Query psy16797
Match_columns 99
No_of_seqs 102 out of 1003
Neff 8.4
Searched_HMMs 46136
Date Fri Aug 16 22:19:37 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy16797.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/16797hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.8 2.3E-19 4.9E-24 127.1 6.1 66 17-82 169-234 (309)
2 KOG0842|consensus 99.8 6.1E-20 1.3E-24 129.0 3.1 73 16-88 149-221 (307)
3 PF00046 Homeobox: Homeobox do 99.8 1.5E-18 3.3E-23 95.0 7.4 57 21-77 1-57 (57)
4 KOG0494|consensus 99.8 5.2E-19 1.1E-23 121.2 5.8 75 23-97 144-218 (332)
5 KOG0489|consensus 99.8 5.2E-19 1.1E-23 123.0 5.9 68 18-85 157-224 (261)
6 KOG0484|consensus 99.8 4.5E-19 9.7E-24 106.7 3.5 73 7-79 4-76 (125)
7 KOG0487|consensus 99.7 6.8E-19 1.5E-23 123.8 3.3 68 18-85 233-300 (308)
8 KOG0850|consensus 99.7 2E-18 4.4E-23 116.4 5.1 64 18-81 120-183 (245)
9 KOG0843|consensus 99.7 2.5E-18 5.4E-23 112.3 5.2 63 19-81 101-163 (197)
10 KOG0485|consensus 99.7 2E-18 4.3E-23 115.8 3.9 74 16-89 100-173 (268)
11 KOG2251|consensus 99.7 3.5E-17 7.6E-22 109.8 4.5 68 15-82 32-99 (228)
12 cd00086 homeodomain Homeodomai 99.7 4.5E-16 9.8E-21 85.3 7.8 57 22-78 2-58 (59)
13 smart00389 HOX Homeodomain. DN 99.7 3E-16 6.4E-21 85.3 7.0 55 22-76 2-56 (56)
14 COG5576 Homeodomain-containing 99.7 1.1E-16 2.4E-21 103.7 6.1 71 13-83 44-114 (156)
15 KOG0492|consensus 99.7 1E-16 2.2E-21 106.9 5.0 63 18-80 142-204 (246)
16 TIGR01565 homeo_ZF_HD homeobox 99.7 1.4E-16 2.9E-21 87.5 4.0 53 20-72 1-57 (58)
17 KOG0493|consensus 99.6 5.2E-16 1.1E-20 106.7 6.3 67 21-87 247-313 (342)
18 KOG3802|consensus 99.6 2.1E-16 4.6E-21 113.6 3.1 78 3-80 265-354 (398)
19 KOG0483|consensus 99.6 2.9E-16 6.3E-21 105.0 3.5 72 20-91 50-121 (198)
20 KOG0491|consensus 99.6 4.2E-16 9E-21 100.7 3.3 64 20-83 100-163 (194)
21 KOG0848|consensus 99.6 6.3E-16 1.4E-20 106.4 2.4 60 23-82 202-261 (317)
22 KOG0486|consensus 99.5 3.9E-15 8.6E-20 104.4 2.5 73 19-91 111-183 (351)
23 KOG0847|consensus 99.5 1.7E-14 3.8E-19 97.2 3.9 66 15-80 162-227 (288)
24 KOG4577|consensus 99.5 5E-14 1.1E-18 98.2 4.6 71 13-83 160-230 (383)
25 KOG0844|consensus 99.3 2.9E-13 6.2E-18 95.1 1.2 64 18-81 179-242 (408)
26 KOG0490|consensus 99.3 2.1E-12 4.6E-17 87.5 3.4 64 17-80 57-120 (235)
27 KOG0775|consensus 99.2 3.5E-11 7.6E-16 83.4 6.3 54 27-80 183-236 (304)
28 KOG0849|consensus 99.2 2.6E-11 5.6E-16 87.7 5.2 66 15-80 171-236 (354)
29 KOG1168|consensus 99.1 4.4E-12 9.5E-17 88.6 -0.8 63 17-79 306-368 (385)
30 PF05920 Homeobox_KN: Homeobox 99.0 6.8E-10 1.5E-14 56.7 4.1 35 40-74 6-40 (40)
31 KOG2252|consensus 99.0 3.6E-09 7.8E-14 79.2 8.2 58 18-75 418-475 (558)
32 KOG0774|consensus 98.9 1.3E-09 2.8E-14 75.4 2.3 60 20-79 188-250 (334)
33 KOG0490|consensus 98.3 1.2E-06 2.6E-11 59.3 4.3 64 17-80 150-213 (235)
34 KOG1146|consensus 98.0 7.8E-06 1.7E-10 66.7 4.8 63 20-82 903-965 (1406)
35 PF11569 Homez: Homeodomain le 97.9 1.8E-05 3.8E-10 43.0 3.8 41 32-72 10-50 (56)
36 KOG0773|consensus 97.4 9.4E-05 2E-09 53.3 2.3 57 20-76 239-298 (342)
37 KOG3623|consensus 96.5 0.01 2.2E-07 47.0 6.4 48 32-79 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.8 0.045 9.8E-07 29.2 5.0 47 21-72 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 93.9 0.4 8.7E-06 24.7 5.4 46 26-76 4-49 (50)
40 PF04967 HTH_10: HTH DNA bindi 89.8 1.9 4.1E-05 23.0 5.4 43 27-69 1-45 (53)
41 PF01527 HTH_Tnp_1: Transposas 89.6 0.71 1.5E-05 25.6 3.5 47 22-72 2-48 (76)
42 PF10668 Phage_terminase: Phag 89.1 0.44 9.5E-06 26.2 2.3 22 49-70 24-45 (60)
43 cd06171 Sigma70_r4 Sigma70, re 88.4 1.7 3.7E-05 21.6 4.3 43 27-74 11-53 (55)
44 PRK03975 tfx putative transcri 87.3 4.5 9.8E-05 25.9 6.5 50 24-79 4-53 (141)
45 PRK10072 putative transcriptio 85.5 2.8 6.1E-05 25.1 4.5 40 26-72 32-71 (96)
46 PF09607 BrkDBD: Brinker DNA-b 84.9 4.6 9.9E-05 22.0 4.8 46 24-70 3-48 (58)
47 PF00196 GerE: Bacterial regul 84.9 4.1 8.9E-05 21.5 5.5 45 26-76 3-47 (58)
48 PRK09413 IS2 repressor TnpA; R 84.8 4.4 9.4E-05 24.9 5.4 45 23-71 9-53 (121)
49 PF08281 Sigma70_r4_2: Sigma-7 84.7 3.9 8.6E-05 21.1 5.6 43 27-74 11-53 (54)
50 PRK06759 RNA polymerase factor 82.5 9.3 0.0002 23.7 6.4 29 49-77 124-152 (154)
51 PF13936 HTH_38: Helix-turn-he 82.0 4.5 9.7E-05 20.4 3.9 40 25-69 3-42 (44)
52 PF13518 HTH_28: Helix-turn-he 81.2 2.9 6.2E-05 21.2 3.0 25 49-73 14-38 (52)
53 PF13384 HTH_23: Homeodomain-l 81.0 2.2 4.8E-05 21.6 2.6 23 48-70 18-40 (50)
54 COG3413 Predicted DNA binding 80.8 6.1 0.00013 26.6 5.3 44 26-69 155-200 (215)
55 KOG0773|consensus 80.0 4.3 9.3E-05 29.3 4.6 48 34-81 111-158 (342)
56 TIGR03879 near_KaiC_dom probab 79.7 1.3 2.8E-05 25.3 1.4 25 46-70 31-55 (73)
57 cd04761 HTH_MerR-SF Helix-Turn 79.6 2.9 6.4E-05 20.9 2.7 22 50-71 3-24 (49)
58 PRK12526 RNA polymerase sigma 78.7 9.7 0.00021 25.3 5.7 33 48-80 170-202 (206)
59 PRK09642 RNA polymerase sigma 77.7 10 0.00022 23.8 5.4 31 50-80 125-155 (160)
60 PRK05602 RNA polymerase sigma 77.6 8.3 0.00018 24.9 5.0 36 49-84 146-181 (186)
61 PRK12514 RNA polymerase sigma 77.3 5.7 0.00012 25.5 4.2 30 49-78 147-176 (179)
62 PF06056 Terminase_5: Putative 76.9 3.5 7.6E-05 22.3 2.6 20 50-69 16-35 (58)
63 PRK09646 RNA polymerase sigma 76.4 12 0.00026 24.4 5.6 31 49-79 160-190 (194)
64 PRK04217 hypothetical protein; 76.1 15 0.00033 22.5 5.9 51 24-79 40-90 (110)
65 PRK11924 RNA polymerase sigma 75.3 7.8 0.00017 24.4 4.4 29 49-77 143-171 (179)
66 PRK09652 RNA polymerase sigma 75.1 15 0.00032 23.2 5.7 47 27-78 129-175 (182)
67 TIGR02937 sigma70-ECF RNA poly 75.1 9.4 0.0002 23.0 4.6 46 27-77 111-156 (158)
68 PRK12512 RNA polymerase sigma 74.5 15 0.00033 23.6 5.7 31 49-79 149-179 (184)
69 TIGR02989 Sig-70_gvs1 RNA poly 74.4 18 0.00039 22.5 6.0 30 48-77 128-157 (159)
70 PF00376 MerR: MerR family reg 73.4 4.4 9.5E-05 19.9 2.2 19 51-69 3-21 (38)
71 cd04762 HTH_MerR-trunc Helix-T 73.1 6 0.00013 19.3 2.8 23 50-72 3-25 (49)
72 PRK09639 RNA polymerase sigma 73.1 20 0.00042 22.5 5.8 30 49-78 129-158 (166)
73 PRK00118 putative DNA-binding 72.9 18 0.0004 21.9 5.9 48 27-79 18-65 (104)
74 PRK12530 RNA polymerase sigma 72.4 19 0.00042 23.4 5.8 29 50-78 153-181 (189)
75 TIGR02999 Sig-70_X6 RNA polyme 71.7 22 0.00047 22.7 5.9 29 50-78 153-181 (183)
76 cd00569 HTH_Hin_like Helix-tur 71.7 7.6 0.00017 17.0 5.0 37 27-68 6-42 (42)
77 PRK09648 RNA polymerase sigma 70.7 21 0.00046 23.0 5.7 30 49-78 157-186 (189)
78 PF13411 MerR_1: MerR HTH fami 70.6 5.2 0.00011 21.6 2.4 19 51-69 4-22 (69)
79 PRK12547 RNA polymerase sigma 70.1 23 0.00051 22.3 5.7 31 49-79 130-160 (164)
80 PRK12537 RNA polymerase sigma 69.4 23 0.0005 22.8 5.6 30 49-78 151-180 (182)
81 PRK12541 RNA polymerase sigma 69.2 25 0.00054 22.0 5.7 29 50-78 131-159 (161)
82 cd04764 HTH_MlrA-like_sg1 Heli 69.1 7 0.00015 21.1 2.7 20 51-70 4-23 (67)
83 TIGR02948 SigW_bacill RNA poly 69.0 23 0.00051 22.6 5.6 31 48-78 153-183 (187)
84 TIGR02985 Sig70_bacteroi1 RNA 68.5 25 0.00054 21.6 6.1 29 49-77 131-159 (161)
85 cd04763 HTH_MlrA-like Helix-Tu 68.3 6.9 0.00015 21.2 2.6 20 51-70 4-23 (68)
86 PF13443 HTH_26: Cro/C1-type H 68.1 6.2 0.00014 20.9 2.3 23 49-71 12-34 (63)
87 TIGR02959 SigZ RNA polymerase 67.9 29 0.00062 22.1 5.9 32 49-80 118-149 (170)
88 PRK12524 RNA polymerase sigma 67.9 27 0.00059 22.8 5.8 32 50-81 155-186 (196)
89 PRK12518 RNA polymerase sigma 67.9 8 0.00017 24.6 3.2 36 45-80 134-169 (175)
90 PRK08301 sporulation sigma fac 67.8 21 0.00045 24.1 5.3 31 48-78 199-229 (234)
91 TIGR02859 spore_sigH RNA polym 67.5 30 0.00066 22.3 6.0 33 46-78 164-196 (198)
92 TIGR02939 RpoE_Sigma70 RNA pol 67.5 9.9 0.00022 24.4 3.6 34 46-79 153-186 (190)
93 PRK12519 RNA polymerase sigma 67.4 11 0.00023 24.5 3.8 32 47-78 157-188 (194)
94 cd01392 HTH_LacI Helix-turn-he 67.4 4.4 9.4E-05 20.6 1.5 20 52-71 2-21 (52)
95 COG4367 Uncharacterized protei 67.3 16 0.00034 21.7 4.0 39 27-65 3-41 (97)
96 PRK12515 RNA polymerase sigma 67.2 30 0.00065 22.3 5.9 31 50-80 150-180 (189)
97 PRK06930 positive control sigm 67.1 30 0.00066 22.6 5.8 49 26-79 114-162 (170)
98 PRK06986 fliA flagellar biosyn 66.5 17 0.00038 24.6 4.8 31 49-79 202-232 (236)
99 PRK09644 RNA polymerase sigma 66.4 12 0.00026 23.7 3.8 33 48-80 125-157 (165)
100 TIGR02950 SigM_subfam RNA poly 66.0 13 0.00027 23.0 3.8 34 44-77 118-151 (154)
101 KOG1146|consensus 65.8 14 0.0003 31.9 4.7 66 20-85 705-770 (1406)
102 PRK09480 slmA division inhibit 65.2 10 0.00022 24.4 3.3 40 33-73 17-56 (194)
103 PRK08583 RNA polymerase sigma 64.9 20 0.00043 24.6 4.8 47 27-78 206-252 (257)
104 PRK09047 RNA polymerase factor 64.8 31 0.00068 21.4 5.9 30 50-79 125-154 (161)
105 cd01104 HTH_MlrA-CarA Helix-Tu 64.5 11 0.00025 20.1 3.0 20 50-69 3-22 (68)
106 PRK05657 RNA polymerase sigma 64.5 31 0.00067 24.9 5.9 54 26-80 262-315 (325)
107 TIGR02947 SigH_actino RNA poly 64.3 13 0.00028 24.2 3.7 34 46-79 146-179 (193)
108 PRK12546 RNA polymerase sigma 64.0 14 0.00031 24.2 3.8 35 49-83 131-165 (188)
109 PRK08295 RNA polymerase factor 63.9 38 0.00082 22.1 6.1 32 48-79 171-202 (208)
110 PRK06811 RNA polymerase factor 63.7 32 0.00069 22.3 5.5 32 49-80 149-180 (189)
111 PF08280 HTH_Mga: M protein tr 63.6 21 0.00045 19.0 4.6 37 30-70 6-42 (59)
112 PRK09637 RNA polymerase sigma 62.8 38 0.00083 21.9 5.7 31 49-79 124-154 (181)
113 PRK13870 transcriptional regul 62.8 22 0.00048 24.4 4.7 48 24-77 171-218 (234)
114 PRK12543 RNA polymerase sigma 62.7 38 0.00083 21.7 5.8 31 49-79 135-165 (179)
115 PRK12513 RNA polymerase sigma 62.5 15 0.00033 23.9 3.8 35 45-79 153-187 (194)
116 smart00421 HTH_LUXR helix_turn 62.1 19 0.0004 17.9 6.1 44 26-75 3-46 (58)
117 TIGR02479 FliA_WhiG RNA polyme 61.8 24 0.00052 23.7 4.7 47 27-78 176-222 (224)
118 PRK13919 putative RNA polymera 61.5 23 0.00051 22.7 4.5 30 49-78 153-182 (186)
119 TIGR03020 EpsA transcriptional 61.2 42 0.00092 23.4 5.9 48 24-77 188-235 (247)
120 TIGR03541 reg_near_HchA LuxR f 61.1 46 0.001 22.6 6.1 49 24-78 169-217 (232)
121 TIGR02941 Sigma_B RNA polymera 61.1 27 0.00058 24.0 4.9 47 27-78 206-252 (255)
122 TIGR00721 tfx DNA-binding prot 60.8 41 0.00089 21.4 6.5 49 24-78 4-52 (137)
123 PRK07408 RNA polymerase sigma 60.6 24 0.00052 24.4 4.7 48 28-80 205-252 (256)
124 PF01381 HTH_3: Helix-turn-hel 60.6 9.2 0.0002 19.5 2.0 22 50-71 12-33 (55)
125 TIGR02393 RpoD_Cterm RNA polym 60.2 39 0.00084 22.9 5.6 52 26-78 176-227 (238)
126 PRK09645 RNA polymerase sigma 60.0 41 0.0009 21.2 5.7 31 50-80 137-167 (173)
127 PRK12538 RNA polymerase sigma 60.0 35 0.00077 23.3 5.3 32 49-80 189-220 (233)
128 PF14549 P22_Cro: DNA-binding 59.9 11 0.00023 20.6 2.2 18 50-67 12-29 (60)
129 PF13551 HTH_29: Winged helix- 59.4 33 0.00071 19.9 6.0 47 23-69 54-109 (112)
130 PRK07670 RNA polymerase sigma 58.4 29 0.00062 23.8 4.7 30 49-78 219-248 (251)
131 PRK12535 RNA polymerase sigma 58.4 50 0.0011 21.7 6.2 35 50-84 152-186 (196)
132 PRK09640 RNA polymerase sigma 58.4 20 0.00043 23.2 3.8 32 47-78 150-181 (188)
133 PRK12533 RNA polymerase sigma 58.3 44 0.00096 22.5 5.5 33 49-81 152-184 (216)
134 TIGR02983 SigE-fam_strep RNA p 58.1 21 0.00045 22.3 3.7 31 49-79 128-158 (162)
135 PRK12536 RNA polymerase sigma 57.7 21 0.00045 23.0 3.8 30 49-78 147-176 (181)
136 PRK12511 RNA polymerase sigma 57.7 50 0.0011 21.4 5.7 32 50-81 130-161 (182)
137 PRK12532 RNA polymerase sigma 57.7 21 0.00045 23.3 3.8 30 50-79 155-184 (195)
138 PRK12539 RNA polymerase sigma 57.6 49 0.0011 21.3 5.8 32 48-79 148-179 (184)
139 PF04936 DUF658: Protein of un 57.5 9.5 0.0002 25.3 2.0 33 48-80 15-47 (186)
140 TIGR02394 rpoS_proteo RNA poly 57.4 56 0.0012 22.9 6.1 52 27-79 223-274 (285)
141 TIGR02392 rpoH_proteo alternat 57.4 40 0.00087 23.4 5.3 50 26-78 218-267 (270)
142 PRK09649 RNA polymerase sigma 57.4 50 0.0011 21.4 6.1 28 50-77 149-176 (185)
143 TIGR01764 excise DNA binding d 57.2 19 0.00041 17.5 2.8 22 50-71 4-25 (49)
144 PF13730 HTH_36: Helix-turn-he 57.1 26 0.00055 17.9 3.5 22 49-70 27-48 (55)
145 PRK12542 RNA polymerase sigma 57.1 20 0.00044 23.1 3.6 33 50-82 141-173 (185)
146 PRK10100 DNA-binding transcrip 57.1 58 0.0013 22.0 6.0 46 26-77 155-200 (216)
147 TIGR02980 SigBFG RNA polymeras 57.0 36 0.00077 22.8 4.9 47 26-77 178-224 (227)
148 TIGR02952 Sig70_famx2 RNA poly 57.0 46 0.00099 20.8 6.0 30 48-77 139-168 (170)
149 PRK10403 transcriptional regul 57.0 34 0.00073 21.6 4.7 46 25-76 152-197 (215)
150 PRK11923 algU RNA polymerase s 56.8 22 0.00047 23.0 3.8 31 49-79 156-186 (193)
151 PRK12545 RNA polymerase sigma 56.6 54 0.0012 21.5 5.9 31 49-79 157-187 (201)
152 PRK12522 RNA polymerase sigma 56.1 23 0.0005 22.5 3.7 29 50-78 138-166 (173)
153 PF12728 HTH_17: Helix-turn-he 56.0 19 0.00041 18.2 2.8 22 50-71 4-25 (51)
154 TIGR02954 Sig70_famx3 RNA poly 55.8 23 0.00051 22.4 3.7 30 49-78 137-166 (169)
155 PRK09641 RNA polymerase sigma 55.1 24 0.00053 22.5 3.8 31 48-78 153-183 (187)
156 TIGR02984 Sig-70_plancto1 RNA 54.9 41 0.00088 21.4 4.8 31 48-78 157-187 (189)
157 TIGR02835 spore_sigmaE RNA pol 54.8 64 0.0014 21.8 6.1 31 48-78 199-229 (234)
158 TIGR03070 couple_hipB transcri 54.4 12 0.00027 18.9 1.9 22 50-71 18-39 (58)
159 TIGR02943 Sig70_famx1 RNA poly 54.3 58 0.0013 21.2 5.8 31 49-79 149-179 (188)
160 PRK07122 RNA polymerase sigma 54.3 36 0.00079 23.7 4.7 47 27-78 216-262 (264)
161 PRK12523 RNA polymerase sigma 54.2 27 0.00058 22.2 3.8 31 49-79 137-167 (172)
162 PRK07037 extracytoplasmic-func 54.2 51 0.0011 20.5 5.8 29 50-78 128-156 (163)
163 COG1905 NuoE NADH:ubiquinone o 54.0 37 0.0008 22.3 4.3 37 29-65 25-61 (160)
164 COG2963 Transposase and inacti 53.9 46 0.00099 19.9 5.1 45 24-72 5-50 (116)
165 smart00422 HTH_MERR helix_turn 53.8 18 0.00039 19.3 2.6 19 51-69 4-22 (70)
166 PRK12534 RNA polymerase sigma 53.7 37 0.00079 21.8 4.4 31 48-78 154-184 (187)
167 PRK12516 RNA polymerase sigma 53.7 26 0.00057 22.8 3.8 32 50-81 135-166 (187)
168 PRK12520 RNA polymerase sigma 53.7 26 0.00057 22.7 3.8 31 50-80 150-180 (191)
169 COG2944 Predicted transcriptio 53.6 32 0.00069 21.0 3.7 40 26-72 43-82 (104)
170 PRK12529 RNA polymerase sigma 53.5 57 0.0012 20.9 5.8 28 50-77 146-173 (178)
171 COG5484 Uncharacterized conser 53.4 13 0.00029 26.3 2.3 25 49-73 21-45 (279)
172 PRK12544 RNA polymerase sigma 52.8 66 0.0014 21.4 5.9 30 50-79 167-196 (206)
173 PRK09647 RNA polymerase sigma 52.7 27 0.00059 23.2 3.7 31 50-80 157-187 (203)
174 cd00093 HTH_XRE Helix-turn-hel 52.1 17 0.00038 17.4 2.2 22 50-71 15-36 (58)
175 PRK09638 RNA polymerase sigma 52.1 28 0.00061 22.0 3.7 34 45-78 140-173 (176)
176 TIGR03001 Sig-70_gmx1 RNA poly 52.1 25 0.00053 24.3 3.5 30 50-79 180-209 (244)
177 PRK05803 sporulation sigma fac 51.9 58 0.0013 22.0 5.3 31 48-78 196-226 (233)
178 TIGR02957 SigX4 RNA polymerase 51.1 70 0.0015 22.3 5.8 30 50-79 127-156 (281)
179 PRK12531 RNA polymerase sigma 51.1 66 0.0014 20.9 5.8 30 49-78 159-188 (194)
180 cd01106 HTH_TipAL-Mta Helix-Tu 51.0 18 0.00039 21.4 2.5 21 51-71 4-24 (103)
181 PF07638 Sigma70_ECF: ECF sigm 50.0 32 0.0007 22.4 3.7 30 48-77 152-181 (185)
182 PF07037 DUF1323: Putative tra 50.0 19 0.00041 22.6 2.4 27 50-76 3-29 (122)
183 PRK05988 formate dehydrogenase 49.3 56 0.0012 21.1 4.7 36 30-65 24-59 (156)
184 COG1595 RpoE DNA-directed RNA 49.3 34 0.00075 22.0 3.8 33 49-81 145-177 (182)
185 PRK08215 sporulation sigma fac 49.3 53 0.0012 22.6 4.9 47 26-77 209-255 (258)
186 PF13542 HTH_Tnp_ISL3: Helix-t 49.0 29 0.00063 17.5 2.8 20 50-69 30-49 (52)
187 PRK06288 RNA polymerase sigma 49.0 43 0.00092 23.2 4.4 47 27-78 213-259 (268)
188 PRK07500 rpoH2 RNA polymerase 48.8 61 0.0013 22.9 5.2 51 26-79 227-277 (289)
189 PHA01976 helix-turn-helix prot 48.6 20 0.00043 19.1 2.2 22 50-71 18-39 (67)
