Query psy14049
Match_columns 93
No_of_seqs 117 out of 1057
Neff 8.8
Searched_HMMs 46136
Date Fri Aug 16 18:16:41 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy14049.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/14049hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.8 5.8E-21 1.3E-25 130.9 7.9 67 21-87 167-233 (309)
2 KOG0850|consensus 99.8 1.1E-20 2.4E-25 123.2 6.7 68 20-87 116-183 (245)
3 KOG0489|consensus 99.8 1E-20 2.2E-25 127.4 6.1 66 24-89 157-222 (261)
4 KOG0484|consensus 99.8 7.6E-21 1.7E-25 110.7 4.3 66 22-87 13-78 (125)
5 PF00046 Homeobox: Homeobox do 99.8 1.9E-19 4.2E-24 95.7 7.4 57 27-83 1-57 (57)
6 KOG0842|consensus 99.8 3.6E-20 7.8E-25 126.0 4.7 67 23-89 150-216 (307)
7 KOG0843|consensus 99.8 1.8E-19 3.9E-24 113.9 5.9 63 25-87 101-163 (197)
8 KOG2251|consensus 99.8 1.4E-19 3E-24 117.5 5.1 68 21-88 32-99 (228)
9 KOG0493|consensus 99.8 6.4E-19 1.4E-23 117.1 6.9 61 26-86 246-306 (342)
10 KOG0485|consensus 99.8 9.9E-19 2.1E-23 113.5 5.9 65 22-86 100-164 (268)
11 KOG0494|consensus 99.8 1.2E-18 2.6E-23 115.7 5.9 65 26-90 141-205 (332)
12 KOG0487|consensus 99.8 4.6E-19 1E-23 120.7 3.9 66 24-89 233-298 (308)
13 smart00389 HOX Homeodomain. DN 99.7 3.4E-17 7.3E-22 86.5 7.0 55 28-82 2-56 (56)
14 KOG0492|consensus 99.7 8.1E-18 1.8E-22 108.6 5.2 62 25-86 143-204 (246)
15 cd00086 homeodomain Homeodomai 99.7 6E-17 1.3E-21 86.2 7.6 57 28-84 2-58 (59)
16 KOG0848|consensus 99.7 8.2E-18 1.8E-22 112.0 3.2 63 26-88 199-261 (317)
17 TIGR01565 homeo_ZF_HD homeobox 99.7 3E-17 6.5E-22 87.4 4.2 52 27-78 2-57 (58)
18 COG5576 Homeodomain-containing 99.6 4.6E-16 1E-20 97.7 6.4 66 22-87 47-112 (156)
19 KOG0491|consensus 99.6 1.2E-16 2.6E-21 100.0 3.0 64 25-88 99-162 (194)
20 KOG0483|consensus 99.6 2.5E-16 5.5E-21 102.0 4.6 62 27-88 51-112 (198)
21 KOG0844|consensus 99.6 1.3E-16 2.7E-21 108.2 2.4 66 21-86 176-241 (408)
22 KOG3802|consensus 99.6 1.1E-16 2.5E-21 111.3 1.9 75 11-86 280-354 (398)
23 KOG0486|consensus 99.6 6.8E-16 1.5E-20 104.8 3.3 63 25-87 111-173 (351)
24 KOG4577|consensus 99.6 4.4E-15 9.6E-20 100.1 5.0 66 25-90 166-231 (383)
25 KOG0847|consensus 99.5 2E-14 4.2E-19 93.9 3.9 62 24-85 165-226 (288)
26 KOG0490|consensus 99.4 3.5E-13 7.6E-18 88.6 2.8 64 23-86 57-120 (235)
27 KOG0849|consensus 99.3 2.7E-12 5.9E-17 89.8 6.1 66 21-86 171-236 (354)
28 KOG0775|consensus 99.3 4.9E-12 1.1E-16 84.8 4.9 53 33-85 183-235 (304)
29 PF05920 Homeobox_KN: Homeobox 99.1 1.2E-10 2.6E-15 57.7 4.2 34 47-80 7-40 (40)
30 KOG1168|consensus 99.1 2.6E-11 5.6E-16 82.2 0.2 62 25-86 308-369 (385)
31 KOG0774|consensus 99.0 1.6E-10 3.4E-15 77.4 2.4 61 26-86 188-251 (334)
32 KOG2252|consensus 99.0 1.5E-09 3.3E-14 78.7 6.5 57 25-81 419-475 (558)
33 KOG0490|consensus 98.4 3.5E-07 7.6E-12 60.1 4.6 63 23-85 150-212 (235)
34 KOG1146|consensus 98.1 4.2E-06 9.1E-11 66.2 5.2 62 25-86 902-963 (1406)
35 PF11569 Homez: Homeodomain le 97.9 2.7E-05 5.9E-10 41.0 3.9 42 37-78 9-50 (56)
36 KOG0773|consensus 97.7 2.6E-05 5.6E-10 54.5 2.7 58 26-83 239-299 (342)
37 KOG3623|consensus 97.0 0.0019 4.2E-08 49.3 5.8 48 38-85 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.1 0.026 5.7E-07 29.2 4.9 47 27-78 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 92.3 0.76 1.7E-05 22.9 5.6 46 32-82 4-49 (50)
40 PF01527 HTH_Tnp_1: Transposas 89.3 0.49 1.1E-05 25.5 2.6 46 29-78 3-48 (76)
41 KOG1146|consensus 88.9 1.5 3.3E-05 36.2 5.9 71 15-85 694-764 (1406)
42 PF08281 Sigma70_r4_2: Sigma-7 88.1 2.2 4.7E-05 21.4 5.5 42 33-79 11-52 (54)
43 cd06171 Sigma70_r4 Sigma70, re 88.0 1.9 4.2E-05 20.7 4.3 43 33-80 11-53 (55)
44 PF10668 Phage_terminase: Phag 87.7 0.63 1.4E-05 24.8 2.3 21 55-75 24-44 (60)
45 PRK03975 tfx putative transcri 86.2 6.1 0.00013 24.6 6.6 50 31-86 5-54 (141)
46 PF04967 HTH_10: HTH DNA bindi 85.2 3.8 8.1E-05 21.2 5.3 42 33-74 1-44 (53)
47 PRK11924 RNA polymerase sigma 84.5 6.1 0.00013 24.3 6.0 33 55-87 143-175 (179)
48 PRK09646 RNA polymerase sigma 84.2 6.6 0.00014 25.0 6.2 32 55-86 160-191 (194)
49 PF13518 HTH_28: Helix-turn-he 82.7 2.5 5.4E-05 20.8 3.1 24 56-79 15-38 (52)
50 PRK09639 RNA polymerase sigma 82.3 9 0.0002 23.4 6.3 34 55-88 129-162 (166)
51 PRK06759 RNA polymerase factor 81.4 8.6 0.00019 23.2 5.7 29 55-83 124-152 (154)
52 PRK05602 RNA polymerase sigma 80.6 11 0.00023 23.7 6.1 34 55-88 146-179 (186)
53 TIGR02943 Sig70_famx1 RNA poly 80.1 11 0.00023 23.9 6.0 38 55-92 149-186 (188)
54 PF06056 Terminase_5: Putative 79.8 2.7 5.8E-05 22.1 2.6 20 56-75 16-35 (58)
55 PRK12512 RNA polymerase sigma 79.5 12 0.00026 23.4 6.1 32 55-86 149-180 (184)
56 PRK06288 RNA polymerase sigma 79.5 12 0.00026 25.2 6.4 39 55-93 230-268 (268)
57 cd04761 HTH_MerR-SF Helix-Turn 79.3 3.3 7E-05 20.1 2.8 22 56-77 3-24 (49)
58 PRK09413 IS2 repressor TnpA; R 79.3 8.9 0.00019 22.8 5.1 44 30-77 10-53 (121)
59 PF13384 HTH_23: Homeodomain-l 79.1 2.7 5.8E-05 20.7 2.4 21 55-75 19-39 (50)
60 PRK09652 RNA polymerase sigma 78.8 12 0.00027 22.9 6.1 31 55-85 146-176 (182)
61 PRK12526 RNA polymerase sigma 78.7 14 0.00031 23.7 6.3 32 55-86 171-202 (206)
62 PF00196 GerE: Bacterial regul 78.4 7.2 0.00016 19.9 5.4 45 32-82 3-47 (58)
63 PRK12546 RNA polymerase sigma 77.9 12 0.00026 23.9 5.7 33 55-87 131-163 (188)
64 PF13936 HTH_38: Helix-turn-he 77.4 6.8 0.00015 19.1 3.8 40 31-75 3-42 (44)
65 TIGR02939 RpoE_Sigma70 RNA pol 77.2 11 0.00025 23.5 5.4 32 54-85 155-186 (190)
66 KOG0773|consensus 77.2 4.6 0.0001 28.3 3.9 42 46-87 117-158 (342)
67 TIGR03879 near_KaiC_dom probab 77.2 1.5 3.4E-05 24.2 1.2 32 45-76 24-55 (73)
68 TIGR02959 SigZ RNA polymerase 76.2 16 0.00035 22.7 6.0 32 55-86 118-149 (170)
69 PRK10072 putative transcriptio 75.9 9.1 0.0002 22.2 4.3 40 33-79 33-72 (96)
70 PRK00118 putative DNA-binding 75.8 14 0.0003 21.8 6.3 48 32-84 17-64 (104)
71 PRK12514 RNA polymerase sigma 75.7 17 0.00036 22.6 6.1 30 55-84 147-176 (179)
72 TIGR02948 SigW_bacill RNA poly 74.5 16 0.00035 22.7 5.6 32 54-85 153-184 (187)
73 PRK12519 RNA polymerase sigma 74.0 16 0.00034 23.1 5.5 32 54-85 158-189 (194)
74 PRK09642 RNA polymerase sigma 73.7 18 0.00038 22.0 6.1 30 56-85 125-154 (160)
75 PF13411 MerR_1: MerR HTH fami 73.5 5 0.00011 21.0 2.7 21 56-76 3-23 (69)
76 PRK12541 RNA polymerase sigma 73.5 14 0.0003 22.5 5.0 29 55-83 130-158 (161)
77 PRK06811 RNA polymerase factor 73.2 17 0.00038 22.9 5.6 34 55-88 149-182 (189)
78 PRK09644 RNA polymerase sigma 72.3 20 0.00043 22.0 5.9 32 55-86 126-157 (165)
79 PRK09648 RNA polymerase sigma 72.0 22 0.00047 22.3 6.0 30 55-84 157-186 (189)
80 TIGR02989 Sig-70_gvs1 RNA poly 71.9 19 0.00042 21.7 5.8 29 54-82 128-156 (159)
81 PF00376 MerR: MerR family reg 71.9 6.5 0.00014 18.7 2.6 19 57-75 3-21 (38)
82 cd04762 HTH_MerR-trunc Helix-T 71.8 7.2 0.00016 18.4 2.9 23 56-78 3-25 (49)
83 COG3413 Predicted DNA binding 71.6 17 0.00037 23.7 5.3 40 32-71 155-196 (215)
84 PRK06930 positive control sigm 71.5 22 0.00049 22.6 5.7 51 32-87 114-164 (170)
85 PRK12530 RNA polymerase sigma 71.2 23 0.00051 22.4 6.1 31 55-85 152-182 (189)
86 PRK12524 RNA polymerase sigma 71.2 24 0.00051 22.4 5.9 32 55-86 154-185 (196)
87 TIGR02985 Sig70_bacteroi1 RNA 70.8 20 0.00043 21.4 5.4 29 55-83 131-159 (161)
88 cd00569 HTH_Hin_like Helix-tur 70.7 7.5 0.00016 16.5 5.0 38 32-74 5-42 (42)
89 TIGR02999 Sig-70_X6 RNA polyme 70.3 23 0.0005 22.0 6.1 30 55-84 152-181 (183)
90 PRK09047 RNA polymerase factor 69.5 22 0.00048 21.5 5.6 31 56-86 125-155 (161)
91 PRK07037 extracytoplasmic-func 69.5 23 0.00049 21.6 6.5 31 55-85 127-157 (163)
92 COG4367 Uncharacterized protei 69.3 14 0.0003 21.4 3.8 40 33-72 3-42 (97)
93 PRK12515 RNA polymerase sigma 68.7 26 0.00057 22.0 6.2 32 55-86 149-180 (189)
94 PRK09637 RNA polymerase sigma 68.2 23 0.00049 22.3 5.3 31 55-85 124-154 (181)
95 cd04764 HTH_MlrA-like_sg1 Heli 68.1 9.7 0.00021 19.9 3.0 21 56-76 3-23 (67)
96 cd04763 HTH_MlrA-like Helix-Tu 67.9 9.1 0.0002 20.1 2.9 21 56-76 3-23 (68)
97 PRK12518 RNA polymerase sigma 67.8 13 0.00029 22.9 4.1 34 53-86 136-169 (175)
98 COG2944 Predicted transcriptio 67.8 19 0.00042 21.3 4.4 42 32-80 43-84 (104)
99 TIGR02937 sigma70-ECF RNA poly 67.6 22 0.00048 20.7 5.7 29 55-83 128-156 (158)
100 PF09607 BrkDBD: Brinker DNA-b 67.5 17 0.00036 19.2 4.4 17 59-75 31-47 (58)
101 PRK12537 RNA polymerase sigma 67.4 28 0.0006 21.8 5.9 30 55-84 151-180 (182)
102 PF13443 HTH_26: Cro/C1-type H 67.1 6.3 0.00014 20.2 2.1 24 55-78 12-35 (63)
103 PRK06986 fliA flagellar biosyn 66.3 34 0.00075 22.5 6.1 31 55-85 202-232 (236)
104 PRK12542 RNA polymerase sigma 65.9 22 0.00048 22.3 4.8 31 55-85 140-170 (185)
105 TIGR02947 SigH_actino RNA poly 65.7 14 0.0003 23.3 3.9 34 54-87 148-181 (193)
106 PRK08301 sporulation sigma fac 64.3 35 0.00075 22.3 5.7 32 54-85 199-230 (234)
107 PRK04217 hypothetical protein; 64.2 28 0.00061 20.7 6.3 51 30-85 40-90 (110)
108 cd01104 HTH_MlrA-CarA Helix-Tu 64.1 12 0.00026 19.4 2.9 20 56-75 3-22 (68)
109 PRK12538 RNA polymerase sigma 63.9 35 0.00075 22.6 5.7 32 55-86 189-220 (233)
110 TIGR02950 SigM_subfam RNA poly 63.8 17 0.00036 21.9 3.9 33 51-83 119-151 (154)
111 cd01392 HTH_LacI Helix-turn-he 63.2 5.7 0.00012 19.5 1.5 20 58-77 2-21 (52)
112 PRK09649 RNA polymerase sigma 63.2 32 0.00069 21.7 5.2 29 55-83 148-176 (185)
113 PRK12547 RNA polymerase sigma 62.5 34 0.00073 21.0 6.2 31 55-85 130-160 (164)
114 PRK12527 RNA polymerase sigma 62.5 32 0.0007 20.8 6.3 34 55-88 123-156 (159)
115 COG1905 NuoE NADH:ubiquinone o 62.5 22 0.00048 22.7 4.3 37 35-71 25-61 (160)
116 PF00424 REV: REV protein (ant 62.5 15 0.00032 21.3 3.1 37 38-88 14-50 (91)
117 PRK11923 algU RNA polymerase s 62.4 20 0.00044 22.5 4.2 32 55-86 156-187 (193)
118 TIGR02983 SigE-fam_strep RNA p 62.4 33 0.00071 20.8 5.9 31 55-85 128-158 (162)
119 PRK13919 putative RNA polymera 62.1 36 0.00078 21.2 6.1 30 55-84 153-182 (186)
120 smart00595 MADF subfamily of S 61.3 23 0.00049 19.5 3.9 32 57-88 31-62 (89)
121 PRK12523 RNA polymerase sigma 61.1 37 0.00079 21.0 5.8 31 55-85 137-167 (172)
122 PRK12532 RNA polymerase sigma 60.3 41 0.00088 21.2 6.0 32 55-86 154-185 (195)
123 TIGR02954 Sig70_famx3 RNA poly 60.0 38 0.00082 20.8 5.9 30 55-84 137-166 (169)
124 PRK12535 RNA polymerase sigma 59.8 43 0.00094 21.4 6.0 32 55-86 151-182 (196)
125 PRK12533 RNA polymerase sigma 59.7 47 0.001 21.8 5.9 31 55-85 152-182 (216)
126 PF01381 HTH_3: Helix-turn-hel 59.6 9.1 0.0002 19.0 1.8 23 56-78 12-34 (55)
127 PRK09638 RNA polymerase sigma 59.3 22 0.00048 21.9 4.0 33 52-84 141-173 (176)
128 PRK12513 RNA polymerase sigma 59.1 23 0.00051 22.3 4.1 34 52-85 154-187 (194)
129 PF04936 DUF658: Protein of un 58.8 8.5 0.00018 24.7 1.9 31 54-84 15-45 (186)
130 PRK09647 RNA polymerase sigma 58.7 47 0.001 21.4 6.2 32 55-86 156-187 (203)
131 PRK08583 RNA polymerase sigma 58.5 52 0.0011 21.9 6.1 30 55-84 223-252 (257)
132 PRK09640 RNA polymerase sigma 58.4 24 0.00053 22.2 4.1 33 54-86 151-183 (188)
133 PRK05657 RNA polymerase sigma 58.3 62 0.0013 22.7 6.3 54 32-86 262-315 (325)
134 PRK05988 formate dehydrogenase 57.9 35 0.00076 21.5 4.6 36 36-71 24-59 (156)
135 TIGR02859 spore_sigH RNA polym 57.9 22 0.00049 22.3 3.8 31 53-83 165-195 (198)
136 PRK12520 RNA polymerase sigma 57.6 45 0.00098 20.9 6.2 33 55-87 149-181 (191)
137 PRK12516 RNA polymerase sigma 57.6 46 0.001 21.0 6.4 32 55-86 134-165 (187)
138 PRK12539 RNA polymerase sigma 57.4 45 0.00098 20.8 6.1 32 54-85 148-179 (184)
139 PRK12536 RNA polymerase sigma 57.3 45 0.00097 20.8 6.1 30 55-84 147-176 (181)
140 KOG3755|consensus 57.0 8.3 0.00018 29.7 1.9 44 42-85 708-758 (769)
141 PF13730 HTH_36: Helix-turn-he 56.8 24 0.00052 17.5 3.3 44 33-77 3-49 (55)
142 PRK12543 RNA polymerase sigma 56.7 46 0.00099 20.7 6.1 32 55-86 135-166 (179)
143 TIGR02952 Sig70_famx2 RNA poly 56.6 43 0.00093 20.3 6.0 29 55-83 140-168 (170)
144 PF07638 Sigma70_ECF: ECF sigm 56.4 27 0.00059 22.1 4.0 30 55-84 153-182 (185)
145 smart00422 HTH_MERR helix_turn 56.0 17 0.00036 18.9 2.6 20 56-75 3-22 (70)
146 TIGR01764 excise DNA binding d 55.8 22 0.00047 16.7 2.9 23 56-78 4-26 (49)
147 PF14549 P22_Cro: DNA-binding 55.8 18 0.00038 19.1 2.6 18 56-73 12-29 (60)
148 PRK09645 RNA polymerase sigma 55.6 46 0.001 20.4 6.2 30 56-85 137-166 (173)
149 TIGR01958 nuoE_fam NADH-quinon 55.6 39 0.00085 20.8 4.5 35 37-71 18-52 (148)
150 TIGR03001 Sig-70_gmx1 RNA poly 55.2 61 0.0013 21.7 6.2 31 55-85 179-209 (244)
151 PRK09641 RNA polymerase sigma 55.0 49 0.0011 20.5 5.9 32 54-85 153-184 (187)
152 PF08280 HTH_Mga: M protein tr 54.7 29 0.00063 17.8 3.9 37 36-76 6-42 (59)
153 PRK12531 RNA polymerase sigma 54.6 53 0.0011 20.8 6.2 31 55-85 159-189 (194)
154 TIGR03070 couple_hipB transcri 54.4 13 0.00029 18.2 2.0 23 56-78 18-40 (58)
155 TIGR02980 SigBFG RNA polymeras 54.2 58 0.0013 21.1 6.1 46 33-83 179-224 (227)
156 smart00027 EH Eps15 homology d 54.1 38 0.00082 19.0 5.5 44 32-75 3-51 (96)
157 cd00093 HTH_XRE Helix-turn-hel 54.0 16 0.00034 17.1 2.2 22 56-77 15-36 (58)
158 PF13551 HTH_29: Winged helix- 53.5 23 0.00049 20.0 3.1 24 55-78 14-37 (112)
159 PRK12529 RNA polymerase sigma 53.1 54 0.0012 20.4 6.0 29 55-83 145-173 (178)
160 PRK07539 NADH dehydrogenase su 52.9 46 0.00099 20.7 4.5 35 37-71 24-58 (154)
161 TIGR02941 Sigma_B RNA polymera 52.8 66 0.0014 21.4 6.0 29 55-83 223-251 (255)
162 PRK09480 slmA division inhibit 52.8 19 0.00042 22.4 2.9 36 43-79 21-56 (194)
163 PF12728 HTH_17: Helix-turn-he 52.7 20 0.00044 17.5 2.5 22 56-77 4-25 (51)
164 PF02796 HTH_7: Helix-turn-hel 52.6 27 0.00059 16.9 4.0 38 32-74 5-42 (45)
165 PF06971 Put_DNA-bind_N: Putat 52.2 17 0.00037 18.5 2.1 17 56-72 31-47 (50)
166 PRK12511 RNA polymerase sigma 51.8 59 0.0013 20.5 6.1 32 55-86 129-160 (182)
167 TIGR02957 SigX4 RNA polymerase 51.7 59 0.0013 22.1 5.3 29 56-84 127-155 (281)
168 PRK10403 transcriptional regul 51.5 53 0.0011 20.1 4.8 45 32-82 153-197 (215)
169 PRK08295 RNA polymerase factor 51.3 61 0.0013 20.5 6.5 32 54-85 171-202 (208)
170 TIGR02393 RpoD_Cterm RNA polym 51.2 69 0.0015 21.1 5.9 51 33-84 177-227 (238)
171 PRK07571 bidirectional hydroge 51.1 52 0.0011 21.1 4.6 34 38-71 39-72 (169)
