||
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVK 217 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVK 217 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHH
Confidence 4677889999999999999999999999999999999999999999998
No 31
>KOG0775|consensus
Probab=98.90 E-value=1.4e-09 Score=83.00 Aligned_cols=47 Identities=34% Similarity=0.429 Sum_probs=44.2
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007 55 HQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS 101 (165)
Q Consensus 55 ~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~ 101 (165)
.-...|.++|..++||+..++.+||..+||+..||-+||.|||.+++
T Consensus 186 kSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 186 KSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 34579999999999999999999999999999999999999999987
No 32
>KOG0484|consensus
Probab=98.81 E-value=1.1e-09 Score=71.97 Aligned_cols=51 Identities=29% Similarity=0.477 Sum_probs=47.6
Q ss_pred cccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 113 KHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 113 ~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..+++++-|+.||..|+.+||+.|..++||++-.|++||..|+|+++.||-
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQV 63 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQV 63 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHH
Confidence 356778899999999999999999999999999999999999999999984
No 33
>KOG0489|consensus
Probab=98.78 E-value=4.1e-09 Score=81.84 Aligned_cols=68 Identities=31% Similarity=0.544 Sum_probs=54.9
Q ss_pred hhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 88 QVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 88 ~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+|.-|+.....- ..........+|.|+.||..|+.+||+.|+.|+|++...|.+||..|.|+|+|||=
T Consensus 138 ~~~p~~~~~~~~--------~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKI 205 (261)
T KOG0489|consen 138 QIYPWMKSTANY--------LSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKI 205 (261)
T ss_pred ccccchhhhhcc--------cccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHH
Confidence 677787654322 12222333467889999999999999999999999999999999999999999983
No 34
>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=98.74 E-value=6.1e-09 Score=62.25 Aligned_cols=45 Identities=42% Similarity=0.530 Sum_probs=42.9
Q ss_pred cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+.++.||.+|+..|+..|..++||+..+++.||..+||+..+|+.
T Consensus 2 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 46 (57)
T PF00046_consen 2 RKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKN 46 (57)
T ss_dssp SSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHH
T ss_pred cCCCCCCHHHHHHHHHHHHHhcccccccccccccccccccccccc
Confidence 568899999999999999999999999999999999999999975
No 35
>KOG0843|consensus
Probab=98.72 E-value=6.5e-09 Score=74.84 Aligned_cols=48 Identities=44% Similarity=0.621 Sum_probs=45.6
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+.++.||.||.+|+..||.+|+.++|....+|++||..|+|++.|||-
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkv 148 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKV 148 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhh
Confidence 567789999999999999999999999999999999999999999984
No 36
>KOG2251|consensus
Probab=98.72 E-value=6.7e-09 Score=77.07 Aligned_cols=52 Identities=35% Similarity=0.430 Sum_probs=49.3
Q ss_pred ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 112 ~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..+++.+|.||.|+-.|+++||..|.+++||+...|++||.+|+|.+.+||-
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqV 83 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQV 83 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhh
Confidence 6677889999999999999999999999999999999999999999999984
No 37
>KOG0487|consensus
Probab=98.72 E-value=4.7e-09 Score=82.28 Aligned_cols=53 Identities=36% Similarity=0.493 Sum_probs=49.1
Q ss_pred cCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 110 LGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 110 ~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
........|++|+.+|..|+.+||+.|..|.|++.+.|.+|+..|+||++|||
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVK 280 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVK 280 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhhee
Confidence 33455788999999999999999999999999999999999999999999998
No 38
>KOG0848|consensus
Probab=98.69 E-value=8.5e-09 Score=78.47 Aligned_cols=52 Identities=40% Similarity=0.563 Sum_probs=47.2
Q ss_pred ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 112 SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 112 ~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.+.+...+.|.++|++|+.+||+.|..++|+++..+.+||.-|||+|+|||-
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 3445566889999999999999999999999999999999999999999983
No 39
>KOG0842|consensus
Probab=98.69 E-value=9.7e-09 Score=80.48 Aligned_cols=49 Identities=49% Similarity=0.752 Sum_probs=46.3
Q ss_pred ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
..+.|+.|.-||..|+.+||+.|...+|++..||++||..|+||+.|||
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVK 198 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVK 198 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchhee
Confidence 5567778889999999999999999999999999999999999999998
No 40
>KOG0850|consensus
Probab=98.68 E-value=1e-08 Score=76.51 Aligned_cols=53 Identities=43% Similarity=0.673 Sum_probs=48.6
Q ss_pred CccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 111 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 111 ~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..+..+-|+.||.|+..||..|.+.|++++|+...||++||.+||||-.|||-
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKI 168 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKI 168 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhh
Confidence 34556678889999999999999999999999999999999999999999983
No 41
>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=98.59 E-value=1.1e-08 Score=56.68 Aligned_cols=33 Identities=36% Similarity=0.514 Sum_probs=27.9
Q ss_pred hcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 66 AQRYLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 66 ~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
.++||+.++++.||..+||+..||..||-|.|.
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 479999999999999999999999999999774
No 42
>KOG0774|consensus
Probab=98.59 E-value=4e-08 Score=74.62 Aligned_cols=57 Identities=28% Similarity=0.384 Sum_probs=52.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007 45 RRKARTVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQVKTWFQNRLPFGS 101 (165)
Q Consensus 45 ~rr~R~~~s~~q~~~Le~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~ 101 (165)
.+|+|..|++.-.++|.++|- .++||+.+.+++||.++|++..||-.||.|+|-+.+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIryk 247 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYK 247 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehh
Confidence 367888999999999999996 689999999999999999999999999999987654
No 43
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.57 E-value=5.5e-08 Score=57.70 Aligned_cols=45 Identities=47% Similarity=0.579 Sum_probs=41.9
Q ss_pred cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+.++.|+.+|+..|+..|+.++||+..++..||..+||+..||+.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKV 46 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 356779999999999999999999999999999999999999975
No 44
>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=98.51 E-value=9.8e-08 Score=57.10 Aligned_cols=45 Identities=47% Similarity=0.583 Sum_probs=42.1
Q ss_pred cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+.+..++.+|+..|+..|..++||+..+++.||..+||+..||+.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~ 46 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKI 46 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHH
Confidence 356789999999999999999999999999999999999999974
No 45
>KOG2252|consensus
Probab=98.46 E-value=2.2e-07 Score=77.24 Aligned_cols=58 Identities=24% Similarity=0.303 Sum_probs=54.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007 43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG 100 (165)
Q Consensus 43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~ 100 (165)
-+.++.|.+||+.|...|...|+.+++|+.+..+.|+..|||....|.+||-|-|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3456779999999999999999999999999999999999999999999999988775
No 46
>KOG0492|consensus
Probab=98.45 E-value=7.7e-08 Score=70.83 Aligned_cols=50 Identities=44% Similarity=0.696 Sum_probs=46.5
Q ss_pred ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
....|+.|+.||..|+..||+.|...+|+++++|.+++..|.||+.|||-
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKI 190 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKI 190 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheeh
Confidence 34567889999999999999999999999999999999999999999983
No 47
>KOG0493|consensus
Probab=98.43 E-value=1.7e-07 Score=71.35 Aligned_cols=76 Identities=29% Similarity=0.373 Sum_probs=55.9
Q ss_pred hhhhhhccCCCCccccCCCCCccC----ccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 88 QVKTWFQNRLPFGSLFSTSPHELG----SKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 88 ~V~~WF~nrr~~~~~~~~~~~~~~----~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..-.|.-..|..++.......... ......++.||-||.+|+..|...|..|+|++...|.+||.+|||.+.|||-
T Consensus 213 mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKI 292 (342)
T KOG0493|consen 213 MWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKI 292 (342)
T ss_pred ccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhH
Confidence 344676666665544332222111 1222345779999999999999999999999999999999999999999984
No 48
>KOG0491|consensus
Probab=98.36 E-value=1.5e-07 Score=66.91 Aligned_cols=50 Identities=82% Similarity=1.118 Sum_probs=47.3
Q ss_pred ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.|+.++.|++|++.|+..|++.|+.-+|++..++.+||..|+|++.|||-
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKT 146 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKT 146 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHH
Confidence 56778899999999999999999999999999999999999999999984
No 49
>KOG0485|consensus
Probab=98.34 E-value=1.6e-07 Score=69.70 Aligned_cols=48 Identities=54% Similarity=0.745 Sum_probs=45.1
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+.++.||+|+..|+..||..|+..+|++..+|..||.+|.|||.|||-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKI 150 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKI 150 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhh
Confidence 556779999999999999999999999999999999999999999983
No 50
>KOG0494|consensus
Probab=98.25 E-value=6.7e-07 Score=68.03 Aligned_cols=50 Identities=32% Similarity=0.459 Sum_probs=44.6
Q ss_pred cccccc-ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 114 HCRRRK-ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 114 ~~~~rr-~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
+++.|| .||.||..|+.+||++|...+||+...|+-||..++|.+++||-
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqV 187 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQV 187 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhH
Confidence 343444 49999999999999999999999999999999999999999874
No 51
>KOG0490|consensus
Probab=97.95 E-value=5.3e-06 Score=62.97 Aligned_cols=67 Identities=33% Similarity=0.462 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCC
Q psy17007 39 GSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFST 105 (165)
Q Consensus 39 ~~~~~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~ 105 (165)
.....+.++.|+.+...|+..+...|..+++|+...++.|+..+|++...|++||+|+|.+.+....
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4445677888999999999999999999999999999999999999999999999999999976443
No 52
>KOG1146|consensus
Probab=97.83 E-value=5.3e-05 Score=68.91 Aligned_cols=60 Identities=32% Similarity=0.343 Sum_probs=55.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcccc
Q psy17007 44 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLF 103 (165)
Q Consensus 44 ~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~ 103 (165)
.++..|+.+++.|+..+...|....+|...+.+.|...+++..+.|++||+|-|.+.+..
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~ 961 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKA 961 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhh
Confidence 456789999999999999999999999999999999999999999999999999998653
No 53
>KOG0849|consensus
Probab=97.73 E-value=3.1e-05 Score=62.71 Aligned_cols=50 Identities=32% Similarity=0.381 Sum_probs=45.6
Q ss_pred ccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 114 HCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 114 ~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
....++.|+.|+..|+..|++.|++++||+...|+.||.++|+++..|+-
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqv 222 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQV 222 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHH
Confidence 34566778999999999999999999999999999999999999998873
No 54
>KOG0486|consensus
Probab=97.73 E-value=1e-05 Score=63.24 Aligned_cols=47 Identities=34% Similarity=0.540 Sum_probs=44.6
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
++++-|+.||..|+.+||..|.+|+||+...|++||.-+.|++..|.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvr 157 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVR 157 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhh
Confidence 67788999999999999999999999999999999999999999875
No 55
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.68 E-value=3e-05 Score=45.70 Aligned_cols=43 Identities=26% Similarity=0.475 Sum_probs=31.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 56 q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
.+..|+.+|....++...+...|+.+.+|+..||+.||..+..
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 3567999999999999999999999999999999999987644
No 56
>KOG0844|consensus
Probab=97.65 E-value=9.3e-06 Score=63.25 Aligned_cols=48 Identities=44% Similarity=0.652 Sum_probs=44.8
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.-++.||-||.+|+-.||+.|.+..|.+.+.|++||..|+|.+..||-
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKV 227 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKV 227 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeeh
Confidence 446889999999999999999999999999999999999999998874
No 57
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=97.50 E-value=0.00011 Score=52.78 Aligned_cols=48 Identities=27% Similarity=0.382 Sum_probs=43.2
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
...+.+.+-|.+|+..|++.|+.++||+..+|..|+..++|++.-||-
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqI 97 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQI 97 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhh
Confidence 345567788999999999999999999999999999999999988873
No 58
>KOG0483|consensus
Probab=97.46 E-value=0.00011 Score=54.74 Aligned_cols=45 Identities=27% Similarity=0.384 Sum_probs=41.9
Q ss_pred ccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 118 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 118 rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
..++.+||.+|...||+.|+.+.++....+..||..|||..+||.
