Query psy10486
Match_columns 183
No_of_seqs 155 out of 1745
Neff 8.7
Searched_HMMs 46136
Date Fri Aug 16 19:23:46 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10486.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10486hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0490|consensus 99.7 2.1E-18 4.6E-23 134.8 6.7 123 18-140 57-213 (235)
2 KOG0484|consensus 99.7 6.6E-18 1.4E-22 112.6 4.7 70 77-146 14-83 (125)
3 KOG2251|consensus 99.7 3.1E-17 6.8E-22 123.6 4.7 64 16-79 32-95 (228)
4 KOG0850|consensus 99.7 4.8E-17 1E-21 123.2 3.8 65 17-81 118-182 (245)
5 PF00046 Homeobox: Homeobox do 99.7 1E-16 2.2E-21 98.6 4.2 56 22-77 1-56 (57)
6 KOG0488|consensus 99.7 1.4E-16 3.1E-21 128.7 5.8 76 78-153 170-245 (309)
7 KOG0484|consensus 99.6 4.7E-17 1E-21 108.6 1.9 62 17-78 13-74 (125)
8 KOG0487|consensus 99.6 1.2E-16 2.7E-21 127.4 4.6 69 16-84 230-298 (308)
9 KOG0488|consensus 99.6 1.8E-16 4E-21 128.1 5.6 64 16-79 167-230 (309)
10 KOG0489|consensus 99.6 1.6E-16 3.5E-21 126.2 5.0 82 64-145 138-224 (261)
11 KOG0843|consensus 99.6 5E-16 1.1E-20 113.6 6.9 65 79-143 101-165 (197)
12 KOG2251|consensus 99.6 8E-16 1.7E-20 116.1 7.7 67 76-142 33-99 (228)
13 KOG0842|consensus 99.6 2.1E-16 4.6E-21 126.0 4.8 64 17-80 149-212 (307)
14 PF00046 Homeobox: Homeobox do 99.6 5.4E-16 1.2E-20 95.4 5.5 57 81-137 1-57 (57)
15 KOG0850|consensus 99.6 3.3E-16 7.1E-21 118.7 5.1 67 76-142 118-184 (245)
16 KOG0494|consensus 99.6 7.2E-16 1.6E-20 118.6 5.4 65 19-83 138-203 (332)
17 KOG0843|consensus 99.6 5.1E-16 1.1E-20 113.6 4.2 66 17-82 98-163 (197)
18 KOG0487|consensus 99.6 4.2E-16 9E-21 124.4 2.9 69 78-146 233-301 (308)
19 KOG0489|consensus 99.6 6.4E-16 1.4E-20 122.7 3.9 66 19-84 157-222 (261)
20 TIGR01565 homeo_ZF_HD homeobox 99.6 2.6E-15 5.6E-20 91.7 5.2 51 22-72 2-56 (58)
21 KOG0494|consensus 99.6 1.4E-15 3E-20 117.0 4.6 67 76-142 137-203 (332)
22 KOG0842|consensus 99.6 1.6E-15 3.5E-20 121.0 4.8 75 77-151 150-224 (307)
23 KOG0848|consensus 99.6 3.6E-15 7.8E-20 115.2 6.5 65 78-142 197-261 (317)
24 smart00389 HOX Homeodomain. DN 99.6 8.6E-15 1.9E-19 89.6 5.9 55 22-76 1-55 (56)
25 KOG0492|consensus 99.5 3.7E-15 8.1E-20 111.3 4.4 68 76-143 140-207 (246)
26 KOG0848|consensus 99.5 1E-15 2.2E-20 118.2 1.3 63 22-84 200-262 (317)
27 KOG0492|consensus 99.5 5.5E-15 1.2E-19 110.4 4.0 61 19-79 142-202 (246)
28 cd00086 homeodomain Homeodomai 99.5 2.2E-14 4.7E-19 88.6 5.5 55 23-77 2-56 (59)
29 COG5576 Homeodomain-containing 99.5 1.1E-14 2.4E-19 106.5 4.4 100 15-132 45-144 (156)
30 KOG0485|consensus 99.5 1.4E-14 3.1E-19 108.9 4.3 67 79-145 103-169 (268)
31 KOG0491|consensus 99.5 1.4E-14 2.9E-19 104.6 4.0 80 79-158 99-178 (194)
32 KOG0485|consensus 99.5 1.4E-14 3E-19 108.9 4.1 63 17-79 100-162 (268)
33 KOG3802|consensus 99.5 4.3E-15 9.4E-20 121.0 0.1 127 14-140 210-354 (398)
34 cd00086 homeodomain Homeodomai 99.5 8.2E-14 1.8E-18 86.0 5.7 57 82-138 2-58 (59)
35 smart00389 HOX Homeodomain. DN 99.5 6.2E-14 1.3E-18 85.7 5.0 55 82-136 2-56 (56)
36 KOG0493|consensus 99.5 3.9E-14 8.5E-19 109.2 4.4 61 79-139 245-305 (342)
37 KOG0486|consensus 99.4 5.4E-14 1.2E-18 111.0 3.9 62 20-81 111-172 (351)
38 KOG0486|consensus 99.4 7.7E-14 1.7E-18 110.2 3.4 68 79-146 111-178 (351)
39 KOG0491|consensus 99.4 5E-14 1.1E-18 101.7 0.9 65 20-84 99-163 (194)
40 TIGR01565 homeo_ZF_HD homeobox 99.4 2.2E-13 4.7E-18 83.2 3.1 52 81-132 2-57 (58)
41 KOG0483|consensus 99.4 2.7E-13 5.8E-18 102.6 3.9 75 21-95 50-124 (198)
42 COG5576 Homeodomain-containing 99.4 6.1E-13 1.3E-17 97.4 5.4 68 78-145 49-116 (156)
43 KOG0844|consensus 99.4 1.9E-13 4.1E-18 107.6 1.8 68 14-81 174-241 (408)
44 KOG3802|consensus 99.4 7.5E-13 1.6E-17 108.0 4.8 66 16-81 289-354 (398)
45 KOG0483|consensus 99.3 7.6E-13 1.7E-17 100.1 4.4 59 81-139 51-109 (198)
46 KOG0844|consensus 99.3 2E-13 4.3E-18 107.5 1.2 61 79-139 180-240 (408)
47 KOG0493|consensus 99.3 1.3E-12 2.8E-17 100.9 5.6 59 22-80 247-305 (342)
48 KOG4577|consensus 99.3 1.9E-12 4.1E-17 101.3 3.5 63 17-79 163-225 (383)
49 KOG0847|consensus 99.2 1.2E-11 2.5E-16 93.4 5.3 73 83-155 170-242 (288)
50 KOG4577|consensus 99.2 2.8E-11 6.1E-16 94.8 4.0 64 79-142 166-229 (383)
51 KOG0849|consensus 99.0 2.6E-10 5.6E-15 94.3 5.2 65 16-80 171-235 (354)
52 KOG0490|consensus 98.9 4.2E-10 9E-15 87.8 2.6 63 78-140 58-120 (235)
53 KOG0849|consensus 98.9 1.2E-09 2.6E-14 90.4 4.3 72 66-140 165-236 (354)
54 KOG0775|consensus 98.9 2E-09 4.3E-14 84.0 3.6 51 89-139 185-235 (304)
55 KOG0847|consensus 98.8 1.7E-09 3.7E-14 81.8 2.5 55 24-78 170-224 (288)
56 KOG0775|consensus 98.8 9.6E-09 2.1E-13 80.2 4.8 59 28-86 183-241 (304)
57 PF05920 Homeobox_KN: Homeobox 98.7 1.4E-08 2.9E-13 57.5 3.8 35 100-134 6-40 (40)
58 KOG1168|consensus 98.6 7E-09 1.5E-13 81.6 0.6 62 79-140 308-369 (385)
59 PF05920 Homeobox_KN: Homeobox 98.6 2.3E-08 5.1E-13 56.6 1.9 33 42-74 7-39 (40)
60 KOG1168|consensus 98.5 1.7E-08 3.6E-13 79.5 0.4 60 19-78 307-366 (385)
61 KOG2252|consensus 98.5 1.4E-07 3.1E-12 80.2 5.0 56 20-75 419-474 (558)
62 KOG0774|consensus 98.4 1.4E-07 3.1E-12 73.3 2.9 64 79-142 187-253 (334)
63 KOG1146|consensus 98.3 2.9E-06 6.3E-11 78.6 9.3 136 6-142 691-965 (1406)
64 KOG0774|consensus 98.3 5.2E-07 1.1E-11 70.2 3.4 55 21-75 188-245 (334)
65 KOG2252|consensus 98.0 1E-05 2.2E-10 69.2 4.8 56 80-135 420-475 (558)
66 KOG3623|consensus 97.7 6.4E-05 1.4E-09 66.3 4.8 107 33-139 568-685 (1007)
67 KOG1146|consensus 97.5 0.00011 2.3E-09 68.7 4.0 59 20-78 902-960 (1406)
68 PF11569 Homez: Homeodomain le 97.4 0.00011 2.5E-09 44.2 2.2 41 92-132 10-50 (56)
69 KOG0773|consensus 97.2 0.0003 6.6E-09 58.2 3.4 109 37-145 113-307 (342)
70 PF11569 Homez: Homeodomain le 97.1 0.00046 9.9E-09 41.6 2.7 41 33-73 10-50 (56)
71 KOG0773|consensus 96.2 0.0045 9.8E-08 51.2 3.6 54 21-74 239-295 (342)
72 PF04218 CENP-B_N: CENP-B N-te 95.1 0.046 1E-06 32.6 4.0 46 22-72 1-46 (53)
73 PF13551 HTH_29: Winged helix- 94.5 0.16 3.5E-06 34.4 6.1 80 50-129 14-109 (112)
74 PF04218 CENP-B_N: CENP-B N-te 94.1 0.11 2.3E-06 31.0 3.9 46 82-132 2-47 (53)
75 KOG3623|consensus 94.1 0.074 1.6E-06 47.7 4.3 48 92-139 568-615 (1007)
76 cd00131 PAX Paired Box domain 93.9 0.62 1.4E-05 33.0 8.2 101 26-131 16-127 (128)
77 PF04967 HTH_10: HTH DNA bindi 93.5 0.14 3E-06 30.6 3.6 43 28-70 1-45 (53)
78 smart00351 PAX Paired Box doma 93.5 1 2.2E-05 31.8 8.7 97 27-128 17-124 (125)
79 PF01710 HTH_Tnp_IS630: Transp 92.6 0.36 7.8E-06 33.7 5.2 91 28-130 3-94 (119)
80 cd04763 HTH_MlrA-like Helix-Tu 91.9 1 2.2E-05 27.9 6.2 64 52-128 4-67 (68)
81 KOG3755|consensus 91.7 0.5 1.1E-05 41.7 6.0 100 22-139 648-758 (769)
82 cd04764 HTH_MlrA-like_sg1 Heli 91.6 0.89 1.9E-05 28.0 5.7 63 52-128 4-66 (67)
83 PRK06424 transcription factor; 90.5 3.7 8.1E-05 29.8 8.7 20 52-71 101-120 (144)
84 cd01106 HTH_TipAL-Mta Helix-Tu 90.4 1.3 2.7E-05 30.0 6.0 67 52-131 4-70 (103)
85 cd01104 HTH_MlrA-CarA Helix-Tu 90.1 1.9 4E-05 26.5 6.1 62 52-126 4-65 (68)
86 PF13411 MerR_1: MerR HTH fami 89.9 1.1 2.4E-05 27.6 5.0 65 52-130 4-68 (69)
87 PF01381 HTH_3: Helix-turn-hel 89.7 0.9 2E-05 26.6 4.3 41 52-122 13-53 (55)
88 PF13443 HTH_26: Cro/C1-type H 89.3 0.7 1.5E-05 28.0 3.7 45 51-124 13-57 (63)
89 PF04967 HTH_10: HTH DNA bindi 88.9 0.73 1.6E-05 27.5 3.4 42 87-128 1-44 (53)
90 PHA01976 helix-turn-helix prot 88.2 1.7 3.7E-05 26.6 4.9 41 52-122 19-59 (67)
91 cd04765 HTH_MlrA-like_sg2 Heli 87.0 3.1 6.7E-05 28.0 6.0 69 52-132 4-72 (99)
92 PF01527 HTH_Tnp_1: Transposas 86.5 0.82 1.8E-05 28.8 2.8 47 23-73 2-48 (76)
93 COG3413 Predicted DNA binding 86.4 0.94 2E-05 34.9 3.6 45 27-71 155-201 (215)
94 cd04773 HTH_TioE_rpt2 Second H 84.6 5.1 0.00011 27.4 6.2 47 52-98 4-50 (108)
95 cd04768 HTH_BmrR-like Helix-Tu 84.1 5.2 0.00011 26.7 6.0 66 52-130 4-69 (96)
96 TIGR02047 CadR-PbrR Cd(II)/Pb( 84.0 6.3 0.00014 27.8 6.7 46 52-97 4-49 (127)
97 PRK09726 antitoxin HipB; Provi 84.0 9.5 0.00021 24.9 7.1 63 27-122 7-69 (88)
98 cd04761 HTH_MerR-SF Helix-Turn 83.8 1.7 3.7E-05 24.6 3.1 44 52-96 4-47 (49)
99 cd01109 HTH_YyaN Helix-Turn-He 83.3 6.5 0.00014 26.9 6.4 65 52-129 4-68 (113)
100 smart00422 HTH_MERR helix_turn 83.3 3.9 8.5E-05 25.0 4.8 64 52-128 4-67 (70)
101 TIGR03070 couple_hipB transcri 82.7 4 8.7E-05 23.7 4.5 20 52-71 19-38 (58)
102 TIGR02044 CueR Cu(I)-responsiv 82.3 6.3 0.00014 27.7 6.1 45 52-96 4-48 (127)
103 TIGR02607 antidote_HigA addict 82.0 5.7 0.00012 24.9 5.4 40 52-121 22-61 (78)
104 COG3415 Transposase and inacti 82.0 4.1 8.9E-05 29.4 5.0 88 50-137 23-116 (138)
105 PF04545 Sigma70_r4: Sigma-70, 81.8 3.8 8.3E-05 23.5 4.1 44 86-134 4-47 (50)
106 TIGR02043 ZntR Zn(II)-responsi 81.8 6.6 0.00014 27.8 6.1 46 52-97 5-50 (131)
107 PF04545 Sigma70_r4: Sigma-70, 81.7 2.6 5.7E-05 24.3 3.4 40 27-71 4-43 (50)
108 PRK09706 transcriptional repre 81.5 4 8.7E-05 28.9 4.9 20 52-71 22-41 (135)
109 PF09607 BrkDBD: Brinker DNA-b 81.3 4.3 9.3E-05 24.7 4.1 45 25-71 3-48 (58)
110 cd00569 HTH_Hin_like Helix-tur 81.2 5.1 0.00011 20.1 4.3 39 26-69 4-42 (42)
111 cd04767 HTH_HspR-like_MBC Heli 81.1 7.2 0.00016 27.4 5.9 64 52-129 5-68 (120)
112 cd04788 HTH_NolA-AlbR Helix-Tu 81.0 7.6 0.00016 25.8 5.9 65 52-129 4-68 (96)
113 PF10668 Phage_terminase: Phag 80.7 1.5 3.2E-05 26.9 2.0 21 109-129 24-44 (60)
114 PF12844 HTH_19: Helix-turn-he 80.3 5 0.00011 24.2 4.5 44 51-124 15-58 (64)
115 PF01527 HTH_Tnp_1: Transposas 80.3 1.5 3.3E-05 27.5 2.1 44 83-130 3-46 (76)
116 PRK13890 conjugal transfer pro 79.9 5.1 0.00011 28.0 4.9 42 51-122 21-62 (120)
117 cd04779 HTH_MerR-like_sg4 Heli 79.6 7.5 0.00016 27.8 5.7 65 52-130 4-68 (134)
118 cd01108 HTH_CueR Helix-Turn-He 79.2 8.8 0.00019 27.0 6.0 46 52-97 4-49 (127)
119 PF10668 Phage_terminase: Phag 79.0 1.6 3.4E-05 26.8 1.7 27 50-76 24-50 (60)
120 cd04762 HTH_MerR-trunc Helix-T 78.9 4.2 9.1E-05 22.5 3.6 44 52-96 4-47 (49)
121 cd04785 HTH_CadR-PbrR-like Hel 78.5 12 0.00026 26.2 6.5 46 52-97 4-49 (126)
122 cd00592 HTH_MerR-like Helix-Tu 77.4 10 0.00022 25.1 5.7 47 52-99 4-50 (100)
123 PRK10072 putative transcriptio 77.1 7.2 0.00016 26.2 4.7 37 29-72 34-70 (96)
124 PRK09514 zntR zinc-responsive 76.9 10 0.00022 27.2 5.9 47 52-98 5-51 (140)
125 cd04770 HTH_HMRTR Helix-Turn-H 76.7 15 0.00032 25.5 6.5 45 52-96 4-48 (123)
126 cd04789 HTH_Cfa Helix-Turn-Hel 76.0 21 0.00046 24.0 7.7 65 52-130 5-69 (102)
127 cd04781 HTH_MerR-like_sg6 Heli 75.9 12 0.00026 25.9 5.9 65 52-130 4-68 (120)
128 cd04787 HTH_HMRTR_unk Helix-Tu 75.4 13 0.00028 26.3 6.0 45 52-96 4-48 (133)
129 cd04784 HTH_CadR-PbrR Helix-Tu 75.1 14 0.0003 25.9 6.0 46 52-97 4-49 (127)
130 cd00093 HTH_XRE Helix-turn-hel 75.1 9.3 0.0002 21.1 4.4 20 52-71 16-35 (58)
131 cd04782 HTH_BltR Helix-Turn-He 74.9 22 0.00047 23.7 8.1 46 52-97 4-49 (97)
132 TIGR02054 MerD mercuric resist 74.8 17 0.00037 25.4 6.3 48 51-98 6-53 (120)
133 PF08281 Sigma70_r4_2: Sigma-7 74.6 8.3 0.00018 22.4 4.1 41 87-132 11-51 (54)
134 smart00530 HTH_XRE Helix-turn- 74.4 10 0.00022 20.8 4.5 20 52-71 14-33 (56)
135 cd04783 HTH_MerR1 Helix-Turn-H 74.2 14 0.00031 25.8 6.0 66 52-130 4-69 (126)
136 cd04780 HTH_MerR-like_sg5 Heli 74.1 19 0.0004 24.0 6.2 67 52-130 4-70 (95)
137 PRK08359 transcription factor; 74.1 14 0.00031 27.7 6.1 41 52-122 102-142 (176)
138 cd06171 Sigma70_r4 Sigma70, re 73.4 8.3 0.00018 21.5 3.9 42 87-133 11-52 (55)
139 PRK09413 IS2 repressor TnpA; R 72.8 23 0.00049 24.6 6.6 47 24-74 9-55 (121)
140 cd04774 HTH_YfmP Helix-Turn-He 72.8 20 0.00043 23.9 6.1 68 52-132 4-71 (96)
141 cd01105 HTH_GlnR-like Helix-Tu 72.2 24 0.00053 23.0 6.7 67 52-132 5-72 (88)
142 TIGR02051 MerR Hg(II)-responsi 71.3 16 0.00035 25.5 5.6 65 52-129 3-67 (124)
143 PF13936 HTH_38: Helix-turn-he 70.6 6.6 0.00014 22.1 2.9 40 85-129 3-42 (44)
144 PF13560 HTH_31: Helix-turn-he 70.6 10 0.00022 22.9 4.0 46 51-125 17-62 (64)
145 cd01111 HTH_MerD Helix-Turn-He 69.9 23 0.00049 24.1 6.0 47 52-98 4-50 (107)
146 TIGR00270 conserved hypothetic 69.6 41 0.0009 24.6 9.1 42 52-123 86-127 (154)
147 COG3413 Predicted DNA binding 68.9 6.4 0.00014 30.3 3.4 43 86-128 155-199 (215)
148 PF08279 HTH_11: HTH domain; 67.1 9.5 0.00021 22.2 3.2 36 32-70 2-37 (55)
149 cd01110 HTH_SoxR Helix-Turn-He 67.1 26 0.00056 25.1 6.0 46 51-97 4-49 (139)
150 PF07022 Phage_CI_repr: Bacter 67.0 6.5 0.00014 24.2 2.5 40 52-122 16-56 (66)
151 cd04775 HTH_Cfa-like Helix-Tur 66.2 37 0.0008 22.7 7.5 65 52-130 5-69 (102)
152 PF13518 HTH_28: Helix-turn-he 65.7 8.1 0.00017 22.0 2.7 22 109-130 14-35 (52)
153 PF13443 HTH_26: Cro/C1-type H 65.6 13 0.00029 22.1 3.8 32 109-140 12-43 (63)
154 PF08667 BetR: BetR domain; I 64.9 29 0.00063 25.3 5.8 57 33-101 7-63 (147)
155 PF08280 HTH_Mga: M protein tr 64.8 11 0.00024 22.6 3.2 36 31-70 6-41 (59)
156 PRK03975 tfx putative transcri 64.7 20 0.00043 25.9 5.0 51 84-140 4-54 (141)
157 PF13384 HTH_23: Homeodomain-l 64.3 8.2 0.00018 22.0 2.5 23 108-130 18-40 (50)
158 PF06056 Terminase_5: Putative 63.8 7.9 0.00017 23.4 2.4 21 109-129 15-35 (58)
159 PHA02955 hypothetical protein; 63.6 11 0.00025 29.0 3.7 43 30-72 60-103 (213)
160 cd01282 HTH_MerR-like_sg3 Heli 63.4 37 0.00081 23.2 6.1 44 52-96 4-47 (112)
161 cd04766 HTH_HspR Helix-Turn-He 63.4 39 0.00084 22.0 7.8 65 52-129 5-69 (91)
162 PF00376 MerR: MerR family reg 63.4 8.7 0.00019 21.0 2.3 20 110-129 2-21 (38)
163 cd04769 HTH_MerR2 Helix-Turn-H 63.1 33 0.00072 23.5 5.8 65 52-130 4-68 (116)
164 TIGR01950 SoxR redox-sensitive 63.0 32 0.00069 24.8 5.8 45 51-96 4-48 (142)
165 PRK15002 redox-sensitivie tran 62.4 27 0.00059 25.6 5.5 44 52-96 15-58 (154)
166 PRK10227 DNA-binding transcrip 61.2 49 0.0011 23.5 6.5 46 52-97 4-49 (135)
167 PRK10072 putative transcriptio 61.1 8.3 0.00018 25.9 2.3 40 87-133 33-72 (96)
168 PF00196 GerE: Bacterial regul 60.8 20 0.00043 21.1 3.9 45 86-136 3-47 (58)
169 PF02796 HTH_7: Helix-turn-hel 60.5 15 0.00032 20.7 3.1 39 26-69 4-42 (45)
170 cd01279 HTH_HspR-like Helix-Tu 60.5 48 0.001 22.1 8.2 66 52-130 5-70 (98)
171 cd04786 HTH_MerR-like_sg7 Heli 60.2 43 0.00093 23.7 6.1 45 52-96 4-48 (131)
172 PF13411 MerR_1: MerR HTH fami 59.7 10 0.00022 23.1 2.4 20 110-129 3-22 (69)
173 PRK00118 putative DNA-binding 58.7 36 0.00077 23.3 5.2 49 86-139 17-65 (104)
174 cd04777 HTH_MerR-like_sg1 Heli 57.8 55 0.0012 22.0 6.1 64 52-130 4-67 (107)
175 PRK09943 DNA-binding transcrip 57.3 27 0.00059 26.0 4.9 42 52-123 24-65 (185)
176 cd01392 HTH_LacI Helix-turn-he 57.0 18 0.00039 20.5 3.1 19 53-71 2-20 (52)
177 TIGR03879 near_KaiC_dom probab 56.9 4.3 9.4E-05 25.9 0.4 34 38-71 22-55 (73)
178 TIGR02684 dnstrm_HI1420 probab 55.9 28 0.00061 23.0 4.2 38 54-121 49-86 (89)
179 COG0789 SoxR Predicted transcr 55.6 48 0.001 22.6 5.7 45 52-96 4-48 (124)
180 PRK06759 RNA polymerase factor 55.5 25 0.00055 24.8 4.3 28 109-136 124-151 (154)
181 COG2944 Predicted transcriptio 55.1 18 0.0004 24.7 3.2 40 28-74 44-83 (104)
182 PRK11924 RNA polymerase sigma 55.1 34 0.00073 24.6 5.0 31 109-139 143-173 (179)
183 TIGR02937 sigma70-ECF RNA poly 54.3 30 0.00066 23.7 4.6 46 87-137 111-156 (158)
184 PRK13749 transcriptional regul 53.7 75 0.0016 22.3 6.6 47 51-97 6-52 (121)
185 PRK13182 racA polar chromosome 53.4 43 0.00094 25.1 5.3 46 52-98 4-49 (175)
186 smart00421 HTH_LUXR helix_turn 53.3 28 0.00061 19.6 3.6 39 27-71 3-41 (58)
187 PRK03975 tfx putative transcri 53.2 17 0.00036 26.3 3.0 44 25-74 4-47 (141)
188 PRK09413 IS2 repressor TnpA; R 53.1 24 0.00053 24.4 3.8 43 83-130 9-52 (121)
189 PRK09642 RNA polymerase sigma 53.0 34 0.00074 24.4 4.7 32 109-140 124-155 (160)
190 PRK12543 RNA polymerase sigma 53.0 51 0.0011 24.1 5.7 40 109-148 135-174 (179)
191 PF13551 HTH_29: Winged helix- 52.9 45 0.00098 22.0 5.1 49 22-70 52-109 (112)
192 TIGR03879 near_KaiC_dom probab 52.2 6.1 0.00013 25.2 0.5 23 108-130 33-55 (73)
193 PF04936 DUF658: Protein of un 52.1 4.7 0.0001 29.8 -0.0 82 49-130 15-111 (186)
194 cd04790 HTH_Cfa-like_unk Helix 52.0 80 0.0017 23.4 6.6 46 52-97 5-50 (172)
195 PRK08154 anaerobic benzoate ca 51.9 33 0.00071 28.0 4.9 21 51-71 44-64 (309)
196 PRK09646 RNA polymerase sigma 51.7 34 0.00073 25.5 4.6 30 109-138 160-189 (194)
197 PF13730 HTH_36: Helix-turn-he 51.7 45 0.00098 19.2 4.8 41 28-71 3-48 (55)
198 PRK13752 putative transcriptio 51.6 65 0.0014 23.2 5.9 48 51-98 10-57 (144)
199 COG4367 Uncharacterized protei 51.5 28 0.00061 23.0 3.5 41 28-68 3-43 (97)
200 PRK09652 RNA polymerase sigma 50.8 36 0.00077 24.6 4.6 30 109-138 146-175 (182)
201 PRK12526 RNA polymerase sigma 50.6 36 0.00079 25.7 4.7 31 109-139 171-201 (206)
202 PHA01083 hypothetical protein 50.4 91 0.002 22.8 6.3 33 36-71 7-39 (149)
203 TIGR02612 mob_myst_A mobile my 49.7 49 0.0011 24.1 5.0 42 52-121 42-83 (150)
204 PF14549 P22_Cro: DNA-binding 49.4 46 0.001 20.2 4.1 35 111-147 13-47 (60)
205 PF13565 HTH_32: Homeodomain-l 49.1 62 0.0013 20.0 6.0 40 29-68 32-76 (77)
206 TIGR01764 excise DNA binding d 48.9 26 0.00056 19.2 2.9 41 52-94 5-45 (49)
207 PRK12512 RNA polymerase sigma 47.8 28 0.0006 25.6 3.6 32 109-140 149-180 (184)
208 PRK12519 RNA polymerase sigma 47.4 40 0.00086 25.0 4.4 31 108-138 158-188 (194)
209 COG4367 Uncharacterized protei 46.6 23 0.00051 23.4 2.6 39 87-125 3-41 (97)
210 PRK13558 bacterio-opsin activa 46.3 24 0.00053 31.6 3.6 45 26-70 606-652 (665)
211 PRK09644 RNA polymerase sigma 46.2 54 0.0012 23.5 4.9 31 109-139 126-156 (165)
212 PRK04217 hypothetical protein; 46.0 60 0.0013 22.4 4.7 50 84-138 40-89 (110)
213 PF04936 DUF658: Protein of un 45.9 17 0.00038 26.9 2.1 37 108-144 15-51 (186)
214 TIGR02943 Sig70_famx1 RNA poly 45.7 67 0.0015 23.8 5.4 35 109-143 149-183 (188)
215 PF13412 HTH_24: Winged helix- 45.5 54 0.0012 18.3 4.2 38 29-70 2-39 (48)
216 PRK12514 RNA polymerase sigma 45.3 50 0.0011 24.1 4.6 30 109-138 147-176 (179)
217 TIGR02989 Sig-70_gvs1 RNA poly 44.5 50 0.0011 23.4 4.5 45 87-136 112-156 (159)
218 PRK06930 positive control sigm 44.4 65 0.0014 23.9 5.1 49 87-140 115-163 (170)
219 smart00027 EH Eps15 homology d 43.7 71 0.0015 20.8 4.8 45 27-71 3-52 (96)
220 PF12728 HTH_17: Helix-turn-he 43.0 31 0.00067 19.6 2.6 23 52-74 5-27 (51)
221 PRK02866 cyanate hydratase; Va 42.9 73 0.0016 23.2 4.9 20 52-71 22-41 (147)
222 PRK09648 RNA polymerase sigma 42.6 57 0.0012 24.0 4.6 29 109-137 157-185 (189)
223 PRK04217 hypothetical protein; 42.4 41 0.00088 23.2 3.4 41 26-71 41-81 (110)
224 TIGR02999 Sig-70_X6 RNA polyme 42.2 62 0.0014 23.6 4.8 29 109-137 152-180 (183)
225 PRK05602 RNA polymerase sigma 41.9 63 0.0014 23.7 4.7 32 109-140 146-177 (186)
226 PRK09639 RNA polymerase sigma 41.5 89 0.0019 22.2 5.4 31 109-139 129-159 (166)
227 TIGR02948 SigW_bacill RNA poly 41.5 57 0.0012 23.8 4.5 31 108-138 153-183 (187)
228 cd06170 LuxR_C_like C-terminal 41.4 52 0.0011 18.5 3.5 37 29-71 2-38 (57)
229 PF15063 TC1: Thyroid cancer p 41.1 58 0.0013 20.9 3.7 38 26-63 32-69 (79)
230 PRK11511 DNA-binding transcrip 40.6 29 0.00063 24.2 2.6 23 49-71 26-48 (127)
231 TIGR02939 RpoE_Sigma70 RNA pol 40.1 65 0.0014 23.6 4.6 31 108-138 155-185 (190)
232 PRK12530 RNA polymerase sigma 39.7 83 0.0018 23.3 5.1 31 109-139 152-182 (189)
233 PF07037 DUF1323: Putative tra 39.7 23 0.0005 24.8 1.8 24 52-75 4-27 (122)
234 PRK12515 RNA polymerase sigma 39.6 84 0.0018 23.1 5.1 32 109-140 149-180 (189)
235 TIGR02985 Sig70_bacteroi1 RNA 39.5 69 0.0015 22.4 4.5 28 109-136 131-158 (161)
236 PRK15043 transcriptional regul 39.2 1.2E+02 0.0026 24.1 6.0 46 51-96 6-51 (243)
237 PRK12516 RNA polymerase sigma 38.6 81 0.0018 23.4 4.9 33 109-141 134-166 (187)
238 TIGR02952 Sig70_famx2 RNA poly 38.5 77 0.0017 22.6 4.7 29 109-137 140-168 (170)
239 PRK09047 RNA polymerase factor 38.3 85 0.0018 22.2 4.9 30 109-138 124-153 (161)
240 TIGR03001 Sig-70_gmx1 RNA poly 38.1 1.3E+02 0.0028 23.6 6.2 40 109-148 179-218 (244)
241 PRK12532 RNA polymerase sigma 37.9 93 0.002 23.0 5.2 33 109-141 154-186 (195)
242 TIGR02959 SigZ RNA polymerase 37.6 96 0.0021 22.5 5.1 32 109-140 118-149 (170)
243 PRK09480 slmA division inhibit 37.3 30 0.00065 25.4 2.4 34 99-133 23-56 (194)
244 PF00440 TetR_N: Bacterial reg 36.9 36 0.00077 19.1 2.1 24 109-132 18-41 (47)
245 cd01107 HTH_BmrR Helix-Turn-He 36.6 1.3E+02 0.0029 20.2 8.3 45 52-96 4-49 (108)
246 TIGR02954 Sig70_famx3 RNA poly 36.4 78 0.0017 22.7 4.5 29 109-137 137-165 (169)
247 smart00354 HTH_LACI helix_turn 36.3 94 0.002 19.1 4.2 21 51-71 3-23 (70)
248 PRK06986 fliA flagellar biosyn 36.2 87 0.0019 24.1 4.9 30 109-138 202-231 (236)
249 PRK12518 RNA polymerase sigma 36.2 56 0.0012 23.6 3.7 35 106-140 135-169 (175)
250 smart00342 HTH_ARAC helix_turn 36.0 62 0.0013 19.6 3.4 68 52-129 5-73 (84)
251 smart00595 MADF subfamily of S 35.9 1.2E+02 0.0025 19.3 4.8 40 109-148 29-68 (89)
252 PRK12524 RNA polymerase sigma 35.7 86 0.0019 23.3 4.7 31 109-139 154-184 (196)
