Query psy11996
Match_columns 222
No_of_seqs 214 out of 2467
Neff 8.9
Searched_HMMs 46136
Date Fri Aug 16 15:57:17 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy11996.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/11996hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 4.9E-20 1.1E-24 125.7 6.3 70 5-74 12-81 (125)
2 KOG0490|consensus 99.8 2.1E-19 4.5E-24 145.8 10.4 157 7-194 57-213 (235)
3 KOG0850|consensus 99.7 6.2E-18 1.3E-22 131.6 7.4 70 5-74 117-186 (245)
4 KOG0489|consensus 99.7 1E-17 2.2E-22 137.6 7.9 87 110-199 138-224 (261)
5 KOG2251|consensus 99.7 5.7E-17 1.2E-21 125.8 9.7 68 5-72 32-99 (228)
6 KOG0850|consensus 99.7 3.7E-17 8E-22 127.4 8.1 69 130-198 118-186 (245)
7 KOG0484|consensus 99.7 1.3E-17 2.9E-22 113.9 3.9 66 130-195 13-78 (125)
8 KOG0489|consensus 99.7 8.1E-17 1.8E-21 132.3 8.5 71 5-75 154-224 (261)
9 PF00046 Homeobox: Homeobox do 99.7 8.3E-17 1.8E-21 102.0 6.6 57 11-67 1-57 (57)
10 KOG0842|consensus 99.7 6.5E-17 1.4E-21 133.0 6.4 74 131-204 150-223 (307)
11 KOG0843|consensus 99.7 9.1E-17 2E-21 120.7 6.4 64 9-72 101-164 (197)
12 PF00046 Homeobox: Homeobox do 99.7 1.7E-16 3.7E-21 100.6 6.5 57 135-191 1-57 (57)
13 KOG0488|consensus 99.7 1.4E-16 3E-21 133.1 7.3 67 129-195 167-233 (309)
14 KOG0488|consensus 99.7 1.2E-16 2.7E-21 133.4 6.6 66 6-71 168-233 (309)
15 KOG0842|consensus 99.7 5.9E-17 1.3E-21 133.3 4.3 70 8-77 151-220 (307)
16 KOG0485|consensus 99.7 9.4E-17 2E-21 123.8 4.7 65 7-71 101-165 (268)
17 KOG0843|consensus 99.6 2E-16 4.3E-21 118.8 5.6 64 133-196 101-164 (197)
18 KOG0494|consensus 99.6 2.2E-16 4.8E-21 124.7 6.0 65 10-74 140-205 (332)
19 KOG2251|consensus 99.6 1.3E-15 2.8E-20 118.3 8.5 67 130-196 33-99 (228)
20 KOG0485|consensus 99.6 2.8E-15 6.2E-20 115.7 8.0 65 131-195 101-165 (268)
21 KOG0492|consensus 99.6 1.4E-15 3.1E-20 116.6 5.3 65 7-71 141-205 (246)
22 KOG0487|consensus 99.6 1.2E-15 2.7E-20 125.6 4.1 65 8-72 233-297 (308)
23 TIGR01565 homeo_ZF_HD homeobox 99.6 4E-15 8.6E-20 93.2 4.8 53 10-62 1-57 (58)
24 KOG0487|consensus 99.6 4.9E-15 1.1E-19 122.0 6.4 64 132-195 233-296 (308)
25 KOG0492|consensus 99.6 3.8E-15 8.2E-20 114.3 5.0 65 130-194 140-204 (246)
26 KOG0848|consensus 99.6 3.6E-15 7.9E-20 118.5 5.0 63 134-196 199-261 (317)
27 smart00389 HOX Homeodomain. DN 99.5 1.2E-14 2.7E-19 91.6 5.8 55 11-65 1-55 (56)
28 KOG0494|consensus 99.5 2.6E-14 5.7E-19 113.1 8.4 65 133-197 140-204 (332)
29 cd00086 homeodomain Homeodomai 99.5 2.3E-14 5.1E-19 91.2 6.7 57 11-67 1-57 (59)
30 smart00389 HOX Homeodomain. DN 99.5 1.8E-14 3.9E-19 90.8 6.0 55 136-190 2-56 (56)
31 cd00086 homeodomain Homeodomai 99.5 3.3E-14 7.1E-19 90.5 6.7 57 136-192 2-58 (59)
32 KOG0493|consensus 99.5 1.2E-14 2.6E-19 115.1 5.3 64 6-69 242-305 (342)
33 KOG0848|consensus 99.5 6.4E-15 1.4E-19 117.1 3.2 65 8-72 197-261 (317)
34 KOG0491|consensus 99.5 1.2E-13 2.6E-18 102.4 8.5 70 133-202 99-168 (194)
35 KOG0493|consensus 99.5 2.8E-14 6.1E-19 113.1 4.9 62 134-195 246-307 (342)
36 TIGR01565 homeo_ZF_HD homeobox 99.5 3E-14 6.5E-19 89.2 4.1 52 135-186 2-57 (58)
37 KOG3802|consensus 99.5 1.4E-14 3E-19 121.7 3.2 70 132-201 292-361 (398)
38 KOG0844|consensus 99.4 1.8E-14 3.9E-19 116.5 1.4 70 6-75 177-246 (408)
39 KOG0491|consensus 99.4 8.4E-14 1.8E-18 103.2 4.7 64 10-73 100-163 (194)
40 KOG0486|consensus 99.4 4.5E-14 9.9E-19 114.7 3.5 66 8-73 110-175 (351)
41 COG5576 Homeodomain-containing 99.4 2.3E-13 5E-18 102.7 6.1 68 5-72 46-113 (156)
42 KOG3802|consensus 99.4 8.8E-14 1.9E-18 116.9 3.7 67 4-70 288-354 (398)
43 KOG4577|consensus 99.4 1.7E-13 3.7E-18 110.1 5.0 71 4-74 161-231 (383)
44 COG5576 Homeodomain-containing 99.4 5.5E-13 1.2E-17 100.7 6.3 72 129-200 46-117 (156)
45 KOG0844|consensus 99.4 2.8E-14 6.1E-19 115.4 -1.4 62 132-193 179-240 (408)
46 KOG0483|consensus 99.4 5.7E-13 1.2E-17 104.0 5.2 60 134-193 50-109 (198)
47 KOG0483|consensus 99.4 9E-13 2E-17 102.8 5.2 60 10-69 50-109 (198)
48 KOG4577|consensus 99.4 9E-13 2E-17 106.0 5.2 70 127-196 160-229 (383)
49 KOG0847|consensus 99.3 1.1E-12 2.5E-17 101.5 4.3 67 129-195 162-228 (288)
50 KOG0486|consensus 99.3 9.8E-13 2.1E-17 107.0 3.0 65 133-197 111-175 (351)
51 KOG0847|consensus 99.3 2E-12 4.4E-17 100.1 4.3 66 6-71 163-228 (288)
52 KOG1168|consensus 99.0 4.9E-11 1.1E-15 96.1 0.4 63 130-192 305-367 (385)
53 KOG0849|consensus 99.0 9.5E-10 2.1E-14 94.1 8.3 65 6-70 172-236 (354)
54 KOG0775|consensus 99.0 3E-09 6.4E-14 85.4 8.1 49 19-67 185-233 (304)
55 KOG0775|consensus 99.0 7.1E-10 1.5E-14 88.9 4.6 53 141-193 183-235 (304)
56 KOG1168|consensus 99.0 1.7E-10 3.6E-15 93.1 1.0 67 6-72 305-371 (385)
57 KOG0490|consensus 98.9 8.6E-10 1.9E-14 89.3 4.2 64 131-194 57-120 (235)
58 KOG0849|consensus 98.8 8E-09 1.7E-13 88.5 7.4 63 131-193 173-235 (354)
59 KOG0774|consensus 98.8 1.1E-08 2.3E-13 81.6 5.7 60 10-69 188-250 (334)
60 PF05920 Homeobox_KN: Homeobox 98.7 1.1E-08 2.3E-13 59.4 3.5 34 155-188 7-40 (40)
61 PF05920 Homeobox_KN: Homeobox 98.7 2.3E-08 5.1E-13 58.0 3.3 34 31-64 7-40 (40)
62 KOG0774|consensus 98.5 6.2E-08 1.3E-12 77.4 2.9 61 133-193 187-250 (334)
63 KOG1146|consensus 98.5 2E-06 4.4E-11 82.2 13.2 187 10-196 705-965 (1406)
64 KOG2252|consensus 98.4 6.7E-07 1.5E-11 78.6 7.8 60 130-189 416-475 (558)
65 KOG2252|consensus 98.3 1.5E-06 3.3E-11 76.4 7.3 60 6-65 416-475 (558)
66 KOG0773|consensus 98.0 2E-05 4.4E-10 67.6 8.2 165 30-194 117-302 (342)
67 KOG1146|consensus 98.0 1.5E-05 3.3E-10 76.5 7.2 64 9-72 902-965 (1406)
68 KOG3623|consensus 97.7 8.6E-05 1.9E-09 67.5 6.3 117 22-192 568-684 (1007)
69 PF11569 Homez: Homeodomain le 97.6 6.8E-05 1.5E-09 46.3 3.2 42 22-63 10-51 (56)
70 PF11569 Homez: Homeodomain le 97.5 0.00011 2.3E-09 45.4 3.3 42 146-187 10-51 (56)
71 KOG0773|consensus 96.3 0.0029 6.3E-08 54.3 2.9 58 10-67 239-299 (342)
72 KOG3623|consensus 96.1 0.012 2.7E-07 54.0 5.9 52 146-197 568-619 (1007)
73 PF04218 CENP-B_N: CENP-B N-te 95.4 0.041 8.9E-07 33.8 4.5 47 11-62 1-47 (53)
74 PF04218 CENP-B_N: CENP-B N-te 94.4 0.11 2.4E-06 31.8 4.5 47 135-186 1-47 (53)
75 KOG3755|consensus 92.1 0.3 6.5E-06 44.3 5.2 59 9-67 646-708 (769)
76 PF04545 Sigma70_r4: Sigma-70, 87.8 1.8 4E-05 25.7 4.8 46 140-190 4-49 (50)
77 PF04967 HTH_10: HTH DNA bindi 85.8 1.4 3E-05 27.0 3.4 41 141-181 1-43 (53)
78 PF01527 HTH_Tnp_1: Transposas 84.0 1 2.2E-05 29.3 2.4 43 12-59 2-45 (76)
79 PF04545 Sigma70_r4: Sigma-70, 83.9 3.6 7.8E-05 24.4 4.7 44 16-64 4-47 (50)
80 PF04967 HTH_10: HTH DNA bindi 81.0 4.3 9.4E-05 24.8 4.2 42 17-58 1-44 (53)
81 PF08281 Sigma70_r4_2: Sigma-7 79.8 7.1 0.00015 23.4 5.0 43 140-187 10-52 (54)
82 PF13551 HTH_29: Winged helix- 79.5 18 0.00038 25.0 8.6 43 141-183 58-109 (112)
83 cd06171 Sigma70_r4 Sigma70, re 79.2 3.2 6.8E-05 24.2 3.3 43 140-187 10-52 (55)
84 PF10668 Phage_terminase: Phag 76.7 2.2 4.7E-05 26.9 2.0 21 163-183 24-44 (60)
85 PF01527 HTH_Tnp_1: Transposas 76.5 2.2 4.8E-05 27.6 2.1 44 137-184 3-46 (76)
86 cd00131 PAX Paired Box domain 75.9 28 0.0006 25.4 11.6 46 140-185 75-127 (128)
87 PF09607 BrkDBD: Brinker DNA-b 75.7 9.9 0.00022 23.7 4.7 44 14-59 3-47 (58)
88 PF09607 BrkDBD: Brinker DNA-b 73.8 11 0.00024 23.5 4.5 44 138-183 3-47 (58)
89 cd06171 Sigma70_r4 Sigma70, re 72.8 8.6 0.00019 22.2 4.0 42 16-62 10-51 (55)
90 PRK03975 tfx putative transcri 72.7 14 0.00031 27.5 5.8 49 138-192 4-52 (141)
91 PF10668 Phage_terminase: Phag 72.6 3.6 7.7E-05 25.9 2.2 20 39-58 24-43 (60)
92 PRK09413 IS2 repressor TnpA; R 72.0 17 0.00036 26.1 6.0 41 14-59 10-51 (121)
93 cd00569 HTH_Hin_like Helix-tur 70.2 13 0.00029 19.1 4.8 38 16-58 5-42 (42)
94 PF13936 HTH_38: Helix-turn-he 68.7 9.6 0.00021 22.1 3.4 40 139-183 3-42 (44)
95 PF08281 Sigma70_r4_2: Sigma-7 65.3 21 0.00046 21.2 4.6 41 17-62 11-51 (54)
96 PRK10072 putative transcriptio 65.0 19 0.00042 24.9 4.8 41 16-63 32-72 (96)
97 PRK03975 tfx putative transcri 64.7 32 0.00069 25.7 6.2 50 14-69 4-53 (141)
98 PRK00118 putative DNA-binding 64.4 24 0.00053 24.8 5.3 49 139-192 16-64 (104)
99 PF02796 HTH_7: Helix-turn-hel 64.4 16 0.00034 21.2 3.7 40 139-183 4-43 (45)
100 PF00196 GerE: Bacterial regul 63.7 22 0.00047 21.7 4.5 44 140-189 3-46 (58)
101 PRK09646 RNA polymerase sigma 63.2 21 0.00046 27.6 5.5 49 140-193 142-190 (194)
102 PRK04217 hypothetical protein; 61.8 29 0.00062 24.7 5.3 52 138-194 40-91 (110)
103 PRK09642 RNA polymerase sigma 60.1 27 0.00058 25.9 5.4 50 140-194 106-155 (160)
104 cd04761 HTH_MerR-SF Helix-Turn 60.1 11 0.00024 21.7 2.6 20 40-59 3-22 (49)
105 smart00351 PAX Paired Box doma 60.0 63 0.0014 23.3 11.2 39 16-59 17-55 (125)
106 PRK12512 RNA polymerase sigma 59.4 29 0.00063 26.4 5.5 51 140-195 131-181 (184)
107 COG3413 Predicted DNA binding 59.2 16 0.00036 29.0 4.2 42 16-57 155-198 (215)
108 PF00196 GerE: Bacterial regul 59.0 30 0.00066 21.0 4.6 43 16-64 3-45 (58)
109 PF13518 HTH_28: Helix-turn-he 58.8 12 0.00026 22.0 2.6 22 163-184 14-35 (52)
110 PF06056 Terminase_5: Putative 58.5 10 0.00022 23.6 2.3 22 162-183 14-35 (58)
111 PRK12526 RNA polymerase sigma 58.1 28 0.00061 27.3 5.4 50 140-194 153-202 (206)
112 COG4367 Uncharacterized protei 57.7 18 0.0004 24.5 3.5 41 140-180 2-42 (97)
113 PRK06759 RNA polymerase factor 57.6 26 0.00057 25.7 4.9 47 140-191 106-152 (154)
114 COG3413 Predicted DNA binding 57.4 20 0.00044 28.4 4.5 39 140-178 155-195 (215)
115 COG3415 Transposase and inacti 56.9 72 0.0016 23.7 6.9 55 137-191 60-116 (138)
116 smart00421 HTH_LUXR helix_turn 56.6 38 0.00082 19.7 4.7 41 140-186 3-43 (58)
117 KOG3755|consensus 56.2 22 0.00048 32.8 4.7 60 133-192 646-709 (769)
118 TIGR02937 sigma70-ECF RNA poly 55.2 31 0.00066 24.7 4.9 47 140-191 110-156 (158)
119 PF08280 HTH_Mga: M protein tr 54.5 31 0.00066 21.3 4.0 37 143-183 5-41 (59)
120 PRK04217 hypothetical protein; 54.4 45 0.00098 23.7 5.3 49 15-68 41-89 (110)
121 PRK11924 RNA polymerase sigma 54.3 33 0.00071 25.6 5.0 48 141-193 126-173 (179)
122 PRK09413 IS2 repressor TnpA; R 54.1 30 0.00065 24.8 4.5 41 138-183 10-51 (121)
123 PF00376 MerR: MerR family reg 52.8 15 0.00033 20.6 2.2 20 164-183 2-21 (38)
124 PRK09652 RNA polymerase sigma 52.6 37 0.0008 25.4 5.1 48 140-192 128-175 (182)
125 smart00027 EH Eps15 homology d 52.1 48 0.001 22.4 5.1 44 16-59 3-51 (96)
126 PF13384 HTH_23: Homeodomain-l 52.0 16 0.00035 21.3 2.4 22 162-183 18-39 (50)
127 TIGR03879 near_KaiC_dom probab 51.6 7.8 0.00017 25.4 1.0 25 160-184 31-55 (73)
128 PF13411 MerR_1: MerR HTH fami 51.4 17 0.00037 22.8 2.6 20 164-183 3-22 (69)
129 PRK12547 RNA polymerase sigma 51.3 48 0.001 24.7 5.5 50 140-194 112-161 (164)
130 PRK12514 RNA polymerase sigma 51.2 42 0.00091 25.4 5.2 48 140-192 129-176 (179)
131 PRK12520 RNA polymerase sigma 50.7 47 0.001 25.5 5.5 58 140-202 131-188 (191)
132 TIGR02989 Sig-70_gvs1 RNA poly 50.6 42 0.0009 24.7 5.0 47 139-190 110-156 (159)
133 PRK00118 putative DNA-binding 49.8 58 0.0012 22.9 5.2 48 16-68 17-64 (104)
134 COG4367 Uncharacterized protei 49.6 37 0.0008 23.1 3.9 40 17-56 3-42 (97)
135 PF13443 HTH_26: Cro/C1-type H 49.6 19 0.00042 22.1 2.6 24 39-62 12-35 (63)
136 TIGR02948 SigW_bacill RNA poly 48.7 43 0.00092 25.4 4.9 48 140-192 136-183 (187)
137 TIGR03879 near_KaiC_dom probab 48.6 9.9 0.00022 24.9 1.1 32 29-60 24-55 (73)
138 TIGR02999 Sig-70_X6 RNA polyme 48.4 52 0.0011 24.9 5.3 46 141-191 135-180 (183)
139 PRK12519 RNA polymerase sigma 48.0 39 0.00085 25.9 4.6 48 140-192 141-188 (194)
140 PF04297 UPF0122: Putative hel 47.7 57 0.0012 22.8 4.8 43 139-186 16-58 (101)
141 PRK09648 RNA polymerase sigma 47.6 51 0.0011 25.2 5.2 48 139-191 138-185 (189)
142 cd04762 HTH_MerR-trunc Helix-T 47.6 24 0.00052 19.9 2.7 22 40-61 3-24 (49)
143 TIGR02939 RpoE_Sigma70 RNA pol 47.3 41 0.00089 25.6 4.6 48 141-193 139-186 (190)
144 PRK10072 putative transcriptio 46.6 53 0.0011 22.7 4.5 41 140-187 32-72 (96)
145 PRK12530 RNA polymerase sigma 46.5 53 0.0011 25.3 5.2 49 140-193 134-182 (189)
146 TIGR02959 SigZ RNA polymerase 46.4 60 0.0013 24.4 5.4 50 140-194 100-149 (170)
147 PRK06930 positive control sigm 46.2 59 0.0013 24.9 5.3 50 140-194 114-163 (170)
148 PRK05602 RNA polymerase sigma 46.0 50 0.0011 25.2 4.9 50 140-194 128-177 (186)
149 PRK09644 RNA polymerase sigma 45.9 53 0.0011 24.5 5.0 50 139-193 107-156 (165)
150 smart00027 EH Eps15 homology d 45.9 71 0.0015 21.6 5.2 43 141-183 4-51 (96)
151 PRK12515 RNA polymerase sigma 45.6 58 0.0013 24.9 5.3 51 139-194 130-180 (189)
152 TIGR02943 Sig70_famx1 RNA poly 45.2 57 0.0012 25.1 5.1 54 140-198 131-184 (188)
153 PRK09047 RNA polymerase factor 45.2 75 0.0016 23.3 5.7 51 139-194 105-155 (161)
154 PF08671 SinI: Anti-repressor 45.1 44 0.00095 17.8 3.1 17 167-183 11-27 (30)
155 PRK12512 RNA polymerase sigma 45.0 62 0.0013 24.6 5.3 32 39-70 149-180 (184)
156 PRK09480 slmA division inhibit 45.0 24 0.00053 26.9 3.0 36 151-187 21-56 (194)
157 PRK06759 RNA polymerase factor 44.8 56 0.0012 23.8 4.9 45 17-66 107-151 (154)
158 TIGR02985 Sig70_bacteroi1 RNA 44.5 63 0.0014 23.5 5.2 47 140-191 113-159 (161)
159 PF01381 HTH_3: Helix-turn-hel 44.4 28 0.0006 20.6 2.6 23 40-62 12-34 (55)
160 PRK09639 RNA polymerase sigma 44.3 61 0.0013 24.0 5.1 48 140-193 112-159 (166)
161 PRK09642 RNA polymerase sigma 44.1 75 0.0016 23.4 5.6 31 39-69 124-154 (160)
162 PF04936 DUF658: Protein of un 43.8 17 0.00037 27.7 1.8 33 162-194 15-47 (186)
163 PRK12538 RNA polymerase sigma 43.8 39 0.00085 27.2 4.1 52 140-196 171-222 (233)
164 PRK12541 RNA polymerase sigma 43.2 56 0.0012 24.2 4.7 47 140-191 112-158 (161)
165 TIGR02937 sigma70-ECF RNA poly 42.7 62 0.0013 23.0 4.8 46 17-67 111-156 (158)
166 cd04763 HTH_MlrA-like Helix-Tu 42.3 28 0.00061 21.9 2.5 20 164-183 3-22 (68)
167 PRK11924 RNA polymerase sigma 42.1 83 0.0018 23.4 5.6 31 39-69 143-173 (179)
168 PRK09646 RNA polymerase sigma 42.1 69 0.0015 24.7 5.2 30 39-68 160-189 (194)
169 PRK09637 RNA polymerase sigma 41.9 66 0.0014 24.6 5.0 50 140-194 106-155 (181)
170 PRK12546 RNA polymerase sigma 41.6 70 0.0015 24.7 5.1 52 140-196 113-164 (188)
171 PRK07037 extracytoplasmic-func 41.5 78 0.0017 23.3 5.3 48 140-192 109-156 (163)
172 PRK12529 RNA polymerase sigma 41.3 74 0.0016 24.1 5.2 49 139-192 126-174 (178)
173 PF13551 HTH_29: Winged helix- 41.2 1.1E+02 0.0023 20.8 5.7 48 12-59 53-109 (112)
174 COG2944 Predicted transcriptio 41.1 80 0.0017 22.2 4.7 41 16-63 43-83 (104)
175 PRK12526 RNA polymerase sigma 41.0 80 0.0017 24.6 5.5 31 39-69 171-201 (206)
176 PRK09652 RNA polymerase sigma 41.0 80 0.0017 23.5 5.4 47 17-68 129-175 (182)
177 PRK12536 RNA polymerase sigma 40.9 76 0.0017 24.1 5.2 49 140-193 129-177 (181)
178 TIGR02983 SigE-fam_strep RNA p 40.8 71 0.0015 23.5 5.0 48 140-192 110-157 (162)
179 TIGR02954 Sig70_famx3 RNA poly 40.7 73 0.0016 23.8 5.0 48 140-192 119-166 (169)
180 cd00131 PAX Paired Box domain 40.6 1.4E+02 0.003 21.6 7.3 47 15-61 74-127 (128)
181 cd04764 HTH_MlrA-like_sg1 Heli 40.3 32 0.00069 21.5 2.6 21 164-184 3-23 (67)
182 PRK12523 RNA polymerase sigma 39.9 92 0.002 23.3 5.5 51 139-194 118-168 (172)
183 cd01392 HTH_LacI Helix-turn-he 39.5 26 0.00056 20.5 1.9 21 42-62 2-22 (52)
184 PRK12531 RNA polymerase sigma 39.2 92 0.002 23.9 5.5 50 140-194 141-190 (194)
185 PRK13919 putative RNA polymera 39.2 86 0.0019 23.8 5.3 47 140-191 135-181 (186)
186 TIGR00721 tfx DNA-binding prot 39.1 1.3E+02 0.0027 22.4 5.8 48 138-191 4-51 (137)
187 TIGR03070 couple_hipB transcri 39.0 38 0.00082 20.0 2.7 23 40-62 18-40 (58)
188 PRK12537 RNA polymerase sigma 39.0 83 0.0018 23.9 5.2 47 140-191 133-179 (182)
189 PRK12543 RNA polymerase sigma 38.8 84 0.0018 23.8 5.2 50 140-194 117-166 (179)
190 PRK12524 RNA polymerase sigma 38.5 84 0.0018 24.2 5.2 49 140-193 136-184 (196)
191 PRK09645 RNA polymerase sigma 38.3 97 0.0021 23.1 5.4 49 140-193 118-166 (173)
192 COG2963 Transposase and inacti 38.3 81 0.0018 22.1 4.7 42 138-183 5-47 (116)
193 PRK09480 slmA division inhibit 38.1 41 0.00089 25.5 3.4 36 27-63 21-56 (194)
194 TIGR02952 Sig70_famx2 RNA poly 37.9 90 0.0019 23.1 5.2 47 140-191 122-168 (170)
195 PRK06986 fliA flagellar biosyn 37.4 83 0.0018 25.2 5.1 48 140-192 184-231 (236)
196 PHA02955 hypothetical protein; 37.4 32 0.00068 27.5 2.5 75 143-217 60-135 (213)