172 PF01257 2Fe-2S_thioredx: Thio 50.9 35 0.00075 21.0 3.7 34 38-71 16-49 (145)
173 PRK12545 RNA polymerase sigma 50.8 64 0.0014 20.6 6.2 31 55-85 157-187 (201)
174 PRK12544 RNA polymerase sigma 50.4 67 0.0015 20.7 6.2 31 56-86 167-197 (206)
175 cd01106 HTH_TipAL-Mta Helix-Tu 50.1 24 0.00052 20.2 2.8 22 56-77 3-24 (103)
176 PRK07670 RNA polymerase sigma 50.0 74 0.0016 21.1 6.2 30 55-84 219-248 (251)
177 PRK12522 RNA polymerase sigma 49.9 59 0.0013 20.0 6.0 30 55-84 137-166 (173)
178 TIGR02479 FliA_WhiG RNA polyme 49.9 70 0.0015 20.8 6.0 29 55-83 193-221 (224)
179 smart00421 HTH_LUXR helix_turn 49.6 30 0.00066 16.6 6.2 43 32-80 3-45 (58)
180 TIGR02835 spore_sigmaE RNA pol 49.5 40 0.00086 22.2 4.1 32 55-86 200-231 (234)
181 cd04774 HTH_YfmP Helix-Turn-He 49.1 27 0.0006 19.9 2.9 21 56-76 3-23 (96)
182 cd01105 HTH_GlnR-like Helix-Tu 48.8 24 0.00052 19.7 2.6 20 56-75 4-23 (88)
183 PRK09651 RNA polymerase sigma 48.8 63 0.0014 20.0 5.4 29 55-83 137-165 (172)
184 PRK09415 RNA polymerase factor 48.6 65 0.0014 20.0 5.1 30 55-84 145-174 (179)
185 PRK07408 RNA polymerase sigma 48.5 81 0.0018 21.1 6.4 33 54-86 220-252 (256)
186 PF01710 HTH_Tnp_IS630: Transp 48.0 22 0.00048 21.0 2.5 37 34-75 4-40 (119)
187 PRK07122 RNA polymerase sigma 48.0 65 0.0014 21.8 5.0 31 54-84 232-262 (264)
188 cd04766 HTH_HspR Helix-Turn-He 47.9 25 0.00054 19.7 2.6 21 56-76 4-24 (91)
189 TIGR00721 tfx DNA-binding prot 47.4 67 0.0015 19.9 6.5 47 31-83 5-51 (137)
190 PHA01976 helix-turn-helix prot 47.3 21 0.00046 18.4 2.1 23 56-78 18-40 (67)
191 TIGR02607 antidote_HigA addict 47.0 21 0.00046 19.0 2.1 23 56-78 21-43 (78)
192 PRK09636 RNA polymerase sigma 47.0 90 0.002 21.2 5.8 30 56-85 134-163 (293)
193 COG1595 RpoE DNA-directed RNA 46.5 56 0.0012 20.4 4.3 33 55-87 145-177 (182)
194 PRK12528 RNA polymerase sigma 46.3 66 0.0014 19.5 5.8 26 56-81 132-157 (161)
195 TIGR02392 rpoH_proteo alternat 45.8 92 0.002 21.0 5.6 49 33-84 219-267 (270)
196 TIGR02960 SigX5 RNA polymerase 45.3 96 0.0021 21.2 5.6 31 56-86 161-191 (324)
197 COG5484 Uncharacterized conser 45.1 21 0.00044 24.7 2.2 26 54-81 20-45 (279)
198 COG2963 Transposase and inacti 45.0 61 0.0013 18.8 5.9 46 30-79 5-51 (116)
199 cd04779 HTH_MerR-like_sg4 Heli 44.3 33 0.00071 21.0 2.9 22 56-77 3-24 (134)
200 PRK11552 putative DNA-binding 44.0 30 0.00066 22.6 2.9 41 40-82 21-61 (225)
201 PRK07500 rpoH2 RNA polymerase 43.8 1.1E+02 0.0023 21.1 5.6 51 33-86 228-278 (289)
202 PRK05803 sporulation sigma fac 43.6 92 0.002 20.4 5.9 32 54-85 196-227 (233)
203 PRK11511 DNA-binding transcrip 43.3 71 0.0015 19.0 4.9 25 53-77 25-49 (127)
204 PRK12525 RNA polymerase sigma 43.0 78 0.0017 19.4 5.9 29 55-83 136-164 (168)
205 smart00530 HTH_XRE Helix-turn- 42.8 36 0.00079 15.5 2.6 22 56-77 13-34 (56)
206 TIGR03541 reg_near_HchA LuxR f 42.7 98 0.0021 20.4 5.5 48 31-84 170-217 (232)
207 PF07037 DUF1323: Putative tra 42.5 34 0.00074 20.8 2.6 20 56-75 3-22 (122)
208 cd04768 HTH_BmrR-like Helix-Tu 42.4 41 0.00088 19.1 2.9 21 56-76 3-23 (96)
209 PRK11922 RNA polymerase sigma 42.4 59 0.0013 21.3 4.1 37 50-86 162-198 (231)
210 PRK10360 DNA-binding transcrip 42.3 79 0.0017 19.2 4.9 45 32-82 137-181 (196)
211 PRK14996 TetR family transcrip 41.2 43 0.00092 21.0 3.2 39 40-79 16-54 (192)
212 PRK09643 RNA polymerase sigma 40.7 94 0.002 19.6 6.4 32 55-86 152-183 (192)
213 PRK09935 transcriptional regul 40.6 86 0.0019 19.2 4.8 45 32-82 149-193 (210)
214 PF07022 Phage_CI_repr: Bacter 40.0 17 0.00038 19.2 1.0 21 56-76 15-36 (66)
215 PF05269 Phage_CII: Bacterioph 40.0 51 0.0011 19.0 3.0 26 56-81 26-51 (91)
216 PF12244 DUF3606: Protein of u 40.0 53 0.0012 17.0 2.9 18 54-71 21-38 (57)
217 PRK09706 transcriptional repre 39.8 28 0.00061 20.9 2.1 23 56-78 21-43 (135)
218 PRK12540 RNA polymerase sigma 39.7 96 0.0021 19.5 6.0 32 55-86 129-160 (182)
219 PF01726 LexA_DNA_bind: LexA D 39.7 61 0.0013 17.2 3.5 40 33-74 4-47 (65)
220 cd00592 HTH_MerR-like Helix-Tu 39.3 41 0.00088 18.9 2.6 22 56-77 3-24 (100)
221 TIGR02394 rpoS_proteo RNA poly 39.3 1.2E+02 0.0027 20.6 6.5 33 54-86 243-275 (285)
222 PF13542 HTH_Tnp_ISL3: Helix-t 39.0 50 0.0011 16.0 3.0 21 55-75 29-49 (52)
223 PF13404 HTH_AsnC-type: AsnC-t 38.8 38 0.00082 16.3 2.1 17 55-71 19-35 (42)
224 cd04780 HTH_MerR-like_sg5 Heli 38.7 42 0.00091 19.1 2.6 20 56-75 3-22 (95)
225 TIGR03020 EpsA transcriptional 38.4 1.3E+02 0.0027 20.5 6.1 48 30-83 188-235 (247)
226 cd04775 HTH_Cfa-like Helix-Tur 38.4 43 0.00092 19.2 2.6 21 56-76 4-24 (102)
227 cd04789 HTH_Cfa Helix-Turn-Hel 38.3 43 0.00093 19.2 2.6 21 56-76 4-24 (102)
228 PF14229 DUF4332: Domain of un 38.3 54 0.0012 19.6 3.1 26 50-75 26-51 (122)
229 PRK06704 RNA polymerase factor 37.4 87 0.0019 20.9 4.3 31 55-85 134-164 (228)
230 TIGR03826 YvyF flagellar opero 37.2 43 0.00094 20.7 2.6 27 54-80 47-73 (137)
231 cd04773 HTH_TioE_rpt2 Second H 37.1 49 0.0011 19.2 2.8 22 56-77 3-24 (108)
232 cd04782 HTH_BltR Helix-Turn-He 37.1 55 0.0012 18.6 2.9 21 56-76 3-23 (97)
233 PRK09744 DNA-binding transcrip 36.7 53 0.0012 18.3 2.6 18 56-73 13-30 (75)
234 PF13613 HTH_Tnp_4: Helix-turn 36.7 39 0.00085 16.9 2.0 22 56-77 22-43 (53)
235 cd04788 HTH_NolA-AlbR Helix-Tu 36.6 57 0.0012 18.5 2.9 21 56-76 3-23 (96)
236 TIGR02054 MerD mercuric resist 36.4 47 0.001 19.9 2.6 21 56-76 6-26 (120)
237 cd04767 HTH_HspR-like_MBC Heli 36.4 55 0.0012 19.8 2.9 22 56-77 4-25 (120)
238 PF04703 FaeA: FaeA-like prote 35.4 69 0.0015 17.0 2.9 21 56-76 18-38 (62)
239 PRK09975 DNA-binding transcrip 35.2 54 0.0012 20.8 3.0 40 39-79 18-57 (213)
240 cd04765 HTH_MlrA-like_sg2 Heli 34.9 66 0.0014 18.5 3.0 21 56-76 3-23 (99)
241 cd01107 HTH_BmrR Helix-Turn-He 34.8 52 0.0011 19.1 2.6 21 56-76 3-23 (108)
242 cd01111 HTH_MerD Helix-Turn-He 34.6 53 0.0012 19.1 2.6 21 56-76 3-23 (107)
243 cd01109 HTH_YyaN Helix-Turn-He 34.2 53 0.0011 19.1 2.6 21 56-76 3-23 (113)
244 PRK10100 DNA-binding transcrip 34.0 1.4E+02 0.003 19.6 5.9 45 32-82 155-199 (216)
245 cd01279 HTH_HspR-like Helix-Tu 33.9 60 0.0013 18.5 2.7 22 56-77 4-25 (98)
246 PRK08241 RNA polymerase factor 33.9 1.5E+02 0.0033 20.5 5.2 29 55-83 171-199 (339)
247 PF12793 SgrR_N: Sugar transpo 33.4 97 0.0021 18.4 3.6 33 38-72 6-38 (115)
248 PF00440 TetR_N: Bacterial reg 33.2 36 0.00077 16.4 1.5 23 56-78 19-41 (47)
249 PF11388 DotA: Phagosome traff 33.1 39 0.00084 19.7 1.8 25 61-85 23-47 (105)
250 PF13560 HTH_31: Helix-turn-he 33.0 42 0.00091 17.2 1.8 25 55-79 16-40 (64)
251 PRK13890 conjugal transfer pro 32.7 41 0.0009 20.1 2.0 23 56-78 21-43 (120)
252 PRK09726 antitoxin HipB; Provi 32.7 43 0.00094 18.6 2.0 22 56-77 28-49 (88)
253 PRK08215 sporulation sigma fac 32.6 1.5E+02 0.0033 19.7 6.0 47 32-83 209-255 (258)
254 PRK10430 DNA-binding transcrip 32.5 1.4E+02 0.0029 19.4 4.6 45 32-77 158-202 (239)
255 PF07471 Phage_Nu1: Phage DNA 32.3 51 0.0011 21.0 2.4 21 56-76 5-25 (164)
256 KOG3755|consensus 32.2 50 0.0011 25.8 2.6 57 26-82 647-707 (769)
257 TIGR02885 spore_sigF RNA polym 32.1 1.5E+02 0.0032 19.3 6.0 45 33-82 184-228 (231)
258 PF12844 HTH_19: Helix-turn-he 32.1 44 0.00096 16.9 1.8 24 55-78 14-37 (64)
259 PF08671 SinI: Anti-repressor 32.1 58 0.0013 14.7 2.9 20 56-75 8-27 (30)
260 PRK12534 RNA polymerase sigma 31.9 1.3E+02 0.0028 18.7 6.0 29 55-83 155-183 (187)
261 PRK09635 sigI RNA polymerase s 31.8 1.7E+02 0.0037 20.1 5.1 29 56-84 137-165 (290)
262 COG0789 SoxR Predicted transcr 31.6 62 0.0013 18.8 2.6 19 56-74 3-21 (124)
263 PF04539 Sigma70_r3: Sigma-70 31.6 74 0.0016 16.9 2.7 21 55-75 22-42 (78)
264 PF12833 HTH_18: Helix-turn-he 31.5 53 0.0012 17.4 2.2 15 60-74 17-31 (81)
265 PRK05572 sporulation sigma fac 31.5 1.6E+02 0.0034 19.6 6.1 48 32-84 202-249 (252)
266 PF09862 DUF2089: Protein of u 31.5 1.2E+02 0.0026 18.2 4.4 38 32-74 33-70 (113)
267 cd01282 HTH_MerR-like_sg3 Heli 31.1 65 0.0014 18.8 2.6 21 56-76 3-23 (112)
268 PHA02955 hypothetical protein; 31.1 61 0.0013 21.7 2.7 44 35-78 60-104 (213)
269 PRK13182 racA polar chromosome 31.0 71 0.0015 20.6 2.9 22 56-77 3-24 (175)
270 cd01110 HTH_SoxR Helix-Turn-He 30.8 62 0.0013 19.8 2.6 21 56-76 4-24 (139)
271 TIGR02997 Sig70-cyanoRpoD RNA 30.7 1.8E+02 0.0039 20.0 5.5 47 33-80 250-296 (298)
272 cd04772 HTH_TioE_rpt1 First He 30.7 68 0.0015 18.3 2.6 21 56-76 3-23 (99)
273 PRK10651 transcriptional regul 30.6 1.3E+02 0.0028 18.3 5.8 45 32-82 155-199 (216)
274 PRK12517 RNA polymerase sigma 30.6 1.4E+02 0.0031 18.8 6.1 32 55-86 146-177 (188)
275 PRK06596 RNA polymerase factor 30.6 1.8E+02 0.0039 19.9 5.8 49 33-84 231-279 (284)
276 PF04297 UPF0122: Putative hel 30.5 1.2E+02 0.0026 17.8 5.1 42 32-78 17-58 (101)
277 TIGR01557 myb_SHAQKYF myb-like 30.4 87 0.0019 16.2 5.1 50 29-78 2-54 (57)
278 TIGR01950 SoxR redox-sensitive 30.3 76 0.0016 19.5 2.9 21 56-76 4-24 (142)
279 PF12200 DUF3597: Domain of un 30.0 1.4E+02 0.003 18.4 4.2 30 51-80 83-117 (127)
280 PRK05911 RNA polymerase sigma 30.0 1.7E+02 0.0038 19.6 6.2 30 55-84 223-252 (257)
281 TIGR03830 CxxCG_CxxCG_HTH puta 29.9 1.2E+02 0.0026 17.6 4.5 22 57-78 82-103 (127)
282 PF08971 GlgS: Glycogen synthe 29.9 68 0.0015 17.4 2.3 24 65-89 37-60 (66)
283 PF08880 QLQ: QLQ; InterPro: 29.7 64 0.0014 15.3 2.0 14 31-44 1-14 (37)
284 cd04776 HTH_GnyR Helix-Turn-He 29.5 71 0.0015 18.9 2.6 20 56-75 3-22 (118)
285 TIGR02846 spore_sigmaK RNA pol 29.3 1.7E+02 0.0036 19.1 6.3 29 55-83 196-224 (227)
286 TIGR02051 MerR Hg(II)-responsi 29.3 69 0.0015 19.1 2.5 19 56-74 2-20 (124)
287 cd01108 HTH_CueR Helix-Turn-He 28.9 71 0.0015 19.0 2.6 21 56-76 3-23 (127)
288 cd06170 LuxR_C_like C-terminal 28.7 78 0.0017 15.1 5.9 24 55-78 17-40 (57)
289 PRK12373 NADH dehydrogenase su 28.5 1.6E+02 0.0035 21.7 4.6 34 38-71 40-73 (400)
290 PF10078 DUF2316: Uncharacteri 28.4 57 0.0012 18.7 2.0 30 38-71 12-41 (89)
291 cd04781 HTH_MerR-like_sg6 Heli 28.3 76 0.0016 18.7 2.6 21 56-76 3-23 (120)
292 TIGR02044 CueR Cu(I)-responsiv 27.8 76 0.0017 18.9 2.6 21 56-76 3-23 (127)
293 PRK15008 HTH-type transcriptio 27.7 81 0.0017 20.2 2.8 39 42-81 28-66 (212)
294 TIGR03613 RutR pyrimidine util 27.5 81 0.0018 19.7 2.8 37 42-79 18-54 (202)
295 PRK09514 zntR zinc-responsive 27.5 91 0.002 19.0 2.9 21 56-76 4-24 (140)
296 PF01325 Fe_dep_repress: Iron 27.3 60 0.0013 16.8 1.8 39 37-75 6-44 (60)
297 TIGR02043 ZntR Zn(II)-responsi 27.2 95 0.0021 18.7 2.9 21 56-76 4-24 (131)
298 PF13223 DUF4031: Protein of u 26.9 79 0.0017 17.9 2.3 20 53-76 23-42 (83)
299 PF12802 MarR_2: MarR family; 26.8 94 0.002 15.4 3.0 39 33-73 3-41 (62)
300 PRK10227 DNA-binding transcrip 26.8 83 0.0018 19.2 2.6 20 56-75 3-22 (135)
301 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.8 83 0.0018 18.8 2.6 21 56-76 3-23 (127)
302 PF08279 HTH_11: HTH domain; 26.7 91 0.002 15.2 3.7 22 55-76 17-38 (55)
303 PF08452 DNAP_B_exo_N: DNA pol 26.7 19 0.00042 15.0 -0.1 8 71-78 6-13 (22)
304 cd04770 HTH_HMRTR Helix-Turn-H 26.6 85 0.0018 18.4 2.6 21 56-76 3-23 (123)
305 PHA00542 putative Cro-like pro 26.4 75 0.0016 17.5 2.2 23 55-77 33-55 (82)
306 PRK07405 RNA polymerase sigma 26.0 2.3E+02 0.0051 19.7 5.6 51 33-84 257-307 (317)
307 PF01476 LysM: LysM domain; I 26.0 82 0.0018 14.5 2.5 19 55-73 8-26 (44)
308 KOG0044|consensus 26.0 1.4E+02 0.003 19.6 3.6 30 49-78 7-36 (193)
309 TIGR02984 Sig-70_plancto1 RNA 25.6 1.7E+02 0.0037 18.0 6.0 29 55-83 158-186 (189)
310 PF00325 Crp: Bacterial regula 25.4 84 0.0018 14.4 2.1 20 55-74 4-23 (32)
311 smart00354 HTH_LACI helix_turn 25.3 73 0.0016 16.8 2.0 23 56-78 3-25 (70)
312 PF11516 DUF3220: Protein of u 25.0 46 0.001 18.8 1.1 11 67-77 30-40 (106)
313 PF13022 HTH_Tnp_1_2: Helix-tu 24.9 94 0.002 19.5 2.6 23 53-75 34-56 (142)
314 cd04786 HTH_MerR-like_sg7 Heli 24.8 95 0.0021 18.8 2.6 20 56-75 3-22 (131)
315 PRK15369 two component system 24.4 1.7E+02 0.0037 17.5 5.9 46 31-82 148-193 (211)
316 cd04785 HTH_CadR-PbrR-like Hel 24.3 98 0.0021 18.4 2.6 21 56-76 3-23 (126)
317 cd04783 HTH_MerR1 Helix-Turn-H 24.2 97 0.0021 18.4 2.6 20 56-75 3-22 (126)
318 PRK13558 bacterio-opsin activa 24.1 1.3E+02 0.0029 22.7 3.8 41 31-71 606-648 (665)
319 cd04784 HTH_CadR-PbrR Helix-Tu 24.1 1E+02 0.0022 18.3 2.6 21 56-76 3-23 (127)
320 PF07750 GcrA: GcrA cell cycle 23.7 1.4E+02 0.0029 19.0 3.2 34 32-70 2-36 (162)
321 PRK13870 transcriptional regul 23.6 2.3E+02 0.005 18.8 6.2 27 57-83 192-218 (234)
322 cd04787 HTH_HMRTR_unk Helix-Tu 23.1 1.1E+02 0.0023 18.4 2.6 20 56-75 3-22 (133)
323 PRK10668 DNA-binding transcrip 22.8 1.2E+02 0.0025 19.3 2.9 42 38-80 17-58 (215)
324 PF01047 MarR: MarR family; I 22.7 1.1E+02 0.0025 15.0 3.9 39 33-75 1-39 (59)
325 PTZ00183 centrin; Provisional 22.4 1.8E+02 0.0039 17.1 5.4 40 26-65 4-48 (158)
326 PF08765 Mor: Mor transcriptio 22.1 1.7E+02 0.0038 16.9 3.4 26 55-80 74-99 (108)
327 PRK00767 transcriptional regul 22.1 1.5E+02 0.0033 18.2 3.3 38 41-79 18-55 (197)
328 PRK13749 transcriptional regul 22.0 1.2E+02 0.0026 18.2 2.6 19 56-74 6-24 (121)
329 cd04777 HTH_MerR-like_sg1 Heli 21.8 1.2E+02 0.0027 17.3 2.6 20 56-75 3-22 (107)
330 PRK05949 RNA polymerase sigma 21.7 3E+02 0.0065 19.4 5.9 50 33-83 267-316 (327)
331 TIGR03629 arch_S13P archaeal r 21.7 98 0.0021 19.3 2.3 15 32-46 51-65 (144)
332 PF03457 HA: Helicase associat 21.6 1.3E+02 0.0028 15.6 2.5 18 67-84 35-52 (68)
333 TIGR02850 spore_sigG RNA polym 21.6 2.6E+02 0.0056 18.6 5.0 46 32-82 206-251 (254)
334 cd04769 HTH_MerR2 Helix-Turn-H 21.6 1.5E+02 0.0031 17.3 2.9 21 56-76 3-23 (116)
335 PRK00215 LexA repressor; Valid 21.4 1.7E+02 0.0037 18.7 3.5 43 33-77 2-48 (205)
336 PHA01083 hypothetical protein 21.1 1.1E+02 0.0024 19.3 2.4 32 42-76 8-39 (149)
337 cd00131 PAX Paired Box domain 20.9 2E+02 0.0044 17.2 7.4 46 32-77 75-127 (128)
338 PRK15451 tRNA cmo(5)U34 methyl 20.5 2.7E+02 0.0058 18.4 5.4 43 33-77 190-233 (247)
339 PF00356 LacI: Bacterial regul 20.4 1.3E+02 0.0028 14.8 2.2 22 56-77 2-23 (46)
340 PF09301 DUF1970: Domain of un 20.3 62 0.0013 18.6 1.1 12 69-80 18-29 (117)
341 cd04778 HTH_MerR-like_sg2 Heli 20.0 1.2E+02 0.0026 20.1 2.6 20 56-75 4-23 (219)
No 1
>KOG0488|consensus
Probab=99.84 E-value=5.8e-21 Score=130.92 Aligned_cols=67 Identities=31% Similarity=0.486 Sum_probs=63.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 21 ~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