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVa 95 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVA 95 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHH
Confidence 445677999999999999999999999999999999999999996
No 59
>KOG3623|consensus
Probab=96.96 E-value=0.0015 Score=56.66 Aligned_cols=52 Identities=21% Similarity=0.261 Sum_probs=47.0
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC
Q psy17007 57 LTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH 108 (165)
Q Consensus 57 ~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~ 108 (165)
+..|..+|..|..|+.++...+|..+||+.+.|+.||+++++.....+..+.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 7899999999999999999999999999999999999999999876654443
No 60
>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=96.96 E-value=0.00074 Score=37.26 Aligned_cols=26 Identities=35% Similarity=0.339 Sum_probs=21.0
Q ss_pred ccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 138 AQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 138 ~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.++||+.++++.||..+||+..||.-
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~ 32 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISN 32 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHH
Confidence 47999999999999999999999964
No 61
>KOG3802|consensus
Probab=96.80 E-value=0.0023 Score=51.95 Aligned_cols=47 Identities=30% Similarity=0.332 Sum_probs=44.4
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
+.|++||-++...+..||+.|.+|+.|+..|.-.||.+|+|.++.|.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVR 339 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVR 339 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEE
Confidence 77889999999999999999999999999999999999999998774
No 62
>KOG0847|consensus
Probab=96.71 E-value=0.0008 Score=50.35 Aligned_cols=44 Identities=36% Similarity=0.690 Sum_probs=41.1
Q ss_pred ccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 120 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 120 ~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.+-.|+..|+..|++.|+..+|+..+++.+||..+|+++.||+-
T Consensus 170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkV 213 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKV 213 (288)
T ss_pred cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHH
Confidence 45679999999999999999999999999999999999999974
No 63
>KOG0773|consensus
Probab=96.69 E-value=0.0019 Score=52.14 Aligned_cols=57 Identities=23% Similarity=0.253 Sum_probs=48.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007 45 RRKARTVFSDHQLTGLEKRFEA---QRYLSTPERVELATALQLSETQVKTWFQNRLPFGS 101 (165)
Q Consensus 45 ~rr~R~~~s~~q~~~Le~~f~~---~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~ 101 (165)
..|.+..+......+|+.+... .+||+..+...|+..+||+..||.+||-|.|.+..
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 4455668899999999987543 58999999999999999999999999999887764
No 64
>KOG4577|consensus
Probab=96.22 E-value=0.0028 Score=49.40 Aligned_cols=48 Identities=17% Similarity=0.241 Sum_probs=44.2
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..++.||.+|..|++.|..++...+-|..+.|++|+.++||.-+.||-
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQV 213 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQV 213 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhh
Confidence 456789999999999999999999999999999999999999988873
No 65
>KOG2252|consensus
Probab=96.10 E-value=0.0088 Score=50.44 Aligned_cols=50 Identities=22% Similarity=0.304 Sum_probs=44.7
Q ss_pred cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
...++.|.+||+.|...|...|..+++|+.+..+.|+.+|||....|.-|
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~Nf 467 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINF 467 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHH
Confidence 34556699999999999999999999999999999999999999887643
No 66
>KOG0774|consensus
Probab=96.00 E-value=0.0049 Score=47.39 Aligned_cols=46 Identities=26% Similarity=0.332 Sum_probs=41.3
Q ss_pred cccccccccccchhhhhhhcc---ccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 117 RRKARTVFSDHQLTGLEKRFE---AQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 117 ~rr~rt~ft~~Q~~~Le~~F~---~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
.+|+|..|+..-.+.|...|. .|+||+.+++++||+++|++..||-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvs 236 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVS 236 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhc
Confidence 457788899999999999995 6999999999999999999999874
No 67
>KOG0775|consensus
Probab=95.09 E-value=0.018 Score=44.66 Aligned_cols=37 Identities=30% Similarity=0.294 Sum_probs=33.2
Q ss_pred ccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 126 DHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 126 ~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
+.-+..|.+.|..++||+..++.+||..+||+..||-
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVs 221 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVS 221 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhh
Confidence 3446789999999999999999999999999999983
No 68
>KOG1146|consensus
Probab=94.97 E-value=0.11 Score=48.24 Aligned_cols=119 Identities=19% Similarity=0.113 Sum_probs=95.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCC--------------
Q psy17007 43 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPH-------------- 108 (165)
Q Consensus 43 ~~~rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~-------------- 108 (165)
-+.++.+..+-.++...|-.+|-.+..|+......|......+.+++.+||.|-+.+.+... ..+
T Consensus 703 ~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~-v~g~~~~c~l~~y~t~~ 781 (1406)
T KOG1146|consen 703 PRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ-VPGDVPSCKLKPYATNT 781 (1406)
T ss_pred cccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc-ccCCCCcceeccccccc
Confidence 34567788888999999999999999999999999999999999999999999765432211 000
Q ss_pred --------------------------------------------------------------------------------
Q psy17007 109 -------------------------------------------------------------------------------- 108 (165)
Q Consensus 109 -------------------------------------------------------------------------------- 108 (165)
T Consensus 782 kanfqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~~he~~~~~~ks~ 861 (1406)
T KOG1146|consen 782 KANFQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPSEHEGPEEIYKSL 861 (1406)
T ss_pred chhhhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCCccccccccchhH
Confidence
Q ss_pred ---------------------------------ccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcC
Q psy17007 109 ---------------------------------ELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQ 155 (165)
Q Consensus 109 ---------------------------------~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lg 155 (165)
......+..+..++.+++.|+..|...|..-.|+...+-+.|-..++
T Consensus 862 ~~l~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~ 941 (1406)
T KOG1146|consen 862 LSLACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIG 941 (1406)
T ss_pred HHHHHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhccccc
Confidence 00000123346789999999999999999999999999999999999
Q ss_pred CChhhhh
Q psy17007 156 LSETQLF 162 (165)
Q Consensus 156 l~~~qVq 162 (165)
+..+.|+
T Consensus 942 ~~~~~i~ 948 (1406)
T KOG1146|consen 942 LPKRVIQ 948 (1406)
T ss_pred CCcchhH
Confidence 9998775
No 69
>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=94.58 E-value=0.077 Score=30.95 Aligned_cols=46 Identities=20% Similarity=0.356 Sum_probs=35.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007 46 RKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 46 rr~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr 96 (165)
++.|..+|-++...+-..++... ....||..+|++..+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788999999888888887776 47788999999999999999885
No 70
>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=92.38 E-value=0.064 Score=31.39 Aligned_cols=39 Identities=23% Similarity=0.248 Sum_probs=32.4
Q ss_pred ccccchhhhhhhccccCC--CCHHHHHHHHHHcCCChhhhh
Q psy17007 124 FSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQLF 162 (165)
Q Consensus 124 ft~~Q~~~Le~~F~~~~y--p~~~~r~~La~~lgl~~~qVq 162 (165)
+|+.|+..|..+++.+.| |-.-.-.+||..+|++..-|.
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 478899999999999887 555566899999999987654
No 71
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=85.17 E-value=0.4 Score=36.07 Aligned_cols=41 Identities=22% Similarity=0.237 Sum_probs=34.6
Q ss_pred cccccchhhhhhhccccCC--CCHHHHHHHHHHcCCChhhhhh
Q psy17007 123 VFSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 123 ~ft~~Q~~~Le~~F~~~~y--p~~~~r~~La~~lgl~~~qVq~ 163 (165)
.+|+.|+..|..+|..+.| |-...-.+||+++|+++.-+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 6999999999999999877 5555668999999999876543
No 72
>KOG1168|consensus
Probab=84.98 E-value=0.42 Score=37.61 Aligned_cols=47 Identities=21% Similarity=0.264 Sum_probs=40.6
Q ss_pred ccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhh
Q psy17007 116 RRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLF 162 (165)
Q Consensus 116 ~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq 162 (165)
..+|+||-+-..+-..||..|...+-|+.+..+.+|.+|+|.+..|.
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVR 354 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVR 354 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEE
Confidence 34567888888888999999999999999999999999999876553
No 73
>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=84.84 E-value=1.8 Score=26.52 Aligned_cols=47 Identities=13% Similarity=0.179 Sum_probs=31.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007 47 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 47 r~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
+.|..||.++...+-..+.... .....+|..+||+...+..|-..-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHHh
Confidence 4567899988887777663322 3577889999999999999986543
No 74
>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=84.27 E-value=0.49 Score=27.49 Aligned_cols=41 Identities=15% Similarity=0.263 Sum_probs=30.0
Q ss_pred cccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 119 KARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 119 r~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
+.|..+|-++-..+-+.++.+. ...+||..+|+...+|..|
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I 42 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTI 42 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHH
Confidence 4567788888888888888886 6789999999999999765
No 75
>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=84.24 E-value=1.9 Score=25.15 Aligned_cols=39 Identities=26% Similarity=0.286 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhccchhhhh
Q psy17007 52 FSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQVK 90 (165)
Q Consensus 52 ~s~~q~~~Le~~f~~~~~--p~~~~~~~la~~l~l~~~~V~ 90 (165)
+|+.|.++|...+..--| |-.....+||..+|++..-|.
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 578999999999887554 667778899999999886654
No 76
>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=83.31 E-value=4.1 Score=24.38 Aligned_cols=64 Identities=14% Similarity=0.229 Sum_probs=41.1
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL 154 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l 154 (165)
..++|..+|++...++.|-++-.-.. + +.......|+.+++..|.. ..-....
T Consensus 3 i~evA~~~gvs~~tlR~~~~~g~l~~------~--------~~~~g~R~y~~~~l~~l~~-------------i~~l~~~ 55 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKEFNLYI------P--------RTENGRRYYTDEDIELLKK-------------IKTLLEK 55 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCC------C--------CCCCCceeeCHHHHHHHHH-------------HHHHHHC
Confidence 45789999999999999976421110 0 1122344588888777633 3334458
Q ss_pred CCChhhhhhcC
Q psy17007 155 QLSETQLFYVI 165 (165)
Q Consensus 155 gl~~~qVq~~~ 165 (165)
|++-.+|+-+|
T Consensus 56 g~~l~~i~~~l 66 (67)
T cd04764 56 GLSIKEIKEIL 66 (67)
T ss_pred CCCHHHHHHHh
Confidence 88888887654
No 77
>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=81.19 E-value=11 Score=25.58 Aligned_cols=87 Identities=23% Similarity=0.261 Sum_probs=49.7
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhh
Q psy17007 53 SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGL 132 (165)
Q Consensus 53 s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~L 132 (165)
|-+-...+-.++.... ...++|..++++..-|..|++ +......... + +.+ + .+. ...|
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k-~--------r~~--~-Kid---~~~L 62 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK-RKETGDLEPK-P--------RGR--K-KID---RDEL 62 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH-hccccccccc-c--------ccc--c-ccc---HHHH
Confidence 3344444445555433 355678999999999999998 4333211000 0 011 1 222 3456
Q ss_pred hhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 133 EKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 133 e~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
....+.++-.+.. +||..+|++..-|-+
T Consensus 63 ~~~v~~~pd~tl~---Ela~~l~Vs~~ti~~ 90 (119)
T PF01710_consen 63 KALVEENPDATLR---ELAERLGVSPSTIWR 90 (119)
T ss_pred HHHHHHCCCcCHH---HHHHHcCCCHHHHHH
Confidence 6666666655443 567889998776644
No 78
>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=80.93 E-value=5.6 Score=23.66 Aligned_cols=64 Identities=14% Similarity=0.176 Sum_probs=38.9
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL 154 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l 154 (165)
..++|..+|++...++.|-+.- .. ..+.+.......|+.+++..|.. .....+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~~---g~----------~~~~r~~~~~r~yt~~~v~~l~~-------------i~~l~~~ 56 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERRY---GL----------PAPQRTDGGHRLYSEADVARLRL-------------IRRLTSE 56 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhC---CC----------CCCCcCCCCCeecCHHHHHHHHH-------------HHHHHHC
Confidence 3578999999999999998531 00 00011112334588888777743 3334457
Q ss_pred CCChhhhhhc
Q psy17007 155 QLSETQLFYV 164 (165)
Q Consensus 155 gl~~~qVq~~ 164 (165)
|++-.+|+-+
T Consensus 57 g~~l~~i~~~ 66 (68)
T cd01104 57 GVRISQAAAL 66 (68)
T ss_pred CCCHHHHHHH
Confidence 7777776643
No 79
>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=80.77 E-value=6 Score=23.72 Aligned_cols=63 Identities=11% Similarity=0.128 Sum_probs=39.9
Q ss_pred HHHHHHHhccchhhhhhhhccC-CCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHH
Q psy17007 75 RVELATALQLSETQVKTWFQNR-LPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA 153 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr-r~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~ 153 (165)
..++|..+|++...++.|...- .-. +.+.......||.+++..|.. ......