253 PRK05988 formate dehydrogenase 35.5 78 0.0017 23.2 4.2 36 31-66 24-59 (156)
254 PF08880 QLQ: QLQ; InterPro: 35.5 34 0.00074 18.7 1.8 15 27-41 2-16 (37)
255 PF05263 DUF722: Protein of un 35.5 61 0.0013 23.1 3.5 41 28-71 82-122 (130)
256 PRK09647 RNA polymerase sigma 35.3 98 0.0021 23.4 5.0 32 109-140 156-187 (203)
257 COG2963 Transposase and inacti 35.3 1.4E+02 0.0031 20.1 6.0 46 25-74 5-51 (116)
258 PRK07037 extracytoplasmic-func 35.3 95 0.0021 22.0 4.7 30 109-138 127-156 (163)
259 PF07037 DUF1323: Putative tra 34.6 39 0.00085 23.7 2.3 20 110-129 3-22 (122)
260 COG2944 Predicted transcriptio 34.1 96 0.0021 21.2 4.1 42 86-134 43-84 (104)
261 PRK12536 RNA polymerase sigma 33.8 97 0.0021 22.6 4.6 30 109-138 147-176 (181)
262 cd04779 HTH_MerR-like_sg4 Heli 33.7 42 0.00091 23.9 2.5 21 110-130 3-23 (134)
263 PF04297 UPF0122: Putative hel 33.7 1.1E+02 0.0023 20.9 4.3 42 86-132 17-58 (101)
264 PRK12547 RNA polymerase sigma 33.7 1E+02 0.0022 22.1 4.6 29 109-137 130-158 (164)
265 PRK12520 RNA polymerase sigma 33.6 1.4E+02 0.003 22.0 5.5 35 109-143 149-183 (191)
266 cd04776 HTH_GnyR Helix-Turn-He 33.5 1.6E+02 0.0035 20.2 6.1 43 52-96 4-46 (118)
267 PRK12546 RNA polymerase sigma 33.3 94 0.002 23.1 4.5 31 109-139 131-161 (188)
268 PRK12533 RNA polymerase sigma 33.2 1.7E+02 0.0036 22.5 6.0 31 109-139 152-182 (216)
269 PRK12537 RNA polymerase sigma 33.2 97 0.0021 22.7 4.6 29 109-137 151-179 (182)
270 PRK10403 transcriptional regul 33.1 43 0.00093 24.3 2.7 43 27-75 153-195 (215)
271 COG1905 NuoE NADH:ubiquinone o 33.1 85 0.0018 23.2 4.0 37 30-66 25-61 (160)
272 PRK09637 RNA polymerase sigma 33.1 94 0.002 22.9 4.5 30 109-138 124-153 (181)
273 PRK09651 RNA polymerase sigma 33.1 1E+02 0.0022 22.3 4.6 29 109-137 137-165 (172)
274 PRK12529 RNA polymerase sigma 32.9 99 0.0022 22.6 4.6 28 109-136 145-172 (178)
275 PRK07539 NADH dehydrogenase su 32.9 89 0.0019 22.7 4.2 36 31-66 23-58 (154)
276 PRK12538 RNA polymerase sigma 32.8 1.1E+02 0.0024 23.7 5.0 32 109-140 189-220 (233)
277 TIGR02950 SigM_subfam RNA poly 32.7 66 0.0014 22.6 3.5 32 106-137 120-151 (154)
278 PF14174 YycC: YycC-like prote 32.6 57 0.0012 19.1 2.4 24 46-69 6-29 (53)
279 PF01726 LexA_DNA_bind: LexA D 32.6 1E+02 0.0023 18.9 3.9 43 27-71 3-49 (65)
280 PRK09480 slmA division inhibit 32.5 50 0.0011 24.1 2.9 38 34-72 17-54 (194)
281 PRK13919 putative RNA polymera 32.5 1E+02 0.0023 22.4 4.7 29 109-137 153-181 (186)
282 TIGR02983 SigE-fam_strep RNA p 32.0 99 0.0021 21.9 4.4 29 109-137 128-156 (162)
283 PRK04140 hypothetical protein; 31.9 97 0.0021 25.6 4.6 20 52-71 143-162 (317)
284 COG5484 Uncharacterized conser 31.7 36 0.00079 27.1 2.0 25 51-75 22-46 (279)
285 PRK09645 RNA polymerase sigma 31.7 1.1E+02 0.0024 22.0 4.6 30 109-138 136-165 (173)
286 cd00131 PAX Paired Box domain 31.5 1.8E+02 0.004 20.3 6.5 45 27-71 75-126 (128)
287 TIGR01321 TrpR trp operon repr 31.4 46 0.001 22.3 2.2 45 27-71 32-78 (94)
288 TIGR01958 nuoE_fam NADH-quinon 31.2 99 0.0021 22.2 4.2 36 31-66 17-52 (148)
289 PF13022 HTH_Tnp_1_2: Helix-tu 31.1 58 0.0013 23.5 2.8 25 47-71 33-57 (142)
290 PF01257 2Fe-2S_thioredx: Thio 30.9 82 0.0018 22.6 3.7 35 32-66 15-49 (145)
291 TIGR02980 SigBFG RNA polymeras 30.7 1.1E+02 0.0024 23.3 4.7 45 87-136 179-223 (227)
292 PRK12539 RNA polymerase sigma 30.6 1.1E+02 0.0023 22.5 4.4 31 109-139 149-179 (184)
293 PRK07408 RNA polymerase sigma 30.2 1.1E+02 0.0023 24.1 4.6 31 108-138 220-250 (256)
294 PRK12541 RNA polymerase sigma 30.2 1E+02 0.0022 21.9 4.2 28 109-136 130-157 (161)
295 PF14229 DUF4332: Domain of un 30.1 55 0.0012 22.8 2.6 27 45-71 26-52 (122)
296 PRK12535 RNA polymerase sigma 29.8 90 0.0019 23.4 3.9 34 109-142 151-184 (196)
297 PF13921 Myb_DNA-bind_6: Myb-l 29.8 1.2E+02 0.0026 17.7 6.0 58 28-95 1-60 (60)
298 PF06971 Put_DNA-bind_N: Putat 29.8 47 0.001 19.4 1.8 17 110-126 31-47 (50)
299 PRK07571 bidirectional hydroge 29.5 1.1E+02 0.0024 22.8 4.2 35 32-66 38-72 (169)
300 PRK12540 RNA polymerase sigma 29.5 2E+02 0.0043 21.1 5.7 32 109-140 129-160 (182)
301 COG5484 Uncharacterized conser 29.4 44 0.00096 26.7 2.1 25 109-135 21-45 (279)
302 PRK05988 formate dehydrogenase 29.3 76 0.0017 23.2 3.3 36 90-125 24-59 (156)
303 PRK09649 RNA polymerase sigma 29.3 1.1E+02 0.0023 22.6 4.2 29 109-137 148-176 (185)
304 PHA00542 putative Cro-like pro 29.2 1.6E+02 0.0034 18.8 4.9 21 51-71 34-54 (82)
305 PRK12542 RNA polymerase sigma 29.1 1.2E+02 0.0026 22.2 4.5 31 109-139 140-170 (185)
306 PRK12523 RNA polymerase sigma 29.0 1.4E+02 0.003 21.6 4.7 30 109-138 137-166 (172)
307 PF03444 HrcA_DNA-bdg: Winged 28.9 1.5E+02 0.0032 19.2 4.2 41 28-70 2-45 (78)
308 PRK08583 RNA polymerase sigma 28.7 1.2E+02 0.0027 23.6 4.7 46 87-137 206-251 (257)
309 TIGR01557 myb_SHAQKYF myb-like 28.6 1.1E+02 0.0023 18.4 3.3 52 83-134 2-56 (57)
310 TIGR03830 CxxCG_CxxCG_HTH puta 28.5 74 0.0016 21.8 3.1 20 52-71 82-101 (127)
311 TIGR02941 Sigma_B RNA polymera 28.4 1.3E+02 0.0029 23.4 4.8 47 86-137 205-251 (255)
312 PF01476 LysM: LysM domain; I 28.3 53 0.0012 17.7 1.9 23 49-71 7-29 (44)
313 TIGR02479 FliA_WhiG RNA polyme 28.0 1.4E+02 0.003 22.8 4.8 45 87-136 176-220 (224)
314 TIGR02947 SigH_actino RNA poly 27.7 87 0.0019 23.1 3.5 33 108-140 148-180 (193)
315 COG1725 Predicted transcriptio 27.7 1E+02 0.0022 21.8 3.5 80 44-129 34-117 (125)
316 PF07471 Phage_Nu1: Phage DNA 27.6 44 0.00095 24.8 1.8 21 51-71 5-25 (164)
317 PRK12513 RNA polymerase sigma 27.6 1.1E+02 0.0023 22.6 4.0 34 106-139 154-187 (194)
318 PRK12531 RNA polymerase sigma 27.4 1.5E+02 0.0032 22.0 4.7 30 109-138 159-188 (194)
319 PRK09706 transcriptional repre 27.3 57 0.0012 22.9 2.3 24 110-133 21-44 (135)
320 PRK15369 two component system 27.2 1E+02 0.0022 22.0 3.8 44 26-75 148-191 (211)
321 PF12824 MRP-L20: Mitochondria 27.1 2.6E+02 0.0057 20.7 6.0 44 84-129 83-126 (164)
322 TIGR02859 spore_sigH RNA polym 26.9 88 0.0019 23.0 3.4 30 108-137 166-195 (198)
323 PRK06811 RNA polymerase factor 26.8 1.3E+02 0.0028 22.2 4.3 26 109-134 149-174 (189)
324 COG3093 VapI Plasmid maintenan 26.8 2.1E+02 0.0046 19.5 5.1 35 34-71 12-46 (104)
325 PRK08301 sporulation sigma fac 26.7 1.7E+02 0.0038 22.3 5.2 30 109-138 200-229 (234)
326 TIGR01958 nuoE_fam NADH-quinon 26.7 88 0.0019 22.5 3.2 35 90-124 17-51 (148)
327 PRK12522 RNA polymerase sigma 26.6 1.7E+02 0.0037 21.1 4.9 30 109-138 137-166 (173)
328 PF09862 DUF2089: Protein of u 26.5 1E+02 0.0022 21.4 3.3 37 87-128 34-70 (113)
329 TIGR01636 phage_rinA phage tra 26.4 1.5E+02 0.0033 20.9 4.4 38 28-68 83-120 (134)
330 PF13542 HTH_Tnp_ISL3: Helix-t 26.3 81 0.0018 17.8 2.5 21 109-129 29-49 (52)
331 PRK13869 plasmid-partitioning 26.3 79 0.0017 26.9 3.3 51 50-100 50-100 (405)
332 PRK07122 RNA polymerase sigma 26.0 1.6E+02 0.0036 23.3 5.0 29 109-137 233-261 (264)
333 PF06413 Neugrin: Neugrin; In 26.0 1.5E+02 0.0032 23.3 4.5 43 23-67 6-48 (225)
334 COG1476 Predicted transcriptio 25.8 1.8E+02 0.0038 18.3 4.8 44 51-124 17-60 (68)
335 PF00325 Crp: Bacterial regula 25.8 59 0.0013 17.1 1.6 21 50-70 4-24 (32)
336 PF08671 SinI: Anti-repressor 25.5 1.1E+02 0.0024 15.9 2.6 19 111-129 9-27 (30)
337 PRK09641 RNA polymerase sigma 25.5 1.6E+02 0.0035 21.3 4.6 31 108-138 153-183 (187)
338 PRK07539 NADH dehydrogenase su 25.4 95 0.0021 22.5 3.2 34 91-124 24-57 (154)
339 PRK07670 RNA polymerase sigma 25.3 1.7E+02 0.0036 22.8 4.9 29 109-137 219-247 (251)
340 TIGR00721 tfx DNA-binding prot 25.0 2.6E+02 0.0057 20.0 5.9 48 84-137 4-51 (137)
341 PRK10360 DNA-binding transcrip 24.9 72 0.0016 23.0 2.6 43 27-75 137-179 (196)
342 PRK11552 putative DNA-binding 24.7 59 0.0013 24.9 2.2 41 94-136 21-61 (225)
343 PRK12525 RNA polymerase sigma 24.7 1.6E+02 0.0034 21.2 4.3 28 109-136 136-163 (168)
344 PRK12545 RNA polymerase sigma 24.4 2.2E+02 0.0048 21.2 5.2 31 109-139 157-187 (201)
345 PRK09640 RNA polymerase sigma 24.3 1.3E+02 0.0029 22.1 4.0 31 108-138 151-181 (188)
346 PRK09415 RNA polymerase factor 24.3 1.4E+02 0.0031 21.7 4.1 29 109-137 145-173 (179)
347 PF08452 DNAP_B_exo_N: DNA pol 24.2 23 0.00049 16.8 -0.2 8 125-132 6-13 (22)
348 PF12793 SgrR_N: Sugar transpo 24.1 1.1E+02 0.0024 21.1 3.2 35 90-126 4-38 (115)
349 PRK12528 RNA polymerase sigma 23.9 1.7E+02 0.0036 20.7 4.4 24 109-132 131-154 (161)
350 PF04539 Sigma70_r3: Sigma-70 23.9 59 0.0013 20.2 1.7 25 44-71 19-43 (78)
351 PRK12517 RNA polymerase sigma 23.8 2.7E+02 0.0058 20.5 5.5 35 109-143 146-180 (188)
352 COG1905 NuoE NADH:ubiquinone o 23.7 1.1E+02 0.0025 22.6 3.3 36 89-124 25-60 (160)
353 PRK08241 RNA polymerase factor 23.7 1.7E+02 0.0036 23.9 4.8 62 52-113 173-238 (339)
354 PRK12511 RNA polymerase sigma 23.6 2.1E+02 0.0045 21.0 4.9 30 109-138 129-158 (182)
355 PRK07571 bidirectional hydroge 23.6 1.2E+02 0.0026 22.6 3.5 33 92-124 39-71 (169)
356 PF01257 2Fe-2S_thioredx: Thio 23.6 88 0.0019 22.4 2.7 35 91-125 15-49 (145)
357 PF11304 DUF3106: Protein of u 23.6 2.4E+02 0.0053 19.1 6.2 30 87-116 59-88 (107)
358 PF11212 DUF2999: Protein of u 23.6 2.1E+02 0.0045 18.2 4.0 36 27-66 12-47 (82)
359 PRK11922 RNA polymerase sigma 23.4 1.7E+02 0.0038 22.4 4.6 36 105-140 163-198 (231)
360 PRK12544 RNA polymerase sigma 23.4 2.3E+02 0.005 21.4 5.2 32 109-140 166-197 (206)
361 TIGR03826 YvyF flagellar opero 23.3 75 0.0016 22.9 2.2 27 108-134 47-73 (137)
362 PRK05657 RNA polymerase sigma 23.2 1.7E+02 0.0037 24.1 4.6 53 86-139 262-314 (325)
363 PRK12527 RNA polymerase sigma 23.1 1.7E+02 0.0036 20.7 4.2 30 109-138 123-152 (159)
364 PRK11923 algU RNA polymerase s 23.0 1.4E+02 0.0031 21.9 3.9 32 109-140 156-187 (193)
365 PF09301 DUF1970: Domain of un 22.6 46 0.001 21.9 1.0 13 122-134 17-29 (117)
366 PF13404 HTH_AsnC-type: AsnC-t 22.4 66 0.0014 17.9 1.5 17 52-68 21-37 (42)
367 TIGR03020 EpsA transcriptional 22.4 1.6E+02 0.0035 23.3 4.2 53 84-142 188-240 (247)
368 COG2938 Uncharacterized conser 22.4 1.6E+02 0.0034 19.8 3.5 42 32-73 28-71 (94)
369 PRK08295 RNA polymerase factor 22.2 1.4E+02 0.0031 22.1 3.8 31 108-138 171-201 (208)
370 PRK09636 RNA polymerase sigma 22.0 1.9E+02 0.0042 23.0 4.8 80 28-113 116-195 (293)
371 TIGR03020 EpsA transcriptional 22.0 89 0.0019 24.7 2.7 45 25-75 188-232 (247)
372 COG1595 RpoE DNA-directed RNA 21.9 1.5E+02 0.0032 21.7 3.8 32 109-140 145-176 (182)
373 PHA02535 P terminase ATPase su 21.7 2E+02 0.0043 26.0 5.0 44 27-75 2-45 (581)
374 PRK10878 hypothetical protein; 21.7 1.9E+02 0.004 18.3 3.6 41 32-72 3-45 (72)
375 TIGR02960 SigX5 RNA polymerase 21.6 1.9E+02 0.0041 23.3 4.7 81 28-113 143-228 (324)
376 PRK13558 bacterio-opsin activa 21.6 1.2E+02 0.0026 27.2 3.8 44 85-128 606-651 (665)
377 PF13223 DUF4031: Protein of u 21.5 1E+02 0.0022 20.2 2.4 20 48-71 23-42 (83)
378 COG3711 BglG Transcriptional a 21.3 5.3E+02 0.012 22.2 8.5 36 29-67 3-38 (491)
379 TIGR02957 SigX4 RNA polymerase 21.2 1.9E+02 0.0041 23.1 4.5 28 110-137 127-154 (281)
380 PF12244 DUF3606: Protein of u 21.0 1.3E+02 0.0027 18.0 2.6 20 107-126 20-39 (57)
381 PF06163 DUF977: Bacterial pro 21.0 1.9E+02 0.0042 20.5 3.9 50 26-75 3-53 (127)
382 TIGR00673 cynS cyanate hydrata 20.9 2.7E+02 0.0059 20.4 4.8 22 102-123 45-66 (150)
383 PRK09638 RNA polymerase sigma 20.8 1.4E+02 0.0031 21.4 3.5 32 106-137 141-172 (176)
384 PRK13182 racA polar chromosome 20.8 97 0.0021 23.2 2.5 21 110-130 3-23 (175)
385 cd04778 HTH_MerR-like_sg2 Heli 20.8 4.1E+02 0.0088 20.6 6.4 46 52-98 5-50 (219)
386 PRK06288 RNA polymerase sigma 20.7 2.8E+02 0.0061 21.8 5.4 48 87-139 213-260 (268)
387 PRK05803 sporulation sigma fac 20.6 3.1E+02 0.0068 21.0 5.5 30 108-137 196-225 (233)
388 PHA02947 S-S bond formation pa 20.6 1.7E+02 0.0037 22.7 3.8 42 30-71 60-102 (215)
389 PF01325 Fe_dep_repress: Iron 20.4 53 0.0011 19.8 0.9 42 28-69 2-43 (60)
390 TIGR02393 RpoD_Cterm RNA polym 20.4 2.4E+02 0.0051 21.8 4.8 51 87-138 177-227 (238)
391 PRK10430 DNA-binding transcrip 20.1 1.5E+02 0.0032 22.7 3.6 45 27-72 158-202 (239)
392 PRK10651 transcriptional regul 20.1 1E+02 0.0023 22.2 2.7 43 27-75 155-197 (216)
No 1
>KOG0490|consensus
Probab=99.75 E-value=2.1e-18 Score=134.75 Aligned_cols=123 Identities=30% Similarity=0.362 Sum_probs=112.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc-----------------
Q psy10486 18 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV----------------- 80 (183)
Q Consensus 18 ~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~----------------- 80 (183)
..+.++.|+.|+..|+++|+..|..++||+...++.||..+++++..|++||+|+|++.++..
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 567889999999999999999999999999999999999999999999999999999866433
Q ss_pred -----------------cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 81 -----------------RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 81 -----------------rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
++.++.+...++..+...|....+|+...++.|+..+|++...|++||+|+|.+.++...
T Consensus 137 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 137 PSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 223457778899999999999999999999999999999999999999999999998877
No 2
>KOG0484|consensus
Probab=99.72 E-value=6.6e-18 Score=112.65 Aligned_cols=70 Identities=34% Similarity=0.492 Sum_probs=64.2
Q ss_pred cccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486 77 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA 146 (183)
Q Consensus 77 ~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~ 146 (183)
+++.++-|+.|+..|+.+|+..|...+||++-++++||..+.|++..|++||||||+|.||+.+......
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~ 83 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM 83 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence 4567788999999999999999999999999999999999999999999999999999999997665543
No 3
>KOG2251|consensus
Probab=99.68 E-value=3.1e-17 Score=123.65 Aligned_cols=64 Identities=30% Similarity=0.415 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT 79 (183)
Q Consensus 16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~ 79 (183)
..+++.||+||.|+..|+++||+.|.++.|||...+++||.+|+|.+-+|++||.|||+|.+..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~q 95 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQ 95 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHh
Confidence 6789999999999999999999999999999999999999999999999999999999996553
No 4
>KOG0850|consensus
Probab=99.66 E-value=4.8e-17 Score=123.23 Aligned_cols=65 Identities=40% Similarity=0.463 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR 81 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r 81 (183)
...|.|++||.|+..||..|+.+|+.+.|+...||.+||..|||+..||+|||||||.|-|+..+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 44677899999999999999999999999999999999999999999999999999998776554
No 5
>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=99.66 E-value=1e-16 Score=98.64 Aligned_cols=56 Identities=48% Similarity=0.639 Sum_probs=53.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ 77 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~ 77 (183)
+++|+.||.+|+.+|++.|..++||+..+++.||..|||+..+|.+||+|+|.+.+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 56 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEK 56 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhC
Confidence 57899999999999999999999999999999999999999999999999987643
No 6
>KOG0488|consensus
Probab=99.65 E-value=1.4e-16 Score=128.73 Aligned_cols=76 Identities=46% Similarity=0.593 Sum_probs=68.1
Q ss_pred ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCC
Q psy10486 78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTS 153 (183)
Q Consensus 78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~ 153 (183)
++.++.|+.||.-|+..||..|++..|++..+|++||..|||+..||++||||||+|||++...........++.+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~~~~ 245 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAGNSS 245 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcccccccccc
Confidence 6778889999999999999999999999999999999999999999999999999999999988655555444443
No 7
>KOG0484|consensus
Probab=99.64 E-value=4.7e-17 Score=108.60 Aligned_cols=62 Identities=31% Similarity=0.394 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV 78 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~ 78 (183)
...++||-||.||..||.+||..|.++.||+.-.+++||.+|.|++..|++||||||+|-++
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRK 74 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRK 74 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHH
Confidence 45788999999999999999999999999999999999999999999999999999998543
No 8
>KOG0487|consensus
Probab=99.64 E-value=1.2e-16 Score=127.43 Aligned_cols=69 Identities=59% Similarity=0.888 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR 84 (183)
Q Consensus 16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r 84 (183)
......||+|.-||..|+.+||+-|-.|.|++++.|.+|+..|+|+++||+|||||||.|.|+..+..+
T Consensus 230 ~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 230 SSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 455788999999999999999999999999999999999999999999999999999999998776444
No 9
>KOG0488|consensus
Probab=99.64 E-value=1.8e-16 Score=128.07 Aligned_cols=64 Identities=44% Similarity=0.546 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT 79 (183)
Q Consensus 16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~ 79 (183)
..+.|.|+.||.||+.||..||++|+...|++..+|++||..|||+..||++||||||.|+++.
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 3457888999999999999999999999999999999999999999999999999999987753
No 10
>KOG0489|consensus
Probab=99.64 E-value=1.6e-16 Score=126.16 Aligned_cols=82 Identities=43% Similarity=0.739 Sum_probs=71.2
Q ss_pred hhhhhhhhccc-----cccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 64 QVKIWFQNIEW-----TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 64 qV~~WF~nrr~-----k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
+|--|+..... ......++.|+.||..|+.+||++|..|.|++...|.+||..|+|++.||+|||||||+||||.
T Consensus 138 ~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~ 217 (261)
T KOG0489|consen 138 QIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKE 217 (261)
T ss_pred ccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHh
Confidence 67778876542 2223467889999999999999999999999999999999999999999999999999999999
Q ss_pred HhHHHHH
Q psy10486 139 TQRQAAQ 145 (183)
Q Consensus 139 ~~~~~~~ 145 (183)
.+.....
T Consensus 218 ~k~~~~~ 224 (261)
T KOG0489|consen 218 NKAKSSQ 224 (261)
T ss_pred hcccccc
Confidence 9776655
No 11
>KOG0843|consensus
Probab=99.64 E-value=5e-16 Score=113.61 Aligned_cols=65 Identities=43% Similarity=0.650 Sum_probs=60.6
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA 143 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~ 143 (183)
..++.|+.|+.+|+..|+..|+.++|....+|+.||..|+|++.||++||||||+|.||++...+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~k 165 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQEDK 165 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHhh
Confidence 35567999999999999999999999999999999999999999999999999999999987753
No 12
>KOG2251|consensus
Probab=99.63 E-value=8e-16 Score=116.07 Aligned_cols=67 Identities=36% Similarity=0.543 Sum_probs=63.5
Q ss_pred ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
..++.++.|+.|+-.|+++|+..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++.+
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4556788899999999999999999999999999999999999999999999999999999999876
No 13
>KOG0842|consensus
Probab=99.63 E-value=2.1e-16 Score=126.00 Aligned_cols=64 Identities=42% Similarity=0.593 Sum_probs=59.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV 80 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~ 80 (183)
.+.+.||.|..||..|+.+||.+|....|.+..||+.||..|+||+.||+|||||||.|.|+..
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 3567778889999999999999999999999999999999999999999999999999977644
No 14
>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=99.63 E-value=5.4e-16 Score=95.39 Aligned_cols=57 Identities=56% Similarity=0.750 Sum_probs=54.5
Q ss_pred cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
+++++.|+.+|+.+|+..|..++||+..+++.||..+||+..+|.+||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 357889999999999999999999999999999999999999999999999999986
No 15
>KOG0850|consensus
Probab=99.63 E-value=3.3e-16 Score=118.72 Aligned_cols=67 Identities=46% Similarity=0.571 Sum_probs=63.1
Q ss_pred ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
..++.|+.|+.++.-|+..|...|+.++|+-..+|.+||..|||+-.||++||||||.|.||..+..