..++|.|+.||.||..|+..||..|+...|++..+|..||..|||+..||++||||||+|||++...
T Consensus 167 ~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 167 STPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 3457888999999999999999999999999999999999999999999999999999999998765
No 2
>KOG0850|consensus
Probab=99.83 E-value=1.1e-20 Score=123.21 Aligned_cols=68 Identities=29% Similarity=0.458 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 20 GMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 20 ~~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
...++|.|++||.++..|+..|...|+.++|+...||.+||..|||+..||+|||||||.|.||..+.
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 46677899999999999999999999999999999999999999999999999999999999998873
No 3
>KOG0489|consensus
Probab=99.83 E-value=1e-20 Score=127.39 Aligned_cols=66 Identities=32% Similarity=0.469 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhccc
Q psy14049 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMS 89 (93)
Q Consensus 24 ~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~ 89 (93)
.+.+|.|+.||..|+-.||..|..|.|++...|.+||..|.|+++||+|||||||+||||..+...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 457889999999999999999999999999999999999999999999999999999999776543
No 4
>KOG0484|consensus
Probab=99.82 E-value=7.6e-21 Score=110.73 Aligned_cols=66 Identities=26% Similarity=0.458 Sum_probs=61.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 22 ~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
..+|.+|.|+.||..|+..|+..|...+||++..+++||..+.|+++.|++||||||++.+++.+.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 355788999999999999999999999999999999999999999999999999999999997653
No 5
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.81 E-value=1.9e-19 Score=95.73 Aligned_cols=57 Identities=35% Similarity=0.640 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 27 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
++.|+.|+.+|+..|+..|..++||+..++..||..+||+..+|.+||+|+|.++|+
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 467899999999999999999999999999999999999999999999999999885
No 6
>KOG0842|consensus
Probab=99.80 E-value=3.6e-20 Score=126.02 Aligned_cols=67 Identities=30% Similarity=0.414 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhccc
Q psy14049 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMS 89 (93)
Q Consensus 23 ~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~ 89 (93)
..++||.|..|+..|+.+||..|....|++..||+.||..+.|++.||+|||||||.|.||+.....
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 5567888899999999999999999999999999999999999999999999999999999776543
No 7
>KOG0843|consensus
Probab=99.79 E-value=1.8e-19 Score=113.89 Aligned_cols=63 Identities=32% Similarity=0.530 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
+.+|.||.|+.+|+..|+..|+.++|....++..||..|+|++.||+|||||||.|-||....
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 788999999999999999999999999999999999999999999999999999999987654
No 8
>KOG2251|consensus
Probab=99.79 E-value=1.4e-19 Score=117.52 Aligned_cols=68 Identities=29% Similarity=0.500 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 21 ~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
+.+++.||+||.|+..|+++|+..|.+.+||+...+++||.+++|.+.+|+|||+|||+|++++..+.
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 56778999999999999999999999999999999999999999999999999999999999988764
No 9
>KOG0493|consensus
Probab=99.78 E-value=6.4e-19 Score=117.12 Aligned_cols=61 Identities=34% Similarity=0.607 Sum_probs=57.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
-+|+||.||.+|+..|+..|+.|.|++...+.+||.+|+|.+.||++||||+|+|.||...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 3678999999999999999999999999999999999999999999999999999998654
No 10
>KOG0485|consensus
Probab=99.76 E-value=9.9e-19 Score=113.54 Aligned_cols=65 Identities=29% Similarity=0.427 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 22 ~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|+.||+|+..|+..||..|+...|++..++.-||.+|.|++.||++||||||.|||++..
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 44478889999999999999999999999999999999999999999999999999999999754
No 11
>KOG0494|consensus
Probab=99.76 E-value=1.2e-18 Score=115.69 Aligned_cols=65 Identities=28% Similarity=0.410 Sum_probs=60.1
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcccC
Q psy14049 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMSK 90 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~~ 90 (93)
+|+.||.||..|+..||..|....||+...++.||..+.|.++.|+|||||||+||||..+....
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 44459999999999999999999999999999999999999999999999999999998876654
No 12
>KOG0487|consensus
Probab=99.76 E-value=4.6e-19 Score=120.68 Aligned_cols=66 Identities=24% Similarity=0.338 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhccc
Q psy14049 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMS 89 (93)
Q Consensus 24 ~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~ 89 (93)
+..|++|-.+|+.|+..||..|..|.|++...|.+|+..|+|+++||+|||||||+|.||..+...
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 456677788999999999999999999999999999999999999999999999999999886444
No 13
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.72 E-value=3.4e-17 Score=86.52 Aligned_cols=55 Identities=42% Similarity=0.751 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 28 KRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 28 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
+.|+.|+.+++..|+..|..++||+..++..||..+||+..+|++||+|+|++.+
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 4567899999999999999999999999999999999999999999999998753
No 14
>KOG0492|consensus
Probab=99.72 E-value=8.1e-18 Score=108.58 Aligned_cols=62 Identities=31% Similarity=0.431 Sum_probs=58.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
..|++|+.||..|+..||.-|...+|+++.++.+++..|.|++.||+|||||||+|.||.+.
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 35778999999999999999999999999999999999999999999999999999998654
No 15
>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=99.72 E-value=6e-17 Score=86.22 Aligned_cols=57 Identities=44% Similarity=0.772 Sum_probs=53.6
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 28 KRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 28 r~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
+.+..++..++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456789999999999999999999999999999999999999999999999998763
No 16
>KOG0848|consensus
Probab=99.70 E-value=8.2e-18 Score=112.02 Aligned_cols=63 Identities=24% Similarity=0.350 Sum_probs=58.2
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 26 KRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
+-+-|.++|..|.-.||+.|..++|.++..+.+||.-|||+++||+|||||||+|+||..+..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 344578999999999999999999999999999999999999999999999999999977654
No 17
>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=99.69 E-value=3e-17 Score=87.37 Aligned_cols=52 Identities=25% Similarity=0.546 Sum_probs=50.1
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 27 RKRRTSFTPQALELLNAHFERNTH----PSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 27 rr~r~~~t~~q~~~L~~~f~~~~~----p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
+|.||.||.+|+..|+..|..++| |+..++.+||..+||++.+|++||||.+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 788999999999999999999999 9999999999999999999999999964
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.65 E-value=4.6e-16 Score=97.68 Aligned_cols=66 Identities=29% Similarity=0.381 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 22 EPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 22 ~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
..+..++.|.+.+..|+.+|+..|..++||+...+..|+..++|+++.|++||||+|++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 344566777888999999999999999999999999999999999999999999999999986543
No 19
>KOG0491|consensus
Probab=99.64 E-value=1.2e-16 Score=100.00 Aligned_cols=64 Identities=33% Similarity=0.471 Sum_probs=59.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
++++.|++|+..|+..|+..|+...|.+..++.+||..++|++.||+.||||+|+|-||..+..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 4567799999999999999999999999999999999999999999999999999999976643
No 20
>KOG0483|consensus
Probab=99.64 E-value=2.5e-16 Score=101.99 Aligned_cols=62 Identities=21% Similarity=0.425 Sum_probs=56.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 27 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
...+.+|+.+|+..|+..|..+.+..+..+..||..|||.++||.+|||||||+||..+...
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~ 112 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEK 112 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhh
Confidence 33445799999999999999999999999999999999999999999999999999866543
No 21
>KOG0844|consensus
Probab=99.63 E-value=1.3e-16 Score=108.22 Aligned_cols=66 Identities=27% Similarity=0.387 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 21 ~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
+.....||.||.||.+|+..||+.|-+..|.+...+.+||..|+|.+..|++||||||+|+|++..
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRl 241 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRL 241 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhh
Confidence 345567899999999999999999999999999999999999999999999999999999999764
No 22
>KOG3802|consensus
Probab=99.62 E-value=1.1e-16 Score=111.33 Aligned_cols=75 Identities=41% Similarity=0.702 Sum_probs=64.6
Q ss_pred CCCCCccccCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 11 GQNHLTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 11 ~~~~~~~~~~~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
++....+...... ++|+.||.|.......||.+|..|+.|+..++..||.+|+|.+.+|+|||||||.|.||...
T Consensus 280 ~~~~~~e~i~a~~-RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 280 GSPNSIEKIGAQS-RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred CCCCCHHHhhccc-cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3444444444334 67788999999999999999999999999999999999999999999999999999999765
No 23
>KOG0486|consensus
Probab=99.59 E-value=6.8e-16 Score=104.77 Aligned_cols=63 Identities=33% Similarity=0.541 Sum_probs=59.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
|++|.|+.|+..|+..||..|++|.||+...+++||.-.+|++..|++||+|||+||++...-
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 678899999999999999999999999999999999999999999999999999999986543
No 24
>KOG4577|consensus
Probab=99.56 E-value=4.4e-15 Score=100.14 Aligned_cols=66 Identities=23% Similarity=0.472 Sum_probs=61.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcccC
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMSK 90 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~~ 90 (93)
..+|+||.+|..|++.|+..|..++.|....+++|+..+||..+.|++||||||+|+|+..+...+
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 468899999999999999999999999999999999999999999999999999999998776543
No 25
>KOG0847|consensus
Probab=99.50 E-value=2e-14 Score=93.87 Aligned_cols=62 Identities=23% Similarity=0.520 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 24 SKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 24 ~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
.+++..|..|+..|+..|+..|+...|+...++.++|..+|+++.+|+|||||||.||||..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 45677788999999999999999999999999999999999999999999999999999854
No 26
>KOG0490|consensus
Probab=99.36 E-value=3.5e-13 Score=88.62 Aligned_cols=64 Identities=28% Similarity=0.335 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 23 ~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
..+.++.|+.|+..|++.|+..|+.++||+...++.||..+++++..|++||||+|+++++...
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 4578889999999999999999999999999999999999999999999999999999998764
No 27
>KOG0849|consensus
Probab=99.33 E-value=2.7e-12 Score=89.81 Aligned_cols=66 Identities=32% Similarity=0.532 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 21 MEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 21 ~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++.++.|+.|+..|+..|+..|..++||++..++.||.++++++..|++||+|+|+++++...
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 445567788999999999999999999999999999999999999999999999999999999774
No 28
>KOG0775|consensus
Probab=99.29 E-value=4.9e-12 Score=84.82 Aligned_cols=53 Identities=28% Similarity=0.429 Sum_probs=47.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
|...-...|..+|..++||++.++.+||+++||+..||-+||+|||.++|...
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 44444778999999999999999999999999999999999999999999543
No 29
>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=99.13 E-value=1.2e-10 Score=57.67 Aligned_cols=34 Identities=41% Similarity=0.607 Sum_probs=29.2
Q ss_pred hCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 47 RNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 47 ~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
.+|||+..++..||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999999975
No 30
>KOG1168|consensus
Probab=99.06 E-value=2.6e-11 Score=82.18 Aligned_cols=62 Identities=37% Similarity=0.718 Sum_probs=57.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
-++|.||.+...+.+.||++|...+.|+...+..||+.|.|.+..|++||+|.|.|.||...
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 35677899999999999999999999999999999999999999999999999999998543
No 31
>KOG0774|consensus
Probab=99.01 E-value=1.6e-10 Score=77.41 Aligned_cols=61 Identities=34% Similarity=0.488 Sum_probs=55.2
Q ss_pred CCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 26 KRKRRTSFTPQALELLNAHF---ERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
.+|.|..|+....++|..+| ..||||+..++++||.+++++..||.+||.|+|-+++|...