190 PRK09935 transcriptional regul 48.4 59 0.0013 20.5 4.8 46 25-76 148-193 (210)
191 PLN03162 golden-2 like transcr 48.4 92 0.002 23.6 6.1 77 3-79 216-294 (526)
192 PRK09636 RNA polymerase sigma 48.2 82 0.0018 22.0 5.8 30 50-79 134-163 (293)
193 PF01710 HTH_Tnp_IS630: Transp 48.1 22 0.00047 21.7 2.5 21 49-69 20-40 (119)
194 TIGR02885 spore_sigF RNA polym 48.1 72 0.0016 21.4 5.3 47 26-77 183-229 (231)
195 PRK05572 sporulation sigma fac 47.8 57 0.0012 22.3 4.8 47 26-77 202-248 (252)
196 PRK05911 RNA polymerase sigma 47.5 55 0.0012 22.6 4.7 47 27-78 206-252 (257)
197 KOG3623|consensus 47.3 9.6 0.00021 31.0 1.0 60 21-80 627-686 (1007)
198 TIGR02607 antidote_HigA addict 47.1 21 0.00046 19.5 2.2 23 50-72 21-43 (78)
199 cd04766 HTH_HspR Helix-Turn-He 46.9 21 0.00046 20.6 2.2 20 50-69 4-23 (91)
200 PRK10360 DNA-binding transcrip 46.6 68 0.0015 20.1 4.8 44 26-75 137-180 (196)
201 cd01105 HTH_GlnR-like Helix-Tu 46.5 26 0.00056 20.2 2.6 19 50-68 4-22 (88)
202 PRK10430 DNA-binding transcrip 46.2 59 0.0013 21.7 4.7 45 26-71 158-202 (239)
203 TIGR02846 spore_sigmaK RNA pol 46.2 90 0.0019 21.0 5.9 50 27-77 175-224 (227)
204 PRK11511 DNA-binding transcrip 46.0 21 0.00045 22.0 2.2 25 47-71 25-49 (127)
205 PRK12540 RNA polymerase sigma 46.0 41 0.00089 21.8 3.8 35 49-83 129-163 (182)
206 cd04774 HTH_YfmP Helix-Turn-He 46.0 31 0.00067 20.3 2.9 20 51-70 4-23 (96)
207 PRK09415 RNA polymerase factor 45.8 42 0.00091 21.5 3.8 28 50-77 146-173 (179)
208 PRK11552 putative DNA-binding 45.5 30 0.00066 23.2 3.2 41 32-74 19-59 (225)
209 cd04779 HTH_MerR-like_sg4 Heli 45.3 25 0.00054 22.2 2.5 20 51-70 4-23 (134)
210 PRK09651 RNA polymerase sigma 44.7 45 0.00098 21.2 3.8 31 48-78 136-166 (172)
211 PRK15411 rcsA colanic acid cap 44.5 93 0.002 20.7 5.7 45 26-76 137-181 (207)
212 PF07471 Phage_Nu1: Phage DNA 44.5 25 0.00054 23.1 2.5 21 50-70 5-25 (164)
213 PRK10188 DNA-binding transcrip 44.3 1E+02 0.0022 21.1 6.2 48 24-77 177-224 (240)
214 PRK10651 transcriptional regul 44.0 81 0.0018 19.8 5.7 45 26-76 155-199 (216)
215 cd04768 HTH_BmrR-like Helix-Tu 43.9 30 0.00064 20.3 2.6 20 51-70 4-23 (96)
216 TIGR01958 nuoE_fam NADH-quinon 43.8 75 0.0016 20.2 4.6 36 30-65 17-52 (148)
217 PRK09706 transcriptional repre 43.8 22 0.00049 22.0 2.1 23 50-72 21-43 (135)
218 PRK07539 NADH dehydrogenase su 43.6 75 0.0016 20.3 4.6 36 30-65 23-58 (154)
219 PRK15369 two component system 43.6 79 0.0017 19.6 5.9 46 25-76 148-193 (211)
220 PRK11922 RNA polymerase sigma 43.5 45 0.00097 22.5 3.7 37 44-80 162-198 (231)
221 PF06971 Put_DNA-bind_N: Putat 42.9 28 0.0006 18.2 2.1 17 50-66 31-47 (50)
222 PRK06596 RNA polymerase factor 42.8 91 0.002 22.0 5.3 50 26-78 230-279 (284)
223 PF01257 2Fe-2S_thioredx: Thio 42.4 61 0.0013 20.5 4.0 35 31-65 15-49 (145)
224 PRK12528 RNA polymerase sigma 42.2 84 0.0018 19.5 5.8 26 50-75 132-157 (161)
225 PF07022 Phage_CI_repr: Bacter 42.1 16 0.00035 19.9 1.2 20 50-69 15-35 (66)
226 TIGR02997 Sig70-cyanoRpoD RNA 42.0 96 0.0021 21.9 5.4 47 27-74 250-296 (298)
227 cd04789 HTH_Cfa Helix-Turn-Hel 41.5 29 0.00062 20.6 2.3 21 50-70 4-24 (102)
228 PRK06704 RNA polymerase factor 41.5 50 0.0011 22.7 3.7 31 50-80 135-165 (228)
229 cd04775 HTH_Cfa-like Helix-Tur 41.1 29 0.00063 20.5 2.3 21 50-70 4-24 (102)
230 PRK09744 DNA-binding transcrip 41.0 39 0.00085 19.3 2.6 18 50-67 13-30 (75)
231 PRK12517 RNA polymerase sigma 40.5 56 0.0012 21.2 3.8 31 49-79 146-176 (188)
232 TIGR02960 SigX5 RNA polymerase 40.5 56 0.0012 23.0 4.0 32 50-81 161-192 (324)
233 PRK09975 DNA-binding transcrip 40.4 26 0.00057 22.9 2.2 41 32-73 17-57 (213)
234 PF02796 HTH_7: Helix-turn-hel 40.4 50 0.0011 16.4 4.1 37 27-68 6-42 (45)
235 PRK07571 bidirectional hydroge 40.4 92 0.002 20.5 4.7 35 31-65 38-72 (169)
236 cd04788 HTH_NolA-AlbR Helix-Tu 40.3 31 0.00067 20.2 2.3 19 51-69 4-22 (96)
237 PRK15008 HTH-type transcriptio 39.9 58 0.0013 21.4 3.8 42 32-74 24-65 (212)
238 KOG3755|consensus 39.5 19 0.00042 28.7 1.6 47 36-82 708-761 (769)
239 PRK12525 RNA polymerase sigma 39.5 98 0.0021 19.5 5.9 28 50-77 137-164 (168)
240 cd04782 HTH_BltR Helix-Turn-He 39.3 39 0.00084 19.8 2.6 20 51-70 4-23 (97)
241 cd04765 HTH_MlrA-like_sg2 Heli 39.0 41 0.00089 19.9 2.7 20 51-70 4-23 (99)
242 cd00592 HTH_MerR-like Helix-Tu 38.8 34 0.00074 19.8 2.3 20 51-70 4-23 (100)
243 cd01111 HTH_MerD Helix-Turn-He 38.8 33 0.00072 20.6 2.3 20 51-70 4-23 (107)
244 cd04773 HTH_TioE_rpt2 Second H 38.8 35 0.00077 20.4 2.4 21 50-70 3-23 (108)
245 PF09862 DUF2089: Protein of u 38.5 96 0.0021 19.2 4.4 42 26-72 33-74 (113)
246 smart00530 HTH_XRE Helix-turn- 38.4 35 0.00076 16.0 2.1 22 50-71 13-34 (56)
247 cd00131 PAX Paired Box domain 38.1 99 0.0021 19.2 7.3 45 26-70 75-126 (128)
248 smart00027 EH Eps15 homology d 37.8 81 0.0018 18.1 5.4 43 27-69 4-51 (96)
249 cd04780 HTH_MerR-like_sg5 Heli 37.7 36 0.00078 20.0 2.3 20 50-69 3-22 (95)
250 PF00325 Crp: Bacterial regula 36.9 44 0.00095 15.8 2.1 21 49-69 4-24 (32)
251 cd01109 HTH_YyaN Helix-Turn-He 36.9 36 0.00079 20.4 2.3 20 50-69 3-22 (113)
252 PF14229 DUF4332: Domain of un 36.8 58 0.0013 20.1 3.2 26 44-69 26-51 (122)
253 cd06170 LuxR_C_like C-terminal 36.7 58 0.0013 16.1 5.8 25 49-73 17-41 (57)
254 cd04767 HTH_HspR-like_MBC Heli 36.7 43 0.00093 20.8 2.6 21 50-70 4-24 (120)
255 cd01107 HTH_BmrR Helix-Turn-He 36.7 37 0.0008 20.3 2.2 20 51-70 4-23 (108)
256 COG0789 SoxR Predicted transcr 36.6 38 0.00081 20.3 2.3 19 51-69 4-22 (124)
257 PF13613 HTH_Tnp_4: Helix-turn 36.5 40 0.00086 17.4 2.1 22 50-71 22-43 (53)
258 PF01726 LexA_DNA_bind: LexA D 36.4 76 0.0016 17.3 4.3 40 27-68 4-47 (65)
259 PF08279 HTH_11: HTH domain; 36.1 63 0.0014 16.3 3.8 35 33-70 4-38 (55)
260 PRK07405 RNA polymerase sigma 35.9 1.7E+02 0.0036 21.1 6.0 50 27-77 257-306 (317)
261 PF13404 HTH_AsnC-type: AsnC-t 35.8 43 0.00093 16.6 2.1 18 49-66 19-36 (42)
262 PRK14996 TetR family transcrip 35.8 61 0.0013 20.8 3.4 41 32-73 14-54 (192)
263 PRK09643 RNA polymerase sigma 34.8 1.3E+02 0.0028 19.5 5.8 32 49-80 152-183 (192)
264 PRK13182 racA polar chromosome 34.4 54 0.0012 21.7 2.9 20 51-70 4-23 (175)
265 PHA02955 hypothetical protein; 34.3 51 0.0011 22.7 2.8 43 30-72 61-104 (213)
266 PF03444 HrcA_DNA-bdg: Winged 34.3 96 0.0021 17.9 4.7 40 27-68 2-44 (78)
267 cd01279 HTH_HspR-like Helix-Tu 34.2 47 0.001 19.5 2.4 21 50-70 4-24 (98)
268 PRK05949 RNA polymerase sigma 34.0 1.8E+02 0.0039 21.1 5.7 50 27-77 267-316 (327)
269 cd04772 HTH_TioE_rpt1 First He 33.9 45 0.00098 19.6 2.3 19 51-69 4-22 (99)
270 cd01282 HTH_MerR-like_sg3 Heli 33.6 45 0.00098 20.0 2.3 20 51-70 4-23 (112)
271 TIGR02054 MerD mercuric resist 33.5 53 0.0012 20.3 2.6 21 50-70 6-26 (120)
272 PRK10840 transcriptional regul 33.5 1.4E+02 0.003 19.4 5.7 43 26-74 150-192 (216)
273 PF13560 HTH_31: Helix-turn-he 33.4 44 0.00095 17.7 2.0 24 49-72 16-39 (64)
274 PF08452 DNAP_B_exo_N: DNA pol 33.4 11 0.00024 16.3 -0.3 7 66-72 7-13 (22)
275 PF01325 Fe_dep_repress: Iron 33.0 33 0.00071 18.4 1.4 42 28-69 3-44 (60)
276 PRK12527 RNA polymerase sigma 32.6 1.2E+02 0.0027 18.7 5.8 29 50-78 124-152 (159)
277 TIGR02850 spore_sigG RNA polym 32.4 1.4E+02 0.0031 20.4 4.9 47 26-77 206-252 (254)
278 TIGR02051 MerR Hg(II)-responsi 32.4 46 0.001 20.4 2.2 18 51-68 3-20 (124)
279 PRK09726 antitoxin HipB; Provi 32.3 45 0.00098 19.1 2.1 22 50-71 28-49 (88)
280 cd01110 HTH_SoxR Helix-Turn-He 31.9 47 0.001 20.9 2.2 21 50-70 4-24 (139)
281 TIGR01950 SoxR redox-sensitive 31.9 55 0.0012 20.8 2.6 21 50-70 4-24 (142)
282 PRK13890 conjugal transfer pro 31.7 44 0.00096 20.5 2.0 23 50-72 21-43 (120)
283 PRK08241 RNA polymerase factor 31.5 82 0.0018 22.4 3.7 29 49-77 171-199 (339)
284 PF01476 LysM: LysM domain; I 31.5 65 0.0014 15.3 2.3 20 48-67 7-26 (44)
285 cd04776 HTH_GnyR Helix-Turn-He 31.4 50 0.0011 20.1 2.3 19 51-69 4-22 (118)
286 PRK13719 conjugal transfer tra 31.4 1.4E+02 0.003 20.7 4.5 44 25-74 142-185 (217)
287 PF00440 TetR_N: Bacterial reg 31.1 44 0.00095 16.6 1.7 33 39-72 9-41 (47)
288 COG2197 CitB Response regulato 31.1 89 0.0019 20.9 3.6 44 25-74 147-190 (211)
289 TIGR01321 TrpR trp operon repr 30.9 93 0.002 18.6 3.2 43 26-68 32-76 (94)
290 cd01108 HTH_CueR Helix-Turn-He 30.7 51 0.0011 20.3 2.2 20 51-70 4-23 (127)
291 PRK15201 fimbriae regulatory p 30.6 1.7E+02 0.0037 19.9 4.7 44 25-74 132-175 (198)
292 PF04703 FaeA: FaeA-like prote 30.3 88 0.0019 17.1 2.9 21 50-70 18-38 (62)
293 PF10078 DUF2316: Uncharacteri 30.3 55 0.0012 19.4 2.2 31 32-66 12-42 (89)
294 TIGR02044 CueR Cu(I)-responsiv 30.2 53 0.0012 20.2 2.2 20 51-70 4-23 (127)
295 PRK09514 zntR zinc-responsive 30.2 61 0.0013 20.4 2.6 21 50-70 4-24 (140)
296 COG0568 RpoD DNA-directed RNA 30.1 2.3E+02 0.005 21.0 5.8 50 27-77 280-329 (342)
297 cd04770 HTH_HMRTR Helix-Turn-H 29.7 56 0.0012 19.8 2.3 19 51-69 4-22 (123)
298 PF12244 DUF3606: Protein of u 29.4 94 0.002 16.5 2.9 14 51-64 24-37 (57)
299 cd04781 HTH_MerR-like_sg6 Heli 29.3 57 0.0012 19.8 2.3 19 51-69 4-22 (120)
300 PF12793 SgrR_N: Sugar transpo 29.2 1.1E+02 0.0024 18.7 3.5 34 33-68 7-40 (115)
301 PF12844 HTH_19: Helix-turn-he 29.2 57 0.0012 17.0 2.0 24 49-72 14-37 (64)
302 smart00354 HTH_LACI helix_turn 29.2 58 0.0012 17.7 2.1 23 50-72 3-25 (70)
303 PRK13558 bacterio-opsin activa 29.1 1.8E+02 0.0039 22.7 5.4 44 25-68 606-651 (665)
304 PF12824 MRP-L20: Mitochondria 28.8 1.7E+02 0.0037 19.1 5.3 42 23-66 82-123 (164)
305 TIGR03613 RutR pyrimidine util 28.6 82 0.0018 20.3 3.1 40 33-73 15-54 (202)
306 TIGR02043 ZntR Zn(II)-responsi 28.6 69 0.0015 19.8 2.6 21 50-70 4-24 (131)
307 cd04783 HTH_MerR1 Helix-Turn-H 28.6 59 0.0013 19.9 2.2 19 51-69 4-22 (126)
308 PRK10227 DNA-binding transcrip 28.5 59 0.0013 20.4 2.3 20 50-69 3-22 (135)
309 PRK09635 sigI RNA polymerase s 28.2 1E+02 0.0023 21.8 3.7 30 50-79 137-166 (290)
310 PRK11475 DNA-binding transcrip 27.9 1.9E+02 0.0041 19.3 5.9 43 26-74 134-176 (207)
311 cd04784 HTH_CadR-PbrR Helix-Tu 27.8 63 0.0014 19.8 2.3 20 51-70 4-23 (127)
312 TIGR02047 CadR-PbrR Cd(II)/Pb( 27.6 63 0.0014 19.9 2.3 21 50-70 3-23 (127)
313 PF12833 HTH_18: Helix-turn-he 27.6 69 0.0015 17.5 2.3 21 54-74 17-37 (81)
314 KOG0044|consensus 27.4 1.2E+02 0.0026 20.5 3.7 32 42-73 6-37 (193)
315 cd04787 HTH_HMRTR_unk Helix-Tu 26.5 68 0.0015 19.9 2.3 19 51-69 4-22 (133)
316 PF12200 DUF3597: Domain of un 26.4 1.8E+02 0.0038 18.4 4.1 29 45-73 83-116 (127)
317 cd04785 HTH_CadR-PbrR-like Hel 26.4 68 0.0015 19.7 2.2 20 51-70 4-23 (126)
318 cd04786 HTH_MerR-like_sg7 Heli 26.3 70 0.0015 19.9 2.3 19 51-69 4-22 (131)
319 PF04297 UPF0122: Putative hel 26.2 1.6E+02 0.0034 17.8 5.1 43 27-74 18-60 (101)
320 PRK07598 RNA polymerase sigma 26.1 2.8E+02 0.006 21.1 5.7 51 27-78 351-401 (415)
321 PF03457 HA: Helicase associat 25.9 1E+02 0.0022 16.4 2.7 45 31-81 11-55 (68)
322 TIGR03826 YvyF flagellar opero 25.8 84 0.0018 20.0 2.6 27 48-74 47-73 (137)
323 PF05269 Phage_CII: Bacterioph 25.7 1.1E+02 0.0025 18.1 3.0 25 50-74 26-50 (91)
324 PRK00767 transcriptional regul 25.7 1.4E+02 0.003 19.0 3.7 41 32-73 15-55 (197)
325 PF04539 Sigma70_r3: Sigma-70 24.5 1.1E+02 0.0024 16.6 2.7 22 49-70 22-43 (78)
326 PHA00542 putative Cro-like pro 24.5 78 0.0017 17.9 2.1 23 49-71 33-55 (82)
327 PRK10668 DNA-binding transcrip 24.3 1.1E+02 0.0024 19.9 3.1 43 31-74 16-58 (215)
328 PF06163 DUF977: Bacterial pro 24.1 2E+02 0.0043 18.2 4.1 43 25-70 3-49 (127)
329 PRK09958 DNA-binding transcrip 24.1 1.9E+02 0.0042 18.1 5.3 45 25-75 142-186 (204)
330 PRK07921 RNA polymerase sigma 24.0 2.9E+02 0.0062 20.0 5.4 52 26-78 262-313 (324)
331 cd04769 HTH_MerR2 Helix-Turn-H 23.8 99 0.0021 18.6 2.6 20 51-70 4-23 (116)
332 PRK09390 fixJ response regulat 23.6 1.9E+02 0.004 17.7 5.3 28 50-77 159-186 (202)
333 cd04777 HTH_MerR-like_sg1 Heli 23.5 87 0.0019 18.5 2.3 19 51-69 4-22 (107)
334 PF05263 DUF722: Protein of un 23.4 2E+02 0.0044 18.1 5.4 44 27-73 82-125 (130)
335 PF13412 HTH_24: Winged helix- 23.3 1.1E+02 0.0024 15.0 4.6 37 29-69 3-39 (48)
336 PF11516 DUF3220: Protein of u 23.0 53 0.0011 19.1 1.2 12 62-73 31-42 (106)
337 PRK12373 NADH dehydrogenase su 22.9 2.2E+02 0.0049 21.5 4.7 34 32-65 40-73 (400)
338 PF12802 MarR_2: MarR family; 22.9 1.2E+02 0.0027 15.4 2.9 40 27-68 3-42 (62)
339 PF00356 LacI: Bacterial regul 22.9 1.2E+02 0.0025 15.4 2.4 22 50-71 2-23 (46)
340 PRK13749 transcriptional regul 22.8 92 0.002 19.3 2.3 19 50-68 6-24 (121)
341 PF00249 Myb_DNA-binding: Myb- 22.7 1.2E+02 0.0025 15.0 5.0 44 24-70 1-46 (48)
342 PRK15002 redox-sensitivie tran 22.6 88 0.0019 20.2 2.3 21 50-70 14-34 (154)
343 PF00165 HTH_AraC: Bacterial r 22.4 1.1E+02 0.0024 14.6 3.0 24 46-69 7-30 (42)
344 PRK09483 response regulator; P 22.2 2.2E+02 0.0047 18.0 5.7 45 25-75 147-191 (217)
345 smart00595 MADF subfamily of S 21.9 1.6E+02 0.0035 16.4 3.7 28 51-78 31-58 (89)
346 PF13022 HTH_Tnp_1_2: Helix-tu 21.8 1.1E+02 0.0024 19.7 2.6 23 47-69 34-56 (142)
347 PHA01083 hypothetical protein 21.8 96 0.0021 20.2 2.3 21 50-70 19-39 (149)
348 TIGR03384 betaine_BetI transcr 21.6 1.5E+02 0.0031 18.7 3.2 41 32-73 14-54 (189)
349 PF08822 DUF1804: Protein of u 21.4 2.5E+02 0.0054 18.6 4.2 40 28-71 4-43 (165)
350 TIGR03830 CxxCG_CxxCG_HTH puta 21.2 1.2E+02 0.0026 18.1 2.6 21 51-71 82-102 (127)
351 COG1476 Predicted transcriptio 21.1 1.4E+02 0.0029 16.8 2.5 20 49-68 16-35 (68)
352 PRK09210 RNA polymerase sigma 20.6 3.5E+02 0.0077 19.8 5.4 51 26-77 305-355 (367)
353 PF05703 Auxin_canalis: Auxin 20.6 1.9E+02 0.0041 20.4 3.7 15 60-74 99-113 (242)
354 PRK13752 putative transcriptio 20.4 1E+02 0.0022 19.5 2.2 21 49-69 9-29 (144)
355 COG4197 Uncharacterized protei 20.3 86 0.0019 18.8 1.7 21 52-72 17-37 (96)
356 PF08880 QLQ: QLQ; InterPro: 20.2 1.2E+02 0.0026 14.7 2.0 14 25-38 1-14 (37)
357 PRK00215 LexA repressor; Valid 20.2 2E+02 0.0043 18.9 3.7 46 27-74 2-51 (205)
No 1
>KOG0488|consensus
Probab=99.78 E-value=2.3e-19 Score=127.14 Aligned_cols=66 Identities=42% Similarity=0.708 Sum_probs=61.6
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
.+|+++.|+.||..|+..||+.|+...|++..+|++||..|||+..||++||||||+|||+.....
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 366677899999999999999999999999999999999999999999999999999999977663
No 2
>KOG0842|consensus
Probab=99.78 E-value=6.1e-20 Score=129.03 Aligned_cols=73 Identities=36% Similarity=0.602 Sum_probs=65.7
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhc
Q psy16797 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYK 88 (99)
Q Consensus 16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~ 88 (99)
...++||.|..||..|..+||+.|..+.|++..+|+.||..|+||+.||+|||||+|-|.||...........
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~ 221 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALL 221 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhccc
Confidence 3557777889999999999999999999999999999999999999999999999999999988776654433
No 3
>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=99.78 E-value=1.5e-18 Score=95.00 Aligned_cols=57 Identities=54% Similarity=0.809 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
++.|+.|+.+|+..|+.+|..++||+..++..||..+||+..+|.+||+|+|.++|+
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 468899999999999999999999999999999999999999999999999999885
No 4
>KOG0494|consensus
Probab=99.77 E-value=5.2e-19 Score=121.22 Aligned_cols=75 Identities=35% Similarity=0.438 Sum_probs=71.4
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhccccCCCcCC
Q psy16797 23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHYTTHSHL 97 (99)
Q Consensus 23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~~~~~~~ 97 (99)
.|+.||..|+..||+.|++.+||+...|+.||..+.|.+..|++||||||+||||.++.++.......|+..+.|