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 4457888999999999999999999999999999999999999999999999999999999999843
No 16
>KOG0494|consensus
Probab=99.61 E-value=7.2e-16 Score=118.62 Aligned_cols=65 Identities=29% Similarity=0.343 Sum_probs=58.3
Q ss_pred CCCCCC-CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccccc
Q psy10486 19 VTVRKK-RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKK 83 (183)
Q Consensus 19 ~~~rr~-r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~ 83 (183)
.+.||. ||.||..|++.||+.|.+..|||.-.|+.||.++.|.+++|++||||||+|.+++.++-
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 334444 99999999999999999999999999999999999999999999999999988766543
No 17
>KOG0843|consensus
Probab=99.61 E-value=5.1e-16 Score=113.56 Aligned_cols=66 Identities=35% Similarity=0.507 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRK 82 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr 82 (183)
...+.+|.||.||.+||..||..|+.+.|..-.||+.||..|+|++.||++||||||-|.++...+
T Consensus 98 ~~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 98 RSMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 344889999999999999999999999999999999999999999999999999999987765544
No 18
>KOG0487|consensus
Probab=99.59 E-value=4.2e-16 Score=124.40 Aligned_cols=69 Identities=65% Similarity=0.974 Sum_probs=63.1
Q ss_pred ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486 78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA 146 (183)
Q Consensus 78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~ 146 (183)
+..||+|..+|+.|+.+||++|..|.|++...|.+|+..|+|+++||+|||||||.|.||..+......
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~~ 301 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLKE 301 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhccc
Confidence 346778999999999999999999999999999999999999999999999999999999997655443
No 19
>KOG0489|consensus
Probab=99.59 E-value=6.4e-16 Score=122.75 Aligned_cols=66 Identities=41% Similarity=0.689 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486 19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR 84 (183)
Q Consensus 19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r 84 (183)
...||.||.||..||.+||+-|+-+.|.++..|.+||..|.|+++||+|||||||+|.|+..+...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 347899999999999999999999999999999999999999999999999999999887555443
No 20
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.59 E-value=2.6e-15 Score=91.68 Aligned_cols=51 Identities=14% Similarity=0.333 Sum_probs=49.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
+|.||.||.+|+..|+..|+.+.| |+..++++||..|||++.+|++||+|-
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~ 56 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNN 56 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccC
Confidence 789999999999999999999999 999999999999999999999999993
No 21
>KOG0494|consensus
Probab=99.58 E-value=1.4e-15 Score=117.04 Aligned_cols=67 Identities=34% Similarity=0.429 Sum_probs=61.5
Q ss_pred ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
.++++|..|+.||.-|+..||+.|...+||+...++.||..++|++++|+|||||||+||||.++..
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 3445556699999999999999999999999999999999999999999999999999999998765
No 22
>KOG0842|consensus
Probab=99.58 E-value=1.6e-15 Score=121.03 Aligned_cols=75 Identities=43% Similarity=0.570 Sum_probs=67.2
Q ss_pred cccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCC
Q psy10486 77 QVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNN 151 (183)
Q Consensus 77 ~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~ 151 (183)
+.++||.|.-|+..|+.+||..|....|++..+|+.||..|.||+.||+|||||||-|+||+.+...........
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~ 224 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS 224 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence 445666778899999999999999999999999999999999999999999999999999999888777665443
No 23
>KOG0848|consensus
Probab=99.58 E-value=3.6e-15 Score=115.24 Aligned_cols=65 Identities=51% Similarity=0.778 Sum_probs=60.6
Q ss_pred ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
++..+.|.++|+-|.-+||++|..++|+++..+.+||.-|||+++||++||||||+|+||.+++.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34556788999999999999999999999999999999999999999999999999999999666
No 24
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.56 E-value=8.6e-15 Score=89.57 Aligned_cols=55 Identities=51% Similarity=0.696 Sum_probs=51.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTG 76 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~ 76 (183)
++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|..||+|+|.+.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 3567889999999999999999999999999999999999999999999988753
No 25
>KOG0492|consensus
Probab=99.55 E-value=3.7e-15 Score=111.27 Aligned_cols=68 Identities=44% Similarity=0.652 Sum_probs=62.3
Q ss_pred ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486 76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA 143 (183)
Q Consensus 76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~ 143 (183)
+.+..|++|+.||..|+..||..|...+|+++.++.+++..|.|++.||++||||||+|.||.++.+.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 34567788999999999999999999999999999999999999999999999999999999885443
No 26
>KOG0848|consensus
Probab=99.55 E-value=1e-15 Score=118.22 Aligned_cols=63 Identities=49% Similarity=0.693 Sum_probs=58.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR 84 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r 84 (183)
-|.|.+||+.|..+||+.|+.+.|++...+.+||..|||+++||++||||||+|+++..++++
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 367889999999999999999999999999999999999999999999999999988776664
No 27
>KOG0492|consensus
Probab=99.53 E-value=5.5e-15 Score=110.38 Aligned_cols=61 Identities=43% Similarity=0.602 Sum_probs=56.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486 19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT 79 (183)
Q Consensus 19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~ 79 (183)
.+.|++||.||.+||..||..|...+|.+..|+.+++..|.|++.||++||||||+|.++.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 4457889999999999999999999999999999999999999999999999999987653
No 28
>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=99.52 E-value=2.2e-14 Score=88.59 Aligned_cols=55 Identities=53% Similarity=0.691 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc
Q psy10486 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ 77 (183)
Q Consensus 23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~ 77 (183)
+.+..|+..|+.+|++.|..++||+..++..||..+||+..+|..||+|+|.+.+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLK 56 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHh
Confidence 5678999999999999999999999999999999999999999999999987654
No 29
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.52 E-value=1.1e-14 Score=106.53 Aligned_cols=100 Identities=26% Similarity=0.301 Sum_probs=77.6
Q ss_pred cCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHH
Q psy10486 15 WTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLE 94 (183)
Q Consensus 15 ~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~ 94 (183)
..+....+++|++-|.+|+.+|+..|..++||+..++..|+..|||+++-|++||||+|++.++.....
T Consensus 45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~----------- 113 (156)
T COG5576 45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK----------- 113 (156)
T ss_pred ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc-----------
Confidence 345567888999999999999999999999999999999999999999999999999999876544433
Q ss_pred HHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 95 LEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 95 Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
...++.. +-..++....+...++.+||.+..
T Consensus 114 ------~~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~ 144 (156)
T COG5576 114 ------VEQRPGE-EEADLAKIGSLSTGQISIIETLEF 144 (156)
T ss_pred ------hhccccc-ccccccccccccccchhhHHhhhc
Confidence 2333333 334456666666667777775443
No 30
>KOG0485|consensus
Probab=99.50 E-value=1.4e-14 Score=108.89 Aligned_cols=67 Identities=43% Similarity=0.598 Sum_probs=60.8
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ 145 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~ 145 (183)
..++.|++|+..|+..||..|+...|++..++..||..|.|++.||++||||||.|||++-......
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea 169 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEA 169 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhh
Confidence 3456688999999999999999999999999999999999999999999999999999998655443
No 31
>KOG0491|consensus
Probab=99.50 E-value=1.4e-14 Score=104.59 Aligned_cols=80 Identities=41% Similarity=0.566 Sum_probs=70.5
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCCCCCCC
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNTNNN 158 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~~~~~~ 158 (183)
..++.|++|+..|+..|+..|+...|++..++.+||..|+|++.||+.||||||.|.||..+.......+.....++...
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~~~t~~a~a~t 178 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSNGVTQKASAPT 178 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCCcccccccCcc
Confidence 34566899999999999999999999999999999999999999999999999999999999888777666655555443
No 32
>KOG0485|consensus
Probab=99.50 E-value=1.4e-14 Score=108.93 Aligned_cols=63 Identities=41% Similarity=0.553 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT 79 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~ 79 (183)
+..+.+|.||.|+..|+..||..|+...|.+..+|..||..|.|++.||++||||||.|.++.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 445778889999999999999999999999999999999999999999999999999887653
No 33
>KOG3802|consensus
Probab=99.48 E-value=4.3e-15 Score=121.00 Aligned_cols=127 Identities=24% Similarity=0.344 Sum_probs=101.2
Q ss_pred ccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHcCCChhh-hhhhhhhcccc-------------
Q psy10486 14 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQ-VKIWFQNIEWT------------- 75 (183)
Q Consensus 14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~q-V~~WF~nrr~k------------- 75 (183)
.+....|+||-+.-||..++-.-...-.-+.| +++.|...|.-+-.+..+- +..|...-...
T Consensus 210 qFAK~FKqRRIkLGfTQaDVGlALG~lyGn~FSQTTIcRFEALqLSFKNMCKLKPLL~KWLeEAes~~~~~~~~~~e~i~ 289 (398)
T KOG3802|consen 210 QFAKTFKQRRIKLGFTQADVGLALGALYGNVFSQTTICRFEALQLSFKNMCKLKPLLEKWLEEAESRESTGSPNSIEKIG 289 (398)
T ss_pred HHHHHHHhheeccccchhHHHHHHHhhhCcccchhhhhHhHhhccCHHHHhhhHHHHHHHHHHHhcccccCCCCCHHHhh
Confidence 33466888999999999998766655444444 7777766666555555544 35898764331
Q ss_pred ccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 76 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 76 ~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|++|+.|.......||.+|..|+.|+..++..||.+|+|....|+|||+|||.|.||...
T Consensus 290 a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 290 AQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 22256788999999999999999999999999999999999999999999999999999999887
No 34
>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=99.48 E-value=8.2e-14 Score=85.96 Aligned_cols=57 Identities=58% Similarity=0.807 Sum_probs=53.4
Q ss_pred ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
+.+..++..++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456789999999999999999999999999999999999999999999999998763
No 35
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=6.2e-14 Score=85.73 Aligned_cols=55 Identities=56% Similarity=0.794 Sum_probs=51.3
Q ss_pred ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
+.++.+++.++.+|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4566799999999999999999999999999999999999999999999998753
No 36
>KOG0493|consensus
Probab=99.47 E-value=3.9e-14 Score=109.21 Aligned_cols=61 Identities=44% Similarity=0.691 Sum_probs=57.4
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
..+++|+.|+.+|+..|..+|..+.|++...+.+||.+|||.+.||++||||+|+|-||..
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 4467799999999999999999999999999999999999999999999999999998865
No 37
>KOG0486|consensus
Probab=99.45 E-value=5.4e-14 Score=111.05 Aligned_cols=62 Identities=32% Similarity=0.441 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486 20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR 81 (183)
Q Consensus 20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r 81 (183)
|+||.||.||.+||.+||..|.++.||++..+++||..++|++..|.+||.|||+|.++..+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 77899999999999999999999999999999999999999999999999999999877554
No 38
>KOG0486|consensus
Probab=99.43 E-value=7.7e-14 Score=110.17 Aligned_cols=68 Identities=37% Similarity=0.542 Sum_probs=63.9
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHh
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQA 146 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~ 146 (183)
+.++.|+.|+..|+.+||..|.++.||++..+++||.-++|++..|++||+|||+||||.++.+..+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~ 178 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAEL 178 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHh
Confidence 56777899999999999999999999999999999999999999999999999999999998888443
No 39
>KOG0491|consensus
Probab=99.40 E-value=5e-14 Score=101.69 Aligned_cols=65 Identities=40% Similarity=0.530 Sum_probs=59.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC
Q psy10486 20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR 84 (183)
Q Consensus 20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r 84 (183)
+.++-||.|++.|+..|+++|+...|.+..++.+||..|+|++.||+.||||||+|.++-.++..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 44677999999999999999999999999999999999999999999999999999887666543
No 40
>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=2.2e-13 Score=83.19 Aligned_cols=52 Identities=13% Similarity=0.364 Sum_probs=49.6
Q ss_pred cccCCCCChhHHHHHHHccccCCc----cCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 81 RKKRKPYSKHQTLELEKEFLYNAY----VSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 81 rr~r~~~t~~q~~~Le~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
++.|+.||.+|+..|+..|+.+.| |+..++++||..+||++.+|++||+|-+
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 577999999999999999999999 9999999999999999999999999854
No 41
>KOG0483|consensus
Probab=99.38 E-value=2.7e-13 Score=102.60 Aligned_cols=75 Identities=28% Similarity=0.310 Sum_probs=61.7
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHH
Q psy10486 21 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLEL 95 (183)
Q Consensus 21 ~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~L 95 (183)
..+++.+|+.+|+..||..|+...+.....+..||..|||.++||.+||||||++.+.+..-..-.+...++..|
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l 124 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESL 124 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHH
Confidence 457778999999999999999999999999999999999999999999999999887655444333333333333
No 42
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=6.1e-13 Score=97.41 Aligned_cols=68 Identities=35% Similarity=0.542 Sum_probs=61.3
Q ss_pred ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486 78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ 145 (183)
Q Consensus 78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~ 145 (183)
...+++|++.+.+|+.+|+..|+.++||+..++..|+..++|+++.|++||||+|++.|+........
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~ 116 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQ 116 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhc
Confidence 34566788999999999999999999999999999999999999999999999999999988654433
No 43
>KOG0844|consensus
Probab=99.36 E-value=1.9e-13 Score=107.57 Aligned_cols=68 Identities=34% Similarity=0.546 Sum_probs=61.3
Q ss_pred ccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486 14 EWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR 81 (183)
Q Consensus 14 ~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r 81 (183)
.-...+-.||.||.||-+|+.-||+.|.+..|.++..|.+||..|+|.+..|++||||||+|.++.+-
T Consensus 174 a~sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 174 ANSADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred ccCccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 33455667999999999999999999999999999999999999999999999999999999876443
No 44
>KOG3802|consensus
Probab=99.35 E-value=7.5e-13 Score=108.04 Aligned_cols=66 Identities=30% Similarity=0.344 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc
Q psy10486 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR 81 (183)
Q Consensus 16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r 81 (183)
..+.+.||+||.|......+||+.|..|+.|+.+|+..||..|+|..++|++||+|||.|.|+...
T Consensus 289 ~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 289 GAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 344588999999999999999999999999999999999999999999999999999999877554
No 45
>KOG0483|consensus
Probab=99.35 E-value=7.6e-13 Score=100.14 Aligned_cols=59 Identities=34% Similarity=0.522 Sum_probs=55.4
Q ss_pred cccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 81 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 81 rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
..++.+++.+|...|+..|+.+.++....+..||..|||.++||.+||||||++||.++
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 44567899999999999999999999999999999999999999999999999999876
No 46
>KOG0844|consensus
Probab=99.35 E-value=2e-13 Score=107.45 Aligned_cols=61 Identities=46% Similarity=0.808 Sum_probs=58.6
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
..++.|+.||.+|+..||++|-+..|.+...+.+||..|+|++..|++||||||.|+|++.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 5678899999999999999999999999999999999999999999999999999999986
No 47
>KOG0493|consensus
Probab=99.35 E-value=1.3e-12 Score=100.90 Aligned_cols=59 Identities=37% Similarity=0.583 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV 80 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~ 80 (183)
+|+||.||.+||+-|...|..+.|++...|.+||.+|||.+-||++||||.|+|-++..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 57899999999999999999999999999999999999999999999999999866533
No 48
>KOG4577|consensus
Probab=99.29 E-value=1.9e-12 Score=101.32 Aligned_cols=63 Identities=21% Similarity=0.313 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccc
Q psy10486 17 GQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVT 79 (183)
Q Consensus 17 ~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~ 79 (183)
+....+|+||.+|..||+.|..+|...+.|.+..|++|+..+||..+.|++||||||+|.++-
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRL 225 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRL 225 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhh
Confidence 345678999999999999999999999999999999999999999999999999999997653
No 49
>KOG0847|consensus
Probab=99.23 E-value=1.2e-11 Score=93.44 Aligned_cols=73 Identities=36% Similarity=0.600 Sum_probs=64.1
Q ss_pred cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcCCCCCCCC
Q psy10486 83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASNNNNTSNT 155 (183)
Q Consensus 83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~~~~~~~~ 155 (183)
.+..|+-.|+..|+..|+...|+-.+++.+||..+|+++.+|++||||||+||||+...+...+..-.+..+.
T Consensus 170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ae 242 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSGAE 242 (288)
T ss_pred cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCccc
Confidence 3557999999999999999999999999999999999999999999999999999998887776554444333
No 50
>KOG4577|consensus
Probab=99.15 E-value=2.8e-11 Score=94.81 Aligned_cols=64 Identities=25% Similarity=0.398 Sum_probs=60.1
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
..+++|+.++..|++.|..+|...+.|..+.++.|+.++||.-+.|++||||||+|+|+-.+..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 5678899999999999999999999999999999999999999999999999999999877544
No 51
>KOG0849|consensus
Probab=99.04 E-value=2.6e-10 Score=94.30 Aligned_cols=65 Identities=29% Similarity=0.308 Sum_probs=59.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc
Q psy10486 16 TGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV 80 (183)
Q Consensus 16 ~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~ 80 (183)
....+.++.||.|+..|++.|++.|+.++||+...++.||..+++++..|++||+|+|++.++..
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 45567788899999999999999999999999999999999999999999999999998766544
No 52
>KOG0490|consensus
Probab=98.94 E-value=4.2e-10 Score=87.83 Aligned_cols=63 Identities=33% Similarity=0.360 Sum_probs=59.3
Q ss_pred ccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 78 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 78 ~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
.+.++.|+.++..|+++|+..|...+||+...++.||..+++++..|++||+|+|++++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 355677889999999999999999999999999999999999999999999999999999886
No 53
>KOG0849|consensus
Probab=98.91 E-value=1.2e-09 Score=90.40 Aligned_cols=72 Identities=31% Similarity=0.348 Sum_probs=62.6
Q ss_pred hhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 66 KIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 66 ~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
..|+.+.. ++..++.|+.|+..|+..|++.|+.++||+...++.||.++++++..|.+||+|+|+++++...
T Consensus 165 ~~~p~~~~---~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 165 EEPPGYAL---QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccc---cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 34554432 2345566899999999999999999999999999999999999999999999999999999994
No 54
>KOG0775|consensus
Probab=98.85 E-value=2e-09 Score=83.97 Aligned_cols=51 Identities=33% Similarity=0.505 Sum_probs=45.9
Q ss_pred hhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 89 KHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 89 ~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
..-..+|...|..++||+..++.+||+.+||+..||-+||+|||.++|-..
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 334578999999999999999999999999999999999999999999333
No 55
>KOG0847|consensus
Probab=98.83 E-value=1.7e-09 Score=81.84 Aligned_cols=55 Identities=36% Similarity=0.579 Sum_probs=51.2
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486 24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV 78 (183)
Q Consensus 24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~ 78 (183)
.|-.|+-.|+..|+..|+.+.|+--+++.+||..+|+++-+|.+||||||-|.++
T Consensus 170 srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRK 224 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRK 224 (288)
T ss_pred cCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhh
Confidence 3557999999999999999999999999999999999999999999999887655
No 56
>KOG0775|consensus
Probab=98.76 E-value=9.6e-09 Score=80.21 Aligned_cols=59 Identities=27% Similarity=0.376 Sum_probs=50.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCC
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKP 86 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~ 86 (183)
|-+.-...|.+.|..++||+..++.+||+++||+..||.+||.|||.+.+....+.+..
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ak~~~~ 241 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAAKNSSN 241 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccccccCC
Confidence 55556789999999999999999999999999999999999999999887555544433
No 57
>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=98.74 E-value=1.4e-08 Score=57.53 Aligned_cols=35 Identities=40% Similarity=0.635 Sum_probs=29.3
Q ss_pred ccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 100 LYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 100 ~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
..++||+..++..||..+||+..||.+||.|.|.+
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 35799999999999999999999999999998864
No 58
>KOG1168|consensus
Probab=98.63 E-value=7e-09 Score=81.57 Aligned_cols=62 Identities=27% Similarity=0.401 Sum_probs=57.2
Q ss_pred cccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
..+++|+.+...+...||++|...+.|+.+.+..+|++|+|....|++||+|+|.|.||+..
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 45677888999999999999999999999999999999999999999999999999998654
No 59
>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=98.60 E-value=2.3e-08 Score=56.57 Aligned_cols=33 Identities=36% Similarity=0.561 Sum_probs=27.5
Q ss_pred hcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486 42 YNAYVSKQKRWELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 42 ~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
.+|||+.+++..||..+||+..||..||-|.|.
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHc
Confidence 469999999999999999999999999999653
No 60
>KOG1168|consensus
Probab=98.54 E-value=1.7e-08 Score=79.46 Aligned_cols=60 Identities=23% Similarity=0.285 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486 19 VTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV 78 (183)
Q Consensus 19 ~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~ 78 (183)
.-.+|+||.+-.-....||++|...+.|+.+.+..||++|.|....|++||.|.|.|.++
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHH
Confidence 445788999999999999999999999999999999999999999999999999987665
No 61
>KOG2252|consensus
Probab=98.50 E-value=1.4e-07 Score=80.18 Aligned_cols=56 Identities=21% Similarity=0.219 Sum_probs=51.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
..+|+|.+||+.|.+.|.+.|..+++|+.++++.|+..|||....|.+||=|-|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRR 474 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRR 474 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhh
Confidence 45677999999999999999999999999999999999999999999999995543
No 62
>KOG0774|consensus
Probab=98.43 E-value=1.4e-07 Score=73.30 Aligned_cols=64 Identities=38% Similarity=0.576 Sum_probs=57.4
Q ss_pred cccccCCCCChhHHHHHHHccc---cCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 79 TVRKKRKPYSKHQTLELEKEFL---YNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 79 ~~rr~r~~~t~~q~~~Le~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
..+++|+.|++.-.++|..+|. .++||+.+.+++||++.+++..||.+||.|+|-+.+|..-..
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 3567788999999999999984 689999999999999999999999999999999999877433
No 63
>KOG1146|consensus
Probab=98.33 E-value=2.9e-06 Score=78.61 Aligned_cols=136 Identities=18% Similarity=0.182 Sum_probs=116.3
Q ss_pred CCCCCCccccCCCCCCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccc--------
Q psy10486 6 VNSSSSTLEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQ-------- 77 (183)
Q Consensus 6 ~~~s~~~~~~~~~~~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~-------- 77 (183)
+++..+. +++.+...+..+...-.+++.+|-..|..+..|+......|.-....+.+++..||.+-+.+..
T Consensus 691 t~s~~g~-~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~ 769 (1406)
T KOG1146|consen 691 TGSEVGG-GESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDV 769 (1406)
T ss_pred CCCCCCC-CCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCC
Confidence 3444444 6666667778888899999999999999999999999999988888899999999987532200
Q ss_pred --------------------------------------------------------------------------------
Q psy10486 78 -------------------------------------------------------------------------------- 77 (183)
Q Consensus 78 -------------------------------------------------------------------------------- 77 (183)
T Consensus 770 ~~c~l~~y~t~~kanfqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~ 849 (1406)
T KOG1146|consen 770 PSCKLKPYATNTKANFQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPS 849 (1406)
T ss_pred CcceecccccccchhhhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCC
Confidence
Q ss_pred ---------------------------------------------------ccccccCCCCChhHHHHHHHccccCCccC
Q psy10486 78 ---------------------------------------------------VTVRKKRKPYSKHQTLELEKEFLYNAYVS 106 (183)
Q Consensus 78 ---------------------------------------------------~~~rr~r~~~t~~q~~~Le~~F~~~~~p~ 106 (183)
..++.+|+.++..|+..+...|....+|.
T Consensus 850 ~he~~~~~~ks~~~l~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~ 929 (1406)
T KOG1146|consen 850 EHEGPEEIYKSLLSLACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPT 929 (1406)
T ss_pred ccccccccchhHHHHHHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCCh
Confidence 05667889999999999999999999999
Q ss_pred HHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 107 KQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 107 ~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
..+.+.|...+++..+.|.+||+|-|.+.++....+
T Consensus 930 ~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 930 MQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred HHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 999999999999999999999999999999988744
No 64
>KOG0774|consensus
Probab=98.30 E-value=5.2e-07 Score=70.22 Aligned_cols=55 Identities=36% Similarity=0.507 Sum_probs=50.1
Q ss_pred CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
.+|+|..|+..-.++|..+|.. +|||+.+++++||...||+.-||.+||.|.|..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIr 245 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIR 245 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceee
Confidence 4688999999999999999975 699999999999999999999999999996543
No 65
>KOG2252|consensus
Probab=97.96 E-value=1e-05 Score=69.17 Aligned_cols=56 Identities=23% Similarity=0.267 Sum_probs=52.0
Q ss_pred ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHH
Q psy10486 80 VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKN 135 (183)
Q Consensus 80 ~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~ 135 (183)
.+++|.+|++.|...|...|+.+++|+.+..+.|+..|+|....|.+||-|-|.+.
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 35668899999999999999999999999999999999999999999999877664
No 66
>KOG3623|consensus
Probab=97.66 E-value=6.4e-05 Score=66.33 Aligned_cols=107 Identities=21% Similarity=0.248 Sum_probs=77.5
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc-----------ccCCCCChhHHHHHHHcccc
Q psy10486 33 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR-----------KKRKPYSKHQTLELEKEFLY 101 (183)
Q Consensus 33 l~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r-----------r~r~~~t~~q~~~Le~~F~~ 101 (183)
+..|.+.|..+..|+.++...+|...||+.+.|+.||++++.......+ +-++.....+-..|..+++.
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 8899999999999999999999999999999999999998766322111 11233344444556666665
Q ss_pred CCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 102 NAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 102 ~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
+..++--+....+..+-..+..|.+||.+|+..-+...
T Consensus 648 q~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 648 QASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred ccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 55544444444455577777788999999988766554
No 67
>KOG1146|consensus
Probab=97.48 E-value=0.00011 Score=68.66 Aligned_cols=59 Identities=20% Similarity=0.202 Sum_probs=55.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc
Q psy10486 20 TVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV 78 (183)
Q Consensus 20 ~~rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~ 78 (183)
.++++|+.+++.||.+|...|....||...+++.|...+++..+.|.+||+|-|.+.++
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k 960 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKK 960 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhh
Confidence 45788999999999999999999999999999999999999999999999998887655
No 68
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.41 E-value=0.00011 Score=44.18 Aligned_cols=41 Identities=24% Similarity=0.358 Sum_probs=31.0
Q ss_pred HHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 92 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 92 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
+..|+..|....++.......|+.+.+|+..+|+.||..+.
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 34599999999999999999999999999999999997664
No 69
>KOG0773|consensus
Probab=97.21 E-value=0.0003 Score=58.17 Aligned_cols=109 Identities=26% Similarity=0.283 Sum_probs=78.3
Q ss_pred HHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc--------------------------cc-------------
Q psy10486 37 EKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT--------------------------GQ------------- 77 (183)
Q Consensus 37 e~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k--------------------------~~------------- 77 (183)
...-..++||+..+...|+...+++..+|..||-|-++. ..
T Consensus 113 ~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~ 192 (342)
T KOG0773|consen 113 LEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEE 192 (342)
T ss_pred hhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccc
Confidence 344566789999898889999999999988999874322 00
Q ss_pred --------------------------------------------ccccccCCCCChhHHHHHHHcc-c--cCCccCHHHH
Q psy10486 78 --------------------------------------------VTVRKKRKPYSKHQTLELEKEF-L--YNAYVSKQKR 110 (183)
Q Consensus 78 --------------------------------------------~~~rr~r~~~t~~q~~~Le~~F-~--~~~~p~~~~~ 110 (183)
....+....+......+|.... + ..+||+..++
T Consensus 193 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K 272 (342)
T KOG0773|consen 193 LLGESEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEK 272 (342)
T ss_pred ccccccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhc
Confidence 0011223356666677777653 2 3679999999
Q ss_pred HHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHH
Q psy10486 111 WELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQ 145 (183)
Q Consensus 111 ~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~ 145 (183)
..|+.++||+..||.+||.|.|.+.-+-.......
T Consensus 273 ~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~~~ 307 (342)
T KOG0773|consen 273 LMLAKQTGLSRPQVSNWFINARVRLWKPMIEEMYL 307 (342)
T ss_pred cccchhcCCCcccCCchhhhcccccCCchHHHHHH
Confidence 99999999999999999999998866555443333
No 70
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.12 E-value=0.00046 Score=41.57 Aligned_cols=41 Identities=22% Similarity=0.298 Sum_probs=31.2
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486 33 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIE 73 (183)
Q Consensus 33 l~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr 73 (183)
+..|+.+|....++.......|..+.+|+..||+.||-.+.
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 45699999999999999999999999999999999997654
No 71
>KOG0773|consensus
Probab=96.25 E-value=0.0045 Score=51.21 Aligned_cols=54 Identities=22% Similarity=0.290 Sum_probs=46.0
Q ss_pred CCCCCCCCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486 21 VRKKRKPYSKHQTLELEKEFLY---NAYVSKQKRWELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 21 ~rr~r~~ft~~Ql~~Le~~F~~---~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
..++...|......+|++.... .+||+..++..||..+||+..||.+||.|.|.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~ 295 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARV 295 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhccc
Confidence 4455668999999999987433 48999999999999999999999999999553
No 72
>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=95.12 E-value=0.046 Score=32.64 Aligned_cols=46 Identities=22% Similarity=0.356 Sum_probs=36.2
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
+++|+.+|.++...+-..++... ....||..+|++..+|..|..|+
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 57889999999999999998877 34679999999999999999884
No 73
>PF13551 HTH_29: Winged helix-turn helix
Probab=94.54 E-value=0.16 Score=34.44 Aligned_cols=80 Identities=20% Similarity=0.216 Sum_probs=53.8
Q ss_pred HHHHHHHHcCCChhhhhhhhhhcccccc-------ccccccCCCCChhHHHHHHHccccCC-----ccCHHHHHH-H-HH
Q psy10486 50 KRWELARSLMLTERQVKIWFQNIEWTGQ-------VTVRKKRKPYSKHQTLELEKEFLYNA-----YVSKQKRWE-L-AR 115 (183)
Q Consensus 50 ~~~~La~~l~l~~~qV~~WF~nrr~k~~-------~~~rr~r~~~t~~q~~~Le~~F~~~~-----~p~~~~~~~-L-a~ 115 (183)
...++|..+|++...|..|....+..+- ....+++..+++++...|...+...+ ..+...... | ..