197 TIGR01764 excise DNA binding d 37.2 45 0.00097 18.8 2.7 22 40-61 4-25 (49)
198 PRK12516 RNA polymerase sigma 37.1 97 0.0021 23.8 5.3 51 140-195 116-166 (187)
199 PRK09644 RNA polymerase sigma 36.9 1.1E+02 0.0024 22.7 5.5 31 39-69 126-156 (165)
200 PF12824 MRP-L20: Mitochondria 36.9 1.7E+02 0.0037 22.4 6.4 45 14-60 83-127 (164)
201 PRK12539 RNA polymerase sigma 36.9 96 0.0021 23.6 5.2 49 140-193 131-179 (184)
202 PRK09647 RNA polymerase sigma 36.7 97 0.0021 24.2 5.3 51 140-195 138-188 (203)
203 PRK05602 RNA polymerase sigma 36.7 1E+02 0.0022 23.4 5.4 32 39-70 146-177 (186)
204 PRK12532 RNA polymerase sigma 36.5 90 0.002 24.0 5.1 51 140-195 136-186 (195)
205 PRK09649 RNA polymerase sigma 36.0 85 0.0018 24.0 4.8 47 140-191 130-176 (185)
206 cd01104 HTH_MlrA-CarA Helix-Tu 35.9 40 0.00087 20.9 2.5 20 164-183 3-22 (68)
207 PRK06811 RNA polymerase factor 35.9 1.1E+02 0.0024 23.4 5.5 50 139-193 130-179 (189)
208 TIGR02989 Sig-70_gvs1 RNA poly 35.8 95 0.0021 22.7 5.0 27 39-65 129-155 (159)
209 PRK08583 RNA polymerase sigma 35.8 97 0.0021 25.1 5.4 49 140-193 205-253 (257)
210 cd06170 LuxR_C_like C-terminal 35.5 91 0.002 18.0 4.5 37 142-184 2-38 (57)
211 PRK12535 RNA polymerase sigma 35.5 1E+02 0.0022 23.9 5.3 52 140-196 133-184 (196)
212 PRK12515 RNA polymerase sigma 35.3 1.2E+02 0.0027 23.0 5.7 32 39-70 149-180 (189)
213 PRK09651 RNA polymerase sigma 35.1 86 0.0019 23.6 4.7 47 140-191 119-165 (172)
214 COG2963 Transposase and inacti 35.0 1.1E+02 0.0024 21.4 4.9 42 14-59 5-47 (116)
215 TIGR02980 SigBFG RNA polymeras 34.7 1E+02 0.0022 24.4 5.2 48 139-191 177-224 (227)
216 PF12824 MRP-L20: Mitochondria 34.6 1E+02 0.0022 23.6 4.9 44 137-182 82-125 (164)
217 PRK09648 RNA polymerase sigma 34.3 1.1E+02 0.0024 23.3 5.3 29 39-67 157-185 (189)
218 smart00595 MADF subfamily of S 34.3 54 0.0012 21.7 3.1 35 163-197 29-63 (89)
219 PRK12545 RNA polymerase sigma 34.1 1.3E+02 0.0028 23.4 5.6 51 140-195 139-189 (201)
220 TIGR02479 FliA_WhiG RNA polyme 33.8 1.1E+02 0.0023 24.2 5.2 47 140-191 175-221 (224)
221 PRK12519 RNA polymerase sigma 33.8 97 0.0021 23.7 4.9 31 38-68 158-188 (194)
222 PRK12522 RNA polymerase sigma 33.5 1.2E+02 0.0026 22.7 5.2 30 163-192 137-166 (173)
223 PRK06930 positive control sigm 33.3 1.4E+02 0.0031 22.8 5.6 49 16-69 114-162 (170)
224 PRK12542 RNA polymerase sigma 33.0 1.1E+02 0.0025 23.1 5.1 48 140-192 122-169 (185)
225 PRK11511 DNA-binding transcrip 32.8 93 0.002 22.3 4.3 24 37-60 25-48 (127)
226 PF12728 HTH_17: Helix-turn-he 32.5 57 0.0012 19.0 2.7 22 40-61 4-25 (51)
227 PRK09047 RNA polymerase factor 32.3 1.7E+02 0.0036 21.4 5.8 31 39-69 124-154 (161)
228 TIGR03830 CxxCG_CxxCG_HTH puta 32.2 1E+02 0.0022 21.8 4.4 41 15-62 63-103 (127)
229 PRK12518 RNA polymerase sigma 32.1 62 0.0014 24.2 3.5 34 162-195 137-170 (175)
230 TIGR02859 spore_sigH RNA polym 32.1 1.4E+02 0.0029 22.8 5.5 31 161-191 165-195 (198)
231 TIGR00721 tfx DNA-binding prot 32.0 2E+02 0.0043 21.3 5.9 48 14-67 4-51 (137)
232 PRK12528 RNA polymerase sigma 32.0 1.2E+02 0.0026 22.3 5.0 46 139-189 112-157 (161)
233 PF13730 HTH_36: Helix-turn-he 32.0 73 0.0016 18.8 3.1 43 141-184 3-48 (55)
234 TIGR02948 SigW_bacill RNA poly 31.9 1.1E+02 0.0025 23.0 4.9 31 38-68 153-183 (187)
235 PRK12513 RNA polymerase sigma 31.8 57 0.0012 25.0 3.2 33 162-194 156-188 (194)
236 PRK12514 RNA polymerase sigma 31.4 1.3E+02 0.0029 22.6 5.2 29 39-67 147-175 (179)
237 TIGR02985 Sig70_bacteroi1 RNA 31.4 1.3E+02 0.0029 21.7 5.2 28 39-66 131-158 (161)
238 TIGR02943 Sig70_famx1 RNA poly 31.4 1.7E+02 0.0036 22.4 5.8 33 39-71 149-181 (188)
239 PRK09641 RNA polymerase sigma 31.2 1.2E+02 0.0027 22.7 5.1 47 141-192 137-183 (187)
240 PHA01976 helix-turn-helix prot 31.2 59 0.0013 20.1 2.7 23 40-62 18-40 (67)
241 TIGR02999 Sig-70_X6 RNA polyme 31.2 1.4E+02 0.003 22.5 5.3 29 39-67 152-180 (183)
242 PRK12533 RNA polymerase sigma 31.2 1.1E+02 0.0025 24.2 4.9 50 140-194 134-183 (216)
243 PRK12532 RNA polymerase sigma 31.2 1.7E+02 0.0038 22.3 5.9 32 39-70 154-185 (195)
244 PRK12525 RNA polymerase sigma 31.0 1.3E+02 0.0028 22.5 5.0 48 139-191 117-164 (168)
245 TIGR02941 Sigma_B RNA polymera 31.0 1.2E+02 0.0026 24.6 5.1 47 140-191 205-251 (255)
246 PRK11923 algU RNA polymerase s 31.0 1.3E+02 0.0027 23.0 5.1 32 163-194 156-187 (193)
247 TIGR02939 RpoE_Sigma70 RNA pol 30.9 1.1E+02 0.0024 23.1 4.7 31 38-68 155-185 (190)
248 PF13309 HTH_22: HTH domain 30.6 1.4E+02 0.003 18.7 4.3 38 20-57 25-62 (64)
249 PF13412 HTH_24: Winged helix- 30.6 1.1E+02 0.0024 17.5 3.9 38 142-183 2-39 (48)
250 PRK12530 RNA polymerase sigma 30.6 1.5E+02 0.0033 22.6 5.5 31 39-69 152-182 (189)
251 cd00093 HTH_XRE Helix-turn-hel 30.5 64 0.0014 18.0 2.7 22 40-61 15-36 (58)
252 PRK07408 RNA polymerase sigma 30.4 1.4E+02 0.003 24.4 5.4 49 140-193 203-251 (256)
253 PF08279 HTH_11: HTH domain; 30.4 64 0.0014 19.1 2.7 35 146-183 3-37 (55)
254 PF07037 DUF1323: Putative tra 30.4 47 0.001 24.0 2.2 20 40-59 3-22 (122)
255 TIGR02959 SigZ RNA polymerase 30.2 1.7E+02 0.0036 21.9 5.5 32 39-70 118-149 (170)
256 TIGR02607 antidote_HigA addict 30.2 60 0.0013 20.7 2.7 23 40-62 21-43 (78)
257 PRK12527 RNA polymerase sigma 30.2 1.8E+02 0.0038 21.3 5.6 50 140-194 105-154 (159)
258 PRK06424 transcription factor; 30.1 66 0.0014 24.1 3.1 24 40-63 100-123 (144)
259 PRK09637 RNA polymerase sigma 30.0 1.6E+02 0.0034 22.4 5.4 32 39-70 124-155 (181)
260 PF01710 HTH_Tnp_IS630: Transp 30.0 2E+02 0.0044 20.3 8.4 36 19-59 5-40 (119)
261 PF13022 HTH_Tnp_1_2: Helix-tu 29.9 66 0.0014 24.0 3.0 23 161-183 34-56 (142)
262 PRK12540 RNA polymerase sigma 29.9 1.5E+02 0.0033 22.6 5.3 53 140-197 111-163 (182)
263 PHA02955 hypothetical protein; 29.9 59 0.0013 26.0 2.9 43 19-61 60-103 (213)
264 PRK08301 sporulation sigma fac 29.9 1.1E+02 0.0025 24.2 4.8 52 140-192 178-229 (234)
265 TIGR03001 Sig-70_gmx1 RNA poly 29.8 1.3E+02 0.0027 24.5 5.0 50 140-194 161-210 (244)
266 PRK12547 RNA polymerase sigma 29.8 1.6E+02 0.0035 21.8 5.4 30 39-68 130-159 (164)
267 PRK12511 RNA polymerase sigma 29.6 1.4E+02 0.003 22.9 5.0 50 140-194 111-160 (182)
268 PRK12544 RNA polymerase sigma 29.6 1.5E+02 0.0033 23.2 5.3 50 140-194 148-197 (206)
269 PRK08295 RNA polymerase factor 29.4 1.7E+02 0.0037 22.5 5.7 48 140-193 155-202 (208)
270 PRK09645 RNA polymerase sigma 29.1 1.8E+02 0.0039 21.6 5.6 31 39-69 136-166 (173)
271 PRK09639 RNA polymerase sigma 29.1 1.8E+02 0.0039 21.4 5.5 31 39-69 129-159 (166)
272 TIGR02947 SigH_actino RNA poly 29.0 70 0.0015 24.5 3.3 33 162-194 148-180 (193)
273 PRK07670 RNA polymerase sigma 29.0 1.4E+02 0.0031 24.1 5.3 47 140-191 201-247 (251)
274 PF06971 Put_DNA-bind_N: Putat 28.8 45 0.00098 20.1 1.7 17 164-180 31-47 (50)
275 smart00422 HTH_MERR helix_turn 28.7 55 0.0012 20.3 2.3 20 164-183 3-22 (70)
276 PRK12541 RNA polymerase sigma 28.6 1.3E+02 0.0029 22.1 4.7 29 39-67 130-158 (161)
277 PF14549 P22_Cro: DNA-binding 28.5 66 0.0014 20.1 2.5 18 40-57 12-29 (60)
278 PRK11552 putative DNA-binding 28.2 64 0.0014 25.7 3.0 42 146-189 19-60 (225)
279 PRK06986 fliA flagellar biosyn 28.0 1.6E+02 0.0034 23.5 5.3 30 39-68 202-231 (236)
280 PF12793 SgrR_N: Sugar transpo 28.0 91 0.002 22.3 3.4 35 144-180 4-38 (115)
281 COG1905 NuoE NADH:ubiquinone o 28.0 1E+02 0.0023 23.5 3.9 37 143-179 25-61 (160)
282 PRK05657 RNA polymerase sigma 27.9 1.3E+02 0.0028 25.6 5.0 55 139-194 261-315 (325)
283 PRK07037 extracytoplasmic-func 27.7 2E+02 0.0043 21.1 5.5 29 39-67 127-155 (163)
284 PRK09415 RNA polymerase factor 27.6 1.3E+02 0.0029 22.7 4.6 48 140-192 127-174 (179)
285 PRK12518 RNA polymerase sigma 27.4 88 0.0019 23.4 3.6 35 36-70 135-169 (175)
286 TIGR02954 Sig70_famx3 RNA poly 27.3 1.6E+02 0.0035 21.8 5.0 29 39-67 137-165 (169)
287 TIGR03826 YvyF flagellar opero 27.2 94 0.002 23.0 3.5 26 162-187 47-72 (137)
288 TIGR02957 SigX4 RNA polymerase 26.7 1.5E+02 0.0031 24.6 5.0 48 140-192 108-155 (281)
289 PRK05657 RNA polymerase sigma 26.5 1.7E+02 0.0036 25.0 5.4 54 16-70 262-315 (325)
290 TIGR03826 YvyF flagellar opero 26.4 1.1E+02 0.0024 22.7 3.7 26 39-64 48-73 (137)
291 PRK05988 formate dehydrogenase 26.3 1.4E+02 0.003 22.6 4.4 35 145-179 25-59 (156)
292 PRK12520 RNA polymerase sigma 26.2 2.4E+02 0.0052 21.4 5.9 35 39-73 149-183 (191)
293 PRK12543 RNA polymerase sigma 26.2 2.1E+02 0.0046 21.5 5.5 32 39-70 135-166 (179)
294 PF10078 DUF2316: Uncharacteri 26.1 50 0.0011 22.6 1.7 38 141-182 3-44 (89)
295 PRK12524 RNA polymerase sigma 26.0 1.8E+02 0.004 22.3 5.2 31 39-69 154-184 (196)
296 PRK12546 RNA polymerase sigma 26.0 1.8E+02 0.0038 22.4 5.1 32 39-70 131-162 (188)
297 TIGR02983 SigE-fam_strep RNA p 26.0 1.8E+02 0.0038 21.4 5.0 30 39-68 128-157 (162)
298 PRK12537 RNA polymerase sigma 25.9 1.8E+02 0.0039 22.0 5.1 29 39-67 151-179 (182)
299 PRK07122 RNA polymerase sigma 25.8 1.7E+02 0.0036 24.1 5.1 47 140-191 215-261 (264)
300 PF08880 QLQ: QLQ; InterPro: 25.8 70 0.0015 17.9 2.0 13 16-28 2-14 (37)
301 TIGR02952 Sig70_famx2 RNA poly 25.7 1.9E+02 0.0042 21.2 5.2 28 39-66 140-167 (170)
302 PF07037 DUF1323: Putative tra 25.5 60 0.0013 23.4 2.1 20 164-183 3-22 (122)
303 cd01105 HTH_GlnR-like Helix-Tu 25.4 66 0.0014 21.6 2.2 19 164-182 4-22 (88)
304 PRK11511 DNA-binding transcrip 25.4 83 0.0018 22.6 2.9 25 161-185 25-49 (127)
305 smart00530 HTH_XRE Helix-turn- 25.2 90 0.002 17.2 2.7 23 40-62 13-35 (56)
306 TIGR02950 SigM_subfam RNA poly 25.1 98 0.0021 22.5 3.4 32 160-191 120-151 (154)
307 PRK08295 RNA polymerase factor 25.0 2.7E+02 0.0059 21.3 6.1 33 37-69 170-202 (208)
308 PF00440 TetR_N: Bacterial reg 24.9 83 0.0018 18.1 2.4 24 39-62 18-41 (47)
309 PRK12538 RNA polymerase sigma 24.8 1.8E+02 0.0039 23.4 5.1 32 39-70 189-220 (233)
310 TIGR02980 SigBFG RNA polymeras 24.7 1.9E+02 0.0042 22.7 5.3 45 17-66 179-223 (227)
311 PF03444 HrcA_DNA-bdg: Winged 24.5 2.2E+02 0.0048 18.9 5.8 60 141-212 2-64 (78)
312 PRK06288 RNA polymerase sigma 24.2 2.1E+02 0.0045 23.4 5.4 48 140-192 212-259 (268)
313 PRK13919 putative RNA polymera 24.2 2.2E+02 0.0047 21.5 5.3 29 39-67 153-181 (186)
314 TIGR02392 rpoH_proteo alternat 24.2 1.6E+02 0.0036 24.1 4.8 50 140-192 218-267 (270)
315 TIGR02393 RpoD_Cterm RNA polym 24.2 1.8E+02 0.0038 23.3 4.9 52 140-192 176-227 (238)
316 PRK14996 TetR family transcrip 24.2 97 0.0021 23.6 3.3 39 148-187 16-54 (192)
317 PRK08583 RNA polymerase sigma 24.2 2E+02 0.0043 23.3 5.3 47 17-68 206-252 (257)
318 TIGR02941 Sigma_B RNA polymera 24.0 1.9E+02 0.0042 23.3 5.2 46 17-67 206-251 (255)
319 cd04774 HTH_YfmP Helix-Turn-He 23.9 80 0.0017 21.6 2.5 20 164-183 3-22 (96)
320 PRK06704 RNA polymerase factor 23.9 1.9E+02 0.0042 23.3 5.0 51 140-195 116-166 (228)
321 PRK12545 RNA polymerase sigma 23.9 2.5E+02 0.0055 21.6 5.7 32 39-70 157-188 (201)
322 PF12244 DUF3606: Protein of u 23.8 1.1E+02 0.0023 18.9 2.8 20 37-56 20-39 (57)
323 PRK07539 NADH dehydrogenase su 23.7 1.6E+02 0.0034 22.1 4.3 35 145-179 24-58 (154)
324 PF07638 Sigma70_ECF: ECF sigm 23.6 1.7E+02 0.0037 22.4 4.6 47 141-192 136-182 (185)
325 PRK06811 RNA polymerase factor 23.6 2E+02 0.0043 21.9 5.0 30 39-68 149-178 (189)
326 PRK12534 RNA polymerase sigma 23.5 2.2E+02 0.0047 21.5 5.2 47 140-191 137-183 (187)
327 cd04766 HTH_HspR Helix-Turn-He 23.5 75 0.0016 21.3 2.3 20 164-183 4-23 (91)
328 PRK05803 sporulation sigma fac 23.4 2E+02 0.0044 22.9 5.1 52 140-192 175-226 (233)
329 TIGR01958 nuoE_fam NADH-quinon 23.4 1.6E+02 0.0035 21.8 4.3 35 145-179 18-52 (148)
330 cd01106 HTH_TipAL-Mta Helix-Tu 23.4 2.5E+02 0.0054 19.2 7.9 20 40-59 3-22 (103)
331 PRK12516 RNA polymerase sigma 23.2 2.9E+02 0.0062 21.1 5.8 32 39-70 134-165 (187)
332 PRK09636 RNA polymerase sigma 23.2 1.8E+02 0.004 24.0 5.0 48 140-192 115-162 (293)
333 PRK11922 RNA polymerase sigma 23.1 1.2E+02 0.0026 24.2 3.7 50 141-195 150-199 (231)
334 PRK10403 transcriptional regul 22.9 1.4E+02 0.0031 22.3 4.1 45 139-189 152-196 (215)
335 PRK12536 RNA polymerase sigma 22.7 2.4E+02 0.0052 21.2 5.3 30 39-68 147-176 (181)
336 PF01047 MarR: MarR family; I 22.7 1.4E+02 0.0031 17.7 3.3 39 141-183 1-39 (59)
337 COG2944 Predicted transcriptio 22.7 2.1E+02 0.0045 20.2 4.3 41 140-187 43-83 (104)
338 PRK12522 RNA polymerase sigma 22.6 2.6E+02 0.0057 20.8 5.4 30 39-68 137-166 (173)
339 PRK09643 RNA polymerase sigma 22.6 2.4E+02 0.0053 21.5 5.3 48 140-192 134-181 (192)
340 PRK11923 algU RNA polymerase s 22.5 2.4E+02 0.0052 21.4 5.3 32 39-70 156-187 (193)
341 PRK10360 DNA-binding transcrip 22.5 1.5E+02 0.0032 22.1 4.1 45 139-189 136-180 (196)
342 PF04936 DUF658: Protein of un 22.4 69 0.0015 24.5 2.0 31 39-69 16-46 (186)
343 COG5484 Uncharacterized conser 22.3 69 0.0015 26.4 2.1 27 161-189 19-45 (279)
344 PF01257 2Fe-2S_thioredx: Thio 22.3 1.3E+02 0.0029 22.2 3.6 36 145-180 15-50 (145)
345 PRK07571 bidirectional hydroge 22.0 1.8E+02 0.004 22.3 4.3 35 145-179 38-72 (169)
346 PF13565 HTH_32: Homeodomain-l 21.9 2.2E+02 0.0048 17.9 6.5 40 18-57 32-76 (77)
347 TIGR02479 FliA_WhiG RNA polyme 21.8 2.4E+02 0.0051 22.2 5.2 46 17-67 176-221 (224)
348 PF06569 DUF1128: Protein of u 21.8 1.7E+02 0.0037 19.0 3.5 34 139-172 31-67 (71)
349 TIGR02885 spore_sigF RNA polym 21.8 2.3E+02 0.005 22.4 5.1 46 139-189 182-227 (231)
350 COG1595 RpoE DNA-directed RNA 21.7 1.9E+02 0.0042 21.8 4.5 50 141-195 128-177 (182)
351 cd04779 HTH_MerR-like_sg4 Heli 21.7 88 0.0019 23.0 2.4 21 164-184 3-23 (134)
352 PF12844 HTH_19: Helix-turn-he 21.5 1.1E+02 0.0024 18.6 2.6 24 39-62 14-37 (64)
353 PRK09647 RNA polymerase sigma 21.5 3E+02 0.0065 21.4 5.7 31 39-69 156-186 (203)
354 PRK10100 DNA-binding transcrip 21.4 2.3E+02 0.0051 22.4 5.1 45 140-190 155-199 (216)
355 PRK12539 RNA polymerase sigma 21.4 2.5E+02 0.0054 21.2 5.1 30 39-68 149-178 (184)
356 PRK05988 formate dehydrogenase 21.4 2.2E+02 0.0048 21.5 4.7 36 20-55 24-59 (156)
357 TIGR01557 myb_SHAQKYF myb-like 21.3 2.1E+02 0.0046 17.6 4.5 51 13-63 2-55 (57)
358 PRK07408 RNA polymerase sigma 21.3 2.5E+02 0.0055 22.8 5.4 31 38-68 220-250 (256)
359 PF06163 DUF977: Bacterial pro 21.3 1.4E+02 0.0029 21.9 3.2 44 16-59 4-48 (127)
360 PRK12513 RNA polymerase sigma 21.3 1.4E+02 0.003 22.9 3.6 35 36-70 154-188 (194)
361 PF13404 HTH_AsnC-type: AsnC-t 21.2 93 0.002 17.7 2.0 18 39-56 19-36 (42)
362 PRK05572 sporulation sigma fac 21.1 2.4E+02 0.0053 22.7 5.2 48 139-191 201-248 (252)
363 PRK10651 transcriptional regul 21.0 2.4E+02 0.0053 21.0 5.1 44 140-189 155-198 (216)
364 PF05263 DUF722: Protein of un 21.0 2.2E+02 0.0049 20.8 4.4 41 140-183 81-121 (130)
365 TIGR03001 Sig-70_gmx1 RNA poly 20.9 2.9E+02 0.0063 22.3 5.6 33 39-71 179-211 (244)
366 TIGR02960 SigX5 RNA polymerase 20.9 2E+02 0.0043 24.0 4.8 50 140-194 142-191 (324)
367 PRK12540 RNA polymerase sigma 20.8 3.8E+02 0.0083 20.3 6.7 32 39-70 129-160 (182)
368 PRK05911 RNA polymerase sigma 20.7 2.5E+02 0.0054 22.9 5.2 48 140-192 205-252 (257)
369 PRK12529 RNA polymerase sigma 20.7 2.8E+02 0.0061 20.8 5.3 28 39-66 145-172 (178)
370 cd04780 HTH_MerR-like_sg5 Heli 20.7 2.8E+02 0.0062 18.8 7.9 19 40-58 3-21 (95)
371 PRK12523 RNA polymerase sigma 20.6 3E+02 0.0064 20.5 5.3 30 39-68 137-166 (172)
372 PRK09706 transcriptional repre 20.5 1E+02 0.0023 22.3 2.7 24 40-63 21-44 (135)
373 TIGR02984 Sig-70_plancto1 RNA 20.5 2.7E+02 0.0058 20.9 5.1 47 140-191 140-186 (189)
374 TIGR02846 spore_sigmaK RNA pol 20.4 3E+02 0.0065 21.8 5.6 52 139-191 173-224 (227)
375 PF07022 Phage_CI_repr: Bacter 20.4 79 0.0017 19.8 1.8 20 40-59 15-35 (66)
376 PRK13890 conjugal transfer pro 20.4 1.1E+02 0.0023 22.0 2.6 23 40-62 21-43 (120)
377 TIGR02950 SigM_subfam RNA poly 20.3 1.3E+02 0.0027 21.9 3.1 33 35-67 119-151 (154)
378 TIGR02835 spore_sigmaE RNA pol 20.1 3.4E+02 0.0074 21.6 5.8 53 139-192 177-229 (234)
379 TIGR03020 EpsA transcriptional 20.1 2.6E+02 0.0057 22.9 5.1 47 138-190 188-234 (247)
380 PRK12531 RNA polymerase sigma 20.0 3.3E+02 0.0071 20.8 5.6 30 39-68 159-188 (194)
No 1
>KOG0484|consensus
Probab=99.81 E-value=4.9e-20 Score=125.75 Aligned_cols=70 Identities=37% Similarity=0.562 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 74 (222)
Q Consensus 5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~ 74 (222)
...+++||-||+||..||..||..|.+.+||++..|++||.++.|++.+|++||||||+|.+++++....
