Query psy2704
Match_columns 256
No_of_seqs 315 out of 1464
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 23:05:02 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy2704.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/2704hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 3.8E-21 8.2E-26 149.3 7.5 70 109-178 12-81 (125)
2 KOG2251|consensus 99.8 3.8E-20 8.3E-25 160.8 10.8 68 109-176 32-99 (228)
3 KOG0488|consensus 99.8 3.5E-19 7.6E-24 164.3 14.3 72 108-179 166-237 (309)
4 KOG0489|consensus 99.8 8.8E-20 1.9E-24 164.9 7.8 68 112-179 157-224 (261)
5 KOG0842|consensus 99.8 3.7E-19 8.1E-24 162.7 11.7 78 108-185 147-224 (307)
6 KOG0850|consensus 99.8 1E-18 2.2E-23 152.7 11.0 71 107-177 115-185 (245)
7 KOG0487|consensus 99.8 2.2E-18 4.8E-23 157.7 10.3 73 107-179 228-300 (308)
8 KOG0491|consensus 99.8 2E-18 4.3E-23 144.1 8.5 138 39-176 22-162 (194)
9 KOG0494|consensus 99.7 2.5E-18 5.4E-23 152.5 7.4 66 113-178 140-205 (332)
10 KOG0848|consensus 99.7 3.7E-18 8.1E-23 151.9 5.2 68 110-177 195-262 (317)
11 KOG0843|consensus 99.7 9.3E-18 2E-22 141.9 5.7 65 112-176 100-164 (197)
12 KOG0485|consensus 99.7 5.3E-17 1.1E-21 140.9 8.7 67 110-176 100-166 (268)
13 PF00046 Homeobox: Homeobox do 99.7 6.1E-17 1.3E-21 113.1 6.1 57 115-171 1-57 (57)
14 KOG0492|consensus 99.7 1.3E-16 2.7E-21 137.7 7.1 68 112-179 142-209 (246)
15 KOG0844|consensus 99.6 3.2E-16 6.9E-21 141.9 4.8 67 109-175 176-242 (408)
16 KOG0486|consensus 99.6 3.8E-16 8.2E-21 141.8 5.1 66 112-177 110-175 (351)
17 KOG0493|consensus 99.6 2E-15 4.3E-20 134.3 6.0 60 115-174 247-306 (342)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 2.7E-15 5.9E-20 106.1 4.3 53 114-166 1-57 (58)
19 cd00086 homeodomain Homeodomai 99.6 8.5E-15 1.9E-19 102.1 6.1 57 116-172 2-58 (59)
20 smart00389 HOX Homeodomain. DN 99.5 7.1E-15 1.5E-19 101.8 5.3 56 115-170 1-56 (56)
21 KOG3802|consensus 99.5 2E-15 4.4E-20 141.2 3.3 63 112-174 292-354 (398)
22 COG5576 Homeodomain-containing 99.5 3.7E-14 8.1E-19 119.1 6.0 68 110-177 47-114 (156)
23 KOG0483|consensus 99.5 2.3E-14 4.9E-19 124.5 4.0 56 118-173 54-109 (198)
24 KOG0847|consensus 99.4 1.7E-13 3.7E-18 119.4 3.3 65 111-175 164-228 (288)
25 KOG4577|consensus 99.4 1.5E-12 3.2E-17 117.5 8.3 67 110-176 163-229 (383)
26 KOG0490|consensus 99.4 2.9E-13 6.3E-18 118.3 3.3 64 111-174 57-120 (235)
27 KOG0849|consensus 99.2 3E-11 6.5E-16 113.8 9.9 68 108-175 170-237 (354)
28 KOG1168|consensus 99.1 4.5E-11 9.7E-16 108.0 2.1 63 112-174 307-369 (385)
29 KOG0775|consensus 99.0 2.1E-09 4.5E-14 96.6 9.8 52 121-172 183-234 (304)
30 KOG0774|consensus 99.0 1.5E-09 3.2E-14 97.0 7.5 63 114-176 188-253 (334)
