Query psy15514
Match_columns 187
No_of_seqs 279 out of 1814
Neff 9.6
Searched_HMMs 46136
Date Fri Aug 16 23:15:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15514.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15514hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 1.2E-22 2.5E-27 129.6 2.7 63 124-186 9-71 (125)
2 KOG0849|consensus 99.8 4.4E-21 9.5E-26 152.6 8.2 135 1-186 94-230 (354)
3 KOG0490|consensus 99.8 7.6E-19 1.6E-23 133.4 5.5 128 59-186 57-207 (235)
4 KOG0843|consensus 99.7 8.2E-19 1.8E-23 123.1 4.0 56 131-186 101-156 (197)
5 KOG2251|consensus 99.7 1.7E-18 3.7E-23 125.5 4.9 59 128-186 33-91 (228)
6 KOG0850|consensus 99.7 2.3E-18 5.1E-23 125.3 3.6 58 129-186 119-176 (245)
7 TIGR01565 homeo_ZF_HD homeobox 99.7 1.2E-17 2.5E-22 97.9 5.5 52 133-184 2-57 (58)
8 KOG0488|consensus 99.7 6.3E-18 1.4E-22 131.8 5.5 58 129-186 169-226 (309)
9 KOG0484|consensus 99.7 2.8E-18 6.1E-23 109.6 2.6 59 57-115 12-70 (125)
10 KOG0842|consensus 99.7 6.6E-18 1.4E-22 129.8 4.4 58 129-186 150-207 (307)
11 KOG0489|consensus 99.7 3.2E-18 6.9E-23 131.4 2.1 57 130-186 157-213 (261)
12 KOG0494|consensus 99.7 1.6E-17 3.6E-22 122.7 4.7 55 132-186 141-195 (332)
13 PF00046 Homeobox: Homeobox do 99.7 1.8E-17 3.9E-22 98.5 3.4 54 133-186 1-54 (57)
14 KOG0492|consensus 99.7 2.4E-17 5.3E-22 118.1 3.4 58 130-187 142-199 (246)
15 KOG0487|consensus 99.7 6.8E-17 1.5E-21 124.2 4.5 58 129-186 232-289 (308)
16 KOG0485|consensus 99.6 8.6E-17 1.9E-21 116.0 3.7 58 129-186 101-158 (268)
17 smart00389 HOX Homeodomain. DN 99.6 6.2E-16 1.4E-20 91.5 5.1 53 134-186 2-54 (56)
18 KOG0493|consensus 99.6 4.5E-16 9.7E-21 115.2 4.9 55 132-186 246-300 (342)
19 cd00086 homeodomain Homeodomai 99.6 3E-15 6.4E-20 89.5 4.5 53 134-186 2-54 (59)
20 KOG0848|consensus 99.5 1.3E-15 2.7E-20 113.3 1.4 54 133-186 200-253 (317)
21 KOG0491|consensus 99.5 1.1E-15 2.4E-20 105.8 0.3 57 131-187 99-155 (194)
22 KOG0486|consensus 99.5 8.4E-15 1.8E-19 111.3 4.3 56 131-186 111-166 (351)
23 KOG3862|consensus 99.5 5.3E-15 1.1E-19 110.2 1.3 31 1-31 103-135 (327)
24 KOG3802|consensus 99.5 3.6E-14 7.7E-19 111.5 5.6 128 58-186 213-348 (398)
25 KOG0844|consensus 99.5 1.3E-14 2.8E-19 109.8 2.8 59 128-186 177-235 (408)
26 KOG3517|consensus 99.5 6.3E-15 1.4E-19 108.6 0.3 32 1-32 98-131 (334)
27 KOG2251|consensus 99.5 5.5E-14 1.2E-18 102.2 4.3 62 57-118 32-93 (228)
28 COG5576 Homeodomain-containing 99.5 5.2E-14 1.1E-18 99.3 3.9 57 130-186 49-105 (156)
29 KOG0494|consensus 99.4 2.2E-13 4.8E-18 101.0 6.7 56 61-116 140-195 (332)
30 KOG0850|consensus 99.4 6.6E-14 1.4E-18 102.2 3.8 60 58-117 118-177 (245)
31 KOG0842|consensus 99.4 1E-13 2.2E-18 106.9 4.0 63 59-121 150-212 (307)
32 KOG0483|consensus 99.4 2.2E-13 4.8E-18 99.3 4.5 52 135-186 53-104 (198)
33 KOG0843|consensus 99.4 1.8E-13 4E-18 96.3 3.9 58 61-118 101-158 (197)
34 TIGR01565 homeo_ZF_HD homeobox 99.4 4.1E-13 9E-18 78.7 4.2 52 63-114 2-57 (58)
35 KOG4577|consensus 99.4 3.2E-13 6.9E-18 101.6 3.5 58 129-186 164-221 (383)
36 KOG0488|consensus 99.4 8.2E-13 1.8E-17 103.3 5.2 61 58-118 168-228 (309)
37 KOG0490|consensus 99.3 6.8E-13 1.5E-17 100.7 2.0 58 129-186 57-114 (235)
38 KOG0489|consensus 99.3 1.5E-12 3.2E-17 100.1 3.5 59 60-118 157-215 (261)
39 PF00046 Homeobox: Homeobox do 99.2 1.1E-11 2.5E-16 73.4 4.3 52 63-114 1-52 (57)
40 KOG0485|consensus 99.2 1.1E-11 2.4E-16 89.8 5.0 59 59-117 101-159 (268)
41 KOG0847|consensus 99.2 3.7E-12 8.1E-17 92.4 2.4 57 130-186 165-221 (288)
42 KOG0492|consensus 99.2 7.4E-12 1.6E-16 90.1 3.8 56 61-116 143-198 (246)
43 KOG0486|consensus 99.2 4.3E-11 9.3E-16 91.3 5.3 61 57-117 107-167 (351)
44 smart00389 HOX Homeodomain. DN 99.1 2.1E-10 4.5E-15 67.6 5.0 52 64-115 2-53 (56)
45 KOG0493|consensus 99.1 1.2E-10 2.6E-15 86.7 3.7 56 63-118 247-302 (342)
46 cd00086 homeodomain Homeodomai 99.0 8E-10 1.7E-14 65.7 4.7 53 64-116 2-54 (59)
47 COG5576 Homeodomain-containing 99.0 5.6E-10 1.2E-14 78.9 4.1 56 61-116 50-105 (156)
48 KOG0844|consensus 98.9 5.2E-10 1.1E-14 85.1 3.4 63 60-122 179-241 (408)
49 KOG0487|consensus 98.9 6.8E-10 1.5E-14 85.9 4.1 65 55-119 228-292 (308)
50 KOG0848|consensus 98.9 5.3E-10 1.1E-14 83.6 1.4 54 64-117 201-254 (317)
51 KOG0849|consensus 98.9 3.5E-09 7.5E-14 84.8 5.9 63 53-115 167-229 (354)
52 KOG0775|consensus 98.9 2.5E-09 5.5E-14 80.3 4.0 48 139-186 183-230 (304)
53 KOG0491|consensus 98.8 9.3E-10 2E-14 76.6 0.7 57 61-117 99-155 (194)
54 KOG1168|consensus 98.7 1.6E-09 3.4E-14 82.0 -0.1 58 129-186 306-363 (385)
55 PF05920 Homeobox_KN: Homeobox 98.7 2.8E-09 6.1E-14 57.9 0.4 34 153-186 7-40 (40)
56 KOG2252|consensus 98.5 1.1E-07 2.4E-12 78.1 5.2 59 129-187 417-475 (558)
57 KOG0847|consensus 98.5 9.8E-08 2.1E-12 69.7 2.9 58 60-117 165-222 (288)
58 KOG0483|consensus 98.4 4.2E-07 9.1E-12 66.6 4.4 54 67-120 55-108 (198)
59 KOG4577|consensus 98.4 2.5E-07 5.4E-12 70.2 2.8 60 61-120 166-225 (383)
60 KOG3802|consensus 98.3 1.1E-06 2.4E-11 69.8 4.4 62 61-122 293-354 (398)
61 KOG0774|consensus 98.2 1.6E-06 3.5E-11 65.0 3.7 54 132-185 188-244 (334)
62 KOG1146|consensus 97.8 2.2E-05 4.7E-10 70.7 4.2 59 129-187 900-958 (1406)
63 KOG2252|consensus 97.6 9E-05 1.9E-09 61.4 5.3 55 61-115 419-473 (558)
64 KOG3623|consensus 97.6 0.00015 3.2E-09 62.0 5.8 113 74-186 568-680 (1007)
65 KOG0775|consensus 97.5 0.00022 4.7E-09 54.2 4.7 57 59-115 164-229 (304)
66 PF11569 Homez: Homeodomain le 97.4 0.00011 2.4E-09 42.4 2.2 41 144-184 10-50 (56)
67 PF05920 Homeobox_KN: Homeobox 97.3 9.7E-05 2.1E-09 40.0 1.3 32 83-114 7-38 (40)
68 KOG0773|consensus 96.6 0.0016 3.4E-08 52.4 2.9 54 133-186 240-296 (342)
69 KOG1168|consensus 96.5 0.00069 1.5E-08 52.0 0.2 56 61-116 308-363 (385)
70 KOG0774|consensus 96.1 0.0054 1.2E-07 46.5 2.9 54 62-115 188-244 (334)
71 PF04218 CENP-B_N: CENP-B N-te 95.8 0.022 4.7E-07 32.8 4.0 46 133-183 1-46 (53)
72 KOG3623|consensus 95.6 0.014 3.1E-07 50.4 3.7 43 144-186 568-610 (1007)
73 PF11569 Homez: Homeodomain le 95.2 0.03 6.4E-07 32.4 3.1 43 73-115 9-51 (56)
74 KOG1146|consensus 95.1 0.029 6.4E-07 51.5 4.3 57 61-117 902-958 (1406)
75 PF04967 HTH_10: HTH DNA bindi 93.6 0.12 2.7E-06 29.6 3.3 39 139-177 1-41 (53)
76 PF13551 HTH_29: Winged helix- 87.6 1.6 3.6E-05 28.5 4.9 86 91-181 14-109 (112)
77 PF01527 HTH_Tnp_1: Transposas 85.7 2 4.3E-05 26.1 4.2 43 134-181 2-45 (76)
78 COG3413 Predicted DNA binding 84.0 1.4 3E-05 33.0 3.4 40 138-177 155-196 (215)
79 KOG0773|consensus 82.7 1.4 3E-05 35.5 3.2 55 62-116 239-296 (342)
80 PF10668 Phage_terminase: Phag 82.5 1 2.2E-05 26.5 1.7 20 161-180 24-43 (60)
81 cd00131 PAX Paired Box domain 79.2 16 0.00034 25.0 7.0 104 68-183 17-127 (128)
82 PF13411 MerR_1: MerR HTH fami 79.1 6.7 0.00015 23.2 4.7 66 91-181 2-67 (69)
83 PF04967 HTH_10: HTH DNA bindi 79.0 4.8 0.0001 23.1 3.7 40 69-108 1-42 (53)
84 PF04545 Sigma70_r4: Sigma-70, 77.9 5.1 0.00011 22.2 3.6 39 138-181 4-42 (50)
85 cd04763 HTH_MlrA-like Helix-Tu 76.0 14 0.0003 21.9 6.5 65 92-180 3-67 (68)
86 PF13936 HTH_38: Helix-turn-he 75.2 4 8.6E-05 22.2 2.6 40 137-181 3-42 (44)
87 cd04764 HTH_MlrA-like_sg1 Heli 73.3 16 0.00035 21.5 6.0 64 92-180 3-66 (67)
88 TIGR03879 near_KaiC_dom probab 72.8 2 4.3E-05 26.4 1.1 36 148-183 21-56 (73)
89 PF08281 Sigma70_r4_2: Sigma-7 72.2 3.7 8E-05 23.1 2.1 39 139-182 11-49 (54)
90 PF04218 CENP-B_N: CENP-B N-te 71.6 14 0.0003 21.0 4.4 45 64-113 2-46 (53)
91 cd06171 Sigma70_r4 Sigma70, re 71.6 4.7 0.0001 21.9 2.5 41 138-183 10-50 (55)
92 PRK10072 putative transcriptio 70.2 12 0.00026 24.3 4.3 40 139-185 33-72 (96)
93 PRK09413 IS2 repressor TnpA; R 70.2 14 0.00031 24.9 4.9 43 136-182 10-52 (121)
94 PF02796 HTH_7: Helix-turn-hel 69.6 8.3 0.00018 21.0 3.0 40 137-181 4-43 (45)
95 cd01106 HTH_TipAL-Mta Helix-Tu 68.7 28 0.00061 22.6 6.0 48 92-150 3-50 (103)
96 cd00569 HTH_Hin_like Helix-tur 68.3 12 0.00027 18.0 4.2 38 138-180 5-42 (42)
97 smart00351 PAX Paired Box doma 66.8 37 0.00081 23.0 7.1 100 69-180 18-124 (125)
98 cd01104 HTH_MlrA-CarA Helix-Tu 66.0 24 0.00053 20.6 6.1 48 92-150 3-50 (68)
99 COG4367 Uncharacterized protei 65.5 12 0.00026 23.8 3.4 40 138-177 2-41 (97)
100 cd04761 HTH_MerR-SF Helix-Turn 63.8 6.2 0.00013 21.4 1.8 21 162-182 3-23 (49)
101 PF06056 Terminase_5: Putative 63.7 2.2 4.9E-05 24.9 -0.0 21 161-181 15-35 (58)
102 PF01710 HTH_Tnp_IS630: Transp 63.4 35 0.00075 22.9 5.8 73 91-180 20-92 (119)
103 PF09607 BrkDBD: Brinker DNA-b 62.2 25 0.00054 20.6 4.1 18 164-181 30-47 (58)
104 PF00196 GerE: Bacterial regul 61.8 13 0.00029 21.2 3.1 39 138-182 3-41 (58)
105 cd04765 HTH_MlrA-like_sg2 Heli 59.7 45 0.00098 21.6 5.9 48 92-150 3-50 (99)
106 PF13384 HTH_23: Homeodomain-l 57.8 9.2 0.0002 21.0 1.8 24 161-184 19-42 (50)
107 cd04781 HTH_MerR-like_sg6 Heli 57.8 55 0.0012 21.9 6.2 45 92-148 3-47 (120)
108 PF13518 HTH_28: Helix-turn-he 57.7 8.9 0.00019 21.1 1.8 22 161-182 14-35 (52)
109 COG3413 Predicted DNA binding 57.5 17 0.00038 27.1 3.8 41 68-108 155-197 (215)
110 PRK03975 tfx putative transcri 56.7 10 0.00023 26.5 2.3 41 137-183 5-45 (141)
111 COG2944 Predicted transcriptio 56.1 29 0.00064 22.9 4.2 41 138-185 43-83 (104)
112 PF13443 HTH_26: Cro/C1-type H 56.1 10 0.00022 22.0 1.9 23 161-183 12-34 (63)
113 COG3415 Transposase and inacti 55.9 67 0.0015 22.4 6.4 80 88-174 20-99 (138)
114 COG3028 Uncharacterized protei 55.8 3.7 8E-05 29.5 -0.1 10 3-12 122-131 (187)
115 PF08280 HTH_Mga: M protein tr 55.4 22 0.00047 20.6 3.2 34 142-179 6-39 (59)
116 PF12824 MRP-L20: Mitochondria 54.1 35 0.00075 24.6 4.7 42 135-178 82-123 (164)
117 cd04767 HTH_HspR-like_MBC Heli 53.9 53 0.0012 22.3 5.3 47 91-150 3-49 (120)
118 PF12824 MRP-L20: Mitochondria 53.8 69 0.0015 23.0 6.1 43 66-110 83-125 (164)
119 PF01381 HTH_3: Helix-turn-hel 53.5 15 0.00032 20.5 2.3 23 162-184 12-34 (55)
120 cd04762 HTH_MerR-trunc Helix-T 51.5 17 0.00038 19.2 2.3 23 162-184 3-25 (49)
121 PF00376 MerR: MerR family reg 50.5 15 0.00032 19.3 1.8 18 163-180 3-20 (38)
122 cd01110 HTH_SoxR Helix-Turn-He 50.3 69 0.0015 22.2 5.6 48 91-150 3-50 (139)
123 cd01392 HTH_LacI Helix-turn-he 50.3 12 0.00025 20.7 1.5 21 164-184 2-22 (52)
124 smart00027 EH Eps15 homology d 50.0 44 0.00094 21.2 4.3 43 139-181 4-51 (96)
125 TIGR03070 couple_hipB transcri 48.8 20 0.00044 19.9 2.4 23 162-184 18-40 (58)
126 smart00421 HTH_LUXR helix_turn 48.5 44 0.00096 18.1 4.2 39 138-182 3-41 (58)
127 PRK13558 bacterio-opsin activa 46.7 22 0.00048 31.2 3.3 40 137-176 606-647 (665)
128 smart00422 HTH_MERR helix_turn 46.5 59 0.0013 18.9 5.9 51 92-153 3-53 (70)
129 cd04789 HTH_Cfa Helix-Turn-Hel 46.0 81 0.0018 20.4 6.3 48 91-150 3-50 (102)
130 cd04779 HTH_MerR-like_sg4 Heli 45.6 99 0.0022 21.3 5.8 47 92-150 3-49 (134)
131 PRK05988 formate dehydrogenase 44.9 48 0.001 23.6 4.2 36 142-177 24-59 (156)
132 PRK05255 hypothetical protein; 44.6 6.7 0.00014 28.4 -0.2 10 2-11 111-120 (171)
133 TIGR02044 CueR Cu(I)-responsiv 44.3 98 0.0021 20.9 6.2 47 92-149 3-49 (127)
134 PF04751 DUF615: Protein of un 43.8 6.5 0.00014 28.1 -0.4 11 2-12 100-110 (157)
135 TIGR01958 nuoE_fam NADH-quinon 43.7 50 0.0011 23.1 4.1 36 142-177 17-52 (148)
136 TIGR02043 ZntR Zn(II)-responsi 43.4 1E+02 0.0023 21.0 5.9 50 90-150 2-51 (131)
137 KOG3755|consensus 43.1 28 0.00062 30.3 3.2 96 62-186 647-753 (769)
138 PRK07539 NADH dehydrogenase su 42.8 52 0.0011 23.2 4.1 35 143-177 24-58 (154)
139 TIGR01764 excise DNA binding d 42.4 28 0.0006 18.5 2.2 23 162-184 4-26 (49)
140 COG2963 Transposase and inacti 42.2 66 0.0014 21.2 4.4 42 136-181 5-47 (116)
141 PF08880 QLQ: QLQ; InterPro: 41.6 28 0.00062 18.2 2.0 13 138-150 2-14 (37)
142 PRK04217 hypothetical protein; 41.4 52 0.0011 22.0 3.7 40 137-181 41-80 (110)
143 cd04768 HTH_BmrR-like Helix-Tu 41.3 94 0.002 19.8 6.1 49 91-150 2-50 (96)
144 cd04785 HTH_CadR-PbrR-like Hel 40.6 1.1E+02 0.0025 20.6 6.2 48 92-150 3-50 (126)
145 PF12728 HTH_17: Helix-turn-he 40.4 29 0.00062 19.1 2.1 23 162-184 4-26 (51)
146 PF01726 LexA_DNA_bind: LexA D 40.3 67 0.0015 19.1 3.7 38 138-177 3-44 (65)
147 COG2944 Predicted transcriptio 40.2 65 0.0014 21.3 3.9 41 69-116 44-84 (104)