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 3456789999999999999999999999999999999999999999999999999999999998876643
No 2
>KOG0490|consensus
Probab=99.80 E-value=2.1e-19 Score=145.80 Aligned_cols=157 Identities=29% Similarity=0.337 Sum_probs=123.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccC
Q psy11996 7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQ 86 (222)
Q Consensus 7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~ 86 (222)
..++|+.|+.|+..|+.+|+..|+..+||+...++.||..+++++..|++||+|+|+++++.+........ ..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~--~~----- 129 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGEN--LP----- 129 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhcccccccc--CC-----
Confidence 45678999999999999999999999999999999999999999999999999999999987650000000 00
Q ss_pred CCCCCCCcccCCCCCCCCCCCCCcccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHH
Q psy11996 87 GKSCTGRYQVRPITSPHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIE 166 (222)
Q Consensus 87 ~~~~~~~~~~~p~~sp~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~ 166 (222)
......+.. .............+.++.++.+...|+..|...|..+++|+...+..
T Consensus 130 ---------~~~~~~~~~---------------~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~ 185 (235)
T KOG0490|consen 130 ---------DLSGTAPPS---------------ASRDKLDKGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQ 185 (235)
T ss_pred ---------CCCCCCCcc---------------ccccccccCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHH
Confidence 000000000 00011112233446677899999999999999999999999999999
Q ss_pred HHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 167 IAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 167 la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
|+..+|+....|++||+|+|.+.++...
T Consensus 186 l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 186 LAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred HHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 9999999999999999999999998765
No 3
>KOG0850|consensus
Probab=99.73 E-value=6.2e-18 Score=131.65 Aligned_cols=70 Identities=40% Similarity=0.617 Sum_probs=64.9
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 74 (222)
Q Consensus 5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~ 74 (222)
..+++-|+.||.|+..||..|+..|+++.|+...||.+||+.|||+.+||+|||||||.|.||.++.+..
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 4567789999999999999999999999999999999999999999999999999999999999885543
No 4
>KOG0489|consensus
Probab=99.72 E-value=1e-17 Score=137.55 Aligned_cols=87 Identities=64% Similarity=1.016 Sum_probs=73.0
Q ss_pred cccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 110 LRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 110 ~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
.++||+...... .+.....+..+|.|+.||..|+.+||..|..|.|.+...|.+||..|.|+++||+|||||||+||
T Consensus 138 ~~~p~~~~~~~~---~~~~~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~ 214 (261)
T KOG0489|consen 138 QIYPWMKSTANY---LSSSETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKW 214 (261)
T ss_pred ccccchhhhhcc---cccccccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHH
Confidence 455555444332 12223345678999999999999999999999999999999999999999999999999999999
Q ss_pred HHhhhcccCC
Q psy11996 190 KKEHKMASMN 199 (222)
Q Consensus 190 kk~~~~~~~~ 199 (222)
||..+...+.
T Consensus 215 Kk~~k~~~~~ 224 (261)
T KOG0489|consen 215 KKENKAKSSQ 224 (261)
T ss_pred HHhhcccccc
Confidence 9999988877
No 5
>KOG2251|consensus
Probab=99.71 E-value=5.7e-17 Score=125.76 Aligned_cols=68 Identities=32% Similarity=0.524 Sum_probs=64.1
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
...++.||.||+|+..|+.+||.+|.++.||+...+++||.+|+|.+.+|+|||+|||+|++++.+..
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 45678899999999999999999999999999999999999999999999999999999999987764
No 6
>KOG0850|consensus
Probab=99.70 E-value=3.7e-17 Score=127.36 Aligned_cols=69 Identities=41% Similarity=0.624 Sum_probs=63.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 198 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~ 198 (222)
+..+.|+.||.++.-||..|...|++++|+-..||.+||+.|||+..||+|||||||.|.||..+.++.
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~ 186 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSG 186 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCC
Confidence 345677889999999999999999999999999999999999999999999999999999999985443
No 7
>KOG0484|consensus
Probab=99.69 E-value=1.3e-17 Score=113.89 Aligned_cols=66 Identities=38% Similarity=0.593 Sum_probs=61.8
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
...+.++.|+.||..|+..|+..|...+||++-.+++||.++.|++..|++||||||+|.+|+++.
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 345678889999999999999999999999999999999999999999999999999999999665
No 8
>KOG0489|consensus
Probab=99.69 E-value=8.1e-17 Score=132.26 Aligned_cols=71 Identities=76% Similarity=1.191 Sum_probs=65.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccC
Q psy11996 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN 75 (222)
Q Consensus 5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~ 75 (222)
....+.||.||.||..||-+||+-|..|.|+++..|.++|..|.|+++||+|||||||+|+||..+.....
T Consensus 154 ~~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 154 ETGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred cccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 44566899999999999999999999999999999999999999999999999999999999987766544
No 9
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.69 E-value=8.3e-17 Score=102.04 Aligned_cols=57 Identities=53% Similarity=0.704 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
|++|+.||.+|+..|+..|..++||+..+++.||..+||+..+|.+||+|+|.+.++
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 578999999999999999999999999999999999999999999999999999875
No 10
>KOG0842|consensus
Probab=99.67 E-value=6.5e-17 Score=133.01 Aligned_cols=74 Identities=35% Similarity=0.609 Sum_probs=67.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCCCC
Q psy11996 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYH 204 (222)
Q Consensus 131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~~~ 204 (222)
..++||.|..|+..|+.+||+.|...+|++..||+.||..|.|+..||+|||||||.|+||.++...+......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~ 223 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLA 223 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCC
Confidence 33667788899999999999999999999999999999999999999999999999999999998887776644
No 11
>KOG0843|consensus
Probab=99.67 E-value=9.1e-17 Score=120.67 Aligned_cols=64 Identities=42% Similarity=0.675 Sum_probs=60.7
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
+.||.||.||.+||..||..|+.+.|....+|+.||..|+|++.||++||||||.|.||.....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6789999999999999999999999999999999999999999999999999999999976554
No 12
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.67 E-value=1.7e-16 Score=100.62 Aligned_cols=57 Identities=53% Similarity=0.704 Sum_probs=54.8
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
++.|+.|+.+|+.+|+..|..+++|+..+++.||..+||+..+|.+||+|+|.+.|+
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 467899999999999999999999999999999999999999999999999999886
No 13
>KOG0488|consensus
Probab=99.66 E-value=1.4e-16 Score=133.12 Aligned_cols=67 Identities=42% Similarity=0.747 Sum_probs=62.2
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
....+.++.|+.||..|+..||..|++.+|.+..+|..||..|||+..||++||||||+|||+....
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 3446778899999999999999999999999999999999999999999999999999999998554
No 14
>KOG0488|consensus
Probab=99.66 E-value=1.2e-16 Score=133.38 Aligned_cols=66 Identities=42% Similarity=0.754 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
..+++|+.||.||..||..||+.|+...|++..+|.+||..|||+..||++||||||+|||+....
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 346788889999999999999999999999999999999999999999999999999999997654
No 15
>KOG0842|consensus
Probab=99.66 E-value=5.9e-17 Score=133.28 Aligned_cols=70 Identities=37% Similarity=0.628 Sum_probs=64.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCC
Q psy11996 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNP 77 (222)
Q Consensus 8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~ 77 (222)
.++||.|..||..|+.+||..|....|++..||+.||..|+||++||+|||||||.|.||..+...+...
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 3567778899999999999999999999999999999999999999999999999999999887766544
No 16
>KOG0485|consensus
Probab=99.65 E-value=9.4e-17 Score=123.82 Aligned_cols=65 Identities=45% Similarity=0.797 Sum_probs=60.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
++++||.||+|+..|+..||..|+...|++..+|..||+.|.|++.||++||||||.||||+...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 34788899999999999999999999999999999999999999999999999999999997543
No 17
>KOG0843|consensus
Probab=99.65 E-value=2e-16 Score=118.84 Aligned_cols=64 Identities=42% Similarity=0.675 Sum_probs=60.9
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
+.+|.||.|+.+|+..||..|+.++|....+++.||..|+|++.||++||||||.|.||.....
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6788999999999999999999999999999999999999999999999999999999986654
No 18
>KOG0494|consensus
Probab=99.64 E-value=2.2e-16 Score=124.75 Aligned_cols=65 Identities=42% Similarity=0.619 Sum_probs=59.7
Q ss_pred CCCC-CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996 10 TKRQ-RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 74 (222)
Q Consensus 10 ~~r~-R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~ 74 (222)
+||. ||.||..|+..||+.|++.+||+...|+-||..+.|.+++|++||||||+||||.++.-..
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~ 205 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGG 205 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCc
Confidence 3444 9999999999999999999999999999999999999999999999999999998776543
No 19
>KOG2251|consensus
Probab=99.63 E-value=1.3e-15 Score=118.28 Aligned_cols=67 Identities=33% Similarity=0.527 Sum_probs=62.9
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
...+.+|.||.|+-.|+.+||.+|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++..
T Consensus 33 ~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 33 GPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 4457788999999999999999999999999999999999999999999999999999999998864
No 20
>KOG0485|consensus
Probab=99.60 E-value=2.8e-15 Score=115.69 Aligned_cols=65 Identities=45% Similarity=0.797 Sum_probs=60.6
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
...+|+.|++|+..|+..||..|+...|.+..++..||.+|.|++.||++||||||.|||++...
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 44677889999999999999999999999999999999999999999999999999999998543
No 21
>KOG0492|consensus
Probab=99.59 E-value=1.4e-15 Score=116.57 Aligned_cols=65 Identities=42% Similarity=0.654 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 7 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 7 ~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
-+..|++||-||..||..||.-|...+|.++.++.+++..|.|++.||+|||||||+|.||....
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQea 205 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEA 205 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHH
Confidence 35568899999999999999999999999999999999999999999999999999999986443
No 22
>KOG0487|consensus
Probab=99.57 E-value=1.2e-15 Score=125.59 Aligned_cols=65 Identities=55% Similarity=0.889 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
+..||||--+|..|+.+||+-|..|.|++.+.|.+|++.|+|+++||+|||||||+|.||..+..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 56789999999999999999999999999999999999999999999999999999999987533
No 23
>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=99.56 E-value=4e-15 Score=93.20 Aligned_cols=53 Identities=23% Similarity=0.373 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCC----CCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996 10 TKRQRTSYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f~~~~~----p~~~~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
+||.||.||.+|+..|+..|..+.| |+..++++||..+||++.+|++||+|-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3789999999999999999999999 9999999999999999999999999965
No 24
>KOG0487|consensus
Probab=99.56 E-value=4.9e-15 Score=122.04 Aligned_cols=64 Identities=56% Similarity=0.905 Sum_probs=60.5
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
...||+|--+|+.|+.+||..|..|.|++.+.|-+|+..|+|+++||+|||||||+|.||..+.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 4667888999999999999999999999999999999999999999999999999999998863
No 25
>KOG0492|consensus
Probab=99.56 E-value=3.8e-15 Score=114.26 Aligned_cols=65 Identities=42% Similarity=0.655 Sum_probs=60.9
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
+....++.|+-||..|+..||..|...+|.+++++.+++..|.|++.||++||||||+|.||.+.
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 45567889999999999999999999999999999999999999999999999999999999754
No 26
>KOG0848|consensus
Probab=99.56 E-value=3.6e-15 Score=118.46 Aligned_cols=63 Identities=56% Similarity=0.840 Sum_probs=59.0
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
+-+.|.++|+-|+.+||+.|..++|.++..+.+||..|||+++||+|||||||+|+||..|..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 346788999999999999999999999999999999999999999999999999999987765
No 27
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.54 E-value=1.2e-14 Score=91.57 Aligned_cols=55 Identities=58% Similarity=0.912 Sum_probs=51.9
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65 (222)
Q Consensus 11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 65 (222)
++.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|+|++.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 3567889999999999999999999999999999999999999999999999864
No 28
>KOG0494|consensus
Probab=99.54 E-value=2.6e-14 Score=113.11 Aligned_cols=65 Identities=40% Similarity=0.601 Sum_probs=59.8
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 197 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~ 197 (222)
+.+..||.||..|+..||..|++.+||+...++.||.++.|.+..|++||||||+||||.++.-.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 33445899999999999999999999999999999999999999999999999999999987744
No 29
>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=99.54 E-value=2.3e-14 Score=91.22 Aligned_cols=57 Identities=58% Similarity=0.830 Sum_probs=53.9
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
++.|+.|+..|+.+|++.|..++||+..++..||..+||+..+|++||+|+|.+.++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 356789999999999999999999999999999999999999999999999998775
No 30
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.53 E-value=1.8e-14 Score=90.82 Aligned_cols=55 Identities=60% Similarity=0.915 Sum_probs=51.7
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190 (222)
Q Consensus 136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 190 (222)
+.++.|+.+|+.+|+..|..++||+..++..||..+||+..+|.+||+|+|.+.+
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 4577899999999999999999999999999999999999999999999998753
No 31
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.52 E-value=3.3e-14 Score=90.53 Aligned_cols=57 Identities=58% Similarity=0.816 Sum_probs=53.7
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 136 RQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 136 ~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
+.+..++..++.+|+..|..++||+..++..||..+||+..+|.+||+|+|.+.++.
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 457889999999999999999999999999999999999999999999999998763
No 32
>KOG0493|consensus
Probab=99.52 E-value=1.2e-14 Score=115.14 Aligned_cols=64 Identities=53% Similarity=0.759 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
....-||+||.||.+||..|+..|..+.|+....|.+||.+|||.+.||+|||||+|+|.||..
T Consensus 242 ~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 242 SSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred ccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 3445688999999999999999999999999999999999999999999999999999999843
No 33
>KOG0848|consensus
Probab=99.51 E-value=6.4e-15 Score=117.09 Aligned_cols=65 Identities=54% Similarity=0.809 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
+++-|.|.++|..|.-+||+.|.-++|+.+..+.+||..|||+++||+|||||||+|+||..+.+
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34445688999999999999999999999999999999999999999999999999999876655
No 34
>KOG0491|consensus
Probab=99.50 E-value=1.2e-13 Score=102.39 Aligned_cols=70 Identities=41% Similarity=0.621 Sum_probs=64.0
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCC
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIP 202 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~ 202 (222)
..++.|++|+..|+..|++.|+...|.+..++.+||..|+|++.||+.||||||+|.||..+.......+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~p~nS~ 168 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQPKNSN 168 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccCCCCCC
Confidence 4567799999999999999999999999999999999999999999999999999999998887654444
No 35
>KOG0493|consensus
Probab=99.49 E-value=2.8e-14 Score=113.05 Aligned_cols=62 Identities=53% Similarity=0.746 Sum_probs=58.1
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
-||.|+.||.+||..|+..|..+.|.+...+..||.+|||.+.||++||||+|+|.||-...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 46789999999999999999999999999999999999999999999999999999996443
No 36
>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=99.49 E-value=3e-14 Score=89.24 Aligned_cols=52 Identities=23% Similarity=0.379 Sum_probs=50.2
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996 135 KRQRTSYTRYQTLELEKEFHFNRY----LTRRRRIEIAHALCLTERQIKIWFQNRR 186 (222)
Q Consensus 135 ~~~r~~~~~~q~~~L~~~F~~~~~----p~~~~~~~la~~l~l~~~~V~~WF~nrR 186 (222)
++.||.||.+|+..|+..|+.++| |+..++++||..+||++.+|++||+|-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 688999999999999999999999 9999999999999999999999999965
No 37
>KOG3802|consensus
Probab=99.48 E-value=1.4e-14 Score=121.71 Aligned_cols=70 Identities=30% Similarity=0.358 Sum_probs=64.0
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCC
Q psy11996 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVI 201 (222)
Q Consensus 132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~ 201 (222)
+++||+||.|+...+..||.+|.+|+.|+.+|+..||++|+|.+++|+|||||||.|.||......+..+
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~~~~~~~P 361 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITPFPSAGSP 361 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCCCccCCCC
Confidence 3778899999999999999999999999999999999999999999999999999999998884444444
No 38
>KOG0844|consensus
Probab=99.45 E-value=1.8e-14 Score=116.46 Aligned_cols=70 Identities=47% Similarity=0.690 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccC
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMN 75 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~ 75 (222)
+.+..||.||.||.+|+..||+.|-+..|-++..|++||..|+|++..|++||||||+|+||+.-...+.
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWP 246 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWP 246 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCC
Confidence 4556799999999999999999999999999999999999999999999999999999999976554443
No 39
>KOG0491|consensus
Probab=99.45 E-value=8.4e-14 Score=103.16 Aligned_cols=64 Identities=45% Similarity=0.711 Sum_probs=59.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 73 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~ 73 (222)
.++-||+|+..|+..|++.|+...|.+..++.+||..|+|+++||+.||||||+|-||..+...
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4677999999999999999999999999999999999999999999999999999999876554
No 40
>KOG0486|consensus
Probab=99.45 E-value=4.5e-14 Score=114.71 Aligned_cols=66 Identities=42% Similarity=0.681 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996 8 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 73 (222)
Q Consensus 8 ~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~ 73 (222)
.++||.||.||..||..||..|.++.||+...|+++|..++|++.+|++||+|||+||++++....
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 367899999999999999999999999999999999999999999999999999999999876654
No 41
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.43 E-value=2.3e-13 Score=102.68 Aligned_cols=68 Identities=32% Similarity=0.521 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 5 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 5 ~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
+.....+++|++.|.+|+.+|+..|..++||+...+..|+..++|+++-|++||||+|++.++....+
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 34456788899999999999999999999999999999999999999999999999999999876544
No 42
>KOG3802|consensus
Probab=99.42 E-value=8.8e-14 Score=116.94 Aligned_cols=67 Identities=31% Similarity=0.405 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
+.+..++||+||.|......+||++|.+|+.|+..|+..||.+|+|..++|+|||+|||.|.||...
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 4455588999999999999999999999999999999999999999999999999999999999655
No 43
>KOG4577|consensus
Probab=99.42 E-value=1.7e-13 Score=110.07 Aligned_cols=71 Identities=30% Similarity=0.415 Sum_probs=65.4
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhcc
Q psy11996 4 VNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 74 (222)
Q Consensus 4 ~~~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~ 74 (222)
.+.....||+||++|..||+.|+..|...+.|.+..|+.|+.++||.-+.|++||||||+|.||-++.++-
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 45667789999999999999999999999999999999999999999999999999999999987776654
No 44
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.40 E-value=5.5e-13 Score=100.66 Aligned_cols=72 Identities=31% Similarity=0.473 Sum_probs=64.0
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCC
Q psy11996 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNV 200 (222)
Q Consensus 129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~ 200 (222)
+.....++.|...+.+|+.+|+..|..+++|+..++..|+..++|+++-|++||||+|++.|+....+....