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~~gl~~--------------~~r~~~g~R~yt~~di~~l~~-------------i~~l~~ 55 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWEREFGLLK--------------PQRSDGGHRLFNDADIDRILE-------------IKRWID 55 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCC--------------CCcCCCCCcccCHHHHHHHHH-------------HHHHHH
Confidence 4578999999999999997531 100 011122334688888777733 333455
Q ss_pred cCCChhhhhhc
Q psy17007 154 LQLSETQLFYV 164 (165)
Q Consensus 154 lgl~~~qVq~~ 164 (165)
.|++-.+|+-+
T Consensus 56 ~g~~l~~i~~~ 66 (68)
T cd04763 56 NGVQVSKVKKL 66 (68)
T ss_pred cCCCHHHHHHH
Confidence 88888877654
No 80
>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=79.52 E-value=5.5 Score=23.69 Aligned_cols=46 Identities=17% Similarity=0.260 Sum_probs=24.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
|..|+........+++..+..--...| ..|.++|+.+.+|+-|-+.
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQR-AAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HH-HHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHH-HHHHHhCccHHHHHHHHHH
Confidence 456676554444445544443322233 3489999999999999863
No 81
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=76.84 E-value=8.8 Score=26.07 Aligned_cols=44 Identities=9% Similarity=0.064 Sum_probs=31.4
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 48 ARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 48 ~R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
.|..|+.++....-.....+..+ ...+|..+|++...|..|...
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~s----v~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGMT----VSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCCC----HHHHHHHHCcCHHHHHHHHHH
Confidence 35668888766555544444442 556799999999999999764
No 82
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=76.25 E-value=1.6 Score=25.78 Aligned_cols=34 Identities=21% Similarity=0.177 Sum_probs=25.1
Q ss_pred hhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 130 TGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 130 ~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.-|+..|....++...+-..|..+.||+..||+-
T Consensus 11 ~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~ 44 (56)
T PF11569_consen 11 QPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRD 44 (56)
T ss_dssp HHHHHHHHHT----TTHHHHHHHHTT--HHHHHH
T ss_pred HHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHH
Confidence 4589999999999999999999999999999973
No 83
>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=75.74 E-value=2.2 Score=25.58 Aligned_cols=24 Identities=21% Similarity=0.441 Sum_probs=19.4
Q ss_pred HHHHHHHHhccchhhhhhhhccCC
Q psy17007 74 ERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
.-..||..||++..+|..|=..-.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dk 47 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDK 47 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcc
Confidence 456789999999999999965433
No 84
>PF13551 HTH_29: Winged helix-turn helix
Probab=75.67 E-value=3.7 Score=26.87 Aligned_cols=85 Identities=20% Similarity=0.242 Sum_probs=49.1
Q ss_pred HHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccC-----CCCHHHHH
Q psy17007 74 ERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQR-----YLSTPERV 148 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~-----yp~~~~r~ 148 (165)
....+|..+|++...|..|...=+...- ...........+.+..+++++...|.+.+..++ ..+.....
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~------~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~ 87 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGI------EGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELA 87 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccH------HHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHH
Confidence 3677899999999999999975332220 001110111222333389999999999888765 23444443
Q ss_pred H-H-HHHc--CCChhhhhhc
Q psy17007 149 E-L-ATAL--QLSETQLFYV 164 (165)
Q Consensus 149 ~-L-a~~l--gl~~~qVq~~ 164 (165)
+ | .... .++...|.-+
T Consensus 88 ~~l~~~~~~~~~s~~ti~r~ 107 (112)
T PF13551_consen 88 EWLIEEEFGIDVSPSTIRRI 107 (112)
T ss_pred HHHHHhccCccCCHHHHHHH
Confidence 3 4 3333 4555555443
No 85
>KOG0773|consensus
Probab=73.53 E-value=3.4 Score=33.32 Aligned_cols=33 Identities=39% Similarity=0.534 Sum_probs=28.6
Q ss_pred HhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007 65 EAQRYLSTPERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 65 ~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
..++|++..+...++...+++..+|.+||-|-+
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~ 149 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANAR 149 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHH
Confidence 458899999999999999999999999998864
No 86
>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=72.99 E-value=7.3 Score=21.80 Aligned_cols=39 Identities=15% Similarity=0.190 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhc
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 94 (165)
.+++.+..+|...|... ..-.++|..+|++...|+.+..
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 46788999999988222 2367789999999999987754
No 87
>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=71.56 E-value=11 Score=24.68 Aligned_cols=21 Identities=14% Similarity=0.003 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999864
No 88
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.46 E-value=10 Score=22.12 Aligned_cols=23 Identities=13% Similarity=0.270 Sum_probs=17.0
Q ss_pred HHHHHHHHhccchhhhhhhhccC
Q psy17007 74 ERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nr 96 (165)
....||..+|++...|..|+.++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 46678999999999999999753
No 89
>cd00131 PAX Paired Box domain
Probab=67.26 E-value=32 Score=23.70 Aligned_cols=93 Identities=10% Similarity=0.011 Sum_probs=56.7
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccch
Q psy17007 50 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQL 129 (165)
Q Consensus 50 ~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~ 129 (165)
..++.+....+...+.... ....+|..+|++...|..|-+.-+..... ...+...+ .+...++.+.
T Consensus 16 ~~lS~d~R~rIv~~~~~G~-----s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v--------~pk~~gg~-rpr~~~~~~~ 81 (128)
T cd00131 16 RPLPDSIRQRIVELAQSGI-----RPCDISRQLRVSHGCVSKILNRYYETGSI--------RPGAIGGS-KPRVATPEVV 81 (128)
T ss_pred CcCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHcCCc--------CCCCCCCC-CCCcCCHHHH
Confidence 4677777777767775332 35667999999999999998754433311 11111111 1223455566
Q ss_pred hhhhhhccccCCCCHHHHHHHHHHcCC
Q psy17007 130 TGLEKRFEAQRYLSTPERVELATALQL 156 (165)
Q Consensus 130 ~~Le~~F~~~~yp~~~~r~~La~~lgl 156 (165)
..++.....++..+..+..++...-|+
T Consensus 82 ~~i~~~v~~~p~~Tl~El~~~L~~~gv 108 (128)
T cd00131 82 KKIEIYKQENPGMFAWEIRDRLLQEGV 108 (128)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHcCC
Confidence 666666788888888877654234465
No 90
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=67.01 E-value=4 Score=22.56 Aligned_cols=37 Identities=16% Similarity=0.119 Sum_probs=18.6
Q ss_pred ccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 122 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 122 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..+|.+|+..++.....+. ...++|..+|++..-|-.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G~-----s~~~IA~~lg~s~sTV~r 39 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQGM-----SIREIAKRLGRSRSTVSR 39 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHH
T ss_pred cchhhhHHHHHHHHHHcCC-----CHHHHHHHHCcCcHHHHH
Confidence 3578888888888876553 667899999999987754
No 91
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=66.39 E-value=12 Score=22.19 Aligned_cols=63 Identities=17% Similarity=0.174 Sum_probs=38.2
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL 154 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l 154 (165)
..++|..+|++.+.|+.|-..-.-. +.+.......|+.+.+..|.. -..|-. .
T Consensus 3 i~eva~~~gvs~~tlr~y~~~gll~--------------~~~~~~g~r~y~~~dv~~l~~------------i~~l~~-~ 55 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREGLLP--------------PPRDENGYRYYSEEDVERLRE------------IKELRK-Q 55 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTTSST--------------TBESTTSSEEE-HHHHHHHHH------------HHHHHH-T
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCcc--------------cccccCceeeccHHHHHHHHH------------HHHHHH-C
Confidence 3578999999999999997542211 111223346788888877743 223333 6
Q ss_pred CCChhhhhhc
Q psy17007 155 QLSETQLFYV 164 (165)
Q Consensus 155 gl~~~qVq~~ 164 (165)
|++..+|+-+
T Consensus 56 G~sl~~I~~~ 65 (69)
T PF13411_consen 56 GMSLEEIKKL 65 (69)
T ss_dssp TTHHHHHHHH
T ss_pred cCCHHHHHHH
Confidence 7776666543
No 92
>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=65.71 E-value=16 Score=25.13 Aligned_cols=45 Identities=20% Similarity=0.335 Sum_probs=30.7
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhh
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEK 134 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~ 134 (165)
..++|..+|++...++.|.+.-.-.-. .......|+.+++..|+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~GLl~p~---------------r~~G~R~Ys~~dv~rL~~ 48 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERHGLIKPA---------------RRNGQRLYSNNDLKRLRF 48 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCc---------------CCCCcEEECHHHHHHHHH
Confidence 467899999999999999874211110 012455688888887754
No 93
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=65.53 E-value=13 Score=26.23 Aligned_cols=75 Identities=19% Similarity=0.138 Sum_probs=46.6
Q ss_pred HHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHH
Q psy17007 74 ERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATA 153 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~ 153 (165)
-..++|..+|++...|..|-..-+..... .............+.+|...|....+...+-+......|..+
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~r~~e~G~~---------l~~~~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e 93 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVRRYRETGLD---------LPPKPRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLE 93 (138)
T ss_pred cHHHHHHHhCccHHHHHHHHHHhcccccc---------ccCccCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhh
Confidence 36677999999999999999643322211 111112223445788888888777666654444444566777
Q ss_pred cCCC
Q psy17007 154 LQLS 157 (165)
Q Consensus 154 lgl~ 157 (165)
.|+.
T Consensus 94 ~gv~ 97 (138)
T COG3415 94 FGVW 97 (138)
T ss_pred cCeE
Confidence 7654
No 94
>smart00351 PAX Paired Box domain.
Probab=64.13 E-value=43 Score=22.83 Aligned_cols=91 Identities=10% Similarity=0.030 Sum_probs=56.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchh
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLT 130 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~ 130 (165)
.++.++...+-..+... . ....||..+|++...|..|.+.-+..... ...+... ......++.+..