148 TIGR01950 SoxR redox-sensitive 40.2 1.3E+02 0.0027 21.0 5.7 22 91-112 3-24 (142)
149 PRK15002 redox-sensitivie tran 39.6 1.4E+02 0.003 21.2 5.8 24 90-113 12-35 (154)
150 PRK07571 bidirectional hydroge 39.5 64 0.0014 23.3 4.2 35 143-177 38-72 (169)
151 cd04775 HTH_Cfa-like Helix-Tur 39.1 1.1E+02 0.0023 19.8 6.2 49 90-150 2-50 (102)
152 PHA01976 helix-turn-helix prot 38.8 33 0.0007 20.0 2.3 23 162-184 18-40 (67)
153 cd04777 HTH_MerR-like_sg1 Heli 38.8 1.1E+02 0.0024 19.9 6.3 64 92-181 3-66 (107)
154 PF01257 2Fe-2S_thioredx: Thio 38.6 52 0.0011 22.9 3.6 34 144-177 16-49 (145)
155 TIGR02607 antidote_HigA addict 38.1 33 0.00071 20.7 2.2 23 162-184 21-43 (78)
156 PRK00118 putative DNA-binding 37.9 33 0.00072 22.6 2.3 40 138-182 17-56 (104)
157 PRK06759 RNA polymerase factor 36.8 60 0.0013 22.3 3.7 39 138-181 106-144 (154)
158 COG1905 NuoE NADH:ubiquinone o 36.6 73 0.0016 22.8 4.0 37 141-177 25-61 (160)
159 PF08279 HTH_11: HTH domain; 36.0 64 0.0014 17.9 3.1 31 145-178 4-34 (55)
160 PF06971 Put_DNA-bind_N: Putat 35.9 27 0.00059 19.7 1.4 17 162-178 31-47 (50)
161 cd01109 HTH_YyaN Helix-Turn-He 35.7 1.3E+02 0.0028 19.8 6.3 48 92-150 3-50 (113)
162 TIGR03629 arch_S13P archaeal r 35.6 40 0.00087 23.7 2.5 17 137-153 50-66 (144)
163 cd00093 HTH_XRE Helix-turn-hel 34.9 42 0.00091 17.7 2.2 23 162-184 15-37 (58)
164 cd04783 HTH_MerR1 Helix-Turn-H 34.8 1.4E+02 0.0031 20.0 6.2 66 92-181 3-68 (126)
165 cd04773 HTH_TioE_rpt2 Second H 34.3 1.4E+02 0.0029 19.6 5.9 48 92-150 3-50 (108)
166 cd06170 LuxR_C_like C-terminal 34.3 81 0.0018 17.1 4.1 36 140-181 2-37 (57)
167 cd04770 HTH_HMRTR Helix-Turn-H 33.6 1.5E+02 0.0032 19.8 6.2 48 92-150 3-50 (123)
168 TIGR02051 MerR Hg(II)-responsi 33.5 1.5E+02 0.0033 19.9 5.3 46 92-148 2-47 (124)
169 PRK09652 RNA polymerase sigma 33.4 66 0.0014 22.6 3.5 39 138-181 128-166 (182)
170 cd04787 HTH_HMRTR_unk Helix-Tu 32.9 1.6E+02 0.0035 20.0 6.1 47 92-149 3-49 (133)
171 cd01108 HTH_CueR Helix-Turn-He 32.6 1.6E+02 0.0034 19.9 6.1 48 92-150 3-50 (127)
172 cd00592 HTH_MerR-like Helix-Tu 32.4 1.3E+02 0.0029 19.0 6.4 49 92-152 3-51 (100)
173 PRK12526 RNA polymerase sigma 31.8 41 0.00088 24.8 2.3 22 161-182 171-192 (206)
174 PF12244 DUF3606: Protein of u 31.7 54 0.0012 18.9 2.3 18 160-177 21-38 (57)
175 TIGR00721 tfx DNA-binding prot 31.5 94 0.002 21.6 3.8 40 137-182 5-44 (137)
176 PF13560 HTH_31: Helix-turn-he 31.4 48 0.001 19.2 2.1 25 161-185 16-40 (64)
177 PRK09646 RNA polymerase sigma 31.2 43 0.00093 24.3 2.3 39 139-182 143-181 (194)
178 cd01279 HTH_HspR-like Helix-Tu 31.0 1.5E+02 0.0032 19.0 6.1 49 91-151 3-51 (98)
179 TIGR02054 MerD mercuric resist 31.0 1.7E+02 0.0037 19.7 6.1 50 90-150 4-53 (120)
180 TIGR02047 CadR-PbrR Cd(II)/Pb( 31.0 1.7E+02 0.0037 19.8 6.4 47 92-149 3-49 (127)
181 smart00530 HTH_XRE Helix-turn- 30.8 58 0.0013 16.9 2.4 23 162-184 13-35 (56)
182 TIGR02989 Sig-70_gvs1 RNA poly 30.7 46 0.00099 23.0 2.3 39 138-181 111-149 (159)
183 PRK09514 zntR zinc-responsive 30.5 1.9E+02 0.004 20.0 5.9 50 90-150 2-51 (140)
184 PF13309 HTH_22: HTH domain 30.0 1.1E+02 0.0024 18.0 3.5 38 142-179 25-62 (64)
185 PRK11924 RNA polymerase sigma 29.8 79 0.0017 22.1 3.5 22 161-182 143-164 (179)
186 PF00440 TetR_N: Bacterial reg 29.5 50 0.0011 17.8 1.8 34 149-183 7-40 (47)
187 TIGR02959 SigZ RNA polymerase 29.1 97 0.0021 21.9 3.8 39 138-181 100-138 (170)
188 PF10078 DUF2316: Uncharacteri 29.0 43 0.00094 21.4 1.7 30 145-178 13-42 (89)
189 PF06163 DUF977: Bacterial pro 28.9 64 0.0014 22.1 2.6 45 138-182 4-49 (127)
190 TIGR02937 sigma70-ECF RNA poly 28.8 45 0.00097 22.3 2.0 40 138-182 110-149 (158)
191 PF04539 Sigma70_r3: Sigma-70 28.8 55 0.0012 19.7 2.2 21 161-181 22-42 (78)
192 PHA02955 hypothetical protein; 28.6 99 0.0021 23.3 3.7 43 140-182 59-102 (213)
193 PRK13890 conjugal transfer pro 28.2 57 0.0012 22.0 2.3 23 162-184 21-43 (120)
194 PF13404 HTH_AsnC-type: AsnC-t 28.1 45 0.00097 17.9 1.4 16 162-177 20-35 (42)
195 PRK12519 RNA polymerase sigma 28.0 39 0.00084 24.4 1.6 22 161-182 159-180 (194)
196 cd04766 HTH_HspR Helix-Turn-He 27.7 1.6E+02 0.0035 18.4 5.8 49 91-151 3-51 (91)
197 PF12844 HTH_19: Helix-turn-he 27.4 62 0.0013 18.5 2.1 24 161-184 14-37 (64)
198 PRK11552 putative DNA-binding 27.3 70 0.0015 23.9 2.9 38 144-183 19-56 (225)
199 PRK12537 RNA polymerase sigma 27.3 1.1E+02 0.0023 21.9 3.8 21 161-181 151-171 (182)
200 PRK12512 RNA polymerase sigma 27.3 55 0.0012 23.4 2.2 22 161-182 149-170 (184)
201 PF02042 RWP-RK: RWP-RK domain 27.2 1.1E+02 0.0024 17.4 3.0 27 144-177 7-33 (52)
202 cd01282 HTH_MerR-like_sg3 Heli 27.2 1.9E+02 0.0041 19.0 6.3 47 92-150 3-49 (112)
203 PRK09706 transcriptional repre 26.7 60 0.0013 22.1 2.3 23 162-184 21-43 (135)
204 PRK11511 DNA-binding transcrip 26.5 60 0.0013 21.9 2.2 25 158-182 24-48 (127)
205 PF13412 HTH_24: Winged helix- 26.3 1.1E+02 0.0025 16.3 3.1 37 140-180 2-38 (48)
206 PRK09726 antitoxin HipB; Provi 26.3 70 0.0015 20.0 2.4 24 161-184 27-50 (88)
207 PRK09642 RNA polymerase sigma 26.0 60 0.0013 22.5 2.2 20 162-181 125-144 (160)
208 PF14549 P22_Cro: DNA-binding 25.3 56 0.0012 19.2 1.6 17 163-179 13-29 (60)
209 PF07022 Phage_CI_repr: Bacter 25.3 38 0.00083 20.0 0.9 20 162-181 15-35 (66)
210 PRK12514 RNA polymerase sigma 25.0 1.2E+02 0.0026 21.4 3.7 22 161-182 147-168 (179)
211 cd04788 HTH_NolA-AlbR Helix-Tu 24.9 1.9E+02 0.0042 18.4 5.9 48 92-150 3-50 (96)
212 PRK12529 RNA polymerase sigma 24.6 1.3E+02 0.0029 21.3 3.8 39 138-181 127-165 (178)
213 cd04774 HTH_YfmP Helix-Turn-He 24.6 2E+02 0.0043 18.4 6.0 47 92-150 3-49 (96)
214 cd01111 HTH_MerD Helix-Turn-He 24.6 2.1E+02 0.0046 18.7 5.8 49 91-150 2-50 (107)
215 PF13542 HTH_Tnp_ISL3: Helix-t 24.3 71 0.0015 17.4 1.9 21 161-181 29-49 (52)
216 PRK09648 RNA polymerase sigma 24.2 1.3E+02 0.0028 21.5 3.8 39 138-181 139-177 (189)
217 PF08452 DNAP_B_exo_N: DNA pol 24.0 28 0.00061 15.8 0.1 8 177-184 6-13 (22)
218 TIGR02999 Sig-70_X6 RNA polyme 24.0 70 0.0015 22.7 2.3 22 161-182 152-173 (183)
219 PRK06930 positive control sigm 23.9 69 0.0015 23.1 2.2 41 137-182 113-153 (170)
220 PF13022 HTH_Tnp_1_2: Helix-tu 23.8 1E+02 0.0022 21.6 2.9 45 137-181 9-56 (142)
221 cd08315 Death_TRAILR_DR4_DR5 D 23.6 1.1E+02 0.0024 19.7 2.9 34 145-178 4-38 (96)
222 PF13730 HTH_36: Helix-turn-he 23.3 86 0.0019 17.3 2.2 21 161-181 27-47 (55)
223 cd04780 HTH_MerR-like_sg5 Heli 23.1 2.1E+02 0.0046 18.2 6.4 48 92-150 3-50 (95)
224 PRK12530 RNA polymerase sigma 23.0 1.4E+02 0.003 21.5 3.7 21 161-181 152-172 (189)
225 TIGR02983 SigE-fam_strep RNA p 22.9 1.3E+02 0.0029 20.7 3.6 21 161-181 128-148 (162)
226 TIGR03830 CxxCG_CxxCG_HTH puta 22.8 1.8E+02 0.004 19.2 4.1 22 162-183 81-102 (127)
227 TIGR02948 SigW_bacill RNA poly 22.7 62 0.0014 23.0 1.8 22 161-182 154-175 (187)
228 PRK09644 RNA polymerase sigma 22.7 69 0.0015 22.4 2.0 22 161-182 126-147 (165)
229 PRK10100 DNA-binding transcrip 22.6 1.6E+02 0.0034 22.0 4.0 39 138-182 155-193 (216)
230 PRK09047 RNA polymerase factor 22.2 1.6E+02 0.0035 20.2 3.8 39 138-181 106-144 (161)
231 cd04769 HTH_MerR2 Helix-Turn-H 22.1 2.4E+02 0.0053 18.6 6.3 46 92-149 3-48 (116)
232 PF12802 MarR_2: MarR family; 21.9 95 0.0021 17.5 2.2 37 139-177 3-39 (62)
233 PRK12524 RNA polymerase sigma 21.9 1.4E+02 0.0031 21.5 3.6 21 161-181 154-174 (196)
234 PRK09639 RNA polymerase sigma 21.9 1.5E+02 0.0033 20.4 3.7 38 138-181 112-149 (166)
235 PRK05602 RNA polymerase sigma 21.8 70 0.0015 22.8 1.9 21 161-181 146-166 (186)
236 PRK09651 RNA polymerase sigma 21.7 1.2E+02 0.0027 21.3 3.2 21 161-181 137-157 (172)
237 TIGR02954 Sig70_famx3 RNA poly 21.3 1.6E+02 0.0034 20.6 3.6 21 161-181 137-157 (169)
238 PF14229 DUF4332: Domain of un 21.1 1.1E+02 0.0023 20.7 2.6 24 157-180 27-50 (122)
239 PRK07037 extracytoplasmic-func 21.1 1.7E+02 0.0038 20.1 3.8 20 161-180 127-146 (163)
240 TIGR03826 YvyF flagellar opero 21.1 1.5E+02 0.0032 20.7 3.3 25 160-184 47-71 (137)
241 cd04784 HTH_CadR-PbrR Helix-Tu 21.1 2.7E+02 0.0058 18.7 6.1 47 92-149 3-49 (127)
242 TIGR02985 Sig70_bacteroi1 RNA 21.0 88 0.0019 21.3 2.3 21 161-181 131-151 (161)
243 cd01105 HTH_GlnR-like Helix-Tu 21.0 2.2E+02 0.0049 17.7 6.9 49 91-150 3-51 (88)
244 PRK10403 transcriptional regul 20.8 67 0.0014 22.8 1.7 41 138-184 153-193 (215)
245 PF08671 SinI: Anti-repressor 20.8 60 0.0013 16.2 1.0 18 164-181 10-27 (30)
246 PRK10227 DNA-binding transcrip 20.7 2.9E+02 0.0064 18.9 6.1 48 92-150 3-50 (135)
247 PF01047 MarR: MarR family; I 20.5 1.4E+02 0.003 16.6 2.7 37 139-179 1-37 (59)
248 COG1427 Predicted periplasmic 20.4 1.5E+02 0.0032 23.0 3.4 39 145-184 185-223 (252)
249 TIGR02980 SigBFG RNA polymeras 20.4 1.7E+02 0.0036 21.8 3.8 39 138-181 178-216 (227)
250 cd02413 40S_S3_KH K homology R 20.3 48 0.001 20.7 0.7 21 162-182 56-76 (81)
251 PRK08583 RNA polymerase sigma 20.0 1.7E+02 0.0036 22.3 3.8 39 138-181 205-243 (257)
No 1
>KOG0484|consensus
Probab=99.86 E-value=1.2e-22 Score=129.58 Aligned_cols=63 Identities=59% Similarity=0.874 Sum_probs=59.3
Q ss_pred CCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 124 PGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 124 ~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+...++|++|.||+||..||.+||++|...+||++..|++||.+++|++.+|||||||||+|
T Consensus 9 ~~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAK 71 (125)
T KOG0484|consen 9 LGLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAK 71 (125)
T ss_pred CChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHH
Confidence 344567899999999999999999999999999999999999999999999999999999987
No 2
>KOG0849|consensus
Probab=99.84 E-value=4.4e-21 Score=152.58 Aligned_cols=135 Identities=38% Similarity=0.578 Sum_probs=95.2
Q ss_pred Ccc--ccchhhcCCCCCCCCCccchhhhcccCCCCCCCCcccccCCCCCCCCCCCCCCCcccCCCCCCCCcCHHHHHHHH
Q psy15514 1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGHEGDDTSSEKKLSDGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE 78 (187)
Q Consensus 1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~rt~ft~~ql~~Le 78 (187)
|+| ||+|+.+++|+++++|||++|||++++........ . +....
T Consensus 94 ~~~~ir~~l~~~~~~~~~t~Ps~ssi~r~~r~~~~~~d~~---~----------------~~~~~--------------- 139 (354)
T KOG0849|consen 94 FAWEIRDQLLHEGLCTQATLPSVSSINRVLRNGALGKDQG---L----------------PSQQV--------------- 139 (354)
T ss_pred cchhhhhcccCcccccCCCCCChhhhhHHhhccccccccc---c----------------ccccc---------------
Confidence 789 99999999999999999999999999876543220 0 00000
Q ss_pred HHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCC
Q psy15514 79 RAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPD 158 (187)
Q Consensus 79 ~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~ 158 (187)
+....++. ...++.. .. ......+....++....++.+|.||+|+..|+..|+..|++++||+
T Consensus 140 --~~~~~~~~-------~~~~gs~-------~~-~s~~~~~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~ 202 (354)
T KOG0849|consen 140 --TKEKSPSI-------SGALGSQ-------AG-ASLLSADDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPD 202 (354)
T ss_pred --cccccCCc-------ccccCCc-------cc-cccccCCccccccccccccccccccccccchHHHHHHHhcCCCCCc
Confidence 00000000 0000000 11 1122223333444455677888899999999999999999999999
Q ss_pred HHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 159 IYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 159 ~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
...|+.||.++++++..|++||+|||+|
T Consensus 203 i~~Re~La~~i~l~e~riqvwf~nrra~ 230 (354)
T KOG0849|consen 203 IVGRETLAKETGLPEPRVQVWFQNRRAK 230 (354)
T ss_pred hhhHHHHhhhccCCchHHHHHHhhhhhh
Confidence 9999999999999999999999999986
No 3
>KOG0490|consensus
Probab=99.76 E-value=7.6e-19 Score=133.45 Aligned_cols=128 Identities=37% Similarity=0.435 Sum_probs=110.1
Q ss_pred ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCC----------C------
Q psy15514 59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD----------S------ 122 (187)
Q Consensus 59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~----------~------ 122 (187)
..++++.|+.|+..|+++|++.|+..|||+.+.++.||..+++++..|++||+|++...-... .