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~ 117 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR 117 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhcc
Confidence 344566778889999999999999999999999999999999999999999999999999999877754443
No 45
>KOG0844|consensus
Probab=99.39 E-value=2.8e-14 Score=115.37 Aligned_cols=62 Identities=52% Similarity=0.777 Sum_probs=59.0
Q ss_pred CCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 132 GETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 132 ~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
...+|.||.||.+|+..||+.|.+..|.+...+.+||..|+|.+.-|++||||||+|+|+++
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQR 240 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQR 240 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhh
Confidence 35688999999999999999999999999999999999999999999999999999999974
No 46
>KOG0483|consensus
Probab=99.37 E-value=5.7e-13 Score=103.95 Aligned_cols=60 Identities=37% Similarity=0.621 Sum_probs=55.7
Q ss_pred CCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 134 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 134 ~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
...+...|+.+|+..|+..|+...+.....+..||.+|||..+||.+||||||++||.++
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 345567899999999999999999999999999999999999999999999999999874
No 47
>KOG0483|consensus
Probab=99.35 E-value=9e-13 Score=102.84 Aligned_cols=60 Identities=37% Similarity=0.621 Sum_probs=55.8
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
..+++.+|+.+|+..||..|+...+....++..||..|||.++||.+||||||+++|.+.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 455667899999999999999999999999999999999999999999999999999753
No 48
>KOG4577|consensus
Probab=99.35 E-value=9e-13 Score=105.96 Aligned_cols=70 Identities=30% Similarity=0.427 Sum_probs=64.1
Q ss_pred cccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 127 TVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 127 ~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
+.+..+..||+|+.||..|++.|+..|...+.|....++.|+.++||..+.|++||||||+|+|+-.|.+
T Consensus 160 ~l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 160 ELEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 3445668899999999999999999999999999999999999999999999999999999999876543
No 49
>KOG0847|consensus
Probab=99.33 E-value=1.1e-12 Score=101.52 Aligned_cols=67 Identities=43% Similarity=0.820 Sum_probs=62.5
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 129 NANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 129 ~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
...++.+..|..|+..|+..|+..|+..+|+-.+++.+||..+|+++.||++||||||.||||+...
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 3567888889999999999999999999999999999999999999999999999999999998654
No 50
>KOG0486|consensus
Probab=99.31 E-value=9.8e-13 Score=107.03 Aligned_cols=65 Identities=43% Similarity=0.689 Sum_probs=61.5
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 197 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~ 197 (222)
+.++.|+.|+..|+..||..|.++.||+...+++||.-++|++..|++||+|||+||+|.+....
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 45677899999999999999999999999999999999999999999999999999999988766
No 51
>KOG0847|consensus
Probab=99.30 E-value=2e-12 Score=100.14 Aligned_cols=66 Identities=42% Similarity=0.813 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
.+++++..|.+|+..|+..|+..|+...|+-..++.+||..+|+++.+|++||||||.||||+...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 456677788999999999999999999999999999999999999999999999999999997543
No 52
>KOG1168|consensus
Probab=99.02 E-value=4.9e-11 Score=96.13 Aligned_cols=63 Identities=32% Similarity=0.451 Sum_probs=59.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
..+.+||+|+.+.......||.+|...+.|+.+.+..||++|+|.+..|++||||.|+|.||.
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 455778899999999999999999999999999999999999999999999999999999884
No 53
>KOG0849|consensus
Probab=99.02 E-value=9.5e-10 Score=94.11 Aligned_cols=65 Identities=34% Similarity=0.601 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
-+++.+|.||+|+.+|+..|++.|+.++||+...|+.||.++++++..|++||+|+|+++++...
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 45567888999999999999999999999999999999999999999999999999999999764
No 54
>KOG0775|consensus
Probab=98.96 E-value=3e-09 Score=85.42 Aligned_cols=49 Identities=31% Similarity=0.405 Sum_probs=45.4
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 19 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 19 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
..-...|.++|..++||+..++.+||+.+||+..||.+||+|||.++|-
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3346789999999999999999999999999999999999999999983
No 55
>KOG0775|consensus
Probab=98.96 E-value=7.1e-10 Score=88.93 Aligned_cols=53 Identities=28% Similarity=0.403 Sum_probs=48.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
|-..-+.+|+++|..++||+..++.+||+.+||+..||-+||+|||+++|-..
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 44557889999999999999999999999999999999999999999999543
No 56
>KOG1168|consensus
Probab=98.95 E-value=1.7e-10 Score=93.08 Aligned_cols=67 Identities=31% Similarity=0.446 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
.++.+||+||.+...+...||++|...+.|+.+.+..+|++|.|....|++||+|.|.|.||.....
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~Sa 371 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKRSA 371 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhhhh
Confidence 4567899999999999999999999999999999999999999999999999999999999965543
No 57
>KOG0490|consensus
Probab=98.93 E-value=8.6e-10 Score=89.33 Aligned_cols=64 Identities=31% Similarity=0.343 Sum_probs=60.5
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
..+.++.|+.|+..|+.+|+..|+.++||+...++.||..+++++..|++||+|+|+++++..+
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 4467889999999999999999999999999999999999999999999999999999999875
No 58
>KOG0849|consensus
Probab=98.84 E-value=8e-09 Score=88.48 Aligned_cols=63 Identities=35% Similarity=0.612 Sum_probs=59.1
Q ss_pred CCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 131 NGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 131 ~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
....++.|+.|+..|+..|+..|+.++||+...++.||.++++++..|.+||+|+|++++|..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 335566789999999999999999999999999999999999999999999999999999998
No 59
>KOG0774|consensus
Probab=98.78 E-value=1.1e-08 Score=81.63 Aligned_cols=60 Identities=28% Similarity=0.523 Sum_probs=55.2
Q ss_pred CCCCCCCCCHHHHHHHHHHh---hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 10 TKRQRTSYTRYQTLELEKEF---HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
.+|+|..|+..-..+|..+| -.++||+.+.+++||.+.|++..||..||.|+|-+.+|..
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 46888999999999999999 4588999999999999999999999999999999988753
No 60
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.74 E-value=1.1e-08 Score=59.41 Aligned_cols=34 Identities=32% Similarity=0.589 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhh
Q psy11996 155 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 188 (222)
Q Consensus 155 ~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k 188 (222)
.++||+.+++..||.++||+..||.+||-|.|.+
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 4799999999999999999999999999999864
No 61
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.67 E-value=2.3e-08 Score=57.99 Aligned_cols=34 Identities=32% Similarity=0.589 Sum_probs=28.5
Q ss_pred hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996 31 FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64 (222)
Q Consensus 31 ~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 64 (222)
.+|||+.++++.||..+||+..||..||-|.|.+
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 4799999999999999999999999999998853
No 62
>KOG0774|consensus
Probab=98.51 E-value=6.2e-08 Score=77.35 Aligned_cols=61 Identities=28% Similarity=0.527 Sum_probs=56.5
Q ss_pred CCCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
..+|+|..|++.-.++|..+|. .++||+.+.+++||.+++++..||.+||.|+|-+.+|..
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~ 250 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNM 250 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhh
Confidence 3578899999999999999996 699999999999999999999999999999999998873
No 63
>KOG1146|consensus
Probab=98.51 E-value=2e-06 Score=82.24 Aligned_cols=187 Identities=18% Similarity=0.176 Sum_probs=119.2
Q ss_pred CCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCC-----------
Q psy11996 10 TKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPN----------- 78 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~----------- 78 (222)
.++.++.+-.+++..|-.+|-.+..|+...+..|....+.+.+++.+||.+-+.+.++....+..-...
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~~~~c~l~~y~t~~kan 784 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGDVPSCKLKPYATNTKAN 784 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCCCCcceecccccccchh
Confidence 356678888899999999999999999999999999999999999999999998888765111111000
Q ss_pred ---------------cc---------------------cccccCCCCCCCCcccCCC--CCCCCCCCCCc--cc------
Q psy11996 79 ---------------LY---------------------TQYQTQGKSCTGRYQVRPI--TSPHGAYHGDL--RY------ 112 (222)
Q Consensus 79 ---------------~~---------------------~~~~~~~~~~~~~~~~~p~--~sp~~~~~~~~--~~------ 112 (222)
.. .+...-+..|.-....... .......+... .+
T Consensus 785 fqlh~Ktdkh~qk~~~~~hikegg~a~~~~t~~la~~~~P~~l~cn~cd~~Tns~~~L~lh~~~~~he~~~~~~ks~~~l 864 (1406)
T KOG1146|consen 785 FQLHNKTDKHVQKYQLRAHIKEGGPANEYPTKTLASGPNPVHLKCNACDTPTNSPEPLLLHTPPSEHEGPEEIYKSLLSL 864 (1406)
T ss_pred hhhhcccchhhhccchhhhhhccCCccCCcchhhhcCCCccccccccccCCCCCccccccCCCCCccccccccchhHHHH
Confidence 00 0011111111111000000 00000111100 00
Q ss_pred ----ccccCC------------Cc-cccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCCh
Q psy11996 113 ----HWTNRA------------PL-KYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTE 175 (222)
Q Consensus 113 ----p~~~~~------------~~-~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~ 175 (222)
..++-+ +. ........-..--.+..|+.++..|+..|...|....+|...+.+.|...+++..
T Consensus 865 ~~~ls~~~~s~~~as~~~s~~~~~~~~s~~s~~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~ 944 (1406)
T KOG1146|consen 865 ACSLSAGDLSDSSASSLASPESPGGGPSGGSGVPDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPK 944 (1406)
T ss_pred HHHhhccccccccccccccccCCCCCCCCCcccchhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCc
Confidence 000000 00 0000001111113456789999999999999999999999999999999999999
Q ss_pred hhHHHHHhhhhhhHHHhhhcc
Q psy11996 176 RQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 176 ~~V~~WF~nrR~k~kk~~~~~ 196 (222)
+.|.+||+|-|.+.++..-.+
T Consensus 945 ~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 945 RVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred chhHHhhhhhhhhhhhhhhcc
Confidence 999999999999999986644
No 64
>KOG2252|consensus
Probab=98.45 E-value=6.7e-07 Score=78.61 Aligned_cols=60 Identities=25% Similarity=0.264 Sum_probs=54.9
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 130 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 130 ~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
.....|+.|.+||..|...|...|+.+++|+.+..+.|+.+|+|...-|.+||-|-|.|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344667889999999999999999999999999999999999999999999999977663
No 65
>KOG2252|consensus
Probab=98.33 E-value=1.5e-06 Score=76.41 Aligned_cols=60 Identities=25% Similarity=0.264 Sum_probs=54.9
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996 6 ANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 65 (222)
Q Consensus 6 ~~~~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~ 65 (222)
..-..||.|.+||..|...|...|..+++|+.+..+.|+..|||....|.+||-|-|.+.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344568889999999999999999999999999999999999999999999999987653
No 66
>KOG0773|consensus
Probab=98.04 E-value=2e-05 Score=67.59 Aligned_cols=165 Identities=19% Similarity=0.172 Sum_probs=94.2
Q ss_pred hhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccCCCCC----CCCccc---------
Q psy11996 30 HFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSC----TGRYQV--------- 96 (222)
Q Consensus 30 ~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~~~~~----~~~~~~--------- 96 (222)
..++||...+..-|+...+++..+|..||-|-|.......+......+............. +...+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~q~~~~~~~~~~ 196 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLALDGISRHFSDLEKEKAIGGQLSSSEELLGE 196 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccccchhhhhhhhhhccccccccccccccccc
Confidence 5588999999999999999999999999999887766654443333222111100000000 000000
Q ss_pred CCCCCCCCCCCCCcccccccCC----Cccc-cccccccCCCCCCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHH
Q psy11996 97 RPITSPHGAYHGDLRYHWTNRA----PLKY-VKRGTVNANGETKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIA 168 (222)
Q Consensus 97 ~p~~sp~~~~~~~~~~p~~~~~----~~~~-~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la 168 (222)
.+..............+..... .... .............+....+......+|+.+.. ..+||+..++..||
T Consensus 197 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La 276 (342)
T KOG0773|consen 197 SEQDDSEDESGPSGSEPPLRLAKQSLRQQRSAYDGSGGKKQSKWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLA 276 (342)
T ss_pred ccccccccccCcccccCCcccccccccccccccccccccccCCCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccc
Confidence 0000000000000000000000 0000 00111111223455567899999999998843 36799999999999
Q ss_pred HHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 169 HALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 169 ~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.++||+..||.+||-|.|.+..+-..
T Consensus 277 ~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 277 KQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred hhcCCCcccCCchhhhcccccCCchH
Confidence 99999999999999999988776544
No 67
>KOG1146|consensus
Probab=98.00 E-value=1.5e-05 Score=76.51 Aligned_cols=64 Identities=25% Similarity=0.306 Sum_probs=59.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhh
Q psy11996 9 ETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 72 (222)
Q Consensus 9 ~~~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~ 72 (222)
.++++|+.++..||..|...|....+|...+.+.|-..+++..+.|++||+|-|.+.++.....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n~ 965 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLNG 965 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhcc
Confidence 4678899999999999999999999999999999999999999999999999999998875533
No 68
>KOG3623|consensus
Probab=97.69 E-value=8.6e-05 Score=67.53 Aligned_cols=117 Identities=16% Similarity=0.223 Sum_probs=79.3
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhccCCCCcccccccCCCCCCCCcccCCCCC
Q psy11996 22 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNNPNLYTQYQTQGKSCTGRYQVRPITS 101 (222)
Q Consensus 22 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~s 101 (222)
+..|+.+|..|..|+.++...+|...||+.+.|+.||.++++..........+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps~--------------------------- 620 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQ--------------------------- 620 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCccC---------------------------
Confidence 78899999999999999999999999999999999999998886653221100
Q ss_pred CCCCCCCCcccccccCCCccccccccccCCCCCCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHH
Q psy11996 102 PHGAYHGDLRYHWTNRAPLKYVKRGTVNANGETKRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 181 (222)
Q Consensus 102 p~~~~~~~~~~p~~~~~~~~~~~~~~~~~~~~~~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~W 181 (222)
|.+. ...+.++-+..++-.-|...++.+..++-.+...++..|-.....|.+|
T Consensus 621 psg~---------------------------~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~ 673 (1007)
T KOG3623|consen 621 PSGE---------------------------RPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVW 673 (1007)
T ss_pred CCCC---------------------------CCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhc
Confidence 0000 0011112222233334455555555555555556666677778889999
Q ss_pred HhhhhhhHHHh
Q psy11996 182 FQNRRMKWKKE 192 (222)
Q Consensus 182 F~nrR~k~kk~ 192 (222)
|.+|+..-+..
T Consensus 674 dhsrsstpsp~ 684 (1007)
T KOG3623|consen 674 DHSRSSTPSPM 684 (1007)
T ss_pred ccCCCCCCCCC
Confidence 99998766553
No 69
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.61 E-value=6.8e-05 Score=46.26 Aligned_cols=42 Identities=19% Similarity=0.300 Sum_probs=31.4
Q ss_pred HHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996 22 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 22 ~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
+..|+++|....++...+...|+.+.+|+..||+.||..+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 466999999999999999999999999999999999976643
No 70
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.53 E-value=0.00011 Score=45.40 Aligned_cols=42 Identities=19% Similarity=0.300 Sum_probs=31.5
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
...|+..|....++...+...|..+.+|+..||+.||..+..
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 456999999999999999999999999999999999987653
No 71
>KOG0773|consensus
Probab=96.32 E-value=0.0029 Score=54.33 Aligned_cols=58 Identities=19% Similarity=0.306 Sum_probs=49.0
Q ss_pred CCCCCCCCCHHHHHHHHHHhh---hCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 10 TKRQRTSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 10 ~~r~R~~~t~~q~~~L~~~f~---~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
..|.+..+......+|+.++. ..+||+..++..|+.++||+..||.+||.|.|.+.-+
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 445566899999999998843 3579999999999999999999999999998876554
No 72
>KOG3623|consensus
Probab=96.13 E-value=0.012 Score=54.02 Aligned_cols=52 Identities=19% Similarity=0.260 Sum_probs=48.0
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996 146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 197 (222)
Q Consensus 146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~ 197 (222)
+.+|+..|..|..|+.++...+|...||..+.|+.||.++++.....++..+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 8899999999999999999999999999999999999999999888765544
No 73
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.39 E-value=0.041 Score=33.80 Aligned_cols=47 Identities=23% Similarity=0.357 Sum_probs=36.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996 11 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 11 ~r~R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
||+|..+|-++...+-..++... ....||..+|++..+|..|..|+.
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 57889999999998888888886 477899999999999999998753
No 74
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=94.41 E-value=0.11 Score=31.84 Aligned_cols=47 Identities=23% Similarity=0.357 Sum_probs=35.4
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996 135 KRQRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186 (222)
Q Consensus 135 ~~~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR 186 (222)
+++|..+|-++-..+-..++... ....||.++|++..+|..|..|+.
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 46788999998888888887775 577889999999999999998854
No 75
>KOG3755|consensus
Probab=92.12 E-value=0.3 Score=44.31 Aligned_cols=59 Identities=22% Similarity=0.250 Sum_probs=47.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHh-hhCCCCCHHH---HHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 9 ETKRQRTSYTRYQTLELEKEF-HFNRYLTRRR---RIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 9 ~~~r~R~~~t~~q~~~L~~~f-~~~~~p~~~~---~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|+.++.+-+..|...- ...=||+.+. ..-|...++++.+.+...|+|.|...+.
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred cCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 356778889999999888775 3455888777 7789999999999999999999977553
No 76
>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=87.79 E-value=1.8 Score=25.72 Aligned_cols=46 Identities=11% Similarity=0.095 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 190 (222)
.+++.+..+|...|... ....++|..+|++...|+.+...-..+-|
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 47888999999998333 35778899999999999998865544433
No 77
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=85.78 E-value=1.4 Score=27.03 Aligned_cols=41 Identities=17% Similarity=0.149 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHhhhhcC--CCCHHHHHHHHHHcCCChhhHHHH
Q psy11996 141 YTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIW 181 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~--~p~~~~~~~la~~l~l~~~~V~~W 181 (222)
+|+.|+.+|...|...- +|-.....+||+++|++..-|..=
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 57899999999998654 477788899999999998765443
No 78
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=84.03 E-value=1 Score=29.29 Aligned_cols=43 Identities=19% Similarity=0.341 Sum_probs=28.4
Q ss_pred CCCCCCCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 12 RQRTSYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 12 r~R~~~t~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
++|..||+++...+-..+ ... .....+|..+||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 457789999777666665 332 4678899999999999999964
No 79
>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=83.86 E-value=3.6 Score=24.40 Aligned_cols=44 Identities=11% Similarity=0.084 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 64 (222)
.+++.+..+|...|..+ ....++|..+|++...|..+...-..+
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 47888999999998433 246788999999999999886544433
No 80
>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=80.99 E-value=4.3 Score=24.84 Aligned_cols=42 Identities=17% Similarity=0.161 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCChHHHHHHh
Q psy11996 17 YTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIWF 58 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~--~p~~~~~~~la~~~~l~~~~v~~WF 58 (222)
+|+.|..+|...|+..- +|-.....+||..+|++..-+..-.
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 57899999999988765 4767788999999999998776543
No 81
>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=79.84 E-value=7.1 Score=23.39 Aligned_cols=43 Identities=19% Similarity=0.155 Sum_probs=29.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
.+++.+..++...|-.. ....++|..+|++...|+.|...-|.
T Consensus 10 ~L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp CS-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 35667777777665544 46788899999999999999975443
No 82
>PF13551 HTH_29: Winged helix-turn helix
Probab=79.45 E-value=18 Score=24.96 Aligned_cols=43 Identities=14% Similarity=0.105 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHhhhhcC-----CCCHHHHHH-H-HHHc--CCChhhHHHHHh
Q psy11996 141 YTRYQTLELEKEFHFNR-----YLTRRRRIE-I-AHAL--CLTERQIKIWFQ 183 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~-----~p~~~~~~~-l-a~~l--~l~~~~V~~WF~ 183 (222)
+++++...|.+.+..++ ..+...... | .... .++..-|..|+.
T Consensus 58 l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 58 LSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 89999999999998776 344454444 3 3333 467888888875
No 83
>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=79.21 E-value=3.2 Score=24.18 Aligned_cols=43 Identities=12% Similarity=0.055 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
.+++.+..++...|... .....+|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46777888887776433 24667799999999999999875543
No 84
>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=76.68 E-value=2.2 Score=26.88 Aligned_cols=21 Identities=29% Similarity=0.507 Sum_probs=18.0
Q ss_pred HHHHHHHHcCCChhhHHHHHh
Q psy11996 163 RRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 163 ~~~~la~~l~l~~~~V~~WF~ 183 (222)
....||++||++..+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999953
No 85
>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=76.47 E-value=2.2 Score=27.64 Aligned_cols=44 Identities=16% Similarity=0.274 Sum_probs=28.8
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996 137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 184 (222)
.+..|++++...+-..+... ......+|.++||+...|..|-..
T Consensus 3 ~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 3 KRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHH
Confidence 46788888776666555222 357888999999999999999753
No 86
>cd00131 PAX Paired Box domain
Probab=75.87 E-value=28 Score=25.35 Aligned_cols=46 Identities=11% Similarity=-0.099 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCC-------ChhhHHHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-------TERQIKIWFQNR 185 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l-------~~~~V~~WF~nr 185 (222)
..+..+...+...-..++..+..++.++...-|+ +...|..||+++
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 4466666666666678888887777665334455 788888888653
No 87
>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=75.70 E-value=9.9 Score=23.71 Aligned_cols=44 Identities=25% Similarity=0.320 Sum_probs=23.1
Q ss_pred CCCCCHH-HHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 14 RTSYTRY-QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 14 R~~~t~~-q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
|..|+.. .|.+++....-+. --...|. .|.++|+++.+|+.|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4456655 5555555443332 1222333 49999999999999974
No 88
>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=73.80 E-value=11 Score=23.48 Aligned_cols=44 Identities=23% Similarity=0.292 Sum_probs=22.1
Q ss_pred CCcCCHHH-HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 138 RTSYTRYQ-TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 138 r~~~~~~q-~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
|..|+... +.+++. |.....--...+ ..|.++|+.+.+|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~-a~~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEY-AEKDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHH-HHH-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHH-HHHccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 44566653 444444 333322222223 349999999999999985
No 89
>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=72.77 E-value=8.6 Score=22.18 Aligned_cols=42 Identities=12% Similarity=0.067 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
.+++.+..++...|... .....+|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777777777776433 2366779999999999999975443
No 90
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=72.73 E-value=14 Score=27.49 Aligned_cols=49 Identities=18% Similarity=0.073 Sum_probs=38.4
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
...+++.|..+|... ... ....++|..+|++...|..|-...+.+.++.