T Consensus 144 ~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyglyGam 218 (332)
T KOG0494|consen 144 FRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYGLYGAM 218 (332)
T ss_pred ccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhcccchh
Confidence 499999999999999999999999999999999999999999999999999999999999999988888887755
No 5
>KOG0489|consensus
Probab=99.77 E-value=5.2e-19 Score=122.97 Aligned_cols=68 Identities=54% Similarity=0.800 Sum_probs=63.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL 85 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~ 85 (99)
++.+|.|+.||..|+..||+.|..|.|++...|.+||..|.|+++||+|||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45788999999999999999999999999999999999999999999999999999999988776655
No 6
>KOG0484|consensus
Probab=99.76 E-value=4.5e-19 Score=106.69 Aligned_cols=73 Identities=40% Similarity=0.634 Sum_probs=65.6
Q ss_pred hhhhhhhccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 7 YLDDSLIADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 7 ~~~~~~~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
+-++...+..+++.+|-|+.|+..|+..|+..|-+.+||++..|++||..+.|++..|++||||||+|.++..
T Consensus 4 ~~~~~~~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 4 YGDDPLGLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred cCCCCCChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 3345555666778888999999999999999999999999999999999999999999999999999998864
No 7
>KOG0487|consensus
Probab=99.75 E-value=6.8e-19 Score=123.81 Aligned_cols=68 Identities=49% Similarity=0.721 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL 85 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~ 85 (99)
+..||+|+.+|+.|+..||+.|-.|.|++.+.|.+|+..|+||++||+|||||||.|+||+..+....
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 56678899999999999999999999999999999999999999999999999999999998654443
No 8
>KOG0850|consensus
Probab=99.74 E-value=2e-18 Score=116.36 Aligned_cols=64 Identities=47% Similarity=0.684 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
+|-|+.||-++..||..|+..|+.++|+.-.+|.+||..|||+..||+|||||||.|.||..+.
T Consensus 120 KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 120 KKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred ccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 3445689999999999999999999999999999999999999999999999999999998873
No 9
>KOG0843|consensus
Probab=99.74 E-value=2.5e-18 Score=112.28 Aligned_cols=63 Identities=49% Similarity=0.796 Sum_probs=60.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
+-+|.||.|+.+|+..||..|+.++|-...+|..||..|+|++.||+|||||||.|.||....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 667789999999999999999999999999999999999999999999999999999998766
No 10
>KOG0485|consensus
Probab=99.73 E-value=2e-18 Score=115.78 Aligned_cols=74 Identities=36% Similarity=0.544 Sum_probs=65.2
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcc
Q psy16797 16 EKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKL 89 (99)
Q Consensus 16 ~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~ 89 (99)
.+.+|+|.|++|+..|+..||..|+...|++..+|..||.+|.|++.||++||||||.||||............
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~sl~ 173 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAASLH 173 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhhcc
Confidence 44578889999999999999999999999999999999999999999999999999999999765544333333
No 11
>KOG2251|consensus
Probab=99.68 E-value=3.5e-17 Score=109.82 Aligned_cols=68 Identities=34% Similarity=0.564 Sum_probs=63.6
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
...++.+|.||.|+-.|+++||..|.+..||+...+++||..|+|.+.+|+|||+|||+|+|+.+..+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 45677788999999999999999999999999999999999999999999999999999999987754
No 12
>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=99.67 E-value=4.5e-16 Score=85.25 Aligned_cols=57 Identities=58% Similarity=0.873 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+.+..++..++..|+.+|..++||+..++..||..+||+..+|++||+|+|.+.++.
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 567789999999999999999999999999999999999999999999999998763
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.67 E-value=3e-16 Score=85.33 Aligned_cols=55 Identities=55% Similarity=0.848 Sum_probs=51.6
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
+.|+.+++.++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
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 5677899999999999999999999999999999999999999999999998753
No 14
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.67 E-value=1.1e-16 Score=103.67 Aligned_cols=71 Identities=34% Similarity=0.505 Sum_probs=63.9
Q ss_pred hccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797 13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED 83 (99)
Q Consensus 13 ~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~ 83 (99)
..+.+...+++|.+.+..|+.+|+..|..++||+...+..|+..++|+++.|++||||+|++.|+......
T Consensus 44 ~~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 44 KQDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred cccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 34566677788999999999999999999999999999999999999999999999999999988766533
No 15
>KOG0492|consensus
Probab=99.66 E-value=1e-16 Score=106.88 Aligned_cols=63 Identities=44% Similarity=0.777 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
+.-|+.|+.||..|+..||+-|...+|++++++.+++..|.|++.||+|||||||+|.||-+.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 344568999999999999999999999999999999999999999999999999999988653
No 16
>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=99.65 E-value=1.4e-16 Score=87.51 Aligned_cols=53 Identities=23% Similarity=0.463 Sum_probs=50.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 20 KKRARTAYTSNQLLALEKEFNQQNY----ILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~~~~~----p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
++|.||.||.+|+..|+.+|..++| |+...+.+||..+||+..+|++||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999965
No 17
>KOG0493|consensus
Probab=99.64 E-value=5.2e-16 Score=106.72 Aligned_cols=67 Identities=48% Similarity=0.773 Sum_probs=60.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhh
Q psy16797 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEY 87 (99)
Q Consensus 21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~ 87 (99)
+|.|+.|+.+|+..|...|+.|.|++...|.+||.+|+|.+.||+|||||+|+|.||.........+
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~ 313 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLAL 313 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhh
Confidence 4679999999999999999999999999999999999999999999999999999997766555443
No 18
>KOG3802|consensus
Probab=99.62 E-value=2.1e-16 Score=113.63 Aligned_cols=78 Identities=27% Similarity=0.409 Sum_probs=68.4
Q ss_pred hhhhhhhhhhhc------------cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 3 RVQKYLDDSLIA------------DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 3 ~~~~~~~~~~~~------------~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
.+.+|+++.... ....+|||+||.|.......||.+|.+|+.|+..++..||.+|+|....|+|||||
T Consensus 265 LL~KWLeEAes~~~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCN 344 (398)
T KOG3802|consen 265 LLEKWLEEAESRESTGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCN 344 (398)
T ss_pred HHHHHHHHHhcccccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeec
Confidence 456677665551 23346788999999999999999999999999999999999999999999999999
Q ss_pred HHhHHhhcCC
Q psy16797 71 RRMKKKKGKT 80 (99)
Q Consensus 71 rR~k~kr~~~ 80 (99)
||.|.||...
T Consensus 345 RRQkeKR~~~ 354 (398)
T KOG3802|consen 345 RRQKEKRITP 354 (398)
T ss_pred cccccccCCC
Confidence 9999999877
No 19
>KOG0483|consensus
Probab=99.62 E-value=2.9e-16 Score=105.00 Aligned_cols=72 Identities=35% Similarity=0.500 Sum_probs=64.4
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcccc
Q psy16797 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHY 91 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~ 91 (99)
..+++.+++.+|...|+..|..+.++.+..+..||..|||.++||.+||||||++||.++...+...+...+
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~ 121 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL 121 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence 344566799999999999999999999999999999999999999999999999999999888776665544
No 20
>KOG0491|consensus
Probab=99.61 E-value=4.2e-16 Score=100.72 Aligned_cols=64 Identities=45% Similarity=0.786 Sum_probs=59.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED 83 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~ 83 (99)
+++.|++|+..|+..|++.|+...|++..++.+||..|+|++.||+.||||+|.|.||......
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4567999999999999999999999999999999999999999999999999999999776544
No 21
>KOG0848|consensus
Probab=99.58 E-value=6.3e-16 Score=106.43 Aligned_cols=60 Identities=48% Similarity=0.781 Sum_probs=56.1
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
=|.++|..|..+||+.|..++|.++..+-+||.-|||+++||+|||||||+|+||..+..
T Consensus 202 YRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 202 YRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 477899999999999999999999999999999999999999999999999999877654
No 22
>KOG0486|consensus
Probab=99.52 E-value=3.9e-15 Score=104.37 Aligned_cols=73 Identities=33% Similarity=0.503 Sum_probs=64.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCchhhcccc
Q psy16797 19 GKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNLEYKLHY 91 (99)
Q Consensus 19 ~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~~~~~~~ 91 (99)
|++|.|+.|+..|+..||..|..|.||+...+++||...++++..|++||.|||+||++++.-+.....+..+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f 183 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGF 183 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCC
Confidence 4566899999999999999999999999999999999999999999999999999999988766633344433
No 23
>KOG0847|consensus
Probab=99.50 E-value=1.7e-14 Score=97.16 Aligned_cols=66 Identities=42% Similarity=0.740 Sum_probs=60.8
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+++++-.|..|+..|+..|+..|+...|+..+++.++|..+|++..+|++||||||+|||++..
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 345667778899999999999999999999999999999999999999999999999999999753
No 24
>KOG4577|consensus
Probab=99.47 E-value=5e-14 Score=98.18 Aligned_cols=71 Identities=35% Similarity=0.494 Sum_probs=64.8
Q ss_pred hccccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797 13 IADEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED 83 (99)
Q Consensus 13 ~~~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~ 83 (99)
..+++...+|.|+.+|..|++.|...|+..+.|....|+.|+.++||..+.|++||||||+|+||-++..+
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 34567788899999999999999999999999999999999999999999999999999999998766544
No 25
>KOG0844|consensus
Probab=99.33 E-value=2.9e-13 Score=95.05 Aligned_cols=64 Identities=50% Similarity=0.800 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
..-+|=|+.||-+|+..||+.|....|-+...|.+||..|+|.+..|++||||||.|+||+..-
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3446678999999999999999999999999999999999999999999999999999997643
No 26
>KOG0490|consensus
Probab=99.29 E-value=2.1e-12 Score=87.51 Aligned_cols=64 Identities=38% Similarity=0.460 Sum_probs=60.1
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..++++.|+.|+..|++.|+..|+..+||+...++.+|..+++++..|++||||+|+++++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4567789999999999999999999999999999999999999999999999999999998774
No 27
>KOG0775|consensus
Probab=99.21 E-value=3.5e-11 Score=83.35 Aligned_cols=54 Identities=22% Similarity=0.409 Sum_probs=48.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
|...-...|..+|..++||++.++.+||..+||+..||.+||+|||+++|....
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 555567899999999999999999999999999999999999999999995544
No 28
>KOG0849|consensus
Probab=99.19 E-value=2.6e-11 Score=87.67 Aligned_cols=66 Identities=38% Similarity=0.603 Sum_probs=60.4
Q ss_pred cccCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 15 DEKKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 15 ~~~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
...++.++.|+.|+..|++.|+..|..++||+...++.||..++++...|.+||+|+|+++++...
T Consensus 171 ~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 171 ALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 344556677899999999999999999999999999999999999999999999999999999773
No 29
>KOG1168|consensus
Probab=99.14 E-value=4.4e-12 Score=88.62 Aligned_cols=63 Identities=32% Similarity=0.427 Sum_probs=58.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
-+.++|+|+.+-..+...||.+|...+.|+.+.+..||+.|.|....|++||+|.|+|.||+.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 345678899999999999999999999999999999999999999999999999999998854
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=99.01 E-value=6.8e-10 Score=56.67 Aligned_cols=35 Identities=31% Similarity=0.568 Sum_probs=29.4
Q ss_pred hhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 40 NQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 40 ~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
..+|||+.+++..||..+|++..||..||-|.|.+
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 35799999999999999999999999999999864
No 31
>KOG2252|consensus
Probab=98.96 E-value=3.6e-09 Score=79.21 Aligned_cols=58 Identities=22% Similarity=0.306 Sum_probs=54.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 18 KGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 18 ~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
-+.+|.|.+|+..|.+-|...|+.+++|+.+..+.|+..|+|....|.+||.|.|.+.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3456679999999999999999999999999999999999999999999999999875
No 32
>KOG0774|consensus
Probab=98.85 E-value=1.3e-09 Score=75.42 Aligned_cols=60 Identities=27% Similarity=0.483 Sum_probs=54.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 20 KKRARTAYTSNQLLALEKEFN---QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~---~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
.+|+|..|++...++|..+|. .|+||+.+.+++||.+++++..||.+||.|+|-+.++-.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 456778899999999999995 689999999999999999999999999999998877744
No 33
>KOG0490|consensus
Probab=98.27 E-value=1.2e-06 Score=59.30 Aligned_cols=64 Identities=45% Similarity=0.620 Sum_probs=58.7
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 17 KKGKKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 17 ~~~~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+.++.++.+...++..+...|...++|+...+..|+..+|++...+++||+|+|.+.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 4556678899999999999999999999999999999999999999999999999999988655
No 34
>KOG1146|consensus
Probab=98.02 E-value=7.8e-06 Score=66.74 Aligned_cols=63 Identities=29% Similarity=0.385 Sum_probs=58.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
++..|+.++..|+..+...|....||...+.+.+...+++..+.|.+||+|.|.+.++.....
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 345789999999999999999999999999999999999999999999999999999877744
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.94 E-value=1.8e-05 Score=42.96 Aligned_cols=41 Identities=17% Similarity=0.396 Sum_probs=31.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
+..|+.+|...+++.......|....+|+..+|+.||-.+.