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 457889999999999999999999999999999999999999999999999998765332111 0
Q ss_pred -------CCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 123 -------EPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 123 -------~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
........+.++.|+.+...|+..|...|..+++|+...++.|+..+|++...|++||+|+|++
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~ 207 (235)
T KOG0490|consen 137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAK 207 (235)
T ss_pred ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHH
Confidence 0011223566778899999999999999999999999999999999999999999999999865
No 4
>KOG0843|consensus
Probab=99.75 E-value=8.2e-19 Score=123.06 Aligned_cols=56 Identities=38% Similarity=0.547 Sum_probs=54.5
Q ss_pred cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
+.+|.||.||.+||..||..|+.++|..-.+|+.||+.|+|++.||+|||||||+|
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk 156 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTK 156 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHH
Confidence 77889999999999999999999999999999999999999999999999999987
No 5
>KOG2251|consensus
Probab=99.74 E-value=1.7e-18 Score=125.45 Aligned_cols=59 Identities=51% Similarity=0.783 Sum_probs=57.0
Q ss_pred ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
..++.+|.||+|+..|+++||..|.+.+||++..+++||.+|+|++.+|+|||+|||+|
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK 91 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAK 91 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccch
Confidence 45788999999999999999999999999999999999999999999999999999997
No 6
>KOG0850|consensus
Probab=99.72 E-value=2.3e-18 Score=125.30 Aligned_cols=58 Identities=36% Similarity=0.560 Sum_probs=55.4
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+|.|+.||.|+..||..|.+.|++++|+-..+|.+||..|||+.+||||||||||.|
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK 176 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSK 176 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHH
Confidence 4677888999999999999999999999999999999999999999999999999987
No 7
>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=99.72 E-value=1.2e-17 Score=97.89 Aligned_cols=52 Identities=19% Similarity=0.261 Sum_probs=50.5
Q ss_pred cccCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514 133 RRSRTTFSAQQLDELERAFERTQY----PDIYTREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 133 ~r~r~~~t~~q~~~Le~~f~~~~~----p~~~~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
+|.||.||.+|+..|+..|+.++| |+..++++||..+||++.+|+|||||.+
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 688999999999999999999999 9999999999999999999999999976
No 8
>KOG0488|consensus
Probab=99.72 E-value=6.3e-18 Score=131.85 Aligned_cols=58 Identities=43% Similarity=0.641 Sum_probs=56.1
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+|.++.||.||..|+.+||+.|++..|.+..+|++||..|||+..||++||||||+|
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtK 226 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTK 226 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHH
Confidence 3788889999999999999999999999999999999999999999999999999997
No 9
>KOG0484|consensus
Probab=99.71 E-value=2.8e-18 Score=109.57 Aligned_cols=59 Identities=51% Similarity=0.693 Sum_probs=55.5
Q ss_pred CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
.-.+++||.||+||..||.+||++|..+||||+++|++||.++.|++..|++||||++.
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRA 70 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRA 70 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHH
Confidence 34568999999999999999999999999999999999999999999999999998764
No 10
>KOG0842|consensus
Probab=99.71 E-value=6.6e-18 Score=129.75 Aligned_cols=58 Identities=38% Similarity=0.581 Sum_probs=55.1
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
..++||.|..||..|+.+||+.|...+|.+..||++||..|.||++||||||||||.|
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK 207 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYK 207 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhh
Confidence 4567778899999999999999999999999999999999999999999999999987
No 11
>KOG0489|consensus
Probab=99.70 E-value=3.2e-18 Score=131.36 Aligned_cols=57 Identities=39% Similarity=0.525 Sum_probs=54.9
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+.+|.||.||..|+.+||+.|..|+|.+...|.+||..|.|+|.||||||||||||
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK 213 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMK 213 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHH
Confidence 457889999999999999999999999999999999999999999999999999997
No 12
>KOG0494|consensus
Probab=99.69 E-value=1.6e-17 Score=122.68 Aligned_cols=55 Identities=49% Similarity=0.821 Sum_probs=52.0
Q ss_pred ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.|+.||.||..|+++||+.|...+||+...|+.||.++.|++.+|+|||||||+|
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 3334999999999999999999999999999999999999999999999999997
No 13
>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=99.69 E-value=1.8e-17 Score=98.55 Aligned_cols=54 Identities=39% Similarity=0.613 Sum_probs=51.7
Q ss_pred cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
++.|+.||.+|+..|+..|..++||+..+++.||..+||+..+|++||+|+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 54 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRK 54 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHH
Confidence 467899999999999999999999999999999999999999999999999975
No 14
>KOG0492|consensus
Probab=99.67 E-value=2.4e-17 Score=118.07 Aligned_cols=58 Identities=36% Similarity=0.582 Sum_probs=54.9
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187 (187)
Q Consensus 130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 187 (187)
+..|+.||.||..||..||+.|...+|.++.++.+++..|.|++.||++||||||+|+
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKa 199 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKA 199 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHH
Confidence 4457789999999999999999999999999999999999999999999999999986
No 15
>KOG0487|consensus
Probab=99.66 E-value=6.8e-17 Score=124.24 Aligned_cols=58 Identities=31% Similarity=0.457 Sum_probs=55.5
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+..|++|..+|..|+.+||+.|-.|.|++...|.+|++.|+|+++||+|||||||+|
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK 289 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMK 289 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhH
Confidence 4667888999999999999999999999999999999999999999999999999998
No 16
>KOG0485|consensus
Probab=99.65 E-value=8.6e-17 Score=116.03 Aligned_cols=58 Identities=31% Similarity=0.482 Sum_probs=54.9
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
..++++.||+|+..|+..||..|+...|.+..+|..||..|.|++.||++||||||.|
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnK 158 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNK 158 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHH
Confidence 3466778999999999999999999999999999999999999999999999999986
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.62 E-value=6.2e-16 Score=91.53 Aligned_cols=53 Identities=40% Similarity=0.712 Sum_probs=50.7
Q ss_pred ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
+.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|||++
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 46778999999999999999999999999999999999999999999999986
No 18
>KOG0493|consensus
Probab=99.62 E-value=4.5e-16 Score=115.25 Aligned_cols=55 Identities=35% Similarity=0.581 Sum_probs=53.0
Q ss_pred ccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 132 QRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 132 ~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+|.||.||.+||..|+..|+.+.|.....|++||.+|+|.+.||++||||+|+|
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAK 300 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAK 300 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhh
Confidence 4678999999999999999999999999999999999999999999999999987
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=99.57 E-value=3e-15 Score=89.52 Aligned_cols=53 Identities=43% Similarity=0.712 Sum_probs=50.5
Q ss_pred ccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 134 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 134 r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
+.++.|+.+|+..|+..|..++||+..++..||..+||+..+|++||+|+|.+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK 54 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45788999999999999999999999999999999999999999999999975
No 20
>KOG0848|consensus
Probab=99.54 E-value=1.3e-15 Score=113.28 Aligned_cols=54 Identities=28% Similarity=0.465 Sum_probs=51.4
Q ss_pred cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
-+.|.++|+.|..+||+.|..++|.++..+.+||..|||+|+||+|||||||+|
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAK 253 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAK 253 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHH
Confidence 346789999999999999999999999999999999999999999999999997
No 21
>KOG0491|consensus
Probab=99.53 E-value=1.1e-15 Score=105.75 Aligned_cols=57 Identities=40% Similarity=0.652 Sum_probs=53.9
Q ss_pred cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187 (187)
Q Consensus 131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 187 (187)
+.++.||+|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~ 155 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKH 155 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 456679999999999999999999999999999999999999999999999999983
No 22
>KOG0486|consensus
Probab=99.52 E-value=8.4e-15 Score=111.26 Aligned_cols=56 Identities=55% Similarity=0.842 Sum_probs=54.7
Q ss_pred cccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 131 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 131 ~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
|++|.||.||..|+.+||..|+++.||+...|++||.-++|++.+|+|||.|||+|
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrak 166 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAK 166 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhh
Confidence 78889999999999999999999999999999999999999999999999999987
No 23
>KOG3862|consensus
Probab=99.49 E-value=5.3e-15 Score=110.16 Aligned_cols=31 Identities=45% Similarity=0.967 Sum_probs=29.5
Q ss_pred Ccc--ccchhhcCCCCCCCCCccchhhhcccCC
Q psy15514 1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGH 31 (187)
Q Consensus 1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~ 31 (187)
||| ||+|++|+|||+|+||||||||||||++
T Consensus 103 faweiR~~l~~~~ic~~d~vpsVssinri~r~~ 135 (327)
T KOG3862|consen 103 FAWEIRDRLLAEPICDNDTVPSVSSINRIIRTK 135 (327)
T ss_pred hhhhhhhhhhcccccCCCCCchHHHHHHHHHHh
Confidence 899 9999999999999999999999999953
No 24
>KOG3802|consensus
Probab=99.49 E-value=3.6e-14 Score=111.55 Aligned_cols=128 Identities=18% Similarity=0.227 Sum_probs=85.3
Q ss_pred cccCCCCCCCCcCHHHHHH-HHHH----hhhcCCCChhhhHHHHHh-hcCCchhhHhHhhccCC--CCCCCCCCCCCccc
Q psy15514 58 LKRKQRRSRTTFSAQQLDE-LERA----FERTQYPDIYTREELAQR-TKLFPHFLIIIEQQSSG--EGSDCDSEPGIPLK 129 (187)
Q Consensus 58 ~~~~~~r~rt~ft~~ql~~-Le~~----F~~~~yp~~~~r~~la~~-~~l~~~~v~~wfq~~~~--~~~~~~~~~~~~~~ 129 (187)
+..|+||..-.||..++.. |... |.++. ++.++--.|.-+ +.--.--++.|..+... ..............
T Consensus 213 K~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTT-IcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~a~ 291 (398)
T KOG3802|consen 213 KTFKQRRIKLGFTQADVGLALGALYGNVFSQTT-ICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIGAQ 291 (398)
T ss_pred HHHHhheeccccchhHHHHHHHhhhCcccchhh-hhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhhcc
Confidence 4448888888999888874 3322 22222 222221112111 11011125778765444 22222222222233
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.++|++||.|.......||++|.+|+.|+..++..||.+|+|....|+|||.|||.|
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQk 348 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQK 348 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccc
Confidence 477889999999999999999999999999999999999999999999999999987
No 25
>KOG0844|consensus
Probab=99.49 E-value=1.3e-14 Score=109.83 Aligned_cols=59 Identities=36% Similarity=0.510 Sum_probs=56.0
Q ss_pred ccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 128 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 128 ~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.....||.||.||.+|+..||+.|-+..|-+...|-+||..|+|++..|+|||||||+|
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMK 235 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMK 235 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhh
Confidence 34567999999999999999999999999999999999999999999999999999998
No 26
>KOG3517|consensus
Probab=99.47 E-value=6.3e-15 Score=108.60 Aligned_cols=32 Identities=50% Similarity=1.007 Sum_probs=30.8
Q ss_pred Ccc--ccchhhcCCCCCCCCCccchhhhcccCCC
Q psy15514 1 MCW--GDRLIKEGLCDRGSAPSVSAISRLLRGHE 32 (187)
Q Consensus 1 ~~~--rdrll~e~vc~~~~vPSvsSinrilr~~~ 32 (187)
||| |||||++||||+-||||||||.|||||+-
T Consensus 98 FAWEIRDRLlsdgiCDk~NvPSVSSISRILRNKi 131 (334)
T KOG3517|consen 98 FAWEIRDRLLSDGICDKYNVPSVSSISRILRNKI 131 (334)
T ss_pred eeehhhhhhhhcccccccCCcchHHHHHHHHhhh
Confidence 899 99999999999999999999999999874
No 27
>KOG2251|consensus
Probab=99.46 E-value=5.5e-14 Score=102.17 Aligned_cols=62 Identities=40% Similarity=0.562 Sum_probs=58.5
Q ss_pred CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514 57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS 118 (187)
Q Consensus 57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~ 118 (187)
..++++||.||+|+..|+++||..|.+++|||+..+++||.+++|.+..|++||.|++.+..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r 93 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCR 93 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhh
Confidence 46779999999999999999999999999999999999999999999999999999987664
No 28
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.45 E-value=5.2e-14 Score=99.29 Aligned_cols=57 Identities=26% Similarity=0.379 Sum_probs=52.8
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
...++.|.+.|.+|+.+|++.|..++||+..++..|+..++|++.-|++||||+|++
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~ 105 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence 345667778899999999999999999999999999999999999999999999986
No 29
>KOG0494|consensus
Probab=99.44 E-value=2.2e-13 Score=100.98 Aligned_cols=56 Identities=41% Similarity=0.651 Sum_probs=51.8
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
+.|+.||.||..|+++||+.|...||||++.|+-||.++.|.++.|++||||++..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAK 195 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAK 195 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHH
Confidence 44455999999999999999999999999999999999999999999999998754
No 30
>KOG0850|consensus
Probab=99.44 E-value=6.6e-14 Score=102.22 Aligned_cols=60 Identities=33% Similarity=0.375 Sum_probs=55.5
Q ss_pred cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
..+|.|..||.|+..||..|.+.|++++|+-..+|.+||..+||+..+|+|||||++++-
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~ 177 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKF 177 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHH
Confidence 345778899999999999999999999999999999999999999999999999998643
No 31
>KOG0842|consensus
Probab=99.43 E-value=1e-13 Score=106.86 Aligned_cols=63 Identities=35% Similarity=0.423 Sum_probs=57.8
Q ss_pred ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCC
Q psy15514 59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCD 121 (187)
Q Consensus 59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~ 121 (187)
+.++|+.|-.||..|+-+||+.|..+.|++..+|++||..++||++||+|||||++.+.+...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 457778889999999999999999999999999999999999999999999999998776443
No 32
>KOG0483|consensus
Probab=99.41 E-value=2.2e-13 Score=99.31 Aligned_cols=52 Identities=21% Similarity=0.364 Sum_probs=49.3
Q ss_pred cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
++.+|+.+|+..||..|+.+.+.....+..||..|||.+.||.|||||||||
T Consensus 53 kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRAR 104 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRAR 104 (198)
T ss_pred ccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhcccc
Confidence 3456899999999999999999999999999999999999999999999997
No 33
>KOG0843|consensus
Probab=99.41 E-value=1.8e-13 Score=96.30 Aligned_cols=58 Identities=33% Similarity=0.358 Sum_probs=54.8
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS 118 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~ 118 (187)
+.+|.||.||.+|+..||..|+.++|..-.+|+.||..++|++.+|++||||++..-.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~k 158 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHK 158 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHH
Confidence 7789999999999999999999999999999999999999999999999999986543
No 34
>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=99.39 E-value=4.1e-13 Score=78.67 Aligned_cols=52 Identities=15% Similarity=0.247 Sum_probs=49.8
Q ss_pred CCCCCCcCHHHHHHHHHHhhhcCC----CChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514 63 RRSRTTFSAQQLDELERAFERTQY----PDIYTREELAQRTKLFPHFLIIIEQQSS 114 (187)
Q Consensus 63 ~r~rt~ft~~ql~~Le~~F~~~~y----p~~~~r~~la~~~~l~~~~v~~wfq~~~ 114 (187)
+|.||.||.+|+..|+..|+..+| |+...+++||..+||++..|++||+|..
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 688999999999999999999999 9999999999999999999999999853
No 35
>KOG4577|consensus
Probab=99.37 E-value=3.2e-13 Score=101.62 Aligned_cols=58 Identities=31% Similarity=0.481 Sum_probs=55.0
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
....+|.||++|..||+.|+.+|...+.|....|+.|+.++||.-+.|||||||||+|
T Consensus 164 d~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAK 221 (383)
T KOG4577|consen 164 DASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAK 221 (383)
T ss_pred ccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHH
Confidence 3456889999999999999999999999999999999999999999999999999997
No 36
>KOG0488|consensus
Probab=99.36 E-value=8.2e-13 Score=103.32 Aligned_cols=61 Identities=34% Similarity=0.382 Sum_probs=56.7
Q ss_pred cccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514 58 LKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS 118 (187)
Q Consensus 58 ~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~ 118 (187)
.++|.|+.||.||..|+.+||+.|+.+.|....+|.+||..+||+..||+.||||++.+..
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWK 228 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWK 228 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHH
Confidence 4478888999999999999999999999999999999999999999999999999886654
No 37
>KOG0490|consensus
Probab=99.31 E-value=6.8e-13 Score=100.74 Aligned_cols=58 Identities=41% Similarity=0.512 Sum_probs=55.6
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
..+.++.|+.|+..|+++|+++|+..+||+...++.||..+++++..|++||||||+|
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak 114 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAK 114 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHh
Confidence 5678899999999999999999999999999999999999999999999999999986
No 38
>KOG0489|consensus
Probab=99.30 E-value=1.5e-12 Score=100.14 Aligned_cols=59 Identities=31% Similarity=0.303 Sum_probs=55.1
Q ss_pred cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514 60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS 118 (187)
Q Consensus 60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~ 118 (187)
.+.+|.||.||..|+.+||+.|+.+.|+....|.+||..+.|++.+|+|||||++.+..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K 215 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK 215 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999999999999999999999999999999999986543
No 39
>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=99.24 E-value=1.1e-11 Score=73.37 Aligned_cols=52 Identities=35% Similarity=0.431 Sum_probs=49.3
Q ss_pred CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514 63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSS 114 (187)
Q Consensus 63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~ 114 (187)
++.|+.||..|+..|+..|..++||+...++.||..+||+..+|..||+|++
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRR 52 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhH
Confidence 4678999999999999999999999999999999999999999999999865
No 40
>KOG0485|consensus
Probab=99.24 E-value=1.1e-11 Score=89.81 Aligned_cols=59 Identities=27% Similarity=0.316 Sum_probs=54.7
Q ss_pred ccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 59 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 59 ~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
..++++.||+|+..|+..||..|+...|.+..+|..||..+.|++.||++||||++.+.
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKw 159 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKW 159 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHH
Confidence 34677889999999999999999999999999999999999999999999999998654
No 41
>KOG0847|consensus
Probab=99.23 E-value=3.7e-12 Score=92.38 Aligned_cols=57 Identities=35% Similarity=0.579 Sum_probs=53.0
Q ss_pred ccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 130 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 130 ~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+++-.|.+|+-.|+..||..|+..+|+--.++.+||..+|+++.+|+|||||||+|
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTK 221 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTK 221 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhh
Confidence 445556889999999999999999999999999999999999999999999999987
No 42
>KOG0492|consensus
Probab=99.23 E-value=7.4e-12 Score=90.14 Aligned_cols=56 Identities=34% Similarity=0.431 Sum_probs=52.7
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
..|.+||.||..||..||+.|...+|.++.+|.+++..+.|++.+|++||||++..
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAK 198 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAK 198 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHH
Confidence 45678999999999999999999999999999999999999999999999999854
No 43
>KOG0486|consensus
Probab=99.16 E-value=4.3e-11 Score=91.31 Aligned_cols=61 Identities=41% Similarity=0.536 Sum_probs=56.2
Q ss_pred CcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 57 PLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 57 ~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
.+..|++|.||.||.+|+.+||..|.++.||++.+|++||.-++|++..|.+||.+++.+.