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 35667899999999999999 46899999999999999999999999999999999988543
No 32
>KOG2252|consensus
Probab=98.98 E-value=1.5e-09 Score=78.66 Aligned_cols=57 Identities=30% Similarity=0.388 Sum_probs=54.1
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHh
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQAL 81 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~ 81 (93)
..+++|.+||..|...|...|+.+++|+....+.|+.+|+|....|.+||.|.|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 467779999999999999999999999999999999999999999999999999885
No 33
>KOG0490|consensus
Probab=98.44 E-value=3.5e-07 Score=60.11 Aligned_cols=63 Identities=33% Similarity=0.624 Sum_probs=58.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 23 PSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 23 ~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..+.++.++.+...++..+...|..+++|+...+..|+..+|++...|++||+|+|.+.++..
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 446778889999999999999999999999999999999999999999999999999998753
No 34
>KOG1146|consensus
Probab=98.14 E-value=4.2e-06 Score=66.16 Aligned_cols=62 Identities=27% Similarity=0.478 Sum_probs=58.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 25 KKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 25 k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
.++..|+.++..|+..+...|....||...+.+.|...+++.++.|++||+|.|.+.++...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 46778999999999999999999999999999999999999999999999999999998655
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.89 E-value=2.7e-05 Score=40.96 Aligned_cols=42 Identities=12% Similarity=0.347 Sum_probs=31.2
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 37 ALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 37 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
.+..|+.+|...+++...+...|+.+.+|+..+|+.||-.+.
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999999999999999999999999999997654
No 36
>KOG0773|consensus
Probab=97.72 E-value=2.6e-05 Score=54.46 Aligned_cols=58 Identities=31% Similarity=0.454 Sum_probs=49.1
Q ss_pred CCCCCCCCCHHHHHHHHHHh-h--hCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 26 KRKRRTSFTPQALELLNAHF-E--RNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f-~--~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
..+....+......+|+.+. + ..+||+..++..||.++||+..||.+||-|.|.+.-+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 45555688999999999874 2 3589999999999999999999999999999987654
No 37
>KOG3623|consensus
Probab=97.04 E-value=0.0019 Score=49.33 Aligned_cols=48 Identities=27% Similarity=0.468 Sum_probs=44.7
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...|..+|..|..|+..+...+|.+.|++.+.|+.||.+.++......
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 678999999999999999999999999999999999999999877654
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=96.13 E-value=0.026 Score=29.20 Aligned_cols=47 Identities=19% Similarity=0.301 Sum_probs=34.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 27 RKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 27 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
++.|..+|-++...+-..++... ....||..+|++..+|..|..|+-
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 35677899988877777777665 477899999999999999998853
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=92.34 E-value=0.76 Score=22.92 Aligned_cols=46 Identities=17% Similarity=0.369 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.+++.+..++...|..+ ....++|..+|++...|..+...-..+.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 46788888998888322 34678899999999999999876655544
No 40
>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=89.28 E-value=0.49 Score=25.52 Aligned_cols=46 Identities=17% Similarity=0.351 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 29 RRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 29 ~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
.+..|+.++...+-..+.. +......+|..+|+++..+..|-.--+
T Consensus 3 ~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence 3567888887766555421 224677899999999999999986443
No 41
>KOG1146|consensus
Probab=88.91 E-value=1.5 Score=36.18 Aligned_cols=71 Identities=14% Similarity=0.204 Sum_probs=59.5
Q ss_pred CccccCCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 15 LTEFIGMEPSKKRKRRTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 15 ~~~~~~~~~~k~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..+...+.+-..+..+..+-.++...|-.+|-.+.-|+......|......+.+.+.+||+|-+.+.++..
T Consensus 694 ~~g~~~~~~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 694 EVGGGESLSPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CCCCCCCCCcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 33333334445677778888899999999999999999999999999999999999999999999998866
No 42
>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=88.10 E-value=2.2 Score=21.42 Aligned_cols=42 Identities=14% Similarity=0.279 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
+++.+...+...|. ......++|..+|++...|+.|...-+.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45555666655443 3346788999999999999999985554
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=88.02 E-value=1.9 Score=20.73 Aligned_cols=43 Identities=16% Similarity=0.258 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
++..+...+...|... .....+|..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 5666677776665322 245677999999999999999765543
No 44
>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=87.71 E-value=0.63 Score=24.81 Aligned_cols=21 Identities=29% Similarity=0.621 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFq 75 (93)
....||.+||+++.+|..|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 356789999999999999964
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=86.24 E-value=6.1 Score=24.61 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=38.8
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
+.+++.|...|...+. . ....++|..+|++...|..|-...+.+.++...
T Consensus 5 ~~Lt~rqreVL~lr~~--G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 5 SFLTERQIEVLRLRER--G----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred cCCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5688889999877432 1 235688999999999999999988887776543
No 46
>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=85.15 E-value=3.8 Score=21.20 Aligned_cols=42 Identities=24% Similarity=0.412 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCChHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTH--PSGTEITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~v~~WF 74 (93)
+|+.|.+.|...+...-| |-......||..+|+++..+..-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 578899999999876644 555567889999999998765544
No 47
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=84.52 E-value=6.1 Score=24.26 Aligned_cols=33 Identities=18% Similarity=0.264 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
...++|..+|++...|..|..--+.+.++....
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999999888877765443
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=84.19 E-value=6.6 Score=24.97 Aligned_cols=32 Identities=9% Similarity=0.143 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-|.+.+....
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 45688999999999999999888887776543
No 49
>PF13518 HTH_28: Helix-turn-helix domain
Probab=82.70 E-value=2.5 Score=20.84 Aligned_cols=24 Identities=21% Similarity=0.545 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
...+|..+|++..+|..|.+.-+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~~ 38 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYRE 38 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHHh
Confidence 556899999999999999975443
No 50
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=82.30 E-value=9 Score=23.41 Aligned_cols=34 Identities=12% Similarity=0.269 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
...+||..+|++...|+.+...-+.+.+......
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~~~ 162 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIYEQM 162 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHh
Confidence 4567899999999999999988888877765543
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=81.37 E-value=8.6 Score=23.20 Aligned_cols=29 Identities=10% Similarity=0.158 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.+...-+.+.++
T Consensus 124 s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 124 TMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 46789999999999999999876666554
No 52
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=80.56 E-value=11 Score=23.73 Aligned_cols=34 Identities=12% Similarity=0.171 Sum_probs=27.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
...++|..+|++...|+.+...-|.+.++.....
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLADL 179 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHhc
Confidence 3568899999999999999998888887765543
No 53
>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=80.14 E-value=11 Score=23.95 Aligned_cols=38 Identities=13% Similarity=0.211 Sum_probs=30.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcccCCC
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMSKGS 92 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~~~~ 92 (93)
...+||..+|++...|++....-|.+.++.......||
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~~~ 186 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACLSINWFGE 186 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhhhc
Confidence 45789999999999999999888888877666554443
No 54
>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=79.78 E-value=2.7 Score=22.08 Aligned_cols=20 Identities=30% Similarity=0.541 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..+||..+|++...|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 56789999999999999986
No 55
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=79.49 E-value=12 Score=23.38 Aligned_cols=32 Identities=22% Similarity=0.267 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...+||..+|++...|+.++..-+.+.+....
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999999988888776543
No 56
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=79.48 E-value=12 Score=25.22 Aligned_cols=39 Identities=18% Similarity=0.263 Sum_probs=32.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcccCCCC
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMMSKGSL 93 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~~~~~~ 93 (93)
...++|..+|++...|......-+.+.++.......|.|
T Consensus 230 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l~~~~~~~~ 268 (268)
T PRK06288 230 TLKEIGKVLGVTESRISQLHTKAVLQLRAKLAEIKKGIL 268 (268)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHhccCC
Confidence 357889999999999999999888888887777766654
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=79.33 E-value=3.3 Score=20.10 Aligned_cols=22 Identities=23% Similarity=0.196 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|+++..|..|.+..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999997654
No 58
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=79.33 E-value=8.9 Score=22.83 Aligned_cols=44 Identities=16% Similarity=0.108 Sum_probs=29.4
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy14049 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 30 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnr 77 (93)
+.+|+.+.....-.....+.. ....+|..+|+++..|..|...-
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y 53 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQY 53 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHH
Confidence 456788775544433333332 35567999999999999998643
No 59
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=79.07 E-value=2.7 Score=20.72 Aligned_cols=21 Identities=29% Similarity=0.589 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFq 75 (93)
...++|..+|++...|..|.+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 467789999999999999985
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=78.85 E-value=12 Score=22.89 Aligned_cols=31 Identities=19% Similarity=0.322 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|..|...-+.+.++..
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766644
No 61
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=78.68 E-value=14 Score=23.72 Aligned_cols=32 Identities=19% Similarity=0.105 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-+.+.++...
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45788999999999999999877777776543
No 62
>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=78.36 E-value=7.2 Score=19.88 Aligned_cols=45 Identities=20% Similarity=0.218 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.||..+...|.....-. ...++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 57888888887765433 3678899999999999999987766654
No 63
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=77.85 E-value=12 Score=23.86 Aligned_cols=33 Identities=12% Similarity=0.128 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
...++|..+|++...|+++...-|.+.++....
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~ 163 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQL 163 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhc
Confidence 356889999999999999999888877765543
No 64
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=77.43 E-value=6.8 Score=19.10 Aligned_cols=40 Identities=23% Similarity=0.355 Sum_probs=20.6
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
..+|.++...++..+... ....+||..+|.++..|..+.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 357777877777775433 4466799999999999988875
No 65
>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=77.21 E-value=11 Score=23.47 Aligned_cols=32 Identities=13% Similarity=0.165 Sum_probs=26.3
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|+++...-|.+.+...
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34578999999999999999987777776654
No 66
>KOG0773|consensus
Probab=77.20 E-value=4.6 Score=28.28 Aligned_cols=42 Identities=31% Similarity=0.420 Sum_probs=36.5
Q ss_pred hhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 46 ERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 46 ~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
..++||+..+...++....++..++.+||-|.+.+.......
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~ 158 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKM 158 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCC
Confidence 558999999999999999999999999999999887765443
No 67
>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=77.16 E-value=1.5 Score=24.23 Aligned_cols=32 Identities=16% Similarity=0.263 Sum_probs=23.3
Q ss_pred hhhCCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy14049 45 FERNTHPSGTEITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 45 f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqn 76 (93)
|....|...-...+||..+|++...|+.|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33333333345778999999999999999974
No 68
>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=76.16 E-value=16 Score=22.69 Aligned_cols=32 Identities=19% Similarity=0.221 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-|.+.+....
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877777776554
No 69
>PRK10072 putative transcriptional regulator; Provisional
Probab=75.92 E-value=9.1 Score=22.19 Aligned_cols=40 Identities=18% Similarity=0.255 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
.+...+..|......+ ..+||..+|++...|..|...++.
T Consensus 33 ~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3566666665543222 678899999999999999987764
No 70
>PRK00118 putative DNA-binding protein; Validated
Probab=75.83 E-value=14 Score=21.81 Aligned_cols=48 Identities=8% Similarity=0.143 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
.++..+...+...|... ....++|..+|+++..|..|....+.+.+..
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34566666665554332 2456789999999999999998777766653
No 71
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=75.66 E-value=17 Score=22.64 Aligned_cols=30 Identities=17% Similarity=0.302 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+++...-|.+.++.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777776664
No 72
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=74.51 E-value=16 Score=22.68 Aligned_cols=32 Identities=13% Similarity=0.267 Sum_probs=26.0
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|++++..-|.+.+...
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 34578899999999999999987777766643
No 73
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=73.98 E-value=16 Score=23.08 Aligned_cols=32 Identities=13% Similarity=0.153 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|+.++..-+.+.++..
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999999987777776643
No 74
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=73.71 E-value=18 Score=22.03 Aligned_cols=30 Identities=17% Similarity=0.155 Sum_probs=25.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..++|..+|++...|++....-|.+.+...
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999987777766644
No 75
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=73.51 E-value=5 Score=21.03 Aligned_cols=21 Identities=24% Similarity=0.349 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|=..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999653
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=73.50 E-value=14 Score=22.55 Aligned_cols=29 Identities=17% Similarity=0.233 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.+...-|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35688999999999999999877766654
No 77
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=73.23 E-value=17 Score=22.90 Aligned_cols=34 Identities=24% Similarity=0.368 Sum_probs=27.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
...++|..+|++...|.+..+--+.+.++...-.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~~~~ 182 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNKLNI 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcccCc
Confidence 3568899999999999999987777777755433
No 78
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=72.33 E-value=20 Score=22.00 Aligned_cols=32 Identities=16% Similarity=0.189 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++..--|.+.++...
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877777776543
No 79
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=71.95 E-value=22 Score=22.34 Aligned_cols=30 Identities=13% Similarity=0.134 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+.+...-+.+.++.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999998777766653
No 80
>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=71.94 E-value=19 Score=21.71 Aligned_cols=29 Identities=28% Similarity=0.329 Sum_probs=23.0
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
....++|..+|++...|.++...-|.+.+
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 34678899999999999999876665544
No 81
>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=71.87 E-value=6.5 Score=18.68 Aligned_cols=19 Identities=21% Similarity=0.282 Sum_probs=15.3
Q ss_pred HHHHHHhCCChHHHHHHHH
Q psy14049 57 TTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 57 ~~la~~~~l~~~~v~~WFq 75 (93)
.++|..+|++...|+.|=.
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 4679999999999999954
No 82
>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=71.82 E-value=7.2 Score=18.41 Aligned_cols=23 Identities=22% Similarity=0.400 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
..++|..+|++...|..|.++..
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 35789999999999999987654
No 83
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=71.60 E-value=17 Score=23.73 Aligned_cols=40 Identities=23% Similarity=0.452 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCChHHHH
Q psy14049 32 SFTPQALELLNAHFERNTH--PSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~v~ 71 (93)
.+|..|++.|...|...-| |=......||..+|+++..+.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ 196 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS 196 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 6999999999999976543 555667889999999997644
No 84
>PRK06930 positive control sigma-like factor; Validated
Probab=71.50 E-value=22 Score=22.58 Aligned_cols=51 Identities=10% Similarity=0.141 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
.+++.+..++...|... ....++|..+|++...|+.+...-+.+.+.....
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~~ 164 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQINE 164 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 34555555555433211 2356789999999999999999888887765543
No 85
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=71.19 E-value=23 Score=22.37 Aligned_cols=31 Identities=6% Similarity=0.185 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|+++..|+++...-|.+.+...
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999987777776643
No 86
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=71.17 E-value=24 Score=22.42 Aligned_cols=32 Identities=13% Similarity=0.127 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...+||..+|++...|+++..--|.+.++...
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999988887776544
No 87
>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=70.83 E-value=20 Score=21.43 Aligned_cols=29 Identities=14% Similarity=0.305 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|+++..|+.+...-+.+.++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999998866666554
No 88
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=70.69 E-value=7.5 Score=16.50 Aligned_cols=38 Identities=18% Similarity=0.396 Sum_probs=25.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 74 (93)
.++.+....+...+.. .+ ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 3556666666555542 22 45577899999999888873
No 89
>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=70.29 E-value=23 Score=21.97 Aligned_cols=30 Identities=17% Similarity=0.172 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|++....-|.+.++.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 346889999999999999998777776653
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=69.53 E-value=22 Score=21.47 Aligned_cols=31 Identities=13% Similarity=0.277 Sum_probs=25.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
..++|..+|++...|++....-+.+.+....
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5688999999999999999877777666543
No 91
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=69.51 E-value=23 Score=21.56 Aligned_cols=31 Identities=10% Similarity=0.205 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+....-.+.+.++..
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999887777766644
No 92
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=69.30 E-value=14 Score=21.36 Aligned_cols=40 Identities=10% Similarity=0.135 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRI 72 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 72 (93)
+.++|...-.+.|+.|--.+......+|..++.++..|+.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 4567776666666666555556778899999998876553
No 93
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=68.69 E-value=26 Score=21.99 Aligned_cols=32 Identities=9% Similarity=0.291 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|++-...-|.+.+....
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999888877776543
No 94
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=68.24 E-value=23 Score=22.33 Aligned_cols=31 Identities=19% Similarity=0.192 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+..+..-|.+.++..
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999987777766644
No 95
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=68.08 E-value=9.7 Score=19.92 Aligned_cols=21 Identities=14% Similarity=0.311 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|+++..++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 356899999999999999764
No 96
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=67.90 E-value=9.1 Score=20.13 Aligned_cols=21 Identities=29% Similarity=0.444 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|+.+|+++..++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999864
No 97
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=67.78 E-value=13 Score=22.91 Aligned_cols=34 Identities=12% Similarity=0.168 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 53 GTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 53 ~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
.....++|..+|++...|++.+..-|.+.++...
T Consensus 136 g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 136 DLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3346789999999999999999888887776543
No 98
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=67.75 E-value=19 Score=21.28 Aligned_cols=42 Identities=14% Similarity=0.395 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
.++..++..+...+..+ ...+|.-+|++...|+.|=++|+.-
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 37888888888877544 4678999999999999999987653
No 99
>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=67.56 E-value=22 Score=20.67 Aligned_cols=29 Identities=17% Similarity=0.287 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|+++..|..+...-+.+.++
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45688999999999999999876666554
No 100
>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=67.46 E-value=17 Score=19.24 Aligned_cols=17 Identities=24% Similarity=0.438 Sum_probs=14.5
Q ss_pred HHHHhCCChHHHHHHHH
Q psy14049 59 LAHQLGYEREVIRIWFC 75 (93)
Q Consensus 59 la~~~~l~~~~v~~WFq 75 (93)
.|.++|++..+|+-|-+
T Consensus 31 aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 31 AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp HHHHTTS-HHHHHHHHT
T ss_pred HHHHhCccHHHHHHHHH
Confidence 48999999999999985
No 101
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=67.36 E-value=28 Score=21.77 Aligned_cols=30 Identities=20% Similarity=0.422 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+++...-+.+.+..
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 356789999999999999998777666543
No 102
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=67.05 E-value=6.3 Score=20.23 Aligned_cols=24 Identities=21% Similarity=0.246 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
....||...|++...|..|+.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 356789999999999999998773
No 103
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=66.33 E-value=34 Score=22.45 Aligned_cols=31 Identities=10% Similarity=0.206 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+.+...-+.+.++..
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578999999999999999998888877654
No 104
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=65.85 E-value=22 Score=22.27 Aligned_cols=31 Identities=16% Similarity=0.326 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|++....-|.+.+...
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999987777776644
No 105
>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=65.68 E-value=14 Score=23.35 Aligned_cols=34 Identities=12% Similarity=0.128 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
....+||..+|++...|+++...-|.+.++....