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 36
>KOG0773|consensus
Probab=97.42 E-value=9.4e-05 Score=53.27 Aligned_cols=57 Identities=25% Similarity=0.347 Sum_probs=47.5
Q ss_pred CCCCCCCCCHHHHHHHHHH-Hh--hcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 20 KKRARTAYTSNQLLALEKE-FN--QQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~-f~--~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
+.+.+..+.+....+|..+ |. ..+||+..++..|+.++|++..||.+||.|.|.+.-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w 298 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLW 298 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccC
Confidence 4455667888888888877 33 368999999999999999999999999999997643
No 37
>KOG3623|consensus
Probab=96.51 E-value=0.01 Score=47.01 Aligned_cols=48 Identities=13% Similarity=0.231 Sum_probs=44.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+|..+|..|..|+..+...+|.+.|+....|+.||.+.++......
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 678999999999999999999999999999999999999999877655
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.80 E-value=0.045 Score=29.17 Aligned_cols=47 Identities=19% Similarity=0.408 Sum_probs=34.1
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
++.|..+|-++...+-..++... ....||..+|++..+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46778899998777777777655 477899999999999999998854
No 39
>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=93.90 E-value=0.4 Score=24.72 Aligned_cols=46 Identities=7% Similarity=0.145 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
.+++.+..++...|.. .....++|..+|++...|+.+...-..+.|
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 4678888999988832 234677899999999999999887766655
No 40
>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=89.84 E-value=1.9 Score=22.99 Aligned_cols=43 Identities=19% Similarity=0.264 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 27 YTSNQLLALEKEFNQQNY--ILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~--p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
+|+.|..+|...|...-| |-.....+||..+|++...+..-..
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 478899999999886544 6667778899999999998876553
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=89.57 E-value=0.71 Score=25.62 Aligned_cols=47 Identities=19% Similarity=0.345 Sum_probs=29.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 22 RARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 22 r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
+.|..||+++...+-..+.. .......+|..+|+++.++..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence 35677999986655555421 225577889999999999999986544
No 42
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=89.05 E-value=0.44 Score=26.20 Aligned_cols=22 Identities=27% Similarity=0.543 Sum_probs=18.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqN 70 (99)
.-..||..||+++.+|+.|=..
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~~ 45 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKSR 45 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhhh
Confidence 3567899999999999999643
No 43
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=88.39 E-value=1.7 Score=21.57 Aligned_cols=43 Identities=9% Similarity=0.149 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
+++.+..++...|... .....+|..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5666777776666322 235667999999999999999765544
No 44
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=87.34 E-value=4.5 Score=25.93 Aligned_cols=50 Identities=14% Similarity=0.141 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+++.|..+|...+. . ....++|..+|++...|..|..+.+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr~~--G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLRER--G----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35688999999977432 2 33568999999999999999998888766643
No 45
>PRK10072 putative transcriptional regulator; Provisional
Probab=85.48 E-value=2.8 Score=25.07 Aligned_cols=40 Identities=20% Similarity=0.245 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
+.+...+..|...-.. ...++|..+|++...|..|...++
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 4566666666544322 257789999999999999998665
No 46
>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=84.95 E-value=4.6 Score=22.03 Aligned_cols=46 Identities=24% Similarity=0.414 Sum_probs=23.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
|..|+.......-.+|....---...|. .|..+|++..+|+-|-+-
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHTT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHHH
Confidence 4567777644444444433322223333 499999999999999853
No 47
>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=84.94 E-value=4.1 Score=21.47 Aligned_cols=45 Identities=20% Similarity=0.197 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
.+|+.+..+|.-...- ....++|..+|+++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 5788888888776543 33678999999999999999988776654
No 48
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=84.82 E-value=4.4 Score=24.92 Aligned_cols=45 Identities=13% Similarity=0.242 Sum_probs=30.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797 23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNr 71 (99)
.+.+++.++....-.....+. .....+|..+|+++.+|..|..--
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 356688887554433333333 235678999999999999997543
No 49
>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=84.67 E-value=3.9 Score=21.05 Aligned_cols=43 Identities=19% Similarity=0.185 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
+++.+..++...|-. .-...++|..+|++...|+.|....+.+
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 455555555555432 3456789999999999999999876643
No 50
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=82.54 E-value=9.3 Score=23.71 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+||..+|++...|+.+...-+.+.|+
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 36788999999999999999887777665
No 51
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=82.02 E-value=4.5 Score=20.38 Aligned_cols=40 Identities=15% Similarity=0.150 Sum_probs=21.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
..+|..+...++..+.. .....+||..+|++...|..+..
T Consensus 3 ~~Lt~~eR~~I~~l~~~-----G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ-----GMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc-----CCCHHHHHHHHCcCcHHHHHHHh
Confidence 35777887888777653 24466799999999999998875
No 52
>PF13518 HTH_28: Helix-turn-helix domain
Probab=81.17 E-value=2.9 Score=21.22 Aligned_cols=25 Identities=16% Similarity=0.453 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
...++|..+|++..+|..|.+.-+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHh
Confidence 3556899999999999999975443
No 53
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=81.05 E-value=2.2 Score=21.65 Aligned_cols=23 Identities=17% Similarity=0.397 Sum_probs=17.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHH
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqN 70 (99)
....++|..+|++...|..|...
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 44677899999999999999854
No 54
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=80.78 E-value=6.1 Score=26.60 Aligned_cols=44 Identities=25% Similarity=0.330 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQN--YILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~--~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
.+|+.|+.+|...|...= +|-......||..+|+++..+..-.+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehLR 200 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHLR 200 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHHH
Confidence 699999999999998654 37777778899999999988766443
No 55
>KOG0773|consensus
Probab=79.99 E-value=4.3 Score=29.28 Aligned_cols=48 Identities=27% Similarity=0.301 Sum_probs=39.6
Q ss_pred HHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 34 ALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 34 ~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
.+...-..++|++......++....++..++.+||-|.+.+.+.....
T Consensus 111 ~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 111 AWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred cchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 344455678999999999999999999999999999999887765443
No 56
>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=79.70 E-value=1.3 Score=25.29 Aligned_cols=25 Identities=16% Similarity=0.286 Sum_probs=20.8
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 46 LRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 46 ~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
..-...+||..+|++...|+.|+.+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3345678999999999999999964
No 57
>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=79.64 E-value=2.9 Score=20.88 Aligned_cols=22 Identities=14% Similarity=0.119 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..+|+++..|+.|..+-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999997543
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=78.70 E-value=9.7 Score=25.25 Aligned_cols=33 Identities=24% Similarity=0.152 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
....+||..+|++...|+++....+.+.++...
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 345678999999999999999988888777553
No 59
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=77.71 E-value=10 Score=23.79 Aligned_cols=31 Identities=13% Similarity=0.079 Sum_probs=26.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..++|..+|++...|++.+...|.+.|....
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999988888877543
No 60
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=77.58 E-value=8.3 Score=24.93 Aligned_cols=36 Identities=6% Similarity=0.034 Sum_probs=29.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN 84 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~ 84 (99)
...+||..+|++...|+.+...-|.+.++.....+.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 181 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLADLPG 181 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhccc
Confidence 356789999999999999999999888886655443
No 61
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=77.31 E-value=5.7 Score=25.50 Aligned_cols=30 Identities=13% Similarity=0.347 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+||..+|++...|+++...-|.+.|..
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888887764
No 62
>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=76.87 E-value=3.5 Score=22.29 Aligned_cols=20 Identities=20% Similarity=0.404 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
..+||..||++...|..|-.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56789999999999999986
No 63
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=76.44 E-value=12 Score=24.41 Aligned_cols=31 Identities=10% Similarity=0.146 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|++...|+++....|.+.+...
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 3567899999999999999998888877654
No 64
>PRK04217 hypothetical protein; Provisional
Probab=76.07 E-value=15 Score=22.48 Aligned_cols=51 Identities=12% Similarity=0.004 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
-..++..+..++...|...- ...+||..+|++...|...+...+.+.+...
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 44578888887776664322 4667999999999999999988888776644
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=75.32 E-value=7.8 Score=24.43 Aligned_cols=29 Identities=14% Similarity=0.163 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+||..+|++...|..|...-+.+.++
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999888877765
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=75.12 E-value=15 Score=23.18 Aligned_cols=47 Identities=6% Similarity=-0.077 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|- ......++|..+|++...|+.|...-+.+.++.
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44555555544432 122355789999999999999998777777653
No 67
>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=75.06 E-value=9.4 Score=22.96 Aligned_cols=46 Identities=13% Similarity=0.128 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
+++.+..++...|- ......++|..+|+++..|..+...-+.+.++
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555544332 12345678999999999999999887777664
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=74.46 E-value=15 Score=23.58 Aligned_cols=31 Identities=10% Similarity=0.102 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|++...|+.++...+.+.+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999998888877643
No 69
>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=74.42 E-value=18 Score=22.47 Aligned_cols=30 Identities=13% Similarity=0.140 Sum_probs=24.7
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
....++|..+|++...|.++...-|.+.+.
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 345678999999999999999877777664
No 70
>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=73.45 E-value=4.4 Score=19.90 Aligned_cols=19 Identities=21% Similarity=0.385 Sum_probs=15.3
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|=.
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4679999999999999964
No 71
>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=73.14 E-value=6 Score=19.27 Aligned_cols=23 Identities=13% Similarity=0.419 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR 72 (99)
..++|..+|++...|..|..+..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35689999999999999997644
No 72
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=73.09 E-value=20 Score=22.52 Aligned_cols=30 Identities=17% Similarity=0.191 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+||..+|++...|+.+...-+.+.|..
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888777764
No 73
>PRK00118 putative DNA-binding protein; Validated
Probab=72.93 E-value=18 Score=21.91 Aligned_cols=48 Identities=13% Similarity=0.069 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
+++.+..++...|... ....+||..+|++...|..|....+.+.+...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4566666665554432 23556899999999999999988887766643
No 74
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=72.37 E-value=19 Score=23.41 Aligned_cols=29 Identities=10% Similarity=0.313 Sum_probs=25.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..++|..+|+++..|+++....|.+.|..
T Consensus 153 ~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 153 SEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999999888877764
No 75
>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=71.71 E-value=22 Score=22.75 Aligned_cols=29 Identities=14% Similarity=0.101 Sum_probs=24.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..++|..+|++...|++.....|.+.++.
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999888877653
No 76
>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=71.65 E-value=7.6 Score=16.98 Aligned_cols=37 Identities=11% Similarity=0.209 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
++......+...|.. .. ....++..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 556666666566653 22 35577899999999988873
No 77
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=70.72 E-value=21 Score=23.03 Aligned_cols=30 Identities=3% Similarity=0.054 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+||..+|++...|+.+...-+.+.++.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888777653
No 78
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=70.60 E-value=5.2 Score=21.58 Aligned_cols=19 Identities=16% Similarity=0.335 Sum_probs=16.8
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
.++|..+|++...|+.|=.
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999964
No 79
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=70.07 E-value=23 Score=22.34 Aligned_cols=31 Identities=13% Similarity=-0.042 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|+++..|+++...-|.+.+...
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999998888777644
No 80
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=69.36 E-value=23 Score=22.78 Aligned_cols=30 Identities=13% Similarity=0.258 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...++|..+|++...|+++....+.+.+..
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 356789999999999999999888777654
No 81
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=69.18 E-value=25 Score=22.01 Aligned_cols=29 Identities=21% Similarity=0.210 Sum_probs=24.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..++|..+|++...|+.+...-|.+.++.
T Consensus 131 ~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 131 YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999998888777654
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=69.07 E-value=7 Score=21.09 Aligned_cols=20 Identities=0% Similarity=0.225 Sum_probs=17.5
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|+++..++.|-..
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999864
No 83
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=69.00 E-value=23 Score=22.58 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....++|..+|++...|++++..-|.+.+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4456789999999999999999888877664
No 84
>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=68.53 E-value=25 Score=21.61 Aligned_cols=29 Identities=14% Similarity=0.281 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+||..+|++...|+.+...-+.+.++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999887777664
No 85
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=68.27 E-value=6.9 Score=21.22 Aligned_cols=20 Identities=10% Similarity=0.247 Sum_probs=17.5
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|+++..++.|...
T Consensus 4 ~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 4 GEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46899999999999999863
No 86
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=68.12 E-value=6.2 Score=20.86 Aligned_cols=23 Identities=9% Similarity=0.293 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNr 71 (99)
....||...|++...|..|+.++
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~ 34 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGK 34 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcc
Confidence 35678999999999999999876
No 87
>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=67.91 E-value=29 Score=22.14 Aligned_cols=32 Identities=25% Similarity=0.209 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
...+||..+|++...|+++...-|.+.+....
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999888887777543
No 88
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=67.90 E-value=27 Score=22.76 Aligned_cols=32 Identities=3% Similarity=-0.027 Sum_probs=27.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
..+||..+|++...|++++...|.+.++....
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~~ 186 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAALLAG 186 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 56789999999999999999888888875543
No 89
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=67.88 E-value=8 Score=24.60 Aligned_cols=36 Identities=17% Similarity=0.107 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 45 ILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 45 p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
.......++|..+|++...|++.+..-|.+.++...
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 333446789999999999999999988888877544
No 90
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=67.77 E-value=21 Score=24.08 Aligned_cols=31 Identities=16% Similarity=0.133 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
-...++|..+|++...|+.+....+.+.|+.
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467789999999999999998888777664
No 91
>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=67.54 E-value=30 Score=22.31 Aligned_cols=33 Identities=21% Similarity=0.101 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 46 LRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 46 ~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
......+||..+|++...|++.+..-|.+.+..
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 334466899999999999999998877776653
No 92
>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=67.53 E-value=9.9 Score=24.43 Aligned_cols=34 Identities=6% Similarity=-0.072 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 46 LRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 46 ~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
....-.+||..+|++...|+++...-|.+.+...
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3344568899999999999999998888877654
No 93
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=67.41 E-value=11 Score=24.53 Aligned_cols=32 Identities=16% Similarity=0.148 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 47 RAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 47 ~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.....+||..+|++...|+.++...+.+.++.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34456789999999999999999888877763
No 94
>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=67.38 E-value=4.4 Score=20.59 Aligned_cols=20 Identities=5% Similarity=0.192 Sum_probs=18.2
Q ss_pred HHHHHhCCChHHHHHHHHHH
Q psy16797 52 QLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 52 ~la~~l~l~~~~V~~WFqNr 71 (99)
.||..+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 47999999999999999876
No 95
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=67.28 E-value=16 Score=21.74 Aligned_cols=39 Identities=15% Similarity=0.196 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
++++|...-...|..|--.+.....++|..|++++..|+
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 566776666666655555555777889999999987655
No 96
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=67.21 E-value=30 Score=22.34 Aligned_cols=31 Identities=13% Similarity=0.068 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..++|..+|++...|++-...-|.+.+....
T Consensus 150 ~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 150 VEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999988888777533
No 97
>PRK06930 positive control sigma-like factor; Validated
Probab=67.13 E-value=30 Score=22.62 Aligned_cols=49 Identities=10% Similarity=0.034 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
.+++.+..++...|-.. ....++|..+|++...|+.+....+.+.++..
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45666666665543221 23567899999999999999998888877643
No 98
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=66.54 E-value=17 Score=24.58 Aligned_cols=31 Identities=6% Similarity=0.097 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...++|..+|++...|+.+....+.+.+...
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999998888877643
No 99
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=66.41 E-value=12 Score=23.66 Aligned_cols=33 Identities=18% Similarity=0.027 Sum_probs=27.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
....+||..+|++...|+++...-|.+.++...
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 335678999999999999999988888777543
No 100
>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=66.05 E-value=13 Score=23.05 Aligned_cols=34 Identities=24% Similarity=0.172 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 44 YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 44 ~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
|.......++|..+|+++..|+++...-+.+.+.
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3444556789999999999999999887777665
No 101
>KOG1146|consensus
Probab=65.79 E-value=14 Score=31.92 Aligned_cols=66 Identities=20% Similarity=0.277 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCch
Q psy16797 20 KKRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDNL 85 (99)
Q Consensus 20 ~~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~~ 85 (99)
.++.+..+-.++...|-.+|-.+.-|+......|....+.+.+.+.+||+|-+.+.++.....+..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~~ 770 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDVP 770 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCCC
Confidence 345567777899999999999999999999999999999999999999999999988876333333
No 102
>PRK09480 slmA division inhibitor protein; Provisional
Probab=65.20 E-value=10 Score=24.37 Aligned_cols=40 Identities=18% Similarity=0.193 Sum_probs=31.1
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 33 LALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 33 ~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
......|...+. .......||...|++...+-.+|.|+-.
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 333344555555 7788899999999999999999998763
No 103
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=64.93 E-value=20 Score=24.63 Aligned_cols=47 Identities=6% Similarity=0.109 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|- ......+||..+|++...|+.|...-+.+.|..
T Consensus 206 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44455555554442 122356789999999999999998888877654
No 104
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=64.80 E-value=31 Score=21.40 Aligned_cols=30 Identities=13% Similarity=0.062 Sum_probs=25.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..++|..+|++...|++....-+.+.+...
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999988887777643
No 105
>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=64.54 E-value=11 Score=20.10 Aligned_cols=20 Identities=10% Similarity=0.282 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
..++|..+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999985
No 106
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=64.51 E-value=31 Score=24.92 Aligned_cols=54 Identities=13% Similarity=0.129 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
.+++.+..+|...|.... .......+||..+|++...|+.+....+.+.|+...
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 355666666666553322 233456789999999999999999999988887553
No 107
>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=64.27 E-value=13 Score=24.16 Aligned_cols=34 Identities=9% Similarity=-0.006 Sum_probs=28.0
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 46 LRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 46 ~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
......+||..+|++...|+++...-|.+.++..
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3344568999999999999999998888887754
No 108
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=64.02 E-value=14 Score=24.22 Aligned_cols=35 Identities=11% Similarity=0.031 Sum_probs=28.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED 83 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~ 83 (99)
...++|..+|++...|++++..-|.+.|+......
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~~ 165 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQLEE 165 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhccc
Confidence 35678999999999999999999988887665433
No 109
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=63.91 E-value=38 Score=22.08 Aligned_cols=32 Identities=25% Similarity=0.185 Sum_probs=26.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
....+||..+|++...|++-+...|.+.++..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44567899999999999999988888877643
No 110
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=63.74 E-value=32 Score=22.31 Aligned_cols=32 Identities=31% Similarity=0.349 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
...+||..+|++...|++..+.-+.+.++...
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~ 180 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKL 180 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHccc
Confidence 35678999999999999999888888777553
No 111
>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=63.58 E-value=21 Score=18.97 Aligned_cols=37 Identities=38% Similarity=0.444 Sum_probs=27.6
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 30 ~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
.++..|+-.+. +...+. .+||..+|++.+.|+....+
T Consensus 6 rq~~Ll~~L~~-~~~~~~---~ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITL---KELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBH---HHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcH---HHHHHHHCCCHHHHHHHHHH
Confidence 46777777788 666654 38999999999999987654
No 112
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=62.80 E-value=38 Score=21.91 Aligned_cols=31 Identities=26% Similarity=0.243 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...++|..+|++...|+..+..-|.+.+...
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999988888777644
No 113
>PRK13870 transcriptional regulator TraR; Provisional
Probab=62.77 E-value=22 Score=24.36 Aligned_cols=48 Identities=4% Similarity=-0.040 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+|+.++++|.=.- ....-.+||..+|++++.|..-..|-+.|.--
T Consensus 171 ~~~LT~RE~E~L~W~A------~GKT~~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 171 AAWLDPKEATYLRWIA------VGKTMEEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred cCCCCHHHHHHHHHHH------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 3468888888874331 12334678999999999999999998877544
No 114
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=62.68 E-value=38 Score=21.69 Aligned_cols=31 Identities=13% Similarity=0.156 Sum_probs=26.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|++...|++....-+.+.++..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999998888877754
No 115
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=62.54 E-value=15 Score=23.86 Aligned_cols=35 Identities=11% Similarity=-0.015 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 45 ILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 45 p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
.......++|..+|++...|+++...-+.+.+...
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445678999999999999999988888877643
No 116
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=62.10 E-value=19 Score=17.91 Aligned_cols=44 Identities=18% Similarity=0.212 Sum_probs=30.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
.+++.+..++...+. . ....++|..+|++...|..|...-+.+.
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~kl 46 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMRKL 46 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 356777777655432 2 2457789999999999999987654443
No 117
>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=61.83 E-value=24 Score=23.65 Aligned_cols=47 Identities=13% Similarity=0.147 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|- ......++|..+|++...|+.+....+.+.|+.