T Consensus 107 kki~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakw 167 (351)
T KOG0486|consen 107 KKISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKW 167 (351)
T ss_pred chhhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhh
Confidence 3445899999999999999999999999999999999999999999999999999887553
No 44
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.09 E-value=2.1e-10 Score=67.59 Aligned_cols=52 Identities=37% Similarity=0.561 Sum_probs=48.9
Q ss_pred CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
+.|+.|+..|+..|+..|..++||+..++..||..+|++..+|..||++++.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~ 53 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRA 53 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhh
Confidence 4567899999999999999999999999999999999999999999998874
No 45
>KOG0493|consensus
Probab=99.06 E-value=1.2e-10 Score=86.71 Aligned_cols=56 Identities=32% Similarity=0.401 Sum_probs=52.8
Q ss_pred CCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCC
Q psy15514 63 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGS 118 (187)
Q Consensus 63 ~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~ 118 (187)
+|+||.||.+||..|...|+.+.|+.-..|.+||..++|.+.+|++||||.+..-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiK 302 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIK 302 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhh
Confidence 57899999999999999999999999999999999999999999999999986644
No 46
>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=98.99 E-value=8e-10 Score=65.71 Aligned_cols=53 Identities=40% Similarity=0.565 Sum_probs=49.1
Q ss_pred CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
+.++.|+..|+..|+..|..++||+..++..||..+||+..+|..||++++..
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAK 54 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35678999999999999999999999999999999999999999999987643
No 47
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.97 E-value=5.6e-10 Score=78.91 Aligned_cols=56 Identities=29% Similarity=0.340 Sum_probs=50.9
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
..++.|+.-|..|+..|++.|..++||+..++.+|+..+++++..|++||||++..
T Consensus 50 ~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~ 105 (156)
T COG5576 50 PPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAK 105 (156)
T ss_pred cCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHH
Confidence 45566677899999999999999999999999999999999999999999998743
No 48
>KOG0844|consensus
Probab=98.95 E-value=5.2e-10 Score=85.11 Aligned_cols=63 Identities=27% Similarity=0.281 Sum_probs=57.6
Q ss_pred cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCC
Q psy15514 60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDS 122 (187)
Q Consensus 60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~ 122 (187)
...||.||.||.+|+..||+.|-+..|.+...|-+||..++|.+..|++||||++.+++....
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 357899999999999999999999999999999999999999999999999999987654433
No 49
>KOG0487|consensus
Probab=98.95 E-value=6.8e-10 Score=85.88 Aligned_cols=65 Identities=23% Similarity=0.230 Sum_probs=57.2
Q ss_pred CCCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCC
Q psy15514 55 GIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSD 119 (187)
Q Consensus 55 ~~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~ 119 (187)
.+...++.|..|-.||-.|+.+||+.|-.+.|+...-|-+|+..++|+++||+|||||++.+.+.
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK 292 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKK 292 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhh
Confidence 34444566677788999999999999999999999999999999999999999999999977543
No 50
>KOG0848|consensus
Probab=98.89 E-value=5.3e-10 Score=83.64 Aligned_cols=54 Identities=26% Similarity=0.319 Sum_probs=50.4
Q ss_pred CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
..|.+||..|.-+||+.|+-..|+.+....+||..++|++++|++||||++.++
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKE 254 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKE 254 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHH
Confidence 457789999999999999999999999999999999999999999999998654
No 51
>KOG0849|consensus
Probab=98.88 E-value=3.5e-09 Score=84.79 Aligned_cols=63 Identities=44% Similarity=0.634 Sum_probs=57.3
Q ss_pred CCCCCcccCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 53 EPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 53 ~~~~~~~~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
.++....++.+|.||.|++.|+..|+..|+.++||+++.|+.||..+++++..|++||++++.
T Consensus 167 ~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra 229 (354)
T KOG0849|consen 167 PPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRA 229 (354)
T ss_pred cccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhh
Confidence 344555667888899999999999999999999999999999999999999999999999775
No 52
>KOG0775|consensus
Probab=98.85 E-value=2.5e-09 Score=80.32 Aligned_cols=48 Identities=27% Similarity=0.406 Sum_probs=43.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
|...-...|..+|..++||+..++.+||+.+||+..||-+||+|||.+
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQR 230 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQR 230 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhh
Confidence 444556799999999999999999999999999999999999999975
No 53
>KOG0491|consensus
Probab=98.82 E-value=9.3e-10 Score=76.62 Aligned_cols=57 Identities=33% Similarity=0.408 Sum_probs=52.8
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
+.+..||+|+..|+..|++.|+.+.|.+..++.+||..++|++.+|+.||||++...
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~ 155 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKH 155 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHH
Confidence 456679999999999999999999999999999999999999999999999987543
No 54
>KOG1168|consensus
Probab=98.74 E-value=1.6e-09 Score=82.03 Aligned_cols=58 Identities=19% Similarity=0.296 Sum_probs=54.1
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
...++|+||.+-......||..|...+.|+.+.+..+|++|+|....|+|||.|.|.|
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 4556788999999999999999999999999999999999999999999999999976
No 55
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.72 E-value=2.8e-09 Score=57.89 Aligned_cols=34 Identities=35% Similarity=0.554 Sum_probs=28.4
Q ss_pred hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 153 RTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 153 ~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.++||+..+++.||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4789999999999999999999999999998853
No 56
>KOG2252|consensus
Probab=98.54 E-value=1.1e-07 Score=78.06 Aligned_cols=59 Identities=19% Similarity=0.336 Sum_probs=54.2
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 187 (187)
....++.|.+||+.|...|..+|+.+++|+.+..+.|+..|+|....|.+||.|-|.|+
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34556679999999999999999999999999999999999999999999999988763
No 57
>KOG0847|consensus
Probab=98.48 E-value=9.8e-08 Score=69.68 Aligned_cols=58 Identities=29% Similarity=0.379 Sum_probs=53.3
Q ss_pred cCCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 60 RKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 60 ~~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
.+.+..|.+|+..|+..|+..|+.++|+--.++.+||..+++++.+|++||||++...
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKW 222 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKW 222 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhh
Confidence 4556678899999999999999999999999999999999999999999999998654
No 58
>KOG0483|consensus
Probab=98.39 E-value=4.2e-07 Score=66.62 Aligned_cols=54 Identities=19% Similarity=0.228 Sum_probs=49.2
Q ss_pred CCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCC
Q psy15514 67 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDC 120 (187)
Q Consensus 67 t~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~ 120 (187)
-.|+.+|+..||..|+..+|.....+..||..+||.+.+|.+||||++......
T Consensus 55 ~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 55 RRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred ccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 458999999999999999999999999999999999999999999998665433
No 59
>KOG4577|consensus
Probab=98.36 E-value=2.5e-07 Score=70.25 Aligned_cols=60 Identities=27% Similarity=0.364 Sum_probs=55.0
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDC 120 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~ 120 (187)
..+|+||++|+.||+.|...+...+-|....|+.|+..+||.-+.|++||||++..+..-
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 456889999999999999999999999999999999999999999999999998776543
No 60
>KOG3802|consensus
Probab=98.26 E-value=1.1e-06 Score=69.83 Aligned_cols=62 Identities=15% Similarity=0.192 Sum_probs=58.1
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDS 122 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~ 122 (187)
++|+.||.+.......||..|..++-|+..+...||..++|....|++||+|++-.++....
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 67778899999999999999999999999999999999999999999999999988877665
No 61
>KOG0774|consensus
Probab=98.19 E-value=1.6e-06 Score=65.00 Aligned_cols=54 Identities=30% Similarity=0.487 Sum_probs=49.2
Q ss_pred ccccCCCCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514 132 QRRSRTTFSAQQLDELERAFE---RTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185 (187)
Q Consensus 132 ~~r~r~~~t~~q~~~Le~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 185 (187)
.+|+|..|+..-.++|..+|- .++||+..++++||++.+++..||-.||.|.|-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI 244 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI 244 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee
Confidence 467788899999999999994 578999999999999999999999999999874
No 62
>KOG1146|consensus
Probab=97.80 E-value=2.2e-05 Score=70.75 Aligned_cols=59 Identities=24% Similarity=0.258 Sum_probs=55.0
Q ss_pred cccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCCC
Q psy15514 129 KRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMRG 187 (187)
Q Consensus 129 ~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 187 (187)
.-..++.|+.++..||..|...|....||...+.+.|...++++...|++||||-|.|+
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s 958 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKS 958 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhh
Confidence 34567789999999999999999999999999999999999999999999999999875
No 63
>KOG2252|consensus
Probab=97.64 E-value=9e-05 Score=61.41 Aligned_cols=55 Identities=18% Similarity=0.247 Sum_probs=51.1
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
..+++|.+||..|...|...|..+++|+....+.|+..++|....|..||.|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRR 473 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARR 473 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhh
Confidence 5566799999999999999999999999999999999999999999999998653
No 64
>KOG3623|consensus
Probab=97.58 E-value=0.00015 Score=62.05 Aligned_cols=113 Identities=14% Similarity=0.135 Sum_probs=82.6
Q ss_pred HHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhh
Q psy15514 74 LDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFER 153 (187)
Q Consensus 74 l~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~ 153 (187)
+..|...|..+..|..++...++...|++-..|+.||++.....-+..-.+..+....+-+.++....++-..|..+++.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~el 647 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYEL 647 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhc
Confidence 67788899999999999999999999999999999999877654433333333333344445566666666667777776
Q ss_pred cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 154 TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 154 ~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
+.-+.-.+--..+.++...+..|.+||++|+..
T Consensus 648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsst 680 (1007)
T KOG3623|consen 648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSST 680 (1007)
T ss_pred ccCccCcccchhhhhccCCCcchhhcccCCCCC
Confidence 665554444444555777788889999999864
No 65
>KOG0775|consensus
Probab=97.45 E-value=0.00022 Score=54.22 Aligned_cols=57 Identities=23% Similarity=0.219 Sum_probs=47.7
Q ss_pred ccCCCCCCCC---------cCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 59 KRKQRRSRTT---------FSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 59 ~~~~~r~rt~---------ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
.+|-.-+||. |-+.....|...|..++||...+..+||..+||+..+|..||.|++-
T Consensus 164 RrKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQ 229 (304)
T KOG0775|consen 164 RRKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQ 229 (304)
T ss_pred eccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhh
Confidence 3455556776 45566678999999999999999999999999999999999998763
No 66
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.42 E-value=0.00011 Score=42.43 Aligned_cols=41 Identities=15% Similarity=0.292 Sum_probs=31.0
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514 144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
+..|+..|...+++.......|..+.+|+..+|+.||-.+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 35599999999999999999999999999999999997664
No 67
>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=97.34 E-value=9.7e-05 Score=40.03 Aligned_cols=32 Identities=25% Similarity=0.242 Sum_probs=26.0
Q ss_pred hcCCCChhhhHHHHHhhcCCchhhHhHhhccC
Q psy15514 83 RTQYPDIYTREELAQRTKLFPHFLIIIEQQSS 114 (187)
Q Consensus 83 ~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~ 114 (187)
.++||+..+++.|+..+|++..+|..||-|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaR 38 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINAR 38 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhH
Confidence 36799999999999999999999999998753
No 68
>KOG0773|consensus
Probab=96.63 E-value=0.0016 Score=52.44 Aligned_cols=54 Identities=20% Similarity=0.309 Sum_probs=45.2
Q ss_pred cccCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 133 RRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 133 ~r~r~~~t~~q~~~Le~~f~~---~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
.+....+......+|+.+... .+||+..++..|+.++||+..||.+||.|.|-+
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R 296 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR 296 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence 344457888888888877433 579999999999999999999999999999865
No 69
>KOG1168|consensus
Probab=96.53 E-value=0.00069 Score=51.96 Aligned_cols=56 Identities=18% Similarity=0.208 Sum_probs=49.8
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
-++|.||..-.-....||..|..++-|+..-...+|.+++|....|.+||.|.+..
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQK 363 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQK 363 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHH
Confidence 45567788888888999999999999999999999999999999999999987743
No 70
>KOG0774|consensus
Probab=96.10 E-value=0.0054 Score=46.49 Aligned_cols=54 Identities=26% Similarity=0.280 Sum_probs=47.1
Q ss_pred CCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 62 QRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 62 ~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
.+|.|-.|+-.--+.|...|.. ++||+-.+.++||+.-+++..+|..||.+.+-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrI 244 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRI 244 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhcccccccee
Confidence 4566677999999999999954 68999999999999999999999999987653
No 71
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.80 E-value=0.022 Score=32.80 Aligned_cols=46 Identities=15% Similarity=0.376 Sum_probs=35.6
Q ss_pred cccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 133 RRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 133 ~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
++.|..+|.++...+-..++.+. ....||..+|++..+|..|..|+
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 46788999999888888888876 57789999999999999999886
No 72
>KOG3623|consensus
Probab=95.57 E-value=0.014 Score=50.40 Aligned_cols=43 Identities=16% Similarity=0.142 Sum_probs=40.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCCC
Q psy15514 144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKMR 186 (187)
Q Consensus 144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 186 (187)
+..|...|..|..|...+...+|..+||+...|+.||.+++++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~ 610 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAE 610 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhh
Confidence 6788999999999999999999999999999999999998764
No 73
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.20 E-value=0.03 Score=32.43 Aligned_cols=43 Identities=9% Similarity=0.061 Sum_probs=31.1
Q ss_pred HHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCC
Q psy15514 73 QLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSG 115 (187)
Q Consensus 73 ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~ 115 (187)
.+..|+..|...+++.-.....|..+.+|+..+|+.||..+..
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 4567999999999999999999999999999999999976543
No 74
>KOG1146|consensus
Probab=95.10 E-value=0.029 Score=51.52 Aligned_cols=57 Identities=21% Similarity=0.225 Sum_probs=52.4
Q ss_pred CCCCCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCC
Q psy15514 61 KQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEG 117 (187)
Q Consensus 61 ~~~r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~ 117 (187)
.+++.||.++..||..|...|....||...+.+.|...+++..+.|++||+|.+...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s 958 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKS 958 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhh
Confidence 466789999999999999999999999999999999999999999999999877544
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=93.58 E-value=0.12 Score=29.65 Aligned_cols=39 Identities=26% Similarity=0.416 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhh
Q psy15514 139 FSAQQLDELERAFERTQY--PDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~--p~~~~~~~la~~~~l~~~~v~ 177 (187)
+|+.|.+.|..+++..-| |-.....+||..+|++..-+.
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 588999999999999886 666777899999999987654
No 76
>PF13551 HTH_29: Winged helix-turn helix
Probab=87.57 E-value=1.6 Score=28.49 Aligned_cols=86 Identities=17% Similarity=0.171 Sum_probs=52.4
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcc-cccccccCCCCCHHHHHHHHHHhhhcCC-----CCHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPL-KRKQRRSRTTFSAQQLDELERAFERTQY-----PDIYTREE 164 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~-~~~~~r~r~~~t~~q~~~Le~~f~~~~~-----p~~~~~~~ 164 (187)
+..++|..+|++...|..|...-...+... ... .....+.+..+++++...|...+..++. .+......
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~-----l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~ 88 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEG-----LLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAE 88 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHH-----HHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHH
Confidence 467889999999999999976544333111 111 1112233333899999999999987752 22332222
Q ss_pred -H-HHH--cCCChhhhhhhhc
Q psy15514 165 -L-AQR--TKLTEARIQTIFI 181 (187)
Q Consensus 165 -l-a~~--~~l~~~~v~~WF~ 181 (187)
| ... +.++...|..|++
T Consensus 89 ~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 89 WLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred HHHHhccCccCCHHHHHHHHH
Confidence 3 222 2577788888774
No 77
>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=85.68 E-value=2 Score=26.12 Aligned_cols=43 Identities=16% Similarity=0.183 Sum_probs=28.4
Q ss_pred ccCCCCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 134 RSRTTFSAQQLDELERAF-ERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 134 r~r~~~t~~q~~~Le~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
+.|..||+++...+-..+ ... .....+|.++||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 356789988887776555 333 3677899999999999999964
No 78
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=83.97 E-value=1.4 Score=33.05 Aligned_cols=40 Identities=18% Similarity=0.385 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhh
Q psy15514 138 TFSAQQLDELERAFERTQY--PDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~--p~~~~~~~la~~~~l~~~~v~ 177 (187)
.+|+.|++.|..+|...-| |-.....+||+.+|++..-+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 6999999999999999875 777778899999999987554
No 79
>KOG0773|consensus
Probab=82.69 E-value=1.4 Score=35.46 Aligned_cols=55 Identities=15% Similarity=0.059 Sum_probs=44.5
Q ss_pred CCCCCCCcCHHHHHHHHHHhhh---cCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 62 QRRSRTTFSAQQLDELERAFER---TQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 62 ~~r~rt~ft~~ql~~Le~~F~~---~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
..+....+.......|...... .+||...+...|+..+||+..+|..||-|.+..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R 296 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVR 296 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccc
Confidence 4455667888888888877433 469999999899999999999999999876643
No 80
>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=82.54 E-value=1 Score=26.54 Aligned_cols=20 Identities=15% Similarity=0.290 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCChhhhhhhh
Q psy15514 161 TREELAQRTKLTEARIQTIF 180 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF 180 (187)
.-.+||.+||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 35688999999999999994
No 81
>cd00131 PAX Paired Box domain
Probab=79.21 E-value=16 Score=25.03 Aligned_cols=104 Identities=6% Similarity=-0.010 Sum_probs=60.5
Q ss_pred CcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHH
Q psy15514 68 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDEL 147 (187)
Q Consensus 68 ~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~L 147 (187)
.++...-..+-..++.. ....++|..++++...|..|-..-...++-... ..... .+...+..+...+
T Consensus 17 ~lS~d~R~rIv~~~~~G-----~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk------~~gg~-rpr~~~~~~~~~i 84 (128)
T cd00131 17 PLPDSIRQRIVELAQSG-----IRPCDISRQLRVSHGCVSKILNRYYETGSIRPG------AIGGS-KPRVATPEVVKKI 84 (128)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCC------CCCCC-CCCcCCHHHHHHH
Confidence 45555444444444322 355678999999999999997654433321110 00011 1224566776777
Q ss_pred HHHhhhcCCCCHHHHHHHHHHcCC-------Chhhhhhhhccc
Q psy15514 148 ERAFERTQYPDIYTREELAQRTKL-------TEARIQTIFIVR 183 (187)
Q Consensus 148 e~~f~~~~~p~~~~~~~la~~~~l-------~~~~v~~WF~nr 183 (187)
+.....++..+..+..++...-|+ +...|..||+++
T Consensus 85 ~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 85 EIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred HHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 766677777666666544224465 788888887653
No 82
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=79.13 E-value=6.7 Score=23.19 Aligned_cols=66 Identities=17% Similarity=0.233 Sum_probs=40.9
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK 170 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~ 170 (187)
...++|..+|++.+.+..|....--. . .+....+..|+.+.+..|... ..|-. .|
T Consensus 2 ti~eva~~~gvs~~tlr~y~~~gll~-----------~-~~~~~g~r~y~~~dv~~l~~i------------~~l~~-~G 56 (69)
T PF13411_consen 2 TIKEVAKLLGVSPSTLRYYEREGLLP-----------P-PRDENGYRYYSEEDVERLREI------------KELRK-QG 56 (69)
T ss_dssp EHHHHHHHTTTTHHHHHHHHHTTSST-----------T-BESTTSSEEE-HHHHHHHHHH------------HHHHH-TT
T ss_pred cHHHHHHHHCcCHHHHHHHHHhcCcc-----------c-ccccCceeeccHHHHHHHHHH------------HHHHH-Cc
Confidence 35678999999999999997533311 1 112334467999999988533 33333 66
Q ss_pred CChhhhhhhhc
Q psy15514 171 LTEARIQTIFI 181 (187)
Q Consensus 171 l~~~~v~~WF~ 181 (187)
++..+|+-+++
T Consensus 57 ~sl~~I~~~l~ 67 (69)
T PF13411_consen 57 MSLEEIKKLLK 67 (69)
T ss_dssp THHHHHHHHH-
T ss_pred CCHHHHHHHHc
Confidence 66666665554
No 83
>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=79.04 E-value=4.8 Score=23.06 Aligned_cols=40 Identities=25% Similarity=0.277 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHhhhcCC--CChhhhHHHHHhhcCCchhhHh
Q psy15514 69 FSAQQLDELERAFERTQY--PDIYTREELAQRTKLFPHFLII 108 (187)
Q Consensus 69 ft~~ql~~Le~~F~~~~y--p~~~~r~~la~~~~l~~~~v~~ 108 (187)
+|+.|.+.|...++..-| |-.....+||..+|++...+..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 478899999999988765 7788899999999999876643
No 84
>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=77.88 E-value=5.1 Score=22.18 Aligned_cols=39 Identities=15% Similarity=0.309 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..+|...|..+ ....++|..+|++...|+.+..