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 181 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLVD 181 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4467899999999999999999888887776543
No 106
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=64.25 E-value=35 Score=22.34 Aligned_cols=32 Identities=19% Similarity=0.149 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|+.+...-+.+.|+..
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999987777777643
No 107
>PRK04217 hypothetical protein; Provisional
Probab=64.16 E-value=28 Score=20.70 Aligned_cols=51 Identities=12% Similarity=0.096 Sum_probs=38.2
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 30 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
-..++.++...+...|...- ...+||..+|++...|...+...+.+.+...
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 45678888877776653322 4677999999999999999987777766543
No 108
>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=64.07 E-value=12 Score=19.44 Aligned_cols=20 Identities=25% Similarity=0.463 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...+..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35689999999999999986
No 109
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=63.87 E-value=35 Score=22.63 Aligned_cols=32 Identities=16% Similarity=0.210 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...+||..+|++...|++....-|.+.++...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999888887776543
No 110
>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=63.79 E-value=17 Score=21.87 Aligned_cols=33 Identities=15% Similarity=0.135 Sum_probs=26.0
Q ss_pred CCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 51 PSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 51 p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
.......++|..+|+++..|.++..--+.+.++
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999999866666554
No 111
>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=63.20 E-value=5.7 Score=19.52 Aligned_cols=20 Identities=15% Similarity=0.165 Sum_probs=18.2
Q ss_pred HHHHHhCCChHHHHHHHHHH
Q psy14049 58 TLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 58 ~la~~~~l~~~~v~~WFqnr 77 (93)
.||..+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 47999999999999999887
No 112
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=63.18 E-value=32 Score=21.66 Aligned_cols=29 Identities=24% Similarity=0.182 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...+||..+|++...|++....-|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35689999999999999999877766665
No 113
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=62.53 E-value=34 Score=21.00 Aligned_cols=31 Identities=16% Similarity=0.161 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+++...-|.+.+...
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999987777766543
No 114
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=62.52 E-value=32 Score=20.83 Aligned_cols=34 Identities=18% Similarity=0.283 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
...++|..+|++...|+......+.+.+......
T Consensus 123 s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~~~ 156 (159)
T PRK12527 123 SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMRQW 156 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHhc
Confidence 3468899999999999999987777777665433
No 115
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=62.49 E-value=22 Score=22.66 Aligned_cols=37 Identities=22% Similarity=0.223 Sum_probs=31.5
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 35 PQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 35 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
..-+..|........|.+......+|..+|++...|.
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 4557788888888889999999999999999987753
No 116
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=62.49 E-value=15 Score=21.28 Aligned_cols=37 Identities=16% Similarity=0.272 Sum_probs=19.2
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
+...+-.|+.|+||+..--.. ==.|||.+|++...++
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~--------------aRRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ--------------ARRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH--------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc--------------cccchhhhHHHHHHHH
Confidence 334455588899997431111 0258888888766554
No 117
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=62.39 E-value=20 Score=22.51 Aligned_cols=32 Identities=13% Similarity=0.233 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|++....-|.+.++...
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999988888777654
No 118
>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=62.37 E-value=33 Score=20.82 Aligned_cols=31 Identities=13% Similarity=0.209 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+++...-+.+.++..
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999988777777644
No 119
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=62.09 E-value=36 Score=21.20 Aligned_cols=30 Identities=17% Similarity=0.108 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+++...-|.+.+..
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998766666554
No 120
>smart00595 MADF subfamily of SANT domain.
Probab=61.28 E-value=23 Score=19.47 Aligned_cols=32 Identities=19% Similarity=0.330 Sum_probs=27.1
Q ss_pred HHHHHHhCCChHHHHHHHHHHHHHhhHhhhcc
Q psy14049 57 TTLAHQLGYEREVIRIWFCNKRQALKNTVRMM 88 (93)
Q Consensus 57 ~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~~ 88 (93)
..||..+|.+...|+.-+.|-|..+++.....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999988875443
No 121
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=61.12 E-value=37 Score=20.97 Aligned_cols=31 Identities=13% Similarity=0.192 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
.-.++|..+|++...|+++....+.+.+...
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999988777776543
No 122
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=60.26 E-value=41 Score=21.23 Aligned_cols=32 Identities=9% Similarity=0.199 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+.....-|.+.++...
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35789999999999999999888877776544
No 123
>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=59.97 E-value=38 Score=20.77 Aligned_cols=30 Identities=13% Similarity=0.277 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|++...--+.+.++.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999998777766653
No 124
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=59.84 E-value=43 Score=21.40 Aligned_cols=32 Identities=16% Similarity=0.064 Sum_probs=26.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-+.+.++...
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 35688999999999999999877777776543
No 125
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=59.67 E-value=47 Score=21.76 Aligned_cols=31 Identities=10% Similarity=0.067 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|++....-|.+.+...
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4568899999999999999987777777654
No 126
>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=59.59 E-value=9.1 Score=18.97 Aligned_cols=23 Identities=35% Similarity=0.343 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||..+|+++..|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 46789999999999999998754
No 127
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=59.34 E-value=22 Score=21.89 Aligned_cols=33 Identities=12% Similarity=0.174 Sum_probs=26.2
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 52 SGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 52 ~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
......+||..+|++...|+.+...-+.+.++.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 334567899999999999999998777776654
No 128
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=59.13 E-value=23 Score=22.30 Aligned_cols=34 Identities=18% Similarity=0.254 Sum_probs=27.1
Q ss_pred CHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 52 SGTEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 52 ~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
......++|..+|++...|+++...-|.+.+...
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345678999999999999999987777777644
No 129
>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=58.76 E-value=8.5 Score=24.74 Aligned_cols=31 Identities=19% Similarity=0.410 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
..+.+|+.-++++..+|-.|..|.+...+..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999987766543
No 130
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=58.67 E-value=47 Score=21.42 Aligned_cols=32 Identities=22% Similarity=0.315 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-|.+.++...
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999877777766443
No 131
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=58.47 E-value=52 Score=21.90 Aligned_cols=30 Identities=10% Similarity=0.104 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+.|...-+.+.+..
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777776654
No 132
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=58.35 E-value=24 Score=22.17 Aligned_cols=33 Identities=9% Similarity=0.165 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
....++|..+|++...|+++...-+.+.+....
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 183 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKFA 183 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345789999999999999999877777766543
No 133
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=58.34 E-value=62 Score=22.72 Aligned_cols=54 Identities=17% Similarity=0.271 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
.++..+..+|...|... +.......+||..+|++...|+.+....+.+.|+...
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34555555565554222 2233456789999999999999999988888776543
No 134
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=57.91 E-value=35 Score=21.46 Aligned_cols=36 Identities=17% Similarity=0.205 Sum_probs=28.3
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 36 QALELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 36 ~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
.-+..|...=....|.+......+|..+|++...|.
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 335555555566789999999999999999998764
No 135
>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=57.86 E-value=22 Score=22.30 Aligned_cols=31 Identities=16% Similarity=0.189 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 53 GTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 53 ~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
.....++|..+|++...|.+.+.--|.+.+.
T Consensus 165 ~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 165 GKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445789999999999999988766666554
No 136
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=57.62 E-value=45 Score=20.94 Aligned_cols=33 Identities=12% Similarity=0.246 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
...++|..+|++...|++....-|.+.+.....
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 357889999999999999998888877765443
No 137
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=57.62 E-value=46 Score=21.05 Aligned_cols=32 Identities=19% Similarity=0.189 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|++....-|.+.++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999888877776554
No 138
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=57.41 E-value=45 Score=20.84 Aligned_cols=32 Identities=13% Similarity=0.215 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|+.+...-+.+.++..
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34578899999999999999987777766643
No 139
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=57.31 E-value=45 Score=20.79 Aligned_cols=30 Identities=13% Similarity=0.220 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|++....-|.+.+..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998777777664
No 140
>KOG3755|consensus
Probab=56.99 E-value=8.3 Score=29.74 Aligned_cols=44 Identities=14% Similarity=0.228 Sum_probs=28.6
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhC-------CChHHHHHHHHHHHHHhhHhh
Q psy14049 42 NAHFERNTHPSGTEITTLAHQLG-------YEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 42 ~~~f~~~~~p~~~~~~~la~~~~-------l~~~~v~~WFqnrR~k~kr~~ 85 (93)
+.+|..+..++.....+.-.... .....|+.||.+||.++++..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 45555666666555444333332 345679999999999998854
No 141
>PF13730 HTH_36: Helix-turn-helix domain
Probab=56.82 E-value=24 Score=17.49 Aligned_cols=44 Identities=20% Similarity=0.153 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHF---ERNTHPSGTEITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 33 ~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnr 77 (93)
+++.+...+.... ..+.. ..+....||..+|++...|..+...-
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~L 49 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKEL 49 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHHH
Confidence 4455544444332 22223 33357789999999999999888643
No 142
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=56.67 E-value=46 Score=20.70 Aligned_cols=32 Identities=9% Similarity=0.095 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|++....-+.+.++...
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999888888776443
No 143
>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=56.59 E-value=43 Score=20.34 Aligned_cols=29 Identities=21% Similarity=0.268 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|++...--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45688999999999999988766666554
No 144
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=56.41 E-value=27 Score=22.15 Aligned_cols=30 Identities=20% Similarity=0.361 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|+++..|+..+..-|...++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456889999999999999998888666554
No 145
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=56.03 E-value=17 Score=18.91 Aligned_cols=20 Identities=20% Similarity=0.230 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|+++..|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35678999999999999965
No 146
>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=55.80 E-value=22 Score=16.73 Aligned_cols=23 Identities=13% Similarity=0.234 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
..++|..+|++...|..|.....
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45678899999999999986553
No 147
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=55.75 E-value=18 Score=19.13 Aligned_cols=18 Identities=28% Similarity=0.599 Sum_probs=15.4
Q ss_pred HHHHHHHhCCChHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIW 73 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~W 73 (93)
...||..+|++..-|..|
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 457899999999999999
No 148
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=55.61 E-value=46 Score=20.42 Aligned_cols=30 Identities=17% Similarity=0.262 Sum_probs=24.8
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..++|..+|++...|+.....-+.+.++..
T Consensus 137 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 137 TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 568899999999999999987777766644
No 149
>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=55.55 E-value=39 Score=20.85 Aligned_cols=35 Identities=17% Similarity=0.135 Sum_probs=27.0
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 37 ALELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 37 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
-+..|...=....|.+......+|..+|++...|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34555554455679999999999999999987754
No 150
>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=55.21 E-value=61 Score=21.70 Aligned_cols=31 Identities=13% Similarity=0.337 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+++...-|.+.++..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999999999999998877766543
No 151
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=54.95 E-value=49 Score=20.48 Aligned_cols=32 Identities=13% Similarity=0.267 Sum_probs=25.7
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|.+....-|.+.++..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 184 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQL 184 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34578899999999999999887777776643
No 152
>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=54.73 E-value=29 Score=17.84 Aligned_cols=37 Identities=22% Similarity=0.228 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy14049 36 QALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 36 ~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqn 76 (93)
.++..|+-.+. ++..+.. +||..+|++...|+.-..+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHHH
Confidence 35666666676 6666544 7899999999999877654
No 153
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=54.60 E-value=53 Score=20.76 Aligned_cols=31 Identities=6% Similarity=0.087 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|++-...-+.+.+...
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999887777666543
No 154
>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=54.38 E-value=13 Score=18.25 Aligned_cols=23 Identities=26% Similarity=0.075 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997654
No 155
>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=54.23 E-value=58 Score=21.14 Aligned_cols=46 Identities=13% Similarity=0.205 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
+++.+...+...|. ......++|..+|++...|..|...-+.+.++
T Consensus 179 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444445544432 22346789999999999999999866666554
No 156
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=54.06 E-value=38 Score=18.97 Aligned_cols=44 Identities=9% Similarity=0.240 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFER-----NTHPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~-----~~~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
.++.+++..+...|.. +.+.+..+...+....|++...|...|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 3677888888888843 4577888887777778898888887775
No 157
>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=54.04 E-value=16 Score=17.06 Aligned_cols=22 Identities=32% Similarity=0.279 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
...+|..+|+++..|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 3578999999999999998765
No 158
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.48 E-value=23 Score=20.01 Aligned_cols=24 Identities=29% Similarity=0.585 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
....+|..+|++...|..|.+.-+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467789999999999999997543
No 159
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=53.07 E-value=54 Score=20.43 Aligned_cols=29 Identities=7% Similarity=0.102 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+......+.+...
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999877766654
No 160
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=52.93 E-value=46 Score=20.74 Aligned_cols=35 Identities=17% Similarity=0.167 Sum_probs=27.2
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 37 ALELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 37 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
-+..|...=....|.+......+|..+|++...|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34555555455689999999999999999988764
No 161
>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=52.82 E-value=66 Score=21.38 Aligned_cols=29 Identities=14% Similarity=0.092 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.+...-+.+.+.
T Consensus 223 s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 223 SQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999877776655
No 162
>PRK09480 slmA division inhibitor protein; Provisional
Probab=52.78 E-value=19 Score=22.36 Aligned_cols=36 Identities=17% Similarity=0.206 Sum_probs=28.9
Q ss_pred HHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 43 AHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 43 ~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
..|...+. .......||...|++...+-.+|.|+-.
T Consensus 21 ~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 33544545 7778899999999999999999998764
No 163
>PF12728 HTH_17: Helix-turn-helix domain
Probab=52.67 E-value=20 Score=17.53 Aligned_cols=22 Identities=23% Similarity=0.450 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...|..|....
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3567889999999999998654
No 164
>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=52.58 E-value=27 Score=16.88 Aligned_cols=38 Identities=16% Similarity=0.404 Sum_probs=23.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 74 (93)
.++.++.+.+...+... .....+|..+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 34554455555544433 346788999999999887765
No 165
>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=52.17 E-value=17 Score=18.50 Aligned_cols=17 Identities=29% Similarity=0.350 Sum_probs=13.4
Q ss_pred HHHHHHHhCCChHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRI 72 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~ 72 (93)
-.+||..+|+++.||+-
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 46789999999999864
No 166
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=51.79 E-value=59 Score=20.50 Aligned_cols=32 Identities=19% Similarity=0.114 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++..--|.+.++...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999877777665443
No 167
>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=51.72 E-value=59 Score=22.08 Aligned_cols=29 Identities=17% Similarity=0.202 Sum_probs=24.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
..++|..+|+++..|+..+..-|.+.+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999998777776653
No 168
>PRK10403 transcriptional regulator NarP; Provisional
Probab=51.45 E-value=53 Score=20.10 Aligned_cols=45 Identities=16% Similarity=0.244 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.+|..+...|...... ....++|..+++++..|++...+=+.|..
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 5788888888765432 23567899999999999999988777654
No 169
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=51.27 E-value=61 Score=20.51 Aligned_cols=32 Identities=13% Similarity=0.140 Sum_probs=25.9
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|++-....|.+.++..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44678899999999999999887777766643
No 170
>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=51.22 E-value=69 Score=21.11 Aligned_cols=51 Identities=14% Similarity=0.193 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
++..+..+|...|....+ ......++|..+|++...|+.....-..+.|..
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 455555566655532222 223477899999999999999998888777764
No 171
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=51.11 E-value=52 Score=21.07 Aligned_cols=34 Identities=18% Similarity=0.056 Sum_probs=26.3
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
+..|...=....|.+......+|..+|++...|.
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 4445444455689999999999999999987754
No 172
>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=50.93 E-value=35 Score=21.02 Aligned_cols=34 Identities=18% Similarity=0.188 Sum_probs=24.0
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
+..|...=....|.+......+|..++++..+|.
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 4455555455679999999999999999998865
No 173
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=50.77 E-value=64 Score=20.60 Aligned_cols=31 Identities=16% Similarity=0.308 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|++....-|.+.+...
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999987777777654
No 174
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=50.42 E-value=67 Score=20.74 Aligned_cols=31 Identities=10% Similarity=0.278 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
..++|..+|++...|++....-|.+.++...
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999888877776543
No 175
>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=50.12 E-value=24 Score=20.22 Aligned_cols=22 Identities=9% Similarity=0.052 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...++.|..+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIG 24 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999998754
No 176
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=49.97 E-value=74 Score=21.13 Aligned_cols=30 Identities=17% Similarity=0.143 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+..+..-+.+.+..
T Consensus 219 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 219 TLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999998777776653
No 177
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=49.92 E-value=59 Score=19.99 Aligned_cols=30 Identities=3% Similarity=0.156 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
.-.++|..+|++...|+.....-+.+.++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 346889999999999999998777666653
No 178
>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=49.85 E-value=70 Score=20.77 Aligned_cols=29 Identities=10% Similarity=0.229 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.+...-+.+.++
T Consensus 193 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 193 NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998866666554
No 179
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=49.62 E-value=30 Score=16.56 Aligned_cols=43 Identities=23% Similarity=0.327 Sum_probs=29.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
.++..+...+...+. .+ ...++|..+|++...|..|...-+.+
T Consensus 3 ~l~~~e~~i~~~~~~--g~----s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLAE--GL----TNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHHc--CC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 356777776655332 22 45778999999999999998754443
No 180
>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=49.50 E-value=40 Score=22.20 Aligned_cols=32 Identities=19% Similarity=0.153 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+++...-+.+.|+...
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 46778999999999999999877777766443
No 181
>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=49.15 E-value=27 Score=19.91 Aligned_cols=21 Identities=14% Similarity=0.352 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|...
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999864
No 182
>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=48.84 E-value=24 Score=19.75 Aligned_cols=20 Identities=20% Similarity=0.355 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...++.|-.
T Consensus 4 i~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 183
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=48.84 E-value=63 Score=19.96 Aligned_cols=29 Identities=14% Similarity=0.267 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+++...-+...+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999766665544
No 184
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=48.59 E-value=65 Score=20.05 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|+.+..--+.+.+..
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356889999999999999998766666653
No 185
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=48.49 E-value=81 Score=21.14 Aligned_cols=33 Identities=15% Similarity=0.118 Sum_probs=26.6
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
....++|..+|++...|..+..--+.+.+....
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 346789999999999999999877777766543
No 186
>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=48.03 E-value=22 Score=21.04 Aligned_cols=37 Identities=19% Similarity=0.324 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 34 TPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 34 t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
+-+-....-.++.... ...++|..++++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3344444444554432 356678999999999999998
No 187
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=47.97 E-value=65 Score=21.79 Aligned_cols=31 Identities=13% Similarity=0.233 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
....++|..+|++...|..+...-+.+.+..
T Consensus 232 ~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 232 MTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3457899999999999999998777766653
No 188
>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=47.92 E-value=25 Score=19.67 Aligned_cols=21 Identities=19% Similarity=0.260 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|+++..|..|-..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999754
No 189
>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=47.36 E-value=67 Score=19.87 Aligned_cols=47 Identities=13% Similarity=0.121 Sum_probs=36.3
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
+.++..|...+...+ .. ....++|..+|++...|..+-..-+.+.+.