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G~~~l~~~~~~~g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~ 93 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGGIEGLLPRKPRGGRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEE 93 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHcccHHHHHhccccCCCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHh
Confidence 3567999999999999999988655431 11122233389999999998888765 234444433 3 22
Q ss_pred H--hCCChhhHHHHHh
Q psy10486 116 S--LMLTERQVKIWFQ 129 (183)
Q Consensus 116 ~--l~l~~~~V~~WF~ 129 (183)
. +.++...|..|+.
T Consensus 94 ~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 94 EFGIDVSPSTIRRILK 109 (112)
T ss_pred ccCccCCHHHHHHHHH
Confidence 2 3588888888875
No 74
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.13 E-value=0.11 Score=31.04 Aligned_cols=46 Identities=22% Similarity=0.369 Sum_probs=34.3
Q ss_pred ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 82 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 82 r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
++|..+|-++-..+-..++... ....||..+|++..+|..|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 5677888888888777787775 577899999999999999998754
No 75
>KOG3623|consensus
Probab=94.05 E-value=0.074 Score=47.71 Aligned_cols=48 Identities=21% Similarity=0.286 Sum_probs=44.8
Q ss_pred HHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 92 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 92 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
+.+|.++|..|..|...+...+|...||+...|+.||.++++.....+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999998877655
No 76
>cd00131 PAX Paired Box domain
Probab=93.91 E-value=0.62 Score=33.04 Aligned_cols=101 Identities=10% Similarity=0.029 Sum_probs=66.1
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccccccccc----ccCCCCChhHHHHHHHcccc
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVR----KKRKPYSKHQTLELEKEFLY 101 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~r----r~r~~~t~~q~~~Le~~F~~ 101 (183)
..||.+....+-..|+.. ....++|..+|++...|..|.+..+..+.-..+ ......+..+...+......
T Consensus 16 ~~lS~d~R~rIv~~~~~G-----~s~~~iA~~~~Vs~~tV~r~i~r~~e~G~v~pk~~gg~rpr~~~~~~~~~i~~~v~~ 90 (128)
T cd00131 16 RPLPDSIRQRIVELAQSG-----IRPCDISRQLRVSHGCVSKILNRYYETGSIRPGAIGGSKPRVATPEVVKKIEIYKQE 90 (128)
T ss_pred CcCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCCCCCCCCCCcCCHHHHHHHHHHHHH
Confidence 357777777777777643 233468999999999999998875544321111 11234456666666666677
Q ss_pred CCccCHHHHHHHHHHhCC-------ChhhHHHHHhhh
Q psy10486 102 NAYVSKQKRWELARSLML-------TERQVKIWFQNR 131 (183)
Q Consensus 102 ~~~p~~~~~~~La~~l~l-------~~~~V~~WF~nr 131 (183)
++..+..+..++...-|+ +...|..||+++
T Consensus 91 ~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 91 NPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 877777776665334466 888888888653
No 77
>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=93.52 E-value=0.14 Score=30.60 Aligned_cols=43 Identities=16% Similarity=0.175 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
+|+.|.++|..+|+..-| |-.....+||..||++..-|....+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~LR 45 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHLR 45 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHH
Confidence 588999999999999977 6666668899999999887765553
No 78
>smart00351 PAX Paired Box domain.
Probab=93.50 E-value=1 Score=31.76 Aligned_cols=97 Identities=10% Similarity=0.024 Sum_probs=62.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccc----cccCCCCChhHHHHHHHccccC
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTV----RKKRKPYSKHQTLELEKEFLYN 102 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~----rr~r~~~t~~q~~~Le~~F~~~ 102 (183)
.++.++...+-..|.... ...+||..+|++...|..|.+..+..+.... .......+..+...+......+
T Consensus 17 ~~s~~~R~riv~~~~~G~-----s~~~iA~~~gvs~~tV~kwi~r~~~~G~~~pk~~gg~rp~~~~~~~~~~I~~~~~~~ 91 (125)
T smart00351 17 PLPDEERQRIVELAQNGV-----RPCDISRQLCVSHGCVSKILGRYYETGSIRPGAIGGSKPKVATPKVVKKIADYKQEN 91 (125)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHcCCcCCcCCCCCCCCccCHHHHHHHHHHHHHC
Confidence 478888777777776432 2347999999999999999886544322111 1123345556666666667788
Q ss_pred CccCHHHHHHHHHHhCC-------ChhhHHHHH
Q psy10486 103 AYVSKQKRWELARSLML-------TERQVKIWF 128 (183)
Q Consensus 103 ~~p~~~~~~~La~~l~l-------~~~~V~~WF 128 (183)
+..+..+...+....|+ +...|..||
T Consensus 92 p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 92 PGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 88888776554435555 556666665
No 79
>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=92.61 E-value=0.36 Score=33.74 Aligned_cols=91 Identities=19% Similarity=0.142 Sum_probs=54.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccc-cccccCCCCChhHHHHHHHccccCCccC
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQV-TVRKKRKPYSKHQTLELEKEFLYNAYVS 106 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~-~~rr~r~~~t~~q~~~Le~~F~~~~~p~ 106 (183)
||.+-.+...+.++... ...++|..++++...|..|+. +...+.. ...+.+..+. ...|...-..++-.+
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k-~~~~G~~~~k~r~~~Kid---~~~L~~~v~~~pd~t 73 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK-RKETGDLEPKPRGRKKID---RDELKALVEENPDAT 73 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH-hccccccccccccccccc---HHHHHHHHHHCCCcC
Confidence 44444555556666533 234689999999999999999 4444322 1112221332 344555545544333
Q ss_pred HHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 107 KQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 107 ~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
. .+||..+||+...|-..++.
T Consensus 74 l---~Ela~~l~Vs~~ti~~~Lkr 94 (119)
T PF01710_consen 74 L---RELAERLGVSPSTIWRALKR 94 (119)
T ss_pred H---HHHHHHcCCCHHHHHHHHHH
Confidence 3 36788999999988877743
No 80
>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=91.87 E-value=1 Score=27.90 Aligned_cols=64 Identities=8% Similarity=0.005 Sum_probs=42.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
.++|+.+|++...|+.|...--.-...........|+..++..|.. . ......|++...|+.++
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~~gl~~~~r~~~g~R~yt~~di~~l~~------------i-~~l~~~g~~l~~i~~~l 67 (68)
T cd04763 4 GEVALLTGIKPHVLRAWEREFGLLKPQRSDGGHRLFNDADIDRILE------------I-KRWIDNGVQVSKVKKLL 67 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhcCCCCCCcCCCCCcccCHHHHHHHHH------------H-HHHHHcCCCHHHHHHHh
Confidence 4689999999999999976411111122234456788888887732 2 23445888888887765
No 81
>KOG3755|consensus
Probab=91.72 E-value=0.5 Score=41.68 Aligned_cols=100 Identities=21% Similarity=0.183 Sum_probs=65.5
Q ss_pred CCCCCCCCHHHHHHHHHH-hhhcCCCCHHH---HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 22 RKKRKPYSKHQTLELEKE-FLYNAYVSKQK---RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~-F~~~~~p~~~~---~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|+.++.+-+.+|... -...-||+.+. ...|+..+.+..+.+..-|+|.|.-.+. .
T Consensus 648 p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~------------------~ 709 (769)
T KOG3755|consen 648 PRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH------------------H 709 (769)
T ss_pred ccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch------------------h
Confidence 456777788888888766 34456888877 7889999999999999999996654332 2
Q ss_pred ccccCCccCHHHHHHHHHHh-------CCChhhHHHHHhhhhhHHHHHH
Q psy10486 98 EFLYNAYVSKQKRWELARSL-------MLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 98 ~F~~~~~p~~~~~~~La~~l-------~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
.|..+..+......+-.+.. ......|+.||++||.++++-.
T Consensus 710 w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 710 WKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred heecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 22222222222222211111 2256789999999999988754
No 82
>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=91.56 E-value=0.89 Score=28.02 Aligned_cols=63 Identities=11% Similarity=0.095 Sum_probs=41.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
.++|+.+|++...|+.|-+.-..... .....+..|+.+++..|. .... ....|++..+|+.+.
T Consensus 4 ~evA~~~gvs~~tlR~~~~~g~l~~~-~~~~g~R~y~~~~l~~l~------------~i~~-l~~~g~~l~~i~~~l 66 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKEFNLYIP-RTENGRRYYTDEDIELLK------------KIKT-LLEKGLSIKEIKEIL 66 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHhcCCCCC-CCCCCceeeCHHHHHHHH------------HHHH-HHHCCCCHHHHHHHh
Confidence 46899999999999999765222221 223345678888888773 2222 344788888877664
No 83
>PRK06424 transcription factor; Provisional
Probab=90.51 E-value=3.7 Score=29.78 Aligned_cols=20 Identities=10% Similarity=0.061 Sum_probs=17.6
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
.+||..+|++...|..|..+
T Consensus 101 ~eLA~~iGvs~stIskiE~G 120 (144)
T PRK06424 101 ADLAAKIFERKNVIASIERG 120 (144)
T ss_pred HHHHHHhCCCHHHHHHHHCC
Confidence 56999999999999999877
No 84
>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=90.37 E-value=1.3 Score=30.01 Aligned_cols=67 Identities=10% Similarity=0.101 Sum_probs=42.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nr 131 (183)
.++|+.+|++...|+.|...-..............|+..++..|... .....+|++...|+.++...
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i-------------~~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 4 GEVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQI-------------LFLKELGFSLKEIKELLKDP 70 (103)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHcC
Confidence 46899999999999999875332221112234567888888877433 22344566666666666443
No 85
>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=90.08 E-value=1.9 Score=26.47 Aligned_cols=62 Identities=13% Similarity=0.080 Sum_probs=37.8
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI 126 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 126 (183)
.++|..+|++...+..|-+.-..-...........++.+++..|... ......|++...|+.
T Consensus 4 ~eva~~~gvs~~tlr~w~~~~g~~~~~r~~~~~r~yt~~~v~~l~~i-------------~~l~~~g~~l~~i~~ 65 (68)
T cd01104 4 GAVARLTGVSPDTLRAWERRYGLPAPQRTDGGHRLYSEADVARLRLI-------------RRLTSEGVRISQAAA 65 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHhCCCCCCCcCCCCCeecCHHHHHHHHHH-------------HHHHHCCCCHHHHHH
Confidence 46899999999999999864211111111223456888887777322 223346777666654
No 86
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=89.94 E-value=1.1 Score=27.58 Aligned_cols=65 Identities=14% Similarity=0.128 Sum_probs=42.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|..+|++...|+.|=..---...+ .......|+.+.+..| .....|.. .|++..+|+-++++
T Consensus 4 ~eva~~~gvs~~tlr~y~~~gll~~~~-~~~g~r~y~~~dv~~l------------~~i~~l~~-~G~sl~~I~~~l~~ 68 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYEREGLLPPPR-DENGYRYYSEEDVERL------------REIKELRK-QGMSLEEIKKLLKQ 68 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHTTSSTTBE-STTSSEEE-HHHHHHH------------HHHHHHHH-TTTHHHHHHHHH--
T ss_pred HHHHHHHCcCHHHHHHHHHhcCccccc-ccCceeeccHHHHHHH------------HHHHHHHH-CcCCHHHHHHHHcc
Confidence 468999999999999997653322222 2334467888888877 33444444 88888888777653
No 87
>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=89.72 E-value=0.9 Score=26.61 Aligned_cols=41 Identities=17% Similarity=0.120 Sum_probs=31.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 122 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 122 (183)
.+||..+|++...|..|..+ ...|+......||..+|++..
T Consensus 13 ~~la~~~gis~~~i~~~~~g------------------------------~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 13 KELAEKLGISRSTISRIENG------------------------------KRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HHHHHHHTS-HHHHHHHHTT------------------------------SSTSBHHHHHHHHHHHTSEHH
T ss_pred HHHHHHhCCCcchhHHHhcC------------------------------CCCCCHHHHHHHHHHHCCCHH
Confidence 57999999999999999977 334666677777888777654
No 88
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=89.29 E-value=0.7 Score=27.98 Aligned_cols=45 Identities=13% Similarity=0.130 Sum_probs=29.3
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
...||..+|++...|..|+.++ ...++......||..+|++..++
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~-----------------------------~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGK-----------------------------PSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT----------------------------------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHHHCcCHHHHHHHHhcc-----------------------------cccccHHHHHHHHHHcCCCHHHH
Confidence 4579999999999999999762 12456677888888888887654
No 89
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=88.93 E-value=0.73 Score=27.51 Aligned_cols=42 Identities=17% Similarity=0.167 Sum_probs=35.2
Q ss_pred CChhHHHHHHHccccCCc--cCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
+|+.|..+|..+|+..-| |-.....+||..+|++...|..-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 578899999999887665 777788899999999998877655
No 90
>PHA01976 helix-turn-helix protein
Probab=88.17 E-value=1.7 Score=26.60 Aligned_cols=41 Identities=17% Similarity=0.066 Sum_probs=33.1
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 122 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 122 (183)
.+||..+|++...|..|..+ ...|+......||..+|++..
T Consensus 19 ~~lA~~~gvs~~~v~~~e~g------------------------------~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 19 PELSRRAGVRHSLIYDFEAD------------------------------KRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCcCHH
Confidence 56999999999999998865 234667778888999998875
No 91
>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=86.96 E-value=3.1 Score=28.04 Aligned_cols=69 Identities=17% Similarity=0.055 Sum_probs=45.6
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nr 131 (183)
.++|..+|++...+..|-..--.-........+..|+.+++..|. ....|....|++-..|+.+..+.
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~------------~I~~llr~~G~~l~~i~~~l~~~ 71 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLL------------LIKHLLYEKGYTIEGAKQALKED 71 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHH------------HHHHHHHHCCCCHHHHHHHHHhc
Confidence 468999999999999996541111111223346678888888773 23335567788888888877543
Q ss_pred h
Q psy10486 132 R 132 (183)
Q Consensus 132 R 132 (183)
.
T Consensus 72 ~ 72 (99)
T cd04765 72 G 72 (99)
T ss_pred c
Confidence 3
No 92
>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=86.46 E-value=0.82 Score=28.77 Aligned_cols=47 Identities=23% Similarity=0.395 Sum_probs=31.3
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIE 73 (183)
Q Consensus 23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr 73 (183)
+.|+.||+++...+-..+.... .....+|..+||++..|..|-...+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHHHHh
Confidence 4578899998888777773322 4456799999999999999987654
No 93
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=86.40 E-value=0.94 Score=34.92 Aligned_cols=45 Identities=11% Similarity=0.155 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
-+|+.|+++|..+|+...| |-.-...+||+.||++.--+....++
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRr 201 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLRR 201 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHH
Confidence 6999999999999999966 77777789999999998887765543
No 94
>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=84.63 E-value=5.1 Score=27.37 Aligned_cols=47 Identities=13% Similarity=0.087 Sum_probs=30.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
.++|+.+|++...|..|-..---............|+..++..|...
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I 50 (108)
T cd04773 4 GELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLI 50 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHH
Confidence 47899999999999999875222111111123456888888877433
No 95
>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=84.10 E-value=5.2 Score=26.66 Aligned_cols=66 Identities=15% Similarity=0.093 Sum_probs=42.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|..+|++...|+.|-+.---..........+.++..++..|. .......+|++-..|+-.+..
T Consensus 4 ~eva~~~gvs~~tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~~l~~I~~~l~~ 69 (96)
T cd04768 4 GEFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQ-------------FILFLRELGFSLAEIKELLDT 69 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhc
Confidence 468999999999999999762222111122345678888887773 233355566666666666644
No 96
>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=84.04 E-value=6.3 Score=27.76 Aligned_cols=46 Identities=11% Similarity=0.075 Sum_probs=31.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|+.+|++.+.|..|-+.--...........+.++..++..|.-
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T TIGR02047 4 GELAQKTGVSVETIRFYEKQGLLPPPARTDNNYRVYTVGHVERLAF 49 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCCcCCHHHHHHHHH
Confidence 5789999999999999976532222222234566788888877743
No 97
>PRK09726 antitoxin HipB; Provisional
Probab=83.97 E-value=9.5 Score=24.88 Aligned_cols=63 Identities=17% Similarity=0.131 Sum_probs=43.1
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccC
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVS 106 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~ 106 (183)
.++..++....+.+....-.+. .+||..+|++...|..|..+ ...|+
T Consensus 7 ~~~~~~l~~~lk~~R~~~gltq---~elA~~~gvs~~tis~~e~g------------------------------~~~ps 53 (88)
T PRK09726 7 IYSPTQLANAMKLVRQQNGWTQ---SELAKKIGIKQATISNFENN------------------------------PDNTT 53 (88)
T ss_pred ccCHHHHHHHHHHHHHHcCCCH---HHHHHHHCcCHHHHHHHHCC------------------------------CCCCC
Confidence 4566666555555555555543 56999999999999998865 22456
Q ss_pred HHHHHHHHHHhCCChh
Q psy10486 107 KQKRWELARSLMLTER 122 (183)
Q Consensus 107 ~~~~~~La~~l~l~~~ 122 (183)
......||..+|++..
T Consensus 54 ~~~l~~ia~~lgv~~~ 69 (88)
T PRK09726 54 LTTFFKILQSLELSMT 69 (88)
T ss_pred HHHHHHHHHHcCCCcc
Confidence 6677777888887754
No 98
>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=83.80 E-value=1.7 Score=24.63 Aligned_cols=44 Identities=14% Similarity=0.055 Sum_probs=29.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|+.+|++...|..|.+.-.... .........|+.+++..|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~~~g~l~~-~~~~~~~~~y~~~~v~~l~ 47 (49)
T cd04761 4 GELAKLTGVSPSTLRYYERIGLLSP-ARTEGGYRLYSDADLERLR 47 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCC-CcCCCCCEEeCHHHHHHhh
Confidence 5689999999999999986633221 1111234567877777664
No 99
>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=83.31 E-value=6.5 Score=26.94 Aligned_cols=65 Identities=11% Similarity=0.056 Sum_probs=40.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
.++|+.+|++.+.|..|-+.---..........+.++..++..|. .......+|++-..|+..+.
T Consensus 4 ~e~a~~~gvs~~tlr~ye~~gll~~~~r~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~ 68 (113)
T cd01109 4 KEVAEKTGLSADTLRYYEKEGLLPPVKRDENGIRDFTEEDLEWLE-------------FIKCLRNTGMSIKDIKEYAE 68 (113)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHH
Confidence 468999999999999997642221111112234568888887773 22334556666666666554
No 100
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=83.26 E-value=3.9 Score=25.05 Aligned_cols=64 Identities=14% Similarity=0.078 Sum_probs=39.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
.++|+.+|++...|..|-..--.............|+..++..|..... | ...|++...|...+
T Consensus 4 ~eva~~~gvs~~tlr~~~~~gli~~~~~~~~g~r~y~~~dl~~l~~i~~------------l-r~~g~~~~~i~~~l 67 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYERIGLLPPPIRTEGGYRLYSDEDLERLRFIKR------------L-KELGFSLEEIKELL 67 (70)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCEecCHHHHHHHHHHHH------------H-HHcCCCHHHHHHHH
Confidence 4689999999999999976422221111223345688888887744332 2 34677776665543
No 101
>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=82.68 E-value=4 Score=23.69 Aligned_cols=20 Identities=15% Similarity=-0.080 Sum_probs=17.7
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
.+||..+|++...|..|..+
T Consensus 19 ~~lA~~~gvs~~~vs~~e~g 38 (58)
T TIGR03070 19 ADLADLAGVGLRFIRDVENG 38 (58)
T ss_pred HHHHHHhCCCHHHHHHHHCC
Confidence 57999999999999999866
No 102
>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=82.28 E-value=6.3 Score=27.69 Aligned_cols=45 Identities=11% Similarity=0.134 Sum_probs=30.6
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|+.+|++...|+.|-+.---..........+.|+.+++..|.
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~ 48 (127)
T TIGR02044 4 GQVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELR 48 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence 478999999999999988652221111123446678888888774
No 103
>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=81.99 E-value=5.7 Score=24.91 Aligned_cols=40 Identities=15% Similarity=0.172 Sum_probs=31.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCCh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTE 121 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~ 121 (183)
..||..+|++...|..|..+ ...|+......|+..+|++.
T Consensus 22 ~~lA~~~gis~~tis~~~~g------------------------------~~~~~~~~~~~l~~~l~v~~ 61 (78)
T TIGR02607 22 RALAKALGVSRSTLSRIVNG------------------------------RRGITADMALRLAKALGTSP 61 (78)
T ss_pred HHHHHHhCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHcCCCH
Confidence 56999999999999999866 22355667778899998875
No 104
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=81.97 E-value=4.1 Score=29.36 Aligned_cols=88 Identities=17% Similarity=0.124 Sum_probs=58.7
Q ss_pred HHHHHHHHcCCChhhhhhhhhhccccccc---c-ccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh--h
Q psy10486 50 KRWELARSLMLTERQVKIWFQNIEWTGQV---T-VRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER--Q 123 (183)
Q Consensus 50 ~~~~La~~l~l~~~qV~~WF~nrr~k~~~---~-~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~--~ 123 (183)
-+.++|..+|++...|..|....+-++-. . .+.....++..|..+|........+-.......|..+.|+... .
T Consensus 23 S~re~Ak~~gvs~sTvy~wv~r~~e~G~~l~~~~~~GrP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~ 102 (138)
T COG3415 23 SCREAAKRFGVSISTVYRWVRRYRETGLDLPPKPRKGRPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASA 102 (138)
T ss_pred cHHHHHHHhCccHHHHHHHHHHhccccccccCccCCCCCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHH
Confidence 34568999999999999999765543222 1 2222346888888888877766664444444666888887776 6
Q ss_pred HHHHHhhhhhHHHH
Q psy10486 124 VKIWFQNRRMKNKK 137 (183)
Q Consensus 124 V~~WF~nrR~k~rk 137 (183)
|..+++.--..++|
T Consensus 103 v~~~l~~~GlsykK 116 (138)
T COG3415 103 VRRLLHELGLSYKK 116 (138)
T ss_pred HHHHHHHcCCCcCC
Confidence 77777654444444
No 105
>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=81.83 E-value=3.8 Score=23.53 Aligned_cols=44 Identities=11% Similarity=0.108 Sum_probs=32.1
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
.+++.+..++...|..+ ....++|..+|++...|+.+...-..+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 46788888888888333 356789999999999999887544333
No 106
>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=81.81 E-value=6.6 Score=27.79 Aligned_cols=46 Identities=15% Similarity=0.077 Sum_probs=30.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|+.+|++.+.++.|-+.---..........+.++..++..|.-
T Consensus 5 ~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 50 (131)
T TIGR02043 5 GELAKLCGVTSDTLRFYEKNGLIKPAGRTDSGYRLYTDEDQKRLRF 50 (131)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHH
Confidence 4789999999999999986521111111223456788888877743
No 107
>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=81.70 E-value=2.6 Score=24.25 Aligned_cols=40 Identities=10% Similarity=0.127 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
.+++.+..+|..+|.. + ....++|..+|++...|..+...
T Consensus 4 ~L~~~er~vi~~~y~~----~-~t~~eIa~~lg~s~~~V~~~~~~ 43 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE----G-LTLEEIAERLGISRSTVRRILKR 43 (50)
T ss_dssp TS-HHHHHHHHHHHTS----T--SHHHHHHHHTSCHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC----C-CCHHHHHHHHCCcHHHHHHHHHH
Confidence 4788999999999922 2 33467999999999999877643
No 108
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=81.46 E-value=4 Score=28.94 Aligned_cols=20 Identities=15% Similarity=0.441 Sum_probs=18.2
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
.+||..+|++...|..|..+
T Consensus 22 ~~lA~~~gvs~~~is~~E~g 41 (135)
T PRK09706 22 RSLAKAVKVSHVSISQWERD 41 (135)
T ss_pred HHHHHHhCCCHHHHHHHHcC
Confidence 57999999999999999977
No 109
>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=81.27 E-value=4.3 Score=24.65 Aligned_cols=45 Identities=22% Similarity=0.335 Sum_probs=23.6
Q ss_pred CCCCCHH-HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 25 RKPYSKH-QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 25 r~~ft~~-Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
|..|+.. -|.+++.+...+. .-... ..-|.++|++.++|+.|.+.
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~-RAaarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQ-RAAARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-H-HHHHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhH-HHHHHHhCccHHHHHHHHHH
Confidence 4455554 4455554444433 22222 24589999999999999865
No 110
>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=81.15 E-value=5.1 Score=20.15 Aligned_cols=39 Identities=15% Similarity=0.118 Sum_probs=28.0
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 69 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 69 (183)
..++..+...+...|... + ....+|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346777777777777533 2 34568999999999888874
No 111
>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=81.14 E-value=7.2 Score=27.38 Aligned_cols=64 Identities=19% Similarity=0.141 Sum_probs=45.5
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
.++|+.+|++...+..|-+.---... .+...+.|+..++..| .....|...+|++...|+..+.
T Consensus 5 ~eVA~~~GVs~~TLR~wE~~GLl~p~--r~~G~R~Ys~~dv~rL------------~~I~~L~~e~G~~l~eI~~~L~ 68 (120)
T cd04767 5 GVVAELLNIHPETLRIWERHGLIKPA--RRNGQRLYSNNDLKRL------------RFIKKLINEKGLNIAGVKQILS 68 (120)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCc--CCCCcEEECHHHHHHH------------HHHHHHHHHcCCCHHHHHHHHH
Confidence 46899999999999999875222221 2345667888888887 3444555558888888887763
No 112
>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=80.99 E-value=7.6 Score=25.85 Aligned_cols=65 Identities=17% Similarity=0.107 Sum_probs=39.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
.++|..+|++.+.|..|-..---............++.+++..|.. ......+|++-..|+..+.
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~-------------I~~lr~~G~~l~eI~~~l~ 68 (96)
T cd04788 4 GELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQ-------------IIALRRLGFSLREIGRALD 68 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHh
Confidence 4689999999999999986421111111123345688887777632 2234555666666655553
No 113
>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=80.71 E-value=1.5 Score=26.92 Aligned_cols=21 Identities=24% Similarity=0.444 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCChhhHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~ 129 (183)
....||..||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 455789999999999999953
No 114
>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=80.34 E-value=5 Score=24.18 Aligned_cols=44 Identities=14% Similarity=0.076 Sum_probs=30.8
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
...+|..+|++...|..|-.++ ..|+......||..+|++...+
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~------------------------------~~~~~~~l~~i~~~~~v~~~~l 58 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGK------------------------------RKPSVSTLKKIAEALGVSLDEL 58 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTS------------------------------S--BHHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHCcCHHHHHHHHCCC------------------------------cCCCHHHHHHHHHHhCCCHHHH
Confidence 4678999999999999888772 2355566778889998887643
No 115
>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=80.28 E-value=1.5 Score=27.52 Aligned_cols=44 Identities=27% Similarity=0.407 Sum_probs=28.6
Q ss_pred cCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 83 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 83 ~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.+..|++++...+-..+. ........+|..+||++..|..|-+.
T Consensus 3 ~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHHH
Confidence 456788887776655551 12346778999999999999999853
No 116
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=79.87 E-value=5.1 Score=28.01 Aligned_cols=42 Identities=14% Similarity=-0.053 Sum_probs=33.9
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 122 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 122 (183)
+.+||..+|++...|..|.++ ...|+......||..++++..
T Consensus 21 q~eLA~~~Gis~~~is~iE~g------------------------------~~~ps~~~l~kIa~aL~v~~~ 62 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTG------------------------------KANPSLKVMEAIADALETPLP 62 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHHCCCHH
Confidence 456999999999999988876 234777888889999988875
No 117
>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=79.63 E-value=7.5 Score=27.79 Aligned_cols=65 Identities=14% Similarity=0.067 Sum_probs=40.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++.+.|+.|.+.---+ +.........++..++..|... .....+|++-..|+.++.+
T Consensus 4 ~e~a~~~gvs~~TLR~Ye~~GLl~-p~r~~~g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~ 68 (134)
T cd04779 4 GQLAHLAGVSKRTIDYYTNLGLLT-PERSDSNYRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEE 68 (134)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCC-CccCCCCCeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHh
Confidence 468999999999999998763332 1112224556888877766322 2234555555555555543
No 118
>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=79.20 E-value=8.8 Score=26.95 Aligned_cols=46 Identities=13% Similarity=0.049 Sum_probs=30.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
-++|+.+|++.+.|+.|-+.---..........+.|+..++..|.-
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~GLl~~~~r~~~g~R~Y~~~~~~~l~~ 49 (127)
T cd01108 4 GEAAKLTGLSAKMIRYYEEIGLIPPPSRSDNGYRVYNQRDIEELRF 49 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCceecCHHHHHHHHH
Confidence 4689999999999999876522221111223456788888887743
No 119
>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=78.97 E-value=1.6 Score=26.80 Aligned_cols=27 Identities=22% Similarity=0.482 Sum_probs=22.0
Q ss_pred HHHHHHHHcCCChhhhhhhhhhccccc
Q psy10486 50 KRWELARSLMLTERQVKIWFQNIEWTG 76 (183)
Q Consensus 50 ~~~~La~~l~l~~~qV~~WF~nrr~k~ 76 (183)
....||..||+++.+|..|-..-+|..