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 47888889998888333 3467899999999999987653
No 85
>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=76.01 E-value=14 Score=21.89 Aligned_cols=65 Identities=14% Similarity=0.172 Sum_probs=40.1
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 171 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l 171 (187)
..++|+.+|++...+..|...-.-. ...+....+-.|+..++..|... ......|+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~~gl~-----------~~~r~~~g~R~yt~~di~~l~~i-------------~~l~~~g~ 58 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWEREFGLL-----------KPQRSDGGHRLFNDADIDRILEI-------------KRWIDNGV 58 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCC-----------CCCcCCCCCcccCHHHHHHHHHH-------------HHHHHcCC
Confidence 4678999999999999997532111 01111223346999998888532 22344677
Q ss_pred Chhhhhhhh
Q psy15514 172 TEARIQTIF 180 (187)
Q Consensus 172 ~~~~v~~WF 180 (187)
+-.+|+.++
T Consensus 59 ~l~~i~~~l 67 (68)
T cd04763 59 QVSKVKKLL 67 (68)
T ss_pred CHHHHHHHh
Confidence 776666554
No 86
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=75.20 E-value=4 Score=22.22 Aligned_cols=40 Identities=13% Similarity=0.269 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
..||.++...++..++.+ ....++|..+|++...|..+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 468888888888887655 2466799999999999887653
No 87
>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=73.25 E-value=16 Score=21.46 Aligned_cols=64 Identities=17% Similarity=0.243 Sum_probs=40.7
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 171 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l 171 (187)
..++|..+|++...+..|.....-.. + +....+..|+.+++..|.... . ....|+
T Consensus 3 i~evA~~~gvs~~tlR~~~~~g~l~~------~------~~~~g~R~y~~~~l~~l~~i~------------~-l~~~g~ 57 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKEFNLYI------P------RTENGRRYYTDEDIELLKKIK------------T-LLEKGL 57 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCC------C------CCCCCceeeCHHHHHHHHHHH------------H-HHHCCC
Confidence 46789999999999999976433210 0 111233469999998885332 2 334677
Q ss_pred Chhhhhhhh
Q psy15514 172 TEARIQTIF 180 (187)
Q Consensus 172 ~~~~v~~WF 180 (187)
+-.+|+.+.
T Consensus 58 ~l~~i~~~l 66 (67)
T cd04764 58 SIKEIKEIL 66 (67)
T ss_pred CHHHHHHHh
Confidence 777776654
No 88
>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=72.85 E-value=2 Score=26.43 Aligned_cols=36 Identities=19% Similarity=0.066 Sum_probs=26.6
Q ss_pred HHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 148 ERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 148 e~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
+..|....|-......++|..+|++...|+.|+.+.
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 344555544444567899999999999999998753
No 89
>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=72.15 E-value=3.7 Score=23.10 Aligned_cols=39 Identities=10% Similarity=0.139 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
+++.+...+.-.|-.+ ....++|..+|++...|+.|...
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566666666554433 36789999999999999999864
No 90
>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=71.64 E-value=14 Score=21.01 Aligned_cols=45 Identities=13% Similarity=0.245 Sum_probs=29.9
Q ss_pred CCCCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhcc
Q psy15514 64 RSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQS 113 (187)
Q Consensus 64 r~rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~ 113 (187)
+.|..+|-.+.-.+-..++... ...++|..+|++..+|..|..+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 4567788777776666666554 56789999999999998887553
No 91
>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=71.61 E-value=4.7 Score=21.92 Aligned_cols=41 Identities=10% Similarity=0.173 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
.+++.+...+...|... ....++|..+|++...|..|...-
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 35677777777666322 246678999999999999997653
No 92
>PRK10072 putative transcriptional regulator; Provisional
Probab=70.22 E-value=12 Score=24.29 Aligned_cols=40 Identities=13% Similarity=0.098 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 185 (187)
.+...+..|......+ ..+||..+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3555566664333322 678999999999999999987763
No 93
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=70.20 E-value=14 Score=24.87 Aligned_cols=43 Identities=9% Similarity=-0.032 Sum_probs=29.0
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
|..||.+.....-.....+.+ ...++|.++||+...|..|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 456787775544333333332 3567899999999999999753
No 94
>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=69.61 E-value=8.3 Score=20.98 Aligned_cols=40 Identities=13% Similarity=0.308 Sum_probs=28.6
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
..++.++.+.+...+... + ...++|+.+|++...|.-++.
T Consensus 4 ~~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHHh
Confidence 346676777777777766 2 477899999999999887763
No 95
>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=68.74 E-value=28 Score=22.58 Aligned_cols=48 Identities=15% Similarity=0.165 Sum_probs=31.1
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....--.. . ......+..|+.+++..|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gll~~----------~-~~~~~g~R~y~~~di~~l~~i 50 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGLLKP----------S-RRTENGYRLYTEEDLERLQQI 50 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC----------C-ccCCCCceeeCHHHHHHHHHH
Confidence 46789999999999999975322110 0 111113346999999888654
No 96
>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=68.27 E-value=12 Score=18.00 Aligned_cols=38 Identities=16% Similarity=0.322 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 180 (187)
.++.++...+...+... + ....++..+|++...|..|.
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 35666666666666533 2 45678999999999888874
No 97
>smart00351 PAX Paired Box domain.
Probab=66.80 E-value=37 Score=23.01 Aligned_cols=100 Identities=5% Similarity=-0.020 Sum_probs=56.2
Q ss_pred cCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHH
Q psy15514 69 FSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE 148 (187)
Q Consensus 69 ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le 148 (187)
++.++-..+-..+... ....++|..++++...|..|...-...+.-.... .........+..+...+.
T Consensus 18 ~s~~~R~riv~~~~~G-----~s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~-------~gg~rp~~~~~~~~~~I~ 85 (125)
T smart00351 18 LPDEERQRIVELAQNG-----VRPCDISRQLCVSHGCVSKILGRYYETGSIRPGA-------IGGSKPKVATPKVVKKIA 85 (125)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcC-------CCCCCCCccCHHHHHHHH
Confidence 5555555544444322 2456889999999999999976433332211100 001122345666666677
Q ss_pred HHhhhcCCCCHHHHHHHHHHcCC-------Chhhhhhhh
Q psy15514 149 RAFERTQYPDIYTREELAQRTKL-------TEARIQTIF 180 (187)
Q Consensus 149 ~~f~~~~~p~~~~~~~la~~~~l-------~~~~v~~WF 180 (187)
.....++.....+...+....|+ +...|-.||
T Consensus 86 ~~~~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 86 DYKQENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred HHHHHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 77777777777666443335554 445555554
No 98
>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=65.97 E-value=24 Score=20.59 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=31.3
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|........ ..+.......|+.+++..|...
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~~g~~~-----------~~r~~~~~r~yt~~~v~~l~~i 50 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERRYGLPA-----------PQRTDGGHRLYSEADVARLRLI 50 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHhCCCCC-----------CCcCCCCCeecCHHHHHHHHHH
Confidence 46789999999999999985321110 0011123356899999888644
No 99
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=65.50 E-value=12 Score=23.80 Aligned_cols=40 Identities=15% Similarity=0.211 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
.++++|...-...|+.+--.+....+++|.+|++++-.|+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3567777777777777666666677889999999886654
No 100
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=63.76 E-value=6.2 Score=21.45 Aligned_cols=21 Identities=19% Similarity=0.156 Sum_probs=18.0
Q ss_pred HHHHHHHcCCChhhhhhhhcc
Q psy15514 162 REELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~n 182 (187)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 101
>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=63.74 E-value=2.2 Score=24.90 Aligned_cols=21 Identities=10% Similarity=0.097 Sum_probs=18.2
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..||++...|..|-+
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 356899999999999999964
No 102
>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=63.39 E-value=35 Score=22.90 Aligned_cols=73 Identities=25% Similarity=0.261 Sum_probs=42.9
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTK 170 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~ 170 (187)
...++|..++++...|..|+. ....+.-. . +++ .+..+..+ .|...-.. +|+.... +||..+|
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~-~--------k~r-~~~Kid~~---~L~~~v~~--~pd~tl~-Ela~~l~ 82 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK-RKETGDLE-P--------KPR-GRKKIDRD---ELKALVEE--NPDATLR-ELAERLG 82 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH-hccccccc-c--------ccc-ccccccHH---HHHHHHHH--CCCcCHH-HHHHHcC
Confidence 456788899999999999998 33322211 0 111 11134333 34444333 5666544 6789999
Q ss_pred CChhhhhhhh
Q psy15514 171 LTEARIQTIF 180 (187)
Q Consensus 171 l~~~~v~~WF 180 (187)
++...|-..+
T Consensus 83 Vs~~ti~~~L 92 (119)
T PF01710_consen 83 VSPSTIWRAL 92 (119)
T ss_pred CCHHHHHHHH
Confidence 9887665443
No 103
>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=62.21 E-value=25 Score=20.56 Aligned_cols=18 Identities=6% Similarity=0.117 Sum_probs=15.0
Q ss_pred HHHHHcCCChhhhhhhhc
Q psy15514 164 ELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 164 ~la~~~~l~~~~v~~WF~ 181 (187)
..|.++|+++.+|+-|-+
T Consensus 30 Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 30 AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHHTTS-HHHHHHHHT
T ss_pred HHHHHhCccHHHHHHHHH
Confidence 359999999999999975
No 104
>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=61.79 E-value=13 Score=21.21 Aligned_cols=39 Identities=13% Similarity=0.232 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.||+.++..|.-...-. ...++|..+++++..|..+..+
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~ 41 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRR 41 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHH
Confidence 57888888887666554 3678999999999999887654
No 105
>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=59.74 E-value=45 Score=21.59 Aligned_cols=48 Identities=21% Similarity=0.172 Sum_probs=31.3
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|...-..-.. .+....+-.||.+++..|...
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~~gli~p-----------~r~~~g~R~Yt~~di~~l~~I 50 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETEFPQLKP-----------VKRAGGRRYYRPKDVELLLLI 50 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHHcCCCCC-----------cCCCCCCeeeCHHHHHHHHHH
Confidence 457899999999999999754221100 011123446999999988654
No 106
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=57.80 E-value=9.2 Score=21.01 Aligned_cols=24 Identities=13% Similarity=0.195 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCChhhhhhhhcccC
Q psy15514 161 TREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
...++|..+|++...|..|.+.-+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT---
T ss_pred CHHHHHHHHCcCHHHHHHHHHHcc
Confidence 467899999999999999986533
No 107
>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=57.77 E-value=55 Score=21.91 Aligned_cols=45 Identities=24% Similarity=0.256 Sum_probs=30.0
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE 148 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le 148 (187)
..++|..+|++.+.+.-|....--... +. ....-.|+..++..|.
T Consensus 3 IgevA~~~gvs~~tlRyYe~~GLl~p~-----------~~-~~gyR~Y~~~~l~~l~ 47 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEEKGLIASI-----------GR-RGLRRQYDPQVLDRLA 47 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------cC-CCCceecCHHHHHHHH
Confidence 467899999999999998753221110 11 1244568998888885
No 108
>PF13518 HTH_28: Helix-turn-helix domain
Probab=57.71 E-value=8.9 Score=21.10 Aligned_cols=22 Identities=9% Similarity=0.141 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3557899999999999999864
No 109
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=57.48 E-value=17 Score=27.08 Aligned_cols=41 Identities=22% Similarity=0.293 Sum_probs=35.9
Q ss_pred CcCHHHHHHHHHHhhhcC--CCChhhhHHHHHhhcCCchhhHh
Q psy15514 68 TFSAQQLDELERAFERTQ--YPDIYTREELAQRTKLFPHFLII 108 (187)
Q Consensus 68 ~ft~~ql~~Le~~F~~~~--yp~~~~r~~la~~~~l~~~~v~~ 108 (187)
.+|+.|++.|...|..-- ||-.....+||+.+|++...+..
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 699999999999998876 58889999999999999876643
No 110
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=56.70 E-value=10 Score=26.48 Aligned_cols=41 Identities=22% Similarity=0.253 Sum_probs=31.9
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
..+|+.|...|.. +..+ ....++|..+|++...|..|-+..
T Consensus 5 ~~Lt~rqreVL~l-r~~G-----lTq~EIAe~LGiS~~tVs~ie~ra 45 (141)
T PRK03975 5 SFLTERQIEVLRL-RERG-----LTQQEIADILGTSRANVSSIEKRA 45 (141)
T ss_pred cCCCHHHHHHHHH-HHcC-----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5688999999877 3322 246789999999999999987653
No 111
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=56.15 E-value=29 Score=22.90 Aligned_cols=41 Identities=12% Similarity=0.157 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccCC
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRKM 185 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 185 (187)
.+++..+..+.+.+.-. ...+|..+|++...|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37888888888777665 467899999999999999998864
No 112
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=56.09 E-value=10 Score=21.97 Aligned_cols=23 Identities=22% Similarity=0.449 Sum_probs=18.2
Q ss_pred HHHHHHHHcCCChhhhhhhhccc
Q psy15514 161 TREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~nr 183 (187)
....||+.+|++...|..|+.++
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 45689999999999999999876
No 113
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=55.90 E-value=67 Score=22.39 Aligned_cols=80 Identities=18% Similarity=0.090 Sum_probs=49.0
Q ss_pred ChhhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHH
Q psy15514 88 DIYTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQ 167 (187)
Q Consensus 88 ~~~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~ 167 (187)
.-+...++|+.+|.+...|..|-..-...+...... .... ....++.+|+.+|...-+...+-.......|..
T Consensus 20 ~G~S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~---~~~G----rP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~ 92 (138)
T COG3415 20 EGLSCREAAKRFGVSISTVYRWVRRYRETGLDLPPK---PRKG----RPRKLSEEQLEILLERLREKDWTLKELVEELGL 92 (138)
T ss_pred cCccHHHHHHHhCccHHHHHHHHHHhccccccccCc---cCCC----CCcccCHHHHHHHHHHHhcccchHHHHHHHHhh
Confidence 334556789999999999999987655554441111 1111 113578899888877766665333333345566
Q ss_pred HcCCChh
Q psy15514 168 RTKLTEA 174 (187)
Q Consensus 168 ~~~l~~~ 174 (187)
+.|+...
T Consensus 93 e~gv~y~ 99 (138)
T COG3415 93 EFGVWYH 99 (138)
T ss_pred hcCeEEe
Confidence 6666554
No 114
>COG3028 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=55.85 E-value=3.7 Score=29.54 Aligned_cols=10 Identities=60% Similarity=0.717 Sum_probs=8.3
Q ss_pred cccchhhcCC
Q psy15514 3 WGDRLIKEGL 12 (187)
Q Consensus 3 ~rdrll~e~v 12 (187)
||||||++|.
T Consensus 122 ~RdrLia~GD 131 (187)
T COG3028 122 LRDRLIAEGD 131 (187)
T ss_pred HHHHHHhcCc
Confidence 7899999874
No 115
>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=55.41 E-value=22 Score=20.57 Aligned_cols=34 Identities=26% Similarity=0.398 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhh
Q psy15514 142 QQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTI 179 (187)
Q Consensus 142 ~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~W 179 (187)
.|+..|+-.+. +.+.... +||..+|+++..|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 46778888888 6666544 8999999999988764
No 116
>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=54.12 E-value=35 Score=24.57 Aligned_cols=42 Identities=17% Similarity=0.375 Sum_probs=34.7
Q ss_pred cCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy15514 135 SRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQT 178 (187)
Q Consensus 135 ~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 178 (187)
...++|++++.++.+.-..+ |....+..||+++|++..-|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHH
Confidence 34689999999998887665 7888999999999998876544
No 117
>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=53.92 E-value=53 Score=22.27 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=33.0
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++...+..|....--.. . .......|+.+++..|...
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~~GLl~p------------~-r~~G~R~Ys~~dv~rL~~I 49 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWERHGLIKP------------A-RRNGQRLYSNNDLKRLRFI 49 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCC------------c-CCCCcEEECHHHHHHHHHH
Confidence 456789999999999999986422111 0 1134467999999999755
No 118
>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=53.81 E-value=69 Score=23.03 Aligned_cols=43 Identities=21% Similarity=0.469 Sum_probs=34.6
Q ss_pred CCCcCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHh
Q psy15514 66 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIE 110 (187)
Q Consensus 66 rt~ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wf 110 (187)
....|++++.++.+.-.. -|..+++..||+.+|.+...|.+-.
T Consensus 83 ~y~Lt~e~i~Eir~LR~~--DP~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAE--DPEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred cccCCHHHHHHHHHHHHc--CchHhhHHHHHHHhCCCHHHHHHhc
Confidence 367899999998777644 4677899999999999998886543
No 119
>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=53.46 E-value=15 Score=20.51 Aligned_cols=23 Identities=22% Similarity=0.345 Sum_probs=19.4
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..+||+.+|++...|..|..+.+
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 47899999999999999998765
No 120
>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=51.45 E-value=17 Score=19.21 Aligned_cols=23 Identities=13% Similarity=0.107 Sum_probs=18.8
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..++|..+|++...|..|.++..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 45789999999999999976543
No 121
>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=50.54 E-value=15 Score=19.32 Aligned_cols=18 Identities=11% Similarity=0.071 Sum_probs=14.8
Q ss_pred HHHHHHcCCChhhhhhhh
Q psy15514 163 EELAQRTKLTEARIQTIF 180 (187)
Q Consensus 163 ~~la~~~~l~~~~v~~WF 180 (187)
.++|+.+|++...|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 478999999999999984
No 122
>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=50.34 E-value=69 Score=22.18 Aligned_cols=48 Identities=17% Similarity=0.154 Sum_probs=30.5
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++...+..|....--.. .+ .....-.|+.+++..|...