T Consensus 17 ~~s~~~R~riv~~~~~G-~----s~~~iA~~~gvs~~tV~kwi~r~~~~G~~--------~pk~~gg-~rp~~~~~~~~~ 82 (125)
T smart00351 17 PLPDEERQRIVELAQNG-V----RPCDISRQLCVSHGCVSKILGRYYETGSI--------RPGAIGG-SKPKVATPKVVK 82 (125)
T ss_pred CCCHHHHHHHHHHHHcC-C----CHHHHHHHHCcCHHHHHHHHHHHHHcCCc--------CCcCCCC-CCCCccCHHHHH
Confidence 47888877777777633 2 34578999999999999998753332211 1111111 122234455556
Q ss_pred hhhhhccccCCCCHHHHH-HHHHHcCC
Q psy17007 131 GLEKRFEAQRYLSTPERV-ELATALQL 156 (165)
Q Consensus 131 ~Le~~F~~~~yp~~~~r~-~La~~lgl 156 (165)
.+......++..+..+.. .|+ .-|+
T Consensus 83 ~I~~~~~~~p~~t~~el~~~L~-~~gv 108 (125)
T smart00351 83 KIADYKQENPGIFAWEIRDRLL-SEGV 108 (125)
T ss_pred HHHHHHHHCCCCCHHHHHHHHH-HcCC
Confidence 667777888888887775 455 5554
No 95
>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=64.02 E-value=16 Score=17.66 Aligned_cols=38 Identities=16% Similarity=0.241 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhh
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWF 93 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 93 (165)
.++..+...+...+... . ....++..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35666666666666532 2 35577889999998888874
No 96
>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=61.80 E-value=9.6 Score=20.69 Aligned_cols=41 Identities=17% Similarity=0.224 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr 96 (165)
.++..+..++...|... .....+|..+|++...|..|...-
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35677777777766422 246677999999999999998643
No 97
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=59.96 E-value=12 Score=20.59 Aligned_cols=37 Identities=14% Similarity=0.291 Sum_probs=26.7
Q ss_pred ccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 122 TVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 122 t~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
..+++++...+.+.+..+. ...++|..+|++...|.-
T Consensus 4 ~~~~~~~~~~i~~l~~~G~-----si~~IA~~~gvsr~TvyR 40 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEGM-----SIAEIAKQFGVSRSTVYR 40 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHH
T ss_pred CCCCHHHHHHHHHHHHCCC-----CHHHHHHHHCcCHHHHHH
Confidence 3467777888888887773 678999999999987753
No 98
>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=59.79 E-value=29 Score=22.53 Aligned_cols=21 Identities=24% Similarity=0.226 Sum_probs=18.0
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|...
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 99
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=58.84 E-value=13 Score=27.79 Aligned_cols=39 Identities=23% Similarity=0.301 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHhccchhhh
Q psy17007 51 VFSDHQLTGLEKRFEAQR--YLSTPERVELATALQLSETQV 89 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~--~p~~~~~~~la~~l~l~~~~V 89 (165)
-+|+.|+++|..+|..-- +|-......||..+|++..-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 699999999999998654 477788899999999987654
No 100
>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=58.58 E-value=4.2 Score=20.78 Aligned_cols=17 Identities=18% Similarity=0.137 Sum_probs=12.3
Q ss_pred HHHHHHcCCChhhhhhc
Q psy17007 148 VELATALQLSETQLFYV 164 (165)
Q Consensus 148 ~~La~~lgl~~~qVq~~ 164 (165)
..-|..+||+..+|+.|
T Consensus 9 i~eA~~~Gls~eeir~F 25 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREF 25 (30)
T ss_dssp HHHHHHTT--HHHHHHH
T ss_pred HHHHHHcCCCHHHHHHH
Confidence 45688999999999876
No 101
>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=57.48 E-value=6.2 Score=23.19 Aligned_cols=33 Identities=30% Similarity=0.373 Sum_probs=23.0
Q ss_pred chhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 128 QLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 128 Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
|+..|+-.+. +.+.+.. +||..+|+++..|++-
T Consensus 7 q~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 7 QLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 4555666666 6665444 8999999999988763
No 102
>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=57.38 E-value=9.3 Score=22.58 Aligned_cols=21 Identities=24% Similarity=0.422 Sum_probs=18.6
Q ss_pred HHHHHHHHhccchhhhhhhhc
Q psy17007 74 ERVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~ 94 (165)
...+||..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 367789999999999999986
No 103
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=56.79 E-value=39 Score=19.90 Aligned_cols=64 Identities=19% Similarity=0.107 Sum_probs=37.9
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhccccCCCCHHHHHHHHHHc
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATAL 154 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~l 154 (165)
..++|..+|++...|+.|-..-.-.. ..+.......|+..++..|..... | ...
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~gli~~-------------~~~~~~g~r~y~~~dl~~l~~i~~------------l-r~~ 56 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERIGLLPP-------------PIRTEGGYRLYSDEDLERLRFIKR------------L-KEL 56 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-------------CccCCCCCEecCHHHHHHHHHHHH------------H-HHc
Confidence 35689999999999999975221110 001112234688888777755322 2 346
Q ss_pred CCChhhhhhc
Q psy17007 155 QLSETQLFYV 164 (165)
Q Consensus 155 gl~~~qVq~~ 164 (165)
|++..+|.-+
T Consensus 57 g~~~~~i~~~ 66 (70)
T smart00422 57 GFSLEEIKEL 66 (70)
T ss_pred CCCHHHHHHH
Confidence 7777666544
No 104
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=56.27 E-value=5.4 Score=24.87 Aligned_cols=34 Identities=18% Similarity=0.172 Sum_probs=25.1
Q ss_pred HHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007 63 RFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 63 ~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr 96 (165)
.|....|.......+||..+|++...|+.|+.+.
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 4444444344457789999999999999999753
No 105
>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=55.15 E-value=42 Score=22.31 Aligned_cols=21 Identities=19% Similarity=0.197 Sum_probs=18.0
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-+.
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 106
>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=55.06 E-value=32 Score=21.85 Aligned_cols=47 Identities=15% Similarity=0.161 Sum_probs=29.6
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccc-cccccccccchhhhhhh
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRR-KARTVFSDHQLTGLEKR 135 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~r-r~rt~ft~~Q~~~Le~~ 135 (165)
..++|..+|++...++.|-..- .. . + .... .....|+.+++..|...
T Consensus 4 i~evA~~~gvs~~tLR~ye~~G----ll-~--p-------~r~~~~g~R~Ys~~dv~~l~~I 51 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEEKG----LI-K--S-------IRSDGGGQRKYSLADVDRLLVI 51 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC----CC-C--C-------CccCCCCceecCHHHHHHHHHH
Confidence 4578999999999999995321 00 0 0 1111 13446888888877654
No 107
>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=54.54 E-value=35 Score=22.29 Aligned_cols=47 Identities=17% Similarity=0.145 Sum_probs=30.0
Q ss_pred HHHHHHHhccchhhhhhhhcc-CCCCccccCCCCCccCccccccccccccccccchhhhhhh
Q psy17007 75 RVELATALQLSETQVKTWFQN-RLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKR 135 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n-rr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~ 135 (165)
..++|..+|++...++.|-.+ -.-. +.+.......||.+++..|...
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~~gli~--------------p~r~~~g~R~Yt~~di~~l~~I 50 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETEFPQLK--------------PVKRAGGRRYYRPKDVELLLLI 50 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCC--------------CcCCCCCCeeeCHHHHHHHHHH
Confidence 357899999999999999754 1100 0111223446888888877543
No 108
>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=54.53 E-value=11 Score=20.59 Aligned_cols=21 Identities=19% Similarity=0.120 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999765
No 109
>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=54.06 E-value=37 Score=23.23 Aligned_cols=21 Identities=19% Similarity=0.154 Sum_probs=18.3
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQ 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999865
No 110
>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=53.91 E-value=27 Score=19.63 Aligned_cols=39 Identities=23% Similarity=0.303 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 52 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 52 ~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
+++.+..++.-.| .....-.++|..+|++...|+.|...
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 3445555555443 33345778899999999999999864
No 111
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=53.32 E-value=26 Score=22.69 Aligned_cols=39 Identities=23% Similarity=0.276 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 52 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 52 ~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
++++|...-.+.|+.+--.+....+++|..||+++..|.
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 456776665555555555555567889999999876654
No 112
>PRK10072 putative transcriptional regulator; Provisional
Probab=51.93 E-value=15 Score=24.13 Aligned_cols=41 Identities=24% Similarity=0.262 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
+.+...+..|...- .. ...+||..+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~---gl----TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGT---GL----KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHc---CC----CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 33666666664322 22 2677899999999999999987654
No 113
>PF13518 HTH_28: Helix-turn-helix domain
Probab=51.92 E-value=12 Score=20.71 Aligned_cols=22 Identities=23% Similarity=0.437 Sum_probs=18.8
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
...+|..+|++..+|..|.+.-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHH
Confidence 5568999999999999999753
No 114
>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=51.58 E-value=48 Score=21.41 Aligned_cols=21 Identities=14% Similarity=0.034 Sum_probs=18.5
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999975
No 115
>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=51.40 E-value=37 Score=23.67 Aligned_cols=21 Identities=14% Similarity=0.083 Sum_probs=18.5
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++...++.|-+.
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999864
No 116
>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=51.38 E-value=46 Score=22.01 Aligned_cols=21 Identities=24% Similarity=0.412 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999764
No 117
>PHA02955 hypothetical protein; Provisional
Probab=51.34 E-value=26 Score=26.49 Aligned_cols=43 Identities=12% Similarity=0.132 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007 54 DHQLTGLEKRFEAQ-RYLSTPERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 54 ~~q~~~Le~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WF~nr 96 (165)
..++..|-+.|.+. .-...+++.+++.++|+....|..||.+-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 46777777777765 66778889999999999988889999875
No 118
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=51.04 E-value=14 Score=20.45 Aligned_cols=22 Identities=27% Similarity=0.472 Sum_probs=17.2
Q ss_pred HHHHHHHHhccchhhhhhhhcc
Q psy17007 74 ERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~n 95 (165)
...++|..+|++...|..|...
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4677899999999999999864
No 119
>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=50.63 E-value=29 Score=19.95 Aligned_cols=43 Identities=21% Similarity=0.224 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCC
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPF 99 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~ 99 (165)
.+|..+..+|.-...-. ...++|..+|++...|..+..+-+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 57888888887555322 36778999999999999888764443
No 120
>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=49.26 E-value=47 Score=22.63 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-+.
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEK 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 121
>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=48.70 E-value=50 Score=22.55 Aligned_cols=22 Identities=18% Similarity=0.182 Sum_probs=19.2
Q ss_pred HHHHHHHHhccchhhhhhhhcc
Q psy17007 74 ERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~n 95 (165)
.+.++|..+|++.+.|+.|-+.
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 3678999999999999999864
No 122
>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=48.49 E-value=47 Score=23.11 Aligned_cols=21 Identities=14% Similarity=0.082 Sum_probs=18.5
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|...
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999965
No 123
>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=48.10 E-value=45 Score=23.42 Aligned_cols=21 Identities=14% Similarity=0.078 Sum_probs=18.6
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++...++-|.+.
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999864
No 124
>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=47.47 E-value=44 Score=21.44 Aligned_cols=48 Identities=21% Similarity=0.207 Sum_probs=30.2
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhhc
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKRF 136 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~F 136 (165)
..++|..+|++...|+.|-..-.-. + .+.......|+...+..|....
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gll~-------~-------~~~~~g~r~y~~~dv~~l~~i~ 50 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGLLP-------P-------ERSENGYRLYSEEDLERLRLIR 50 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcC-------C-------CcCCCCCcccCHHHHHHHHHHH
Confidence 3568999999999999997542111 0 1111123458887777776654
No 125
>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=46.96 E-value=61 Score=20.90 Aligned_cols=21 Identities=24% Similarity=0.088 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 126
>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=46.91 E-value=63 Score=21.08 Aligned_cols=21 Identities=5% Similarity=0.028 Sum_probs=18.3
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999864
No 127
>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=46.87 E-value=57 Score=21.69 Aligned_cols=21 Identities=19% Similarity=0.150 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|-+.