T Consensus 4 ~~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999873 222 3466889999999999999998777766654
No 91
>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=72.59 E-value=3.6 Score=25.93 Aligned_cols=20 Identities=30% Similarity=0.529 Sum_probs=17.6
Q ss_pred HHHHHHHHhCCChHHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWF 58 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF 58 (222)
....+|.+||+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 46678999999999999994
No 92
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=71.97 E-value=17 Score=26.13 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=28.6
Q ss_pred CCCCCHHHHH-HHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 14 RTSYTRYQTL-ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 14 R~~~t~~q~~-~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
|..||.++.. ++...+... . ...++|..+|++...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-M----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-C----CHHHHHHHHCcCHHHHHHHHH
Confidence 4567777654 444444433 2 356789999999999999963
No 93
>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=70.17 E-value=13 Score=19.09 Aligned_cols=38 Identities=18% Similarity=0.156 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 58 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF 58 (222)
.++..+...+...|.... ....++..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 466777777777775432 45678899999999998873
No 94
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=68.66 E-value=9.6 Score=22.08 Aligned_cols=40 Identities=15% Similarity=0.062 Sum_probs=21.4
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
..+|.++...++..+... ....+||..+|++..-|..+.+
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 567888888888887644 4567789999999999888764
No 95
>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=65.27 E-value=21 Score=21.19 Aligned_cols=41 Identities=20% Similarity=0.173 Sum_probs=26.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
+++.+..++.-.|-.+ ....++|..+|++...|+.|...-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 4556666665554443 3577889999999999999986443
No 96
>PRK10072 putative transcriptional regulator; Provisional
Probab=64.97 E-value=19 Score=24.88 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
..+...+..|......+ ..+||..+|++...|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 34777777776554444 678999999999999999987764
No 97
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=64.67 E-value=32 Score=25.67 Aligned_cols=50 Identities=18% Similarity=0.076 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...+++.|..+|.-. ... ....++|..+|++...|..|-...+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr-~~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ERG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHH-HcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 357899999999773 222 24678999999999999999987777766654
No 98
>PRK00118 putative DNA-binding protein; Validated
Probab=64.42 E-value=24 Score=24.81 Aligned_cols=49 Identities=12% Similarity=-0.012 Sum_probs=37.1
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
..++..|..++...|... ....+||..+|++..-|..|...-|.+.++.
T Consensus 16 ~~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 16 SLLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred ccCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356777788887666554 2466789999999999999998777666654
No 99
>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=64.35 E-value=16 Score=21.22 Aligned_cols=40 Identities=13% Similarity=0.185 Sum_probs=27.7
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
..++.++...+...+... .....||..+|++...|..++.
T Consensus 4 ~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l~ 43 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYLN 43 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHHC
T ss_pred CCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHh
Confidence 346666666666666655 3577889999999999988774
No 100
>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=63.69 E-value=22 Score=21.67 Aligned_cols=44 Identities=23% Similarity=0.080 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
.+|+.++.+|....... ...++|..+|++..-|..+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 57888889888766554 477889999999999999987766554
No 101
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=63.20 E-value=21 Score=27.56 Aligned_cols=49 Identities=12% Similarity=0.090 Sum_probs=37.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.++..+..+|...|-.. ....++|+.+|++...|+.+...-|.+.++..
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 47777888877655433 35778899999999999999987777776654
No 102
>PRK04217 hypothetical protein; Provisional
Probab=61.81 E-value=29 Score=24.71 Aligned_cols=52 Identities=10% Similarity=-0.132 Sum_probs=40.0
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
-..++.++..++...|...- ...+||+.+|++..-|...+..-+.+.+....
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 34678889888877765442 57788999999999999999877777666543
No 103
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=60.12 E-value=27 Score=25.89 Aligned_cols=50 Identities=14% Similarity=0.041 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|..+|++...|++....-|.+.|+.-+
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 106 ELPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46677777776655333 246788999999999999999877777776544
No 104
>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=60.06 E-value=11 Score=21.74 Aligned_cols=20 Identities=10% Similarity=0.120 Sum_probs=17.3
Q ss_pred HHHHHHHhCCChHHHHHHhh
Q psy11996 40 RIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~ 59 (222)
..++|+.+|++...|+.|.+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 105
>smart00351 PAX Paired Box domain.
Probab=59.98 E-value=63 Score=23.31 Aligned_cols=39 Identities=10% Similarity=0.158 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
.++.++...+-..|.... ...++|+.+|++...|..|.+
T Consensus 17 ~~s~~~R~riv~~~~~G~-----s~~~iA~~~gvs~~tV~kwi~ 55 (125)
T smart00351 17 PLPDEERQRIVELAQNGV-----RPCDISRQLCVSHGCVSKILG 55 (125)
T ss_pred CCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHH
Confidence 477777777777776432 345789999999999999974
No 106
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=59.39 E-value=29 Score=26.42 Aligned_cols=51 Identities=10% Similarity=0.023 Sum_probs=39.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.+++.+..++...|-.. ....+||..+|++...|+.++..-|.+.+.....
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~~ 181 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKFRS 181 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhhc
Confidence 56777777777765443 3567889999999999999998888777765543
No 107
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=59.21 E-value=16 Score=28.98 Aligned_cols=42 Identities=17% Similarity=0.196 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHhhhCC--CCCHHHHHHHHHHhCCChHHHHHH
Q psy11996 16 SYTRYQTLELEKEFHFNR--YLTRRRRIEIAHALCLTERQIKIW 57 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~--~p~~~~~~~la~~~~l~~~~v~~W 57 (222)
-+|+.|+.+|...|+..- +|-.....+||+.+|++..-+..-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~eh 198 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEH 198 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHH
Confidence 699999999999998865 688888999999999999876543
No 108
>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=59.00 E-value=30 Score=20.98 Aligned_cols=43 Identities=23% Similarity=0.088 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMK 64 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k 64 (222)
.||+.++.+|.-...-. ...++|..+|+++..|..+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHH
Confidence 57888999887776555 36788999999999999887654444
No 109
>PF13518 HTH_28: Helix-turn-helix domain
Probab=58.77 E-value=12 Score=21.97 Aligned_cols=22 Identities=18% Similarity=0.397 Sum_probs=18.8
Q ss_pred HHHHHHHHcCCChhhHHHHHhh
Q psy11996 163 RRIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 163 ~~~~la~~l~l~~~~V~~WF~n 184 (222)
...++|.++|++...|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4566899999999999999863
No 110
>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=58.49 E-value=10 Score=23.58 Aligned_cols=22 Identities=23% Similarity=0.293 Sum_probs=18.9
Q ss_pred HHHHHHHHHcCCChhhHHHHHh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~ 183 (222)
....+||+.||++...|..|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3467789999999999999975
No 111
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=58.06 E-value=28 Score=27.25 Aligned_cols=50 Identities=12% Similarity=0.062 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.++..+
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46677777776544333 357788999999999999999877777766543
No 112
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=57.72 E-value=18 Score=24.52 Aligned_cols=41 Identities=29% Similarity=0.187 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 180 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~ 180 (222)
.++++|...-...|+.+--.+....+++|.+|+.++..|..
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 35778887777777776666667788899999988765543
No 113
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=57.65 E-value=26 Score=25.65 Aligned_cols=47 Identities=15% Similarity=0.132 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|..+|++...|+.|...-+.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 56777777776665433 347888999999999999998766555543
No 114
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=57.43 E-value=20 Score=28.43 Aligned_cols=39 Identities=18% Similarity=0.253 Sum_probs=33.4
Q ss_pred cCCHHHHHHHHHhhhhc--CCCCHHHHHHHHHHcCCChhhH
Q psy11996 140 SYTRYQTLELEKEFHFN--RYLTRRRRIEIAHALCLTERQI 178 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~--~~p~~~~~~~la~~l~l~~~~V 178 (222)
.+|+.|+.+|...|... -+|-......||+++|+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 69999999999999864 4588888999999999998643
No 115
>COG3415 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=56.93 E-value=72 Score=23.70 Aligned_cols=55 Identities=9% Similarity=0.083 Sum_probs=37.0
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChh--hHHHHHhhhhhhHHH
Q psy11996 137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTER--QIKIWFQNRRMKWKK 191 (222)
Q Consensus 137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~--~V~~WF~nrR~k~kk 191 (222)
....++.+|+.+|...-....+=...-...|..+.|+... -|..+++..-...+|
T Consensus 60 rP~kl~~~q~~~l~e~~~~k~wTl~~~~~~l~~e~gv~y~~~~v~~~l~~~GlsykK 116 (138)
T COG3415 60 RPRKLSEEQLEILLERLREKDWTLKELVEELGLEFGVWYHASAVRRLLHELGLSYKK 116 (138)
T ss_pred CCcccCHHHHHHHHHHHhcccchHHHHHHHHhhhcCeEEeHHHHHHHHHHcCCCcCC
Confidence 3457889999999888776664444444566888887654 777777655444444
No 116
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=56.58 E-value=38 Score=19.69 Aligned_cols=41 Identities=24% Similarity=0.134 Sum_probs=29.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR 186 (222)
.++..+..++...+.. ....++|..+|++...|..|...-+
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3677777777654322 2457789999999999999987443
No 117
>KOG3755|consensus
Probab=56.16 E-value=22 Score=32.84 Aligned_cols=60 Identities=22% Similarity=0.218 Sum_probs=47.5
Q ss_pred CCCCCCCcCCHHHHHHHHHhhhh-cCCCCHHH---HHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 133 ETKRQRTSYTRYQTLELEKEFHF-NRYLTRRR---RIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 133 ~~~~~r~~~~~~q~~~L~~~F~~-~~~p~~~~---~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
-..+.++.+..+-+..|..+-.. .=||+.+. ..-|...+++.++.+...|+|.|.-.+..
T Consensus 646 ~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~ 709 (769)
T KOG3755|consen 646 HKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHH 709 (769)
T ss_pred cCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecchh
Confidence 35667888999988888776443 44677776 77899999999999999999998876643
No 118
>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=55.16 E-value=31 Score=24.65 Aligned_cols=47 Identities=17% Similarity=0.127 Sum_probs=34.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|..+|++...|..+...-+.+.++
T Consensus 110 ~L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45677777776654332 356688999999999999999876666554
No 119
>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=54.47 E-value=31 Score=21.28 Aligned_cols=37 Identities=32% Similarity=0.396 Sum_probs=28.2
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 143 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 143 ~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
..|+..|+-.+. +.+.+.. +||..+|++.+.|+.-..
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 357888888888 6666554 789999999999887664
No 120
>PRK04217 hypothetical protein; Provisional
Probab=54.43 E-value=45 Score=23.71 Aligned_cols=49 Identities=10% Similarity=-0.110 Sum_probs=37.1
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
..++.+|..++...|...- ...++|+.+|++...|...+..-+.+.+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3578888888877764443 467799999999999998887666666554
No 121
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=54.27 E-value=33 Score=25.63 Aligned_cols=48 Identities=15% Similarity=0.009 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
+++.+..++...|-.. ....++|..+|++...|+.|...-|.+.++.-
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5556666665554322 34678899999999999999987777776643
No 122
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=54.14 E-value=30 Score=24.80 Aligned_cols=41 Identities=15% Similarity=0.225 Sum_probs=28.3
Q ss_pred CCcCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 138 RTSYTRYQTL-ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 138 r~~~~~~q~~-~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
+..++.++.. ++...+... .....+|.++|++...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 5567887654 444334322 2456779999999999999964
No 123
>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=52.84 E-value=15 Score=20.60 Aligned_cols=20 Identities=20% Similarity=0.295 Sum_probs=16.1
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
+.++|+.+|++...|+.|=.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 45789999999999999953
No 124
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=52.63 E-value=37 Score=25.41 Aligned_cols=48 Identities=10% Similarity=-0.051 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-.. ....++|..+|++...|+.|...-+.+.++.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57778888887665322 2466789999999999999998666665554
No 125
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=52.14 E-value=48 Score=22.41 Aligned_cols=44 Identities=11% Similarity=0.078 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhh-----CCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 16 SYTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~-----~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
-++.+|+..|...|.. +-+.+..+...+...+|++...|...|.
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 4688899999998854 2367777888877778999998888774
No 126
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=52.02 E-value=16 Score=21.34 Aligned_cols=22 Identities=23% Similarity=0.368 Sum_probs=17.3
Q ss_pred HHHHHHHHHcCCChhhHHHHHh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~ 183 (222)
....++|..+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 4567889999999999999985
No 127
>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=51.65 E-value=7.8 Score=25.43 Aligned_cols=25 Identities=24% Similarity=0.316 Sum_probs=21.0
Q ss_pred CHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996 160 TRRRRIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 160 ~~~~~~~la~~l~l~~~~V~~WF~n 184 (222)
......+||..+|++..-|+.|+.+
T Consensus 31 eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 31 AGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3345788899999999999999964
No 128
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=51.35 E-value=17 Score=22.82 Aligned_cols=20 Identities=15% Similarity=0.253 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
+.++|..+|++...|+.|=.
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999953
No 129
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=51.25 E-value=48 Score=24.73 Aligned_cols=50 Identities=12% Similarity=-0.133 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ...+++|..+|++...|+++...-|.+.+....
T Consensus 112 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 161 (164)
T PRK12547 112 LLSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQELLK 161 (164)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45667777766654433 246788999999999999999877777665543
No 130
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=51.16 E-value=42 Score=25.36 Aligned_cols=48 Identities=8% Similarity=0.200 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-.. ...+++|..+|++...|+++...-|.+.|+.
T Consensus 129 ~L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 129 ELEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 45666766666555322 2477889999999999999998766666654
No 131
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=50.75 E-value=47 Score=25.45 Aligned_cols=58 Identities=12% Similarity=0.079 Sum_probs=42.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCC
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIP 202 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~ 202 (222)
.+++.+..++...|-.. ....+||..+|++..-|++....-|.+.++.........+|
T Consensus 131 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~~~~~~ 188 (191)
T PRK12520 131 RLPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLDLHWFGNPP 188 (191)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHccCCc
Confidence 46666766666654332 24678899999999999999988888888876666654444
No 132
>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=50.57 E-value=42 Score=24.68 Aligned_cols=47 Identities=13% Similarity=0.077 Sum_probs=33.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 190 (222)
..+++.+..++...|-.. ....++|+.+|++...|+++...-|.+.+
T Consensus 110 ~~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 110 EKLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HHCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 357777777777754332 35778899999999999999875555444
No 133
>PRK00118 putative DNA-binding protein; Validated
Probab=49.84 E-value=58 Score=22.92 Aligned_cols=48 Identities=13% Similarity=-0.023 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
.+++.|..++...|.... ...++|..+|++...|..|...-|.+.+..
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456667777766555443 356789999999999999987766666654
No 134
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.62 E-value=37 Score=23.09 Aligned_cols=40 Identities=28% Similarity=0.174 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 56 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~ 56 (222)
++++|...-.+-|..+--.+....+++|..||+++..|..
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 5667766655555555545556678899999999877653
No 135
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.62 E-value=19 Score=22.10 Aligned_cols=24 Identities=4% Similarity=0.170 Sum_probs=18.2
Q ss_pred HHHHHHHHhCCChHHHHHHhhcch
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
....||..+|++...|..|+.++.
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 467899999999999999998763
No 136
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=48.66 E-value=43 Score=25.40 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-. ....+++|..+|++...|+++...-|.+.+..
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4667777777664432 23567889999999999999998766666654
No 137
>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=48.65 E-value=9.9 Score=24.94 Aligned_cols=32 Identities=22% Similarity=0.225 Sum_probs=23.6
Q ss_pred hhhCCCCCHHHHHHHHHHhCCChHHHHHHhhc
Q psy11996 29 FHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60 (222)
Q Consensus 29 f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 60 (222)
|....+-......++|..+|++...|+.|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 44433333345788999999999999999864
No 138
>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=48.36 E-value=52 Score=24.90 Aligned_cols=46 Identities=20% Similarity=0.087 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
+++.+..++...|-.. ....++|+.+|++...|++....-|.+.++
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6677777777665443 246788999999999999999877766655
No 139
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=47.95 E-value=39 Score=25.93 Aligned_cols=48 Identities=19% Similarity=0.118 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-. .....++|..+|++...|+.|...-|.+.++.
T Consensus 141 ~L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 141 QLPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hCCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3556666666554422 23567889999999999999998777666654
No 140
>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=47.68 E-value=57 Score=22.83 Aligned_cols=43 Identities=19% Similarity=0.085 Sum_probs=31.5
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 186 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR 186 (222)
..+|..|..+|+..|..+ -...+||+.+|++..-|.-|.+.-+
T Consensus 16 ~LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 16 ELLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GGS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 357889999999887766 4677889999999999999986443
No 141
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=47.58 E-value=51 Score=25.18 Aligned_cols=48 Identities=13% Similarity=0.010 Sum_probs=35.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
..+++.+..++...|-.. ....+||..+|++...|+.+...-+.+.|+
T Consensus 138 ~~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 138 DTLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456777777777765443 347788999999999999998766655554
No 142
>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=47.56 E-value=24 Score=19.88 Aligned_cols=22 Identities=18% Similarity=0.388 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHHHHhhcc
Q psy11996 40 RIEIAHALCLTERQIKIWFQNR 61 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nr 61 (222)
..++|..+|++...|..|.++.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4678999999999999998643
No 143
>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=47.28 E-value=41 Score=25.58 Aligned_cols=48 Identities=6% Similarity=-0.115 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
+++.+..++...|- ......++|..+|++...|+++...-|.+-|+..
T Consensus 139 L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 139 LPEDLRTAITLREL-----EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 44555555544432 2235678899999999999999976666666543
No 144
>PRK10072 putative transcriptional regulator; Provisional
Probab=46.64 E-value=53 Score=22.72 Aligned_cols=41 Identities=17% Similarity=0.152 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
..+...+..|...-..+ ..+||..+|++..-|..|...+|.
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 34666677775533332 577899999999999999987764
No 145
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=46.50 E-value=53 Score=25.26 Aligned_cols=49 Identities=6% Similarity=0.036 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..++...|-.. ....++|..+|++...|+.+...-|.+.|+..
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45667777776665433 24678899999999999999987777666654
No 146
>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=46.43 E-value=60 Score=24.44 Aligned_cols=50 Identities=20% Similarity=0.021 Sum_probs=38.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|..+|++...|+++-..-|.+.++..+
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 56777888877765443 257788999999999999999877777666544
No 147
>PRK06930 positive control sigma-like factor; Validated
Probab=46.19 E-value=59 Score=24.93 Aligned_cols=50 Identities=12% Similarity=0.068 Sum_probs=38.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|... ....++|..+|++...|+.+...-+.+.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 57788888887755333 246778999999999999999887777776544
No 148
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=45.96 E-value=50 Score=25.16 Aligned_cols=50 Identities=10% Similarity=0.101 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....+||..+|++...|+.+...-|.+.++...
T Consensus 128 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 128 ALPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred hCCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35666666665544222 246788999999999999999877777666543
No 149
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=45.93 E-value=53 Score=24.45 Aligned_cols=50 Identities=14% Similarity=-0.057 Sum_probs=35.4
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
..+++.+..++...|-.. ....++|..+|++...|+.|...-|.+.++.-
T Consensus 107 ~~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 107 HTLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred HhCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345666666666543222 24678899999999999999987666666643
No 150
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=45.89 E-value=71 Score=21.55 Aligned_cols=43 Identities=12% Similarity=0.071 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHhhhh-----cCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 141 YTRYQTLELEKEFHF-----NRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~-----~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
++.+|+..+...|.. +.+.+..+...+...+|++..+|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 577888899988863 3467788888777778999888888885
No 151
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=45.59 E-value=58 Score=24.88 Aligned_cols=51 Identities=12% Similarity=0.111 Sum_probs=37.6
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
..+++.+..+|...|-.. ....++|+.+|++...|++-...-|.+.++.-+
T Consensus 130 ~~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 130 AKLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 356777777776655433 346788999999999999999877777766543
No 152
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=45.22 E-value=57 Score=25.09 Aligned_cols=54 Identities=7% Similarity=0.037 Sum_probs=39.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccC
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASM 198 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~ 198 (222)
.+++.+..++...|-.. ....+||..+|++..-|+.....-|.+.++.......
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~~~~ 184 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLSINWF 184 (188)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45666777776655433 2577889999999999999998777777776655443
No 153
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=45.17 E-value=75 Score=23.31 Aligned_cols=51 Identities=14% Similarity=0.047 Sum_probs=36.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
..+++.+..++...|-.. ....++|..+|++...|++....-|.+.++..+
T Consensus 105 ~~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 155 (161)
T PRK09047 105 QKLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKALE 155 (161)
T ss_pred HhCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356777777777655333 236788999999999999999877766666543
No 154
>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=45.10 E-value=44 Score=17.83 Aligned_cols=17 Identities=18% Similarity=0.321 Sum_probs=12.8
Q ss_pred HHHHcCCChhhHHHHHh
Q psy11996 167 IAHALCLTERQIKIWFQ 183 (222)
Q Consensus 167 la~~l~l~~~~V~~WF~ 183 (222)
-|...||+..+|+..+.
T Consensus 11 eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 11 EAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHTT--HHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 48899999999998874
No 155
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=45.02 E-value=62 Score=24.55 Aligned_cols=32 Identities=13% Similarity=0.180 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.+...-|.+.+....
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 46778999999999999998777777766543
No 156
>PRK09480 slmA division inhibitor protein; Provisional
Probab=44.99 E-value=24 Score=26.86 Aligned_cols=36 Identities=11% Similarity=0.102 Sum_probs=29.7
Q ss_pred HhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 151 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 151 ~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
..|...+. .......||++.|++..-+..+|.|+-.
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 34555556 7888999999999999999999998763
No 157
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=44.79 E-value=56 Score=23.84 Aligned_cols=45 Identities=16% Similarity=0.139 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~ 66 (222)
+++.+..++.-.|-.+ ....++|..+|++...|..|...-+.+.+
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 3444444444433322 24678899999999999999765554443
No 158
>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=44.48 E-value=63 Score=23.51 Aligned_cols=47 Identities=11% Similarity=0.039 Sum_probs=33.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.++..+..++...|-.. ....++|..+|++...|+.+...-+.+.++
T Consensus 113 ~L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 113 KLPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45667777776644322 245678999999999999998766655554
No 159
>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=44.36 E-value=28 Score=20.63 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
..+||..+|++...|..|..+.+
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 47899999999999999998754
No 160
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=44.35 E-value=61 Score=24.01 Aligned_cols=48 Identities=23% Similarity=0.186 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..+|...| .. ....+||..+|++...|+.+...-+.+.|+..
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46777888887777 33 25677899999999999999987777666653
No 161
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.11 E-value=75 Score=23.40 Aligned_cols=31 Identities=19% Similarity=0.101 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|+.....-|.+.++..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999877676666654
No 162
>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=43.78 E-value=17 Score=27.66 Aligned_cols=33 Identities=15% Similarity=0.296 Sum_probs=28.1
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
-.+++|+.-++++..+|-.|..|-+...+...+
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 357889999999999999999999887776543
No 163
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=43.76 E-value=39 Score=27.22 Aligned_cols=52 Identities=15% Similarity=0.146 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
.++..+..++...|-.. ....+||..+|++...|++....-|.+.|+..+..
T Consensus 171 ~Lp~~~R~v~~L~~~eg-----~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~~~ 222 (233)
T PRK12538 171 RLPEQQRIAVILSYHEN-----MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLRRH 222 (233)
T ss_pred hCCHHHHHHhhhHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHh
Confidence 34556666655444322 24678899999999999999988777777765433
No 164
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=43.24 E-value=56 Score=24.17 Aligned_cols=47 Identities=21% Similarity=0.056 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.|..++.-.|-.. ....++|..+|++...|+.+...-|.+.++
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46677777776654333 246788999999999999998766666554
No 165
>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=42.66 E-value=62 Score=22.96 Aligned_cols=46 Identities=17% Similarity=0.119 Sum_probs=30.1
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
+++.+..++...|-. .....++|..+|+++..|..+...-+.+.++
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455555555444322 2246688999999999999988665555443
No 166
>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=42.27 E-value=28 Score=21.88 Aligned_cols=20 Identities=15% Similarity=0.232 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999975
No 167
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=42.14 E-value=83 Score=23.36 Aligned_cols=31 Identities=19% Similarity=0.133 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|..|...-|.+.++..