T Consensus 3 ~I~EvA~~~Gvs~~tLRyYE~~GLl~p-----------~r-~~~g~R~Y~~~dl~~l~~I 50 (139)
T cd01110 3 SVGEVAKRSGVAVSALHFYEQKGLIAS-----------WR-NAGNQRRYPRDVLRRIAFI 50 (139)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCC-----------Cc-CCCCCeEECHHHHHHHHHH
Confidence 456889999999999999976422111 00 1112234888888877644
No 123
>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=50.26 E-value=12 Score=20.67 Aligned_cols=21 Identities=10% Similarity=0.257 Sum_probs=18.6
Q ss_pred HHHHHcCCChhhhhhhhcccC
Q psy15514 164 ELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 164 ~la~~~~l~~~~v~~WF~nrR 184 (187)
+||..+|++...|..|+.+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998863
No 124
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=50.04 E-value=44 Score=21.22 Aligned_cols=43 Identities=12% Similarity=0.156 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhh-----cCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 139 FSAQQLDELERAFER-----TQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~-----~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
+|.+|+..+...|.. ..+.+..+...+...+|+++..|...|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 578888888888754 2356777777766778888888877774
No 125
>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=48.83 E-value=20 Score=19.86 Aligned_cols=23 Identities=13% Similarity=0.055 Sum_probs=20.2
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56899999999999999997764
No 126
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=48.47 E-value=44 Score=18.13 Aligned_cols=39 Identities=18% Similarity=0.276 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.+++.+...+...+ .. + ...++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~-~g-~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA-EG-L----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH-cC-C----CHHHHHHHHCCCHHHHHHHHHH
Confidence 46777777775533 22 1 4578899999999999988653
No 127
>PRK13558 bacterio-opsin activator; Provisional
Probab=46.74 E-value=22 Score=31.18 Aligned_cols=40 Identities=23% Similarity=0.424 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhh
Q psy15514 137 TTFSAQQLDELERAFERTQY--PDIYTREELAQRTKLTEARI 176 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~--p~~~~~~~la~~~~l~~~~v 176 (187)
..+|..|.+.|+.+|....| |-...-++||..||++...+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~ 647 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTF 647 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 46999999999999999987 77777899999999998754
No 128
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=46.53 E-value=59 Score=18.95 Aligned_cols=51 Identities=14% Similarity=0.018 Sum_probs=32.2
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhh
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFER 153 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~ 153 (187)
..++|..+|+++..+..|....--.. ..+....+-.|+...+..|.....-
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~gli~~-----------~~~~~~g~r~y~~~dl~~l~~i~~l 53 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERIGLLPP-----------PIRTEGGYRLYSDEDLERLRFIKRL 53 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-----------CccCCCCCEecCHHHHHHHHHHHHH
Confidence 45788999999999999974221110 0011122346999999988766433
No 129
>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=45.98 E-value=81 Score=20.43 Aligned_cols=48 Identities=19% Similarity=0.209 Sum_probs=31.5
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++.+.+..|....--.. .+.....-.|+.+++..|...
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~~Gll~~------------~r~~~g~R~Y~~~~l~~l~~I 50 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEKLGLITG------------TRNANGYRLYPDSDLQRLLLI 50 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCC------------CcCCCCCeeCCHHHHHHHHHH
Confidence 456889999999999999976322111 011123356889888888643
No 130
>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=45.58 E-value=99 Score=21.32 Aligned_cols=47 Identities=11% Similarity=0.043 Sum_probs=30.7
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....--... +.......|+..++..|...
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~GLl~p~------------r~~~g~R~Y~~~~l~~l~~I 49 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLGLLTPE------------RSDSNYRYYDETALDRLQLI 49 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCc------------cCCCCCeeECHHHHHHHHHH
Confidence 467899999999999999854222210 11113346888888887644
No 131
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=44.93 E-value=48 Score=23.57 Aligned_cols=36 Identities=17% Similarity=0.131 Sum_probs=29.2
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 142 QQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 142 ~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
.-+..|...-+...|.+......+|..+|++..+|.
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 345566666667789999999999999999998774
No 132
>PRK05255 hypothetical protein; Provisional
Probab=44.63 E-value=6.7 Score=28.40 Aligned_cols=10 Identities=60% Similarity=1.232 Sum_probs=8.2
Q ss_pred ccccchhhcC
Q psy15514 2 CWGDRLIKEG 11 (187)
Q Consensus 2 ~~rdrll~e~ 11 (187)
.||||||++|
T Consensus 111 ~wRdrLi~~~ 120 (171)
T PRK05255 111 RWRDRLLAEG 120 (171)
T ss_pred HHHHHHHhCC
Confidence 4899999876
No 133
>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=44.30 E-value=98 Score=20.89 Aligned_cols=47 Identities=21% Similarity=0.221 Sum_probs=30.0
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELER 149 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~ 149 (187)
..++|..+|++.+.+..|....--... .......-.|+.+++..|..
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~GLl~p~-----------~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEKGLIPPP-----------LRSEGGYRTYTQQHLDELRL 49 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCCeecCHHHHHHHHH
Confidence 467899999999999988753322111 11112334688888887753
No 134
>PF04751 DUF615: Protein of unknown function (DUF615); InterPro: IPR006839 The proteins in this entry are functionally uncharacterised. The entry contains the Escherichia coli (strain K12) protein YjgA (P0A8X0 from SWISSPROT), which has been shown to comigrate with the mature 50S ribosome subunit. Therefore it either represents a novel ribosome-associated protein or it is associated with a different oligomeric complex that comigrates with ribosomal particles [].; PDB: 2P0T_A.
Probab=43.84 E-value=6.5 Score=28.06 Aligned_cols=11 Identities=45% Similarity=0.812 Sum_probs=7.9
Q ss_pred ccccchhhcCC
Q psy15514 2 CWGDRLIKEGL 12 (187)
Q Consensus 2 ~~rdrll~e~v 12 (187)
.||||||++|.
T Consensus 100 ~wRdrLi~~~~ 110 (157)
T PF04751_consen 100 RWRDRLIADDD 110 (157)
T ss_dssp HHHHHHHHS-H
T ss_pred HHHHHHHhCCh
Confidence 48899998765
No 135
>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=43.75 E-value=50 Score=23.13 Aligned_cols=36 Identities=11% Similarity=0.029 Sum_probs=28.4
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 142 QQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 142 ~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
.-+..|...=+...|.+......+|..+||+..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345556666566679999999999999999998764
No 136
>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=43.38 E-value=1e+02 Score=20.95 Aligned_cols=50 Identities=12% Similarity=0.115 Sum_probs=31.5
Q ss_pred hhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 90 YTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 90 ~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
+...++|..+|++...+..|....=-... .+.......|+.+++..|...
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~-----------~r~~~gyR~Y~~~~l~~l~~I 51 (131)
T TIGR02043 2 FQIGELAKLCGVTSDTLRFYEKNGLIKPA-----------GRTDSGYRLYTDEDQKRLRFI 51 (131)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCceecCHHHHHHHHHH
Confidence 34578899999999999999854221110 011122346888888887643
No 137
>KOG3755|consensus
Probab=43.07 E-value=28 Score=30.30 Aligned_cols=96 Identities=21% Similarity=0.186 Sum_probs=0.0
Q ss_pred CCCCCCCcCHHHHHHHHHHhhhcC-CCChhh---hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCC
Q psy15514 62 QRRSRTTFSAQQLDELERAFERTQ-YPDIYT---REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRT 137 (187)
Q Consensus 62 ~~r~rt~ft~~ql~~Le~~F~~~~-yp~~~~---r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~ 137 (187)
..+.++..+.+-+..|.......- ||+... ...|...+++....+...|++......
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~------------------- 707 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK------------------- 707 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecc-------------------
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC-------CChhhhhhhhcccCCC
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTK-------LTEARIQTIFIVRKMR 186 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~-------l~~~~v~~WF~nrR~k 186 (187)
+.+|-++..+.-....+--++.. ...+-|+.||.+||.+
T Consensus 708 ----------~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee 753 (769)
T KOG3755|consen 708 ----------HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREE 753 (769)
T ss_pred ----------hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHH
No 138
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=42.75 E-value=52 Score=23.22 Aligned_cols=35 Identities=11% Similarity=0.090 Sum_probs=28.7
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 143 QLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 143 q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
-+..|...-+...|.+......+|+.+||+..+|.
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 45566666666789999999999999999998874
No 139
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=42.40 E-value=28 Score=18.47 Aligned_cols=23 Identities=13% Similarity=0.133 Sum_probs=18.8
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..++|+.+|++...|..|-++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45789999999999999986654
No 140
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=42.18 E-value=66 Score=21.17 Aligned_cols=42 Identities=19% Similarity=0.161 Sum_probs=32.0
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC-Chhhhhhhhc
Q psy15514 136 RTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL-TEARIQTIFI 181 (187)
Q Consensus 136 r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l-~~~~v~~WF~ 181 (187)
+..||.+....+-..+....+ ....+|.++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678998877766666555443 57789999996 9999998864
No 141
>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=41.62 E-value=28 Score=18.25 Aligned_cols=13 Identities=38% Similarity=0.603 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHHH
Q psy15514 138 TFSAQQLDELERA 150 (187)
Q Consensus 138 ~~t~~q~~~Le~~ 150 (187)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 6999999999854
No 142
>PRK04217 hypothetical protein; Provisional
Probab=41.44 E-value=52 Score=21.97 Aligned_cols=40 Identities=13% Similarity=0.159 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
..++.++..++...|...- ...++|+.+|++...|...+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHH
Confidence 4578888887776664433 567899999999999988764
No 143
>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=41.33 E-value=94 Score=19.84 Aligned_cols=49 Identities=16% Similarity=0.036 Sum_probs=31.2
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++.+.+..|....--... .........|+.+++..|...
T Consensus 2 ti~eva~~~gvs~~tLRyye~~Gll~p~-----------~~~~~gyR~Y~~~~l~~l~~I 50 (96)
T cd04768 2 TIGEFAKLAGVSIRTLRHYDDIGLFKPA-----------KIAENGYRYYSYAQLYQLQFI 50 (96)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCC-----------ccCCCCeeeCCHHHHHHHHHH
Confidence 3567899999999999999854221110 011123346888888887643
No 144
>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=40.57 E-value=1.1e+02 Score=20.57 Aligned_cols=48 Identities=17% Similarity=0.108 Sum_probs=30.5
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++.+.+..|....--... .+.......|+.+++..|...
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~Gll~~~-----------~r~~~g~R~Y~~~~l~~l~~I 50 (126)
T cd04785 3 IGELARRTGVNVETIRYYESIGLLPEP-----------ARTAGGYRLYGAAHVERLRFI 50 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCccccCHHHHHHHHHH
Confidence 467899999999999988753322111 011112345888888888644
No 145
>PF12728 HTH_17: Helix-turn-helix domain
Probab=40.44 E-value=29 Score=19.06 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=18.7
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..++|+.+|++...|..|.+...
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~ 26 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGK 26 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35789999999999999986654
No 146
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=40.31 E-value=67 Score=19.06 Aligned_cols=38 Identities=29% Similarity=0.412 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHH---HhhhcCCCCHHHHHHHHHHcCCC-hhhhh
Q psy15514 138 TFSAQQLDELER---AFERTQYPDIYTREELAQRTKLT-EARIQ 177 (187)
Q Consensus 138 ~~t~~q~~~Le~---~f~~~~~p~~~~~~~la~~~~l~-~~~v~ 177 (187)
.+|.-|.++|+- ....+.||. ...+|+..+|+. ...|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHH
Confidence 367777777763 456677873 566889999997 55444
No 147
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=40.23 E-value=65 Score=21.28 Aligned_cols=41 Identities=10% Similarity=0.067 Sum_probs=31.5
Q ss_pred cCHHHHHHHHHHhhhcCCCChhhhHHHHHhhcCCchhhHhHhhccCCC
Q psy15514 69 FSAQQLDELERAFERTQYPDIYTREELAQRTKLFPHFLIIIEQQSSGE 116 (187)
Q Consensus 69 ft~~ql~~Le~~F~~~~yp~~~~r~~la~~~~l~~~~v~~wfq~~~~~ 116 (187)
+++..+..+-..+.-. +...|..+|.+...|+.|.+.+...
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 6677777776666544 4678999999999999999876654
No 148
>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=40.17 E-value=1.3e+02 Score=20.99 Aligned_cols=22 Identities=32% Similarity=0.288 Sum_probs=18.9
Q ss_pred hhHHHHHhhcCCchhhHhHhhc
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQ 112 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~ 112 (187)
...++|..+|++...+.-|...
T Consensus 3 ~IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 3 TVGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 4578999999999999999864
No 149
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=39.63 E-value=1.4e+02 Score=21.21 Aligned_cols=24 Identities=25% Similarity=0.254 Sum_probs=20.1
Q ss_pred hhhHHHHHhhcCCchhhHhHhhcc
Q psy15514 90 YTREELAQRTKLFPHFLIIIEQQS 113 (187)
Q Consensus 90 ~~r~~la~~~~l~~~~v~~wfq~~ 113 (187)
+...++|+.+|++...+..|....
T Consensus 12 ~~IgevAk~~gvs~~TlRyYE~~G 35 (154)
T PRK15002 12 LTPGEVAKRSGVAVSALHFYESKG 35 (154)
T ss_pred ccHHHHHHHHCcCHHHHHHHHHCC
Confidence 567789999999999999997643
No 150
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=39.50 E-value=64 Score=23.32 Aligned_cols=35 Identities=23% Similarity=0.180 Sum_probs=27.9
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 143 QLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 143 q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
-+..|...=+...|.+....+.+|+.+||+..+|.
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34556655566689999999999999999998764
No 151
>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=39.10 E-value=1.1e+02 Score=19.83 Aligned_cols=49 Identities=16% Similarity=0.207 Sum_probs=31.7
Q ss_pred hhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 90 YTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 90 ~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
+...++|..+|++...+..|....=-. .. +.....-.|+..++..|...
T Consensus 2 ~~i~eva~~~gvs~~tLR~ye~~Gll~-----------~~-r~~~g~R~Y~~~dl~~l~~I 50 (102)
T cd04775 2 YTIGQMSRKFGVSRSTLLYYESIGLIP-----------SA-RSEANYRLYSEADLSRLEKI 50 (102)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHCCCCC-----------CC-CCCCCCeeeCHHHHHHHHHH
Confidence 345788999999999999998632110 00 11113346889888888644
No 152
>PHA01976 helix-turn-helix protein
Probab=38.82 E-value=33 Score=19.99 Aligned_cols=23 Identities=17% Similarity=0.223 Sum_probs=19.6
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..+||..+|++...|..|....+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999986654
No 153
>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=38.80 E-value=1.1e+02 Score=19.88 Aligned_cols=64 Identities=16% Similarity=0.053 Sum_probs=37.7
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 171 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l 171 (187)
..++|+.+|++.+.+.-|....=-.. ......| .|+.+.+..|... ..++.+|+
T Consensus 3 Ige~a~~~gvs~~tlRyYe~~GLl~p------------~~~~g~r-~Y~~~~~~~l~~I-------------~~lr~~G~ 56 (107)
T cd04777 3 IGKFAKKNNITIDTVRHYIDLGLLIP------------EKKGGQY-FFDEKCQDDLEFI-------------LELKGLGF 56 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCC------------ccCCCcc-ccCHHHHHHHHHH-------------HHHHHCCC
Confidence 45789999999999988864322111 0011122 5888887777532 33555555
Q ss_pred Chhhhhhhhc
Q psy15514 172 TEARIQTIFI 181 (187)
Q Consensus 172 ~~~~v~~WF~ 181 (187)
+-..|+.+|.
T Consensus 57 sL~eI~~~l~ 66 (107)
T cd04777 57 SLIEIQKIFS 66 (107)
T ss_pred CHHHHHHHHH
Confidence 5555555554
No 154
>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=38.61 E-value=52 Score=22.95 Aligned_cols=34 Identities=24% Similarity=0.190 Sum_probs=25.3
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
+..|...-+...|.+......+|..++|+..+|.
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 5566666666779999999999999999998875
No 155
>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=38.07 E-value=33 Score=20.66 Aligned_cols=23 Identities=17% Similarity=0.229 Sum_probs=19.9
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..+||..+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997664
No 156
>PRK00118 putative DNA-binding protein; Validated
Probab=37.92 E-value=33 Score=22.64 Aligned_cols=40 Identities=10% Similarity=0.105 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.+++.|...+.-.|.... ...++|..+|++...|..|...
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~R 56 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKR 56 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 356666666655544432 4668999999999999998753
No 157
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.80 E-value=60 Score=22.26 Aligned_cols=39 Identities=18% Similarity=0.136 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+...+...|-.+ ....++|..+|++...|+.|..
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ 144 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYR 144 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 35555555554444322 2467899999999999999864
No 158
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=36.55 E-value=73 Score=22.85 Aligned_cols=37 Identities=22% Similarity=0.158 Sum_probs=31.7
Q ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 141 AQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 141 ~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
..-+..|..++....|........+|..||++...|.
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 4457788899988889999999999999999987663
No 159
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=35.96 E-value=64 Score=17.86 Aligned_cols=31 Identities=23% Similarity=0.264 Sum_probs=19.1
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy15514 145 DELERAFERTQYPDIYTREELAQRTKLTEARIQT 178 (187)
Q Consensus 145 ~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 178 (187)
..|.-.+....+ ....+||..++++...|+.
T Consensus 4 ~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 4 QILKLLLESKEP---ITAKELAEELGVSRRTIRR 34 (55)
T ss_dssp HHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHH
T ss_pred HHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHH
Confidence 344444344443 3456899999999988764
No 160
>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=35.88 E-value=27 Score=19.68 Aligned_cols=17 Identities=29% Similarity=0.464 Sum_probs=13.2
Q ss_pred HHHHHHHcCCChhhhhh
Q psy15514 162 REELAQRTKLTEARIQT 178 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~ 178 (187)
-.+||+.+|++..||+-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 35889999999999863
No 161
>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=35.67 E-value=1.3e+02 Score=19.77 Aligned_cols=48 Identities=25% Similarity=0.237 Sum_probs=30.2
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....--... .+. ....-.|+.+++..|...
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~gll~~~----------~r~-~~gyR~Y~~~~l~~l~~I 50 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKEGLLPPV----------KRD-ENGIRDFTEEDLEWLEFI 50 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC----------CcC-CCCCccCCHHHHHHHHHH
Confidence 467899999999999999753221110 001 112235889888888643
No 162
>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=35.57 E-value=40 Score=23.68 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=13.4
Q ss_pred CCCCHHHHHHHHHHhhh
Q psy15514 137 TTFSAQQLDELERAFER 153 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~ 153 (187)
..+|.+|+..|....+.