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 457899999999999999864
No 128
>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=46.77 E-value=67 Score=20.74 Aligned_cols=21 Identities=14% Similarity=0.059 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 129
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.67 E-value=9.1 Score=24.75 Aligned_cols=40 Identities=25% Similarity=0.237 Sum_probs=26.2
Q ss_pred cccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 125 SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 125 t~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
+++|...-.+.|+.|--...-..+++|.+|++++..|+-|
T Consensus 4 n~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~leki 43 (97)
T COG4367 4 NPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKI 43 (97)
T ss_pred CHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHH
Confidence 3455555555555554444456788999999999877654
No 130
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=46.09 E-value=13 Score=23.05 Aligned_cols=39 Identities=15% Similarity=0.215 Sum_probs=25.7
Q ss_pred cccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 123 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 123 ~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
..|++|+.+|=+.+..|+. .-..+..++|++.+..|.+|
T Consensus 12 nvsd~qi~elFq~lT~NPl----~AMa~i~qLGip~eKLQ~lm 50 (82)
T PF11212_consen 12 NVSDEQINELFQALTQNPL----AAMATIQQLGIPQEKLQQLM 50 (82)
T ss_pred CCCHHHHHHHHHHHhhCHH----HHHHHHHHcCCCHHHHHHHH
Confidence 4567777777777777753 34456677788877766543
No 131
>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=46.08 E-value=13 Score=26.16 Aligned_cols=36 Identities=22% Similarity=0.265 Sum_probs=25.4
Q ss_pred hhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 130 TGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 130 ~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
..|...=+...|++.+....+|..+||+..+|.+|+
T Consensus 17 ~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~v~ 52 (145)
T PF01257_consen 17 PILHEVQEEYGYIPEEALEEIAEALGIPPAEVYGVA 52 (145)
T ss_dssp HHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHHHH
Confidence 334444445669999999999999999999998763
No 132
>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=44.88 E-value=59 Score=22.33 Aligned_cols=21 Identities=19% Similarity=0.192 Sum_probs=18.6
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|.+.
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999974
No 133
>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=44.52 E-value=24 Score=24.91 Aligned_cols=29 Identities=14% Similarity=0.252 Sum_probs=25.0
Q ss_pred cccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 137 EAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 137 ~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
+..-|++.+....+|..+|++..+|-+|+
T Consensus 27 ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~ 55 (148)
T TIGR01958 27 EQKGWVTPEAIAAVAEMLGIPPVWVYEVA 55 (148)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHHHHHH
Confidence 34459999999999999999999998764
No 134
>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=44.43 E-value=63 Score=21.97 Aligned_cols=21 Identities=14% Similarity=0.056 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|-..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 3 IGELARRTGVNVETIRYYESI 23 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999864
No 135
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=44.15 E-value=23 Score=25.41 Aligned_cols=29 Identities=28% Similarity=0.332 Sum_probs=25.1
Q ss_pred cccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 137 EAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 137 ~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
+..-|++.+....+|..+|++..+|.+|+
T Consensus 34 ~~~G~Ip~e~~~~iA~~l~v~~~~V~~va 62 (156)
T PRK05988 34 DEFGYVPEDAVPVIAEALNLSRAEVHGVI 62 (156)
T ss_pred HHcCCCCHHHHHHHHHHhCCCHHHHHHHH
Confidence 44569999999999999999999998763
No 136
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.10 E-value=58 Score=21.55 Aligned_cols=43 Identities=19% Similarity=0.156 Sum_probs=34.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcc-chhhhhhhhcc
Q psy17007 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQL-SETQVKTWFQN 95 (165)
Q Consensus 49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l-~~~~V~~WF~n 95 (165)
|.+|+.+....+-+.+....+ ....+|..+|+ ...++..|-..
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 778999988887777766655 46778999996 99999988864
No 137
>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=44.02 E-value=72 Score=20.21 Aligned_cols=21 Identities=5% Similarity=-0.069 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...|+.|-..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999753
No 138
>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=43.00 E-value=70 Score=21.51 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|-..
T Consensus 3 IgevA~~~gvs~~tlRyYe~~ 23 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEEK 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999864
No 139
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=42.78 E-value=64 Score=22.50 Aligned_cols=21 Identities=14% Similarity=0.180 Sum_probs=18.4
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.|+.|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999864
No 140
>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=42.73 E-value=81 Score=20.58 Aligned_cols=21 Identities=19% Similarity=0.118 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|-..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999864
No 141
>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=41.97 E-value=30 Score=19.36 Aligned_cols=23 Identities=22% Similarity=0.264 Sum_probs=19.0
Q ss_pred HHHHHHHhccchhhhhhhhccCC
Q psy17007 75 RVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr 97 (165)
..+||..+|++...|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47789999999999999998743
No 142
>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=41.84 E-value=75 Score=21.03 Aligned_cols=21 Identities=19% Similarity=0.188 Sum_probs=18.4
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...|+.|-..
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999864
No 143
>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=41.48 E-value=23 Score=18.85 Aligned_cols=22 Identities=23% Similarity=0.450 Sum_probs=18.9
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
..++|..+|++...|..|..+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3578999999999999999764
No 144
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=40.95 E-value=28 Score=24.75 Aligned_cols=29 Identities=14% Similarity=0.137 Sum_probs=25.2
Q ss_pred cccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 137 EAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 137 ~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
+..-|++.+....+|..+|++..+|-+|+
T Consensus 33 ~~~g~ip~~~~~~iA~~l~v~~~~v~~v~ 61 (154)
T PRK07539 33 EQRGWVPDEAIEAVADYLGMPAIDVEEVA 61 (154)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHHHHHH
Confidence 44578999999999999999999998764
No 145
>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=40.60 E-value=21 Score=22.73 Aligned_cols=34 Identities=15% Similarity=0.308 Sum_probs=23.1
Q ss_pred ccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 124 FSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 124 ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
.|.+|+..+.... ..+=..||..||+++.+|..|
T Consensus 5 ~t~~~l~~ia~~i-------G~~Wk~Lar~LGls~~dI~~i 38 (86)
T cd08318 5 VTGEQITVFANKL-------GEDWKTLAPHLEMKDKEIRAI 38 (86)
T ss_pred CCHHHHHHHHHHH-------hhhHHHHHHHcCCCHHHHHHH
Confidence 5566666654322 123467999999999999865
No 146
>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=40.58 E-value=27 Score=18.62 Aligned_cols=21 Identities=19% Similarity=0.200 Sum_probs=16.6
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++.+.|+.|=..
T Consensus 2 i~e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 356899999999999999754
No 147
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=40.51 E-value=27 Score=25.40 Aligned_cols=29 Identities=24% Similarity=0.271 Sum_probs=25.0
Q ss_pred cccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 137 EAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 137 ~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
+..-|++.+..+.+|..+|++..+|.+|+
T Consensus 47 ~~~GyIp~e~~~~iA~~l~v~~a~V~gVa 75 (169)
T PRK07571 47 ELFGYLERDLLLYVARQLKLPLSRVYGVA 75 (169)
T ss_pred HHcCCCCHHHHHHHHHHhCcCHHHHHHHH
Confidence 34569999999999999999999998763
No 148
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=40.13 E-value=34 Score=20.74 Aligned_cols=35 Identities=14% Similarity=0.121 Sum_probs=25.9
Q ss_pred hhhhhhccccCCCCHHHHHHHHHHcC--CChhhhhhc
Q psy17007 130 TGLEKRFEAQRYLSTPERVELATALQ--LSETQLFYV 164 (165)
Q Consensus 130 ~~Le~~F~~~~yp~~~~r~~La~~lg--l~~~qVq~~ 164 (165)
..+++.+..|+-++.+.-..+..+.| .++.||+-+
T Consensus 20 ~~~~k~l~~NPpine~mir~M~~QMG~kpSekqi~Q~ 56 (64)
T PF03672_consen 20 KYMEKQLKENPPINEKMIRAMMMQMGRKPSEKQIKQM 56 (64)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHhCCCccHHHHHHH
Confidence 34667778888888888888999988 455666654
No 149
>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=40.11 E-value=78 Score=21.53 Aligned_cols=21 Identities=19% Similarity=0.066 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++.+.++.|-+.
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999865
No 150
>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=39.95 E-value=84 Score=21.08 Aligned_cols=21 Identities=24% Similarity=0.175 Sum_probs=17.9
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|-..
T Consensus 3 I~eva~~~gvs~~tLRyYe~~ 23 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999988764
No 151
>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=39.54 E-value=22 Score=19.72 Aligned_cols=20 Identities=20% Similarity=0.287 Sum_probs=17.8
Q ss_pred HHHHHhccchhhhhhhhccC
Q psy17007 77 ELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 77 ~la~~l~l~~~~V~~WF~nr 96 (165)
.||..+|++...|..|+.++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 57999999999999999875
No 152
>TIGR03643 conserved hypothetical protein TIGR03643. This model describes an uncharacterized bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae El Tor N16961 has three identical copies.
Probab=39.21 E-value=18 Score=22.46 Aligned_cols=20 Identities=15% Similarity=0.245 Sum_probs=16.8
Q ss_pred HHHHHHHHcCCChhhhhhcC
Q psy17007 146 ERVELATALQLSETQLFYVI 165 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~~ 165 (165)
-.+++..++||++.+|.-+|
T Consensus 15 pFeaI~~~fGL~E~eVi~lM 34 (72)
T TIGR03643 15 PFEAIEQQFGLSEKEVIKLM 34 (72)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 35788899999999998776
No 153
>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=39.08 E-value=67 Score=21.80 Aligned_cols=19 Identities=21% Similarity=0.167 Sum_probs=16.3
Q ss_pred HHHHHHHhccchhhhhhhh
Q psy17007 75 RVELATALQLSETQVKTWF 93 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF 93 (165)
..++|..+|++.+.++.|=
T Consensus 2 I~e~a~~~gvs~~tlR~Ye 20 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYE 20 (124)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999998884
No 154
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.98 E-value=35 Score=24.36 Aligned_cols=38 Identities=18% Similarity=0.242 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007 59 GLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 59 ~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
.....|..++. .......||...|++...+..+|.|+.
T Consensus 18 aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 18 ALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 33344655556 777889999999999999999999974
No 155
>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=38.87 E-value=22 Score=20.35 Aligned_cols=16 Identities=38% Similarity=0.403 Sum_probs=12.9
Q ss_pred HHHHHHHcCCChhhhh
Q psy17007 147 RVELATALQLSETQLF 162 (165)
Q Consensus 147 r~~La~~lgl~~~qVq 162 (165)
-.+||..+|++..||.
T Consensus 31 S~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 31 SQELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCCCHHHhc
Confidence 4689999999999985
No 156
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=38.77 E-value=64 Score=23.33 Aligned_cols=37 Identities=19% Similarity=0.159 Sum_probs=32.1
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 54 DHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 54 ~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
..-+..|........|........+|..||++...|.
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 4567788888899999999999999999999987764
No 157
>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=38.04 E-value=1e+02 Score=19.92 Aligned_cols=47 Identities=15% Similarity=0.113 Sum_probs=30.2
Q ss_pred HHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhh
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKR 135 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~ 135 (165)
..++|..+|++...++.|.+.---.. .+.......|+..++..|...
T Consensus 4 i~eva~~~gVs~~tLR~ye~~Gli~p--------------~r~~~g~R~Ys~~dv~~l~~I 50 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLGLVSP--------------ARTNGGGRRYSNNDLELLRQV 50 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC--------------CcCCCCCeeECHHHHHHHHHH
Confidence 45789999999999999975421100 111123445888887777654
No 158
>PRK13558 bacterio-opsin activator; Provisional
Probab=37.90 E-value=18 Score=31.63 Aligned_cols=41 Identities=27% Similarity=0.398 Sum_probs=35.0
Q ss_pred ccccccchhhhhhhccccCC--CCHHHHHHHHHHcCCChhhhh
Q psy17007 122 TVFSDHQLTGLEKRFEAQRY--LSTPERVELATALQLSETQLF 162 (165)
Q Consensus 122 t~ft~~Q~~~Le~~F~~~~y--p~~~~r~~La~~lgl~~~qVq 162 (165)
..+|+.|+..|+.+++.+.| |-.-.-++||..+|++..-+.