T Consensus 176 L~~~~r~il~l~y~-----~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 176 LSEREQLVLSLYYY-----EELNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred CCHHHHHHHHHHHh-----CCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34444445544442 222357889999999999999998877777653
No 118
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=61.49 E-value=23 Score=22.70 Aligned_cols=30 Identities=17% Similarity=0.060 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+||..+|++...|+.+...-|.+.+..
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 346789999999999999998877776654
No 119
>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=61.19 E-value=42 Score=23.40 Aligned_cols=48 Identities=15% Similarity=0.045 Sum_probs=37.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+|+.+..+|.-... . ..-.+||..+|++...|+....|-+.|...
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 44689999999986542 2 335678999999999999999988776554
No 120
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=61.10 E-value=46 Score=22.59 Aligned_cols=49 Identities=14% Similarity=0.131 Sum_probs=38.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+|+.+..+|.-... ...-.++|..+|++...|+.+..|-+.|....
T Consensus 169 ~~~Lt~re~evl~~~a~------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL------GRRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred hccCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 44689999998877531 23456789999999999999999988776643
No 121
>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=61.09 E-value=27 Score=23.95 Aligned_cols=47 Identities=9% Similarity=0.160 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|.. .....+||..+|++...|+.+....+.+.|..
T Consensus 206 L~~~~r~ii~l~~~~-----g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 206 LSEREKSIIHCTFEE-----NLSQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred CCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 445555555555432 12346889999999999999998888777653
No 122
>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=60.83 E-value=41 Score=21.44 Aligned_cols=49 Identities=20% Similarity=0.201 Sum_probs=38.3
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.+.+++.|..++.-.+ .. ....++|..+|++...|..+-..-+.+.+..
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~a 52 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEKA 52 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHHH
Confidence 3568888988887742 22 2467899999999999999998888877753
No 123
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=60.64 E-value=24 Score=24.37 Aligned_cols=48 Identities=15% Similarity=0.035 Sum_probs=33.3
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 28 s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
++.+..++...|. ......+||..+|++...|+.+...-+.+.+....
T Consensus 205 ~~~~r~vl~l~y~-----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 205 EERTREVLEFVFL-----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CHHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 4444444444442 23345788999999999999999888888776543
No 124
>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=60.56 E-value=9.2 Score=19.53 Aligned_cols=22 Identities=18% Similarity=0.303 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..+|+++..|..|..+.
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~ 33 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGK 33 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTS
T ss_pred HHHHHHHhCCCcchhHHHhcCC
Confidence 4678999999999999999773
No 125
>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=60.22 E-value=39 Score=22.94 Aligned_cols=52 Identities=13% Similarity=0.118 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.+++.+..+|...|....+ ......+||..+|++...|+........+.|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 3566666677766633222 224477899999999999999999888887764
No 126
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=60.03 E-value=41 Score=21.23 Aligned_cols=31 Identities=16% Similarity=0.138 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+||..+|++...|+......+.+.++...
T Consensus 137 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 137 TAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 5678999999999999999888888776543
No 127
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=59.98 E-value=35 Score=23.25 Aligned_cols=32 Identities=6% Similarity=0.105 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
...+||..+|++...|++....-|.+.|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999988888877543
No 128
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=59.91 E-value=11 Score=20.59 Aligned_cols=18 Identities=28% Similarity=0.649 Sum_probs=15.3
Q ss_pred HHHHHHHhCCChHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIW 67 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~W 67 (99)
...||..||++...|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 129
>PF13551 HTH_29: Winged helix-turn helix
Probab=59.37 E-value=33 Score=19.88 Aligned_cols=47 Identities=13% Similarity=0.159 Sum_probs=30.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHH--hCCChHHHHHHHH
Q psy16797 23 ARTAYTSNQLLALEKEFNQQNY-----ILRAKRHQ-L-AKE--LNLCERQIKIWFQ 69 (99)
Q Consensus 23 ~r~~~s~~q~~~L~~~f~~~~~-----p~~~~~~~-l-a~~--l~l~~~~V~~WFq 69 (99)
.+..+++++...|...+..++. .+...... | ... +.++...|..|++
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3334899999999999987763 33333332 2 222 3588889988885
No 130
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=58.42 E-value=29 Score=23.80 Aligned_cols=30 Identities=23% Similarity=0.207 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...+||..+|++...|+..+...+.+.|..
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888777653
No 131
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=58.37 E-value=50 Score=21.70 Aligned_cols=35 Identities=11% Similarity=0.037 Sum_probs=28.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCCc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTPEDN 84 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~~ 84 (99)
..+||..+|++...|+++...-+.+.++.......
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~~~ 186 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLIAATATGQA 186 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccccc
Confidence 56789999999999999999888888876655443
No 132
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=58.36 E-value=20 Score=23.22 Aligned_cols=32 Identities=9% Similarity=0.140 Sum_probs=26.4
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 47 RAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 47 ~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.....+||..+|++...|+++...-+.+.+..
T Consensus 150 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 150 ELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999998888777663
No 133
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=58.27 E-value=44 Score=22.52 Aligned_cols=33 Identities=6% Similarity=-0.069 Sum_probs=27.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
...+||..+|++...|+.....-|.+.+.....
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 356789999999999999999888888876543
No 134
>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=58.06 E-value=21 Score=22.33 Aligned_cols=31 Identities=13% Similarity=0.132 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...++|..+|++...|+.+...-+.+.++..
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999998888877643
No 135
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=57.71 E-value=21 Score=22.98 Aligned_cols=30 Identities=13% Similarity=0.048 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...++|..+|++...|++.....|.+.+..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999999888887764
No 136
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=57.70 E-value=50 Score=21.44 Aligned_cols=32 Identities=9% Similarity=-0.037 Sum_probs=26.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
..+||..+|++...|+++...-|.+.++....
T Consensus 130 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~~ 161 (182)
T PRK12511 130 YQEAAAVLGIPIGTLMSRIGRARAALRAFEEG 161 (182)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 56789999999999999998888887775553
No 137
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=57.68 E-value=21 Score=23.27 Aligned_cols=30 Identities=3% Similarity=0.080 Sum_probs=25.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+||..+|++...|++.....|.+.|+..
T Consensus 155 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 155 SDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888777654
No 138
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=57.65 E-value=49 Score=21.29 Aligned_cols=32 Identities=9% Similarity=-0.027 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
....++|..+|++...|+.+...-+.+.++..
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999988888777643
No 139
>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=57.48 E-value=9.5 Score=25.27 Aligned_cols=33 Identities=15% Similarity=0.403 Sum_probs=27.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
....+|+.-++++..+|-.|..|-+...++...
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 456789999999999999999998887666543
No 140
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=57.42 E-value=56 Score=22.87 Aligned_cols=52 Identities=15% Similarity=0.121 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
+++.+..++...|.... .......+||..+|++...|+......+.+.|+..
T Consensus 223 Lp~~~R~Vl~l~ygL~~-~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 223 LNERQREVLARRFGLLG-YEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCHHHHHHHHHHhCCCC-CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44555555555442111 22244678899999999999999998888877744
No 141
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=57.38 E-value=40 Score=23.44 Aligned_cols=50 Identities=16% Similarity=0.127 Sum_probs=36.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.+++.+..+|..+|-. .......+||..+|++...|+....+...+.|+.
T Consensus 218 ~L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566666677776632 1123457899999999999999998888887764
No 142
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=57.37 E-value=50 Score=21.36 Aligned_cols=28 Identities=11% Similarity=-0.137 Sum_probs=24.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
..+||..+|++...|++....-|.+.++
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5678999999999999999888888777
No 143
>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=57.21 E-value=19 Score=17.48 Aligned_cols=22 Identities=9% Similarity=0.108 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..+|++...|..|....
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4567899999999999998654
No 144
>PF13730 HTH_36: Helix-turn-helix domain
Probab=57.15 E-value=26 Score=17.91 Aligned_cols=22 Identities=23% Similarity=0.421 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqN 70 (99)
....||..+|++.+.|..+...
T Consensus 27 S~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4678899999999999988754
No 145
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=57.13 E-value=20 Score=23.10 Aligned_cols=33 Identities=9% Similarity=0.178 Sum_probs=27.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
..+||..+|++...|++.....|.+.+......
T Consensus 141 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~~ 173 (185)
T PRK12542 141 YQEISSVMGITEANVRKQFERARKRVQNMIGGI 173 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHccc
Confidence 467899999999999999998888887755443
No 146
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=57.06 E-value=58 Score=21.98 Aligned_cols=46 Identities=22% Similarity=0.146 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+|+.+..+|.-... . ..-.++|..+++++..|+.+..+-..|..-
T Consensus 155 ~Lt~rE~~Vl~l~~~--G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRI--G----ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 489999999988765 2 225678999999999999999887766543
No 147
>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=56.99 E-value=36 Score=22.77 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..++...|- ......++|..+|++...|..|...-+.+.++
T Consensus 178 ~L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345555555555442 22346678999999999999999877777664
No 148
>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=56.99 E-value=46 Score=20.79 Aligned_cols=30 Identities=20% Similarity=0.100 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
....+||..+|++...|+....--|.+.|+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 335678999999999999998877777665
No 149
>PRK10403 transcriptional regulator NarP; Provisional
Probab=56.96 E-value=34 Score=21.58 Aligned_cols=46 Identities=24% Similarity=0.284 Sum_probs=35.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
..+|+.+..+|.....- ....+||..++++++.|+....|=+.|..
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 35889898888765432 33567899999999999999988776643
No 150
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=56.78 E-value=22 Score=23.03 Aligned_cols=31 Identities=10% Similarity=0.022 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...++|..+|++...|++....-|.+.|+..
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999988888777643
No 151
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=56.63 E-value=54 Score=21.53 Aligned_cols=31 Identities=13% Similarity=0.232 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|++...|++.....|.+.+...
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999998888877754
No 152
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=56.11 E-value=23 Score=22.52 Aligned_cols=29 Identities=10% Similarity=0.178 Sum_probs=24.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
-.++|..+|++...|+.....-+.+.++.
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 138 YKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998777776653
No 153
>PF12728 HTH_17: Helix-turn-helix domain
Probab=55.96 E-value=19 Score=18.16 Aligned_cols=22 Identities=14% Similarity=0.341 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..||++...|..|....
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567899999999999999643
No 154
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=55.76 E-value=23 Score=22.35 Aligned_cols=30 Identities=23% Similarity=0.269 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...++|..+|++...|++....-+.+.++.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888777664
No 155
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=55.13 E-value=24 Score=22.50 Aligned_cols=31 Identities=16% Similarity=0.177 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....++|..+|++...|++....-|.+.++.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999998888877653
No 156
>TIGR02984 Sig-70_plancto1 RNA polymerase sigma-70 factor, Planctomycetaceae-specific subfamily 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are apparently found only in the Planctomycetaceae family including the genuses Gemmata and Pirellula (in which seven sequences are found).
Probab=54.89 E-value=41 Score=21.44 Aligned_cols=31 Identities=6% Similarity=0.126 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....+||..+|++...|+.=...-|.+.++.
T Consensus 157 ~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 157 LSFAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999888777776653
No 157
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=54.81 E-value=64 Score=21.81 Aligned_cols=31 Identities=16% Similarity=0.135 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....+||..+|++...|+++...-+.+.|+.
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467789999999999999998877777664
No 158
>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=54.37 E-value=12 Score=18.91 Aligned_cols=22 Identities=18% Similarity=0.066 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
...+|..+|++...|..|..++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4678999999999999998654
No 159
>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=54.31 E-value=58 Score=21.15 Aligned_cols=31 Identities=10% Similarity=0.274 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...+||..+|++...|+.....-|.+.++..
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999988887776643
No 160
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=54.31 E-value=36 Score=23.68 Aligned_cols=47 Identities=9% Similarity=0.137 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..+|...|. ......+||..+|++...|+.+....+.+.+..
T Consensus 216 L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 216 LPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34444445555442 223457899999999999999998887777653
No 161
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=54.17 E-value=27 Score=22.24 Aligned_cols=31 Identities=6% Similarity=0.125 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
.-.+||..+|++...|+++....+.+.+...
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999988888776643
No 162
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=54.15 E-value=51 Score=20.52 Aligned_cols=29 Identities=14% Similarity=0.319 Sum_probs=24.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..++|..+|++...|+......+.+.++.
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999988777776654
No 163
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=53.99 E-value=37 Score=22.31 Aligned_cols=37 Identities=14% Similarity=0.126 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 29 SNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 29 ~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
..-+..|........|.+......+|..||++...|.
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 4557888888998999999999999999999997754
No 164
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=53.91 E-value=46 Score=19.87 Aligned_cols=45 Identities=16% Similarity=0.252 Sum_probs=32.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-ChHHHHHHHHHHH
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNL-CERQIKIWFQNRR 72 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l-~~~~V~~WFqNrR 72 (99)
+.+|+.+....+-..+-...+ ....+|..+|+ +..++..|-..-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHH
Confidence 677999986655555544443 56788999996 9999999986443
No 165
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=53.76 E-value=18 Score=19.32 Aligned_cols=19 Identities=16% Similarity=0.270 Sum_probs=16.6
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
.++|..+|+++..++.|-.
T Consensus 4 ~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4678999999999999974
No 166
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=53.71 E-value=37 Score=21.83 Aligned_cols=31 Identities=19% Similarity=0.199 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....++|..+|++...|++-...-|.+.+..
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 184 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLAKLKAC 184 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHHHHHHH
Confidence 3356789999999999999988877776653
No 167
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=53.69 E-value=26 Score=22.85 Aligned_cols=32 Identities=13% Similarity=-0.028 Sum_probs=26.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
..+||..+|++...|++....-+.+.++....
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 45789999999999999999888887775543
No 168
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=53.65 E-value=26 Score=22.67 Aligned_cols=31 Identities=13% Similarity=0.274 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+||..+|++...|++....-|.+.+....
T Consensus 150 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 150 TEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999988887776543
No 169
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=53.55 E-value=32 Score=20.98 Aligned_cols=40 Identities=15% Similarity=0.388 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
.+++.++..+...+... ....|..+|++...|+.|=++++
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~ 82 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRK 82 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCc
Confidence 37888888887776643 35679999999999999998765
No 170
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=53.54 E-value=57 Score=20.89 Aligned_cols=28 Identities=11% Similarity=0.254 Sum_probs=23.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
..+||..+|++...|+......+.+...
T Consensus 146 ~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 146 QKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999877776654
No 171
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=53.37 E-value=13 Score=26.33 Aligned_cols=25 Identities=24% Similarity=0.428 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
....||..+||++.+|+.|=+.-.+
T Consensus 21 k~~dIAeklGvspntiksWKrr~gW 45 (279)
T COG5484 21 KLKDIAEKLGVSPNTIKSWKRRDGW 45 (279)
T ss_pred cHHHHHHHhCCChHHHHHHHHhcCC
Confidence 3467899999999999999864433
No 172
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=52.78 E-value=66 Score=21.37 Aligned_cols=30 Identities=7% Similarity=0.304 Sum_probs=25.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+||..+|++...|++....-|.+.|+..
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888877643
No 173
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=52.67 E-value=27 Score=23.19 Aligned_cols=31 Identities=10% Similarity=0.141 Sum_probs=25.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+||..+|++...|+++...-|.+.++...
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999988887776443
No 174
>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=52.11 E-value=17 Score=17.40 Aligned_cols=22 Identities=18% Similarity=0.285 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3478999999999999998764
No 175
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=52.10 E-value=28 Score=22.03 Aligned_cols=34 Identities=21% Similarity=0.179 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 45 ILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 45 p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.......+||..+|++...|+.+...-+.+.++.
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 3445567899999999999999998888777663
No 176
>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=52.06 E-value=25 Score=24.29 Aligned_cols=30 Identities=7% Similarity=0.213 Sum_probs=25.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+||..+|++...|+++....|.+.+...
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999998888776654
No 177
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=51.88 E-value=58 Score=21.96 Aligned_cols=31 Identities=16% Similarity=0.116 Sum_probs=24.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....+||..+|++...|.++-...+.+.++.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4467889999999999999976666665553
No 178
>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=51.13 E-value=70 Score=22.33 Aligned_cols=30 Identities=10% Similarity=0.103 Sum_probs=25.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+||..+|++...|+..+..-|.+.+...
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 457899999999999999998888887643
No 179
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=51.07 E-value=66 Score=20.88 Aligned_cols=30 Identities=13% Similarity=0.124 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
...++|..+|++...|++-...-+.+.+..
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998888777764
No 180
>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=51.04 E-value=18 Score=21.35 Aligned_cols=21 Identities=14% Similarity=0.143 Sum_probs=17.8
Q ss_pred HHHHHHhCCChHHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqNr 71 (99)
.++|..+|+++..++.|..+-
T Consensus 4 ~eva~~~gvs~~tlR~ye~~G 24 (103)
T cd01106 4 GEVAKLTGVSVRTLHYYDEIG 24 (103)
T ss_pred HHHHHHHCcCHHHHHHHHHCC
Confidence 467999999999999998643
No 181
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=50.04 E-value=32 Score=22.43 Aligned_cols=30 Identities=17% Similarity=0.337 Sum_probs=24.0
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
....+||..+|+++..|+..+..-|...++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999988888765544
No 182
>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=49.96 E-value=19 Score=22.56 Aligned_cols=27 Identities=19% Similarity=0.359 Sum_probs=21.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
.++||..+|++...|.-|.....++.-
T Consensus 3 ~eELA~~tG~srQTINrWvRkegW~T~ 29 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVRKEGWKTE 29 (122)
T ss_pred HHHHHHHhCccHHHHHHHHHhcCceec
Confidence 367999999999999999975554433
No 183
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=49.35 E-value=56 Score=21.14 Aligned_cols=36 Identities=19% Similarity=0.248 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 30 ~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
.-+..|...=+...|.+.+....+|..+|+++..|.
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 446666666667789999999999999999998765
No 184
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=49.34 E-value=34 Score=22.00 Aligned_cols=33 Identities=15% Similarity=0.193 Sum_probs=27.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
.-.++|..+|++...|+.+....|.+.+.....
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~ 177 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLEE 177 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 346789999999999999999888888775543
No 185
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=49.29 E-value=53 Score=22.57 Aligned_cols=47 Identities=17% Similarity=0.224 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..++...|.. .....++|..+|++...|...-.+-..+.++
T Consensus 209 ~L~~~er~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQ-----GKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4666666677666632 2346789999999999999988777666654
No 186
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=49.03 E-value=29 Score=17.46 Aligned_cols=20 Identities=20% Similarity=0.337 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
...+|..+|++...|...|.
T Consensus 30 ~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56789999999999999985
No 187
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=49.01 E-value=43 Score=23.22 Aligned_cols=47 Identities=11% Similarity=0.123 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|.. .....++|..+|++...|+......+.+.++.
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 444444444444422 23356789999999999999988877776664
No 188
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=48.82 E-value=61 Score=22.92 Aligned_cols=51 Identities=12% Similarity=0.081 Sum_probs=36.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
.+++.+..+|...|- +-......+||..+|++...|+..-.....+.|...
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 356666666666652 113345688999999999999999988888877644
No 189
>PHA01976 helix-turn-helix protein
Probab=48.64 E-value=20 Score=19.09 Aligned_cols=22 Identities=9% Similarity=0.125 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..+|++...|..|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 4678999999999999998653
No 190
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=48.45 E-value=59 Score=20.49 Aligned_cols=46 Identities=15% Similarity=0.135 Sum_probs=35.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
..+++.+..+|.-...- ....+||..++++.+.|+.+..+-+.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35788888888654332 44678899999999999999988776653
No 191
>PLN03162 golden-2 like transcription factor; Provisional
Probab=48.36 E-value=92 Score=23.56 Aligned_cols=77 Identities=14% Similarity=0.113 Sum_probs=48.3
Q ss_pred hhhhhhhhhhhccccCCCCCCCCCCCHHH-HHHHHHHHhhc-CCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 3 RVQKYLDDSLIADEKKGKKRARTAYTSNQ-LLALEKEFNQQ-NYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 3 ~~~~~~~~~~~~~~~~~~~r~r~~~s~~q-~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
+..+..+...+......++|.|-+.|++- ...++...... ..-++..+.++-..-||+...|+.-.|--|...++..
T Consensus 216 r~~nq~s~~~~~~~~~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~ 294 (526)
T PLN03162 216 RKDNQASPKSCKNAAPGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLA 294 (526)
T ss_pred ccccCcCcccccccCCCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhccccc
Confidence 34444444444445556777888899885 34444445444 2244445566667779999999999887777655433
No 192
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=48.21 E-value=82 Score=22.03 Aligned_cols=30 Identities=10% Similarity=0.107 Sum_probs=25.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
..+||..+|++...|+...+..|.+.+...