T Consensus 50 ~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 50 GYLDDEEIEKLEEAVEN 66 (144)
T ss_pred ccCCHHHHHHHHHHHHh
Confidence 35889999999877755
No 163
>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=34.90 E-value=42 Score=17.68 Aligned_cols=23 Identities=26% Similarity=0.365 Sum_probs=19.1
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
...+|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999987653
No 164
>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=34.83 E-value=1.4e+02 Score=20.03 Aligned_cols=66 Identities=12% Similarity=0.082 Sum_probs=38.7
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFERTQYPDIYTREELAQRTKL 171 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l 171 (187)
..++|..+|++.+.+..|....--... .+.....-.|+.+++..|.. ....+.+|+
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~GLl~~~-----------~r~~~gyR~Y~~~~l~~l~~-------------I~~lr~~G~ 58 (126)
T cd04783 3 IGELAKAAGVNVETIRYYQRRGLLPEP-----------PRPEGGYRRYPEETVTRLRF-------------IKRAQELGF 58 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCCeecCHHHHHHHHH-------------HHHHHHcCC
Confidence 467899999999999888643221100 11111234688888888852 223455555
Q ss_pred Chhhhhhhhc
Q psy15514 172 TEARIQTIFI 181 (187)
Q Consensus 172 ~~~~v~~WF~ 181 (187)
+-..|+-++.
T Consensus 59 sL~eI~~~l~ 68 (126)
T cd04783 59 TLDEIAELLE 68 (126)
T ss_pred CHHHHHHHHh
Confidence 5555555543
No 165
>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=34.29 E-value=1.4e+02 Score=19.60 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=30.2
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....--.. ........-.|+..++..|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gll~p-----------~~~~~~g~R~Y~~~dl~~l~~I 50 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEGLLSP-----------DREPETGYRVYDPSDVRDARLI 50 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-----------CcCCCCCceeeCHHHHHHHHHH
Confidence 46789999999999999975322110 0011112235888888877654
No 166
>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=34.29 E-value=81 Score=17.07 Aligned_cols=36 Identities=17% Similarity=0.185 Sum_probs=24.2
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 140 SAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 140 t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
+..+...+.-.+ .. ....++|..++++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 445555554433 11 2457889999999999998864
No 167
>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=33.59 E-value=1.5e+02 Score=19.78 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=30.5
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+.-|....--... .+.....-.|+.+++..|...
T Consensus 3 I~eva~~~gvs~~tLRyYe~~GLl~p~-----------~r~~~gyR~Y~~~~i~~l~~I 50 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYERIGLLPPP-----------QRSENGYRLYGEADLARLRFI 50 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CCCCCCCccCCHHHHHHHHHH
Confidence 467899999999999988753221110 011112346899999888644
No 168
>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=33.54 E-value=1.5e+02 Score=19.91 Aligned_cols=46 Identities=11% Similarity=0.111 Sum_probs=27.7
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELE 148 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le 148 (187)
..++|..+|++...+..|....=-... .......-.|+..++..|.
T Consensus 2 I~e~a~~~gvs~~tlR~Ye~~GLl~~~-----------~r~~~g~R~Y~~~~l~~l~ 47 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYERKGLLPEP-----------DRPEGGYRRYPEETVKRLR 47 (124)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------ccCCCCCEeECHHHHHHHH
Confidence 357899999999999888542211100 0111123457888888774
No 169
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=33.37 E-value=66 Score=22.58 Aligned_cols=39 Identities=8% Similarity=0.054 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..++.-.|-.+ ....++|..+|++...|+.|..
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 46666666665544322 2356899999999999998875
No 170
>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=32.94 E-value=1.6e+02 Score=20.04 Aligned_cols=47 Identities=17% Similarity=0.161 Sum_probs=28.4
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELER 149 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~ 149 (187)
..++|+.+|++...+.-|....=-.. .+......-.|+.+++..|..
T Consensus 3 IgE~A~~~gvs~~TLRyYE~~GLl~p-----------~r~~~~gyR~Y~~~~~~~l~~ 49 (133)
T cd04787 3 VKELANAAGVTPDTVRFYTRIGLLRP-----------TRDPVNGYRLYSEKDLSRLRF 49 (133)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-----------CcCCCCCeeeCCHHHHHHHHH
Confidence 46789999999999988853211110 011101123688888888853
No 171
>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=32.60 E-value=1.6e+02 Score=19.88 Aligned_cols=48 Identities=15% Similarity=0.136 Sum_probs=30.4
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++.+.+..|....--... .+.....-.|+.+++..|...
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~GLl~~~-----------~r~~~g~R~Y~~~~~~~l~~I 50 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEIGLIPPP-----------SRSDNGYRVYNQRDIEELRFI 50 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCceecCHHHHHHHHHH
Confidence 467899999999999998754322111 111122345888888877543
No 172
>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=32.37 E-value=1.3e+02 Score=19.00 Aligned_cols=49 Identities=16% Similarity=0.150 Sum_probs=32.3
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHhh
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAFE 152 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f~ 152 (187)
..++|..+|+++..+..|....--. + .+....+-.|+...+..|...+.
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gll~----------~--~~~~~g~r~y~~~dv~~l~~i~~ 51 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGLLP----------P--ERSENGYRLYSEEDLERLRLIRR 51 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcC----------C--CcCCCCCcccCHHHHHHHHHHHH
Confidence 4578999999999999997532211 0 11111334699999998887753
No 173
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.83 E-value=41 Score=24.75 Aligned_cols=22 Identities=18% Similarity=0.348 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|+++...
T Consensus 171 s~~EIA~~lgis~~tV~~~l~R 192 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRL 192 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999988753
No 174
>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=31.74 E-value=54 Score=18.94 Aligned_cols=18 Identities=28% Similarity=0.403 Sum_probs=11.6
Q ss_pred HHHHHHHHHcCCChhhhh
Q psy15514 160 YTREELAQRTKLTEARIQ 177 (187)
Q Consensus 160 ~~~~~la~~~~l~~~~v~ 177 (187)
.+...+++++|+++.+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 455666777777776654
No 175
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=31.46 E-value=94 Score=21.63 Aligned_cols=40 Identities=28% Similarity=0.338 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
+.++..|...|.-. ..+ ....++|..+|++...|..+-..
T Consensus 5 ~~Lte~qr~VL~Lr-~~G-----lTq~EIAe~LgiS~stV~~~e~r 44 (137)
T TIGR00721 5 TFLTERQIKVLELR-EKG-----LSQKEIAKELKTTRANVSAIEKR 44 (137)
T ss_pred CCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCcCHHHHHHHHHh
Confidence 57888898888763 222 25778999999999999877543
No 176
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=31.36 E-value=48 Score=19.17 Aligned_cols=25 Identities=20% Similarity=0.304 Sum_probs=20.2
Q ss_pred HHHHHHHHcCCChhhhhhhhcccCC
Q psy15514 161 TREELAQRTKLTEARIQTIFIVRKM 185 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~nrR~ 185 (187)
...++|..+|++...|..|-+.++.
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 4678999999999999999988774
No 177
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=31.17 E-value=43 Score=24.27 Aligned_cols=39 Identities=18% Similarity=0.197 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
+++.+..+|.-.|-.+ ....++|..+|++...|+++...
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHH
Confidence 4445545544333222 24678999999999999998753
No 178
>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=30.98 E-value=1.5e+02 Score=19.04 Aligned_cols=49 Identities=12% Similarity=0.139 Sum_probs=32.4
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHh
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAF 151 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f 151 (187)
...++|..+|++...+..|....--.. .+....+-.|+..++..|....
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~Gli~p------------~r~~~g~R~Ys~~dv~~l~~I~ 51 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLGLVSP------------ARTNGGGRRYSNNDLELLRQVQ 51 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCC------------CcCCCCCeeECHHHHHHHHHHH
Confidence 456789999999999999965322110 0111233459999999887653
No 179
>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=30.98 E-value=1.7e+02 Score=19.75 Aligned_cols=50 Identities=18% Similarity=0.139 Sum_probs=32.2
Q ss_pred hhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 90 YTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 90 ~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
+...++|..+|++...|..|....=-... .......-.|+.+++..|.-.
T Consensus 4 ~tI~elA~~~gvs~~tlR~Ye~~GLL~p~-----------~r~~~gyR~Y~~~~l~rL~~I 53 (120)
T TIGR02054 4 YTISRLAEDAGVSVHVVRDYLLRGLLHPV-----------RRTTSGYGIFDDASLQRLRFV 53 (120)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCC-----------ccCCCCCeeCCHHHHHHHHHH
Confidence 56788999999999999999764221110 011112345788888877655
No 180
>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=30.96 E-value=1.7e+02 Score=19.76 Aligned_cols=47 Identities=17% Similarity=0.167 Sum_probs=29.6
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELER 149 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~ 149 (187)
..++|+.+|++.+.+..|....--... .......-.|+.+++..|..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~GLl~~~-----------~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQGLLPPP-----------ARTDNNYRVYTVGHVERLAF 49 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCCCcCCHHHHHHHHH
Confidence 467899999999999999753222111 01111234688888887754
No 181
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=30.84 E-value=58 Score=16.89 Aligned_cols=23 Identities=22% Similarity=0.348 Sum_probs=18.8
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
...+|..+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999986653
No 182
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=30.67 E-value=46 Score=22.98 Aligned_cols=39 Identities=15% Similarity=0.185 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+...+.-.|-.. ....++|..+|++...|.++..
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHH
Confidence 45666666665543222 2467899999999999998764
No 183
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=30.48 E-value=1.9e+02 Score=20.01 Aligned_cols=50 Identities=22% Similarity=0.267 Sum_probs=31.5
Q ss_pred hhhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 90 YTREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 90 ~~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
+...++|..+|++...+..|....--... .+.......|+..++..|...
T Consensus 2 ~~I~e~a~~~gvs~~tlR~Ye~~GLl~p~-----------~r~~~gyR~Y~~~~l~~l~~I 51 (140)
T PRK09514 2 YRIGELAKLAEVTPDTLRFYEKQGLMDPE-----------VRTEGGYRLYTEQDLQRLRFI 51 (140)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHCCCCCCc-----------ccCCCCCeeeCHHHHHHHHHH
Confidence 34678899999999999999753221110 011112346888888877644
No 184
>PF13309 HTH_22: HTH domain
Probab=30.04 E-value=1.1e+02 Score=17.99 Aligned_cols=38 Identities=11% Similarity=0.158 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhh
Q psy15514 142 QQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTI 179 (187)
Q Consensus 142 ~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~W 179 (187)
+-+..+...++..-|--......+|+.||+++..|-.+
T Consensus 25 ~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~Y 62 (64)
T PF13309_consen 25 EKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRY 62 (64)
T ss_pred HHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHH
Confidence 34455666677777777778889999999999877543
No 185
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=29.83 E-value=79 Score=22.07 Aligned_cols=22 Identities=9% Similarity=0.114 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|..|...
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~r 164 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRR 164 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 3578999999999999998753
No 186
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=29.54 E-value=50 Score=17.83 Aligned_cols=34 Identities=15% Similarity=0.376 Sum_probs=24.0
Q ss_pred HHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 149 RAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 149 ~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
..|....|-.. ....+++++|++..-+-..|.|+
T Consensus 7 ~l~~~~G~~~~-s~~~Ia~~~gvs~~~~y~~f~~k 40 (47)
T PF00440_consen 7 ELFAEKGYEAV-SIRDIARRAGVSKGSFYRYFPSK 40 (47)
T ss_dssp HHHHHHHTTTS-SHHHHHHHHTSCHHHHHHHCSSH
T ss_pred HHHHHhCHHhC-CHHHHHHHHccchhhHHHHcCCH
Confidence 34444444333 35688999999999999988875
No 187
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=29.13 E-value=97 Score=21.85 Aligned_cols=39 Identities=8% Similarity=0.113 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..+|.-.|-.+ ....++|..+|++...|+++..
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555555444322 2467899999999999988753
No 188
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=29.04 E-value=43 Score=21.44 Aligned_cols=30 Identities=20% Similarity=0.321 Sum_probs=22.0
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy15514 145 DELERAFERTQYPDIYTREELAQRTKLTEARIQT 178 (187)
Q Consensus 145 ~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 178 (187)
.+|...|....+. .+.+|..|+++...|+.
T Consensus 13 ~ELq~nf~~~~ls----~~~ia~dL~~s~~~le~ 42 (89)
T PF10078_consen 13 QELQANFELSGLS----LEQIAADLGTSPEHLEQ 42 (89)
T ss_pred HHHHHHHHHcCCC----HHHHHHHhCCCHHHHHH
Confidence 3677777777654 66788899988887764
No 189
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=28.92 E-value=64 Score=22.11 Aligned_cols=45 Identities=16% Similarity=0.217 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHH-hhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERA-FERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~-f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.||++|..+|... -+.-+--...+..+|+..+|++...|+..|.+
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHH
Confidence 5788888877643 22222223345668899999999999888753
No 190
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=28.83 E-value=45 Score=22.34 Aligned_cols=40 Identities=8% Similarity=0.122 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.+++.+...+...|-.. ....++|..+|++...|..+...
T Consensus 110 ~L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~ 149 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKR 149 (158)
T ss_pred hCCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 45566666665443221 24568999999999999988754
No 191
>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=28.83 E-value=55 Score=19.70 Aligned_cols=21 Identities=19% Similarity=0.390 Sum_probs=16.0
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
..++||..+|++...|...++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 456889999999999886653
No 192
>PHA02955 hypothetical protein; Provisional
Probab=28.62 E-value=99 Score=23.26 Aligned_cols=43 Identities=12% Similarity=0.006 Sum_probs=33.1
Q ss_pred CHHHHHHHHHHhhhc-CCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 140 SAQQLDELERAFERT-QYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 140 t~~q~~~Le~~f~~~-~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++..|-+.|... .-....++.+++.++|+....|..||.+
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 456777777777665 4567788999999999999877888865
No 193
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=28.19 E-value=57 Score=21.96 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=20.7
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
+++||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 67899999999999999998875
No 194
>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=28.10 E-value=45 Score=17.86 Aligned_cols=16 Identities=31% Similarity=0.470 Sum_probs=12.5
Q ss_pred HHHHHHHcCCChhhhh
Q psy15514 162 REELAQRTKLTEARIQ 177 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~ 177 (187)
-.+||+.+||++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 5688999999998775
No 195
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=28.04 E-value=39 Score=24.40 Aligned_cols=22 Identities=14% Similarity=0.196 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|++|+..
T Consensus 159 s~~EIA~~lgis~~tV~~~l~R 180 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQ 180 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 4678999999999999999754
No 196
>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=27.69 E-value=1.6e+02 Score=18.42 Aligned_cols=49 Identities=14% Similarity=0.194 Sum_probs=32.3
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHHh
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERAF 151 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~f 151 (187)
...++|..+|++...+..|....--.. .+.....-.|+..++..|....
T Consensus 3 ~i~e~A~~~gvs~~tLr~ye~~Gli~p------------~r~~~g~R~y~~~dv~~l~~i~ 51 (91)
T cd04766 3 VISVAAELSGMHPQTLRLYERLGLLSP------------SRTDGGTRRYSERDIERLRRIQ 51 (91)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCcCC------------CcCCCCCeeECHHHHHHHHHHH
Confidence 456889999999999999975322111 0001122358999999887664
No 197
>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=27.36 E-value=62 Score=18.53 Aligned_cols=24 Identities=21% Similarity=0.357 Sum_probs=18.9
Q ss_pred HHHHHHHHcCCChhhhhhhhcccC
Q psy15514 161 TREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
....+|..+|++...|..|-.+++
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 356789999999999999988765
No 198
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=27.30 E-value=70 Score=23.91 Aligned_cols=38 Identities=16% Similarity=0.117 Sum_probs=31.6
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhccc
Q psy15514 144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nr 183 (187)
+..-...|....|- .....+|+..|++..-|-.+|.++
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sK 56 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSK 56 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCH
Confidence 44556778888877 467889999999999999999886
No 199
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=27.29 E-value=1.1e+02 Score=21.86 Aligned_cols=21 Identities=19% Similarity=0.234 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+++..
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ 171 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIK 171 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHH
Confidence 467899999999999998864
No 200
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.26 E-value=55 Score=23.36 Aligned_cols=22 Identities=14% Similarity=0.240 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|+.++..
T Consensus 149 s~~eIA~~l~is~~tV~~~l~r 170 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHR 170 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 4578999999999999988754
No 201
>PF02042 RWP-RK: RWP-RK domain; InterPro: IPR003035 This domain is named RWP-RK after a conserved motif at the C terminus of the domain. The domain is found in algal minus dominance proteins as well as plant proteins involved in nitrogen-controlled development [].
Probab=27.19 E-value=1.1e+02 Score=17.43 Aligned_cols=27 Identities=19% Similarity=0.340 Sum_probs=17.5
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 144 LDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 144 ~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
++.|...|... ..+.|.+||+....++
T Consensus 7 ~~~L~~~fhlp-------~~eAA~~Lgv~~T~LK 33 (52)
T PF02042_consen 7 LEDLSQYFHLP-------IKEAAKELGVSVTTLK 33 (52)
T ss_pred HHHHHHHhCCC-------HHHHHHHhCCCHHHHH
Confidence 44566667544 4566888888876554
No 202
>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=27.15 E-value=1.9e+02 Score=19.02 Aligned_cols=47 Identities=19% Similarity=0.163 Sum_probs=30.1
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....=-.. .+.....-.|+..++..|...
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~GLl~p------------~r~~~g~R~Y~~~~~~~l~~I 49 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQGLLVP------------ERSANGYRDYDEAAVDRVRQI 49 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCC------------CcCCCCCeecCHHHHHHHHHH
Confidence 45789999999999999975322111 011122346888888877644
No 203
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=26.67 E-value=60 Score=22.14 Aligned_cols=23 Identities=17% Similarity=0.145 Sum_probs=20.3
Q ss_pred HHHHHHHcCCChhhhhhhhcccC
Q psy15514 162 REELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..+||..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999998765
No 204
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=26.49 E-value=60 Score=21.92 Aligned_cols=25 Identities=16% Similarity=0.300 Sum_probs=20.6
Q ss_pred CHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 158 DIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 158 ~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.....++||..+|+++..+..+|+.
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHH
Confidence 3356678999999999999999864
No 205
>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=26.34 E-value=1.1e+02 Score=16.28 Aligned_cols=37 Identities=19% Similarity=0.241 Sum_probs=22.4
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy15514 140 SAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIF 180 (187)
Q Consensus 140 t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 180 (187)
+..+...|....+ ++. ....+||..+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHH
Confidence 3445666655555 322 346689999999998776543
No 206
>PRK09726 antitoxin HipB; Provisional
Probab=26.30 E-value=70 Score=20.01 Aligned_cols=24 Identities=25% Similarity=0.278 Sum_probs=20.4
Q ss_pred HHHHHHHHcCCChhhhhhhhcccC
Q psy15514 161 TREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
...+||..+|++...|..|...++
T Consensus 27 tq~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 27 TQSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCC
Confidence 367899999999999999987653
No 207
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.95 E-value=60 Score=22.47 Aligned_cols=20 Identities=15% Similarity=0.257 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhhhhhhhc
Q psy15514 162 REELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~ 181 (187)
..++|..+|++...|++...