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~dkW~~ 50 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSRDKWDE 50 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhhcchhh
Confidence 346799999999999999987766543
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=78.87 E-value=4.2 Score=22.54 Aligned_cols=44 Identities=11% Similarity=0.146 Sum_probs=29.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|..+|++...|..|..+-.....+ ....+..++..++..+.
T Consensus 4 ~e~a~~lgvs~~tl~~~~~~g~~~~~~-~~~~~~~~~~~ei~~~~ 47 (49)
T cd04762 4 KEAAELLGVSPSTLRRWVKEGKLKAIR-TPGGHRRFPEEDLERLL 47 (49)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCcee-CCCCceecCHHHHHHHH
Confidence 578999999999999999874433221 11234467777666553
No 121
>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=78.48 E-value=12 Score=26.19 Aligned_cols=46 Identities=13% Similarity=0.023 Sum_probs=30.6
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|+.+|++...|+.|-..---..........+.|+..++..|.-
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~Gll~~~~r~~~g~R~Y~~~~l~~l~~ 49 (126)
T cd04785 4 GELARRTGVNVETIRYYESIGLLPEPARTAGGYRLYGAAHVERLRF 49 (126)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCccccCHHHHHHHHH
Confidence 4789999999999998876522221111123456788888887743
No 122
>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=77.37 E-value=10 Score=25.13 Aligned_cols=47 Identities=15% Similarity=0.075 Sum_probs=32.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHcc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEF 99 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F 99 (183)
.++|..+|++...|..|-..-... ..........|+...+..|...+
T Consensus 4 ~eva~~~gi~~~tlr~~~~~Gll~-~~~~~~g~r~y~~~dv~~l~~i~ 50 (100)
T cd00592 4 GEVAKLLGVSVRTLRYYEEKGLLP-PERSENGYRLYSEEDLERLRLIR 50 (100)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcC-CCcCCCCCcccCHHHHHHHHHHH
Confidence 468999999999999997653332 22222345678998888876554
No 123
>PRK10072 putative transcriptional regulator; Provisional
Probab=77.08 E-value=7.2 Score=26.23 Aligned_cols=37 Identities=24% Similarity=0.126 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 29 SKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 29 t~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
+...+..|...-..+ ..+||..+|++...|..|..++
T Consensus 34 ~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~ 70 (96)
T PRK10072 34 SFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRR 70 (96)
T ss_pred ChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCC
Confidence 666666665544433 3679999999999999999774
No 124
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=76.95 E-value=10 Score=27.19 Aligned_cols=47 Identities=15% Similarity=0.109 Sum_probs=31.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
.++|..+|++.+.|+.|-..---..........+.|+..++..|...
T Consensus 5 ~e~a~~~gvs~~tlR~Ye~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I 51 (140)
T PRK09514 5 GELAKLAEVTPDTLRFYEKQGLMDPEVRTEGGYRLYTEQDLQRLRFI 51 (140)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCCeeeCHHHHHHHHHH
Confidence 57899999999999999865222111112234567888888777443
No 125
>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=76.69 E-value=15 Score=25.46 Aligned_cols=45 Identities=11% Similarity=0.074 Sum_probs=29.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
-++|+.+|++.+.|+.|-..---..........+.++..++..|.
T Consensus 4 ~eva~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~i~~l~ 48 (123)
T cd04770 4 GELAKAAGVSPDTIRYYERIGLLPPPQRSENGYRLYGEADLARLR 48 (123)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCCCCCCCccCCHHHHHHHH
Confidence 468999999999998887542111111112345678888888873
No 126
>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=75.96 E-value=21 Score=23.99 Aligned_cols=65 Identities=14% Similarity=0.033 Sum_probs=42.1
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++...|+.|-+.---.. .........|+..++..|. .......+|++-..|+..+..
T Consensus 5 ~eva~~~gvs~~tlR~ye~~Gll~~-~r~~~g~R~Y~~~~l~~l~-------------~I~~l~~~G~~l~ei~~~l~~ 69 (102)
T cd04789 5 SELAEKAGISRSTLLYYEKLGLITG-TRNANGYRLYPDSDLQRLL-------------LIQQLQAGGLSLKECLACLQG 69 (102)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCC-CcCCCCCeeCCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHcC
Confidence 4689999999999999987522221 1122445678888888773 223355666666666666543
No 127
>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=75.94 E-value=12 Score=25.94 Aligned_cols=65 Identities=15% Similarity=0.133 Sum_probs=43.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+||+...|+.|-..=--..... ....+.|+..++..|. .......+|++-..|+.++..
T Consensus 4 gevA~~~gvs~~tlRyYe~~GLl~p~~~-~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~~L~eI~~~l~~ 68 (120)
T cd04781 4 AEVARQSGLPASTLRYYEEKGLIASIGR-RGLRRQYDPQVLDRLA-------------LIALGRAAGFSLDEIQAMLSH 68 (120)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcC-CCCceecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhc
Confidence 4789999999999999976522221111 2356678888888773 334566667777777666654
No 128
>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=75.37 E-value=13 Score=26.29 Aligned_cols=45 Identities=18% Similarity=0.085 Sum_probs=28.5
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
-++|+.+|++.+.|+.|-+-=--+..+......+.|+..++..|.
T Consensus 4 gE~A~~~gvs~~TLRyYE~~GLl~p~r~~~~gyR~Y~~~~~~~l~ 48 (133)
T cd04787 4 KELANAAGVTPDTVRFYTRIGLLRPTRDPVNGYRLYSEKDLSRLR 48 (133)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeeeCCHHHHHHHH
Confidence 478999999999998885431111111111234578888888773
No 129
>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=75.07 E-value=14 Score=25.89 Aligned_cols=46 Identities=11% Similarity=0.049 Sum_probs=30.5
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
-++|+.+|++.+.|+.|-..---..........+.++..++..|..
T Consensus 4 gevA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 49 (127)
T cd04784 4 GELAKKTGCSVETIRYYEKEGLLPAPARSANNYRLYDEEHLERLLF 49 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHH
Confidence 4689999999999999976522221111223456788888876643
No 130
>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=75.05 E-value=9.3 Score=21.12 Aligned_cols=20 Identities=20% Similarity=0.109 Sum_probs=17.3
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
..+|..+|++...|..|..+
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g 35 (58)
T cd00093 16 EELAEKLGVSRSTISRIENG 35 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcC
Confidence 46899999999999999866
No 131
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=74.93 E-value=22 Score=23.65 Aligned_cols=46 Identities=11% Similarity=0.065 Sum_probs=29.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|..+|++...+..|-..=--............++..++..|..
T Consensus 4 ~eva~~~gvs~~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~ 49 (97)
T cd04782 4 GEFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDI 49 (97)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHH
Confidence 4689999999999999976421111111123456788888777643
No 132
>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=74.77 E-value=17 Score=25.43 Aligned_cols=48 Identities=8% Similarity=-0.089 Sum_probs=31.5
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
..++|..+|++.+.|+.|-+.-=-..........+.|+..++..|.-.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I 53 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFV 53 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHH
Confidence 457999999999999999765111111111234557888888877544
No 133
>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=74.64 E-value=8.3 Score=22.35 Aligned_cols=41 Identities=20% Similarity=0.183 Sum_probs=26.4
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
+++.+..++.-.|..+ -...++|..+|++...|+.|...-+
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4555555555544443 3677899999999999999996544
No 134
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=74.38 E-value=10 Score=20.78 Aligned_cols=20 Identities=20% Similarity=0.087 Sum_probs=16.8
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
..||..+|++...|..|..+
T Consensus 14 ~~la~~~~i~~~~i~~~~~~ 33 (56)
T smart00530 14 EELAEKLGVSRSTLSRIENG 33 (56)
T ss_pred HHHHHHhCCCHHHHHHHHCC
Confidence 46899999999999888755
No 135
>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=74.23 E-value=14 Score=25.76 Aligned_cols=66 Identities=12% Similarity=0.077 Sum_probs=42.1
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
-++|..+|++.+.|+.|-+----..........+.++..++..|. .......+|++-..|+.++..
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~ 69 (126)
T cd04783 4 GELAKAAGVNVETIRYYQRRGLLPEPPRPEGGYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLEL 69 (126)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhc
Confidence 468999999999998885432111111122345678888888773 333456677777777776643
No 136
>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=74.12 E-value=19 Score=24.00 Aligned_cols=67 Identities=15% Similarity=0.101 Sum_probs=42.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++.+.|..|=..---............|+..++..|. ....|...+|++-..|+..+..
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~------------~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 4 SELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLR------------LIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHH------------HHHHHHHHcCCCHHHHHHHHHh
Confidence 479999999999999997642111111112223468888887773 2333334477888777777754
No 137
>PRK08359 transcription factor; Validated
Probab=74.11 E-value=14 Score=27.70 Aligned_cols=41 Identities=12% Similarity=0.054 Sum_probs=31.4
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 122 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 122 (183)
++||..+|++...|..|=.+ ...|+......||..|+++..
T Consensus 102 eeLA~~lgvs~stI~~iE~G------------------------------~~~Ps~~~l~kLak~l~VsL~ 142 (176)
T PRK08359 102 EELSHEVGLSVNDLRRIAHG------------------------------EYEPTIKEAKKLERYFKIKLI 142 (176)
T ss_pred HHHHHHhCCCHHHHHHHHCC------------------------------CcCCCHHHHHHHHHHhCCccc
Confidence 56899999999888877655 334777788888888887743
No 138
>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=73.41 E-value=8.3 Score=21.50 Aligned_cols=42 Identities=12% Similarity=0.037 Sum_probs=29.7
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhh
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~ 133 (183)
+++.+..++...|... .....+|..+|++...|..|...-+.
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 5566666666665332 24567899999999999999865443
No 139
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=72.85 E-value=23 Score=24.62 Aligned_cols=47 Identities=13% Similarity=0.193 Sum_probs=30.8
Q ss_pred CCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486 24 KRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 24 ~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
+|..||.+.....-.....+..+ ..++|..+||+...|..|....+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~s----v~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGMT----VSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCCC----HHHHHHHHCcCHHHHHHHHHHHhh
Confidence 35667777655444333333332 246899999999999999877543
No 140
>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=72.84 E-value=20 Score=23.91 Aligned_cols=68 Identities=19% Similarity=0.191 Sum_probs=43.5
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNR 131 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nr 131 (183)
.++|+.+|++...|..|...---. ..........|+...+..| .....|...+|++...|+......
T Consensus 4 ~e~a~~~gvs~~tLR~ye~~Gll~-p~r~~~g~R~Y~~~dv~~l------------~~I~~L~~~~G~~l~ei~~~l~~~ 70 (96)
T cd04774 4 DEVAKRLGLTKRTLKYYEEIGLVS-PERSEGRYRLYSEEDLKRL------------ERILRLREVLGFSLQEVTHFLERP 70 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCC-CCcCCCCCEEECHHHHHHH------------HHHHHHHHHcCCCHHHHHHHHhcc
Confidence 478999999999999998642211 1112234456777777766 233344444788887777777543
Q ss_pred h
Q psy10486 132 R 132 (183)
Q Consensus 132 R 132 (183)
.
T Consensus 71 ~ 71 (96)
T cd04774 71 L 71 (96)
T ss_pred c
Confidence 3
No 141
>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=72.16 E-value=24 Score=22.97 Aligned_cols=67 Identities=16% Similarity=0.092 Sum_probs=41.7
Q ss_pred HHHHHHcCCChhhhhhhhhhcccccccccc-ccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVR-KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~r-r~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++...++.|-..---. ..... .....++.+++..|.. ... ....|++...|+.-+..
T Consensus 5 ~evA~~~gvs~~tLR~ye~~Gll~-p~r~~~~g~R~Ys~~dv~~l~~------------I~~-Lr~~G~sl~~i~~~l~~ 70 (88)
T cd01105 5 GEVSKLTGVSPRQLRYWEEKGLIK-SIRSDGGGQRKYSLADVDRLLV------------IKE-LLDEGFTLAAAVEKLRR 70 (88)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCC-CCccCCCCceecCHHHHHHHHH------------HHH-HHHCCCCHHHHHHHHHH
Confidence 468999999999999995431111 11112 1456788888887732 222 34467777777666654
Q ss_pred hh
Q psy10486 131 RR 132 (183)
Q Consensus 131 rR 132 (183)
.+
T Consensus 71 ~~ 72 (88)
T cd01105 71 RR 72 (88)
T ss_pred cc
Confidence 44
No 142
>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=71.35 E-value=16 Score=25.49 Aligned_cols=65 Identities=11% Similarity=0.052 Sum_probs=38.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
.++|..+|++...|+.|=+.---............++..++..|. ....+..+|++...|+.++.
T Consensus 3 ~e~a~~~gvs~~tlR~Ye~~GLl~~~~r~~~g~R~Y~~~~l~~l~-------------~I~~l~~~G~sl~eI~~~l~ 67 (124)
T TIGR02051 3 GELAKAAGVNVETIRYYERKGLLPEPDRPEGGYRRYPEETVKRLR-------------FIKRAQELGFSLEEIGGLLG 67 (124)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCEeECHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHh
Confidence 478999999999998883321111111122345568888887772 22234555555555555553
No 143
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=70.63 E-value=6.6 Score=22.14 Aligned_cols=40 Identities=15% Similarity=0.097 Sum_probs=21.0
Q ss_pred CCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 85 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 85 ~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
..+|.++...+...+... ....++|..+|++...|..+.+
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 457788888887776544 3566799999999999998874
No 144
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=70.59 E-value=10 Score=22.90 Aligned_cols=46 Identities=20% Similarity=0.065 Sum_probs=29.8
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 125 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 125 (183)
..++|..+|++...|..|-.+++. .|+......|+..+|++...+.
T Consensus 17 ~~~lA~~~g~s~s~v~~iE~G~~~-----------------------------~p~~~~l~~l~~~l~~~~~~~~ 62 (64)
T PF13560_consen 17 QAQLADRLGVSQSTVSRIERGRRP-----------------------------RPSPDTLQRLARALGVPPDERA 62 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSSS-----------------------------S-BHHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHCCCCC-----------------------------CCCHHHHHHHHHHHCcCHHHHc
Confidence 456999999999999888876321 2555667777777777765543
No 145
>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=69.92 E-value=23 Score=24.14 Aligned_cols=47 Identities=9% Similarity=-0.079 Sum_probs=31.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
-++|..+|++.+.|+.|-..=--............|+.+++..|.-.
T Consensus 4 ge~A~~~gvs~~tlR~ye~~GLl~p~~r~~~g~R~Y~~~~l~~l~~I 50 (107)
T cd01111 4 SQLALDAGVSVHIVRDYLLRGLLHPVARTEGGYGLFDDCALQRLRFV 50 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHH
Confidence 46899999999999999865211111112234567899888877554
No 146
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=69.60 E-value=41 Score=24.61 Aligned_cols=42 Identities=17% Similarity=0.082 Sum_probs=33.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ 123 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~ 123 (183)
++||..+|++...|..|-.+ ...|+......|+..||++...
T Consensus 86 eeLA~~lgvs~s~IsriE~G------------------------------~~~Ps~~~l~kLa~~Lgvsl~e 127 (154)
T TIGR00270 86 EQLAKKIQEKESLIKKIENA------------------------------EIEPEPKVVEKLEKLLKIKLRE 127 (154)
T ss_pred HHHHHHhCCCHHHHHHHHCC------------------------------CCCCCHHHHHHHHHHhCCCHHH
Confidence 56888999998888888866 4457777888888888888765
No 147
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=68.95 E-value=6.4 Score=30.26 Aligned_cols=43 Identities=12% Similarity=0.148 Sum_probs=37.0
Q ss_pred CCChhHHHHHHHccccCCc--cCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 86 PYSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
.+|..|+.+|..+|...-| |-.....+||+.+|++...+..-.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehL 199 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHL 199 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHH
Confidence 6999999999999987664 777888999999999998776655
No 148
>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=67.06 E-value=9.5 Score=22.19 Aligned_cols=36 Identities=19% Similarity=0.138 Sum_probs=24.1
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 32 QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 32 Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
|..+|.-.+....+.+. .+||..||++.+.|..-..
T Consensus 2 ~~~il~~L~~~~~~it~---~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPITA---KELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBEH---HHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcCH---HHHHHHhCCCHHHHHHHHH
Confidence 34556665566666555 4599999999999875443
No 149
>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=67.05 E-value=26 Score=25.06 Aligned_cols=46 Identities=9% Similarity=0.013 Sum_probs=30.1
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
..++|+.+|++...|+.|-+.---.. .......+.|+.+++..|.-
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~GLl~p-~r~~~g~R~Y~~~dl~~l~~ 49 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQKGLIAS-WRNAGNQRRYPRDVLRRIAF 49 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCC-CcCCCCCeEECHHHHHHHHH
Confidence 35799999999999999986521111 11222345688888777643
No 150
>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=67.02 E-value=6.5 Score=24.23 Aligned_cols=40 Identities=15% Similarity=0.143 Sum_probs=24.8
Q ss_pred HHHHHHcCCChhhhh-hhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChh
Q psy10486 52 WELARSLMLTERQVK-IWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 122 (183)
Q Consensus 52 ~~La~~l~l~~~qV~-~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 122 (183)
.+||..||++...|. .|... +..| ......+|..+|++..
T Consensus 16 ~~lA~~lgis~st~s~~~~~r------------------------------~~~P-~~~l~~ia~~~gvsl~ 56 (66)
T PF07022_consen 16 KELAERLGISKSTLSNNWKKR------------------------------GSIP-AEWLIKIALETGVSLD 56 (66)
T ss_dssp HHHHCCTT--HHHHH-HHHHS------------------------------SS---HHHHHHHHHHH---HH
T ss_pred HHHHHHhCcCHHHhhHHHHhC------------------------------CCCC-HHHHHHHHHHHCcCHH
Confidence 479999999999999 88843 3344 5666777888887764
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=66.18 E-value=37 Score=22.75 Aligned_cols=65 Identities=11% Similarity=0.037 Sum_probs=40.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|..+|++...+..|-+.--- ...........|+..++..|.. ......+|++-..|+..+..
T Consensus 5 ~eva~~~gvs~~tLR~ye~~Gll-~~~r~~~g~R~Y~~~dl~~l~~-------------I~~l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 5 GQMSRKFGVSRSTLLYYESIGLI-PSARSEANYRLYSEADLSRLEK-------------IVFLQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCC-CCCCCCCCCeeeCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHcC
Confidence 47899999999999999865211 1111122345688888877732 22345666666666666643
No 152
>PF13518 HTH_28: Helix-turn-helix domain
Probab=65.67 E-value=8.1 Score=22.02 Aligned_cols=22 Identities=23% Similarity=0.442 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhh
Q psy10486 109 KRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~n 130 (183)
...++|..+|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3456899999999999999964
No 153
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=65.56 E-value=13 Score=22.11 Aligned_cols=32 Identities=13% Similarity=0.147 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
....||..+|++...|..|+.++.....-..-
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l 43 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTL 43 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHH
Confidence 45689999999999999999887544444443
No 154
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=64.88 E-value=29 Score=25.30 Aligned_cols=57 Identities=12% Similarity=0.139 Sum_probs=42.3
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHcccc
Q psy10486 33 TLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLY 101 (183)
Q Consensus 33 l~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~ 101 (183)
.+.+.+.+..+-.+......+||..|||+...+..+... ...|+-.++..+-..|..
T Consensus 7 ~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL~G------------~~~ftl~EI~~Ia~~fgv 63 (147)
T PF08667_consen 7 AERVRELLDRKGIPKRKHASELADILGISYSSAYRKLNG------------KSPFTLEEIKKIAKHFGV 63 (147)
T ss_pred HHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHhcC------------CCCCCHHHHHHHHHHhCc
Confidence 455666777788888888889999999999998766644 556777766666655543
No 155
>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=64.84 E-value=11 Score=22.62 Aligned_cols=36 Identities=31% Similarity=0.357 Sum_probs=27.5
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 31 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 31 ~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
.|+..|+-.+. +...+.. +||..+|++.+.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 47788888888 6666665 699999999999986543
No 156
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=64.67 E-value=20 Score=25.94 Aligned_cols=51 Identities=16% Similarity=0.033 Sum_probs=38.1
Q ss_pred CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...+++.|..+|.-. ... ....++|..+|++...|..|-.+-+.+-++...
T Consensus 4 ~~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356888888888773 222 256689999999999999999876666555543
No 157
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=64.31 E-value=8.2 Score=21.96 Aligned_cols=23 Identities=22% Similarity=0.358 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCChhhHHHHHhh
Q psy10486 108 QKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~n 130 (183)
....++|..+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35668899999999999999854
No 158
>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=63.77 E-value=7.9 Score=23.42 Aligned_cols=21 Identities=24% Similarity=0.279 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhhHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~ 129 (183)
...++|..||++...|..|-.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH
Confidence 456899999999999999984
No 159
>PHA02955 hypothetical protein; Provisional
Probab=63.59 E-value=11 Score=29.04 Aligned_cols=43 Identities=9% Similarity=0.029 Sum_probs=36.6
Q ss_pred HHHHHHHHHHhhhc-CCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 30 KHQTLELEKEFLYN-AYVSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 30 ~~Ql~~Le~~F~~~-~~p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
..++..|-+.|.++ .-...+++.++++.||+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 56788888888887 66788899999999999998889999874
No 160
>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=63.41 E-value=37 Score=23.16 Aligned_cols=44 Identities=11% Similarity=0.054 Sum_probs=29.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|+.+|++...|+.|-+.---.. .......+.++..++..|.
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~GLl~p-~r~~~g~R~Y~~~~~~~l~ 47 (112)
T cd01282 4 GELAARTGVSVRSLRYYEEQGLLVP-ERSANGYRDYDEAAVDRVR 47 (112)
T ss_pred HHHHHHHCCCHHHHHHHHHCCCCCC-CcCCCCCeecCHHHHHHHH
Confidence 4789999999999999976421111 1122345568888777763
No 161
>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=63.37 E-value=39 Score=22.03 Aligned_cols=65 Identities=12% Similarity=0.065 Sum_probs=43.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
.++|..+|++...|..|-..---. +.........|+..++..|. ....|...+|++...|+.-+.
T Consensus 5 ~e~A~~~gvs~~tLr~ye~~Gli~-p~r~~~g~R~y~~~dv~~l~------------~i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 5 SVAAELSGMHPQTLRLYERLGLLS-PSRTDGGTRRYSERDIERLR------------RIQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcC-CCcCCCCCeeECHHHHHHHH------------HHHHHHHHcCCCHHHHHHHHH
Confidence 468999999999999998642222 11122234568888888773 344555668888888877774
No 162
>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=63.36 E-value=8.7 Score=21.02 Aligned_cols=20 Identities=20% Similarity=0.260 Sum_probs=16.0
Q ss_pred HHHHHHHhCCChhhHHHHHh
Q psy10486 110 RWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~ 129 (183)
..++|+.+|++...|+.|=+
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999999963
No 163
>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=63.09 E-value=33 Score=23.53 Aligned_cols=65 Identities=18% Similarity=0.150 Sum_probs=39.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++.+.+..|-.-==....... ...+.++..++..|.. ......+|++...|+..+..
T Consensus 4 ge~a~~~gvs~~tLryYe~~GLi~p~~~~-~~yR~Y~~~d~~~l~~-------------I~~lr~~G~sl~eI~~~l~~ 68 (116)
T cd04769 4 GELAQQTGVTIKAIRLYEEKGLLPSPKRS-GNYRVYDAQHVECLRF-------------IKEARQLGFTLAELKAIFAG 68 (116)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCCC-CCceeeCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhc
Confidence 46899999999999999865211111111 1345677777776632 22345566666666665543
No 164
>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=62.96 E-value=32 Score=24.77 Aligned_cols=45 Identities=11% Similarity=0.048 Sum_probs=29.0
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
..++|+.+|++...|+.|-+.---... ......+.|+...+..|.
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~GLl~~~-r~~~g~R~Y~~~di~~l~ 48 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESKGLITSI-RNSGNQRRYKRDVLRRVA 48 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCc-cCCCCCEEECHHHHHHHH
Confidence 357999999999999999875211111 111234567777776663
No 165
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=62.41 E-value=27 Score=25.56 Aligned_cols=44 Identities=9% Similarity=0.010 Sum_probs=28.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
-++|+.+|++...|..|-+.=--...+ .....+.|+..++..|.
T Consensus 15 gevAk~~gvs~~TlRyYE~~GLi~~~r-~~~g~R~Y~~~~i~~L~ 58 (154)
T PRK15002 15 GEVAKRSGVAVSALHFYESKGLITSIR-NSGNQRRYKRDVLRYVA 58 (154)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCcc-CCCCCEEECHHHHHHHH
Confidence 469999999999999997652221111 11233567777776663
No 166
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=61.20 E-value=49 Score=23.53 Aligned_cols=46 Identities=15% Similarity=0.183 Sum_probs=29.8
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
-++|+.+|++...|+.|=..-=-..........+.++..++..|.-
T Consensus 4 ge~a~~~gvs~~tlRyYE~~GLl~p~~r~~~gyR~Y~~~~l~~l~~ 49 (135)
T PRK10227 4 SDVAKITGLTSKAIRFYEEKGLVTPPMRSENGYRTYTQQHLNELTL 49 (135)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCcccCCCCcccCCHHHHHHHHH
Confidence 4799999999999998865421111111223456788888877743
No 167
>PRK10072 putative transcriptional regulator; Provisional
Probab=61.12 E-value=8.3 Score=25.93 Aligned_cols=40 Identities=25% Similarity=0.132 Sum_probs=29.5
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhh
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~ 133 (183)
.+...+..|......+ ..+||..+|++...|..|...+|.
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 3555566665444333 568999999999999999987764
No 168
>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=60.84 E-value=20 Score=21.14 Aligned_cols=45 Identities=18% Similarity=0.020 Sum_probs=32.8
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
.+|+.+..+|....... ...++|..+|+++..|.++..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 46777777776665544 4678999999999999999876665543
No 169
>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=60.49 E-value=15 Score=20.68 Aligned_cols=39 Identities=21% Similarity=0.226 Sum_probs=28.1
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 69 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 69 (183)
..++++|.+.+...+... + + ..+||..+|++...|..++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-~-s---i~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-M-S---IAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-C-C---HHHHHHHHCcCHHHHHHHH
Confidence 346777777788888776 2 2 3579999999999988766
No 170
>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=60.47 E-value=48 Score=22.07 Aligned_cols=66 Identities=11% Similarity=0.015 Sum_probs=43.6
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
.++|+.+|++...+..|-+.---. +.........|+..++..|. ....|...+|++...|+.++..
T Consensus 5 ~eva~~~gVs~~tLR~ye~~Gli~-p~r~~~g~R~Ys~~dv~~l~------------~I~~L~~~~G~~l~~i~~~l~l 70 (98)
T cd01279 5 SVAAELLGIHPQTLRVYDRLGLVS-PARTNGGGRRYSNNDLELLR------------QVQRLSQDEGFNLAGIKRIIEL 70 (98)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCC-CCcCCCCCeeECHHHHHHHH------------HHHHHHHHCCCCHHHHHHHHHh
Confidence 468999999999999997643221 11122345568888888773 3344455577777777777643
No 171
>cd04786 HTH_MerR-like_sg7 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 7) with a conserved cysteine present in the C-terminal portion of the protein. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic su
Probab=60.24 E-value=43 Score=23.69 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=28.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
-++|+.+|++.+.|..|=+.-=-..........+.++..++..|.
T Consensus 4 ge~a~~~gvs~~tLRyYE~~GLl~p~~r~~~gyR~Y~~~~v~~l~ 48 (131)
T cd04786 4 GELAKRSGMAASRIRFYEAEGLLSSVERSANGYRDYPPETVWVLE 48 (131)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHH
Confidence 478999999999999986542111111112234567777777663
No 172
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=59.66 E-value=10 Score=23.14 Aligned_cols=20 Identities=15% Similarity=0.187 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhHHHHHh
Q psy10486 110 RWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~ 129 (183)
..++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 173
>PRK00118 putative DNA-binding protein; Validated
Probab=58.75 E-value=36 Score=23.25 Aligned_cols=49 Identities=12% Similarity=0.032 Sum_probs=34.3
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
.++..+..++.-.|.... ...++|..+|++...|..|...-|.+-+...
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 355666666655554432 4567999999999999999987666655543
No 174
>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=57.78 E-value=55 Score=21.98 Aligned_cols=64 Identities=9% Similarity=-0.008 Sum_probs=41.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
-++|+.+|++.+.|+.|=+.-=-.. . .......++...+..| .....+..+|++-..|+.+|..
T Consensus 4 ge~a~~~gvs~~tlRyYe~~GLl~p-~-~~~g~r~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~ 67 (107)
T cd04777 4 GKFAKKNNITIDTVRHYIDLGLLIP-E-KKGGQYFFDEKCQDDL-------------EFILELKGLGFSLIEIQKIFSY 67 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCcCC-c-cCCCccccCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHh
Confidence 4689999999999987754311111 1 1122335666666555 3445578888888888888864
No 175
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=57.32 E-value=27 Score=25.98 Aligned_cols=42 Identities=14% Similarity=-0.005 Sum_probs=32.1
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQ 123 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~ 123 (183)
.+||..+|++...|..|..+ ...|+......||..||++...