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 457899999999999999998888887754
No 193
>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=48.07 E-value=22 Score=21.72 Aligned_cols=21 Identities=14% Similarity=0.415 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFq 69 (99)
...++|..++++...|..||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 355678999999999999998
No 194
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=48.07 E-value=72 Score=21.37 Aligned_cols=47 Identities=11% Similarity=0.101 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..++...|.. .....++|..+|++...|..+-..-..+.|.
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~ 229 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKKMKE 229 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3455555555555432 2346789999999999999887766665554
No 195
>PRK05572 sporulation sigma factor SigF; Validated
Probab=47.82 E-value=57 Score=22.34 Aligned_cols=47 Identities=13% Similarity=0.151 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..++...|.. .....+||..+|++...|..+-..-..+.++
T Consensus 202 ~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4566666666666532 2345789999999999999988877777665
No 196
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=47.47 E-value=55 Score=22.65 Aligned_cols=47 Identities=9% Similarity=0.092 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++...|. ......+||..+|++...|+.+...-+.+.++.
T Consensus 206 L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 206 LEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44444445555442 223457889999999999999988777776654
No 197
>KOG3623|consensus
Probab=47.27 E-value=9.6 Score=31.03 Aligned_cols=60 Identities=12% Similarity=0.141 Sum_probs=43.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 21 KRARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 21 ~r~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
-+-++....++..-|...|..+-.++-.+...++..+-..+..|.+||++++..-+....
T Consensus 627 ~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 627 VKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred ccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 345566666677778888887777766666666777778888999999998876555443
No 198
>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=47.06 E-value=21 Score=19.54 Aligned_cols=23 Identities=26% Similarity=0.341 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR 72 (99)
...+|..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45789999999999999996543
No 199
>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=46.92 E-value=21 Score=20.57 Aligned_cols=20 Identities=5% Similarity=0.107 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
.-++|..+|+++..++.|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34689999999999999975
No 200
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=46.58 E-value=68 Score=20.06 Aligned_cols=44 Identities=20% Similarity=0.163 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
.+|+.+..+|.-...- .....||..++++.+.|+....+=+.|.
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 5888888888766542 2467889999999999999888776654
No 201
>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=46.51 E-value=26 Score=20.18 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WF 68 (99)
..++|..+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3468999999999999994
No 202
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=46.24 E-value=59 Score=21.72 Aligned_cols=45 Identities=13% Similarity=0.118 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNr 71 (99)
.+++.++..+......+ +-....-.+||..+++++..|+..+.+-
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 47788777776655433 3333456789999999999999998765
No 203
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=46.16 E-value=90 Score=20.98 Aligned_cols=50 Identities=16% Similarity=0.146 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
+++.+..++...|-... .......++|..+|+++..|..+....+.+.++
T Consensus 175 L~~~~r~il~l~y~~~~-~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 175 LDGREREVIEMRYGLGD-GRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CCHHHHHHHHHHHcCCC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444445544442100 022346778999999999999887766666654
No 204
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=46.00 E-value=21 Score=21.97 Aligned_cols=25 Identities=4% Similarity=0.162 Sum_probs=19.7
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797 47 RAKRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 47 ~~~~~~la~~l~l~~~~V~~WFqNr 71 (99)
......||..+|+++..+..+|+..
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3556788999999999888888654
No 205
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=45.98 E-value=41 Score=21.80 Aligned_cols=35 Identities=14% Similarity=-0.057 Sum_probs=28.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCCCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKTPED 83 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~~~ 83 (99)
...+||..+|++...|+.....-|.+.++......
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 35678999999999999999988888877665433
No 206
>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=45.98 E-value=31 Score=20.28 Aligned_cols=20 Identities=30% Similarity=0.469 Sum_probs=17.3
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|++...++.|...
T Consensus 4 ~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 4 DEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999753
No 207
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=45.81 E-value=42 Score=21.51 Aligned_cols=28 Identities=18% Similarity=0.217 Sum_probs=24.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
..++|..+|++...|+.+...-+.+.+.
T Consensus 146 ~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 146 IKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999887777665
No 208
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=45.53 E-value=30 Score=23.25 Aligned_cols=41 Identities=15% Similarity=0.180 Sum_probs=33.6
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
+..-...|....|- .....||...|++...|-.+|.++..-
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L 59 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDL 59 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 44555558888877 568889999999999999999998764
No 209
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=45.29 E-value=25 Score=22.17 Aligned_cols=20 Identities=25% Similarity=0.267 Sum_probs=17.6
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|+++..++.|...
T Consensus 4 ~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 4 GQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999964
No 210
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=44.74 E-value=45 Score=21.22 Aligned_cols=31 Identities=10% Similarity=0.052 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
....+||..+|++...|+++....+.+.+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999998777665543
No 211
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=44.54 E-value=93 Score=20.68 Aligned_cols=45 Identities=13% Similarity=0.132 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
.+|+.+..+|.-.-+ . ..-.++|..++++++.|+....|=..|..
T Consensus 137 ~LT~RE~eVL~lla~--G----~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMA--G----QGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHc--C----CCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 488999888866633 2 22467899999999999998876555543
No 212
>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=44.52 E-value=25 Score=23.10 Aligned_cols=21 Identities=29% Similarity=0.615 Sum_probs=15.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
+..||..+|++++.|..|-.+
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 567999999999999999643
No 213
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=44.27 E-value=1e+02 Score=21.12 Aligned_cols=48 Identities=13% Similarity=0.153 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+|+.+.++|.-... . ..-.+||..+++++..|+.-..|-+.|..-
T Consensus 177 ~~~LT~rE~evl~~~a~--G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 177 EMNFSKREKEILKWTAE--G----KTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34688888888865532 1 234678999999999999999888876543
No 214
>PRK10651 transcriptional regulator NarL; Provisional
Probab=43.99 E-value=81 Score=19.84 Aligned_cols=45 Identities=18% Similarity=0.186 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
.+|+.+..+|.-...- ..-..+|..++++...|++...+-+.|..
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4899998888765421 12456788999999999999988777654
No 215
>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=43.86 E-value=30 Score=20.25 Aligned_cols=20 Identities=15% Similarity=0.155 Sum_probs=17.6
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-+.
T Consensus 4 ~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 4 GEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999964
No 216
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=43.85 E-value=75 Score=20.16 Aligned_cols=36 Identities=14% Similarity=0.076 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 30 ~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
.-+..|...=+...|.+.+....+|..+|++...|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345566555566689999999999999999997654
No 217
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=43.83 E-value=22 Score=22.00 Aligned_cols=23 Identities=22% Similarity=0.456 Sum_probs=19.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR 72 (99)
...+|..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999997754
No 218
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=43.64 E-value=75 Score=20.33 Aligned_cols=36 Identities=14% Similarity=0.151 Sum_probs=28.8
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 30 NQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 30 ~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
.-+.+|...=+...|.+.+....+|..+|++...|.
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 345666666566789999999999999999998754
No 219
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=43.63 E-value=79 Score=19.60 Aligned_cols=46 Identities=15% Similarity=0.192 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHh
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKK 76 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~k 76 (99)
..+|+.+..+|.-. .. .+ ...++|..++++...|+.+.++-+.|..
T Consensus 148 ~~lt~~e~~vl~l~-~~-g~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-TE-GY----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-HC-CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34888888888763 32 22 2567899999999999999998776654
No 220
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=43.52 E-value=45 Score=22.50 Aligned_cols=37 Identities=16% Similarity=0.174 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 44 YILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 44 ~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
|.......+||..+|++...|++....-|.+.|+...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3444556789999999999999999888888877543
No 221
>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=42.85 E-value=28 Score=18.25 Aligned_cols=17 Identities=24% Similarity=0.438 Sum_probs=13.2
Q ss_pred HHHHHHHhCCChHHHHH
Q psy16797 50 RHQLAKELNLCERQIKI 66 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~ 66 (99)
-.+||..+|+++.||+-
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 45789999999999874
No 222
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=42.76 E-value=91 Score=21.95 Aligned_cols=50 Identities=14% Similarity=0.146 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.++..+..+|..+|-.. ......++|..+|++...|+..-.....+.|..
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35566666666666321 233467899999999999999887777666653
No 223
>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=42.38 E-value=61 Score=20.51 Aligned_cols=35 Identities=17% Similarity=0.223 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 31 q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
-+..|...=+...|.+.+....+|..+|+++..|.
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 35566666666789999999999999999998765
No 224
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=42.25 E-value=84 Score=19.54 Aligned_cols=26 Identities=19% Similarity=0.332 Sum_probs=21.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
-.+||..+|++...|+++....+.+.
T Consensus 132 ~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 132 YGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46789999999999999988766554
No 225
>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=42.12 E-value=16 Score=19.86 Aligned_cols=20 Identities=20% Similarity=0.514 Sum_probs=15.4
Q ss_pred HHHHHHHhCCChHHHH-HHHH
Q psy16797 50 RHQLAKELNLCERQIK-IWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~-~WFq 69 (99)
..++|..+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4578999999999999 8885
No 226
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=41.98 E-value=96 Score=21.90 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
+++.+..++...|....+ ......+||..+|++...|+..-...+.+
T Consensus 250 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred CCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 556666666666643222 22457789999999999999987655544
No 227
>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=41.54 E-value=29 Score=20.59 Aligned_cols=21 Identities=10% Similarity=0.143 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|+++..++.|-..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999863
No 228
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=41.49 E-value=50 Score=22.65 Aligned_cols=31 Identities=19% Similarity=0.139 Sum_probs=26.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
..+||..+|++...|+++...-|.+.+....
T Consensus 135 ~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~ 165 (228)
T PRK06704 135 IADIAKVCSVSEGAVKASLFRSRNRLKTVSE 165 (228)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999988888776543
No 229
>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=41.13 E-value=29 Score=20.53 Aligned_cols=21 Identities=5% Similarity=0.142 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999863
No 230
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=41.01 E-value=39 Score=19.34 Aligned_cols=18 Identities=17% Similarity=0.423 Sum_probs=16.3
Q ss_pred HHHHHHHhCCChHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIW 67 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~W 67 (99)
...+|..+|++..-|..|
T Consensus 13 ~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 13 KTKLANAAGVRLASVAAW 30 (75)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 467899999999999999
No 231
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=40.50 E-value=56 Score=21.25 Aligned_cols=31 Identities=16% Similarity=0.197 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
...++|..+|++...|+++..--|.+.++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999988777776644
No 232
>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=40.48 E-value=56 Score=23.02 Aligned_cols=32 Identities=13% Similarity=0.057 Sum_probs=27.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
..+||..+|++...|+.....-|.+.|+....
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 192 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEVGPS 192 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHhccc
Confidence 46789999999999999999888888876553
No 233
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=40.43 E-value=26 Score=22.86 Aligned_cols=41 Identities=15% Similarity=0.179 Sum_probs=32.1
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
++.....|....|.. .....||...|++...+-.+|.++-.
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 455555677777655 44778899999999999999988776
No 234
>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=40.43 E-value=50 Score=16.40 Aligned_cols=37 Identities=8% Similarity=0.275 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
+++.+...+...+... .....||..+|++...|.-++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5555555555555543 346789999999999988776
No 235
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=40.37 E-value=92 Score=20.51 Aligned_cols=35 Identities=20% Similarity=0.180 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 31 q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
-+..|...=+...|.+.+....+|..+|++...|.
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 34555555566789999999999999999997654
No 236
>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=40.26 E-value=31 Score=20.16 Aligned_cols=19 Identities=21% Similarity=0.314 Sum_probs=17.0
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-.
T Consensus 4 ~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 4 GELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999985
No 237
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=39.94 E-value=58 Score=21.44 Aligned_cols=42 Identities=17% Similarity=0.242 Sum_probs=31.9
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
++.....|....|.. .....||...|++...+-..|.|+..-
T Consensus 24 L~AA~~lf~e~Gy~~-~s~~dIA~~aGvs~gtiY~hF~sKe~L 65 (212)
T PRK15008 24 LSAALDTFSQFGFHG-TRLEQIAELAGVSKTNLLYYFPSKEAL 65 (212)
T ss_pred HHHHHHHHHHhCccc-CCHHHHHHHhCcCHHHHHHHCCCHHHH
Confidence 444445578888665 446778999999999999999988763
No 238
>KOG3755|consensus
Probab=39.50 E-value=19 Score=28.65 Aligned_cols=47 Identities=15% Similarity=0.148 Sum_probs=31.4
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhC-------CChHHHHHHHHHHHhHHhhcCCCC
Q psy16797 36 EKEFNQQNYILRAKRHQLAKELN-------LCERQIKIWFQNRRMKKKKGKTPE 82 (99)
Q Consensus 36 ~~~f~~~~~p~~~~~~~la~~l~-------l~~~~V~~WFqNrR~k~kr~~~~~ 82 (99)
+-+|-.+..+......+.-..+. .....|+.||.|+|.+.++.+...
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~~ 761 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMSY 761 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhccC
Confidence 44455666666666555444443 344569999999999999876553
No 239
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=39.49 E-value=98 Score=19.51 Aligned_cols=28 Identities=7% Similarity=0.050 Sum_probs=23.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
-.++|..+|++...|+.+..+.+...+.
T Consensus 137 ~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 137 YVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999999877766553
No 240
>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=39.29 E-value=39 Score=19.79 Aligned_cols=20 Identities=10% Similarity=0.089 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|...
T Consensus 4 ~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 4 GEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999853
No 241
>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=39.02 E-value=41 Score=19.90 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|+++..++.|-.+
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 46799999999999999764
No 242
>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=38.80 E-value=34 Score=19.83 Aligned_cols=20 Identities=20% Similarity=0.360 Sum_probs=17.1
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|+++..|+.|-..
T Consensus 4 ~eva~~~gi~~~tlr~~~~~ 23 (100)
T cd00592 4 GEVAKLLGVSVRTLRYYEEK 23 (100)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46789999999999999753
No 243
>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=38.80 E-value=33 Score=20.61 Aligned_cols=20 Identities=15% Similarity=0.238 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-..
T Consensus 4 ge~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 4 SQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999853
No 244
>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=38.79 E-value=35 Score=20.41 Aligned_cols=21 Identities=19% Similarity=0.327 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
..++|..+|+++..++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999754
No 245
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=38.50 E-value=96 Score=19.15 Aligned_cols=42 Identities=12% Similarity=0.166 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
.++++++..+..+..... ...+++..+|+++..|++=+..=-
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rLd~ii 74 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRLDKII 74 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHHHHHH
Confidence 578889888877765433 345678888999998887664433
No 246
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=38.45 E-value=35 Score=16.03 Aligned_cols=22 Identities=14% Similarity=0.267 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
...+|..+|++...|..|-.+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4578899999999999987543
No 247
>cd00131 PAX Paired Box domain
Probab=38.13 E-value=99 Score=19.16 Aligned_cols=45 Identities=9% Similarity=-0.010 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-------ChHHHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNL-------CERQIKIWFQN 70 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l-------~~~~V~~WFqN 70 (99)
..+..+...+......++..+..+..++...-|+ +...|-.+|++
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 4566666667666778888877777665334465 88888888765
No 248
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=37.77 E-value=81 Score=18.08 Aligned_cols=43 Identities=9% Similarity=0.124 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 27 YTSNQLLALEKEFNQ-----QNYILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~-----~~~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
++..++..+...|.. +.+.+..+...+...+|++...|...|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 567788888888753 3467777777766677888888887775
No 249
>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=37.67 E-value=36 Score=19.98 Aligned_cols=20 Identities=20% Similarity=0.340 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
.-++|..+|++...|+.|-.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34689999999999999985
No 250
>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=36.89 E-value=44 Score=15.81 Aligned_cols=21 Identities=19% Similarity=0.336 Sum_probs=15.4
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFq 69 (99)
.+.+||..+|++...|.-=|.
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 367899999999988876553
No 251
>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=36.88 E-value=36 Score=20.39 Aligned_cols=20 Identities=10% Similarity=0.267 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
.-++|..+|++...++.|-.
T Consensus 3 i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34689999999999999964
No 252
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=36.79 E-value=58 Score=20.06 Aligned_cols=26 Identities=31% Similarity=0.431 Sum_probs=22.4
Q ss_pred CCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 44 YILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 44 ~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
-++...+..||..+|++.+.|..|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 36667788899999999999999964
No 253
>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=36.74 E-value=58 Score=16.07 Aligned_cols=25 Identities=20% Similarity=0.344 Sum_probs=20.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
...++|..++++...|..|...-+.
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~~ 41 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIMR 41 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 4567899999999999999874433
No 254
>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=36.73 E-value=43 Score=20.84 Aligned_cols=21 Identities=24% Similarity=0.461 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
..++|..+|+++..++.|-+.
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~ 24 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERH 24 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999864
No 255
>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=36.69 E-value=37 Score=20.27 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=17.5
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-..
T Consensus 4 ~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 4 GEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHCcCHHHHHHHHHc
Confidence 46899999999999999863
No 256
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=36.56 E-value=38 Score=20.31 Aligned_cols=19 Identities=16% Similarity=0.298 Sum_probs=16.0
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|=.
T Consensus 4 ~eva~~~gvs~~tLRyYE~ 22 (124)
T COG0789 4 GEVAKLTGVSVRTLRFYER 22 (124)
T ss_pred HHHHHHhCCCHHHHHHHHH
Confidence 4678889999999999953
No 257
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=36.52 E-value=40 Score=17.41 Aligned_cols=22 Identities=14% Similarity=0.258 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
-..||..+|++...|..||+.-
T Consensus 22 ~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred HhHHhhheeecHHHHHHHHHHH
Confidence 4568999999999999999754
No 258
>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=36.38 E-value=76 Score=17.32 Aligned_cols=40 Identities=18% Similarity=0.226 Sum_probs=25.0
Q ss_pred CCHHHHHHH---HHHHhhcCCCCHHHHHHHHHHhCCC-hHHHHHHH
Q psy16797 27 YTSNQLLAL---EKEFNQQNYILRAKRHQLAKELNLC-ERQIKIWF 68 (99)
Q Consensus 27 ~s~~q~~~L---~~~f~~~~~p~~~~~~~la~~l~l~-~~~V~~WF 68 (99)
+|+.|..+| ..+...+.||. ...+|+..+|+. ...|..-.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 556665555 44567788874 567889999997 77776654
No 259
>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=36.09 E-value=63 Score=16.34 Aligned_cols=35 Identities=20% Similarity=0.253 Sum_probs=22.4
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 33 LALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 33 ~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
.+|.-.+....+ ....+||..++++.+.|..-...
T Consensus 4 ~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 4 QILKLLLESKEP---ITAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp HHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHHHH
Confidence 444444444443 33568899999999999876643
No 260
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=35.88 E-value=1.7e+02 Score=21.08 Aligned_cols=50 Identities=14% Similarity=0.165 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
+++.+..++...|..... ......++|..+|++...|+..-.....+.|.
T Consensus 257 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~ 306 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRK 306 (317)
T ss_pred CCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 556666666666643322 22357789999999999999999888888776
No 261
>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=35.81 E-value=43 Score=16.62 Aligned_cols=18 Identities=33% Similarity=0.477 Sum_probs=13.1
Q ss_pred HHHHHHHHhCCChHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKI 66 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~ 66 (99)
.-.+||..+|++...|..
T Consensus 19 s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 19 SYAELAEELGLSESTVRR 36 (42)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred cHHHHHHHHCcCHHHHHH
Confidence 356789999999988754
No 262
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=35.77 E-value=61 Score=20.82 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=31.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
+......|....|.. .....||...|++...+-.+|.++..
T Consensus 14 l~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 14 LQAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 344445578888744 55778899999999999999988765
No 263
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=34.76 E-value=1.3e+02 Score=19.51 Aligned_cols=32 Identities=16% Similarity=0.090 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhhcCC
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKKGKT 80 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~ 80 (99)
...+||..+|++...|++=...-|.+.++...
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999887777777666443
No 264
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=34.39 E-value=54 Score=21.72 Aligned_cols=20 Identities=20% Similarity=0.536 Sum_probs=17.7
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
.++|..+|+++..|+.|...