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ 144 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLY 144 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56899999999999998764
No 208
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.32 E-value=56 Score=19.16 Aligned_cols=17 Identities=12% Similarity=0.194 Sum_probs=14.9
Q ss_pred HHHHHHcCCChhhhhhh
Q psy15514 163 EELAQRTKLTEARIQTI 179 (187)
Q Consensus 163 ~~la~~~~l~~~~v~~W 179 (187)
..||+.+|++..-|.-|
T Consensus 13 ~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 13 SKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHh
Confidence 47999999999999999
No 209
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=25.25 E-value=38 Score=19.99 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=11.5
Q ss_pred HHHHHHHcCCChhhhh-hhhc
Q psy15514 162 REELAQRTKLTEARIQ-TIFI 181 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~-~WF~ 181 (187)
..+||+.+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 3466777777777776 6653
No 210
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=24.99 E-value=1.2e+02 Score=21.42 Aligned_cols=22 Identities=23% Similarity=0.280 Sum_probs=18.7
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
..+++|..+|++...|+++...
T Consensus 147 s~~eIA~~lgis~~tV~~~l~R 168 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRR 168 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHH
Confidence 3678999999999999998753
No 211
>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=24.91 E-value=1.9e+02 Score=18.36 Aligned_cols=48 Identities=19% Similarity=0.173 Sum_probs=30.0
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++...+..|....--... .......-.|+.+++..|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gll~p~-----------~r~~~gyR~Y~~~~l~~l~~I 50 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHIGLLSPS-----------QRTEGGHRLYDRADIRRLHQI 50 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------ccCCCCceeeCHHHHHHHHHH
Confidence 457899999999999999753221110 011112345888888877643
No 212
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=24.64 E-value=1.3e+02 Score=21.34 Aligned_cols=39 Identities=10% Similarity=0.106 Sum_probs=26.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.|..++.-.|-.+ ...+++|..+|+++..|++...
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~ 165 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIH 165 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45566655555443322 2467899999999999998764
No 213
>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=24.63 E-value=2e+02 Score=18.40 Aligned_cols=47 Identities=23% Similarity=0.249 Sum_probs=30.3
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++.+.+..|....--.. .+.......|+...+..|...
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~Gll~p------------~r~~~g~R~Y~~~dv~~l~~I 49 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIGLVSP------------ERSEGRYRLYSEEDLKRLERI 49 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC------------CcCCCCCEEECHHHHHHHHHH
Confidence 46789999999999999975321110 011123346888888877643
No 214
>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=24.61 E-value=2.1e+02 Score=18.72 Aligned_cols=49 Identities=12% Similarity=0.015 Sum_probs=31.6
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++...+..|....--... .+.....-.|+.+++..|.-.
T Consensus 2 ~Ige~A~~~gvs~~tlR~ye~~GLl~p~-----------~r~~~g~R~Y~~~~l~~l~~I 50 (107)
T cd01111 2 SISQLALDAGVSVHIVRDYLLRGLLHPV-----------ARTEGGYGLFDDCALQRLRFV 50 (107)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCCeecCHHHHHHHHHH
Confidence 3467899999999999999753221110 111123346888888888754
No 215
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=24.33 E-value=71 Score=17.42 Aligned_cols=21 Identities=14% Similarity=0.278 Sum_probs=18.1
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
....+|..+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356889999999999998884
No 216
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=24.18 E-value=1.3e+02 Score=21.50 Aligned_cols=39 Identities=18% Similarity=0.075 Sum_probs=26.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..++...|-.+ ....++|..+|++...|+++..
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 177 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQH 177 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45555555555443332 2467899999999999998764
No 217
>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=24.01 E-value=28 Score=15.80 Aligned_cols=8 Identities=25% Similarity=0.156 Sum_probs=5.9
Q ss_pred hhhhcccC
Q psy15514 177 QTIFIVRK 184 (187)
Q Consensus 177 ~~WF~nrR 184 (187)
-+||-+|.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 47998875
No 218
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.01 E-value=70 Score=22.71 Aligned_cols=22 Identities=18% Similarity=0.194 Sum_probs=18.3
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|++....
T Consensus 152 s~~EIA~~lgis~~tVk~~l~R 173 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRF 173 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3568999999999999987653
No 219
>PRK06930 positive control sigma-like factor; Validated
Probab=23.85 E-value=69 Score=23.07 Aligned_cols=41 Identities=7% Similarity=0.096 Sum_probs=29.6
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 137 TTFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 137 ~~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
..+++.+..++.-.|..+. ...++|..+|++...|+.+...
T Consensus 113 ~~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~R 153 (170)
T PRK06930 113 SVLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIER 153 (170)
T ss_pred HhCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 3567777777765543332 4678999999999999998754
No 220
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=23.82 E-value=1e+02 Score=21.61 Aligned_cols=45 Identities=13% Similarity=0.073 Sum_probs=24.4
Q ss_pred CCCCHHHHHHHHHH--hhhcCCC-CHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 137 TTFSAQQLDELERA--FERTQYP-DIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 137 ~~~t~~q~~~Le~~--f~~~~~p-~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
..++..|+..-.-. -+...+- ......++|.++|+++..+--|-+
T Consensus 9 ~~L~~~Q~kAa~ll~~ne~~~~~~~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 9 AKLTLQQRKAAQLLVENELMPENGERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp TTS-HHHHHHHHHHHHHHHS------S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHcCHHHHHHHHHHHHHHHhhhccccchHHHHHHHhCCCHHHHHHHHh
Confidence 34666666532211 1112211 335678999999999999999974
No 221
>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=23.60 E-value=1.1e+02 Score=19.72 Aligned_cols=34 Identities=21% Similarity=0.307 Sum_probs=21.0
Q ss_pred HHHHHHhhhcC-CCCHHHHHHHHHHcCCChhhhhh
Q psy15514 145 DELERAFERTQ-YPDIYTREELAQRTKLTEARIQT 178 (187)
Q Consensus 145 ~~Le~~f~~~~-~p~~~~~~~la~~~~l~~~~v~~ 178 (187)
+.|..+|..-. ......=..||..+||++..|..
T Consensus 4 ~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 4 ETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred hHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 44666665432 23333445689999999987753
No 222
>PF13730 HTH_36: Helix-turn-helix domain
Probab=23.31 E-value=86 Score=17.32 Aligned_cols=21 Identities=19% Similarity=0.292 Sum_probs=17.4
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
-...||..+|++...|+.+..
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466889999999999987764
No 223
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.11 E-value=2.1e+02 Score=18.23 Aligned_cols=48 Identities=13% Similarity=0.148 Sum_probs=30.9
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|+.+|++...+..|....--.. ..+.......|+..++..|...
T Consensus 3 I~eva~~~gvs~~tlR~Ye~~GLl~p-----------~~r~~~g~r~Y~~~dv~~l~~I 50 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLREGLLPE-----------GRRLAPNQAEYSEAHVERLRLI 50 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-----------CcCCCCCCeecCHHHHHHHHHH
Confidence 46789999999999999975222111 0111112236999999988754
No 224
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=22.96 E-value=1.4e+02 Score=21.49 Aligned_cols=21 Identities=10% Similarity=0.425 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|+++..|+++..
T Consensus 152 s~~EIA~~lgis~~tVk~~l~ 172 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLY 172 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 367899999999999998864
No 225
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=22.90 E-value=1.3e+02 Score=20.68 Aligned_cols=21 Identities=5% Similarity=0.210 Sum_probs=17.7
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+++-.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ 148 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLS 148 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 356899999999999998764
No 226
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=22.80 E-value=1.8e+02 Score=19.18 Aligned_cols=22 Identities=9% Similarity=-0.200 Sum_probs=14.8
Q ss_pred HHHHHHHcCCChhhhhhhhccc
Q psy15514 162 REELAQRTKLTEARIQTIFIVR 183 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~nr 183 (187)
..+||..+|++...|.-|-...
T Consensus 81 q~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 81 QREAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 3467777777777777776543
No 227
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.75 E-value=62 Score=22.99 Aligned_cols=22 Identities=14% Similarity=0.161 Sum_probs=18.8
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|+++...
T Consensus 154 s~~eIA~~lgis~~~v~~~l~R 175 (187)
T TIGR02948 154 SLKEISEILDLPVGTVKTRIHR 175 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999998754
No 228
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.70 E-value=69 Score=22.36 Aligned_cols=22 Identities=23% Similarity=0.129 Sum_probs=18.6
Q ss_pred HHHHHHHHcCCChhhhhhhhcc
Q psy15514 161 TREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~n 182 (187)
...++|..+|++...|++|...
T Consensus 126 s~~eIA~~lgis~~tv~~~l~R 147 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFR 147 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4678999999999999998753
No 229
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=22.59 E-value=1.6e+02 Score=22.03 Aligned_cols=39 Identities=13% Similarity=0.192 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 182 (187)
.+|+.+.++|.-..+-. ...++|+.+++++..|+.+..+
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~ 193 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYN 193 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHH
Confidence 48999999998777622 3578899999999999988765
No 230
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.23 E-value=1.6e+02 Score=20.20 Aligned_cols=39 Identities=15% Similarity=0.117 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..++.-.|-.. ....++|..+|++...|++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 35555555555433222 2357899999999999988754
No 231
>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=22.13 E-value=2.4e+02 Score=18.56 Aligned_cols=46 Identities=24% Similarity=0.231 Sum_probs=29.0
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELER 149 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~ 149 (187)
..++|..+|++...+.-|....=-... ... . ....|+..++..|..
T Consensus 3 ige~a~~~gvs~~tLryYe~~GLi~p~----------~~~-~-~yR~Y~~~d~~~l~~ 48 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEEKGLLPSP----------KRS-G-NYRVYDAQHVECLRF 48 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC----------CCC-C-CceeeCHHHHHHHHH
Confidence 467899999999999999753211110 011 1 234578888887753
No 232
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=21.94 E-value=95 Score=17.46 Aligned_cols=37 Identities=19% Similarity=0.245 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQ 177 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 177 (187)
+|..|...|...+....- .....+||..++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHH
Confidence 678888888777665542 1245688999998886553
No 233
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=21.92 E-value=1.4e+02 Score=21.53 Aligned_cols=21 Identities=10% Similarity=0.251 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+++..
T Consensus 154 s~~eIA~~lgis~~tV~~~l~ 174 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTA 174 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 356899999999999999874
No 234
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=21.86 E-value=1.5e+02 Score=20.44 Aligned_cols=38 Identities=18% Similarity=0.303 Sum_probs=27.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+...|.-.| .+ ....++|..+|++...|+.+..
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ 149 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLA 149 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666666555 22 2467899999999999998764
No 235
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.76 E-value=70 Score=22.85 Aligned_cols=21 Identities=10% Similarity=0.210 Sum_probs=17.8
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+.+..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~ 166 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLA 166 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHH
Confidence 357899999999999998764
No 236
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=21.67 E-value=1.2e+02 Score=21.31 Aligned_cols=21 Identities=14% Similarity=0.268 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ 157 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVA 157 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 467899999999999998763
No 237
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=21.30 E-value=1.6e+02 Score=20.60 Aligned_cols=21 Identities=24% Similarity=0.289 Sum_probs=17.5
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|++...|+++..
T Consensus 137 s~~eiA~~lgis~~tv~~~l~ 157 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLH 157 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356899999999999988753
No 238
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=21.13 E-value=1.1e+02 Score=20.74 Aligned_cols=24 Identities=17% Similarity=0.237 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHcCCChhhhhhhh
Q psy15514 157 PDIYTREELAQRTKLTEARIQTIF 180 (187)
Q Consensus 157 p~~~~~~~la~~~~l~~~~v~~WF 180 (187)
++...|..||..+|++...|.-|-
T Consensus 27 ~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 27 DTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCHHHHHHHHHhcCCCHHHHHHHH
Confidence 566778889999999999999994
No 239
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=21.11 E-value=1.7e+02 Score=20.12 Aligned_cols=20 Identities=10% Similarity=0.316 Sum_probs=17.0
Q ss_pred HHHHHHHHcCCChhhhhhhh
Q psy15514 161 TREELAQRTKLTEARIQTIF 180 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF 180 (187)
...++|+.+|++...|+...
T Consensus 127 s~~EIA~~lgis~~tV~~~l 146 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMI 146 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHH
Confidence 36789999999999998864
No 240
>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=21.06 E-value=1.5e+02 Score=20.69 Aligned_cols=25 Identities=20% Similarity=0.198 Sum_probs=21.1
Q ss_pred HHHHHHHHHcCCChhhhhhhhcccC
Q psy15514 160 YTREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 160 ~~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
....+++..+|++..+|..|...-|
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGR 71 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGR 71 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCC
Confidence 3456889999999999999987655
No 241
>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=21.05 E-value=2.7e+02 Score=18.65 Aligned_cols=47 Identities=15% Similarity=0.128 Sum_probs=29.4
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELER 149 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~ 149 (187)
..++|..+|++...+.-|....--... .+.....-.|+.+++..|..
T Consensus 3 IgevA~~~gvs~~tLRyYe~~GLl~p~-----------~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T cd04784 3 IGELAKKTGCSVETIRYYEKEGLLPAP-----------ARSANNYRLYDEEHLERLLF 49 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCC-----------CcCCCCCeecCHHHHHHHHH
Confidence 467899999999999988753322111 00011234588888887753
No 242
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=21.04 E-value=88 Score=21.33 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=17.6
Q ss_pred HHHHHHHHcCCChhhhhhhhc
Q psy15514 161 TREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 161 ~~~~la~~~~l~~~~v~~WF~ 181 (187)
...++|..+|+++..|+.+..
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ 151 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHIS 151 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356889999999999988764
No 243
>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=21.03 E-value=2.2e+02 Score=17.72 Aligned_cols=49 Identities=18% Similarity=0.167 Sum_probs=31.5
Q ss_pred hhHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 91 TREELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 91 ~r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
...++|..+|++...+..|....--. + .+.....+..|+.+++..|...
T Consensus 3 ti~evA~~~gvs~~tLR~ye~~Gll~-------p----~r~~~~g~R~Ys~~dv~~l~~I 51 (88)
T cd01105 3 GIGEVSKLTGVSPRQLRYWEEKGLIK-------S----IRSDGGGQRKYSLADVDRLLVI 51 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCCCC-------C----CccCCCCceecCHHHHHHHHHH
Confidence 45688999999999999995422111 0 0111113346999999988755
No 244
>PRK10403 transcriptional regulator NarP; Provisional
Probab=20.83 E-value=67 Score=22.77 Aligned_cols=41 Identities=12% Similarity=0.206 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
.+|..+...|...... ....++|+.+++++..|++...+=+
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~ 193 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLL 193 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHH
Confidence 5888888888755433 3467889999999999988876543
No 245
>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=20.80 E-value=60 Score=16.17 Aligned_cols=18 Identities=17% Similarity=0.296 Sum_probs=12.5
Q ss_pred HHHHHcCCChhhhhhhhc
Q psy15514 164 ELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 164 ~la~~~~l~~~~v~~WF~ 181 (187)
.-|..+||+..+|+..+.
T Consensus 10 ~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 10 KEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 348899999999987653
No 246
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=20.69 E-value=2.9e+02 Score=18.93 Aligned_cols=48 Identities=19% Similarity=0.212 Sum_probs=29.4
Q ss_pred hHHHHHhhcCCchhhHhHhhccCCCCCCCCCCCCCcccccccccCCCCCHHHHHHHHHH
Q psy15514 92 REELAQRTKLFPHFLIIIEQQSSGEGSDCDSEPGIPLKRKQRRSRTTFSAQQLDELERA 150 (187)
Q Consensus 92 r~~la~~~~l~~~~v~~wfq~~~~~~~~~~~~~~~~~~~~~~r~r~~~t~~q~~~Le~~ 150 (187)
..++|..+|++.+.+..|....=-... .+.....-.|+.+++..|...
T Consensus 3 Ige~a~~~gvs~~tlRyYE~~GLl~p~-----------~r~~~gyR~Y~~~~l~~l~~I 50 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEEKGLVTPP-----------MRSENGYRTYTQQHLNELTLL 50 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCc-----------ccCCCCcccCCHHHHHHHHHH
Confidence 467899999999999998753221111 111122345777777777543
No 247
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=20.53 E-value=1.4e+02 Score=16.61 Aligned_cols=37 Identities=22% Similarity=0.374 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhh
Q psy15514 139 FSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTI 179 (187)
Q Consensus 139 ~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~W 179 (187)
+|..|...|...++... ....+||..++++...|-.+
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~ 37 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRI 37 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHH
Confidence 46778888888876655 23448899999888766543
No 248
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=20.37 E-value=1.5e+02 Score=23.02 Aligned_cols=39 Identities=18% Similarity=0.260 Sum_probs=27.8
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhcccC
Q psy15514 145 DELERAFERTQYPDIYTREELAQRTKLTEARIQTIFIVRK 184 (187)
Q Consensus 145 ~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 184 (187)
..++.......|+ .+.-+++++.+||+...++.+|.|=|
T Consensus 185 ~~~~~~~~~~~~~-~ei~~~~a~~lglp~~~~~eYy~~~~ 223 (252)
T COG1427 185 ALLEFEETKAKFP-AEILKEAAKRLGLPRSDVEEYYTNIR 223 (252)
T ss_pred hHHHHHHHHHhhh-HHHHHHHHHHcCCCHHHHHHHHHHhe
Confidence 3344444445555 45556789999999999999998754
No 249
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=20.36 E-value=1.7e+02 Score=21.76 Aligned_cols=39 Identities=15% Similarity=0.251 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+...+...|-.. ....++|..+|++...|..|..
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ 216 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLR 216 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 46666666666555322 2467899999999999998863
No 250
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=20.31 E-value=48 Score=20.67 Aligned_cols=21 Identities=10% Similarity=0.093 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhhhhhhhcc
Q psy15514 162 REELAQRTKLTEARIQTIFIV 182 (187)
Q Consensus 162 ~~~la~~~~l~~~~v~~WF~n 182 (187)
+..|...++|...+|.+|+..
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~~ 76 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAEK 76 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEEE
Confidence 566888889999999999853
No 251
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.00 E-value=1.7e+02 Score=22.32 Aligned_cols=39 Identities=10% Similarity=0.247 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhc
Q psy15514 138 TFSAQQLDELERAFERTQYPDIYTREELAQRTKLTEARIQTIFI 181 (187)
Q Consensus 138 ~~t~~q~~~Le~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 181 (187)
.+++.+..+|.-.|-.. ....++|..+|++...|+.|..
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ 243 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQR 243 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 45666666666554322 2457899999999999998864
Done!