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 46999999999999999987 666677899999999986543
No 159
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=37.17 E-value=36 Score=18.92 Aligned_cols=22 Identities=9% Similarity=0.108 Sum_probs=19.3
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
...||..+|++...|..|...+
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 5778999999999999999764
No 160
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=36.81 E-value=1.1e+02 Score=19.52 Aligned_cols=44 Identities=11% Similarity=0.151 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhccchhhhhhhhc
Q psy17007 51 VFSDHQLTGLEKRFEA-----QRYLSTPERVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~-----~~~p~~~~~~~la~~l~l~~~~V~~WF~ 94 (165)
-++.+|+..|...|.. +.+.+..+...+...+|++...|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3678899999999875 2356777777766667888888887775
No 161
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=36.62 E-value=89 Score=22.31 Aligned_cols=23 Identities=9% Similarity=0.040 Sum_probs=19.5
Q ss_pred HHHHHHHHhccchhhhhhhhccC
Q psy17007 74 ERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nr 96 (165)
.+.++|..+|++.+.|+-|-+.-
T Consensus 13 ~IgevAk~~gvs~~TlRyYE~~G 35 (154)
T PRK15002 13 TPGEVAKRSGVAVSALHFYESKG 35 (154)
T ss_pred cHHHHHHHHCcCHHHHHHHHHCC
Confidence 46678999999999999998753
No 162
>PF15063 TC1: Thyroid cancer protein 1
Probab=36.60 E-value=83 Score=19.77 Aligned_cols=37 Identities=16% Similarity=0.250 Sum_probs=29.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccc
Q psy17007 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLS 85 (165)
Q Consensus 49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~ 85 (165)
-..|....+..|..+|+...-...++|-.+.-.++-.
T Consensus 31 aNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d 67 (79)
T PF15063_consen 31 ANIFENVNLDQLQRLFQKSGDKKAEERARIIWECAQD 67 (79)
T ss_pred hhhhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCC
Confidence 4478889999999999999888888887765555433
No 163
>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=36.59 E-value=26 Score=19.11 Aligned_cols=17 Identities=41% Similarity=0.419 Sum_probs=12.7
Q ss_pred HHHHHHHHcCCChhhhh
Q psy17007 146 ERVELATALQLSETQLF 162 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq 162 (165)
.-.+||..+||++..|.
T Consensus 19 s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 19 SYAELAEELGLSESTVR 35 (42)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHCcCHHHHH
Confidence 45689999999998775
No 164
>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=36.51 E-value=16 Score=24.34 Aligned_cols=20 Identities=40% Similarity=0.514 Sum_probs=14.7
Q ss_pred HHHHHHHHcCCChhhhhhcC
Q psy17007 146 ERVELATALQLSETQLFYVI 165 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~~ 165 (165)
...+||.++|||+.+|.-||
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 46799999999999998764
No 165
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=36.36 E-value=1.1e+02 Score=20.78 Aligned_cols=22 Identities=14% Similarity=0.126 Sum_probs=19.3
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
+++||..+|++...|..|.+++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~ 42 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGK 42 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCC
Confidence 6779999999999999999875
No 166
>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=35.74 E-value=32 Score=20.18 Aligned_cols=20 Identities=25% Similarity=0.064 Sum_probs=16.1
Q ss_pred HHHHHHHHHcCCChhhhhhc
Q psy17007 145 PERVELATALQLSETQLFYV 164 (165)
Q Consensus 145 ~~r~~La~~lgl~~~qVq~~ 164 (165)
.+...+|.++|+|+.|++-.
T Consensus 21 ~ev~ywa~~~gvt~~~L~~A 40 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLREA 40 (57)
T ss_pred HHHHHHHHHHCcCHHHHHHH
Confidence 46778999999999988643
No 167
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=35.63 E-value=7.8 Score=25.14 Aligned_cols=32 Identities=25% Similarity=0.270 Sum_probs=24.5
Q ss_pred hhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhcC
Q psy17007 130 TGLEKRFEAQRYLSTPERVELATALQLSETQLFYVI 165 (165)
Q Consensus 130 ~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~~ 165 (165)
.+|...|+..-+ ..+.+|..||++...|+-|+
T Consensus 13 ~ELq~nf~~~~l----s~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 13 QELQANFELSGL----SLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred HHHHHHHHHcCC----CHHHHHHHhCCCHHHHHHHH
Confidence 456777776655 56789999999999888664
No 168
>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=35.26 E-value=43 Score=21.15 Aligned_cols=21 Identities=24% Similarity=0.253 Sum_probs=17.0
Q ss_pred HHHHHHHHHHcCCChhhhhhc
Q psy17007 144 TPERVELATALQLSETQLFYV 164 (165)
Q Consensus 144 ~~~r~~La~~lgl~~~qVq~~ 164 (165)
...-.++|..+||++.+|..|
T Consensus 11 ~~~wk~~~R~LGlse~~Id~i 31 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIERV 31 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHHH
Confidence 345567999999999999865
No 169
>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=35.08 E-value=1.1e+02 Score=20.64 Aligned_cols=20 Identities=20% Similarity=0.205 Sum_probs=17.1
Q ss_pred HHHHHHHhccchhhhhhhhc
Q psy17007 75 RVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~ 94 (165)
..++|..+|++.+.|+-|-+
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 3 IGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999988864
No 170
>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=35.07 E-value=1.1e+02 Score=20.80 Aligned_cols=21 Identities=19% Similarity=0.112 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|-..
T Consensus 3 IgevA~~~gvs~~tLRyYe~~ 23 (127)
T cd04784 3 IGELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 171
>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=35.01 E-value=29 Score=22.08 Aligned_cols=19 Identities=37% Similarity=0.405 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..+|+++.+|..|
T Consensus 15 ~Wk~laR~LGlse~~Id~i 33 (86)
T cd08306 15 DWRKLARKLGLSETKIESI 33 (86)
T ss_pred hHHHHHHHcCCCHHHHHHH
Confidence 3467999999999998765
No 172
>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=34.96 E-value=30 Score=22.03 Aligned_cols=19 Identities=26% Similarity=0.373 Sum_probs=15.6
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..||+++.+|..|
T Consensus 15 ~W~~Lar~Lgls~~~I~~i 33 (83)
T cd08319 15 EWEQVLLDLGLSQTDIYRC 33 (83)
T ss_pred hHHHHHHHcCCCHHHHHHH
Confidence 3467999999999998765
No 173
>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=33.55 E-value=1.3e+02 Score=21.36 Aligned_cols=58 Identities=14% Similarity=0.198 Sum_probs=41.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCccccCCCCCccCccccccccccccccccchhhhhhh
Q psy17007 56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFGSLFSTSPHELGSKHCRRRKARTVFSDHQLTGLEKR 135 (165)
Q Consensus 56 q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~~~~~~~~~~~~~~~~~~rr~rt~ft~~Q~~~Le~~ 135 (165)
-.+.+.+.+..+..+.......||..||++...+..+.. ....||-.|+..+-+.
T Consensus 6 ~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~-------------------------G~~~ftl~EI~~Ia~~ 60 (147)
T PF08667_consen 6 IAERVRELLDRKGIPKRKHASELADILGISYSSAYRKLN-------------------------GKSPFTLEEIKKIAKH 60 (147)
T ss_pred HHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhc-------------------------CCCCCCHHHHHHHHHH
Confidence 345566778888888888888999999999988755432 2455777666666666
Q ss_pred ccc
Q psy17007 136 FEA 138 (165)
Q Consensus 136 F~~ 138 (165)
|.-
T Consensus 61 fgv 63 (147)
T PF08667_consen 61 FGV 63 (147)
T ss_pred hCc
Confidence 543
No 174
>PF10985 DUF2805: Protein of unknown function (DUF2805); InterPro: IPR019882 This entry represents an uncharacterised bacterial protein family. Members average about 90 amino acids in length with several well-conserved uncommon amino acids (Trp, Met). The majority of species are marine bacteria. Few species have more than one copy, but Vibrio cholerae O1 biovar eltor str. N16961 has three identical copies.
Probab=33.15 E-value=25 Score=21.87 Aligned_cols=19 Identities=16% Similarity=0.263 Sum_probs=16.3
Q ss_pred HHHHHHHcCCChhhhhhcC
Q psy17007 147 RVELATALQLSETQLFYVI 165 (165)
Q Consensus 147 r~~La~~lgl~~~qVq~~~ 165 (165)
.+++-.++||++.+|.-+|
T Consensus 15 FeaI~~qfGl~E~eVi~lM 33 (73)
T PF10985_consen 15 FEAIERQFGLSEKEVIKLM 33 (73)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5778899999999998776
No 175
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.92 E-value=87 Score=16.96 Aligned_cols=39 Identities=26% Similarity=0.255 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
.++..+..++...+ ... ...++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~--~g~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA--EGL----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 46777777775532 222 4577899999999999998764
No 176
>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=32.68 E-value=1.2e+02 Score=20.72 Aligned_cols=20 Identities=25% Similarity=0.287 Sum_probs=17.2
Q ss_pred HHHHHHHhccchhhhhhhhc
Q psy17007 75 RVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~ 94 (165)
+.++|..+|++.+.++-|-.
T Consensus 3 IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 3 VKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999864
No 177
>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=32.39 E-value=21 Score=21.75 Aligned_cols=19 Identities=21% Similarity=0.209 Sum_probs=15.1
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
.-++||..+|++...|+-+
T Consensus 22 t~eEiA~~lgis~~~v~~~ 40 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVREL 40 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHH
Confidence 5678999999999988765
No 178
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=32.18 E-value=48 Score=23.40 Aligned_cols=45 Identities=18% Similarity=0.170 Sum_probs=34.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCC
Q psy17007 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPF 99 (165)
Q Consensus 49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~ 99 (165)
...+++.|.++|.-.+ ..+ ...++|..+|++...|..|-.+.+.+
T Consensus 4 ~~~Lt~rqreVL~lr~--~Gl----Tq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RGL----TQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred ccCCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3578999999997732 222 36678999999999999999865444
No 179
>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=32.18 E-value=43 Score=21.86 Aligned_cols=35 Identities=20% Similarity=0.224 Sum_probs=23.1
Q ss_pred hhhhhhcccc-CCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 130 TGLEKRFEAQ-RYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 130 ~~Le~~F~~~-~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
..|...|..- ......+=..||..+||++.+|..|
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~i 39 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDVA 39 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHHH
Confidence 3455555432 2233455678999999999998765
No 180
>PRK04217 hypothetical protein; Provisional
Probab=31.92 E-value=34 Score=23.09 Aligned_cols=45 Identities=9% Similarity=0.037 Sum_probs=32.1
Q ss_pred cccccccccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 115 CRRRKARTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 115 ~~~rr~rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
|-....-..++.+|...+...+..+. ...++|..+|++...|...