T Consensus 24 ~elA~~~gis~~~is~~E~g------------------------------~~~p~~~~l~~ia~~l~v~~~~ 65 (185)
T PRK09943 24 RRAAELSGLTHSAISTIEQD------------------------------KVSPAISTLQKLLKVYGLSLSE 65 (185)
T ss_pred HHHHHHHCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHhCCCHHH
Confidence 45888889888888888865 3356677788888888888753
No 176
>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=56.96 E-value=18 Score=20.53 Aligned_cols=19 Identities=16% Similarity=0.202 Sum_probs=17.4
Q ss_pred HHHHHcCCChhhhhhhhhh
Q psy10486 53 ELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 53 ~La~~l~l~~~qV~~WF~n 71 (183)
+||..+|++...|..|+.+
T Consensus 2 ~lA~~~gvs~~tvs~~l~g 20 (52)
T cd01392 2 DIARAAGVSVATVSRVLNG 20 (52)
T ss_pred cHHHHHCcCHHHHHHHHcC
Confidence 5899999999999999977
No 177
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=56.87 E-value=4.3 Score=25.89 Aligned_cols=34 Identities=18% Similarity=0.100 Sum_probs=24.7
Q ss_pred HHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 38 KEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 38 ~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
..|....|.......+||..+|++...|..|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3444444433345568999999999999999975
No 178
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=55.94 E-value=28 Score=22.97 Aligned_cols=38 Identities=16% Similarity=0.115 Sum_probs=27.5
Q ss_pred HHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCCh
Q psy10486 54 LARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTE 121 (183)
Q Consensus 54 La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~ 121 (183)
||+.+|++...|..|..+ ...|+......|+..+|++.
T Consensus 49 LAe~~GIs~stLs~iE~g------------------------------~~~Ps~~tL~kI~~aLgi~l 86 (89)
T TIGR02684 49 LARKTGLSRESLYKALSG------------------------------KGNPTFDTILKVTKALGLKL 86 (89)
T ss_pred HHHHHCCCHHHHHHHHcC------------------------------CCCCCHHHHHHHHHHcCCce
Confidence 777777777777776655 44577778888888888764
No 179
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=55.58 E-value=48 Score=22.61 Aligned_cols=45 Identities=11% Similarity=0.054 Sum_probs=28.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|+.+||+.+.++.|=..-=-..........+.++..++..|.
T Consensus 4 ~eva~~~gvs~~tLRyYE~~GLl~p~~~~~~gyR~Ys~~dl~~l~ 48 (124)
T COG0789 4 GEVAKLTGVSVRTLRFYERKGLLSPERRDEGGYRYYTPEDLELLQ 48 (124)
T ss_pred HHHHHHhCCCHHHHHHHHHcCCCCCcccCCCCceecCHHHHHHHH
Confidence 468999999999999886531111111111345568888776663
No 180
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.47 E-value=25 Score=24.83 Aligned_cols=28 Identities=21% Similarity=0.122 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
...++|..+|++...|+.|...-+.+-|
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 4678999999999999999875555443
No 181
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=55.12 E-value=18 Score=24.71 Aligned_cols=40 Identities=18% Similarity=0.159 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
++...+..+...+..++ ..+|..||++...|+.|=++|+.
T Consensus 44 ls~~eIk~iRe~~~lSQ-------~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLSQ-------PVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCCH-------HHHHHHHCCCHHHHHHHHcCCcC
Confidence 88888888888887754 57999999999999999998543
No 182
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=55.08 E-value=34 Score=24.63 Aligned_cols=31 Identities=19% Similarity=0.103 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+.|...-+.+.|+.-
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568999999999999999987666665543
No 183
>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=54.31 E-value=30 Score=23.74 Aligned_cols=46 Identities=20% Similarity=0.150 Sum_probs=30.0
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
+++.+..++...|.. .....++|..+|+++..|+.+...-+.+-++
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 445555554443322 2345689999999999999998765555443
No 184
>PRK13749 transcriptional regulator MerD; Provisional
Probab=53.68 E-value=75 Score=22.26 Aligned_cols=47 Identities=9% Similarity=-0.116 Sum_probs=28.6
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
..++|..+|++.+.|+.|=.--=-..........+.|+...+..|.-
T Consensus 6 IgelA~~~gvS~~tiR~YE~~GLl~p~~r~~~gyR~Y~~~~l~rL~~ 52 (121)
T PRK13749 6 VSRLALDAGVSVHIVRDYLLRGLLRPVACTTGGYGLFDDAALQRLCF 52 (121)
T ss_pred HHHHHHHHCCCHHHHHHHHHCCCCCCCCcCCCCCccCCHHHHHHHHH
Confidence 45799999999999997743210000001123455688888877743
No 185
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=53.39 E-value=43 Score=25.10 Aligned_cols=46 Identities=13% Similarity=0.149 Sum_probs=32.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
.++|..+||+...|..|...-.-.. .........|+...+..|.-.
T Consensus 4 ~evA~~lGVS~~TLRrw~k~g~L~~-~R~~~G~R~y~~~dl~~L~~I 49 (175)
T PRK13182 4 PFVAKKLGVSPKTVQRWVKQLNLPC-EKNEYGHYIFTEEDLQLLEYV 49 (175)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCC-CcCCCCCEEECHHHHHHHHHH
Confidence 4689999999999999997643321 122234567888888776443
No 186
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=53.30 E-value=28 Score=19.60 Aligned_cols=39 Identities=21% Similarity=0.150 Sum_probs=28.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
.+++.+..++...+.. + ...++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~~g--~----s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAEG--L----TNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHcC--C----CHHHHHHHHCCCHHHHHHHHHH
Confidence 4678888887664321 1 3357999999999999988765
No 187
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=53.23 E-value=17 Score=26.33 Aligned_cols=44 Identities=14% Similarity=-0.086 Sum_probs=33.6
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccc
Q psy10486 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
...+|+.|..+|...+.. ....+||..||++...|..|-.+.+.
T Consensus 4 ~~~Lt~rqreVL~lr~~G------lTq~EIAe~LGiS~~tVs~ie~ra~k 47 (141)
T PRK03975 4 ESFLTERQIEVLRLRERG------LTQQEIADILGTSRANVSSIEKRARE 47 (141)
T ss_pred ccCCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 467899999999884321 23457999999999999999876443
No 188
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=53.06 E-value=24 Score=24.43 Aligned_cols=43 Identities=16% Similarity=0.261 Sum_probs=28.9
Q ss_pred cCCCCChhHHHHHHH-ccccCCccCHHHHHHHHHHhCCChhhHHHHHhh
Q psy10486 83 KRKPYSKHQTLELEK-EFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 83 ~r~~~t~~q~~~Le~-~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~n 130 (183)
++..++.+.....-. .+... ....++|..+||+...|..|.+.
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 356677776543333 33332 24557899999999999999753
No 189
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=53.00 E-value=34 Score=24.40 Aligned_cols=32 Identities=19% Similarity=0.085 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|++....-|.+-|+..+
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35578999999999999999876666665543
No 190
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=52.95 E-value=51 Score=24.13 Aligned_cols=40 Identities=18% Similarity=0.106 Sum_probs=31.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcC
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASN 148 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~ 148 (183)
...++|..+|++...|++....-+.+-|+.-.........
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~~~~ 174 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIFLGE 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567899999999999999988888888777666554443
No 191
>PF13551 HTH_29: Winged helix-turn helix
Probab=52.88 E-value=45 Score=22.01 Aligned_cols=49 Identities=16% Similarity=0.154 Sum_probs=32.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhhcCC-----CCHHHHHH-H-HHH--cCCChhhhhhhhh
Q psy10486 22 RKKRKPYSKHQTLELEKEFLYNAY-----VSKQKRWE-L-ARS--LMLTERQVKIWFQ 70 (183)
Q Consensus 22 rr~r~~ft~~Ql~~Le~~F~~~~~-----p~~~~~~~-L-a~~--l~l~~~qV~~WF~ 70 (183)
.+++..+++++...|.+.+...+. .+...... | ... +.++...|..|+.
T Consensus 52 g~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 52 GRPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 344444999999999999998873 44444333 3 222 2567777887774
No 192
>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=52.21 E-value=6.1 Score=25.20 Aligned_cols=23 Identities=26% Similarity=0.283 Sum_probs=20.0
Q ss_pred HHHHHHHHHhCCChhhHHHHHhh
Q psy10486 108 QKRWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~n 130 (183)
-...++|..+|++...|+.|+.+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 35678999999999999999964
No 193
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=52.05 E-value=4.7 Score=29.77 Aligned_cols=82 Identities=13% Similarity=0.179 Sum_probs=53.9
Q ss_pred HHHHHHHHHcCCChhhhhhhhhhcccccccccccc---------------CCCCChhHHHHHHHccccCCccCHHHHHHH
Q psy10486 49 QKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKK---------------RKPYSKHQTLELEKEFLYNAYVSKQKRWEL 113 (183)
Q Consensus 49 ~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~---------------r~~~t~~q~~~Le~~F~~~~~p~~~~~~~L 113 (183)
-...+|+..++++..+|-.|..|=+...+....=+ +..-...-....-..|+...+|-..+-.++
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKhAvlN~E~t~e~~e~~kke~kklp~sVy~~y~kG~~~~TGta~ei 94 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKHAVLNYEKTDELNEQKKKEEKKLPASVYDYYDKGIFIMTGTAREI 94 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhHHHhcccchhhhhhhhcchhhhccHHHHHHHhccccccCccHHHH
Confidence 45678999999999999999999544322211100 000111112223344667777777788889
Q ss_pred HHHhCCChhhHHHHHhh
Q psy10486 114 ARSLMLTERQVKIWFQN 130 (183)
Q Consensus 114 a~~l~l~~~~V~~WF~n 130 (183)
|..+++-..-|-+|.+.
T Consensus 95 sq~~~i~k~~Vy~yis~ 111 (186)
T PF04936_consen 95 SQFFSIKKQNVYYYISV 111 (186)
T ss_pred HhhhccccccEEEEEec
Confidence 99999999988888754
No 194
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domain
Probab=51.96 E-value=80 Score=23.41 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=30.0
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEK 97 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~ 97 (183)
.++|+.+|++...|..|-+.---..........+.++..++..|..
T Consensus 5 ~evA~~~gvs~~tLRyYe~~GLl~p~~r~~~gyR~Y~~~dl~rL~~ 50 (172)
T cd04790 5 SQLARQFGLSRSTLLYYERIGLLSPSARSESNYRLYGERDLERLEQ 50 (172)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHH
Confidence 5799999999999999876421111111223456788888877743
No 195
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=51.89 E-value=33 Score=27.96 Aligned_cols=21 Identities=24% Similarity=0.131 Sum_probs=18.6
Q ss_pred HHHHHHHcCCChhhhhhhhhh
Q psy10486 51 RWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~n 71 (183)
..+||..+|++...|..|-.+
T Consensus 44 q~~lA~~~gvs~~~i~~~E~g 64 (309)
T PRK08154 44 RKVLAQASGVSERYLAQLESG 64 (309)
T ss_pred HHHHHHHHCcCHHHHHHHHCC
Confidence 356999999999999999977
No 196
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.72 E-value=34 Score=25.50 Aligned_cols=30 Identities=17% Similarity=0.182 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+++...-|.+-++.
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 456789999999999999997666655544
No 197
>PF13730 HTH_36: Helix-turn-helix domain
Probab=51.71 E-value=45 Score=19.16 Aligned_cols=41 Identities=22% Similarity=0.186 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhhc-----CCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYN-----AYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~-----~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
+++.++.++-..+... .||+ ...||..+|++.+.|..+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHH
Confidence 4444444444443222 4565 466999999999999988754
No 198
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=51.65 E-value=65 Score=23.19 Aligned_cols=48 Identities=4% Similarity=-0.030 Sum_probs=29.3
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
.-++|+.+|++.+.|+.|=+--=-..........+.|+..++..|.-.
T Consensus 10 IgevAk~~Gvs~~TLRyYE~~GLl~p~~r~~~gyR~Y~~~~l~rl~~I 57 (144)
T PRK13752 10 IGVFAKAAGVNVETIRFYQRKGLLPEPDKPYGSIRRYGEADVTRVRFV 57 (144)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeecCHHHHHHHHHH
Confidence 457999999999999988543111111111123456888888776443
No 199
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=51.52 E-value=28 Score=23.01 Aligned_cols=41 Identities=20% Similarity=0.124 Sum_probs=25.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIW 68 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~W 68 (183)
++++|...-..-|..+--.+....+++|..||.++..|..=
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~leki 43 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEKI 43 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHHH
Confidence 45666655444444443344456678999999998777643
No 200
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.80 E-value=36 Score=24.56 Aligned_cols=30 Identities=13% Similarity=-0.011 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+.|...-+.+-++.
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999997555555543
No 201
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=50.62 E-value=36 Score=25.69 Aligned_cols=31 Identities=23% Similarity=0.099 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+++...-+.+-++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4667899999999999998876666655544
No 202
>PHA01083 hypothetical protein
Probab=50.35 E-value=91 Score=22.76 Aligned_cols=33 Identities=15% Similarity=0.142 Sum_probs=23.8
Q ss_pred HHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 36 LEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 36 Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
|.+.-+...|++. ..||..||++...|..|-.+
T Consensus 7 Lda~K~a~~~~sd---kqLA~~LGVs~q~IS~~R~G 39 (149)
T PHA01083 7 LDAYKKAKNYVQY---KQIAHDLGVSPQKISKMRTG 39 (149)
T ss_pred HHHHHHHHhhccH---HHHHHHhCCCHHHHHHHHcC
Confidence 3344444556665 46999999999999998744
No 203
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=49.72 E-value=49 Score=24.14 Aligned_cols=42 Identities=21% Similarity=0.063 Sum_probs=27.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCCh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTE 121 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~ 121 (183)
.+||..+|++...|..|..+.. ...|+......||..+||+.
T Consensus 42 ~eLAerlGVS~~tIs~iE~G~~----------------------------~~~psl~~L~kIA~aLgv~~ 83 (150)
T TIGR02612 42 AQLAGRLGVTPQRVEALEKSEL----------------------------SGTVTLKTLRAAAEALDCTF 83 (150)
T ss_pred HHHHHHhCCCHHHHHHHHcCCC----------------------------CCCCCHHHHHHHHHHcCCCH
Confidence 4577777777777777775411 12356666777777777765
No 204
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=49.39 E-value=46 Score=20.23 Aligned_cols=35 Identities=20% Similarity=0.361 Sum_probs=23.5
Q ss_pred HHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhc
Q psy10486 111 WELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQAS 147 (183)
Q Consensus 111 ~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~ 147 (183)
..||..||++...|..| ..+--..+.-..+.....
T Consensus 13 ~~lAkalGVs~~aVs~W--~~~IP~~ra~~Ie~~T~G 47 (60)
T PF14549_consen 13 SKLAKALGVSPQAVSQW--GERIPAERAYQIEKLTNG 47 (60)
T ss_dssp HHHHHHHTS-HHHHHHH--HTS--HHHHHHHHHHTTT
T ss_pred HHHHHHHCCCHHHHHHh--cCccCHHHHHHHHHHhCC
Confidence 47999999999999999 555555555555555443
No 205
>PF13565 HTH_32: Homeodomain-like domain
Probab=49.13 E-value=62 Score=19.96 Aligned_cols=40 Identities=8% Similarity=-0.085 Sum_probs=29.7
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHH-HHHHHcCC----Chhhhhhh
Q psy10486 29 SKHQTLELEKEFLYNAYVSKQKRW-ELARSLML----TERQVKIW 68 (183)
Q Consensus 29 t~~Ql~~Le~~F~~~~~p~~~~~~-~La~~l~l----~~~qV~~W 68 (183)
++++.+.|.+.+..++..+..+.. .|...+|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 788889999999999888877765 46777664 55555544
No 206
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=48.91 E-value=26 Score=19.24 Aligned_cols=41 Identities=15% Similarity=0.025 Sum_probs=26.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLE 94 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~ 94 (183)
.++|+.||++...|..|...-.....+. ..+..+..+.+..
T Consensus 5 ~e~a~~lgis~~ti~~~~~~g~i~~~~~--g~~~~~~~~~l~~ 45 (49)
T TIGR01764 5 EEAAEYLGVSKDTVYRLIHEGELPAYRV--GRHYRIPREDVDE 45 (49)
T ss_pred HHHHHHHCCCHHHHHHHHHcCCCCeEEe--CCeEEEeHHHHHH
Confidence 4689999999999999987644332221 2234455554443
No 207
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=47.82 E-value=28 Score=25.59 Aligned_cols=32 Identities=16% Similarity=0.094 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+.++..-+.+-|....
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 45678999999999999999877777665543
No 208
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=47.41 E-value=40 Score=24.97 Aligned_cols=31 Identities=19% Similarity=0.135 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|+.|...-|.+-++.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4566799999999999999997666666554
No 209
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.56 E-value=23 Score=23.40 Aligned_cols=39 Identities=21% Similarity=0.164 Sum_probs=27.5
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 125 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 125 (183)
++++|...-...|..+--.+....+++|..|++++-.|.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 566777666666665555556677889999999887553
No 210
>PRK13558 bacterio-opsin activator; Provisional
Probab=46.35 E-value=24 Score=31.62 Aligned_cols=45 Identities=16% Similarity=0.246 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 26 KPYSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
..+|+.|.++|+.+|+...| |=.....+||..||++...+....+
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~lr 652 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHLR 652 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 46999999999999999988 5555667899999999888775553
No 211
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.16 E-value=54 Score=23.53 Aligned_cols=31 Identities=23% Similarity=0.002 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|++|...-|.+-++.-
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4667999999999999999976666655544
No 212
>PRK04217 hypothetical protein; Provisional
Probab=45.97 E-value=60 Score=22.40 Aligned_cols=50 Identities=10% Similarity=-0.090 Sum_probs=36.3
Q ss_pred CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
-..++.++..++...|...- ...++|..+|++...|...+..-+.+-+..
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44678888877766654332 567899999999999999987655555443
No 213
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=45.85 E-value=17 Score=26.87 Aligned_cols=37 Identities=19% Similarity=0.308 Sum_probs=31.0
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAA 144 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~ 144 (183)
.+..+|+.-++++..+|-.|.+|-+...+....-..+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKhA 51 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKHA 51 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhHH
Confidence 4678999999999999999999999888777654443
No 214
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=45.66 E-value=67 Score=23.79 Aligned_cols=35 Identities=9% Similarity=0.124 Sum_probs=27.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA 143 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~ 143 (183)
...++|..+|++...|+.....-|.+-++......
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~ 183 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACLSINW 183 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56789999999999999988776666666655443
No 215
>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=45.46 E-value=54 Score=18.27 Aligned_cols=38 Identities=21% Similarity=0.203 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 29 SKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 29 t~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
+..+..+|...++ ++..+. .+||..+|++...|..-++
T Consensus 2 ~~~~~~Il~~l~~-~~~~t~---~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRITQ---KELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS-H---HHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCCCH---HHHHHHhCCCHHHHHHHHH
Confidence 4556777766665 555554 5699999999988875543
No 216
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=45.32 E-value=50 Score=24.06 Aligned_cols=30 Identities=17% Similarity=0.267 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+++...-|.+-|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 466799999999999999987666665543
No 217
>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=44.51 E-value=50 Score=23.36 Aligned_cols=45 Identities=18% Similarity=0.056 Sum_probs=28.8
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
+++.+..++.-.|-. .....++|..+|++...|.++...-|.+-+
T Consensus 112 L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 112 LPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 444555555443322 235668899999999999998765554433
No 218
>PRK06930 positive control sigma-like factor; Validated
Probab=44.45 E-value=65 Score=23.88 Aligned_cols=49 Identities=12% Similarity=0.070 Sum_probs=35.0
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
+++.+..++.-.|... ....++|..+|++...|+.+...-+.+-++...
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 6666666666544222 246688999999999999999877776665543
No 219
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=43.65 E-value=71 Score=20.83 Aligned_cols=45 Identities=11% Similarity=0.008 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHhhhc-----CCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYN-----AYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~-----~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
-+|.+|+..|...|..- -+.+..+...+-..+|++...|...|..
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~~ 52 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWNL 52 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHHH
Confidence 36889999999998873 4577777777666678888777777643
No 220
>PF12728 HTH_17: Helix-turn-helix domain
Probab=42.97 E-value=31 Score=19.59 Aligned_cols=23 Identities=22% Similarity=0.231 Sum_probs=19.3
Q ss_pred HHHHHHcCCChhhhhhhhhhccc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEW 74 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~ 74 (183)
.++|..||++...|..|......
T Consensus 5 ~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCC
Confidence 46899999999999999976543
No 221
>PRK02866 cyanate hydratase; Validated
Probab=42.92 E-value=73 Score=23.23 Aligned_cols=20 Identities=20% Similarity=0.159 Sum_probs=16.4
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
+.||+.+|+++--|-.+|.+
T Consensus 22 ~~IA~~iG~S~v~vaaa~lG 41 (147)
T PRK02866 22 ADIAEAIGLSEVWVTAALLG 41 (147)
T ss_pred HHHHHHhCCCHHHHHHHHhC
Confidence 56899999998888877766
No 222
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=42.61 E-value=57 Score=24.01 Aligned_cols=29 Identities=14% Similarity=0.019 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++...-+.+-|+
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46678999999999999988655554443
No 223
>PRK04217 hypothetical protein; Provisional
Probab=42.39 E-value=41 Score=23.22 Aligned_cols=41 Identities=7% Similarity=-0.125 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
..++.+|.+++...|...- ...+||..+|++...|...+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 4688999988887775433 3457999999999999877654
No 224
>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=42.15 E-value=62 Score=23.55 Aligned_cols=29 Identities=21% Similarity=0.043 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|+++..|++....-|.+-++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998766655544
No 225
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=41.89 E-value=63 Score=23.73 Aligned_cols=32 Identities=9% Similarity=0.067 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+.+...-|.+-++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998766666555443
No 226
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=41.53 E-value=89 Score=22.25 Aligned_cols=31 Identities=23% Similarity=0.157 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+.+...-+.+-|+..
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999976666655544
No 227
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=41.52 E-value=57 Score=23.78 Aligned_cols=31 Identities=23% Similarity=0.141 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|+++...-|.+-+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566789999999999999997666555543
No 228
>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=41.40 E-value=52 Score=18.48 Aligned_cols=37 Identities=22% Similarity=0.204 Sum_probs=25.8
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 29 SKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 29 t~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
++.+..++...+ .. . ...++|..+|++...|..|...
T Consensus 2 ~~~e~~i~~~~~--~~-~---s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--EG-K---TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--cC-C---CHHHHHHHHCCCHHHHHHHHHH
Confidence 556667665543 22 2 3356899999999999988864
No 229
>PF15063 TC1: Thyroid cancer protein 1
Probab=41.08 E-value=58 Score=20.89 Aligned_cols=38 Identities=8% Similarity=0.055 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChh
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTER 63 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~ 63 (183)
..|..-.++.|...|+..-=...++|..|--.+.-...
T Consensus 32 NIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~e 69 (79)
T PF15063_consen 32 NIFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDPE 69 (79)
T ss_pred hhhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCHH
Confidence 36888899999999999998899998887666655444
No 230
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.58 E-value=29 Score=24.19 Aligned_cols=23 Identities=4% Similarity=0.034 Sum_probs=19.9
Q ss_pred HHHHHHHHHcCCChhhhhhhhhh
Q psy10486 49 QKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 49 ~~~~~La~~l~l~~~qV~~WF~n 71 (183)
....+||..+|+++..+..+|..
T Consensus 26 ~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 26 LSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 44467999999999999999976
No 231
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=40.08 E-value=65 Score=23.56 Aligned_cols=31 Identities=13% Similarity=-0.032 Sum_probs=23.9
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|+++...-|.+-|+.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999986555555444
No 232
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=39.72 E-value=83 Score=23.28 Aligned_cols=31 Identities=3% Similarity=0.124 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|+++..|+++...-|.+-|+..
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4667899999999999999976666655544
No 233
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=39.66 E-value=23 Score=24.82 Aligned_cols=24 Identities=21% Similarity=0.439 Sum_probs=21.9
Q ss_pred HHHHHHcCCChhhhhhhhhhcccc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
++||..+|++...|..|.....|+
T Consensus 4 eELA~~tG~srQTINrWvRkegW~ 27 (122)
T PF07037_consen 4 EELAELTGYSRQTINRWVRKEGWK 27 (122)
T ss_pred HHHHHHhCccHHHHHHHHHhcCce
Confidence 579999999999999999987776
No 234
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=39.61 E-value=84 Score=23.14 Aligned_cols=32 Identities=19% Similarity=0.063 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|++....-|.+.++...
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988777766666544
No 235
>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=39.51 E-value=69 Score=22.42 Aligned_cols=28 Identities=14% Similarity=0.140 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
...++|..+|+++..|+.+...-+.+-+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998865555544
No 236
>PRK15043 transcriptional regulator MirA; Provisional
Probab=39.23 E-value=1.2e+02 Score=24.10 Aligned_cols=46 Identities=7% Similarity=0.061 Sum_probs=29.6
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
..++|+.+|++...++.|-...-.-.+.......+.++.+++..|.
T Consensus 6 IgeVA~~~GVs~~TLR~wErr~GLL~P~Rt~~G~R~Ys~~dv~rL~ 51 (243)
T PRK15043 6 IGEVALLCDINPVTLRAWQRRYGLLKPQRTDGGHRLFNDADIDRIR 51 (243)
T ss_pred HHHHHHHHCcCHHHHHHHHHhcCCCCCccCCCCCEEECHHHHHHHH
Confidence 3568999999999999997421111111122345568888888774
No 237
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=38.63 E-value=81 Score=23.38 Aligned_cols=33 Identities=15% Similarity=-0.060 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQR 141 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~ 141 (183)
...++|..+|++...|+++...-|.+-++....
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 355789999999999999987666666655543
No 238
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=38.46 E-value=77 Score=22.63 Aligned_cols=29 Identities=34% Similarity=0.123 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+.....-|.+-|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887655554443
No 239
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=38.32 E-value=85 Score=22.18 Aligned_cols=30 Identities=20% Similarity=0.048 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|++....-+.+-|+.
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999887655555543
No 240
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=38.12 E-value=1.3e+02 Score=23.60 Aligned_cols=40 Identities=15% Similarity=0.201 Sum_probs=33.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcC
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASN 148 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~ 148 (183)
...++|..+|++...|+++...-|.+-++..+.+......
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~ 218 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLK 218 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 4567899999999999999998888888887777666554
No 241
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=37.93 E-value=93 Score=23.02 Aligned_cols=33 Identities=9% Similarity=0.018 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQR 141 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~ 141 (183)
...++|..+|++...|++....-|.+-|+....
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456799999999999999998777666665543
No 242
>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=37.60 E-value=96 Score=22.46 Aligned_cols=32 Identities=28% Similarity=0.184 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+++-..-|.+.++...
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46678999999999999998766665555443
No 243
>PRK09480 slmA division inhibitor protein; Provisional
Probab=37.34 E-value=30 Score=25.37 Aligned_cols=34 Identities=12% Similarity=0.059 Sum_probs=27.9
Q ss_pred cccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhh
Q psy10486 99 FLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRM 133 (183)
Q Consensus 99 F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~ 133 (183)
|..... .......||...|++...+..+|.|+-.
T Consensus 23 ~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 23 LESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 444444 6778889999999999999999998773
No 244
>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=36.90 E-value=36 Score=19.11 Aligned_cols=24 Identities=13% Similarity=0.242 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
....++...|++...+...|.|+-
T Consensus 18 s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred CHHHHHHHHccchhhHHHHcCCHH
Confidence 456889999999999999998763
No 245
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=36.64 E-value=1.3e+02 Score=20.20 Aligned_cols=45 Identities=16% Similarity=0.043 Sum_probs=28.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccc-cccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQV-TVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~-~~rr~r~~~t~~q~~~Le 96 (183)
.++|..+|++...|+.|-..=--.... ........|+...+..|.
T Consensus 4 ~eva~~~gis~~tlR~ye~~GLi~p~~~~~~ngyR~Y~~~~i~~l~ 49 (108)
T cd01107 4 GEFAKLSNLSIKALRYYDKIGLLKPAYVDPDTGYRYYSAEQLERLN 49 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHcCCCCCCcCCCCCCccccCHHHHHHHH
Confidence 468999999999999998651111111 111234567888777663
No 246
>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=36.39 E-value=78 Score=22.74 Aligned_cols=29 Identities=28% Similarity=0.227 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++...-|.+-++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988765555544
No 247
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=36.34 E-value=94 Score=19.06 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=18.1
Q ss_pred HHHHHHHcCCChhhhhhhhhh
Q psy10486 51 RWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~n 71 (183)
..+||..+|++...|...+.+
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNG 23 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCC
Confidence 357999999999999998866
No 248
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=36.20 E-value=87 Score=24.14 Aligned_cols=30 Identities=13% Similarity=0.087 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+.+...-+.+-|+.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999998777666654
No 249
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=36.20 E-value=56 Score=23.60 Aligned_cols=35 Identities=23% Similarity=0.117 Sum_probs=27.2
Q ss_pred CHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 106 SKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 106 ~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
......++|..+|++...|++.+..-|.+-++.-.
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33456789999999999999999877766666543
No 250
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=35.99 E-value=62 Score=19.64 Aligned_cols=68 Identities=13% Similarity=0.076 Sum_probs=38.2
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCC-ChhhHHHHHh
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLML-TERQVKIWFQ 129 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l-~~~~V~~WF~ 129 (183)
..||..+|++...+..-|...-...... -+....+.........+ .....+||..+|+ +......-|+
T Consensus 5 ~~la~~~~~s~~~l~~~f~~~~~~s~~~------~~~~~r~~~a~~~l~~~----~~~~~~ia~~~g~~s~~~f~r~Fk 73 (84)
T smart00342 5 EDLAEALGMSPRHLQRLFKKETGTTPKQ------YLRDRRLERARRLLRDT----DLSVTEIALRVGFSSQSYFSRAFK 73 (84)
T ss_pred HHHHHHhCCCHHHHHHHHHHHhCcCHHH------HHHHHHHHHHHHHHHcC----CCCHHHHHHHhCCCChHHHHHHHH
Confidence 5799999999999988776422111000 00111112122222222 2346688999999 8887777774
No 251
>smart00595 MADF subfamily of SANT domain.