T Consensus 5 ~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 567888888887743 22 246788999999999999999877777664
No 190
>PHA01976 helix-turn-helix protein
Probab=47.29 E-value=21 Score=18.39 Aligned_cols=23 Identities=22% Similarity=0.326 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
..+||..+|++...|..|-...+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999986554
No 191
>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=47.02 E-value=21 Score=18.96 Aligned_cols=23 Identities=30% Similarity=0.440 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||..+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45789999999999999997654
No 192
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=46.97 E-value=90 Score=21.23 Aligned_cols=30 Identities=17% Similarity=0.235 Sum_probs=25.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..++|..+|++...|+.....-|.+.+...
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 467899999999999999997777777643
No 193
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=46.48 E-value=56 Score=20.40 Aligned_cols=33 Identities=15% Similarity=0.273 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhhc
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVRM 87 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~~ 87 (93)
.-.++|..+|++...|+.+..-.|.+.+.....
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 346789999999999999999888887765543
No 194
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=46.33 E-value=66 Score=19.48 Aligned_cols=26 Identities=12% Similarity=0.220 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQAL 81 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~ 81 (93)
..++|..+|++...|+++...-+.+.
T Consensus 132 ~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 132 YGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 56789999999999999987555443
No 195
>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=45.84 E-value=92 Score=21.02 Aligned_cols=49 Identities=20% Similarity=0.245 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
++..+..+|...|.. -......++|..+|++...|......-..+.|+.
T Consensus 219 L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 219 LDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred CCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445555556555521 1123467899999999999999998877777654
No 196
>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=45.33 E-value=96 Score=21.21 Aligned_cols=31 Identities=16% Similarity=0.122 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
..+||..+|++...|+....--|.+.++...
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 4688999999999999999877777776544
No 197
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=45.08 E-value=21 Score=24.68 Aligned_cols=26 Identities=23% Similarity=0.505 Sum_probs=21.4
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQAL 81 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~ 81 (93)
-.-..||..+|+++.+|+.|=+ |..|
T Consensus 20 mk~~dIAeklGvspntiksWKr--r~gW 45 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKR--RDGW 45 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHH--hcCC
Confidence 3456799999999999999975 6555
No 198
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.03 E-value=61 Score=18.76 Aligned_cols=46 Identities=15% Similarity=0.304 Sum_probs=34.2
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCC-ChHHHHHHHHHHHH
Q psy14049 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGY-EREVIRIWFCNKRQ 79 (93)
Q Consensus 30 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l-~~~~v~~WFqnrR~ 79 (93)
+..|+.+....+-..+....+ ....+|..+|+ +..++..|-..-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 678899887776666554443 56788999996 99999999864443
No 199
>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=44.32 E-value=33 Score=21.01 Aligned_cols=22 Identities=27% Similarity=0.309 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...++.|.+..
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~G 24 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLG 24 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999999653
No 200
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=44.02 E-value=30 Score=22.60 Aligned_cols=41 Identities=20% Similarity=0.186 Sum_probs=32.8
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 40 LLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 40 ~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.-...|...+|- .....||...|++...|..+|.++..-..
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 334448888887 56888999999999999999999876543
No 201
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=43.80 E-value=1.1e+02 Score=21.11 Aligned_cols=51 Identities=16% Similarity=0.311 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
++..+..+|...|. +-......++|..+|++...|+..-..-..+.+....
T Consensus 228 L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 228 LNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred CCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45555555655552 1133457889999999999999999888777776443
No 202
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=43.61 E-value=92 Score=20.39 Aligned_cols=32 Identities=16% Similarity=0.120 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
....++|..+|++...|.++-...+.+.++..
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999665565555543
No 203
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=43.28 E-value=71 Score=18.98 Aligned_cols=25 Identities=12% Similarity=0.280 Sum_probs=20.4
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHHH
Q psy14049 53 GTEITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 53 ~~~~~~la~~~~l~~~~v~~WFqnr 77 (93)
......||..+|+++..+..+|+.-
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3556788999999999999888754
No 204
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=42.99 E-value=78 Score=19.40 Aligned_cols=29 Identities=10% Similarity=0.172 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.+....+...+.
T Consensus 136 s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 136 TYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999777666554
No 205
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=42.80 E-value=36 Score=15.51 Aligned_cols=22 Identities=27% Similarity=0.261 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
...+|..+|++...|..|-.+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4578899999999999998655
No 206
>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=42.71 E-value=98 Score=20.41 Aligned_cols=48 Identities=15% Similarity=0.133 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
..++..+.++|.-...- ..-.++|..+|+++..|+.+..+-+.|..-.
T Consensus 170 ~~Lt~re~evl~~~a~G------~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~ 217 (232)
T TIGR03541 170 GVLSEREREVLAWTALG------RRQADIAAILGISERTVENHLRSARRKLGVA 217 (232)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCC
Confidence 35677777777654311 2346788999999999999999888776543
No 207
>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=42.46 E-value=34 Score=20.81 Aligned_cols=20 Identities=35% Similarity=0.602 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
-++||..+|++...|.-|..
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 36899999999999999985
No 208
>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=42.39 E-value=41 Score=19.09 Aligned_cols=21 Identities=19% Similarity=0.123 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999865
No 209
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=42.38 E-value=59 Score=21.29 Aligned_cols=37 Identities=16% Similarity=0.300 Sum_probs=29.4
Q ss_pred CCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 50 HPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 50 ~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
|.......++|..+|++...|++....-|.+.|+...
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 3344556789999999999999999888888777554
No 210
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=42.26 E-value=79 Score=19.23 Aligned_cols=45 Identities=13% Similarity=0.220 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.+|+.+...|...... + ....+|..++++.+.|++...+-+.|..
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5777777777765532 2 4678899999999999999887776643
No 211
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=41.21 E-value=43 Score=20.97 Aligned_cols=39 Identities=5% Similarity=0.000 Sum_probs=30.4
Q ss_pred HHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 40 LLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 40 ~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
.-...|...+|.. .....||...|++...+-.+|.++..
T Consensus 16 aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 16 AAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 3444577777754 45778899999999999999988755
No 212
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=40.68 E-value=94 Score=19.63 Aligned_cols=32 Identities=16% Similarity=0.241 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...+||..+|++...|++=...-|.+.++...
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 35678999999999998777666666665443
No 213
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=40.63 E-value=86 Score=19.17 Aligned_cols=45 Identities=13% Similarity=0.093 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.++..+...|...... ....++|..++++...|+++..+-|.|..
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 4777777777654332 34678899999999999999988777643
No 214
>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=40.04 E-value=17 Score=19.16 Aligned_cols=21 Identities=24% Similarity=0.409 Sum_probs=15.9
Q ss_pred HHHHHHHhCCChHHHH-HHHHH
Q psy14049 56 ITTLAHQLGYEREVIR-IWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~-~WFqn 76 (93)
...||..+|++...|. .|...
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCcCHHHhhHHHHhC
Confidence 4578999999999999 89863
No 215
>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=40.03 E-value=51 Score=18.98 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=20.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQAL 81 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~ 81 (93)
...+|..+|+++.+|.-|..+-+.+.
T Consensus 26 q~~vA~~~Gv~eStISR~k~~~~~~~ 51 (91)
T PF05269_consen 26 QKKVAEAMGVDESTISRWKNDFIEKM 51 (91)
T ss_dssp HHHHHHHHTSSTTTHHHHHHHHHHHH
T ss_pred hHHHHHHhCCCHHHHHHHHhhHHHHH
Confidence 45689999999999999986654443
No 216
>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=39.96 E-value=53 Score=16.99 Aligned_cols=18 Identities=28% Similarity=0.444 Sum_probs=11.7
Q ss_pred HHHHHHHHHhCCChHHHH
Q psy14049 54 TEITTLAHQLGYEREVIR 71 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~ 71 (93)
.+...+|..+|++..+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 455566777777776654
No 217
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=39.78 E-value=28 Score=20.93 Aligned_cols=23 Identities=17% Similarity=0.247 Sum_probs=20.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999998765
No 218
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=39.73 E-value=96 Score=19.48 Aligned_cols=32 Identities=16% Similarity=0.088 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|+....--|.+.++...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35688999999999999999877777766544
No 219
>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=39.65 E-value=61 Score=17.19 Aligned_cols=40 Identities=23% Similarity=0.397 Sum_probs=24.3
Q ss_pred CCHHHHHHH---HHHhhhCCCCCHHHHHHHHHHhCCC-hHHHHHHH
Q psy14049 33 FTPQALELL---NAHFERNTHPSGTEITTLAHQLGYE-REVIRIWF 74 (93)
Q Consensus 33 ~t~~q~~~L---~~~f~~~~~p~~~~~~~la~~~~l~-~~~v~~WF 74 (93)
+|..|.++| ..+...+.||. ...+||..+|+. ...|..-.
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 456665554 44457778874 567889999997 77666544
No 220
>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=39.34 E-value=41 Score=18.92 Aligned_cols=22 Identities=23% Similarity=0.271 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|+++..|..|-...
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~G 24 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKG 24 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3568999999999999997543
No 221
>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=39.27 E-value=1.2e+02 Score=20.57 Aligned_cols=33 Identities=18% Similarity=0.328 Sum_probs=27.0
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
....++|..+|++...|+......+.+.++...
T Consensus 243 ~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 243 ATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999999999888877776443
No 222
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=39.03 E-value=50 Score=16.03 Aligned_cols=21 Identities=24% Similarity=0.374 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFq 75 (93)
....+|..+|++...|...|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999999885
No 223
>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=38.79 E-value=38 Score=16.32 Aligned_cols=17 Identities=29% Similarity=0.544 Sum_probs=12.3
Q ss_pred HHHHHHHHhCCChHHHH
Q psy14049 55 EITTLAHQLGYEREVIR 71 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~ 71 (93)
.-..||..+|+++..|.
T Consensus 19 s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 19 SYAELAEELGLSESTVR 35 (42)
T ss_dssp -HHHHHHHHTS-HHHHH
T ss_pred cHHHHHHHHCcCHHHHH
Confidence 35678999999998764
No 224
>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=38.73 E-value=42 Score=19.12 Aligned_cols=20 Identities=15% Similarity=0.378 Sum_probs=17.1
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 225
>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=38.44 E-value=1.3e+02 Score=20.46 Aligned_cols=48 Identities=15% Similarity=0.078 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 30 RTSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 30 r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...+|+.+.++|.-... . ..-.++|..+++++..|+....+-+.|..-
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 34688988898886542 2 235678999999999999999988777554
No 226
>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=38.37 E-value=43 Score=19.23 Aligned_cols=21 Identities=14% Similarity=0.301 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...+..|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999763
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=38.31 E-value=43 Score=19.24 Aligned_cols=21 Identities=24% Similarity=0.284 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|+++..++.|-+.
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 228
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=38.26 E-value=54 Score=19.61 Aligned_cols=26 Identities=19% Similarity=0.286 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 50 HPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 50 ~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
-++...+..||..+|++...|..|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 35566777899999999999999953
No 229
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=37.39 E-value=87 Score=20.88 Aligned_cols=31 Identities=16% Similarity=0.234 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
...++|..+|++...|+++...-|.+.+...
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3468899999999999999987777776544
No 230
>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=37.24 E-value=43 Score=20.74 Aligned_cols=27 Identities=11% Similarity=0.281 Sum_probs=22.2
Q ss_pred HHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 54 TEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 54 ~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
+...+++..+|++...|..|....|-.
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 346778999999999999999876643
No 231
>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=37.08 E-value=49 Score=19.21 Aligned_cols=22 Identities=36% Similarity=0.524 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...|+.|-...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEG 24 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997643
No 232
>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=37.06 E-value=55 Score=18.56 Aligned_cols=21 Identities=10% Similarity=0.034 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999764
No 233
>PRK09744 DNA-binding transcriptional regulator DicC; Provisional
Probab=36.67 E-value=53 Score=18.27 Aligned_cols=18 Identities=28% Similarity=0.469 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIW 73 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~W 73 (93)
...+|..+|++..-|..|
T Consensus 13 ~~kvA~aLGIs~~AVsQW 30 (75)
T PRK09744 13 KTKLANAAGVRLASVAAW 30 (75)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 567899999999999999
No 234
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=36.67 E-value=39 Score=16.90 Aligned_cols=22 Identities=18% Similarity=0.279 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
-..||..+|++...|..||..-
T Consensus 22 ~~~La~~FgIs~stvsri~~~~ 43 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHEW 43 (53)
T ss_pred HhHHhhheeecHHHHHHHHHHH
Confidence 4568999999999999999753
No 235
>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=36.60 E-value=57 Score=18.47 Aligned_cols=21 Identities=19% Similarity=0.191 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999863
No 236
>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=36.39 E-value=47 Score=19.94 Aligned_cols=21 Identities=29% Similarity=0.449 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
+.++|..+|++...|+.|-+.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999753
No 237
>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=36.37 E-value=55 Score=19.76 Aligned_cols=22 Identities=32% Similarity=0.492 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|+++..+..|-+..
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~G 25 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERHG 25 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999998643
No 238
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=35.39 E-value=69 Score=16.98 Aligned_cols=21 Identities=19% Similarity=0.252 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
-.++|..+|++..+++.|...
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 347899999999999999864
No 239
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=35.24 E-value=54 Score=20.75 Aligned_cols=40 Identities=28% Similarity=0.255 Sum_probs=29.8
Q ss_pred HHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 39 ELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 39 ~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
+.....|...+|.... ...||...|+++..+-.+|.++-.
T Consensus 18 ~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 18 ETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHH
Confidence 3344446677766544 677899999999999999988754
No 240
>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=34.86 E-value=66 Score=18.45 Aligned_cols=21 Identities=33% Similarity=0.572 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|+++..+..|-.+
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 346899999999999999764
No 241
>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=34.75 E-value=52 Score=19.06 Aligned_cols=21 Identities=14% Similarity=0.072 Sum_probs=18.0
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 456899999999999999864
No 242
>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=34.58 E-value=53 Score=19.14 Aligned_cols=21 Identities=24% Similarity=0.411 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|-..
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999764
No 243
>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=34.24 E-value=53 Score=19.10 Aligned_cols=21 Identities=19% Similarity=0.363 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...+..|-+.
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~ 23 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKE 23 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 244
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=33.98 E-value=1.4e+02 Score=19.58 Aligned_cols=45 Identities=16% Similarity=0.132 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.+|+.+.++|....+ . ..-.++|..+++++..|+.+..+-..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~--G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRI--G----ASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 478888888877664 2 22467899999999999999987766654
No 245
>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=33.95 E-value=60 Score=18.50 Aligned_cols=22 Identities=23% Similarity=0.312 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...+..|....
T Consensus 4 i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4568999999999999997643
No 246
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=33.92 E-value=1.5e+02 Score=20.49 Aligned_cols=29 Identities=14% Similarity=0.123 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...+||..+|++...|+.-...-|.+.++
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 35689999999999999999877777666
No 247
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=33.36 E-value=97 Score=18.41 Aligned_cols=33 Identities=24% Similarity=0.288 Sum_probs=23.2
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRI 72 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 72 (93)
-..|...|. +.+......+||..+.++.+.++.
T Consensus 6 y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 6 YQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 344555555 445556788999999999987664
No 248
>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=33.24 E-value=36 Score=16.44 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||...|++...+-..|.|+-
T Consensus 19 ~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 19 IRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHHHccchhhHHHHcCCHH
Confidence 56789999999999998887653
No 249
>PF11388 DotA: Phagosome trafficking protein DotA; InterPro: IPR021528 DotA is essential for intracellular growth in Legionella []. DotA is thought to play an important role in regulating initial phagosome trafficking decisions either upon or immediately after macrophage uptake [].
Probab=33.11 E-value=39 Score=19.72 Aligned_cols=25 Identities=20% Similarity=0.319 Sum_probs=17.0
Q ss_pred HHhCCChHHHHHHHHHHHHHhhHhh
Q psy14049 61 HQLGYEREVIRIWFCNKRQALKNTV 85 (93)
Q Consensus 61 ~~~~l~~~~v~~WFqnrR~k~kr~~ 85 (93)
..++-+..-+-+||+|.-.+.-..+
T Consensus 23 ~tc~~~~a~LC~WF~~~s~~l~qiq 47 (105)
T PF11388_consen 23 KTCQGDYALLCTWFQNKSDKLVQIQ 47 (105)
T ss_pred ccccCchHHHHHHHccCCchhhhhh
Confidence 3445567778899999877655433
No 250
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=33.02 E-value=42 Score=17.22 Aligned_cols=25 Identities=20% Similarity=0.252 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
....+|..+|++...|..|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 3567899999999999999887763
No 251
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=32.68 E-value=41 Score=20.06 Aligned_cols=23 Identities=13% Similarity=0.072 Sum_probs=20.2
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
..+||..+|++...|..|.+++.
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56789999999999999998775
No 252
>PRK09726 antitoxin HipB; Provisional
Probab=32.66 E-value=43 Score=18.57 Aligned_cols=22 Identities=23% Similarity=0.327 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
...||..+|++...|..|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 5678999999999999998765
No 253
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=32.57 E-value=1.5e+02 Score=19.71 Aligned_cols=47 Identities=13% Similarity=0.211 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
.++..+...+...|.. .....++|..+|++...|...-..-..+.++
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 4555566666666532 2346789999999999998887766666554
No 254
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=32.53 E-value=1.4e+02 Score=19.39 Aligned_cols=45 Identities=20% Similarity=0.233 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnr 77 (93)
.++..++..+......+ +-....-.++|..+++++..|+..+.+-
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 46777666665544322 2233345779999999999999998755
No 255
>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=32.27 E-value=51 Score=21.01 Aligned_cols=21 Identities=24% Similarity=0.366 Sum_probs=15.7
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
+..||..+|+++..|..|-.+
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 567899999999999999643
No 256
>KOG3755|consensus
Probab=32.15 E-value=50 Score=25.77 Aligned_cols=57 Identities=30% Similarity=0.444 Sum_probs=45.2
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCC-CCCHHH---HHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 26 KRKRRTSFTPQALELLNAHFERNT-HPSGTE---ITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f~~~~-~p~~~~---~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
+.+.|+.+..+.+..|..+...-. ||+... ...|+..+++....+...|+|.|.-.+
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~ 707 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVK 707 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecc
Confidence 455678888888888887754433 777776 788999999999999999999886544
No 257
>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=32.14 E-value=1.5e+02 Score=19.32 Aligned_cols=45 Identities=11% Similarity=0.127 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
++..+...+...|. ......++|..+|++...|..+-..-..+.+
T Consensus 184 L~~~e~~i~~~~~~-----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 184 LDERERQIIMLRYF-----KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34444444444432 2235678999999999999888765554444
No 258
>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=32.11 E-value=44 Score=16.95 Aligned_cols=24 Identities=33% Similarity=0.333 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
....+|..+|++...+..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 356789999999999999988765
No 259
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=32.06 E-value=58 Score=14.73 Aligned_cols=20 Identities=25% Similarity=0.366 Sum_probs=14.2
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
...-|...|++..+|+..+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34458999999999998875
No 260
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=31.94 E-value=1.3e+02 Score=18.67 Aligned_cols=29 Identities=17% Similarity=0.227 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|.+-...-|.+.+.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45678999999999999888766666554
No 261
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=31.77 E-value=1.7e+02 Score=20.14 Aligned_cols=29 Identities=14% Similarity=0.256 Sum_probs=24.0
Q ss_pred HHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
..++|..+|+++..|+...+.-|.+.+..