T Consensus 34 ~~~~~p~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~ 78 (110)
T PRK04217 34 VGPPKPPIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRA 78 (110)
T ss_pred ccCCCCcccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHH
Confidence 44444566788888877766654443 5678999999999888654
No 181
>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=31.81 E-value=35 Score=20.71 Aligned_cols=19 Identities=26% Similarity=0.328 Sum_probs=15.5
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..+|++..+|+.|
T Consensus 12 ~W~~la~~Lgl~~~~I~~i 30 (79)
T cd01670 12 DWKKLARKLGLSDGEIDQI 30 (79)
T ss_pred HHHHHHHHhCCCHHHHHHH
Confidence 3357999999999998765
No 182
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=31.57 E-value=49 Score=23.90 Aligned_cols=37 Identities=19% Similarity=0.206 Sum_probs=31.9
Q ss_pred chhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhhc
Q psy17007 128 QLTGLEKRFEAQRYLSTPERVELATALQLSETQLFYV 164 (165)
Q Consensus 128 Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~~ 164 (165)
-+-.|..+.+..-|.+......+|..||++...|-.|
T Consensus 27 lip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~~V 63 (160)
T COG1905 27 LIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVYGV 63 (160)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHheee
Confidence 3567888888888999999999999999999988765
No 183
>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=30.96 E-value=52 Score=17.55 Aligned_cols=15 Identities=27% Similarity=0.426 Sum_probs=12.0
Q ss_pred CCCCHHHHHHHHHHH
Q psy17007 50 TVFSDHQLTGLEKRF 64 (165)
Q Consensus 50 ~~~s~~q~~~Le~~f 64 (165)
+.||..|+..|+.--
T Consensus 1 s~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 1 SPFTPAQLQELRAQI 15 (37)
T ss_pred CCCCHHHHHHHHHHH
Confidence 368999999998753
No 184
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=30.57 E-value=1.1e+02 Score=21.80 Aligned_cols=36 Identities=25% Similarity=0.223 Sum_probs=29.0
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 55 HQLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 55 ~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
.-+..|...=+...|.+.+....+|..+|++..+|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 445566555567789999999999999999998865
No 185
>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=30.32 E-value=72 Score=17.42 Aligned_cols=37 Identities=27% Similarity=0.251 Sum_probs=25.3
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 53 SDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 53 s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
+..+..++.-.+ ... ...++|..+|++...|..|...
T Consensus 2 ~~~e~~i~~~~~--~~~----s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--EGK----TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHH
Confidence 455666664432 222 4677899999999999998863
No 186
>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=29.93 E-value=53 Score=17.43 Aligned_cols=22 Identities=23% Similarity=0.143 Sum_probs=18.6
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
..++|..+|++...|..|..+.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4567899999999999998654
No 187
>PHA01976 helix-turn-helix protein
Probab=29.72 E-value=55 Score=19.13 Aligned_cols=22 Identities=9% Similarity=0.163 Sum_probs=18.9
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
..+||..+|++...|..|...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 5678999999999999998653
No 188
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=28.65 E-value=57 Score=21.80 Aligned_cols=43 Identities=19% Similarity=0.313 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPFG 100 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~~ 100 (165)
.++..++..+.+.+... ....|..+|++...|+.|=++|+...
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kPs 85 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKPS 85 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCCC
Confidence 37888888887766432 45679999999999999999875443
No 189
>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=28.61 E-value=2.3e+02 Score=20.50 Aligned_cols=41 Identities=12% Similarity=0.106 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhh
Q psy17007 49 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKT 91 (165)
Q Consensus 49 R~~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 91 (165)
.-.++.++++++..+-.+++ ..-.+..||.++|++..-|.+
T Consensus 83 ~y~Lt~e~i~Eir~LR~~DP--~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAEDP--EKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred cccCCHHHHHHHHHHHHcCc--hHhhHHHHHHHhCCCHHHHHH
Confidence 35899999999998887765 445688999999988766554
No 190
>cd00131 PAX Paired Box domain
Probab=28.44 E-value=2e+02 Score=19.68 Aligned_cols=46 Identities=11% Similarity=0.023 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhcc-------chhhhhhhhccC
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQL-------SETQVKTWFQNR 96 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l-------~~~~V~~WF~nr 96 (165)
..+..+...++..-..++..+..+..++...-|+ +...|..|++++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4566776777777788888877766554234455 677787777653
No 191
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=28.33 E-value=1.6e+02 Score=20.37 Aligned_cols=21 Identities=10% Similarity=0.199 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++.+.|+.|=..
T Consensus 3 Ige~a~~~gvs~~tlRyYE~~ 23 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEEK 23 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999754
No 192
>PF12728 HTH_17: Helix-turn-helix domain
Probab=28.27 E-value=53 Score=18.13 Aligned_cols=22 Identities=27% Similarity=0.413 Sum_probs=18.6
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
..++|..+|++...|..|..+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567899999999999999754
No 193
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=28.25 E-value=1.3e+02 Score=21.34 Aligned_cols=35 Identities=14% Similarity=0.182 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 56 q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
-+..|...=+...|.+.+....+|..+|++..+|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 44455555566789999999999999999998865
No 194
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=28.09 E-value=53 Score=17.92 Aligned_cols=35 Identities=14% Similarity=0.262 Sum_probs=25.3
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccC
Q psy17007 61 EKRFEAQRYLSTPERVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 61 e~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nr 96 (165)
.+.|....|-... ...|+...|++..-+...|.|+
T Consensus 6 ~~l~~~~G~~~~s-~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 6 LELFAEKGYEAVS-IRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHHTTTSS-HHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHHhCHHhCC-HHHHHHHHccchhhHHHHcCCH
Confidence 3445555554333 5678999999999999999875
No 195
>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=28.09 E-value=43 Score=20.39 Aligned_cols=17 Identities=35% Similarity=0.415 Sum_probs=13.7
Q ss_pred HHHHHHcCCChhhhhhc
Q psy17007 148 VELATALQLSETQLFYV 164 (165)
Q Consensus 148 ~~La~~lgl~~~qVq~~ 164 (165)
..||..+|++..+|+.|
T Consensus 16 k~La~~Lg~~~~~i~~i 32 (83)
T PF00531_consen 16 KRLARKLGLSESEIENI 32 (83)
T ss_dssp HHHHHHTTS-HHHHHHH
T ss_pred HHHHHHhCcCHHHHHHH
Confidence 57899999999998865
No 196
>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=27.76 E-value=65 Score=16.91 Aligned_cols=22 Identities=23% Similarity=0.291 Sum_probs=18.5
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999998764
No 197
>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=27.57 E-value=1.9e+02 Score=20.84 Aligned_cols=21 Identities=19% Similarity=0.162 Sum_probs=18.1
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...|..|-+.
T Consensus 4 I~evA~~~gvs~~tLRyYe~~ 24 (172)
T cd04790 4 ISQLARQFGLSRSTLLYYERI 24 (172)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999764
No 198
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=27.43 E-value=1.8e+02 Score=20.70 Aligned_cols=22 Identities=23% Similarity=0.232 Sum_probs=18.6
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
.+.||..+|++...|..|-.+.
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~ 106 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAE 106 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 6778999999999999998653
No 199
>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=27.29 E-value=48 Score=21.17 Aligned_cols=19 Identities=16% Similarity=0.198 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..||+++.+|..|
T Consensus 15 ~Wk~lar~LG~s~~eI~~i 33 (86)
T cd08777 15 KWKRCARKLGFTESEIEEI 33 (86)
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 3468999999999998765
No 200
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=27.26 E-value=1.1e+02 Score=20.98 Aligned_cols=22 Identities=18% Similarity=0.204 Sum_probs=19.0
Q ss_pred HHHHHHHHhccchhhhhhhhcc
Q psy17007 74 ERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~n 95 (165)
...++|..+|++...|+.|...
T Consensus 124 s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4778899999999999998764
No 201
>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=27.02 E-value=61 Score=23.49 Aligned_cols=41 Identities=10% Similarity=0.062 Sum_probs=33.2
Q ss_pred cccccccchhhhhhhccccCCCCHHHHHHHHHHcCCChhhhhh
Q psy17007 121 RTVFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQLFY 163 (165)
Q Consensus 121 rt~ft~~Q~~~Le~~F~~~~yp~~~~r~~La~~lgl~~~qVq~ 163 (165)
.-.+|++++.++.+.-..+ |..-.+..||+.+||+..=|.-
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHH
Confidence 4578999999999887766 5667899999999999866543
No 202
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=26.49 E-value=55 Score=18.34 Aligned_cols=18 Identities=28% Similarity=0.233 Sum_probs=13.7
Q ss_pred HHHHHHHHcCCChhhhhh
Q psy17007 146 ERVELATALQLSETQLFY 163 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~ 163 (165)
.-.+||..+|++.+-|+.
T Consensus 17 t~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIRR 34 (55)
T ss_dssp EHHHHHHHCTS-HHHHHH
T ss_pred CHHHHHHHhCCCHHHHHH
Confidence 457899999999987763
No 203
>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=26.47 E-value=1.4e+02 Score=20.87 Aligned_cols=36 Identities=14% Similarity=0.129 Sum_probs=28.0
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 55 HQLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 55 ~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
.-+..|...=+...|.+.+....+|..+|++..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 344555555556779999999999999999988765
No 204
>PF13730 HTH_36: Helix-turn-helix domain
Probab=26.23 E-value=42 Score=18.83 Aligned_cols=19 Identities=21% Similarity=0.188 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
..+.||..+|++...|+..
T Consensus 27 S~~~la~~~g~s~~Tv~~~ 45 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRA 45 (55)
T ss_pred CHHHHHHHHCcCHHHHHHH
Confidence 5778999999999888753
No 205
>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=26.13 E-value=64 Score=23.46 Aligned_cols=28 Identities=29% Similarity=0.329 Sum_probs=24.2
Q ss_pred HHHHHHHHhccchhhhhhhhccCCCCcc
Q psy17007 74 ERVELATALQLSETQVKTWFQNRLPFGS 101 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr~~~~ 101 (165)
.+++|+..++++..+|-.|..|-+...+
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~ 43 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKR 43 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCccc
Confidence 4778999999999999999999876654
No 206
>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=25.64 E-value=69 Score=19.28 Aligned_cols=22 Identities=27% Similarity=0.292 Sum_probs=18.9
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
...||..+|++...|..|..++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~ 42 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGR 42 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 4679999999999999999754
No 207
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=25.59 E-value=2.1e+02 Score=20.95 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=18.4
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++...|+.|...
T Consensus 3 i~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 457899999999999999974
No 208
>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=25.34 E-value=1.9e+02 Score=18.86 Aligned_cols=21 Identities=10% Similarity=0.124 Sum_probs=17.3
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
+.++|..+|++.+.++-|=+.
T Consensus 3 Ige~a~~~gvs~~tlRyYe~~ 23 (107)
T cd04777 3 IGKFAKKNNITIDTVRHYIDL 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999888654
No 209
>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=25.33 E-value=1.3e+02 Score=21.02 Aligned_cols=35 Identities=26% Similarity=0.255 Sum_probs=25.4
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 56 QLTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 56 q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
-+..|...=+...|.+.+....+|..+|++..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 34555555566779999999999999999998876
No 210
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=25.22 E-value=24 Score=16.41 Aligned_cols=9 Identities=33% Similarity=0.815 Sum_probs=6.5
Q ss_pred hhhhccCCC
Q psy17007 90 KTWFQNRLP 98 (165)
Q Consensus 90 ~~WF~nrr~ 98 (165)
-+||.++..
T Consensus 6 iNWFE~~ge 14 (22)
T PF08452_consen 6 INWFESRGE 14 (22)
T ss_pred eehhhhCCc
Confidence 479998753
No 211
>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=25.11 E-value=55 Score=20.54 Aligned_cols=19 Identities=32% Similarity=0.398 Sum_probs=15.4
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..+|++...|..|
T Consensus 17 dW~~LAr~Lg~~~~dI~~i 35 (84)
T cd08317 17 DWPQLARELGVSETDIDLI 35 (84)
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 4467999999999888755
No 212
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=24.91 E-value=1.6e+02 Score=21.38 Aligned_cols=34 Identities=26% Similarity=0.227 Sum_probs=26.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhh
Q psy17007 57 LTGLEKRFEAQRYLSTPERVELATALQLSETQVK 90 (165)
Q Consensus 57 ~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 90 (165)
+..|...=+...|.+.+..+.+|..+|++..+|.
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 3444444456679999999999999999987765
No 213
>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=24.77 E-value=62 Score=16.66 Aligned_cols=16 Identities=25% Similarity=0.405 Sum_probs=11.7
Q ss_pred HHHHHHHHcCCChhhh
Q psy17007 146 ERVELATALQLSETQL 161 (165)
Q Consensus 146 ~r~~La~~lgl~~~qV 161 (165)
.+.+||.-+|++..-|
T Consensus 4 tr~diA~~lG~t~ETV 19 (32)
T PF00325_consen 4 TRQDIADYLGLTRETV 19 (32)
T ss_dssp -HHHHHHHHTS-HHHH
T ss_pred CHHHHHHHhCCcHHHH
Confidence 4678999999998755
No 214
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=24.71 E-value=82 Score=22.90 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=30.2
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCC
Q psy17007 58 TGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 58 ~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
++..+.|....|-... ...||...|++..-+..+|.++.