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999877666666543
No 168
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=42.09 E-value=69 Score=24.67 Aligned_cols=30 Identities=13% Similarity=0.202 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|+.+...-|.+.++.
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 467789999999999999987666666554
No 169
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=41.94 E-value=66 Score=24.58 Aligned_cols=50 Identities=22% Similarity=0.068 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ...+++|..+|++...|+..+..-|.+.++...
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46667777776554332 357788999999999999999876766666443
No 170
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=41.59 E-value=70 Score=24.69 Aligned_cols=52 Identities=12% Similarity=-0.085 Sum_probs=37.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
.+++.+..++...|-.. ....++|..+|++...|+++...-|.+.|+.....
T Consensus 113 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~~~ 164 (188)
T PRK12546 113 QLPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLAELLQLE 164 (188)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhcc
Confidence 45667777766553322 24677899999999999999998887777765543
No 171
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=41.55 E-value=78 Score=23.34 Aligned_cols=48 Identities=10% Similarity=0.117 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-.. ....++|+.+|++...|+.....-+.+.++.
T Consensus 109 ~L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45677777776654333 2467889999999999999877666665553
No 172
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=41.34 E-value=74 Score=24.11 Aligned_cols=49 Identities=10% Similarity=0.026 Sum_probs=37.0
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
..+++.|..++.-.|-.. ...+++|..+|++..-|+.....-+.+++..
T Consensus 126 ~~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 126 DTLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 357788888777765433 2467889999999999999998777766553
No 173
>PF13551 HTH_29: Winged helix-turn helix
Probab=41.18 E-value=1.1e+02 Score=20.85 Aligned_cols=48 Identities=17% Similarity=0.154 Sum_probs=31.4
Q ss_pred CCCCCCCHHHHHHHHHHhhhCCC-----CCHHHHHH-H-HHH--hCCChHHHHHHhh
Q psy11996 12 RQRTSYTRYQTLELEKEFHFNRY-----LTRRRRIE-I-AHA--LCLTERQIKIWFQ 59 (222)
Q Consensus 12 r~R~~~t~~q~~~L~~~f~~~~~-----p~~~~~~~-l-a~~--~~l~~~~v~~WF~ 59 (222)
+++..+++++...|.+.+..++. .+...... | ... +.++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33444999999999999988763 33333333 3 222 2578888888874
No 174
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=41.06 E-value=80 Score=22.23 Aligned_cols=41 Identities=12% Similarity=0.273 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
.+++.++..|.+.+... ....|..+|++..-|+.|=+.|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37888888888887776 467799999999999999877764
No 175
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=41.03 E-value=80 Score=24.64 Aligned_cols=31 Identities=16% Similarity=0.122 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|+.+...-+.+.++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999998876666665543
No 176
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=40.98 E-value=80 Score=23.52 Aligned_cols=47 Identities=9% Similarity=-0.077 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
+++.+..+|.-.|-. .....++|..+|++...|..|...-+.+.++.
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444444555443322 22356789999999999999987555555543
No 177
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=40.88 E-value=76 Score=24.06 Aligned_cols=49 Identities=14% Similarity=0.010 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..++...|-.. ....++|..+|++...|++....-|.+.++..
T Consensus 129 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 129 QLPDRQRLPIVHVKLEG-----LSVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred HCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 34555555544443222 34678899999999999999987777777643
No 178
>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=40.76 E-value=71 Score=23.54 Aligned_cols=48 Identities=10% Similarity=0.068 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-. .....++|..+|++...|+.+-..-|.+.++.
T Consensus 110 ~L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 110 RLPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred hCCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3566777777665533 23467789999999999999998777666653
No 179
>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=40.69 E-value=73 Score=23.77 Aligned_cols=48 Identities=17% Similarity=0.166 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.++..+..++...|-.. ....++|..+|++...|+++...-|.+.++.
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 119 TLNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred hCCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45666777776655333 3467789999999999999987666665553
No 180
>cd00131 PAX Paired Box domain
Probab=40.56 E-value=1.4e+02 Score=21.62 Aligned_cols=47 Identities=11% Similarity=-0.098 Sum_probs=32.6
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCC-------ChHHHHHHhhcc
Q psy11996 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-------TERQIKIWFQNR 61 (222)
Q Consensus 15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l-------~~~~v~~WF~nr 61 (222)
...+..+...+......++..+..+..++...-|+ +...|..||+++
T Consensus 74 r~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 34567777777777788887777776665334466 888888887653
No 181
>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=40.33 E-value=32 Score=21.51 Aligned_cols=21 Identities=5% Similarity=0.210 Sum_probs=18.0
Q ss_pred HHHHHHHcCCChhhHHHHHhh
Q psy11996 164 RIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~n 184 (222)
..++|+.+|++...|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999753
No 182
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.95 E-value=92 Score=23.33 Aligned_cols=51 Identities=8% Similarity=-0.031 Sum_probs=36.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
..+++.+..++...|-.. ....++|+.+|++..-|+.+...-+.+++..-+
T Consensus 118 ~~Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~ 168 (172)
T PRK12523 118 GKLSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIALY 168 (172)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 346667777776654332 246778999999999999999877777765443
No 183
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=39.55 E-value=26 Score=20.52 Aligned_cols=21 Identities=14% Similarity=0.205 Sum_probs=18.8
Q ss_pred HHHHHhCCChHHHHHHhhcch
Q psy11996 42 EIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 42 ~la~~~~l~~~~v~~WF~nrR 62 (222)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998873
No 184
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=39.22 E-value=92 Score=23.94 Aligned_cols=50 Identities=10% Similarity=0.036 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.++..+..++...|-.. ...+++|+.+|++...|+.-...-|.+.++...
T Consensus 141 ~Lp~~~r~v~~l~~~eg-----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 141 RLPKAQRDVLQAVYLEE-----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 45666777776544332 246788999999999999988776666665433
No 185
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=39.19 E-value=86 Score=23.76 Aligned_cols=47 Identities=15% Similarity=0.061 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|..+|++...|+.+...-|.+.+.
T Consensus 135 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 135 ALSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46677777776554332 346788999999999999998765555554
No 186
>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=39.08 E-value=1.3e+02 Score=22.35 Aligned_cols=48 Identities=23% Similarity=0.063 Sum_probs=37.4
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+.++..|..+|...+ .. ....++|+.+|++..-|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999998742 22 256788999999999999998877766665
No 187
>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=39.01 E-value=38 Score=19.96 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=20.0
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
..+||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999986654
No 188
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=38.96 E-value=83 Score=23.89 Aligned_cols=47 Identities=13% Similarity=0.133 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|+.+|++...|+++-..-+.+.++
T Consensus 133 ~L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 133 QLEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 45666666665554332 246788999999999999999866655554
No 189
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=38.84 E-value=84 Score=23.78 Aligned_cols=50 Identities=12% Similarity=0.087 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|+.+|++...|++....-+.+.++...
T Consensus 117 ~Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 117 KLPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666544332 246788999999999999999888888777543
No 190
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=38.48 E-value=84 Score=24.20 Aligned_cols=49 Identities=8% Similarity=-0.053 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..++.-.|-.. ...++||..+|++...|+.+...-|.+.++.-
T Consensus 136 ~L~~~~r~i~~L~~~~g-----~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 136 ALPERQRQAVVLRHIEG-----LSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45666666666554332 24678899999999999999987676666643
No 191
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.31 E-value=97 Score=23.13 Aligned_cols=49 Identities=12% Similarity=0.074 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..+|...|-.. ....++|+.+|++..-|+.....-|.+.++.-
T Consensus 118 ~L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 118 QLSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 46777777777765333 24678899999999999999876666666543
No 192
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=38.29 E-value=81 Score=22.09 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=32.3
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCC-ChhhHHHHHh
Q psy11996 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-TERQIKIWFQ 183 (222)
Q Consensus 138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l-~~~~V~~WF~ 183 (222)
+..|+.+....+-..+..... ....+|.++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678898877666666555443 67889999996 9999998875
No 193
>PRK09480 slmA division inhibitor protein; Provisional
Probab=38.13 E-value=41 Score=25.54 Aligned_cols=36 Identities=11% Similarity=0.102 Sum_probs=29.9
Q ss_pred HHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996 27 KEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 27 ~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
..|...+. .......+|+..|++..-+..+|.|+-.
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 34555556 7778999999999999999999999764
No 194
>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=37.93 E-value=90 Score=23.10 Aligned_cols=47 Identities=26% Similarity=0.123 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|..+|++...|+....--|.+.|+
T Consensus 122 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56777777777654332 346788999999999999988755555554
No 195
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=37.44 E-value=83 Score=25.16 Aligned_cols=48 Identities=15% Similarity=0.137 Sum_probs=37.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|... ....++|..+|++..-|+.+...-+.+.++.
T Consensus 184 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 184 SLPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hCCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45677777777766433 3567889999999999999998777777664
No 196
>PHA02955 hypothetical protein; Provisional
Probab=37.37 E-value=32 Score=27.47 Aligned_cols=75 Identities=9% Similarity=0.036 Sum_probs=45.6
Q ss_pred HHHHHHHHHhhhhc-CCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCCCCCCCCCCCCCCCCC
Q psy11996 143 RYQTLELEKEFHFN-RYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYGNPYQF 217 (222)
Q Consensus 143 ~~q~~~L~~~F~~~-~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~~~~~~~~~~~~~~~~ 217 (222)
..++..|-+.|.+. .-.+.+++.+++.++|+....|..||.+.-.+.-+-........-=.....+.|++.|...
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q~C~A~A~v~n~IdIQ~i~ig~C~aP~g~~ 135 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQLHCEAYANLTQHIDIQHFNIGTCYSPNDKY 135 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhhhccchhhhccceeeeeeeeccccCCCCce
Confidence 45777777777664 5677888999999999988778999976533222111111111111335556666655443
No 197
>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=37.16 E-value=45 Score=18.80 Aligned_cols=22 Identities=14% Similarity=0.077 Sum_probs=18.2
Q ss_pred HHHHHHHhCCChHHHHHHhhcc
Q psy11996 40 RIEIAHALCLTERQIKIWFQNR 61 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nr 61 (222)
..++|+.+|++...|..|..+.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4578999999999999997544
No 198
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=37.06 E-value=97 Score=23.80 Aligned_cols=51 Identities=12% Similarity=-0.089 Sum_probs=37.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.+++.+..++...|-.. ....++|+.||++...|+.....-|.+.++..+.
T Consensus 116 ~Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 116 QLPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 45666666666554332 2467889999999999999998777777776554
No 199
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=36.90 E-value=1.1e+02 Score=22.70 Aligned_cols=31 Identities=23% Similarity=0.054 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
..+++|..+|++...|+.|...-|.+.++..
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999999876666666544
No 200
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=36.90 E-value=1.7e+02 Score=22.38 Aligned_cols=45 Identities=9% Similarity=0.028 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhc
Q psy11996 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 60 (222)
Q Consensus 14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~n 60 (222)
...+|++++..+..+-..++ ....+..||+++|++.--|.+-..-
T Consensus 83 ~y~Lt~e~i~Eir~LR~~DP--~~wTr~~LAkkF~~S~~fV~~v~~~ 127 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAEDP--EKWTRKKLAKKFNCSPLFVSMVAPA 127 (164)
T ss_pred cccCCHHHHHHHHHHHHcCc--hHhhHHHHHHHhCCCHHHHHHhcCC
Confidence 45899999999999998885 5678999999999999877765543
No 201
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=36.90 E-value=96 Score=23.57 Aligned_cols=49 Identities=10% Similarity=-0.044 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.++..
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLEG-----LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777777776554322 35778899999999999999987776666543
No 202
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=36.72 E-value=97 Score=24.23 Aligned_cols=51 Identities=12% Similarity=-0.063 Sum_probs=35.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.+++.+..++...|-.. ....++|+.+|++..-|+++...-|.+.++..+.
T Consensus 138 ~L~~~~r~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~~ 188 (203)
T PRK09647 138 SLPPEFRAAVVLCDIEG-----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALAA 188 (203)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666555544222 2467889999999999999998777777665443
No 203
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=36.66 E-value=1e+02 Score=23.39 Aligned_cols=32 Identities=13% Similarity=0.172 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.+...-|.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999998766766666544
No 204
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=36.46 E-value=90 Score=23.95 Aligned_cols=51 Identities=6% Similarity=0.008 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.+++.+..++...|-.. ....++|+.+|++...|+.....-|.+.|+....
T Consensus 136 ~L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 136 NLPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred hCCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 35666666665443322 2467889999999999999998777777766543
No 205
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=36.01 E-value=85 Score=24.00 Aligned_cols=47 Identities=13% Similarity=-0.079 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.|..++.-.|-.. ....+||..+|++...|+.+...-|.+.++
T Consensus 130 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 130 DLTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred hCCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45667777766554333 246788999999999999999766666665
No 206
>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=35.94 E-value=40 Score=20.94 Aligned_cols=20 Identities=10% Similarity=0.230 Sum_probs=17.6
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999984
No 207
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=35.87 E-value=1.1e+02 Score=23.36 Aligned_cols=50 Identities=20% Similarity=0.249 Sum_probs=36.1
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
..+++.+..++...|-.. -...++|+.+|++...|++....-|.+.++..
T Consensus 130 ~~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 130 NDLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred HhCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 356777888877655332 34678899999999999998876666666543
No 208
>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=35.81 E-value=95 Score=22.69 Aligned_cols=27 Identities=15% Similarity=0.086 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKW 65 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~ 65 (222)
...++|..+|++...|..+...-|.+.
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 467789999999999998865444443
No 209
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=35.75 E-value=97 Score=25.12 Aligned_cols=49 Identities=10% Similarity=0.073 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-+.+.|+..
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46777888887766432 24578899999999999999987666666543
No 210
>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=35.52 E-value=91 Score=18.00 Aligned_cols=37 Identities=24% Similarity=0.257 Sum_probs=25.6
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996 142 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 142 ~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 184 (222)
+..+..++...+. .....++|..++++...|..|...
T Consensus 2 ~~~e~~i~~~~~~------~~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLAE------GKTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHHH
Confidence 4555666654332 125677899999999999999863
No 211
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=35.50 E-value=1e+02 Score=23.89 Aligned_cols=52 Identities=10% Similarity=-0.066 Sum_probs=37.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMA 196 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~ 196 (222)
.+++.+..++...|-.. ....++|+.+|++...|+.+...-|.+.++.....
T Consensus 133 ~Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~~ 184 (196)
T PRK12535 133 ALPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAATATG 184 (196)
T ss_pred cCCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhccc
Confidence 45666666665554333 24678899999999999999987777777654443
No 212
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=35.34 E-value=1.2e+02 Score=23.01 Aligned_cols=32 Identities=19% Similarity=0.150 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|++-...-|.+.++...
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999888766666666543
No 213
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=35.10 E-value=86 Score=23.58 Aligned_cols=47 Identities=13% Similarity=-0.011 Sum_probs=32.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....+||+.+|++...|+++...-+.+++.
T Consensus 119 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 119 GLNGKTREAFLLSQLDG-----LTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred hCCHHHhHHhhhhhccC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45666666665543332 347888999999999999999765555543
No 214
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=35.05 E-value=1.1e+02 Score=21.43 Aligned_cols=42 Identities=19% Similarity=0.210 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCC-ChHHHHHHhh
Q psy11996 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCL-TERQIKIWFQ 59 (222)
Q Consensus 14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l-~~~~v~~WF~ 59 (222)
|..||.+....+-+.+....+ ....+|..+|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678999877666555554433 57789999996 9999999953
No 215
>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=34.68 E-value=1e+02 Score=24.41 Aligned_cols=48 Identities=15% Similarity=0.191 Sum_probs=36.2
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
..+++.+..++...|... ....++|+.+|++...|..|...-+.+.++
T Consensus 177 ~~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 177 AALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred HcCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 357888888888776432 357788999999999999998765555544
No 216
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=34.63 E-value=1e+02 Score=23.56 Aligned_cols=44 Identities=9% Similarity=0.034 Sum_probs=36.2
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHH
Q psy11996 137 QRTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 182 (222)
Q Consensus 137 ~r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 182 (222)
+...++++++..+..+-..+ |....+..||.++||+..=|.+-.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhc
Confidence 34689999999999988877 667789999999999887666554
No 217
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=34.35 E-value=1.1e+02 Score=23.26 Aligned_cols=29 Identities=14% Similarity=0.097 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
..+++|..+|++...|+.+...-+.+.++
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46788999999999999887655555444
No 218
>smart00595 MADF subfamily of SANT domain.
Probab=34.31 E-value=54 Score=21.68 Aligned_cols=35 Identities=29% Similarity=0.329 Sum_probs=28.6
Q ss_pred HHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996 163 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 197 (222)
Q Consensus 163 ~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~ 197 (222)
.-..||.++|.+..+|+.-+.|-|...++..+...
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~ 63 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQ 63 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567999999999999999999988888765543
No 219
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=34.15 E-value=1.3e+02 Score=23.37 Aligned_cols=51 Identities=10% Similarity=0.026 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.+++.+..++...|-.. ....++|..+|++...|++....-|.+.++.-..
T Consensus 139 ~Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~~ 189 (201)
T PRK12545 139 HLPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRTCLSE 189 (201)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666654333 2467889999999999999998777777766543
No 220
>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=33.81 E-value=1.1e+02 Score=24.23 Aligned_cols=47 Identities=21% Similarity=0.159 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 46788888888877433 246788999999999999998766555554
No 221
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=33.76 E-value=97 Score=23.68 Aligned_cols=31 Identities=19% Similarity=0.168 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 38 RRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 38 ~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
....++|..+|++...|+.|...-|.+.++.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3567889999999999999997666666654
No 222
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=33.52 E-value=1.2e+02 Score=22.71 Aligned_cols=30 Identities=10% Similarity=0.168 Sum_probs=24.4
Q ss_pred HHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 163 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 163 ~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
..+++|+.+|++...|+.....-|.+.++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999988666666554
No 223
>PRK06930 positive control sigma-like factor; Validated
Probab=33.28 E-value=1.4e+02 Score=22.82 Aligned_cols=49 Identities=12% Similarity=0.064 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
.+++.+..++.-.|...- ...++|..+|++...|+.+...-+.+.++..
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 355666666655442221 3567899999999999999987777766643
No 224
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=33.01 E-value=1.1e+02 Score=23.12 Aligned_cols=48 Identities=15% Similarity=0.230 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|-.. ....+||..+|++..-|++....-|.+.++.
T Consensus 122 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 122 ELNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46667777776544332 2467889999999999999987666666654
No 225
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=32.84 E-value=93 Score=22.33 Aligned_cols=24 Identities=4% Similarity=0.077 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhCCChHHHHHHhhc
Q psy11996 37 RRRRIEIAHALCLTERQIKIWFQN 60 (222)
Q Consensus 37 ~~~~~~la~~~~l~~~~v~~WF~n 60 (222)
....++||+.+|+++..+..+|+.
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~ 48 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKK 48 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 356788999999999999999953
No 226
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.51 E-value=57 Score=19.02 Aligned_cols=22 Identities=18% Similarity=0.332 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChHHHHHHhhcc
Q psy11996 40 RIEIAHALCLTERQIKIWFQNR 61 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nr 61 (222)
..++|..||++...|..|..+.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4578999999999999998544
No 227
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=32.29 E-value=1.7e+02 Score=21.38 Aligned_cols=31 Identities=19% Similarity=0.108 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|+.....-|.+.+...
T Consensus 124 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 124 DVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3577899999999999988766665555543
No 228
>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=32.23 E-value=1e+02 Score=21.80 Aligned_cols=41 Identities=12% Similarity=0.028 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcch
Q psy11996 15 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 15 ~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
..+++.++..+......+ ..+||..+|++...|..|-..+.
T Consensus 63 ~~~~~~~i~~~r~~~glt-------q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 63 GLLTPPEIRRIRKKLGLS-------QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred CCcCHHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHCCCC
Confidence 455566666665554333 45688889999999999875443
No 229
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=32.14 E-value=62 Score=24.22 Aligned_cols=34 Identities=21% Similarity=0.128 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
....++|..+|++...|++.+..-|.+.++..+.
T Consensus 137 ~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~~ 170 (175)
T PRK12518 137 LPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQQ 170 (175)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3478889999999999999998888887776543
No 230
>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=32.06 E-value=1.4e+02 Score=22.82 Aligned_cols=31 Identities=26% Similarity=0.173 Sum_probs=24.4
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 161 RRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 161 ~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.....++|..+|++...|++.+..-|.+.++
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 3457788999999999999998766655554
No 231
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=31.97 E-value=2e+02 Score=21.32 Aligned_cols=48 Identities=23% Similarity=0.063 Sum_probs=36.7
Q ss_pred CCCCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 14 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 14 R~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
.+.+++.|..+|.-.+ .. ....++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999997742 22 247789999999999999987766666664
No 232
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=31.95 E-value=1.2e+02 Score=22.31 Aligned_cols=46 Identities=13% Similarity=0.030 Sum_probs=32.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
..+++.+..++...|-.. ....++|..+|++...|+.+...-+.+.
T Consensus 112 ~~L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 112 DGLPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred HHCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 346777777776665433 2467889999999999999987554443
No 233
>PF13730 HTH_36: Helix-turn-helix domain
Probab=31.95 E-value=73 Score=18.84 Aligned_cols=43 Identities=12% Similarity=-0.014 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcCCChhhHHHHHhh
Q psy11996 141 YTRYQTLELEKEFH---FNRYLTRRRRIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 141 ~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~l~~~~V~~WF~n 184 (222)
+++.+..++-.... .+.. ..+..+.||+.+|++.+.|..+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 44555555544432 2222 3335778899999999999988753
No 234
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=31.91 E-value=1.1e+02 Score=22.98 Aligned_cols=31 Identities=23% Similarity=0.200 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 38 RRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 38 ~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...+++|..+|++...|+.+...-|.+.+..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999987666665553
No 235
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=31.84 E-value=57 Score=25.04 Aligned_cols=33 Identities=18% Similarity=0.079 Sum_probs=26.6
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
....++|..+|++...|+.+...-|.+.++..+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 156 LELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 457788999999999999998877777666544
No 236
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=31.43 E-value=1.3e+02 Score=22.56 Aligned_cols=29 Identities=14% Similarity=0.326 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
..+++|..+|++...|+++...-|.+.++
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 46788999999999999988665655554
No 237
>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=31.40 E-value=1.3e+02 Score=21.66 Aligned_cols=28 Identities=14% Similarity=0.207 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWK 66 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~ 66 (222)
...++|..+|+++..|+.+...-+.+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567889999999999987754444443
No 238
>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=31.39 E-value=1.7e+02 Score=22.40 Aligned_cols=33 Identities=12% Similarity=0.206 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
...++|..+|++..-|+.....-|.+.++....
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999998877666666665443
No 239
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.23 E-value=1.2e+02 Score=22.75 Aligned_cols=47 Identities=15% Similarity=0.103 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
++..+..+|...|- .....+++|..+|++...|++....-|.+.++.