Probab=35.87 E-value=1.2e+02 Score=19.31 Aligned_cols=40 Identities=23% Similarity=0.242 Sum_probs=32.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHHHHhcC
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQAAQASN 148 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~~~~~~ 148 (183)
.-.++|..+|.+...|+.-+.|=|...++..+........
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~~~~ 68 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNGKSG 68 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4456899999999999999999999999988776554443
No 252
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=35.66 E-value=86 Score=23.29 Aligned_cols=31 Identities=10% Similarity=-0.041 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+++...-|.+-++.-
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999976666666544
No 253
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=35.53 E-value=78 Score=23.17 Aligned_cols=36 Identities=19% Similarity=0.045 Sum_probs=29.9
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 31 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 31 ~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
.-+.+|...=+..-|.+.+....+|..||++.-+|.
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 446666666666779999999999999999999886
No 254
>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=35.52 E-value=34 Score=18.68 Aligned_cols=15 Identities=33% Similarity=0.598 Sum_probs=12.2
Q ss_pred CCCHHHHHHHHHHhh
Q psy10486 27 PYSKHQTLELEKEFL 41 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~ 41 (183)
.||..|+..|+.-..
T Consensus 2 ~FT~~Ql~~L~~Qi~ 16 (37)
T PF08880_consen 2 PFTPAQLQELRAQIL 16 (37)
T ss_pred CCCHHHHHHHHHHHH
Confidence 599999999987643
No 255
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=35.50 E-value=61 Score=23.09 Aligned_cols=41 Identities=15% Similarity=0.353 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
++++...+++.+|..- ....-..+|..++++++++..|...
T Consensus 82 l~de~k~Ii~lry~~r---~~~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRR---SRRTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred hCHHHHHHHHHHHccc---ccchHHHHHHHhCccHHHHHHHHHH
Confidence 5566667777777664 2345567999999999999988754
No 256
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=35.30 E-value=98 Score=23.37 Aligned_cols=32 Identities=16% Similarity=0.098 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+++...-|.+-++...
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45578999999999999999766666555443
No 257
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.29 E-value=1.4e+02 Score=20.12 Aligned_cols=46 Identities=26% Similarity=0.309 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC-Chhhhhhhhhhccc
Q psy10486 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLML-TERQVKIWFQNIEW 74 (183)
Q Consensus 25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l-~~~qV~~WF~nrr~ 74 (183)
|..||.+....+-+.+....+ ....+|..+|+ ...++..|-...+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 778999887666666665554 34579999996 99999999876443
No 258
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=35.29 E-value=95 Score=22.05 Aligned_cols=30 Identities=17% Similarity=0.257 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+.....-+.+.|+.
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999999876555555543
No 259
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=34.57 E-value=39 Score=23.70 Aligned_cols=20 Identities=20% Similarity=0.318 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHh
Q psy10486 110 RWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~ 129 (183)
-++||..+|++...|.-|.+
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 46899999999999999994
No 260
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=34.12 E-value=96 Score=21.21 Aligned_cols=42 Identities=19% Similarity=0.246 Sum_probs=34.0
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
.+++.++..+...+.-. ...+|..||++...|+.|=++|+.-
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 37888888887777655 4578999999999999999887643
No 261
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=33.81 E-value=97 Score=22.65 Aligned_cols=30 Identities=20% Similarity=0.032 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|++....-|.+-++.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999997666665553
No 262
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=33.75 E-value=42 Score=23.92 Aligned_cols=21 Identities=14% Similarity=0.116 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhhHHHHHhh
Q psy10486 110 RWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~n 130 (183)
..++|+.+|++...|++|.+.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999953
No 263
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=33.72 E-value=1.1e+02 Score=20.87 Aligned_cols=42 Identities=17% Similarity=0.071 Sum_probs=31.0
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
-+|..|..+++-.|..+- ...++|..+|++..-|..|.+.-+
T Consensus 17 LLT~kQ~~~l~lyy~eDl-----SlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDL-----SLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478888999988887763 567899999999999999996544
No 264
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=33.70 E-value=1e+02 Score=22.13 Aligned_cols=29 Identities=10% Similarity=-0.060 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|+++..|+++...-|.+-+.
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998765555543
No 265
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=33.62 E-value=1.4e+02 Score=21.95 Aligned_cols=35 Identities=14% Similarity=0.182 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA 143 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~ 143 (183)
...++|..+|++...|++....-|.+-++......
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45679999999999999998777766666655544
No 266
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=33.50 E-value=1.6e+02 Score=20.24 Aligned_cols=43 Identities=23% Similarity=0.304 Sum_probs=27.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELE 96 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le 96 (183)
.++|+.+|++.+.|+.|=+.==- .+. .....+.++..++..|.
T Consensus 4 geva~~~gvs~~tlRyYe~~GLl-~p~-r~~gyR~Y~~~~l~~l~ 46 (118)
T cd04776 4 SELAREFDVTPRTLRFYEDKGLL-SPE-RRGQTRVYSRRDRARLK 46 (118)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCC-CCc-CCCCccccCHHHHHHHH
Confidence 46899999999999988543100 010 11145678888887774
No 267
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=33.25 E-value=94 Score=23.11 Aligned_cols=31 Identities=16% Similarity=-0.064 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+++...-|.+-|+..
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999986666665544
No 268
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=33.22 E-value=1.7e+02 Score=22.46 Aligned_cols=31 Identities=13% Similarity=-0.045 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+.+...-|.+-++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999876666666655
No 269
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.18 E-value=97 Score=22.65 Aligned_cols=29 Identities=21% Similarity=0.258 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++-..-+.+-|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 45678999999999999988755554443
No 270
>PRK10403 transcriptional regulator NarP; Provisional
Probab=33.14 E-value=43 Score=24.31 Aligned_cols=43 Identities=16% Similarity=0.132 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
.+|..+.++|.-.... ....+||..++++++.|.....+-+.|
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5899999988865543 234678999999999999999886554
No 271
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=33.12 E-value=85 Score=23.23 Aligned_cols=37 Identities=14% Similarity=-0.015 Sum_probs=33.2
Q ss_pred HHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 30 KHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 30 ~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
..-+.+|...+...-|........+|..||++...|.
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 5667889999999999999999999999999998875
No 272
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=33.11 E-value=94 Score=22.87 Aligned_cols=30 Identities=30% Similarity=0.216 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+..+..-|.+.++.
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987655555543
No 273
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=33.07 E-value=1e+02 Score=22.31 Aligned_cols=29 Identities=17% Similarity=0.088 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++...-+.+++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998655555443
No 274
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=32.92 E-value=99 Score=22.57 Aligned_cols=28 Identities=18% Similarity=0.232 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
...++|..+|+++..|+.....-+.+.+
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998876555554
No 275
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=32.85 E-value=89 Score=22.69 Aligned_cols=36 Identities=14% Similarity=0.014 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 31 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 31 ~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
.-+.+|...=+.--|.+.+....+|..||++.-+|.
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345566666566689999999999999999999886
No 276
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=32.80 E-value=1.1e+02 Score=23.71 Aligned_cols=32 Identities=16% Similarity=0.110 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|++....-|.+-|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999877766665543
No 277
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=32.67 E-value=66 Score=22.56 Aligned_cols=32 Identities=28% Similarity=0.150 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 106 SKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 106 ~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
......++|..+|+++..|+++...-|.+-++
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34467789999999999999998766555543
No 278
>PF14174 YycC: YycC-like protein
Probab=32.62 E-value=57 Score=19.14 Aligned_cols=24 Identities=17% Similarity=0.120 Sum_probs=19.0
Q ss_pred CCHHHHHHHHHHcCCChhhhhhhh
Q psy10486 46 VSKQKRWELARSLMLTERQVKIWF 69 (183)
Q Consensus 46 p~~~~~~~La~~l~l~~~qV~~WF 69 (183)
++.+....||+.||++..++-.--
T Consensus 6 IS~eTA~kLs~~L~vPlE~lMHmP 29 (53)
T PF14174_consen 6 ISPETAVKLSKKLGVPLEQLMHMP 29 (53)
T ss_pred cCHHHHHHHHHHHCCcHHHHhcCc
Confidence 567788899999999998875433
No 279
>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=32.59 E-value=1e+02 Score=18.85 Aligned_cols=43 Identities=23% Similarity=0.193 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHH---hhhcCCCCHHHHHHHHHHcCCC-hhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKE---FLYNAYVSKQKRWELARSLMLT-ERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~---F~~~~~p~~~~~~~La~~l~l~-~~qV~~WF~n 71 (183)
.+|+-|.++|+-. ...+-||. ...+||..+|+. ...|+.....
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHHHH
Confidence 4677787777654 55566653 445799999997 7777765544
No 280
>PRK09480 slmA division inhibitor protein; Provisional
Probab=32.53 E-value=50 Score=24.12 Aligned_cols=38 Identities=13% Similarity=0.048 Sum_probs=29.8
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 34 LELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 34 ~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
++....|...+. +......||+..|++...+..+|.|+
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K 54 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSK 54 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCH
Confidence 333444666556 77778899999999999999999985
No 281
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=32.46 E-value=1e+02 Score=22.42 Aligned_cols=29 Identities=21% Similarity=0.075 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+.+...-|.+-+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887655544443
No 282
>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=32.01 E-value=99 Score=21.93 Aligned_cols=29 Identities=14% Similarity=0.140 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++-..-+.+-++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988766655554
No 283
>PRK04140 hypothetical protein; Provisional
Probab=31.87 E-value=97 Score=25.60 Aligned_cols=20 Identities=25% Similarity=0.290 Sum_probs=18.3
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
.+||..+|++...|..|-.+
T Consensus 143 ~eLA~~lGVSr~tIskyE~G 162 (317)
T PRK04140 143 GELASELGVSRRTISKYENG 162 (317)
T ss_pred HHHHHHhCCCHHHHHHHHcC
Confidence 57999999999999999977
No 284
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=31.68 E-value=36 Score=27.14 Aligned_cols=25 Identities=20% Similarity=0.462 Sum_probs=22.1
Q ss_pred HHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
...||.+||+++-+|+.|-+..-|+
T Consensus 22 ~~dIAeklGvspntiksWKrr~gWs 46 (279)
T COG5484 22 LKDIAEKLGVSPNTIKSWKRRDGWS 46 (279)
T ss_pred HHHHHHHhCCChHHHHHHHHhcCCC
Confidence 3579999999999999999988774
No 285
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=31.67 E-value=1.1e+02 Score=21.97 Aligned_cols=30 Identities=17% Similarity=0.075 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+.....-|.+-|+.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999886555555543
No 286
>cd00131 PAX Paired Box domain
Probab=31.45 E-value=1.8e+02 Score=20.30 Aligned_cols=45 Identities=7% Similarity=-0.135 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCC-------Chhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLML-------TERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l-------~~~qV~~WF~n 71 (183)
..+..+...++.....++..+..+..++...-|+ +...|..++++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~ 126 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRN 126 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHh
Confidence 4566777777777788888888777543223355 77888888765
No 287
>TIGR01321 TrpR trp operon repressor, proteobacterial. This model represents TrpR, the repressor of the trp operon. It is found so far only in the gamma subdivision of the proteobacteria and in Chlamydia trachomatis. All members belong to species capable of tryptophan biosynthesis.
Probab=31.38 E-value=46 Score=22.32 Aligned_cols=45 Identities=11% Similarity=0.073 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhhcCCC--CHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAYV--SKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p--~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
.+|+..+.+|..+|..-.-. ......+||..+|++...|..|=..
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~sn~ 78 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGSNN 78 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHHhh
Confidence 47888999999998876521 1123457899999999988877644
No 288
>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=31.19 E-value=99 Score=22.24 Aligned_cols=36 Identities=14% Similarity=-0.045 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 31 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 31 ~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
.-+.+|...=+..-|.+.+....+|..|||+.-+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445555555555679999999999999999998876
No 289
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=31.10 E-value=58 Score=23.54 Aligned_cols=25 Identities=16% Similarity=0.352 Sum_probs=18.2
Q ss_pred CHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 47 SKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 47 ~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
......+||..+|++...+-.|-+.
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~~ 57 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQQ 57 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHHH
T ss_pred ccchHHHHHHHhCCCHHHHHHHHhc
Confidence 3345678999999999999999853
No 290
>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=30.91 E-value=82 Score=22.59 Aligned_cols=35 Identities=17% Similarity=0.095 Sum_probs=26.3
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 32 QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 32 Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
-+.+|...=+.--|.+.+....+|..|||+.-+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 35566666666779999999999999999999886
No 291
>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=30.67 E-value=1.1e+02 Score=23.28 Aligned_cols=45 Identities=16% Similarity=0.171 Sum_probs=29.6
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
+++.+..++...|.. .....++|..+|++...|..|...-+.+-+
T Consensus 179 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 179 LPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 444455555444422 235678999999999999999865554444
No 292
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=30.56 E-value=1.1e+02 Score=22.46 Aligned_cols=31 Identities=16% Similarity=-0.036 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|+.+...-+.+-++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 5667899999999999999876666655543
No 293
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.23 E-value=1.1e+02 Score=24.11 Aligned_cols=31 Identities=19% Similarity=0.018 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|+.+...-+.+-|+.
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987666655544
No 294
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.20 E-value=1e+02 Score=21.90 Aligned_cols=28 Identities=29% Similarity=0.221 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
...++|..+|++...|+.+...-|.+-+
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998865555444
No 295
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=30.06 E-value=55 Score=22.84 Aligned_cols=27 Identities=26% Similarity=0.357 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 45 YVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 45 ~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
-++...+.+||..+|++.+.|..|-.-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~ 52 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQ 52 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhH
Confidence 356677788999999999999999643
No 296
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=29.82 E-value=90 Score=23.38 Aligned_cols=34 Identities=12% Similarity=-0.036 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
...++|..+|++...|+++...-|.+-|+.....
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 4567899999999999999876666655554333
No 297
>PF13921 Myb_DNA-bind_6: Myb-like DNA-binding domain; PDB: 1A5J_A 1MBH_A 1GV5_A 1H89_C 1IDY_A 1MBK_A 1IDZ_A 1H88_C 1GVD_A 1MBG_A ....
Probab=29.77 E-value=1.2e+02 Score=17.66 Aligned_cols=58 Identities=19% Similarity=0.234 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcC-CChhhhhhhhhh-ccccccccccccCCCCChhHHHHH
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLM-LTERQVKIWFQN-IEWTGQVTVRKKRKPYSKHQTLEL 95 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~-l~~~qV~~WF~n-rr~k~~~~~rr~r~~~t~~q~~~L 95 (183)
+|++.-..|...+....+ .-..||..|| -+..+|+.-|.+ .+ ....+..++.++...|
T Consensus 1 WT~eEd~~L~~~~~~~g~----~W~~Ia~~l~~Rt~~~~~~r~~~~l~------~~~~~~~wt~eEd~~L 60 (60)
T PF13921_consen 1 WTKEEDELLLELVKKYGN----DWKKIAEHLGNRTPKQCRNRWRNHLR------PKISRGPWTKEEDQRL 60 (60)
T ss_dssp S-HHHHHHHHHHHHHHTS-----HHHHHHHSTTS-HHHHHHHHHHTTS------TTSTSSSSSHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHCc----CHHHHHHHHCcCCHHHHHHHHHHHCc------ccccCCCcCHHHHhcC
Confidence 466777777777776432 3567899999 888888866655 22 2234556777765544
No 298
>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=29.76 E-value=47 Score=19.44 Aligned_cols=17 Identities=41% Similarity=0.393 Sum_probs=13.2
Q ss_pred HHHHHHHhCCChhhHHH
Q psy10486 110 RWELARSLMLTERQVKI 126 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~ 126 (183)
-.+||..+|++..||+-
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 34789999999999874
No 299
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=29.51 E-value=1.1e+02 Score=22.77 Aligned_cols=35 Identities=23% Similarity=0.135 Sum_probs=27.2
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 32 QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 32 Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
-+.+|...=+..-|.+.+....+|+.|||+.-+|.
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 34445555455578999999999999999998876
No 300
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=29.48 E-value=2e+02 Score=21.15 Aligned_cols=32 Identities=13% Similarity=-0.129 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+.....-|.+-++...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988655555554443
No 301
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=29.42 E-value=44 Score=26.69 Aligned_cols=25 Identities=24% Similarity=0.314 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKN 135 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~ 135 (183)
...+||..+||++.+|+.|=+ |-.|
T Consensus 21 k~~dIAeklGvspntiksWKr--r~gW 45 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKR--RDGW 45 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHH--hcCC
Confidence 456799999999999999964 5555
No 302
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=29.29 E-value=76 Score=23.22 Aligned_cols=36 Identities=19% Similarity=0.045 Sum_probs=28.9
Q ss_pred hHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHH
Q psy10486 90 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 125 (183)
Q Consensus 90 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 125 (183)
.-+..|...-....|.+.+....+|..+|++...|.
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 345566666666779999999999999999999873
No 303
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.26 E-value=1.1e+02 Score=22.60 Aligned_cols=29 Identities=7% Similarity=-0.164 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+++...-|.+-|+
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999988655544443
No 304
>PHA00542 putative Cro-like protein
Probab=29.24 E-value=1.6e+02 Score=18.81 Aligned_cols=21 Identities=5% Similarity=0.106 Sum_probs=18.6
Q ss_pred HHHHHHHcCCChhhhhhhhhh
Q psy10486 51 RWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~n 71 (183)
..+||..+|++...|..|..+
T Consensus 34 q~elA~~lgIs~~tIsr~e~g 54 (82)
T PHA00542 34 QEQIADATDVSQPTICRIYSG 54 (82)
T ss_pred HHHHHHHHCcCHHHHHHHHcC
Confidence 356999999999999999976
No 305
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=29.09 E-value=1.2e+02 Score=22.18 Aligned_cols=31 Identities=19% Similarity=0.251 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|++....-|.+-++.-
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998876666655544
No 306
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.95 E-value=1.4e+02 Score=21.58 Aligned_cols=30 Identities=13% Similarity=0.104 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+++...-+.+.+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999997666665543
No 307
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=28.87 E-value=1.5e+02 Score=19.16 Aligned_cols=41 Identities=10% Similarity=0.028 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHH---hhhcCCCCHHHHHHHHHHcCCChhhhhhhhh
Q psy10486 28 YSKHQTLELEKE---FLYNAYVSKQKRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 28 ft~~Ql~~Le~~---F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~ 70 (183)
+|+-|.++|.+. |..+.-|-.. ..||+.+++++..|++=..
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN~M~ 45 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRNEMA 45 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHHHHH
Confidence 456676666655 6666555443 3688889999988875443
No 308
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=28.67 E-value=1.2e+02 Score=23.62 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=30.9
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
+++.+..+|.-.|-.. ....++|..+|++...|+.|...-+.+-|.
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555544222 245789999999999999998655555443
No 309
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=28.64 E-value=1.1e+02 Score=18.37 Aligned_cols=52 Identities=19% Similarity=0.102 Sum_probs=31.1
Q ss_pred cCCCCChhHHHHHHHccccCCc---cCHHHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 83 KRKPYSKHQTLELEKEFLYNAY---VSKQKRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 83 ~r~~~t~~q~~~Le~~F~~~~~---p~~~~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
+|..+|++.-..+...+..... .++..+.++....+|+..+|..-.|.-|.+
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 4566777776666666544444 333544444344567888998877665543
No 310
>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=28.51 E-value=74 Score=21.76 Aligned_cols=20 Identities=15% Similarity=-0.087 Sum_probs=15.1
Q ss_pred HHHHHHcCCChhhhhhhhhh
Q psy10486 52 WELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~n 71 (183)
.+||..+|++...|..|-.+
T Consensus 82 ~~lA~~lg~~~~tis~~e~g 101 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYERG 101 (127)
T ss_pred HHHHHHhCCCHHHHHHHHCC
Confidence 45788888888888888654
No 311
>TIGR02941 Sigma_B RNA polymerase sigma-B factor. This sigma factor is restricted to certain lineages of the order Bacillales including Staphylococcus, Listeria and Bacillus.
Probab=28.39 E-value=1.3e+02 Score=23.42 Aligned_cols=47 Identities=17% Similarity=0.071 Sum_probs=32.0
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
.+++.+..++.-.|... ....++|..+|++...|+.+...-+.+-|+
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35556666665555332 245789999999999999988665555444
No 312
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=28.33 E-value=53 Score=17.72 Aligned_cols=23 Identities=13% Similarity=0.273 Sum_probs=17.0
Q ss_pred HHHHHHHHHcCCChhhhhhhhhh
Q psy10486 49 QKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 49 ~~~~~La~~l~l~~~qV~~WF~n 71 (183)
+.+..||..+|++..++..|-.+
T Consensus 7 Dtl~~IA~~~~~~~~~l~~~N~~ 29 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELMELNPN 29 (44)
T ss_dssp --HHHHHHHTTS-HHHHHHHCCT
T ss_pred CcHHHHHhhhhhhHhHHHHhcCC
Confidence 46778999999999999988733
No 313
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=27.99 E-value=1.4e+02 Score=22.77 Aligned_cols=45 Identities=22% Similarity=0.161 Sum_probs=29.2
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
+++.+..+|...|... ....++|..+|++...|+.+...-+.+-|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4444455555544222 24678999999999999988865554444
No 314
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=27.70 E-value=87 Score=23.14 Aligned_cols=33 Identities=15% Similarity=0.005 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
-...++|..+|++...|+++...-|.+-++...
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356679999999999999999877776666553
No 315
>COG1725 Predicted transcriptional regulators [Transcription]
Probab=27.68 E-value=1e+02 Score=21.85 Aligned_cols=80 Identities=20% Similarity=0.220 Sum_probs=41.6
Q ss_pred CCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccC-CCCChh---HHHHHHHccccCCccCHHHHHHHHHHhCC
Q psy10486 44 AYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKR-KPYSKH---QTLELEKEFLYNAYVSKQKRWELARSLML 119 (183)
Q Consensus 44 ~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r-~~~t~~---q~~~Le~~F~~~~~p~~~~~~~La~~l~l 119 (183)
.-|+. .+||..+|+.+-.|+.-|+.-..-+=-...+.. +-.+.. -+..+...+...- ....-.=+..+|+
T Consensus 34 kLPSv---RelA~~~~VNpnTv~raY~eLE~eG~i~t~rg~G~fV~~~~~~~~~~~~~~~~~~~---l~~~I~~~~~~G~ 107 (125)
T COG1725 34 KLPSV---RELAKDLGVNPNTVQRAYQELEREGIVETKRGKGTFVTEDAKEILDQLKRELAEEE---LEEFIEEAKALGL 107 (125)
T ss_pred CCCcH---HHHHHHhCCCHHHHHHHHHHHHHCCCEEEecCeeEEEcCCchhhHHHHHHHHHHHH---HHHHHHHHHHcCC
Confidence 34666 459999999999999999874332211111111 112211 1111111111110 0111112678899
Q ss_pred ChhhHHHHHh
Q psy10486 120 TERQVKIWFQ 129 (183)
Q Consensus 120 ~~~~V~~WF~ 129 (183)
+..+|.-|+.
T Consensus 108 s~eei~~~~~ 117 (125)
T COG1725 108 SLEEILELLK 117 (125)
T ss_pred CHHHHHHHHH
Confidence 9999988874
No 316
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=27.59 E-value=44 Score=24.78 Aligned_cols=21 Identities=29% Similarity=0.528 Sum_probs=16.6
Q ss_pred HHHHHHHcCCChhhhhhhhhh
Q psy10486 51 RWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~n 71 (183)
+.+||..+|++++.|..|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 568999999999999999755
No 317
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=27.59 E-value=1.1e+02 Score=22.63 Aligned_cols=34 Identities=18% Similarity=0.037 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 106 SKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 106 ~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
......++|..+|++...|+++...-|.+-|+..
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345678999999999999998876666555544
No 318
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=27.35 E-value=1.5e+02 Score=21.97 Aligned_cols=30 Identities=13% Similarity=0.045 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|++....-|.+-|+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999988876555554443
No 319
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=27.31 E-value=57 Score=22.89 Aligned_cols=24 Identities=13% Similarity=0.364 Sum_probs=21.0
Q ss_pred HHHHHHHhCCChhhHHHHHhhhhh
Q psy10486 110 RWELARSLMLTERQVKIWFQNRRM 133 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~nrR~ 133 (183)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 458999999999999999988764
No 320
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=27.18 E-value=1e+02 Score=22.01 Aligned_cols=44 Identities=14% Similarity=0.149 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 26 KPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
..+|+.+.++|.- +..+ +. ..++|..++++...|..+..+-+.|
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~~----~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-YT----NRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-CC----HHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3489999888887 4332 22 4679999999999999999885443
No 321
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=27.15 E-value=2.6e+02 Score=20.68 Aligned_cols=44 Identities=14% Similarity=0.058 Sum_probs=35.1
Q ss_pred CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHh
Q psy10486 84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~ 129 (183)
...++++++..+...-..+ |..-.+..||+.+||+..-|.+=..
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 4679999999888877766 5566788999999999987766553
No 322
>TIGR02859 spore_sigH RNA polymerase sigma-H factor. Members of this protein family are RNA polymerase sigma-H factor for sporulation in endospore-forming bacteria. This protein is also called Sigma-30 and SigH. Although rather close homologs are detected in Listeria, Listeria does not form spores and the role of the related sigma factor in that genus is in doubt.
Probab=26.91 E-value=88 Score=23.03 Aligned_cols=30 Identities=20% Similarity=0.117 Sum_probs=22.7
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
....++|..+|++...|++.+..-|.+-++
T Consensus 166 ~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 166 KSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 356679999999999999988655555443
No 323
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.81 E-value=1.3e+02 Score=22.17 Aligned_cols=26 Identities=31% Similarity=0.288 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
...++|..+|++...|++....-|.+
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~ 174 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKK 174 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 45678999999999888876544433
No 324
>COG3093 VapI Plasmid maintenance system antidote protein [General function prediction only]
Probab=26.79 E-value=2.1e+02 Score=19.53 Aligned_cols=35 Identities=26% Similarity=0.250 Sum_probs=23.2
Q ss_pred HHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 34 LELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 34 ~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
++|...|..---.+. ..||+.||++...|..=..+
T Consensus 12 EiL~eeflep~glt~---~~lA~~lgV~r~~is~ling 46 (104)
T COG3093 12 EILREEFLEPLGLTQ---TELAEALGVTRNTISELING 46 (104)
T ss_pred HHHHHHHhccccCCH---HHHHHHhCCCHHHHHHHHcC
Confidence 456666655333333 45899999999888766655
No 325
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=26.72 E-value=1.7e+02 Score=22.35 Aligned_cols=30 Identities=17% Similarity=0.087 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+.+...-+.+-|+.
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466889999999999999876555555543
No 326
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=26.72 E-value=88 Score=22.51 Aligned_cols=35 Identities=14% Similarity=-0.026 Sum_probs=27.5
Q ss_pred hHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 90 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 90 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
.-+..|...-....|.+......+|..+|++...|
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 33455555555667999999999999999999877
No 327
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.62 E-value=1.7e+02 Score=21.05 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|++....-|.+-++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987655555543
No 328
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=26.54 E-value=1e+02 Score=21.43 Aligned_cols=37 Identities=14% Similarity=0.010 Sum_probs=26.7
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
++++|+..++.+.... ....++++.+|+++-.|++=+
T Consensus 34 L~~E~~~Fi~~Fi~~r-----GnlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 34 LSPEQLEFIKLFIKNR-----GNLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCcHHHHHHH
Confidence 7888888776665443 245677888898888887744
No 329
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=26.45 E-value=1.5e+02 Score=20.86 Aligned_cols=38 Identities=8% Similarity=0.139 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIW 68 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~W 68 (183)
+++.+..+++..|...... ....+|..+|++...|..+
T Consensus 83 Ld~~er~II~~rY~~~~~~---t~~~Ia~~l~iS~~t~~r~ 120 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPL---TLVGLAQQLFISKSTAYRL 120 (134)
T ss_pred CCHHHHHHHHHHHccCCCC---CHHHHHHHhCCCHHHHHHH
Confidence 5667777777776543322 3456888889888887755
No 330
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.34 E-value=81 Score=17.76 Aligned_cols=21 Identities=24% Similarity=0.229 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCChhhHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~ 129 (183)
....+|..+|++...|..+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 355789999999999999985
No 331
>PRK13869 plasmid-partitioning protein RepA; Provisional
Probab=26.31 E-value=79 Score=26.91 Aligned_cols=51 Identities=16% Similarity=0.099 Sum_probs=36.6
Q ss_pred HHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccc
Q psy10486 50 KRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFL 100 (183)
Q Consensus 50 ~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~ 100 (183)
...++|+.+|++...++.|-..-...........++.|+.+++..|...+.
T Consensus 50 t~~e~A~~lgvs~~tlr~~~~~g~~~~~~~~~~grR~yt~~di~~lr~~l~ 100 (405)
T PRK13869 50 TSGEAARLMKISDSTLRKMTLAGEGPQPELASNGRRFYTLGQINEIRQMLA 100 (405)
T ss_pred CHHHHHHHhCcCHHHHHHHHHcCCCCCCccCCCCceeecHHHHHHHHHHHH
Confidence 335689999999999998865533222223334567799999999988775
No 332
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=26.00 E-value=1.6e+02 Score=23.26 Aligned_cols=29 Identities=7% Similarity=0.138 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+.+...-+.+-|.