T Consensus 18 ~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe 56 (213)
T PRK09975 18 ETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKT 56 (213)
T ss_pred HHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHH
Confidence 3444557777775554 67789999999999999999874
No 215
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=24.71 E-value=83 Score=22.29 Aligned_cols=16 Identities=25% Similarity=0.447 Sum_probs=9.0
Q ss_pred CCCHHHHHHHHHHHHh
Q psy17007 51 VFSDHQLTGLEKRFEA 66 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~ 66 (165)
-++.+|+..|....+.
T Consensus 51 ~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 51 YLDDEEIEKLEEAVEN 66 (144)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 4566666666555543
No 216
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=24.50 E-value=2e+02 Score=18.94 Aligned_cols=21 Identities=14% Similarity=0.088 Sum_probs=17.6
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++-|=..
T Consensus 3 I~eva~~~gvs~~tLRyYE~~ 23 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYERK 23 (124)
T ss_pred HHHHHHHhCCCHHHHHHHHHc
Confidence 457899999999999999753
No 217
>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=24.10 E-value=81 Score=18.16 Aligned_cols=24 Identities=17% Similarity=0.243 Sum_probs=19.0
Q ss_pred HHHHHHHHhccchhhhhhhhccCC
Q psy17007 74 ERVELATALQLSETQVKTWFQNRL 97 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr 97 (165)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 467789999999999999998754
No 218
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=23.94 E-value=72 Score=21.64 Aligned_cols=24 Identities=8% Similarity=0.095 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhccchhhhhhhhcc
Q psy17007 72 TPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 72 ~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
....+.||..+|++...+..+|..
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 345788999999999999999974
No 219
>PRK06424 transcription factor; Provisional
Probab=23.84 E-value=1.5e+02 Score=21.00 Aligned_cols=24 Identities=13% Similarity=0.142 Sum_probs=20.4
Q ss_pred HHHHHHHhccchhhhhhhhccCCC
Q psy17007 75 RVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
.++||..+|++...|..|..+.+.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 668999999999999999986543
No 220
>PF13565 HTH_32: Homeodomain-like domain
Probab=23.69 E-value=1.7e+02 Score=17.40 Aligned_cols=32 Identities=16% Similarity=0.135 Sum_probs=23.5
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHH-HHHHhcc
Q psy17007 53 SDHQLTGLEKRFEAQRYLSTPERVE-LATALQL 84 (165)
Q Consensus 53 s~~q~~~Le~~f~~~~~p~~~~~~~-la~~l~l 84 (165)
+.++.+.+.+....++..+..+... |...+|+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGI 64 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC
Confidence 6777799999999988776665555 5666664
No 221
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=23.62 E-value=94 Score=22.25 Aligned_cols=40 Identities=15% Similarity=0.111 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 58 TGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 58 ~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
..-.+.|.++.|.. .....||...|++..-+..+|.++..
T Consensus 15 ~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 15 QAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 34445688888844 44778899999999999999998743
No 222
>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=23.24 E-value=64 Score=20.42 Aligned_cols=18 Identities=33% Similarity=0.499 Sum_probs=14.9
Q ss_pred HHHHHHHcCCChhhhhhc
Q psy17007 147 RVELATALQLSETQLFYV 164 (165)
Q Consensus 147 r~~La~~lgl~~~qVq~~ 164 (165)
=.+||.++|+++..|..|
T Consensus 18 Wk~LAr~Lg~se~dI~~i 35 (84)
T cd08804 18 WTELARELDFTEEQIHQI 35 (84)
T ss_pred HHHHHHHcCCCHHHHHHH
Confidence 457999999999988764
No 223
>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=22.92 E-value=46 Score=18.17 Aligned_cols=19 Identities=26% Similarity=0.263 Sum_probs=14.1
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
...+||..+|++...|...
T Consensus 19 t~~ela~~~~is~~tv~~~ 37 (48)
T PF13412_consen 19 TQKELAEKLGISRSTVNRY 37 (48)
T ss_dssp -HHHHHHHHTS-HHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHH
Confidence 6788999999999877654
No 224
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=22.85 E-value=54 Score=25.62 Aligned_cols=30 Identities=23% Similarity=0.345 Sum_probs=22.7
Q ss_pred CCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 69 YLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 69 ~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
|...-.-..||.++|+++.+|+.|=+.--+
T Consensus 16 yl~gmk~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 16 YLKGMKLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred HHhhccHHHHHHHhCCChHHHHHHHHhcCC
Confidence 334445677999999999999999864433
No 225
>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=22.70 E-value=2.3e+02 Score=18.52 Aligned_cols=21 Identities=19% Similarity=0.067 Sum_probs=18.3
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.++.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 457899999999999999864
No 226
>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=22.55 E-value=62 Score=20.21 Aligned_cols=19 Identities=16% Similarity=0.120 Sum_probs=15.7
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
.=..||..+|++...|..|
T Consensus 17 dW~~LA~~LG~~~~~I~~i 35 (77)
T cd08311 17 DWRSLAGELGYEDEAIDTF 35 (77)
T ss_pred CHHHHHHHcCCCHHHHHHH
Confidence 3468999999999988765
No 227
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=22.41 E-value=96 Score=16.01 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=18.0
Q ss_pred HHHHHHHhccchhhhhhhhccC
Q psy17007 75 RVELATALQLSETQVKTWFQNR 96 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nr 96 (165)
...+|..+|++...|..|-.++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4578899999999999987653
No 228
>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=22.36 E-value=67 Score=19.91 Aligned_cols=20 Identities=35% Similarity=0.338 Sum_probs=15.9
Q ss_pred HHHHHHHHHcCCChhhhhhc
Q psy17007 145 PERVELATALQLSETQLFYV 164 (165)
Q Consensus 145 ~~r~~La~~lgl~~~qVq~~ 164 (165)
..=..||..+|++..+|..|
T Consensus 18 ~~W~~la~~Lg~~~~~i~~i 37 (88)
T smart00005 18 LDWRELARKLGLSEADIDQI 37 (88)
T ss_pred hHHHHHHHHcCCCHHHHHHH
Confidence 34567999999999888765
No 229
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=22.35 E-value=96 Score=23.19 Aligned_cols=39 Identities=8% Similarity=0.108 Sum_probs=31.6
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCC
Q psy17007 58 TGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 58 ~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
..-.+.|..+.|- .....||...|++..-|..+|.++..
T Consensus 20 ~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~ 58 (225)
T PRK11552 20 AAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKED 58 (225)
T ss_pred HHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 3444568888887 56888999999999999999998743
No 230
>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=22.22 E-value=1e+02 Score=19.15 Aligned_cols=20 Identities=15% Similarity=0.202 Sum_probs=16.5
Q ss_pred HHHHHHHHHcCCChhhhhhc
Q psy17007 145 PERVELATALQLSETQLFYV 164 (165)
Q Consensus 145 ~~r~~La~~lgl~~~qVq~~ 164 (165)
..-..||..+||++..|..|
T Consensus 12 ~~Wk~laR~LGls~~~I~~i 31 (79)
T cd08784 12 DQHKRFFRKLGLSDNEIKVA 31 (79)
T ss_pred HHHHHHHHHcCCCHHHHHHH
Confidence 44568999999999998765
No 231
>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=22.18 E-value=68 Score=20.39 Aligned_cols=19 Identities=21% Similarity=0.204 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCChhhhhhc
Q psy17007 146 ERVELATALQLSETQLFYV 164 (165)
Q Consensus 146 ~r~~La~~lgl~~~qVq~~ 164 (165)
+=..||..|||++..|.-|
T Consensus 15 ~Wk~lar~LGlse~~Id~I 33 (86)
T cd08779 15 DWQAIGLHLGLSYRELQRI 33 (86)
T ss_pred HHHHHHHHcCCCHHHHHHH
Confidence 3368999999999988654
No 232
>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=21.99 E-value=1.4e+02 Score=20.77 Aligned_cols=21 Identities=24% Similarity=0.506 Sum_probs=16.7
Q ss_pred HHHHHHHHhccchhhhhhhhc
Q psy17007 74 ERVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~ 94 (165)
.-..+|..+++++++++.|..
T Consensus 101 TW~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 101 TWYQIAQKLHISERTARRWRD 121 (130)
T ss_pred hHHHHHHHhCccHHHHHHHHH
Confidence 455678899999999888764
No 233
>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=21.38 E-value=2.5e+02 Score=18.81 Aligned_cols=20 Identities=15% Similarity=0.257 Sum_probs=17.4
Q ss_pred HHHHHHHhccchhhhhhhhc
Q psy17007 75 RVELATALQLSETQVKTWFQ 94 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~ 94 (165)
+.++|..+|++.+.++-|=+
T Consensus 3 Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 3 ISELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999965
No 234
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=21.12 E-value=1.5e+02 Score=20.58 Aligned_cols=40 Identities=13% Similarity=0.046 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhcc
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 95 (165)
.+++.+..+|.-.|- ......++|..+|++...|+.|...
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~r 167 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFR 167 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 345555555544332 2224667899999999999998863
No 235
>PRK00118 putative DNA-binding protein; Validated
Probab=20.92 E-value=2.1e+02 Score=19.03 Aligned_cols=44 Identities=14% Similarity=0.141 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhccchhhhhhhhccCCCC
Q psy17007 51 VFSDHQLTGLEKRFEAQRYLSTPERVELATALQLSETQVKTWFQNRLPF 99 (165)
Q Consensus 51 ~~s~~q~~~Le~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrr~~ 99 (165)
.++..|..++.-.|.... ...+||..+|++...|..|...-+.+
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkk 60 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKL 60 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 446667777765554432 35678999999999999998754433
No 236
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=20.71 E-value=1e+02 Score=17.84 Aligned_cols=25 Identities=28% Similarity=0.389 Sum_probs=19.4
Q ss_pred HHHHHHHHhccchhhhhhhhccCCC
Q psy17007 74 ERVELATALQLSETQVKTWFQNRLP 98 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr~ 98 (165)
....+|..+|++...|..|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4677899999999999999987653
No 237
>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=20.69 E-value=2.7e+02 Score=18.47 Aligned_cols=21 Identities=14% Similarity=0.153 Sum_probs=18.2
Q ss_pred HHHHHHHhccchhhhhhhhcc
Q psy17007 75 RVELATALQLSETQVKTWFQN 95 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~n 95 (165)
..++|..+|++.+.+.-|...
T Consensus 3 ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 238
>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=20.54 E-value=1.5e+02 Score=20.76 Aligned_cols=27 Identities=11% Similarity=0.036 Sum_probs=22.4
Q ss_pred HHHHHHHHhccchhhhhhhhccCCCCc
Q psy17007 74 ERVELATALQLSETQVKTWFQNRLPFG 100 (165)
Q Consensus 74 ~~~~la~~l~l~~~~V~~WF~nrr~~~ 100 (165)
...+++..+|++..+|..|...-|-..
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL~~ 74 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRLQL 74 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCeec
Confidence 356789999999999999998766544
No 239
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.24 E-value=94 Score=21.25 Aligned_cols=25 Identities=20% Similarity=0.381 Sum_probs=21.3
Q ss_pred HHHHHHHhccchhhhhhhhccCCCC
Q psy17007 75 RVELATALQLSETQVKTWFQNRLPF 99 (165)
Q Consensus 75 ~~~la~~l~l~~~~V~~WF~nrr~~ 99 (165)
...||..+|++...|..|..+++..
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~p 45 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETEP 45 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 4678999999999999999887543
Done!