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 46789999999999999998777776653
No 262
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=31.65 E-value=62 Score=18.78 Aligned_cols=19 Identities=21% Similarity=0.309 Sum_probs=15.8
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WF 74 (93)
..++|..+|++...++.|=
T Consensus 3 I~eva~~~gvs~~tLRyYE 21 (124)
T COG0789 3 IGEVAKLTGVSVRTLRFYE 21 (124)
T ss_pred HHHHHHHhCCCHHHHHHHH
Confidence 3467889999999999884
No 263
>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=31.56 E-value=74 Score=16.87 Aligned_cols=21 Identities=24% Similarity=0.272 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCChHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFq 75 (93)
...+||..+|++...|...+.
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 356789999999999987775
No 264
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=31.53 E-value=53 Score=17.44 Aligned_cols=15 Identities=7% Similarity=-0.084 Sum_probs=6.7
Q ss_pred HHHhCCChHHHHHHH
Q psy14049 60 AHQLGYEREVIRIWF 74 (93)
Q Consensus 60 a~~~~l~~~~v~~WF 74 (93)
...+|+++.+.-...
T Consensus 17 ~~~~g~s~~~~~~~~ 31 (81)
T PF12833_consen 17 KKETGMSFKQYLREL 31 (81)
T ss_dssp HHHHSS-HHHHHHHH
T ss_pred HHHHCcCHHHHHHHH
Confidence 444565555444443
No 265
>PRK05572 sporulation sigma factor SigF; Validated
Probab=31.47 E-value=1.6e+02 Score=19.56 Aligned_cols=48 Identities=8% Similarity=0.100 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
.++..+..++...|. ......++|..+|++...|..+-..-..+.++.
T Consensus 202 ~L~~~~~~v~~l~~~-----~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~ 249 (252)
T PRK05572 202 ELDERERLIVYLRYF-----KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEK 249 (252)
T ss_pred cCCHHHHHHHHHHHh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355555555555542 223467899999999999998887666666543
No 266
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=31.47 E-value=1.2e+02 Score=18.18 Aligned_cols=38 Identities=16% Similarity=0.422 Sum_probs=24.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 74 (93)
.++.+++..++.+..... -..+++..+|+++..|+.=+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHH
Confidence 578888888887764432 34555666666666665444
No 267
>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=31.13 E-value=65 Score=18.78 Aligned_cols=21 Identities=24% Similarity=0.262 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...+..|-+.
T Consensus 3 i~eva~~~gvs~~tlR~Ye~~ 23 (112)
T cd01282 3 IGELAARTGVSVRSLRYYEEQ 23 (112)
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 457899999999999999764
No 268
>PHA02955 hypothetical protein; Provisional
Probab=31.13 E-value=61 Score=21.68 Aligned_cols=44 Identities=11% Similarity=0.077 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 35 PQALELLNAHFERN-THPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 35 ~~q~~~L~~~f~~~-~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
..++..|-+.|... .-.+..++..++..+|+....+..||.+--
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 34566666666444 456778899999999999877888887653
No 269
>PRK13182 racA polar chromosome segregation protein; Reviewed
Probab=30.98 E-value=71 Score=20.57 Aligned_cols=22 Identities=18% Similarity=0.394 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
..++|..+|++...|+.|....
T Consensus 3 i~evA~~lGVS~~TLRrw~k~g 24 (175)
T PRK13182 3 TPFVAKKLGVSPKTVQRWVKQL 24 (175)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3568999999999999998643
No 270
>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=30.84 E-value=62 Score=19.78 Aligned_cols=21 Identities=10% Similarity=0.207 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
+.++|..+|++...|+.|-+.
T Consensus 4 I~EvA~~~Gvs~~tLRyYE~~ 24 (139)
T cd01110 4 VGEVAKRSGVAVSALHFYEQK 24 (139)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 271
>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=30.75 E-value=1.8e+02 Score=19.96 Aligned_cols=47 Identities=17% Similarity=0.279 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
+++.+..++...|....+ ......++|..+|++...|+..-...+.+
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 444445555555532212 22457789999999999999887644443
No 272
>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=30.68 E-value=68 Score=18.30 Aligned_cols=21 Identities=19% Similarity=0.301 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-+.
T Consensus 3 i~e~A~~~gvs~~tlR~Ye~~ 23 (99)
T cd04772 3 TVDLARAIGLSPQTVRNYESL 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 357899999999999999653
No 273
>PRK10651 transcriptional regulator NarL; Provisional
Probab=30.64 E-value=1.3e+02 Score=18.33 Aligned_cols=45 Identities=13% Similarity=0.242 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.+|..+.+.|...... + .-..+|..++++...|.+..++-+.|..
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 4888888888765422 1 2456788999999999999998877754
No 274
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=30.63 E-value=1.4e+02 Score=18.76 Aligned_cols=32 Identities=16% Similarity=0.254 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHhhh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNTVR 86 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~~~ 86 (93)
...++|..+|++...|.++..--|.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45688999999999999999877776665443
No 275
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=30.61 E-value=1.8e+02 Score=19.89 Aligned_cols=49 Identities=18% Similarity=0.287 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
++..+..+|...|... ......++|..+|++...|+..-..-..+.|..
T Consensus 231 L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 231 LDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred CCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4444455555555221 233467899999999999999887766666654
No 276
>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=30.45 E-value=1.2e+02 Score=17.80 Aligned_cols=42 Identities=19% Similarity=0.300 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
-+|..|...++.+|. ..-...++|..+|++..-|--|.+.-+
T Consensus 17 LLT~kQ~~~l~lyy~-----eDlSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 17 LLTEKQREILELYYE-----EDLSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GS-HHHHHHHHHHCT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHc-----cCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 467888888887653 335677899999999999998887444
No 277
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=30.44 E-value=87 Score=16.21 Aligned_cols=50 Identities=16% Similarity=0.149 Sum_probs=29.4
Q ss_pred CCCCCCHHHHHHHHHHhhhCCCCCH---HHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 29 RRTSFTPQALELLNAHFERNTHPSG---TEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 29 ~r~~~t~~q~~~L~~~f~~~~~p~~---~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
.|..+|.+.-..+......-+..+. ..+..+....+|+..+|..=.|.-|
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 4567788776665555555555443 4443433345668888887666444
No 278
>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=30.33 E-value=76 Score=19.54 Aligned_cols=21 Identities=14% Similarity=0.281 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
+.++|..+|++...++.|.+.
T Consensus 4 IgevA~~~Gvs~~tLRyYE~~ 24 (142)
T TIGR01950 4 VGELAKRSGVAVSALHFYESK 24 (142)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 279
>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=30.04 E-value=1.4e+02 Score=18.39 Aligned_cols=30 Identities=27% Similarity=0.470 Sum_probs=20.8
Q ss_pred CCHHHHHHHHHHhCCCh-----HHHHHHHHHHHHH
Q psy14049 51 PSGTEITTLAHQLGYER-----EVIRIWFCNKRQA 80 (93)
Q Consensus 51 p~~~~~~~la~~~~l~~-----~~v~~WFqnrR~k 80 (93)
.+...|.+||.++|++. ....+|....-++
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~ 117 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQ 117 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHH
Confidence 46778999999999875 6788899865544
No 280
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=30.00 E-value=1.7e+02 Score=19.57 Aligned_cols=30 Identities=13% Similarity=0.174 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
...++|..+|++...|..+...-+.+.++.
T Consensus 223 t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 223 VLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999988777666654
No 281
>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=29.91 E-value=1.2e+02 Score=17.62 Aligned_cols=22 Identities=14% Similarity=0.010 Sum_probs=17.6
Q ss_pred HHHHHHhCCChHHHHHHHHHHH
Q psy14049 57 TTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 57 ~~la~~~~l~~~~v~~WFqnrR 78 (93)
..||..+|++...|..|-....
T Consensus 82 ~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 5688889999999999976554
No 282
>PF08971 GlgS: Glycogen synthesis protein; InterPro: IPR015065 Members of this protein are involved in glycogen synthesis in Enterobacteria. The structure of the polypeptide chain comprises a bundle of two parallel amphipathic helices, alpha-1 and alpha-3, and a short hydrophobic helix alpha-2 sandwiched between them []. ; GO: 0005978 glycogen biosynthetic process; PDB: 1RRZ_A.
Probab=29.88 E-value=68 Score=17.40 Aligned_cols=24 Identities=21% Similarity=0.520 Sum_probs=15.1
Q ss_pred CChHHHHHHHHHHHHHhhHhhhccc
Q psy14049 65 YEREVIRIWFCNKRQALKNTVRMMS 89 (93)
Q Consensus 65 l~~~~v~~WFqnrR~k~kr~~~~~~ 89 (93)
|++.+ +.||+.|-+-++.+.....
T Consensus 37 M~ee~-r~~F~~R~~~Yr~q~~~~~ 60 (66)
T PF08971_consen 37 MSEEQ-REWFCERYAHYRQQALQAR 60 (66)
T ss_dssp --TTH-HHHHHHHHHHHHHHHHHH-
T ss_pred CCHHH-HHHHHHHHHHHHHHHHHHH
Confidence 44433 7899999888887555443
No 283
>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=29.70 E-value=64 Score=15.26 Aligned_cols=14 Identities=43% Similarity=0.700 Sum_probs=11.0
Q ss_pred CCCCHHHHHHHHHH
Q psy14049 31 TSFTPQALELLNAH 44 (93)
Q Consensus 31 ~~~t~~q~~~L~~~ 44 (93)
+.||..|+..|+.-
T Consensus 1 s~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 1 SPFTPAQLQELRAQ 14 (37)
T ss_pred CCCCHHHHHHHHHH
Confidence 36899999998764
No 284
>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=29.49 E-value=71 Score=18.91 Aligned_cols=20 Identities=20% Similarity=0.335 Sum_probs=16.5
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...++.|=+
T Consensus 3 Igeva~~~gvs~~tlRyYe~ 22 (118)
T cd04776 3 ISELAREFDVTPRTLRFYED 22 (118)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999998853
No 285
>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=29.31 E-value=1.7e+02 Score=19.11 Aligned_cols=29 Identities=17% Similarity=0.077 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|+++..|..+...-+.+.++
T Consensus 196 S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 196 TQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46778999999999998887655555443
No 286
>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=29.31 E-value=69 Score=19.07 Aligned_cols=19 Identities=37% Similarity=0.433 Sum_probs=16.0
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WF 74 (93)
..++|..+|++...|+.|=
T Consensus 2 I~e~a~~~gvs~~tlR~Ye 20 (124)
T TIGR02051 2 IGELAKAAGVNVETIRYYE 20 (124)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3568999999999998884
No 287
>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=28.91 E-value=71 Score=19.05 Aligned_cols=21 Identities=24% Similarity=0.210 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-+.
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T cd01108 3 IGEAAKLTGLSAKMIRYYEEI 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456899999999999999764
No 288
>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=28.68 E-value=78 Score=15.09 Aligned_cols=24 Identities=17% Similarity=0.234 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...++|..++++...|..|...-+
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~~~ 40 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRNIM 40 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 456789999999999999987433
No 289
>PRK12373 NADH dehydrogenase subunit E; Provisional
Probab=28.47 E-value=1.6e+02 Score=21.70 Aligned_cols=34 Identities=18% Similarity=0.134 Sum_probs=26.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
+..|...=....|.+......+|..|||+..+|.
T Consensus 40 IplL~~~Qe~~GyIp~~ai~~VAe~Lgvp~~~V~ 73 (400)
T PRK12373 40 IPLLMRAQEQEGWVTRAAIEKVADMLDMAYIRVL 73 (400)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 4444444455679999999999999999987765
No 290
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=28.35 E-value=57 Score=18.72 Aligned_cols=30 Identities=27% Similarity=0.362 Sum_probs=21.2
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 71 (93)
...|.+.|....+. ...+|..++++...|.
T Consensus 12 ~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le 41 (89)
T PF10078_consen 12 RQELQANFELSGLS----LEQIAADLGTSPEHLE 41 (89)
T ss_pred HHHHHHHHHHcCCC----HHHHHHHhCCCHHHHH
Confidence 45677778777654 4567888888887765
No 291
>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=28.28 E-value=76 Score=18.69 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|-..
T Consensus 3 IgevA~~~gvs~~tlRyYe~~ 23 (120)
T cd04781 3 IAEVARQSGLPASTLRYYEEK 23 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 292
>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=27.79 E-value=76 Score=18.89 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=17.7
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-+.
T Consensus 3 I~e~a~~~gvs~~tlRyYe~~ 23 (127)
T TIGR02044 3 IGQVAKLTGLSSKMIRYYEEK 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999764
No 293
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=27.66 E-value=81 Score=20.18 Aligned_cols=39 Identities=13% Similarity=0.185 Sum_probs=29.7
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHh
Q psy14049 42 NAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQAL 81 (93)
Q Consensus 42 ~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~ 81 (93)
...|....|.... ...||...|++...|-..|.++-.-.
T Consensus 28 ~~lf~e~Gy~~~s-~~dIA~~aGvs~gtiY~hF~sKe~L~ 66 (212)
T PRK15008 28 LDTFSQFGFHGTR-LEQIAELAGVSKTNLLYYFPSKEALY 66 (212)
T ss_pred HHHHHHhCcccCC-HHHHHHHhCcCHHHHHHHCCCHHHHH
Confidence 3347777776543 66789999999999999999886543
No 294
>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=27.52 E-value=81 Score=19.74 Aligned_cols=37 Identities=16% Similarity=0.231 Sum_probs=27.8
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 42 NAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 42 ~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
...|...+|-.. ....||...|+++..+-..|.++-.
T Consensus 18 ~~lf~e~G~~~~-s~~~IA~~agvs~~~lY~hF~sKe~ 54 (202)
T TIGR03613 18 LDTFSRFGFHGT-SLEQIAELAGVSKTNLLYYFPSKDA 54 (202)
T ss_pred HHHHHHhCcccC-CHHHHHHHhCCCHHHHHHHcCCHHH
Confidence 334666776543 3667899999999999999988744
No 295
>PRK09514 zntR zinc-responsive transcriptional regulator; Provisional
Probab=27.48 E-value=91 Score=19.03 Aligned_cols=21 Identities=19% Similarity=0.215 Sum_probs=18.1
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|-..
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (140)
T PRK09514 4 IGELAKLAEVTPDTLRFYEKQ 24 (140)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 296
>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=27.31 E-value=60 Score=16.83 Aligned_cols=39 Identities=15% Similarity=0.203 Sum_probs=23.9
Q ss_pred HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 37 ALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 37 q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
.-.-|+..|....--.......||..+|+++..|..-++
T Consensus 6 ~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml~ 44 (60)
T PF01325_consen 6 EEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEMLK 44 (60)
T ss_dssp HHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHHH
Confidence 344556666444322233456789999999998877664
No 297
>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=27.24 E-value=95 Score=18.66 Aligned_cols=21 Identities=29% Similarity=0.387 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...+..|...
T Consensus 4 I~e~a~~~gvs~~tlR~Ye~~ 24 (131)
T TIGR02043 4 IGELAKLCGVTSDTLRFYEKN 24 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 298
>PF13223 DUF4031: Protein of unknown function (DUF4031)
Probab=26.89 E-value=79 Score=17.91 Aligned_cols=20 Identities=30% Similarity=0.610 Sum_probs=16.4
Q ss_pred HHHHHHHHHHhCCChHHHHHHHHH
Q psy14049 53 GTEITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 53 ~~~~~~la~~~~l~~~~v~~WFqn 76 (93)
..|...+|..+|+.. .|||.
T Consensus 23 ~~ELHafA~riGv~r----r~fq~ 42 (83)
T PF13223_consen 23 LDELHAFAARIGVPR----RWFQR 42 (83)
T ss_pred HHHHHHHHHHcCCCH----HHHcC
Confidence 466777899999988 69987
No 299
>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=26.81 E-value=94 Score=15.43 Aligned_cols=39 Identities=21% Similarity=0.284 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIW 73 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~W 73 (93)
++..|...|...+...+- .....+||..+++++..|..=
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~~ 41 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSRI 41 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHHH
Confidence 567777888776654432 124667899999998776543
No 300
>PRK10227 DNA-binding transcriptional regulator CueR; Provisional
Probab=26.77 E-value=83 Score=19.16 Aligned_cols=20 Identities=25% Similarity=0.361 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
+.++|..+|++...|+.|=.
T Consensus 3 Ige~a~~~gvs~~tlRyYE~ 22 (135)
T PRK10227 3 ISDVAKITGLTSKAIRFYEE 22 (135)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999998854
No 301
>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=26.76 E-value=83 Score=18.81 Aligned_cols=21 Identities=33% Similarity=0.409 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|..|-..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (127)
T TIGR02047 3 IGELAQKTGVSVETIRFYEKQ 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 302
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=26.72 E-value=91 Score=15.25 Aligned_cols=22 Identities=32% Similarity=0.344 Sum_probs=16.4
Q ss_pred HHHHHHHHhCCChHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqn 76 (93)
...+||..++++.+.|..-...
T Consensus 17 t~~eLa~~l~vS~rTi~~~i~~ 38 (55)
T PF08279_consen 17 TAKELAEELGVSRRTIRRDIKE 38 (55)
T ss_dssp EHHHHHHHCTS-HHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHH
Confidence 3567899999999998876653
No 303
>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=26.66 E-value=19 Score=15.04 Aligned_cols=8 Identities=25% Similarity=0.650 Sum_probs=5.8
Q ss_pred HHHHHHHH
Q psy14049 71 RIWFCNKR 78 (93)
Q Consensus 71 ~~WFqnrR 78 (93)
-+||-++.
T Consensus 6 iNWFE~~g 13 (22)
T PF08452_consen 6 INWFESRG 13 (22)
T ss_pred eehhhhCC
Confidence 47998764
No 304
>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=26.63 E-value=85 Score=18.42 Aligned_cols=21 Identities=29% Similarity=0.305 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-..