T Consensus 4 ~evA~~lGVS~~TLRrw~k~ 23 (175)
T PRK13182 4 PFVAKKLGVSPKTVQRWVKQ 23 (175)
T ss_pred HHHHHHHCcCHHHHHHHHHc
Confidence 46799999999999999964
No 265
>PHA02955 hypothetical protein; Provisional
Probab=34.29 E-value=51 Score=22.71 Aligned_cols=43 Identities=7% Similarity=0.086 Sum_probs=31.9
Q ss_pred HHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 30 NQLLALEKEFNQQ-NYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 30 ~q~~~L~~~f~~~-~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
.++..|-+.|.+. .-.+..++..++.++|+....+..||.+--
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 3566666666543 457788899999999999987788887643
No 266
>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=34.28 E-value=96 Score=17.88 Aligned_cols=40 Identities=18% Similarity=0.135 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHH---HhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 27 YTSNQLLALEKE---FNQQNYILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 27 ~s~~q~~~L~~~---f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
+|+.|..+|... |....-|-.. ..||..+++++..|++=.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHHHH
Confidence 456666666655 6666555443 456778999999887644
No 267
>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=34.20 E-value=47 Score=19.52 Aligned_cols=21 Identities=10% Similarity=0.146 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
..++|..+|++...++.|...
T Consensus 4 i~eva~~~gVs~~tLR~ye~~ 24 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRL 24 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346789999999999999753
No 268
>PRK05949 RNA polymerase sigma factor; Validated
Probab=33.99 E-value=1.8e+02 Score=21.08 Aligned_cols=50 Identities=14% Similarity=0.167 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
+++.+..++...|..... ......++|..+|++...|+......+.+.|.
T Consensus 267 L~~rer~Vi~lr~gl~~~-e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDG-KELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred CCHHHHHHHHHHhccCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 566666677666653322 12346789999999999999998888877776
No 269
>cd04772 HTH_TioE_rpt1 First Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD contains the N-terminal or first repeat (rpt1) of these tandem MerR-like domain proteins.
Probab=33.93 E-value=45 Score=19.63 Aligned_cols=19 Identities=16% Similarity=0.347 Sum_probs=16.6
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-+
T Consensus 4 ~e~A~~~gvs~~tlR~Ye~ 22 (99)
T cd04772 4 VDLARAIGLSPQTVRNYES 22 (99)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999964
No 270
>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=33.64 E-value=45 Score=20.05 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=17.4
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-..
T Consensus 4 ~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 4 GELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred HHHHHHHCCCHHHHHHHHHC
Confidence 46899999999999999863
No 271
>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=33.54 E-value=53 Score=20.29 Aligned_cols=21 Identities=10% Similarity=0.229 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...|+.|-+.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999853
No 272
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=33.45 E-value=1.4e+02 Score=19.43 Aligned_cols=43 Identities=19% Similarity=0.074 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
.+|+.+..+|.-... +..-.++|..++++...|+....|=-.|
T Consensus 150 ~Lt~rE~evl~~~~~------G~s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 150 RLSPKESEVLRLFAE------GFLVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred cCCHHHHHHHHHHHC------CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 589999988877743 2335678999999999999877654444
No 273
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=33.41 E-value=44 Score=17.66 Aligned_cols=24 Identities=25% Similarity=0.349 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
....+|..+|++...|..|-.+++
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~ 39 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRR 39 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCC
Confidence 456789999999999999987765
No 274
>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=33.39 E-value=11 Score=16.27 Aligned_cols=7 Identities=43% Similarity=1.175 Sum_probs=5.4
Q ss_pred HHHHHHH
Q psy16797 66 IWFQNRR 72 (99)
Q Consensus 66 ~WFqNrR 72 (99)
+||.++.
T Consensus 7 NWFE~~g 13 (22)
T PF08452_consen 7 NWFESRG 13 (22)
T ss_pred ehhhhCC
Confidence 7998765
No 275
>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=33.05 E-value=33 Score=18.42 Aligned_cols=42 Identities=10% Similarity=0.083 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 28 s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
++..-+-|+..|....--.......||..+|+++..|..=++
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 334445666666655333334456789999999998876553
No 276
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=32.60 E-value=1.2e+02 Score=18.70 Aligned_cols=29 Identities=14% Similarity=0.186 Sum_probs=24.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..++|..+|++...|+......+.+.+..
T Consensus 124 ~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 124 HQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999988777776654
No 277
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=32.37 E-value=1.4e+02 Score=20.39 Aligned_cols=47 Identities=13% Similarity=0.210 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..++...|.. .....+||..+|++...|...-..-..+.++
T Consensus 206 ~L~~rer~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~ral~kLr~ 252 (254)
T TIGR02850 206 RLNEREKMILNMRFFE-----GKTQMEVAEEIGISQAQVSRLEKAALKHMRK 252 (254)
T ss_pred cCCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 4566666666666632 2346789999999999998876655555443
No 278
>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=32.37 E-value=46 Score=20.39 Aligned_cols=18 Identities=22% Similarity=0.257 Sum_probs=15.8
Q ss_pred HHHHHHhCCChHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWF 68 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WF 68 (99)
-++|..+|+++..++.|=
T Consensus 3 ~e~a~~~gvs~~tlR~Ye 20 (124)
T TIGR02051 3 GELAKAAGVNVETIRYYE 20 (124)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 468999999999999993
No 279
>PRK09726 antitoxin HipB; Provisional
Probab=32.32 E-value=45 Score=19.05 Aligned_cols=22 Identities=23% Similarity=0.345 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
..++|..+|++...|..|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 5678999999999999998754
No 280
>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=31.90 E-value=47 Score=20.92 Aligned_cols=21 Identities=14% Similarity=0.200 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|-+.
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999864
No 281
>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=31.87 E-value=55 Score=20.75 Aligned_cols=21 Identities=14% Similarity=0.195 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|.+-
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999864
No 282
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=31.71 E-value=44 Score=20.53 Aligned_cols=23 Identities=4% Similarity=0.076 Sum_probs=19.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR 72 (99)
+.++|..+|++...+..|.+++.
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56789999999999999998764
No 283
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=31.48 E-value=82 Score=22.44 Aligned_cols=29 Identities=14% Similarity=0.129 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
...+||..+|++...|+.....-|.+.++
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 34678999999999999999888888777
No 284
>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=31.46 E-value=65 Score=15.33 Aligned_cols=20 Identities=10% Similarity=0.112 Sum_probs=14.2
Q ss_pred HHHHHHHHHhCCChHHHHHH
Q psy16797 48 AKRHQLAKELNLCERQIKIW 67 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~W 67 (99)
.....||..++++...+..|
T Consensus 7 Dtl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp --HHHHHHHTTS-HHHHHHH
T ss_pred CcHHHHHhhhhhhHhHHHHh
Confidence 45677899999999887776
No 285
>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=31.44 E-value=50 Score=20.13 Aligned_cols=19 Identities=21% Similarity=0.553 Sum_probs=16.3
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|=.
T Consensus 4 geva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 4 SELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999954
No 286
>PRK13719 conjugal transfer transcriptional regulator TraJ; Provisional
Probab=31.40 E-value=1.4e+02 Score=20.66 Aligned_cols=44 Identities=14% Similarity=-0.149 Sum_probs=33.2
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
..+|+.+..+|.-.-. +..-.++|..+++++..|+....+=..|
T Consensus 142 ~~LS~RE~eVL~Lia~------G~SnkEIA~~L~IS~~TVk~hvs~I~~K 185 (217)
T PRK13719 142 NKVTKYQNDVFILYSF------GFSHEYIAQLLNITVGSSKNKISEILKF 185 (217)
T ss_pred CCCCHHHHHHHHHHHC------CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4689999999977633 2335678999999999999877655444
No 287
>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=31.14 E-value=44 Score=16.58 Aligned_cols=33 Identities=12% Similarity=0.345 Sum_probs=23.6
Q ss_pred HhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 39 FNQQNYILRAKRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 39 f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
|....|-. .....|+...|++...+-..|.|+-
T Consensus 9 ~~~~G~~~-~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 9 FAEKGYEA-VSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHTTT-SSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHhCHHh-CCHHHHHHHHccchhhHHHHcCCHH
Confidence 44334333 3366789999999999999998764
No 288
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=31.09 E-value=89 Score=20.92 Aligned_cols=44 Identities=27% Similarity=0.297 Sum_probs=32.1
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
..+|+.+..+|...-. . ..-.+||.+|++++..|+..-.|=-.|
T Consensus 147 ~~LT~RE~eVL~lla~--G----~snkeIA~~L~iS~~TVk~h~~~i~~K 190 (211)
T COG2197 147 ELLTPRELEVLRLLAE--G----LSNKEIAEELNLSEKTVKTHVSNILRK 190 (211)
T ss_pred CCCCHHHHHHHHHHHC--C----CCHHHHHHHHCCCHhHHHHHHHHHHHH
Confidence 3689999888866622 2 223568999999999999977665444
No 289
>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=30.93 E-value=93 Score=18.57 Aligned_cols=43 Identities=14% Similarity=0.066 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHhhcCCC--CHHHHHHHHHHhCCChHHHHHHH
Q psy16797 26 AYTSNQLLALEKEFNQQNYI--LRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p--~~~~~~~la~~l~l~~~~V~~WF 68 (99)
.+|+.++..+...|....-. ......+||..+|++...|..|=
T Consensus 32 lLTp~E~~~l~~R~~i~~~Ll~~~~tQrEIa~~lGiS~atIsR~s 76 (94)
T TIGR01321 32 ILTRSEREDLGDRIRIVNELLNGNMSQREIASKLGVSIATITRGS 76 (94)
T ss_pred hCCHHHHHHHHHHHHHHHHHHhCCCCHHHHHHHhCCChhhhhHHH
Confidence 36788888888887655411 11234567999999888776654
No 290
>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=30.68 E-value=51 Score=20.25 Aligned_cols=20 Identities=20% Similarity=0.200 Sum_probs=17.3
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-+.
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 4 GEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999854
No 291
>PRK15201 fimbriae regulatory protein FimW; Provisional
Probab=30.64 E-value=1.7e+02 Score=19.89 Aligned_cols=44 Identities=18% Similarity=0.059 Sum_probs=32.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
..+|+.+..+|.-.-+ +..-.++|..++++++.|+....+-..|
T Consensus 132 ~~LSpRErEVLrLLAq------GkTnKEIAe~L~IS~rTVkth~srImkK 175 (198)
T PRK15201 132 RHFSVTERHLLKLIAS------GYHLSETAALLSLSEEQTKSLRRSIMRK 175 (198)
T ss_pred CCCCHHHHHHHHHHHC------CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3488999888876633 2335678999999999999877655444
No 292
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.32 E-value=88 Score=17.07 Aligned_cols=21 Identities=19% Similarity=0.387 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
-.++|..+|++.-+++.|...
T Consensus 18 T~eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 18 TREIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHhCCCHHHHHHHHHH
Confidence 357899999999999999864
No 293
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=30.26 E-value=55 Score=19.35 Aligned_cols=31 Identities=16% Similarity=0.262 Sum_probs=22.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHH
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKI 66 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 66 (99)
...|...|....+ ....+|..||+++..|..
T Consensus 12 ~~ELq~nf~~~~l----s~~~ia~dL~~s~~~le~ 42 (89)
T PF10078_consen 12 RQELQANFELSGL----SLEQIAADLGTSPEHLEQ 42 (89)
T ss_pred HHHHHHHHHHcCC----CHHHHHHHhCCCHHHHHH
Confidence 3467777887664 356788999999887664
No 294
>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=30.20 E-value=53 Score=20.16 Aligned_cols=20 Identities=25% Similarity=0.330 Sum_probs=17.3
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-+.
T Consensus 4 ~e~a~~~gvs~~tlRyYe~~ 23 (127)
T TIGR02044 4 GQVAKLTGLSSKMIRYYEEK 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999853
No 295
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=30.17 E-value=61 Score=20.39 Aligned_cols=21 Identities=14% Similarity=0.221 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999853
No 296
>COG0568 RpoD DNA-directed RNA polymerase, sigma subunit (sigma70/sigma32) [Transcription]
Probab=30.13 E-value=2.3e+02 Score=20.98 Aligned_cols=50 Identities=10% Similarity=0.102 Sum_probs=41.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
+++.+..++...|... ...+....+|+..+|+|...|+..=.+.-.|.|.
T Consensus 280 Lt~rE~~Vi~~R~gl~-~~~~~TLeevg~~~~isrERvRQIE~kAl~KLr~ 329 (342)
T COG0568 280 LTERERRVIRLRFGLD-DGEPKTLEELGEEFGISRERVRQIEAKALRKLRR 329 (342)
T ss_pred CCHHHHHHHHHHhccC-CCCcchHHHHHHHhCCcHHHHHHHHHHHHHHHHH
Confidence 8899999999999876 2335677899999999999999998887777773
No 297
>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=29.67 E-value=56 Score=19.78 Aligned_cols=19 Identities=21% Similarity=0.315 Sum_probs=16.7
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-.
T Consensus 4 ~eva~~~gvs~~tLRyYe~ 22 (123)
T cd04770 4 GELAKAAGVSPDTIRYYER 22 (123)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999875
No 298
>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=29.42 E-value=94 Score=16.53 Aligned_cols=14 Identities=29% Similarity=0.415 Sum_probs=6.4
Q ss_pred HHHHHHhCCChHHH
Q psy16797 51 HQLAKELNLCERQI 64 (99)
Q Consensus 51 ~~la~~l~l~~~~V 64 (99)
..++..+|+|..++
T Consensus 24 ~ywa~~~gvt~~~L 37 (57)
T PF12244_consen 24 RYWAKRFGVTEEQL 37 (57)
T ss_pred HHHHHHHCcCHHHH
Confidence 33444444444443
No 299
>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=29.30 E-value=57 Score=19.80 Aligned_cols=19 Identities=11% Similarity=0.268 Sum_probs=16.9
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-.
T Consensus 4 gevA~~~gvs~~tlRyYe~ 22 (120)
T cd04781 4 AEVARQSGLPASTLRYYEE 22 (120)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999985
No 300
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=29.24 E-value=1.1e+02 Score=18.67 Aligned_cols=34 Identities=15% Similarity=0.159 Sum_probs=24.2
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 33 LALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 33 ~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
..|...|. ..+......+||..+.+|.+.++.=.
T Consensus 7 ~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~lL 40 (115)
T PF12793_consen 7 QRLWQHYG--GQPVEVTLDELAELLFCSRRNARTLL 40 (115)
T ss_pred HHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHHHH
Confidence 34555555 45666678899999999998776543
No 301
>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=29.21 E-value=57 Score=17.01 Aligned_cols=24 Identities=21% Similarity=0.338 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNrR 72 (99)
....+|..+|++...+..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 356789999999999999987754
No 302
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=29.18 E-value=58 Score=17.74 Aligned_cols=23 Identities=4% Similarity=0.082 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR 72 (99)
...||..+|++...|...+.++.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 35789999999999999887654
No 303
>PRK13558 bacterio-opsin activator; Provisional
Probab=29.15 E-value=1.8e+02 Score=22.70 Aligned_cols=44 Identities=20% Similarity=0.329 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 25 TAYTSNQLLALEKEFNQQNY--ILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~--p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
..+|..|...|+..|...-| |-...-.+||..+|++...+..=.
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 36999999999999987654 777778899999999998876543
No 304
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=28.84 E-value=1.7e+02 Score=19.15 Aligned_cols=42 Identities=14% Similarity=0.192 Sum_probs=33.9
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHH
Q psy16797 23 ARTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKI 66 (99)
Q Consensus 23 ~r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~ 66 (99)
....++++++..+...-..+ |....+..||..+||+..-|.+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~ 123 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSM 123 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHH
Confidence 45689999999999887765 4566788999999999876654
No 305
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=28.64 E-value=82 Score=20.27 Aligned_cols=40 Identities=13% Similarity=0.201 Sum_probs=29.9
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 33 LALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 33 ~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
......|....|-. .....||...|++...+-..|.|+-.
T Consensus 15 ~aA~~lf~e~G~~~-~s~~~IA~~agvs~~~lY~hF~sKe~ 54 (202)
T TIGR03613 15 SAALDTFSRFGFHG-TSLEQIAELAGVSKTNLLYYFPSKDA 54 (202)
T ss_pred HHHHHHHHHhCccc-CCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 33444477777544 44778899999999999999988765
No 306
>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=28.63 E-value=69 Score=19.84 Aligned_cols=21 Identities=19% Similarity=0.268 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999964
No 307
>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=28.60 E-value=59 Score=19.91 Aligned_cols=19 Identities=21% Similarity=0.293 Sum_probs=16.4
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-+
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 4 GELAKAAGVNVETIRYYQR 22 (126)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999954
No 308
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=28.53 E-value=59 Score=20.38 Aligned_cols=20 Identities=20% Similarity=0.300 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFq 69 (99)
.-++|..+|++...|+.|=.
T Consensus 3 Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34689999999999999964
No 309
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=28.19 E-value=1e+02 Score=21.77 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=25.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhhcC
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKKGK 79 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr~~ 79 (99)
-.++|..+|++...|+...+.-|.+.+...
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 457899999999999999998888877643
No 310
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=27.87 E-value=1.9e+02 Score=19.32 Aligned_cols=43 Identities=16% Similarity=0.011 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
.+|+.+..+|.-...= ..-.+||..++++++.|+..-.|=-.|
T Consensus 134 ~LT~RE~eVL~ll~~G------~snkeIA~~L~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 134 MLSPTEREILRFMSRG------YSMPQIAEQLERNIKTIRAHKFNVMSK 176 (207)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5899998888777542 235678999999999999866554433
No 311
>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=27.78 E-value=63 Score=19.76 Aligned_cols=20 Identities=20% Similarity=0.267 Sum_probs=17.2
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-..
T Consensus 4 gevA~~~gvs~~tLRyYe~~ 23 (127)
T cd04784 4 GELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999853
No 312
>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=27.61 E-value=63 Score=19.90 Aligned_cols=21 Identities=14% Similarity=0.265 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|-..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQ 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 346899999999999999864
No 313
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=27.58 E-value=69 Score=17.48 Aligned_cols=21 Identities=24% Similarity=0.154 Sum_probs=11.0
Q ss_pred HHHhCCChHHHHHHHHHHHhH
Q psy16797 54 AKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 54 a~~l~l~~~~V~~WFqNrR~k 74 (99)
...+|+++.+.-....-.++.
T Consensus 17 ~~~~g~s~~~~~~~~R~~~a~ 37 (81)
T PF12833_consen 17 KKETGMSFKQYLRELRLQRAK 37 (81)
T ss_dssp HHHHSS-HHHHHHHHHHHHHH
T ss_pred HHHHCcCHHHHHHHHHHHHHH
Confidence 444666666655555444444
No 314
>KOG0044|consensus
Probab=27.44 E-value=1.2e+02 Score=20.47 Aligned_cols=32 Identities=13% Similarity=0.391 Sum_probs=25.1
Q ss_pred cCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 42 QNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 42 ~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
+........+.|......+...|+.|+.|-..
T Consensus 6 ~~~~~~~~~e~l~~~t~f~~~ei~~~Yr~Fk~ 37 (193)
T KOG0044|consen 6 NSKLQPESLEQLVQQTKFSKKEIQQWYRGFKN 37 (193)
T ss_pred cccCCcHHHHHHHHhcCCCHHHHHHHHHHhcc
Confidence 34455566778888999999999999988654
No 315
>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=26.53 E-value=68 Score=19.87 Aligned_cols=19 Identities=11% Similarity=0.342 Sum_probs=16.4
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|-.
T Consensus 4 gE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 4 KELANAAGVTPDTVRFYTR 22 (133)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999963
No 316
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=26.35 E-value=1.8e+02 Score=18.44 Aligned_cols=29 Identities=34% Similarity=0.554 Sum_probs=20.0
Q ss_pred CCHHHHHHHHHHhCCCh-----HHHHHHHHHHHh
Q psy16797 45 ILRAKRHQLAKELNLCE-----RQIKIWFQNRRM 73 (99)
Q Consensus 45 p~~~~~~~la~~l~l~~-----~~V~~WFqNrR~ 73 (99)
.+...|.+||.++|++. .+..+|.+..-.
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm 116 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVM 116 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence 56788999999999876 467789976543
No 317
>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=26.35 E-value=68 Score=19.66 Aligned_cols=20 Identities=15% Similarity=0.185 Sum_probs=17.1
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|-..
T Consensus 4 ~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 4 GELARRTGVNVETIRYYESI 23 (126)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46899999999999999853
No 318
>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=26.29 E-value=70 Score=19.95 Aligned_cols=19 Identities=21% Similarity=0.368 Sum_probs=16.5
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|=+
T Consensus 4 ge~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 4 GELAKRSGMAASRIRFYEA 22 (131)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4689999999999999964
No 319
>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=26.21 E-value=1.6e+02 Score=17.80 Aligned_cols=43 Identities=19% Similarity=0.213 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
+|..|...++-+|..+ -...+||..+|+|...|--|.+..+.+
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~ 60 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKK 60 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 6788888888776543 345678999999999999998765543
No 320
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=26.15 E-value=2.8e+02 Score=21.10 Aligned_cols=51 Identities=12% Similarity=0.125 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
+++.+..++.-.|..... ......+||..+|++...|+.+....+.+.|..