T Consensus 137 L~~~~r~il~l~~~-----~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 137 LPEKYRTVIVLKYI-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHhhhHHh-----hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45555555544332 233567889999999999999987777666654
No 240
>PHA01976 helix-turn-helix protein
Probab=31.23 E-value=59 Score=20.12 Aligned_cols=23 Identities=13% Similarity=0.125 Sum_probs=19.5
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
..+||..+|++...|..|-..++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 57799999999999999986543
No 241
>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=31.18 E-value=1.4e+02 Score=22.49 Aligned_cols=29 Identities=21% Similarity=0.122 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|++....-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35678899999999999988666655554
No 242
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=31.17 E-value=1.1e+02 Score=24.20 Aligned_cols=50 Identities=10% Similarity=-0.151 Sum_probs=36.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....+||..+|++...|+.+...-|.+.++...
T Consensus 134 ~Lp~~~R~v~~L~y~eg-----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~ 183 (216)
T PRK12533 134 KLPVEYREVLVLRELED-----MSYREIAAIADVPVGTVMSRLARARRRLAALLG 183 (216)
T ss_pred cCCHHHHhHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHc
Confidence 45666666666654432 246778999999999999999877777776643
No 243
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=31.15 E-value=1.7e+02 Score=22.31 Aligned_cols=32 Identities=9% Similarity=0.084 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++...
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998777777766554
No 244
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=31.04 E-value=1.3e+02 Score=22.48 Aligned_cols=48 Identities=8% Similarity=-0.025 Sum_probs=34.8
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
..+++.+..++.-.|-.. ...+++|..+|++..-|+.+..+-+..++.
T Consensus 117 ~~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 117 DGLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HhCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346677777776654333 246788999999999999998776666554
No 245
>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=31.00 E-value=1.2e+02 Score=24.56 Aligned_cols=47 Identities=13% Similarity=0.094 Sum_probs=36.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|... ....++|..+|++...|+.+...-+.+.|+
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57788888888776433 245788999999999999998766666554
No 246
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=30.99 E-value=1.3e+02 Score=23.02 Aligned_cols=32 Identities=13% Similarity=0.051 Sum_probs=26.1
Q ss_pred HHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 163 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 163 ~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
...++|+.+|++...|++....-|.+-|+.-+
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999999877777666543
No 247
>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=30.88 E-value=1.1e+02 Score=23.11 Aligned_cols=31 Identities=10% Similarity=-0.038 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 38 RRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 38 ~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
....++|..+|++...|+++...-|.+.++.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999986666655554
No 248
>PF13309 HTH_22: HTH domain
Probab=30.62 E-value=1.4e+02 Score=18.74 Aligned_cols=38 Identities=8% Similarity=0.093 Sum_probs=29.8
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHH
Q psy11996 20 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIW 57 (222)
Q Consensus 20 ~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~W 57 (222)
+.+.++...+++.-|--......+|..||++...|...
T Consensus 25 ~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~Y 62 (64)
T PF13309_consen 25 EKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRY 62 (64)
T ss_pred HHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHH
Confidence 45566667777777777778899999999999888754
No 249
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=30.58 E-value=1.1e+02 Score=17.47 Aligned_cols=38 Identities=16% Similarity=0.140 Sum_probs=24.3
Q ss_pred CHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 142 TRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 142 ~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
+..+..+|..... ++. ....+||..+|++..-|..-++
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 4556777766666 332 4567789999999987766553
No 250
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=30.58 E-value=1.5e+02 Score=22.65 Aligned_cols=31 Identities=6% Similarity=0.159 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|+++..|+.+...-|.+.++..
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 182 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQACL 182 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678899999999999999876666666543
No 251
>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=30.50 E-value=64 Score=18.02 Aligned_cols=22 Identities=18% Similarity=0.197 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChHHHHHHhhcc
Q psy11996 40 RIEIAHALCLTERQIKIWFQNR 61 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nr 61 (222)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999998765
No 252
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=30.41 E-value=1.4e+02 Score=24.36 Aligned_cols=49 Identities=16% Similarity=0.051 Sum_probs=37.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..+|...|... ....+||..+|++...|+.+...-+.+.++..
T Consensus 203 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLHD-----LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 56777788887777542 35778899999999999999987666666543
No 253
>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=30.39 E-value=64 Score=19.09 Aligned_cols=35 Identities=17% Similarity=0.095 Sum_probs=22.2
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
..+|...+..... ....+||+.++++.+-|..-..
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHHH
Confidence 4455554444443 3456789999999988876654
No 254
>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=30.39 E-value=47 Score=23.97 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=17.9
Q ss_pred HHHHHHHhCCChHHHHHHhh
Q psy11996 40 RIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~ 59 (222)
-++||..+|++...|..|..
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 47899999999999999973
No 255
>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=30.20 E-value=1.7e+02 Score=21.94 Aligned_cols=32 Identities=31% Similarity=0.218 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.+-..-|.+.+....
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988666666655443
No 256
>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=30.18 E-value=60 Score=20.74 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=19.7
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
..+||..+|++...|..|...++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56799999999999999986554
No 257
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=30.16 E-value=1.8e+02 Score=21.33 Aligned_cols=50 Identities=8% Similarity=-0.051 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|..+|++..-|+.....-+.+.+....
T Consensus 105 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 105 ELPPACRDSFLLRKLEG-----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 36667667666654332 246788999999999999998866666665533
No 258
>PRK06424 transcription factor; Provisional
Probab=30.06 E-value=66 Score=24.06 Aligned_cols=24 Identities=8% Similarity=0.068 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChHHHHHHhhcchh
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
.++||..+|++...|..|....+.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 678999999999999999977664
No 259
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=30.04 E-value=1.6e+02 Score=22.42 Aligned_cols=32 Identities=31% Similarity=0.247 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+..+..-|.+.++...
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988766666665443
No 260
>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=30.00 E-value=2e+02 Score=20.34 Aligned_cols=36 Identities=8% Similarity=0.091 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 19 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 19 ~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
-.-...+-++++... ...++|..++++..-|..||+
T Consensus 5 ~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 5 LDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 333344445555543 355678999999999999997
No 261
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=29.94 E-value=66 Score=23.96 Aligned_cols=23 Identities=30% Similarity=0.531 Sum_probs=17.8
Q ss_pred HHHHHHHHHHcCCChhhHHHHHh
Q psy11996 161 RRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 161 ~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
.....+||+++|++...+..|-+
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 45678899999999999999974
No 262
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=29.86 E-value=1.5e+02 Score=22.58 Aligned_cols=53 Identities=13% Similarity=-0.125 Sum_probs=38.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhccc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 197 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~ 197 (222)
.+++.+..++...|-.. ....++|+.+|++...|+.....-|.+.++......
T Consensus 111 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~~~~ 163 (182)
T PRK12540 111 KLPQDQREALILVGASG-----FSYEDAAAICGCAVGTIKSRVNRARSKLSALLYVDG 163 (182)
T ss_pred hCCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHhcc
Confidence 45666777766654332 346788999999999999999877777776655444
No 263
>PHA02955 hypothetical protein; Provisional
Probab=29.86 E-value=59 Score=25.95 Aligned_cols=43 Identities=12% Similarity=0.020 Sum_probs=33.5
Q ss_pred HHHHHHHHHHhhhC-CCCCHHHHHHHHHHhCCChHHHHHHhhcc
Q psy11996 19 RYQTLELEKEFHFN-RYLTRRRRIEIAHALCLTERQIKIWFQNR 61 (222)
Q Consensus 19 ~~q~~~L~~~f~~~-~~p~~~~~~~la~~~~l~~~~v~~WF~nr 61 (222)
..++..|-+.|.+. .-...+++.++++++|+....|..||.+.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 35677777777665 45678889999999999998888888654
No 264
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=29.86 E-value=1.1e+02 Score=24.25 Aligned_cols=52 Identities=19% Similarity=0.172 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|... +...-...++|..+|++...|+.+...-+.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56777888877766210 01223467889999999999999987666666654
No 265
>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=29.79 E-value=1.3e+02 Score=24.50 Aligned_cols=50 Identities=10% Similarity=0.122 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.++..+..++.-.|-.. ....++|..+|++..-|+.+...-|.+.++..+
T Consensus 161 ~Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 161 ALSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45566666665554433 246788999999999999999887776666543
No 266
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=29.78 E-value=1.6e+02 Score=21.79 Aligned_cols=30 Identities=13% Similarity=-0.010 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
..+++|..+|++...|+.+...-|.+.+..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999887666555543
No 267
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.65 E-value=1.4e+02 Score=22.86 Aligned_cols=50 Identities=12% Similarity=-0.049 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|..+|++..-|+++...-|.+.++...
T Consensus 111 ~Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46677777776654332 246778999999999999999766666666544
No 268
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=29.60 E-value=1.5e+02 Score=23.20 Aligned_cols=50 Identities=12% Similarity=0.133 Sum_probs=36.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....++|+.+|++...|+.....-|.+.|+..+
T Consensus 148 ~L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 148 GLPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666655433 246788999999999999999877777776544
No 269
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=29.40 E-value=1.7e+02 Score=22.48 Aligned_cols=48 Identities=21% Similarity=0.109 Sum_probs=33.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 193 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~ 193 (222)
.+++.+..++...|+ .....++|..+|++...|++-...-|.+.++..
T Consensus 155 ~L~~~~r~vl~l~~e------~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 155 LLSELEKEVLELYLD------GKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred hCCHHHHHHHHHHHc------cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345566666655332 245678899999999999998887777666643
No 270
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=29.07 E-value=1.8e+02 Score=21.63 Aligned_cols=31 Identities=16% Similarity=0.122 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
..+++|..+|++...|+.....-|.+.++..
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3677899999999999988765565555543
No 271
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.07 E-value=1.8e+02 Score=21.36 Aligned_cols=31 Identities=26% Similarity=0.278 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|..+...-+.+.++..
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998866666655543
No 272
>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=29.03 E-value=70 Score=24.53 Aligned_cols=33 Identities=15% Similarity=0.070 Sum_probs=27.3
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
....+||..+|++...|+++...-|.+.++...
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356788999999999999999877777776643
No 273
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=28.96 E-value=1.4e+02 Score=24.09 Aligned_cols=47 Identities=19% Similarity=0.183 Sum_probs=34.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-.. ....++|..+|++...|+.++..-+.+.|.
T Consensus 201 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 201 QLSEKEQLVISLFYKEE-----LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35677777777665322 346788999999999999999766666554
No 274
>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=28.81 E-value=45 Score=20.05 Aligned_cols=17 Identities=35% Similarity=0.434 Sum_probs=13.3
Q ss_pred HHHHHHHcCCChhhHHH
Q psy11996 164 RIEIAHALCLTERQIKI 180 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~ 180 (222)
-.+||+.+|++..||+-
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 45689999999999974
No 275
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=28.65 E-value=55 Score=20.34 Aligned_cols=20 Identities=15% Similarity=0.185 Sum_probs=17.1
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999963
No 276
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.62 E-value=1.3e+02 Score=22.09 Aligned_cols=29 Identities=28% Similarity=0.217 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|+.+...-|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45778999999999999887655555443
No 277
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=28.50 E-value=66 Score=20.11 Aligned_cols=18 Identities=22% Similarity=0.569 Sum_probs=15.5
Q ss_pred HHHHHHHhCCChHHHHHH
Q psy11996 40 RIEIAHALCLTERQIKIW 57 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~W 57 (222)
...||..+|++..-|..|
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 457999999999999999
No 278
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=28.20 E-value=64 Score=25.68 Aligned_cols=42 Identities=12% Similarity=0.052 Sum_probs=33.5
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 146 TLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 146 ~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
+..-...|....|- .....||...|++..-|..+|.++..-.
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 34444558888876 5788999999999999999999886643
No 279
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=27.98 E-value=1.6e+02 Score=23.51 Aligned_cols=30 Identities=13% Similarity=0.160 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|+.+...-+.+.++.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999988777776654
No 280
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=27.97 E-value=91 Score=22.26 Aligned_cols=35 Identities=17% Similarity=0.076 Sum_probs=25.1
Q ss_pred HHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHH
Q psy11996 144 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 180 (222)
Q Consensus 144 ~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~ 180 (222)
++...|...|. ..+......+||+.+.++.+.++.
T Consensus 4 ~~y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 4 EQYQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 45666777777 456667788999999988865543
No 281
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=27.97 E-value=1e+02 Score=23.47 Aligned_cols=37 Identities=16% Similarity=0.026 Sum_probs=31.4
Q ss_pred HHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHH
Q psy11996 143 RYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179 (222)
Q Consensus 143 ~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 179 (222)
..-+.+|...+....|.+...+..+|..||++...|.
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 4567788888888889999999999999999986553
No 282
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=27.88 E-value=1.3e+02 Score=25.63 Aligned_cols=55 Identities=11% Similarity=0.086 Sum_probs=41.4
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
..+++.+..+|...|.... ......++||..+|++...|+.+...-+.+.|+.-.
T Consensus 261 ~~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 261 FELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred HcCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3578889999987763322 233457888999999999999999877777776543
No 283
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=27.65 E-value=2e+02 Score=21.10 Aligned_cols=29 Identities=14% Similarity=0.287 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|+.....-+.+.++
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 36778999999999999886555555444
No 284
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=27.60 E-value=1.3e+02 Score=22.68 Aligned_cols=48 Identities=17% Similarity=0.023 Sum_probs=34.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.++..+..++...|-.. ....++|..+|++...|+.+...-|.+.+..
T Consensus 127 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE-----LSIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred hCCHHHhhHhHhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46677777765544322 2467889999999999999998666665553
No 285
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=27.44 E-value=88 Score=23.40 Aligned_cols=35 Identities=20% Similarity=0.130 Sum_probs=27.5
Q ss_pred CHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 36 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 36 ~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
.....+++|..+|++...|+..+..-|.+.++..+
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33457789999999999999999777777766544
No 286
>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=27.34 E-value=1.6e+02 Score=21.79 Aligned_cols=29 Identities=28% Similarity=0.293 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|+.+...-|.+.++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46778999999999999887655555544
No 287
>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=27.24 E-value=94 Score=23.05 Aligned_cols=26 Identities=19% Similarity=0.277 Sum_probs=21.8
Q ss_pred HHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 162 RRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 162 ~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
....++++.+|++..+|..|-...|.
T Consensus 47 ati~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 47 ATVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 45677899999999999999976554
No 288
>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=26.68 E-value=1.5e+02 Score=24.56 Aligned_cols=48 Identities=13% Similarity=0.055 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.|..++.-.|-.. ....++|..+|++...|+..+..-|.+.+..
T Consensus 108 ~L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 108 RLSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46777777776554333 2467889999999999999998777666653
No 289
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=26.48 E-value=1.7e+02 Score=25.01 Aligned_cols=54 Identities=11% Similarity=0.101 Sum_probs=37.0
Q ss_pred CCCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 16 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 16 ~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
.+++.+..+|...|.... ......+++|..+|++...|+.+...-+.+.++...
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 355566666665553322 223456889999999999999998777777776554
No 290
>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=26.36 E-value=1.1e+02 Score=22.65 Aligned_cols=26 Identities=19% Similarity=0.304 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMK 64 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k 64 (222)
...+++..+|++..+|..|...-|..
T Consensus 48 ti~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 48 TVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 46778999999999999999777654
No 291
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=26.27 E-value=1.4e+02 Score=22.58 Aligned_cols=35 Identities=20% Similarity=0.078 Sum_probs=27.7
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHH
Q psy11996 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179 (222)
Q Consensus 145 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 179 (222)
-+.+|...=....|.+.+....+|+.+|++..+|.
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 45556555566779999999999999999987664
No 292
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=26.23 E-value=2.4e+02 Score=21.43 Aligned_cols=35 Identities=17% Similarity=0.207 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhhhhc
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMAS 73 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~~~ 73 (222)
...++|..+|++..-|++....-|.+.++......
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35778999999999999998777777766554443
No 293
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=26.22 E-value=2.1e+02 Score=21.51 Aligned_cols=32 Identities=19% Similarity=0.208 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-+.+.++...
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46678999999999999988777777776543
No 294
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.06 E-value=50 Score=22.56 Aligned_cols=38 Identities=18% Similarity=0.184 Sum_probs=24.9
Q ss_pred CCHHHHH----HHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHH
Q psy11996 141 YTRYQTL----ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWF 182 (222)
Q Consensus 141 ~~~~q~~----~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF 182 (222)
++++|.. .|.+.|.... -..+.+|..||++...|..=+
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~----ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSG----LSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHH
Confidence 4555554 4555565554 456778999998888776554
No 295
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=26.04 E-value=1.8e+02 Score=22.26 Aligned_cols=31 Identities=10% Similarity=0.012 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
..+++|..+|++...|+.+...-|.+.++..
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999999876666666543
No 296
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=26.02 E-value=1.8e+02 Score=22.38 Aligned_cols=32 Identities=13% Similarity=0.011 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.+...-|.+.++...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 46778999999999999999877777766543
No 297
>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=26.00 E-value=1.8e+02 Score=21.36 Aligned_cols=30 Identities=13% Similarity=0.200 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|+.+-..-|.+.++.
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999999876666665553
No 298
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=1.8e+02 Score=21.96 Aligned_cols=29 Identities=21% Similarity=0.332 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|+.+-..-+.+.+.
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 46778999999999999887655544443
No 299
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=25.80 E-value=1.7e+02 Score=24.09 Aligned_cols=47 Identities=9% Similarity=0.140 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..+|...|... ....+||..+|++...|+.+...-+.+.++
T Consensus 215 ~L~~rer~vl~l~y~~~-----~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFFES-----MTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57788888888877432 346888999999999999998766666554
No 300
>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=25.79 E-value=70 Score=17.92 Aligned_cols=13 Identities=31% Similarity=0.360 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHHH
Q psy11996 16 SYTRYQTLELEKE 28 (222)
Q Consensus 16 ~~t~~q~~~L~~~ 28 (222)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 6899999999865
No 301
>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=25.74 E-value=1.9e+02 Score=21.22 Aligned_cols=28 Identities=29% Similarity=0.145 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWK 66 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~ 66 (222)
...++|..+|++...|+....--|.+.+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4577888999999999887644444433
No 302
>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=25.45 E-value=60 Score=23.44 Aligned_cols=20 Identities=20% Similarity=0.380 Sum_probs=17.9
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
-++||+.+|++..-|..|-.
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 46899999999999999984
No 303
>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=25.40 E-value=66 Score=21.55 Aligned_cols=19 Identities=21% Similarity=0.392 Sum_probs=16.8
Q ss_pred HHHHHHHcCCChhhHHHHH
Q psy11996 164 RIEIAHALCLTERQIKIWF 182 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF 182 (222)
+.++|+.+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4678999999999999993
No 304
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.39 E-value=83 Score=22.60 Aligned_cols=25 Identities=4% Similarity=0.080 Sum_probs=20.7
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhhh
Q psy11996 161 RRRRIEIAHALCLTERQIKIWFQNR 185 (222)
Q Consensus 161 ~~~~~~la~~l~l~~~~V~~WF~nr 185 (222)
....+.||+.+|++...+..+|+..
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3567888999999999999999653
No 305
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.22 E-value=90 Score=17.15 Aligned_cols=23 Identities=17% Similarity=0.239 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
...||..+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55789999999999999986553
No 306
>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=25.12 E-value=98 Score=22.47 Aligned_cols=32 Identities=28% Similarity=0.194 Sum_probs=25.4
Q ss_pred CHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 160 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 160 ~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
......++|..+|++...|+++...-|.+.++
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44567889999999999999999766655554
No 307
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=25.04 E-value=2.7e+02 Score=21.34 Aligned_cols=33 Identities=24% Similarity=0.136 Sum_probs=25.1
Q ss_pred HHHHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 37 RRRRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 37 ~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
.....++|..+|++...|++....-|.+.++..
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345677899999999999988876666666543
No 308
>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=24.87 E-value=83 Score=18.06 Aligned_cols=24 Identities=13% Similarity=0.214 Sum_probs=20.6
Q ss_pred HHHHHHHHhCCChHHHHHHhhcch
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
....++...|++..-+...|.|+-
T Consensus 18 s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 18 SIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp SHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred CHHHHHHHHccchhhHHHHcCCHH
Confidence 367789999999999999998764
No 309
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.79 E-value=1.8e+02 Score=23.36 Aligned_cols=32 Identities=16% Similarity=0.153 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45778999999999999998777777666543
No 310
>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=24.72 E-value=1.9e+02 Score=22.74 Aligned_cols=45 Identities=16% Similarity=0.164 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 66 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~ 66 (222)
+++.+..++...|.. .....++|..+|++...|..|...-+.+.+
T Consensus 179 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 179 LPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 455555555554432 224678899999999999998754444443
No 311
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=24.50 E-value=2.2e+02 Score=18.91 Aligned_cols=60 Identities=15% Similarity=0.012 Sum_probs=39.9
Q ss_pred CCHHHHHHHHHh---hhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhcccCCCCCCCCCCCCCCC
Q psy11996 141 YTRYQTLELEKE---FHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKMASMNVIPYHYHMSQPYG 212 (222)
Q Consensus 141 ~~~~q~~~L~~~---F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~~~~~~~~~~~~~~~~~~ 212 (222)
+|..|..+|... |....-|-. -..||+.++++..-|++=. ..+.+++.+...+|++-.+.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVg--Sk~ia~~l~~s~aTIRN~M----------~~Le~lGlve~~p~~s~Gri 64 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVG--SKTIAEELGRSPATIRNEM----------ADLEELGLVESQPHPSGGRI 64 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcC--HHHHHHHHCCChHHHHHHH----------HHHHHCCCccCCCCCCCCCC
Confidence 466777777665 666665544 2446778999988777644 45677777776667665554
No 312
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.21 E-value=2.1e+02 Score=23.44 Aligned_cols=48 Identities=15% Similarity=0.111 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..+|...|... ....++|..+|++...|+.....-+.+.|+.
T Consensus 212 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 212 TLPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46777777777766433 3467889999999999998887666666654
No 313
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=24.19 E-value=2.2e+02 Score=21.47 Aligned_cols=29 Identities=21% Similarity=0.129 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
...++|..+|++...|+.+...-|.+.+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678889999999999887655555444
No 314
>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=24.19 E-value=1.6e+02 Score=24.10 Aligned_cols=50 Identities=16% Similarity=0.096 Sum_probs=38.0
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.++..+..+|...|-.. ......++|..+|++...|+....+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888998887431 123567899999999999999888776666653
No 315
>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=24.18 E-value=1.8e+02 Score=23.33 Aligned_cols=52 Identities=12% Similarity=0.078 Sum_probs=39.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..+|...|....+ ......++|..+|++...|+.....-..|.|..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 5788888899888743222 223578889999999999999998777666654
No 316
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=24.16 E-value=97 Score=23.60 Aligned_cols=39 Identities=10% Similarity=0.020 Sum_probs=30.4
Q ss_pred HHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 148 ELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 148 ~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
.....|....| ....+..||...|+++.-|..+|.++..
T Consensus 16 aA~~lf~e~G~-~~tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 16 AAMRVALAEGF-AAMTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHhcCh-hhccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 33445777666 4456888999999999999999998755
No 317
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=24.15 E-value=2e+02 Score=23.27 Aligned_cols=47 Identities=9% Similarity=0.064 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
+++.+..+|.-.|-. .....++|..+|++...|..|...-+.+.+..