T Consensus 233 t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 233 TQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988765555544
No 333
>PF06413 Neugrin: Neugrin; InterPro: IPR010487 This family contains mouse and human neugrin proteins. Neugrin and m-neugrin are mainly expressed in neurons in the nervous system, and are thought to play an important role in the process of neuronal differentiation []. Homologues of neugrin are found in fungi suggesting they have a alternative role or more than one function.
Probab=25.95 E-value=1.5e+02 Score=23.25 Aligned_cols=43 Identities=12% Similarity=0.026 Sum_probs=32.9
Q ss_pred CCCCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy10486 23 KKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI 67 (183)
Q Consensus 23 r~r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~ 67 (183)
.+...+|.++++.+...... +|..-....||..+++++..|+.
T Consensus 6 ~p~k~Ls~~~~~~ir~L~~~--~p~~~t~~~Lae~F~vspe~irr 48 (225)
T PF06413_consen 6 NPPKKLSREAMEQIRYLHKE--DPEEWTVERLAESFKVSPEAIRR 48 (225)
T ss_pred CCCCCCCHHHHHHHHHHHHh--CccccCHHHHHhhCCCCHHHHHH
Confidence 34567888888888887777 45554556799999999988874
No 334
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=25.78 E-value=1.8e+02 Score=18.26 Aligned_cols=44 Identities=16% Similarity=0.095 Sum_probs=31.6
Q ss_pred HHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 51 RWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 51 ~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
.++||..+|++...|..|=.+ ..-|+....-.||..++++...|
T Consensus 17 Q~elA~~vgVsRQTi~~iEkg------------------------------ky~Psl~La~kia~~f~~~iedI 60 (68)
T COG1476 17 QEELAKLVGVSRQTIIAIEKG------------------------------KYNPSLELALKIARVFGKTIEDI 60 (68)
T ss_pred HHHHHHHcCcCHHHHHHHHcC------------------------------CCCchHHHHHHHHHHhCCCHHHH
Confidence 367999999988877766533 23366777777888888777654
No 335
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=25.76 E-value=59 Score=17.11 Aligned_cols=21 Identities=29% Similarity=0.294 Sum_probs=15.2
Q ss_pred HHHHHHHHcCCChhhhhhhhh
Q psy10486 50 KRWELARSLMLTERQVKIWFQ 70 (183)
Q Consensus 50 ~~~~La~~l~l~~~qV~~WF~ 70 (183)
.+.+||..+|++...|..=+.
T Consensus 4 tr~diA~~lG~t~ETVSR~l~ 24 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILK 24 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHH
Confidence 357899999999988875553
No 336
>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=25.51 E-value=1.1e+02 Score=15.85 Aligned_cols=19 Identities=11% Similarity=0.274 Sum_probs=13.7
Q ss_pred HHHHHHhCCChhhHHHHHh
Q psy10486 111 WELARSLMLTERQVKIWFQ 129 (183)
Q Consensus 111 ~~La~~l~l~~~~V~~WF~ 129 (183)
..-|...|++..+|+.++.
T Consensus 9 i~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3458999999999998874
No 337
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=25.45 E-value=1.6e+02 Score=21.30 Aligned_cols=31 Identities=23% Similarity=0.141 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|++....-|.+-++.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566789999999999998887666655543
No 338
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=25.43 E-value=95 Score=22.52 Aligned_cols=34 Identities=15% Similarity=0.010 Sum_probs=27.6
Q ss_pred HHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 91 QTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 91 q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
-+.+|...-....|.+......+|..+|++..+|
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3455555556678999999999999999999987
No 339
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=25.25 E-value=1.7e+02 Score=22.84 Aligned_cols=29 Identities=21% Similarity=0.187 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+.++..-+.+-|.
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999998765555443
No 340
>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=25.00 E-value=2.6e+02 Score=20.01 Aligned_cols=48 Identities=19% Similarity=0.073 Sum_probs=36.0
Q ss_pred CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
.+.++..|..+|.-.+ .. ....++|..+|++...|..+-..-+.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 3457788888887632 22 256789999999999999998777766665
No 341
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.92 E-value=72 Score=22.95 Aligned_cols=43 Identities=23% Similarity=0.154 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
.+|+.+.++|.-.... + ...+||..++++.+.|.....+-+.|
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5888888888776643 2 45678999999999999888875544
No 342
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=24.71 E-value=59 Score=24.94 Aligned_cols=41 Identities=7% Similarity=-0.009 Sum_probs=32.1
Q ss_pred HHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 94 ELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 94 ~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
.-...|....|- .....+|...|++...|.++|.++..=..
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 334447777766 56888999999999999999998876543
No 343
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=24.69 E-value=1.6e+02 Score=21.21 Aligned_cols=28 Identities=7% Similarity=0.004 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNK 136 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~r 136 (183)
...++|..+|++...|+.+-.+-+...+
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998866555544
No 344
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.35 E-value=2.2e+02 Score=21.23 Aligned_cols=31 Identities=13% Similarity=0.185 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
...++|..+|++...|++....-|.+-|+.-
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4667899999999999998876666555544
No 345
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=24.33 E-value=1.3e+02 Score=22.06 Aligned_cols=31 Identities=13% Similarity=0.115 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|+++...-+.+-|+.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987666555554
No 346
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=24.26 E-value=1.4e+02 Score=21.73 Aligned_cols=29 Identities=24% Similarity=0.162 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
...++|..+|++...|+.+...-|.+-+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988755555444
No 347
>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=24.22 E-value=23 Score=16.85 Aligned_cols=8 Identities=38% Similarity=0.941 Sum_probs=5.8
Q ss_pred HHHHhhhh
Q psy10486 125 KIWFQNRR 132 (183)
Q Consensus 125 ~~WF~nrR 132 (183)
-+||.++.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 47998765
No 348
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=24.06 E-value=1.1e+02 Score=21.14 Aligned_cols=35 Identities=20% Similarity=0.122 Sum_probs=26.0
Q ss_pred hHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHH
Q psy10486 90 HQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI 126 (183)
Q Consensus 90 ~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 126 (183)
++...|...|. ..+......+||..+.|+.+.++.
T Consensus 4 ~~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 4 EQYQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 34566777777 556667788999999999976554
No 349
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=23.92 E-value=1.7e+02 Score=20.75 Aligned_cols=24 Identities=21% Similarity=0.195 Sum_probs=19.1
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRR 132 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR 132 (183)
...++|..+|++...|+++...-+
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~ 154 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAA 154 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456789999999999999875443
No 350
>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=23.91 E-value=59 Score=20.18 Aligned_cols=25 Identities=20% Similarity=0.190 Sum_probs=17.1
Q ss_pred CCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 44 AYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 44 ~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
..|+. ++||..|||+...|...+.-
T Consensus 19 r~Pt~---eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 19 REPTD---EEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp S--BH---HHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCH---HHHHHHHcccHHHHHHHHHh
Confidence 34665 45999999999999876653
No 351
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=23.81 E-value=2.7e+02 Score=20.54 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQA 143 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~~ 143 (183)
...++|..+|++...|+++-..-|.+-++......
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 180 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALEKPD 180 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998776666666665443
No 352
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=23.74 E-value=1.1e+02 Score=22.57 Aligned_cols=36 Identities=14% Similarity=0.004 Sum_probs=31.4
Q ss_pred hhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 89 KHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 89 ~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
..-+..|........|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 456778888888888999999999999999999876
No 353
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=23.66 E-value=1.7e+02 Score=23.87 Aligned_cols=62 Identities=16% Similarity=-0.042 Sum_probs=36.9
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccc----cCCCCChhHHHHHHHccccCCccCHHHHHHH
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRK----KRKPYSKHQTLELEKEFLYNAYVSKQKRWEL 113 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr----~r~~~t~~q~~~Le~~F~~~~~p~~~~~~~L 113 (183)
.+||..||++...|+.....-|.+-+...++ ........-..++..+|..-.-.+......|
T Consensus 173 ~EIA~~lgis~~tVk~~l~RAr~~Lr~~~~~~~~~~~~~~~~~~~~~v~~~~~A~~~gD~~~l~~l 238 (339)
T PRK08241 173 AEVAELLDTSVAAVNSALQRARATLAERGPSAADTLREPDDPEERALLARYVAAFEAYDVDALVAL 238 (339)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHhhcCCCcccccCCCCChHHHHHHHHHHHHHhcCCHHHHHHH
Confidence 5799999999999998776533333321111 1224445555566666666665566554443
No 354
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=23.65 E-value=2.1e+02 Score=21.04 Aligned_cols=30 Identities=13% Similarity=-0.053 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|+++...-|.+-++.
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999886555554443
No 355
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=23.63 E-value=1.2e+02 Score=22.61 Aligned_cols=33 Identities=24% Similarity=0.181 Sum_probs=25.8
Q ss_pred HHHHHHccccCCccCHHHHHHHHHHhCCChhhH
Q psy10486 92 TLELEKEFLYNAYVSKQKRWELARSLMLTERQV 124 (183)
Q Consensus 92 ~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V 124 (183)
+..|...-....|.+.+..+.+|..+|++...|
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 344544445567999999999999999999876
No 356
>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=23.61 E-value=88 Score=22.44 Aligned_cols=35 Identities=17% Similarity=0.095 Sum_probs=26.1
Q ss_pred HHHHHHHccccCCccCHHHHHHHHHHhCCChhhHH
Q psy10486 91 QTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 125 (183)
Q Consensus 91 q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 125 (183)
-+.+|...-+...|.+......+|..+|++..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 45666666666779999999999999999999874
No 357
>PF11304 DUF3106: Protein of unknown function (DUF3106); InterPro: IPR021455 Some members in this family of proteins are annotated as transmembrane proteins however this cannot be confirmed. Currently no function is known.
Probab=23.56 E-value=2.4e+02 Score=19.10 Aligned_cols=30 Identities=13% Similarity=0.133 Sum_probs=15.3
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARS 116 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~ 116 (183)
++++|...+...|..-.-+....+..|-..
T Consensus 59 LspeqR~~~R~~~~~~~~Lpp~qR~~lr~~ 88 (107)
T PF11304_consen 59 LSPEQRQQARENYQRFKQLPPEQRQALRAR 88 (107)
T ss_pred CCHHHHHHHHHHHHHHHcCCHHHHHHHHHH
Confidence 555555555555555444555555544333
No 358
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=23.56 E-value=2.1e+02 Score=18.24 Aligned_cols=36 Identities=17% Similarity=0.139 Sum_probs=24.9
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhh
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVK 66 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~ 66 (183)
..|++|+..|=..|-.+| ...+.+-..||++...++
T Consensus 12 nvsd~qi~elFq~lT~NP----l~AMa~i~qLGip~eKLQ 47 (82)
T PF11212_consen 12 NVSDEQINELFQALTQNP----LAAMATIQQLGIPQEKLQ 47 (82)
T ss_pred CCCHHHHHHHHHHHhhCH----HHHHHHHHHcCCCHHHHH
Confidence 467888888888887776 344455667887776554
No 359
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.40 E-value=1.7e+02 Score=22.39 Aligned_cols=36 Identities=25% Similarity=0.200 Sum_probs=27.3
Q ss_pred cCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 105 VSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 105 p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
.......++|..+|++...|++....-|.+-|+...
T Consensus 163 ~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 163 VEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 334466789999999999999988766666666554
No 360
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=23.38 E-value=2.3e+02 Score=21.37 Aligned_cols=32 Identities=9% Similarity=0.248 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|++....-|.+-|+...
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999998766666666543
No 361
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=23.27 E-value=75 Score=22.86 Aligned_cols=27 Identities=11% Similarity=0.234 Sum_probs=22.0
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMK 134 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k 134 (183)
....+++..+|++...|..|.+.-|..
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 456688999999999999999765543
No 362
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=23.18 E-value=1.7e+02 Score=24.09 Aligned_cols=53 Identities=15% Similarity=0.082 Sum_probs=36.2
Q ss_pred CCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 86 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 86 ~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
.+++.+..+|...|.... .......++|..+|++...|+.+...-+.+-|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456666667766553222 22345678999999999999999876666665544
No 363
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=23.12 E-value=1.7e+02 Score=20.71 Aligned_cols=30 Identities=13% Similarity=0.112 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
...++|..+|++...|++....-+.+-+..
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999887555555544
No 364
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=23.01 E-value=1.4e+02 Score=21.87 Aligned_cols=32 Identities=16% Similarity=0.037 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|++....-|.+-|+.-+
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988766666655543
No 365
>PF09301 DUF1970: Domain of unknown function (DUF1970); InterPro: IPR015380 This entry is represented by Bacteriophage PRD1, P16; it is a family of uncharacterised viral proteins.; PDB: 1W8X_P.
Probab=22.56 E-value=46 Score=21.86 Aligned_cols=13 Identities=31% Similarity=0.708 Sum_probs=9.2
Q ss_pred hhHHHHHhhhhhH
Q psy10486 122 RQVKIWFQNRRMK 134 (183)
Q Consensus 122 ~~V~~WF~nrR~k 134 (183)
.-|-.||+||-+.
T Consensus 17 iliwlwfrnrpaa 29 (117)
T PF09301_consen 17 ILIWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHHHTT-S
T ss_pred HHHHHHHccChHH
Confidence 4578999988654
No 366
>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=22.44 E-value=66 Score=17.85 Aligned_cols=17 Identities=41% Similarity=0.364 Sum_probs=13.1
Q ss_pred HHHHHHcCCChhhhhhh
Q psy10486 52 WELARSLMLTERQVKIW 68 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~W 68 (183)
.+||..+||+...|..-
T Consensus 21 ~~la~~lglS~~~v~~R 37 (42)
T PF13404_consen 21 AELAEELGLSESTVRRR 37 (42)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 56999999999888643
No 367
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=22.40 E-value=1.6e+02 Score=23.31 Aligned_cols=53 Identities=17% Similarity=-0.039 Sum_probs=39.3
Q ss_pred CCCCChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHHhHH
Q psy10486 84 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNTQRQ 142 (183)
Q Consensus 84 r~~~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~~~ 142 (183)
...+|+.+.++|.-.... ....++|..||+++..|+.+..+=+.|-.-.++.+
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~q 240 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRAQ 240 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHHH
Confidence 346889999998865432 24667899999999999999988777655544443
No 368
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=22.40 E-value=1.6e+02 Score=19.77 Aligned_cols=42 Identities=14% Similarity=0.167 Sum_probs=34.2
Q ss_pred HHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhhhcc
Q psy10486 32 QTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQNIE 73 (183)
Q Consensus 32 Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~nrr 73 (183)
.++.+...|....+ .+.++..++-..|......+-.|+-|+.
T Consensus 28 ElDlil~~Fae~~~~~lsd~el~~f~~LLe~~D~dL~~Wi~g~~ 71 (94)
T COG2938 28 ELDLILGPFAEKEFDSLSDEELDEFERLLECEDNDLFNWIMGHG 71 (94)
T ss_pred HHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCcHHHHHHHhCCC
Confidence 46777788888766 5667778889999999999999998843
No 369
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=22.23 E-value=1.4e+02 Score=22.11 Aligned_cols=31 Identities=19% Similarity=0.123 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
....++|..+|++...|++....-|.+-++.
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3556789999999999998887666665554
No 370
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=22.03 E-value=1.9e+02 Score=23.04 Aligned_cols=80 Identities=10% Similarity=-0.060 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHccccCCccCH
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKEFLYNAYVSK 107 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~F~~~~~p~~ 107 (183)
+++.|..++.-.|-..--.. +||..||+++..|+.....-|.+-+.... ........+..++..++..-.--+.
T Consensus 116 L~~~~R~v~~L~~~~g~s~~-----EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~-~~~~~~~~~~~~v~~f~~A~~~gD~ 189 (293)
T PRK09636 116 LSPLERAAFLLHDVFGVPFD-----EIASTLGRSPAACRQLASRARKHVRAARP-RFPVSDEEGAELVEAFFAALASGDL 189 (293)
T ss_pred CCHHHHHHHHHHHHhCCCHH-----HHHHHHCCCHHHHHHHHHHHHHHHHhhCC-CCCCCchHHHHHHHHHHHHHHhCCH
Q ss_pred HHHHHH
Q psy10486 108 QKRWEL 113 (183)
Q Consensus 108 ~~~~~L 113 (183)
.....|
T Consensus 190 ~~l~~L 195 (293)
T PRK09636 190 DALVAL 195 (293)
T ss_pred HHHHHH
No 371
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=21.99 E-value=89 Score=24.74 Aligned_cols=45 Identities=18% Similarity=-0.072 Sum_probs=34.4
Q ss_pred CCCCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 25 RKPYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 25 r~~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
...+|+.+.++|.-...- +. -.+||..||+++..|+.+..+-+.|
T Consensus 188 ~~~LT~RE~evl~l~a~G--~s----~~eIA~~L~IS~~TVk~hl~~i~~K 232 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG--KT----NEEIAAILGISSLTVKNHLQHIFKK 232 (247)
T ss_pred ccCCCHHHHHHHHHHHCC--CC----HHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 446899999999975422 22 2468999999999999999885444
No 372
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=21.92 E-value=1.5e+02 Score=21.72 Aligned_cols=32 Identities=22% Similarity=0.188 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCChhhHHHHHhhhhhHHHHHHh
Q psy10486 109 KRWELARSLMLTERQVKIWFQNRRMKNKKNTQ 140 (183)
Q Consensus 109 ~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~~ 140 (183)
...++|..+|++...|+.+...-|.+.++...
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45678999999999999999877777666553
No 373
>PHA02535 P terminase ATPase subunit; Provisional
Probab=21.74 E-value=2e+02 Score=25.99 Aligned_cols=44 Identities=18% Similarity=0.319 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
.|+++-...-...|.. -|. . .++|+.||++...|..|-..-+|.
T Consensus 2 ~yt~EfK~~Av~Ly~~-G~s-v---~eIA~~LGv~~~Tl~~W~kr~~w~ 45 (581)
T PHA02535 2 AYDDDVRRAAKFLYWQ-GWT-V---AEIAEELGLKSRTIYSWKERDGWR 45 (581)
T ss_pred CCCHHHHHHHHHHHHc-CCC-H---HHHHHHhCCChhHHHHHhcccccc
Confidence 4666655555555555 332 2 358999999999999998876555
No 374
>PRK10878 hypothetical protein; Provisional
Probab=21.68 E-value=1.9e+02 Score=18.32 Aligned_cols=41 Identities=17% Similarity=0.220 Sum_probs=33.9
Q ss_pred HHHHHHHHhhhcCC--CCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 32 QTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 32 Ql~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
.+++|...|-...| .+..++.....-|.+....+-.||-++
T Consensus 3 ElDlll~~F~~~~~~~l~~~e~~~Fe~LL~~~D~dL~~W~~g~ 45 (72)
T PRK10878 3 ELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNH 45 (72)
T ss_pred hHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHhCC
Confidence 46788888888887 566777788889999999999999773
No 375
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=21.62 E-value=1.9e+02 Score=23.30 Aligned_cols=81 Identities=16% Similarity=-0.067 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhccccccccccccCCC-----CChhHHHHHHHccccC
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKP-----YSKHQTLELEKEFLYN 102 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~-----~t~~q~~~Le~~F~~~ 102 (183)
+++.|..++.-.|-..--.. +||..||++...|+.....-|.+-++.....+.. ........+...+..-
T Consensus 143 Lp~~~R~v~~L~~~~g~s~~-----EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~~~~~~~~~~~v~~~~~a~ 217 (324)
T TIGR02960 143 LPPRQRAVLLLRDVLGWRAA-----ETAELLGTSTASVNSALQRARATLDEVGPSARDDQLAQPPSPEEQDLLERYIAAF 217 (324)
T ss_pred CCHHHhhHhhhHHHhCCCHH-----HHHHHHCCCHHHHHHHHHHHHHHHHHhcccccccccCCCCCHHHHHHHHHHHHHH
Q ss_pred CccCHHHHHHH
Q psy10486 103 AYVSKQKRWEL 113 (183)
Q Consensus 103 ~~p~~~~~~~L 113 (183)
.--+......|
T Consensus 218 ~~gD~~~l~~L 228 (324)
T TIGR02960 218 ESYDLDALTAL 228 (324)
T ss_pred HcCCHHHHHHH
No 376
>PRK13558 bacterio-opsin activator; Provisional
Probab=21.57 E-value=1.2e+02 Score=27.18 Aligned_cols=44 Identities=16% Similarity=0.240 Sum_probs=37.4
Q ss_pred CCCChhHHHHHHHccccCCc--cCHHHHHHHHHHhCCChhhHHHHH
Q psy10486 85 KPYSKHQTLELEKEFLYNAY--VSKQKRWELARSLMLTERQVKIWF 128 (183)
Q Consensus 85 ~~~t~~q~~~Le~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF 128 (183)
..+|..|.++|..+|...-| |-.....+||..||++...+..=.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~~~l 651 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFHQHL 651 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHH
Confidence 36999999999999988775 777788999999999998766544
No 377
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=21.53 E-value=1e+02 Score=20.19 Aligned_cols=20 Identities=20% Similarity=0.401 Sum_probs=16.5
Q ss_pred HHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 48 KQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 48 ~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
.+|.-.+|..|||.. .||+.
T Consensus 23 ~~ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 23 LDELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred HHHHHHHHHHcCCCH----HHHcC
Confidence 567778999999987 58877
No 378
>COG3711 BglG Transcriptional antiterminator [Transcription]
Probab=21.27 E-value=5.3e+02 Score=22.16 Aligned_cols=36 Identities=22% Similarity=0.253 Sum_probs=29.2
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhh
Q psy10486 29 SKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKI 67 (183)
Q Consensus 29 t~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~ 67 (183)
...+...|...+..+++.+.. +||..+|+|.++|..
T Consensus 3 ~~~~~~~l~~l~~~~~~~~~~---~la~~l~vS~Rti~~ 38 (491)
T COG3711 3 LTRREQLLLLLLLKNPLLTIK---ELAEQLGVSRRTIRY 38 (491)
T ss_pred ccHHHHHHHHHHHhCCCCCHH---HHHHHhCccHHHHHH
Confidence 445667788888999988875 499999999999864
No 379
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=21.16 E-value=1.9e+02 Score=23.05 Aligned_cols=28 Identities=14% Similarity=0.037 Sum_probs=22.6
Q ss_pred HHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 110 RWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
..++|..+|+++..|+..+..-|.+-+.
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999766666554
No 380
>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=20.98 E-value=1.3e+02 Score=17.99 Aligned_cols=20 Identities=20% Similarity=0.137 Sum_probs=14.4
Q ss_pred HHHHHHHHHHhCCChhhHHH
Q psy10486 107 KQKRWELARSLMLTERQVKI 126 (183)
Q Consensus 107 ~~~~~~La~~l~l~~~~V~~ 126 (183)
..+...++..+|+++.+++.
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~ 39 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLRE 39 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHH
Confidence 34666788888888877654
No 381
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.97 E-value=1.9e+02 Score=20.49 Aligned_cols=50 Identities=10% Similarity=0.114 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHhh-hcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 26 KPYSKHQTLELEKEFL-YNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 26 ~~ft~~Ql~~Le~~F~-~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
..||++|...|...-- .-.--.......|+..+|++...|...|..--..
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lreLVa~ 53 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLRELVAR 53 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHHHHHHc
Confidence 3589999988887722 1112233445678999999999999999874443
No 382
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=20.86 E-value=2.7e+02 Score=20.35 Aligned_cols=22 Identities=18% Similarity=0.130 Sum_probs=12.9
Q ss_pred CCccCHHHHHHHHHHhCCChhh
Q psy10486 102 NAYVSKQKRWELARSLMLTERQ 123 (183)
Q Consensus 102 ~~~p~~~~~~~La~~l~l~~~~ 123 (183)
...++.++-..|+..|||+...
T Consensus 45 Q~~ls~e~A~kla~lLgL~~e~ 66 (150)
T TIGR00673 45 QAAAPADEARLVGAKLDLDEDS 66 (150)
T ss_pred CCCCCHHHHHHHHHHhCcCHHH
Confidence 4445556666666666666543
No 383
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.82 E-value=1.4e+02 Score=21.41 Aligned_cols=32 Identities=22% Similarity=0.127 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 106 SKQKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 106 ~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
......++|..+|++...|+.+...-|.+-++
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 33456789999999999999988655555444
No 384
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=20.79 E-value=97 Score=23.22 Aligned_cols=21 Identities=19% Similarity=0.365 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChhhHHHHHhh
Q psy10486 110 RWELARSLMLTERQVKIWFQN 130 (183)
Q Consensus 110 ~~~La~~l~l~~~~V~~WF~n 130 (183)
..++|..+||+...|+.|...
T Consensus 3 i~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 457899999999999999853
No 385
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.76 E-value=4.1e+02 Score=20.59 Aligned_cols=46 Identities=20% Similarity=0.110 Sum_probs=28.7
Q ss_pred HHHHHHcCCChhhhhhhhhhccccccccccccCCCCChhHHHHHHHc
Q psy10486 52 WELARSLMLTERQVKIWFQNIEWTGQVTVRKKRKPYSKHQTLELEKE 98 (183)
Q Consensus 52 ~~La~~l~l~~~qV~~WF~nrr~k~~~~~rr~r~~~t~~q~~~Le~~ 98 (183)
.+||..+|++.+.|+.|=..-=-...+. ......|+...+..|.-.
T Consensus 5 ~elA~~~Gvs~~tIR~Ye~~GLL~p~r~-~~~~r~Y~~~~v~rL~~I 50 (219)
T cd04778 5 DDLARAAGTTVRNVRAYQDRGLLPPPRR-RGRVAIYNDSHLARLRLI 50 (219)
T ss_pred HHHHHHHCcCHHHHHHHHHCCCCCCccc-CCCCcccCHHHHHHHHHH
Confidence 5799999999999998865411111111 112236888888777443
No 386
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=20.70 E-value=2.8e+02 Score=21.80 Aligned_cols=48 Identities=10% Similarity=0.088 Sum_probs=30.4
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKNT 139 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~~ 139 (183)
+++.+..++.-.|.. .....++|..+|++...|+.....-+.+-|+.-
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 444444444444422 234678999999999999988766555555443
No 387
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=20.65 E-value=3.1e+02 Score=20.97 Aligned_cols=30 Identities=20% Similarity=0.119 Sum_probs=21.3
Q ss_pred HHHHHHHHHhCCChhhHHHHHhhhhhHHHH
Q psy10486 108 QKRWELARSLMLTERQVKIWFQNRRMKNKK 137 (183)
Q Consensus 108 ~~~~~La~~l~l~~~~V~~WF~nrR~k~rk 137 (183)
....++|..+|++...|+++-..-+.+-|+
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356788999999999998885443433333
No 388
>PHA02947 S-S bond formation pathway protein; Provisional
Probab=20.59 E-value=1.7e+02 Score=22.72 Aligned_cols=42 Identities=17% Similarity=0.112 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhhc-CCCCHHHHHHHHHHcCCChhhhhhhhhh
Q psy10486 30 KHQTLELEKEFLYN-AYVSKQKRWELARSLMLTERQVKIWFQN 71 (183)
Q Consensus 30 ~~Ql~~Le~~F~~~-~~p~~~~~~~La~~l~l~~~qV~~WF~n 71 (183)
..++..|-+.|.++ ...+.+++.+++++||++...+..=|.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~iaa~lgId~~~~~~d~~t 102 (215)
T PHA02947 60 RLSFTLLIKTFKEVISTLPEKERRELANEIGIDLDNDDPSYVS 102 (215)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccccccc
Confidence 45777777777766 4577899999999999977655444443
No 389
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=20.41 E-value=53 Score=19.78 Aligned_cols=42 Identities=10% Similarity=0.052 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhh
Q psy10486 28 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWF 69 (183)
Q Consensus 28 ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF 69 (183)
+|+..-+.|+..|....--.......||..||+++.-|..=+
T Consensus 2 Lt~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 2 LTESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp CSCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CCcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 344555677777777643333334579999999988776443
No 390
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=20.40 E-value=2.4e+02 Score=21.77 Aligned_cols=51 Identities=8% Similarity=0.029 Sum_probs=33.3
Q ss_pred CChhHHHHHHHccccCCccCHHHHHHHHHHhCCChhhHHHHHhhhhhHHHHH
Q psy10486 87 YSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNRRMKNKKN 138 (183)
Q Consensus 87 ~t~~q~~~Le~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF~nrR~k~rk~ 138 (183)
+++.+..+|.-.|....+ ......++|..+|++...|+.....-..|-|..
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 444455555555532111 223577899999999999999887666665554
No 391
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=20.15 E-value=1.5e+02 Score=22.66 Aligned_cols=45 Identities=9% Similarity=-0.028 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhc
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNI 72 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nr 72 (183)
.+|+.++++|....... +-....-.+||..|++++..|+..+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 47888887776665543 2223345789999999999999888764
No 392
>PRK10651 transcriptional regulator NarL; Provisional
Probab=20.07 E-value=1e+02 Score=22.25 Aligned_cols=43 Identities=19% Similarity=0.081 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHcCCChhhhhhhhhhcccc
Q psy10486 27 PYSKHQTLELEKEFLYNAYVSKQKRWELARSLMLTERQVKIWFQNIEWT 75 (183)
Q Consensus 27 ~ft~~Ql~~Le~~F~~~~~p~~~~~~~La~~l~l~~~qV~~WF~nrr~k 75 (183)
.+|+.+.++|.-.... + ...++|..++++.+.|.....+-+.|
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~K 197 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKK 197 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 4899999999875532 2 23568999999999999999886655
Done!