T Consensus 3 I~eva~~~gvs~~tLRyYe~~ 23 (123)
T cd04770 3 IGELAKAAGVSPDTIRYYERI 23 (123)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999988753
No 305
>PHA00542 putative Cro-like protein
Probab=26.41 E-value=75 Score=17.48 Aligned_cols=23 Identities=9% Similarity=0.124 Sum_probs=19.6
Q ss_pred HHHHHHHHhCCChHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnr 77 (93)
....||..+|++...|..|...+
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCC
Confidence 35568999999999999999765
No 306
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=26.04 E-value=2.3e+02 Score=19.75 Aligned_cols=51 Identities=20% Similarity=0.281 Sum_probs=34.0
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhHh
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKNT 84 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr~ 84 (93)
++..+..++...|..... ......++|..+|++...|+..-.....+.+..
T Consensus 257 L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred CCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 444444555555533222 223577899999999999999988777776653
No 307
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=26.02 E-value=82 Score=14.50 Aligned_cols=19 Identities=11% Similarity=0.188 Sum_probs=13.6
Q ss_pred HHHHHHHHhCCChHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIW 73 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~W 73 (93)
....||..++++...+..|
T Consensus 8 tl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 8 TLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp -HHHHHHHTTS-HHHHHHH
T ss_pred cHHHHHhhhhhhHhHHHHh
Confidence 4667899999988887665
No 308
>KOG0044|consensus
Probab=26.00 E-value=1.4e+02 Score=19.62 Aligned_cols=30 Identities=13% Similarity=0.386 Sum_probs=22.3
Q ss_pred CCCCHHHHHHHHHHhCCChHHHHHHHHHHH
Q psy14049 49 THPSGTEITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 49 ~~p~~~~~~~la~~~~l~~~~v~~WFqnrR 78 (93)
+...+...+.|......+...|+.|+.+=.
T Consensus 7 ~~~~~~~~e~l~~~t~f~~~ei~~~Yr~Fk 36 (193)
T KOG0044|consen 7 SKLQPESLEQLVQQTKFSKKEIQQWYRGFK 36 (193)
T ss_pred ccCCcHHHHHHHHhcCCCHHHHHHHHHHhc
Confidence 344455677778888899999999997643
No 309
>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=25.60 E-value=1.7e+02 Score=17.98 Aligned_cols=29 Identities=7% Similarity=0.240 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
...++|..+|++...|+.=...-|.+.++
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998887766666654
No 310
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=25.38 E-value=84 Score=14.37 Aligned_cols=20 Identities=25% Similarity=0.350 Sum_probs=14.3
Q ss_pred HHHHHHHHhCCChHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WF 74 (93)
.+..||..+|++...|.-=|
T Consensus 4 tr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHH
Confidence 36789999999988876554
No 311
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.34 E-value=73 Score=16.80 Aligned_cols=23 Identities=13% Similarity=0.187 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChHHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNKR 78 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnrR 78 (93)
...||..+|++...|.-.+.++.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 35789999999999998887653
No 312
>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=24.96 E-value=46 Score=18.79 Aligned_cols=11 Identities=18% Similarity=0.661 Sum_probs=8.4
Q ss_pred hHHHHHHHHHH
Q psy14049 67 REVIRIWFCNK 77 (93)
Q Consensus 67 ~~~v~~WFqnr 77 (93)
...|++|.||-
T Consensus 30 qgdvkvwmqnl 40 (106)
T PF11516_consen 30 QGDVKVWMQNL 40 (106)
T ss_dssp -HHHHHHHHHH
T ss_pred cccHHHHHHHH
Confidence 35699999985
No 313
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=24.86 E-value=94 Score=19.47 Aligned_cols=23 Identities=17% Similarity=0.358 Sum_probs=17.9
Q ss_pred HHHHHHHHHHhCCChHHHHHHHH
Q psy14049 53 GTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 53 ~~~~~~la~~~~l~~~~v~~WFq 75 (93)
.....++|..+|++...+-.|-+
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 34577899999999999999984
No 314
>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=24.84 E-value=95 Score=18.79 Aligned_cols=20 Identities=30% Similarity=0.395 Sum_probs=16.8
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
+.++|..+|++...++.|=+
T Consensus 3 Ige~a~~~gvs~~tLRyYE~ 22 (131)
T cd04786 3 IGELAKRSGMAASRIRFYEA 22 (131)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999854
No 315
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=24.43 E-value=1.7e+02 Score=17.55 Aligned_cols=46 Identities=17% Similarity=0.186 Sum_probs=33.7
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 31 TSFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
..+|..+...|.-. ..+ + ...++|..++++...|+.+.++-+.|..
T Consensus 148 ~~lt~~e~~vl~l~-~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKLI-TEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHHH-HCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 34788878877663 222 2 2567899999999999999998776653
No 316
>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=24.26 E-value=98 Score=18.41 Aligned_cols=21 Identities=33% Similarity=0.374 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...++.|-..
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~~ 23 (126)
T cd04785 3 IGELARRTGVNVETIRYYESI 23 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999998753
No 317
>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=24.17 E-value=97 Score=18.37 Aligned_cols=20 Identities=35% Similarity=0.396 Sum_probs=16.7
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...|+.|-+
T Consensus 3 I~e~a~~~gvs~~tlR~Ye~ 22 (126)
T cd04783 3 IGELAKAAGVNVETIRYYQR 22 (126)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45689999999999988864
No 318
>PRK13558 bacterio-opsin activator; Provisional
Probab=24.14 E-value=1.3e+02 Score=22.74 Aligned_cols=41 Identities=22% Similarity=0.338 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHhhhCCC--CCHHHHHHHHHHhCCChHHHH
Q psy14049 31 TSFTPQALELLNAHFERNTH--PSGTEITTLAHQLGYEREVIR 71 (93)
Q Consensus 31 ~~~t~~q~~~L~~~f~~~~~--p~~~~~~~la~~~~l~~~~v~ 71 (93)
..+|..|.+.|+..|...-| |=.....+||..+|++...+.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 46999999999999987655 555567889999999987644
No 319
>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=24.08 E-value=1e+02 Score=18.32 Aligned_cols=21 Identities=33% Similarity=0.385 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...|+.|-..
T Consensus 3 IgevA~~~gvs~~tLRyYe~~ 23 (127)
T cd04784 3 IGELAKKTGCSVETIRYYEKE 23 (127)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 320
>PF07750 GcrA: GcrA cell cycle regulator; InterPro: IPR011681 GcrA, together with CtrA (see IPR001789 from INTERPRO and IPR001867 from INTERPRO), form a master cell cycle regulator. These bacterial regulators are involved in controlling the progression and asymmetric polar morphogenesis []. During this process, there are temporal and spatial variations in the concentrations of GcrA and CtrA. The variation in concentration produces time and space dependent transcriptional regulation of modular functions that implement cell-cycle processes []. More specifically, GcrA acts as an activator of components of the replisome and the segregation machinery [].
Probab=23.67 E-value=1.4e+02 Score=18.96 Aligned_cols=34 Identities=26% Similarity=0.441 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhC-CChHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLG-YEREVI 70 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~-l~~~~v 70 (93)
.+|.+.++.|.+.+... ....+||.+|| ++..-|
T Consensus 2 ~Wtde~~~~L~~lw~~G-----~SasqIA~~lg~vsRnAV 36 (162)
T PF07750_consen 2 SWTDERVERLRKLWAEG-----LSASQIARQLGGVSRNAV 36 (162)
T ss_pred CCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCcchhhh
Confidence 47889999999888544 23556788888 666543
No 321
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.57 E-value=2.3e+02 Score=18.79 Aligned_cols=27 Identities=11% Similarity=0.164 Sum_probs=23.3
Q ss_pred HHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 57 TTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 57 ~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
.++|..+|++++.|..-.+|-+.|.--
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 578899999999999999998887643
No 322
>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=23.15 E-value=1.1e+02 Score=18.43 Aligned_cols=20 Identities=20% Similarity=0.418 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
.-++|..+|++...|+.|-.
T Consensus 3 IgE~A~~~gvs~~TLRyYE~ 22 (133)
T cd04787 3 VKELANAAGVTPDTVRFYTR 22 (133)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999864
No 323
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=22.84 E-value=1.2e+02 Score=19.26 Aligned_cols=42 Identities=21% Similarity=0.275 Sum_probs=31.1
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 38 LELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 38 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
+..-...|...+|-... ...||...|+++.-+-.+|.++-.-
T Consensus 17 l~AA~~lf~e~G~~~~t-~~~Ia~~agvs~~tlY~~F~sKe~L 58 (215)
T PRK10668 17 LDAALRLFSQQGVSATS-LADIAKAAGVTRGAIYWHFKNKSDL 58 (215)
T ss_pred HHHHHHHHHHcCcccCC-HHHHHHHhCCChHHHHHHCCCHHHH
Confidence 33444557777776533 6778999999999999999887543
No 324
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=22.75 E-value=1.1e+02 Score=15.01 Aligned_cols=39 Identities=23% Similarity=0.396 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFq 75 (93)
+|..|...|...+...+ ....+||..++++...|..+..
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHHHH
Confidence 35667777777776554 2344789999999998887765
No 325
>PTZ00183 centrin; Provisional
Probab=22.37 E-value=1.8e+02 Score=17.13 Aligned_cols=40 Identities=18% Similarity=0.352 Sum_probs=29.6
Q ss_pred CCCCCCCCCHHHHHHHHHHhh-----hCCCCCHHHHHHHHHHhCC
Q psy14049 26 KRKRRTSFTPQALELLNAHFE-----RNTHPSGTEITTLAHQLGY 65 (93)
Q Consensus 26 ~rr~r~~~t~~q~~~L~~~f~-----~~~~p~~~~~~~la~~~~l 65 (93)
.+-.+..++..++..+...|. .+.+.+..+...+...+|+
T Consensus 4 ~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 4 RRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred cccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 344567789999999988884 3567788887777777664
No 326
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=22.08 E-value=1.7e+02 Score=16.86 Aligned_cols=26 Identities=19% Similarity=0.241 Sum_probs=16.3
Q ss_pred HHHHHHHHhCCChHHHHHHHHHHHHH
Q psy14049 55 EITTLAHQLGYEREVIRIWFCNKRQA 80 (93)
Q Consensus 55 ~~~~la~~~~l~~~~v~~WFqnrR~k 80 (93)
...+||...||+..+|..=....+.+
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35789999999999877666544443
No 327
>PRK00767 transcriptional regulator BetI; Validated
Probab=22.08 E-value=1.5e+02 Score=18.24 Aligned_cols=38 Identities=16% Similarity=0.177 Sum_probs=30.0
Q ss_pred HHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHH
Q psy14049 41 LNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQ 79 (93)
Q Consensus 41 L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~ 79 (93)
-...|...+|-. .....||...|++...+-..|.|+..
T Consensus 18 A~~lf~~~G~~~-~s~~~Ia~~aGvs~gslY~~F~~Ke~ 55 (197)
T PRK00767 18 TLRAIGEVGLLD-ATIAQIARRAGVSTGIISHYFGGKDG 55 (197)
T ss_pred HHHHHHHcCccc-CCHHHHHHHhCCCHHHHHHHhCCHHH
Confidence 344477788876 44777899999999999999988754
No 328
>PRK13749 transcriptional regulator MerD; Provisional
Probab=22.01 E-value=1.2e+02 Score=18.25 Aligned_cols=19 Identities=21% Similarity=0.455 Sum_probs=16.3
Q ss_pred HHHHHHHhCCChHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWF 74 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WF 74 (93)
+.++|..+|++...|+.|=
T Consensus 6 IgelA~~~gvS~~tiR~YE 24 (121)
T PRK13749 6 VSRLALDAGVSVHIVRDYL 24 (121)
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 5678999999999999884
No 329
>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=21.77 E-value=1.2e+02 Score=17.32 Aligned_cols=20 Identities=15% Similarity=0.233 Sum_probs=15.9
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
..++|..+|++...|+.|=+
T Consensus 3 Ige~a~~~gvs~~tlRyYe~ 22 (107)
T cd04777 3 IGKFAKKNNITIDTVRHYID 22 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35688999999999887754
No 330
>PRK05949 RNA polymerase sigma factor; Validated
Probab=21.68 E-value=3e+02 Score=19.39 Aligned_cols=50 Identities=22% Similarity=0.309 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhhH
Q psy14049 33 FTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALKN 83 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~kr 83 (93)
+++.+..++...|..... ......++|..+|++...|+......+.+.+.
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 444455555555532221 12356789999999999999998877777665
No 331
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=21.65 E-value=98 Score=19.30 Aligned_cols=15 Identities=20% Similarity=0.295 Sum_probs=8.8
Q ss_pred CCCHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFE 46 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~ 46 (93)
-++.+|+..|.....
T Consensus 51 ~Lt~~qi~~l~~~i~ 65 (144)
T TIGR03629 51 YLDDEEIEKLEEAVE 65 (144)
T ss_pred cCCHHHHHHHHHHHH
Confidence 466666666655543
No 332
>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=21.59 E-value=1.3e+02 Score=15.60 Aligned_cols=18 Identities=17% Similarity=0.392 Sum_probs=14.8
Q ss_pred hHHHHHHHHHHHHHhhHh
Q psy14049 67 REVIRIWFCNKRQALKNT 84 (93)
Q Consensus 67 ~~~v~~WFqnrR~k~kr~ 84 (93)
...+..|..+.|.+.++.
T Consensus 35 ~~~Lg~Wl~~qR~~~r~g 52 (68)
T PF03457_consen 35 GFPLGQWLNNQRRKYRKG 52 (68)
T ss_dssp SSHHHHHHHHHHHHHHHT
T ss_pred CCcHHHHHHHHHHHHHcC
Confidence 456889999999998873
No 333
>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=21.57 E-value=2.6e+02 Score=18.61 Aligned_cols=46 Identities=13% Similarity=0.209 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHHHHHHhh
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCNKRQALK 82 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqnrR~k~k 82 (93)
.++..+...+...|. ......++|..+|++...|...-..-..+.+
T Consensus 206 ~L~~rer~vi~~~~~-----~~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 206 RLNEREKMILNMRFF-----EGKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred cCCHHHHHHHHHHHc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 355555556665552 2234678999999999998776654444433
No 334
>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=21.56 E-value=1.5e+02 Score=17.34 Aligned_cols=21 Identities=33% Similarity=0.407 Sum_probs=17.6
Q ss_pred HHHHHHHhCCChHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqn 76 (93)
..++|..+|++...+..|...
T Consensus 3 ige~a~~~gvs~~tLryYe~~ 23 (116)
T cd04769 3 IGELAQQTGVTIKAIRLYEEK 23 (116)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356899999999999999863
No 335
>PRK00215 LexA repressor; Validated
Probab=21.37 E-value=1.7e+02 Score=18.69 Aligned_cols=43 Identities=19% Similarity=0.215 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCC-ChHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHF---ERNTHPSGTEITTLAHQLGY-EREVIRIWFCNK 77 (93)
Q Consensus 33 ~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l-~~~~v~~WFqnr 77 (93)
+|..|...|.... ..+..+ ....+||..+|+ +...|..+.+.-
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHHH
Confidence 4667777776554 333433 235678999999 898888887643
No 336
>PHA01083 hypothetical protein
Probab=21.10 E-value=1.1e+02 Score=19.29 Aligned_cols=32 Identities=19% Similarity=0.123 Sum_probs=22.6
Q ss_pred HHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHHHH
Q psy14049 42 NAHFERNTHPSGTEITTLAHQLGYEREVIRIWFCN 76 (93)
Q Consensus 42 ~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WFqn 76 (93)
...-+...|++. ..||+.+|+++..|..|=..
T Consensus 8 da~K~a~~~~sd---kqLA~~LGVs~q~IS~~R~G 39 (149)
T PHA01083 8 DAYKKAKNYVQY---KQIAHDLGVSPQKISKMRTG 39 (149)
T ss_pred HHHHHHHhhccH---HHHHHHhCCCHHHHHHHHcC
Confidence 333333445553 46899999999999999765
No 337
>cd00131 PAX Paired Box domain
Probab=20.94 E-value=2e+02 Score=17.22 Aligned_cols=46 Identities=22% Similarity=0.112 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCC-------ChHHHHHHHHHH
Q psy14049 32 SFTPQALELLNAHFERNTHPSGTEITTLAHQLGY-------EREVIRIWFCNK 77 (93)
Q Consensus 32 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l-------~~~~v~~WFqnr 77 (93)
..+..+...+......++..+..+...+...-|+ +...|--||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 3456666666666778888877777654334455 788888887653
No 338
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=20.53 E-value=2.7e+02 Score=18.40 Aligned_cols=43 Identities=16% Similarity=0.263 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHhhhCCCC-CHHHHHHHHHHhCCChHHHHHHHHHH
Q psy14049 33 FTPQALELLNAHFERNTHP-SGTEITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 33 ~t~~q~~~L~~~f~~~~~p-~~~~~~~la~~~~l~~~~v~~WFqnr 77 (93)
++..++......+...-.| +..+...+..+.|.. .|.+|||+-
T Consensus 190 ~s~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~--~v~~~~~~~ 233 (247)
T PRK15451 190 YSELEISQKRSMLENVMLTDSVETHKARLHKAGFE--HSELWFQCF 233 (247)
T ss_pred CCHHHHHHHHHHHHhhcccCCHHHHHHHHHHcCch--hHHHHHHHH
Confidence 4444444433334333333 556666677777754 578888754
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=20.43 E-value=1.3e+02 Score=14.77 Aligned_cols=22 Identities=14% Similarity=0.258 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFCNK 77 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFqnr 77 (93)
...+|..+|++...|..-|.+.
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 3568999999999998888664
No 340
>PF09301 DUF1970: Domain of unknown function (DUF1970); InterPro: IPR015380 This entry is represented by Bacteriophage PRD1, P16; it is a family of uncharacterised viral proteins.; PDB: 1W8X_P.
Probab=20.27 E-value=62 Score=18.59 Aligned_cols=12 Identities=42% Similarity=0.938 Sum_probs=8.0
Q ss_pred HHHHHHHHHHHH
Q psy14049 69 VIRIWFCNKRQA 80 (93)
Q Consensus 69 ~v~~WFqnrR~k 80 (93)
-|=.||.||-+.
T Consensus 18 liwlwfrnrpaa 29 (117)
T PF09301_consen 18 LIWLWFRNRPAA 29 (117)
T ss_dssp HHHHHHHHTT-S
T ss_pred HHHHHHccChHH
Confidence 356799998653
No 341
>cd04778 HTH_MerR-like_sg2 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 2). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.05 E-value=1.2e+02 Score=20.13 Aligned_cols=20 Identities=25% Similarity=0.263 Sum_probs=17.0
Q ss_pred HHHHHHHhCCChHHHHHHHH
Q psy14049 56 ITTLAHQLGYEREVIRIWFC 75 (93)
Q Consensus 56 ~~~la~~~~l~~~~v~~WFq 75 (93)
+.+||..+|++...|+.|=.
T Consensus 4 i~elA~~~Gvs~~tIR~Ye~ 23 (219)
T cd04778 4 IDDLARAAGTTVRNVRAYQD 23 (219)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999854
Done!