T Consensus 351 L~~reR~VI~LRygl~d~-~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~ 401 (415)
T PRK07598 351 LTSRERDVIRMRFGLADG-HTYSLAEIGRALDLSRERVRQIESKALQKLRQP 401 (415)
T ss_pred CCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 566666677766653221 112367899999999999999988777776643
No 321
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=25.93 E-value=1e+02 Score=16.44 Aligned_cols=45 Identities=20% Similarity=0.228 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhcCCC
Q psy16797 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKGKTP 81 (99)
Q Consensus 31 q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~~~~ 81 (99)
-+..|..+.....+...+.... .....+..|..+.|.+.++....
T Consensus 11 ~~~~l~~y~~~~G~~~vp~~~~------~~~~~Lg~Wl~~qR~~~r~g~L~ 55 (68)
T PF03457_consen 11 RYEALKAYKEEHGHLNVPRDYV------TDGFPLGQWLNNQRRKYRKGKLT 55 (68)
T ss_dssp HHHHHHHHHHHHS--S-SS-----------SSHHHHHHHHHHHHHHHT---
T ss_pred HHHHHHHHHHHHCCCCCCcccC------cCCCcHHHHHHHHHHHHHcCCCC
Confidence 3456666666555322211111 11456889999999998885543
No 322
>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=25.82 E-value=84 Score=20.04 Aligned_cols=27 Identities=19% Similarity=0.374 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 48 AKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 48 ~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
....+++..+|++...|..|...-|-.
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 346778999999999999999766543
No 323
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=25.71 E-value=1.1e+02 Score=18.06 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=19.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
...+|...|+++.+|.-|..+-+.+
T Consensus 26 q~~vA~~~Gv~eStISR~k~~~~~~ 50 (91)
T PF05269_consen 26 QKKVAEAMGVDESTISRWKNDFIEK 50 (91)
T ss_dssp HHHHHHHHTSSTTTHHHHHHHHHHH
T ss_pred hHHHHHHhCCCHHHHHHHHhhHHHH
Confidence 3567999999999999997664443
No 324
>PRK00767 transcriptional regulator BetI; Validated
Probab=25.65 E-value=1.4e+02 Score=18.99 Aligned_cols=41 Identities=15% Similarity=0.167 Sum_probs=32.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
+..-...|....|-. .....||...|++...+-..|.|+..
T Consensus 15 l~aA~~lf~~~G~~~-~s~~~Ia~~aGvs~gslY~~F~~Ke~ 55 (197)
T PRK00767 15 IDATLRAIGEVGLLD-ATIAQIARRAGVSTGIISHYFGGKDG 55 (197)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHhCCCHHHHHHHhCCHHH
Confidence 444455578888776 55778899999999999999988765
No 325
>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=24.47 E-value=1.1e+02 Score=16.62 Aligned_cols=22 Identities=18% Similarity=0.398 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqN 70 (99)
...+||..+|++...|...+.-
T Consensus 22 t~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHHh
Confidence 3568899999999999987753
No 326
>PHA00542 putative Cro-like protein
Probab=24.47 E-value=78 Score=17.95 Aligned_cols=23 Identities=17% Similarity=0.312 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFqNr 71 (99)
...++|..+|++...|..|..++
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 35568999999999999999654
No 327
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=24.31 E-value=1.1e+02 Score=19.88 Aligned_cols=43 Identities=23% Similarity=0.170 Sum_probs=33.3
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhH
Q psy16797 31 QLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMK 74 (99)
Q Consensus 31 q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k 74 (99)
-+......|....|-. .....||...|++...+-.+|.|+-.-
T Consensus 16 Il~AA~~lf~e~G~~~-~t~~~Ia~~agvs~~tlY~~F~sKe~L 58 (215)
T PRK10668 16 ILDAALRLFSQQGVSA-TSLADIAKAAGVTRGAIYWHFKNKSDL 58 (215)
T ss_pred HHHHHHHHHHHcCccc-CCHHHHHHHhCCChHHHHHHCCCHHHH
Confidence 3455566688888765 447788999999999999999887663
No 328
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=24.14 E-value=2e+02 Score=18.23 Aligned_cols=43 Identities=14% Similarity=0.258 Sum_probs=28.2
Q ss_pred CCCCHHHHHHHHHHH----hhcCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy16797 25 TAYTSNQLLALEKEF----NQQNYILRAKRHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f----~~~~~p~~~~~~~la~~l~l~~~~V~~WFqN 70 (99)
..||++|...|...- ..+...+ ...+...+|++...++..|..
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GRiT---i~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGRIT---IKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCcc---HHHHHHHHCCCHHHHHHHHHH
Confidence 357888877776652 2333333 455677778888888877754
No 329
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=24.06 E-value=1.9e+02 Score=18.07 Aligned_cols=45 Identities=4% Similarity=0.186 Sum_probs=34.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
..+|+.+..+|.-...-. ...+|+..++++...|+..-.+=|.|.
T Consensus 142 ~~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 142 DSLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred ccCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358888888887777532 367889999999999999887766554
No 330
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=24.03 E-value=2.9e+02 Score=20.04 Aligned_cols=52 Identities=12% Similarity=0.149 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
.+++.+..+|..+|...... .....+||..+|+|...|+.--.....|.|..
T Consensus 262 ~L~eREr~Vl~~rygl~~~~-~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~~ 313 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQ-PRTLDQIGKLFGLSRERVRQIEREVMSKLRNG 313 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHHHHhH
Confidence 46777777888878643321 23468899999999999988776666565553
No 331
>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=23.81 E-value=99 Score=18.61 Aligned_cols=20 Identities=15% Similarity=0.373 Sum_probs=17.3
Q ss_pred HHHHHHhCCChHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqN 70 (99)
-++|..+|++...++.|..-
T Consensus 4 ge~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 4 GELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 46799999999999999853
No 332
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=23.58 E-value=1.9e+02 Score=17.73 Aligned_cols=28 Identities=18% Similarity=0.404 Sum_probs=22.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 50 RHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
-..+|..+|++...|+++..+-+.|.+.
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~ 186 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQA 186 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHcc
Confidence 3457889999999999998887776543
No 333
>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=23.50 E-value=87 Score=18.48 Aligned_cols=19 Identities=16% Similarity=0.328 Sum_probs=16.2
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFq 69 (99)
-++|..+|++...++.|=.
T Consensus 4 ge~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 4 GKFAKKNNITIDTVRHYID 22 (107)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 4679999999999998864
No 334
>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=23.41 E-value=2e+02 Score=18.13 Aligned_cols=44 Identities=14% Similarity=0.286 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
+..+...++...|......+ =..+|..++++.+++.-|+..-+.
T Consensus 82 l~de~k~Ii~lry~~r~~~T---W~~IA~~l~i~erta~r~~~~fK~ 125 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRT---WYQIAQKLHISERTARRWRDRFKN 125 (130)
T ss_pred hCHHHHHHHHHHHcccccch---HHHHHHHhCccHHHHHHHHHHHHH
Confidence 34444455555555433233 245788899999999988765443
No 335
>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=23.33 E-value=1.1e+02 Score=14.99 Aligned_cols=37 Identities=14% Similarity=0.205 Sum_probs=23.9
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 29 SNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 29 ~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
..+..+|...++ ++. ....+||..+|++...|..-++
T Consensus 3 ~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 3 ETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 445566655555 443 3466789999999999877664
No 336
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=23.02 E-value=53 Score=19.14 Aligned_cols=12 Identities=33% Similarity=0.745 Sum_probs=9.3
Q ss_pred HHHHHHHHHHHh
Q psy16797 62 RQIKIWFQNRRM 73 (99)
Q Consensus 62 ~~V~~WFqNrR~ 73 (99)
..|++|.||--.
T Consensus 31 gdvkvwmqnled 42 (106)
T PF11516_consen 31 GDVKVWMQNLED 42 (106)
T ss_dssp HHHHHHHHHHHH
T ss_pred ccHHHHHHHHHH
Confidence 569999998543
No 337
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=22.92 E-value=2.2e+02 Score=21.54 Aligned_cols=34 Identities=18% Similarity=0.284 Sum_probs=26.9
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHH
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIK 65 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~ 65 (99)
+.+|...=+...|.+......+|..|||+...|.
T Consensus 40 IplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~ 73 (400)
T PRK12373 40 IPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVL 73 (400)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 4555555566789999999999999999987755
No 338
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=22.89 E-value=1.2e+02 Score=15.41 Aligned_cols=40 Identities=15% Similarity=0.165 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy16797 27 YTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 27 ~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF 68 (99)
++..|..+|...+...+. .....+|+..++++...|..=.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~~v 42 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSRIV 42 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHHHH
Confidence 567787888776654332 1246678999999998876533
No 339
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=22.89 E-value=1.2e+02 Score=15.38 Aligned_cols=22 Identities=9% Similarity=0.200 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqNr 71 (99)
...+|...|++...|..-|.+.
T Consensus 2 i~dIA~~agvS~~TVSr~ln~~ 23 (46)
T PF00356_consen 2 IKDIAREAGVSKSTVSRVLNGP 23 (46)
T ss_dssp HHHHHHHHTSSHHHHHHHHTTC
T ss_pred HHHHHHHHCcCHHHHHHHHhCC
Confidence 3568999999999999888664
No 340
>PRK13749 transcriptional regulator MerD; Provisional
Probab=22.80 E-value=92 Score=19.33 Aligned_cols=19 Identities=11% Similarity=0.218 Sum_probs=16.5
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WF 68 (99)
.-++|..+|++...|+.|=
T Consensus 6 IgelA~~~gvS~~tiR~YE 24 (121)
T PRK13749 6 VSRLALDAGVSVHIVRDYL 24 (121)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4578999999999999985
No 341
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=22.73 E-value=1.2e+02 Score=15.04 Aligned_cols=44 Identities=18% Similarity=0.187 Sum_probs=28.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhC--CChHHHHHHHHH
Q psy16797 24 RTAYTSNQLLALEKEFNQQNYILRAKRHQLAKELN--LCERQIKIWFQN 70 (99)
Q Consensus 24 r~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~--l~~~~V~~WFqN 70 (99)
|..+|.++...|...+...+.... ..||..++ -+..+++.-|++
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W---~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNW---KKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHH---HHHHHHHSSSSTHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHH---HHHHHHcCCCCCHHHHHHHHHh
Confidence 356889999999999887664422 33455554 777777776654
No 342
>PRK15002 redox-sensitivie transcriptional activator SoxR; Provisional
Probab=22.60 E-value=88 Score=20.19 Aligned_cols=21 Identities=10% Similarity=0.178 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
.-++|..+|++...++.|-+.
T Consensus 14 IgevAk~~gvs~~TlRyYE~~ 34 (154)
T PRK15002 14 PGEVAKRSGVAVSALHFYESK 34 (154)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 446899999999999999864
No 343
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=22.40 E-value=1.1e+02 Score=14.60 Aligned_cols=24 Identities=8% Similarity=0.177 Sum_probs=14.6
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHH
Q psy16797 46 LRAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 46 ~~~~~~~la~~l~l~~~~V~~WFq 69 (99)
.......+|..+|++...+..=|+
T Consensus 7 ~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 7 QKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHH
Confidence 334566778888887777666665
No 344
>PRK09483 response regulator; Provisional
Probab=22.18 E-value=2.2e+02 Score=18.02 Aligned_cols=45 Identities=11% Similarity=0.128 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHH
Q psy16797 25 TAYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKK 75 (99)
Q Consensus 25 ~~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~ 75 (99)
..+|+.+..+|.-.. ..+. -.+||..++++...|+..-+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~----~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQK----VNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCC----HHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 458999999986542 2222 23789999999999998776655543
No 345
>smart00595 MADF subfamily of SANT domain.
Probab=21.94 E-value=1.6e+02 Score=16.38 Aligned_cols=28 Identities=25% Similarity=0.392 Sum_probs=22.7
Q ss_pred HHHHHHhCCChHHHHHHHHHHHhHHhhc
Q psy16797 51 HQLAKELNLCERQIKIWFQNRRMKKKKG 78 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqNrR~k~kr~ 78 (99)
..||..+|.+...++.-+.|-|...++.
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e 58 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRE 58 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4578999999999998888888866554
No 346
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=21.78 E-value=1.1e+02 Score=19.69 Aligned_cols=23 Identities=22% Similarity=0.492 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCChHHHHHHHH
Q psy16797 47 RAKRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 47 ~~~~~~la~~l~l~~~~V~~WFq 69 (99)
.....+||..+|++...+-.|=+
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHHh
Confidence 34567899999999999999984
No 347
>PHA01083 hypothetical protein
Probab=21.76 E-value=96 Score=20.17 Aligned_cols=21 Identities=19% Similarity=0.271 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy16797 50 RHQLAKELNLCERQIKIWFQN 70 (99)
Q Consensus 50 ~~~la~~l~l~~~~V~~WFqN 70 (99)
-..||..+|+++..|..|=..
T Consensus 19 dkqLA~~LGVs~q~IS~~R~G 39 (149)
T PHA01083 19 YKQIAHDLGVSPQKISKMRTG 39 (149)
T ss_pred HHHHHHHhCCCHHHHHHHHcC
Confidence 346899999999999888654
No 348
>TIGR03384 betaine_BetI transcriptional repressor BetI. BetI is a DNA-binding transcriptional repressor of the bet (betaine) regulon. In sequence, it is related to TetR (pfam00440). Choline, through BetI, induces the expression of the betaine biosynthesis genes betA and betB by derepression. The choline porter gene betT is also part of this regulon in Escherichia coli. Note that a different transcriptional regulator, ArcA, controls the expression of bet regulon genes in response to oxygen, as BetA is an oxygen-dependent enzyme.
Probab=21.59 E-value=1.5e+02 Score=18.69 Aligned_cols=41 Identities=12% Similarity=0.165 Sum_probs=30.2
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHh
Q psy16797 32 LLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRM 73 (99)
Q Consensus 32 ~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~ 73 (99)
+..-...|....|-. .....||...|++...+-..|.++-.
T Consensus 14 l~aA~~lf~~~G~~~-~s~~~IA~~agvsk~~ly~~F~sK~~ 54 (189)
T TIGR03384 14 IDATIESIGERGSLD-VTIAQIARRAGVSSGIISHYFGGKQG 54 (189)
T ss_pred HHHHHHHHHhcCccc-CCHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 444455577777654 45677899999999999999877654
No 349
>PF08822 DUF1804: Protein of unknown function (DUF1804); InterPro: IPR014926 This entry is represented by Bacteriophage D3112, Orf24. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.38 E-value=2.5e+02 Score=18.57 Aligned_cols=40 Identities=10% Similarity=0.140 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy16797 28 TSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 28 s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNr 71 (99)
.++-...+...|--... ....+|..+|++...++.|=..-
T Consensus 4 ~~e~R~~~R~~YV~~~~----sLe~aA~~~gVs~~TarrWK~~A 43 (165)
T PF08822_consen 4 PQETRDAVRRAYVFDRL----SLEQAAAKCGVSYATARRWKREA 43 (165)
T ss_pred cHHHHHHHHHHHHhCCC----CHHHHHHHhCCCHHHHHHHHHHH
Confidence 34555667777664442 24567999999999999996543
No 350
>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=21.21 E-value=1.2e+02 Score=18.10 Aligned_cols=21 Identities=10% Similarity=-0.008 Sum_probs=16.9
Q ss_pred HHHHHHhCCChHHHHHHHHHH
Q psy16797 51 HQLAKELNLCERQIKIWFQNR 71 (99)
Q Consensus 51 ~~la~~l~l~~~~V~~WFqNr 71 (99)
..+|..+|++...|..|-...
T Consensus 82 ~~lA~~lg~~~~tis~~e~g~ 102 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYERGE 102 (127)
T ss_pred HHHHHHhCCCHHHHHHHHCCC
Confidence 468889999999999987543
No 351
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=21.13 E-value=1.4e+02 Score=16.77 Aligned_cols=20 Identities=20% Similarity=0.200 Sum_probs=16.0
Q ss_pred HHHHHHHHhCCChHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWF 68 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WF 68 (99)
...+||..+|++...|-.|=
T Consensus 16 tQ~elA~~vgVsRQTi~~iE 35 (68)
T COG1476 16 TQEELAKLVGVSRQTIIAIE 35 (68)
T ss_pred CHHHHHHHcCcCHHHHHHHH
Confidence 35678999999998887654
No 352
>PRK09210 RNA polymerase sigma factor RpoD; Validated
Probab=20.60 E-value=3.5e+02 Score=19.84 Aligned_cols=51 Identities=12% Similarity=0.092 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCChHHHHHHHHHHHhHHhh
Q psy16797 26 AYTSNQLLALEKEFNQQNYILRAKRHQLAKELNLCERQIKIWFQNRRMKKKK 77 (99)
Q Consensus 26 ~~s~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WFqNrR~k~kr 77 (99)
.+++.+..+|..+|..... ......++|..+|+|...|+..-...-.|.|.
T Consensus 305 ~L~~rEr~Vl~lrygl~~~-~~~tl~EIa~~lgvs~erVrQi~~~Al~kLr~ 355 (367)
T PRK09210 305 TLTDREENVLRLRFGLDDG-RTRTLEEVGKVFGVTRERIRQIEAKALRKLRH 355 (367)
T ss_pred hCCHHHHHHHHHHhccCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhC
Confidence 4667777777777754321 22346789999999999999886555555554
No 353
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=20.57 E-value=1.9e+02 Score=20.35 Aligned_cols=15 Identities=27% Similarity=0.643 Sum_probs=12.3
Q ss_pred ChHHHHHHHHHHHhH
Q psy16797 60 CERQIKIWFQNRRMK 74 (99)
Q Consensus 60 ~~~~V~~WFqNrR~k 74 (99)
....|..||+.++.+
T Consensus 99 ~~~~i~~w~~~~~~k 113 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEK 113 (242)
T ss_pred ccchHHHHHHHHHHH
Confidence 467899999998874
No 354
>PRK13752 putative transcriptional regulator MerR; Provisional
Probab=20.36 E-value=1e+02 Score=19.53 Aligned_cols=21 Identities=14% Similarity=0.173 Sum_probs=17.5
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy16797 49 KRHQLAKELNLCERQIKIWFQ 69 (99)
Q Consensus 49 ~~~~la~~l~l~~~~V~~WFq 69 (99)
..-++|..+|++...++.|=+
T Consensus 9 ~IgevAk~~Gvs~~TLRyYE~ 29 (144)
T PRK13752 9 TIGVFAKAAGVNVETIRFYQR 29 (144)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 355789999999999999963
No 355
>COG4197 Uncharacterized protein conserved in bacteria, prophage-related [Function unknown]
Probab=20.34 E-value=86 Score=18.80 Aligned_cols=21 Identities=29% Similarity=0.631 Sum_probs=18.2
Q ss_pred HHHHHhCCChHHHHHHHHHHH
Q psy16797 52 QLAKELNLCERQIKIWFQNRR 72 (99)
Q Consensus 52 ~la~~l~l~~~~V~~WFqNrR 72 (99)
.+|..||+++..|..|-..+|
T Consensus 17 a~a~LLgvsp~~vnQw~~g~r 37 (96)
T COG4197 17 ALARLLGVSPPSVNQWIKGRR 37 (96)
T ss_pred HHHHHHccCchHHHHHhhhee
Confidence 468899999999999998765
No 356
>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=20.19 E-value=1.2e+02 Score=14.74 Aligned_cols=14 Identities=29% Similarity=0.484 Sum_probs=11.1
Q ss_pred CCCCHHHHHHHHHH
Q psy16797 25 TAYTSNQLLALEKE 38 (99)
Q Consensus 25 ~~~s~~q~~~L~~~ 38 (99)
+.||+.|+..|+.-
T Consensus 1 s~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 1 SPFTPAQLQELRAQ 14 (37)
T ss_pred CCCCHHHHHHHHHH
Confidence 35899999988765
No 357
>PRK00215 LexA repressor; Validated
Probab=20.19 E-value=2e+02 Score=18.90 Aligned_cols=46 Identities=20% Similarity=0.219 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHH---hhcCCCCHHHHHHHHHHhCC-ChHHHHHHHHHHHhH
Q psy16797 27 YTSNQLLALEKEF---NQQNYILRAKRHQLAKELNL-CERQIKIWFQNRRMK 74 (99)
Q Consensus 27 ~s~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l-~~~~V~~WFqNrR~k 74 (99)
+|+.|..+|.... ..+.++ ....+||..+|+ +...|..+.+.-..+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~L~~~ 51 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKALERK 51 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHHHHHC
Confidence 4667777776654 333433 235678999999 999998887654443
Done!