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444455444322 22457889999999999999976666555543
No 318
>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=23.98 E-value=1.9e+02 Score=23.31 Aligned_cols=46 Identities=13% Similarity=0.109 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
+++.+..+|.-.|... ....++|..+|++...|+.+...-+.+.+.
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455555555554322 235788999999999999988665655554
No 319
>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=23.93 E-value=80 Score=21.60 Aligned_cols=20 Identities=35% Similarity=0.416 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
+.++|+.+|++...|+.|..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 320
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=23.92 E-value=1.9e+02 Score=23.25 Aligned_cols=51 Identities=20% Similarity=0.109 Sum_probs=35.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
.++..+..++.-.|-.. -...+||+.+|++..-|+.+...-|.+.++....
T Consensus 116 ~Lp~~~R~v~lL~~~eg-----~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 116 SLNVQQSAILLLKDVFQ-----YSIADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred hCCHHHhhHhhhHHhhC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 35555555555543322 2467789999999999999998777777766543
No 321
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=23.91 E-value=2.5e+02 Score=21.65 Aligned_cols=32 Identities=16% Similarity=0.190 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++...
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988777777666554
No 322
>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=23.77 E-value=1.1e+02 Score=18.85 Aligned_cols=20 Identities=20% Similarity=0.086 Sum_probs=14.8
Q ss_pred HHHHHHHHHHhCCChHHHHH
Q psy11996 37 RRRRIEIAHALCLTERQIKI 56 (222)
Q Consensus 37 ~~~~~~la~~~~l~~~~v~~ 56 (222)
..+...++.++|+++.+++.
T Consensus 20 ~~ev~ywa~~~gvt~~~L~~ 39 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLRE 39 (57)
T ss_pred HHHHHHHHHHHCcCHHHHHH
Confidence 45677788888888887753
No 323
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=23.70 E-value=1.6e+02 Score=22.09 Aligned_cols=35 Identities=9% Similarity=0.032 Sum_probs=27.5
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHH
Q psy11996 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179 (222)
Q Consensus 145 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 179 (222)
-+.+|...=....|.+.+....+|+.+|++..+|.
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 45555555566789999999999999999987664
No 324
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=23.60 E-value=1.7e+02 Score=22.38 Aligned_cols=47 Identities=23% Similarity=0.242 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
+.+.+..+++-.|-.. ...++||..+|++..-|+..+..-|.+.++.
T Consensus 136 l~~~~~~~v~l~~~~G-----ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 136 LDPRQRRVVELRFFEG-----LSVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred cCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3445555555443222 3567889999999999999888777655543
No 325
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=23.55 E-value=2e+02 Score=21.93 Aligned_cols=30 Identities=33% Similarity=0.327 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|......-|.+.++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 367789999999999998876555555543
No 326
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=2.2e+02 Score=21.50 Aligned_cols=47 Identities=15% Similarity=0.092 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|-. ....+++|..+|++...|++--..-|.+.+.
T Consensus 137 ~L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 137 ELEPPRSELIRTAFFE-----GITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 4566666666665532 2356788999999999998887755555544
No 327
>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=23.52 E-value=75 Score=21.32 Aligned_cols=20 Identities=5% Similarity=0.071 Sum_probs=17.6
Q ss_pred HHHHHHHcCCChhhHHHHHh
Q psy11996 164 RIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~ 183 (222)
+.++|..+|++...|+.|-.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56789999999999999964
No 328
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=23.44 E-value=2e+02 Score=22.88 Aligned_cols=52 Identities=17% Similarity=0.130 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..++...|--.. .......++|..+|++...|+++-..-+.+.++.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 567777777777652110 1223577889999999999999865445455544
No 329
>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=23.39 E-value=1.6e+02 Score=21.83 Aligned_cols=35 Identities=11% Similarity=0.004 Sum_probs=26.5
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHH
Q psy11996 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179 (222)
Q Consensus 145 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 179 (222)
-+.+|...=....|.+.+....+|+.+|++..+|.
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34455544455679999999999999999987654
No 330
>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=23.38 E-value=2.5e+02 Score=19.16 Aligned_cols=20 Identities=15% Similarity=0.149 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChHHHHHHhh
Q psy11996 40 RIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~ 59 (222)
..++|+.+|++...|+.|..
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDE 22 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 331
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=23.21 E-value=2.9e+02 Score=21.12 Aligned_cols=32 Identities=16% Similarity=0.023 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998776766666544
No 332
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=23.20 E-value=1.8e+02 Score=24.04 Aligned_cols=48 Identities=13% Similarity=0.001 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.|..++.-.+-.. ....++|+.+|++..-|+.....-|.+.++.
T Consensus 115 ~L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 115 RLSPLERAAFLLHDVFG-----VPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 46666666665554332 2467889999999999999998777666664
No 333
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.08 E-value=1.2e+02 Score=24.17 Aligned_cols=50 Identities=16% Similarity=0.080 Sum_probs=35.4
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
++..+..++...| .......++|+.+|++...|++....-|.+.|+....
T Consensus 150 L~~~~r~i~~l~~-----~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 150 LPDAFRAVFVLRV-----VEELSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred CCHHHhhhheeeh-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555554322 3334678889999999999999998777777776543
No 334
>PRK10403 transcriptional regulator NarP; Provisional
Probab=22.88 E-value=1.4e+02 Score=22.26 Aligned_cols=45 Identities=20% Similarity=0.145 Sum_probs=34.5
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
..+|..+..+|...... ....+||+.++++.+-|+...++=+.|-
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 35899999998865543 3356789999999999999988766554
No 335
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=22.73 E-value=2.4e+02 Score=21.23 Aligned_cols=30 Identities=17% Similarity=0.118 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|++....-|.+.++.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999887666666553
No 336
>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=22.70 E-value=1.4e+02 Score=17.69 Aligned_cols=39 Identities=15% Similarity=0.092 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
+|..|..+|...+.... ....+||..++++..-|..+-.
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 46788889988887655 3445889999999887777653
No 337
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=22.68 E-value=2.1e+02 Score=20.18 Aligned_cols=41 Identities=12% Similarity=0.273 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRM 187 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~ 187 (222)
.+++.++..+++.+.-. ...+|.-||++..-|+.|=++|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37888888888877655 356799999999999999988763
No 338
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=22.58 E-value=2.6e+02 Score=20.76 Aligned_cols=30 Identities=10% Similarity=0.168 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
.-+++|..+|++...|+.....-|.+.++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999886666555554
No 339
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=22.55 E-value=2.4e+02 Score=21.53 Aligned_cols=48 Identities=15% Similarity=0.002 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..+|...|-.. ....+||..+|++...|++=...-|.+.++.
T Consensus 134 ~Lp~~~r~i~~l~~~~g-----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 134 RLPVEQRAALVAVDMQG-----YSVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35677777776554333 2467789999999998877665445555544
No 340
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=22.54 E-value=2.4e+02 Score=21.40 Aligned_cols=32 Identities=13% Similarity=0.051 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++..+
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46788999999999999988766666666543
No 341
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.48 E-value=1.5e+02 Score=22.07 Aligned_cols=45 Identities=22% Similarity=0.104 Sum_probs=34.9
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
..+|+.+..+|+..... ...+.||..++++.+.|++..++=+.|-
T Consensus 136 ~~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 136 DPLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred cCCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 35888888888876653 2577889999999999999887766553
No 342
>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=22.45 E-value=69 Score=24.48 Aligned_cols=31 Identities=13% Similarity=0.291 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...+|+.-++++..+|-.|..|-+...+...
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 5788999999999999999999988776643
No 343
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=22.33 E-value=69 Score=26.41 Aligned_cols=27 Identities=30% Similarity=0.526 Sum_probs=22.0
Q ss_pred HHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 161 RRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 161 ~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
.-....||++|||+..+|+.|=+ |..|
T Consensus 19 gmk~~dIAeklGvspntiksWKr--r~gW 45 (279)
T COG5484 19 GMKLKDIAEKLGVSPNTIKSWKR--RDGW 45 (279)
T ss_pred hccHHHHHHHhCCChHHHHHHHH--hcCC
Confidence 34567899999999999999974 6666
No 344
>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=22.30 E-value=1.3e+02 Score=22.19 Aligned_cols=36 Identities=19% Similarity=0.077 Sum_probs=25.2
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHH
Q psy11996 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKI 180 (222)
Q Consensus 145 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~ 180 (222)
-+.+|...=....|.+.+....+|+.+||+..+|.-
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~ 50 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVYG 50 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHH
Confidence 345565555567799999999999999999877653
No 345
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=21.96 E-value=1.8e+02 Score=22.29 Aligned_cols=35 Identities=23% Similarity=0.182 Sum_probs=26.3
Q ss_pred HHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHH
Q psy11996 145 QTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 179 (222)
Q Consensus 145 q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~ 179 (222)
-+.+|...=....|.+.+..+.+|+.+|++..+|.
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 34445444455679999999999999999986654
No 346
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.89 E-value=2.2e+02 Score=17.94 Aligned_cols=40 Identities=10% Similarity=0.005 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHhhhCCCCCHHHHHH-HHHHhCC----ChHHHHHH
Q psy11996 18 TRYQTLELEKEFHFNRYLTRRRRIE-IAHALCL----TERQIKIW 57 (222)
Q Consensus 18 t~~q~~~L~~~f~~~~~p~~~~~~~-la~~~~l----~~~~v~~W 57 (222)
++++...|.+.+..++..+..+... |...+|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 6778799999999888666666555 5666563 55555543
No 347
>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=21.79 E-value=2.4e+02 Score=22.24 Aligned_cols=46 Identities=20% Similarity=0.146 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 17 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 17 ~t~~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
+++.+..+|...|-.. ....++|..+|++...|+.+...-+.+.++
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3444455555444222 246788999999999999887555544443
No 348
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=21.79 E-value=1.7e+02 Score=19.04 Aligned_cols=34 Identities=12% Similarity=0.164 Sum_probs=27.1
Q ss_pred CcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHcC
Q psy11996 139 TSYTRYQTLELEKEFH---FNRYLTRRRRIEIAHALC 172 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~---~~~~p~~~~~~~la~~l~ 172 (222)
..|+..+...|...|. .....+..+...+|.+||
T Consensus 31 ~~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG 67 (71)
T PF06569_consen 31 EDFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELG 67 (71)
T ss_pred HhCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 4577777777777774 566788999999999997
No 349
>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=21.77 E-value=2.3e+02 Score=22.42 Aligned_cols=46 Identities=11% Similarity=0.127 Sum_probs=33.4
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
..++..+..++...|... ....++|..+|++...|..+-..-..+.
T Consensus 182 ~~L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~~L 227 (231)
T TIGR02885 182 SKLDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEKKVLKKM 227 (231)
T ss_pred HcCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 357788888887776433 3578889999999999888765444333
No 350
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=21.71 E-value=1.9e+02 Score=21.82 Aligned_cols=50 Identities=16% Similarity=0.102 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhhc
Q psy11996 141 YTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 195 (222)
Q Consensus 141 ~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~~ 195 (222)
+++.+..++.-.+-.. ....++|..+|++..-|+.+...-|.+.+.....
T Consensus 128 Lp~~~R~~~~l~~~~g-----ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~~ 177 (182)
T COG1595 128 LPPRQREAFLLRYLEG-----LSYEEIAEILGISVGTVKSRLHRARKKLREQLEE 177 (182)
T ss_pred CCHHHhHHhhhHhhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHhh
Confidence 4444444444333222 3467789999999999999998888777776543
No 351
>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=21.68 E-value=88 Score=23.00 Aligned_cols=21 Identities=19% Similarity=0.227 Sum_probs=18.5
Q ss_pred HHHHHHHcCCChhhHHHHHhh
Q psy11996 164 RIEIAHALCLTERQIKIWFQN 184 (222)
Q Consensus 164 ~~~la~~l~l~~~~V~~WF~n 184 (222)
+.++|+.+|++...|+.|.+.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 567899999999999999964
No 352
>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=21.53 E-value=1.1e+02 Score=18.58 Aligned_cols=24 Identities=17% Similarity=0.257 Sum_probs=19.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcch
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR 62 (222)
....+|..+|++...|..|-.+++
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 467789999999999999987766
No 353
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=21.51 E-value=3e+02 Score=21.42 Aligned_cols=31 Identities=16% Similarity=0.153 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEH 69 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~ 69 (222)
...++|..+|++...|+.+...-|.+.++..
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999876666666543
No 354
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.45 E-value=2.3e+02 Score=22.41 Aligned_cols=45 Identities=24% Similarity=0.102 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 190 (222)
.+|+.+.++|....... ...++|..++++...|+.+..+-..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 48999999998776632 3567899999999999999977655443
No 355
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=2.5e+02 Score=21.23 Aligned_cols=30 Identities=13% Similarity=0.037 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++...|+.+...-+.+.++.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999886666555543
No 356
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=21.39 E-value=2.2e+02 Score=21.45 Aligned_cols=36 Identities=19% Similarity=0.056 Sum_probs=28.4
Q ss_pred HHHHHHHHHhhhCCCCCHHHHHHHHHHhCCChHHHH
Q psy11996 20 YQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIK 55 (222)
Q Consensus 20 ~q~~~L~~~f~~~~~p~~~~~~~la~~~~l~~~~v~ 55 (222)
.-+..|...=+...|.+.+....+|..+|++..+|.
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 345555555566679999999999999999998876
No 357
>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=21.30 E-value=2.1e+02 Score=17.56 Aligned_cols=51 Identities=18% Similarity=0.102 Sum_probs=28.0
Q ss_pred CCCCCCHHHHHHHHHHhhhCCCCCH---HHHHHHHHHhCCChHHHHHHhhcchh
Q psy11996 13 QRTSYTRYQTLELEKEFHFNRYLTR---RRRIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 13 ~R~~~t~~q~~~L~~~f~~~~~p~~---~~~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
+|...|++.-......+..--..+- ....++....+|+..||..-.|..|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 4667777755444444433333232 33333333456788998877665443
No 358
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=21.30 E-value=2.5e+02 Score=22.77 Aligned_cols=31 Identities=16% Similarity=0.063 Sum_probs=24.2
Q ss_pred HHHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 38 RRRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 38 ~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
....++|..+|++...|..+...-+.+.+..
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3567889999999999999886666665554
No 359
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=21.28 E-value=1.4e+02 Score=21.88 Aligned_cols=44 Identities=14% Similarity=0.160 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHh-hhCCCCCHHHHHHHHHHhCCChHHHHHHhh
Q psy11996 16 SYTRYQTLELEKEF-HFNRYLTRRRRIEIAHALCLTERQIKIWFQ 59 (222)
Q Consensus 16 ~~t~~q~~~L~~~f-~~~~~p~~~~~~~la~~~~l~~~~v~~WF~ 59 (222)
.||++|...|...- +.-.--......+|+..+|++...|+..|.
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 68999998887763 222222345677889999999999998874
No 360
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=21.26 E-value=1.4e+02 Score=22.87 Aligned_cols=35 Identities=17% Similarity=0.061 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 36 TRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 36 ~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
......++|..+|++...|+.+...-|.+.++...
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33457788999999999999887766666666543
No 361
>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=21.17 E-value=93 Score=17.74 Aligned_cols=18 Identities=28% Similarity=0.385 Sum_probs=13.3
Q ss_pred HHHHHHHHhCCChHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKI 56 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~ 56 (222)
--.+||+.+||++..|..
T Consensus 19 s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 19 SYAELAEELGLSESTVRR 36 (42)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred cHHHHHHHHCcCHHHHHH
Confidence 356789999999998763
No 362
>PRK05572 sporulation sigma factor SigF; Validated
Probab=21.08 E-value=2.4e+02 Score=22.74 Aligned_cols=48 Identities=13% Similarity=0.142 Sum_probs=36.1
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
..+++.+..++...|... ....+||..+|++...|..+-..-..+.++
T Consensus 201 ~~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 201 RELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred HcCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 457888888888877433 456788999999999998887655555543
No 363
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.03 E-value=2.4e+02 Score=21.02 Aligned_cols=44 Identities=20% Similarity=0.043 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKW 189 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~ 189 (222)
.+|+.+..+|+...... ...++|.+++++...|++..++=+.|-
T Consensus 155 ~Lt~rE~~vl~~l~~g~------~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERDILKLIAQGL------PNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 48999999998755331 356678999999999999998766654
No 364
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=20.99 E-value=2.2e+02 Score=20.85 Aligned_cols=41 Identities=17% Similarity=0.256 Sum_probs=28.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQ 183 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~ 183 (222)
.++.+...+++..|..-...+. ..+|.++++++++++.|+.
T Consensus 81 ~l~de~k~Ii~lry~~r~~~TW---~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 81 TLIDEEKRIIKLRYDRRSRRTW---YQIAQKLHISERTARRWRD 121 (130)
T ss_pred hhCHHHHHHHHHHHcccccchH---HHHHHHhCccHHHHHHHHH
Confidence 3555666666666665543433 4568899999999999975
No 365
>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=20.92 E-value=2.9e+02 Score=22.34 Aligned_cols=33 Identities=9% Similarity=0.173 Sum_probs=26.7
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHKM 71 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~~ 71 (222)
...++|..+|++...|+.+...-|.+.++....
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~ 211 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRR 211 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 467889999999999999998877777765443
No 366
>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=20.89 E-value=2e+02 Score=24.04 Aligned_cols=50 Identities=16% Similarity=0.019 Sum_probs=34.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHhhh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 194 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~~~ 194 (222)
.+++.+..++...|-.. ....+||..||++..-|+.....-|.+.|+..+
T Consensus 142 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG-----WRAAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred hCCHHHhhHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 45566666665543322 236778999999999999999876666666544
No 367
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=20.75 E-value=3.8e+02 Score=20.29 Aligned_cols=32 Identities=16% Similarity=-0.063 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHHhh
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKEHK 70 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~~~ 70 (222)
...++|..+|++...|+.....-|.+.++...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46778999999999999988766666666544
No 368
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.72 E-value=2.5e+02 Score=22.86 Aligned_cols=48 Identities=10% Similarity=0.068 Sum_probs=35.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
.+++.+..+|...|... ....+||..+|++...|+.+...-+.+.|+.
T Consensus 205 ~L~~~er~vi~l~y~e~-----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYYEE-----LVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46777777777776432 3567889999999999999987666655554
No 369
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=20.69 E-value=2.8e+02 Score=20.84 Aligned_cols=28 Identities=18% Similarity=0.272 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWK 66 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~ 66 (222)
..+++|..+|+++..|+.....-+.+..
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3677899999999999988765554443
No 370
>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=20.67 E-value=2.8e+02 Score=18.78 Aligned_cols=19 Identities=16% Similarity=0.235 Sum_probs=16.6
Q ss_pred HHHHHHHhCCChHHHHHHh
Q psy11996 40 RIEIAHALCLTERQIKIWF 58 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF 58 (222)
..++|+.+|++.+.|+.|=
T Consensus 3 I~eva~~~gvs~~tlR~Ye 21 (95)
T cd04780 3 MSELSKRSGVSVATIKYYL 21 (95)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999994
No 371
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=20.59 E-value=3e+02 Score=20.48 Aligned_cols=30 Identities=13% Similarity=0.171 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
...++|..+|++..-|+.+...-+.+.+..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999886655555443
No 372
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=20.55 E-value=1e+02 Score=22.28 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChHHHHHHhhcchh
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRRM 63 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR~ 63 (222)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 568999999999999999987653
No 373
>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=20.49 E-value=2.7e+02 Score=20.88 Aligned_cols=47 Identities=6% Similarity=0.002 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 140 SYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 140 ~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
.+++.+..++...|- ......++|..+|++...|+.=...-|.+.++
T Consensus 140 ~L~~~~r~vi~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777776543 23356788999999999998877666655554
No 374
>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=20.39 E-value=3e+02 Score=21.76 Aligned_cols=52 Identities=17% Similarity=0.158 Sum_probs=34.1
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHH
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 191 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 191 (222)
..+++.+..++...|-...+ .....+++|+.+|++...|..+...-+.+.++
T Consensus 173 ~~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45777888888776631100 12346778999999999998886544544443
No 375
>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=20.38 E-value=79 Score=19.85 Aligned_cols=20 Identities=20% Similarity=0.434 Sum_probs=14.9
Q ss_pred HHHHHHHhCCChHHHH-HHhh
Q psy11996 40 RIEIAHALCLTERQIK-IWFQ 59 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~-~WF~ 59 (222)
..+||..+|++..-|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4578999999999999 8874
No 376
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=20.37 E-value=1.1e+02 Score=22.00 Aligned_cols=23 Identities=4% Similarity=0.007 Sum_probs=20.7
Q ss_pred HHHHHHHhCCChHHHHHHhhcch
Q psy11996 40 RIEIAHALCLTERQIKIWFQNRR 62 (222)
Q Consensus 40 ~~~la~~~~l~~~~v~~WF~nrR 62 (222)
+++||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 67899999999999999998775
No 377
>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=20.28 E-value=1.3e+02 Score=21.87 Aligned_cols=33 Identities=27% Similarity=0.208 Sum_probs=24.3
Q ss_pred CCHHHHHHHHHHhCCChHHHHHHhhcchhHHHH
Q psy11996 35 LTRRRRIEIAHALCLTERQIKIWFQNRRMKWKK 67 (222)
Q Consensus 35 p~~~~~~~la~~~~l~~~~v~~WF~nrR~k~~~ 67 (222)
......+++|..+|+++..|.++..--|.+.++
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344567889999999999999887655544443
No 378
>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=20.10 E-value=3.4e+02 Score=21.57 Aligned_cols=53 Identities=19% Similarity=0.162 Sum_probs=35.7
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHHHh
Q psy11996 139 TSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWKKE 192 (222)
Q Consensus 139 ~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk~ 192 (222)
..+++.+..++...|-... .......++|+.+|++...|+++...-+.+.|+.
T Consensus 177 ~~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 177 AKLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred HhCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3567777777776652100 1123467789999999999999987666666654
No 379
>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=20.07 E-value=2.6e+02 Score=22.85 Aligned_cols=47 Identities=19% Similarity=0.005 Sum_probs=36.3
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHcCCChhhHHHHHhhhhhhHH
Q psy11996 138 RTSYTRYQTLELEKEFHFNRYLTRRRRIEIAHALCLTERQIKIWFQNRRMKWK 190 (222)
Q Consensus 138 r~~~~~~q~~~L~~~F~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~k 190 (222)
...+|+.+.++|.-.... ....++|..||++..-|+.+..+=+.|..
T Consensus 188 ~~~LT~RE~evl~l~a~G------~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 188 AGLITAREAEILAWVRDG------KTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred ccCCCHHHHHHHHHHHCC------CCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 346899999999865432 24567899999999999999987766544
No 380
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=20.03 E-value=3.3e+02 Score=20.77 Aligned_cols=30 Identities=10% Similarity=0.085 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChHHHHHHhhcchhHHHHH
Q psy11996 39 RRIEIAHALCLTERQIKIWFQNRRMKWKKE 68 (222)
Q Consensus 39 ~~~~la~~~~l~~~~v~~WF~nrR~k~~~~ 68 (222)
.-+++|..+|++...|+.-...-|.+.++.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999988776555555543
Done!