31 PF05920 Homeobox_KN: Homeobox 98.4 1.8E-07 3.9E-12 61.4 2.9 34 135-168 7-40 (40)
32 KOG2252|consensus 98.2 1.9E-06 4.1E-11 84.1 5.6 57 113-169 419-475 (558)
33 KOG0490|consensus 98.2 1.5E-06 3.2E-11 75.9 4.4 66 109-174 148-213 (235)
34 KOG1146|consensus 97.7 6E-05 1.3E-09 80.0 6.9 64 111-174 900-963 (1406)
35 PF11569 Homez: Homeodomain le 97.0 0.00055 1.2E-08 48.1 2.7 43 126-168 10-52 (56)
36 KOG0773|consensus 96.4 0.0024 5.3E-08 59.7 3.1 60 114-173 239-301 (342)
37 KOG3623|consensus 95.9 0.0092 2E-07 60.7 4.5 49 126-174 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.1 0.055 1.2E-06 37.3 4.9 47 115-166 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 86.3 1.8 3.9E-05 28.8 4.6 46 120-170 4-49 (50)
40 cd06171 Sigma70_r4 Sigma70, re 81.1 2.9 6.2E-05 26.7 3.8 44 120-168 10-53 (55)
41 PRK03975 tfx putative transcri 79.9 4.7 0.0001 33.5 5.5 52 119-176 5-56 (141)
42 PF08281 Sigma70_r4_2: Sigma-7 78.9 4.2 9E-05 27.2 4.1 43 121-168 11-53 (54)
43 PF00196 GerE: Bacterial regul 74.1 6.5 0.00014 26.8 4.1 45 120-170 3-47 (58)
44 KOG3755|consensus 72.3 1.5 3.2E-05 44.4 0.6 47 128-174 706-759 (769)
45 cd00569 HTH_Hin_like Helix-tur 71.5 9.3 0.0002 21.6 3.9 37 121-162 6-42 (42)
46 PRK09646 RNA polymerase sigma 71.3 8.6 0.00019 32.5 5.1 49 120-173 142-190 (194)
47 PF01527 HTH_Tnp_1: Transposas 71.3 2.5 5.5E-05 30.1 1.6 45 116-164 2-46 (76)
48 PF04967 HTH_10: HTH DNA bindi 70.3 7.6 0.00017 26.8 3.7 40 121-160 1-42 (53)
49 PRK12526 RNA polymerase sigma 68.1 11 0.00024 32.2 5.2 48 121-173 154-201 (206)
50 PRK09652 RNA polymerase sigma 67.6 11 0.00024 30.7 4.9 48 120-172 128-175 (182)
51 PRK06759 RNA polymerase factor 67.4 11 0.00023 30.3 4.6 47 120-171 106-152 (154)
52 KOG1146|consensus 67.1 8.5 0.00018 42.3 4.9 61 113-173 704-764 (1406)
53 COG3413 Predicted DNA binding 66.6 10 0.00022 33.1 4.6 52 120-173 155-208 (215)
54 PRK09644 RNA polymerase sigma 65.1 16 0.00036 29.7 5.4 49 121-174 109-157 (165)
55 PRK12519 RNA polymerase sigma 65.0 10 0.00023 31.7 4.3 47 121-172 142-188 (194)
56 PRK04217 hypothetical protein; 65.0 16 0.00034 29.1 5.0 49 120-173 42-90 (110)
57 PRK00118 putative DNA-binding 64.2 20 0.00043 28.2 5.4 49 121-174 18-66 (104)
58 PRK11924 RNA polymerase sigma 63.8 18 0.0004 29.2 5.5 48 121-173 126-173 (179)
59 TIGR02937 sigma70-ECF RNA poly 63.0 15 0.00033 28.3 4.6 46 121-171 111-156 (158)
60 PRK12514 RNA polymerase sigma 62.7 17 0.00037 30.0 5.2 47 121-172 130-176 (179)
61 PRK09642 RNA polymerase sigma 62.1 18 0.00038 29.3 5.0 47 121-172 107-153 (160)
62 PRK12512 RNA polymerase sigma 61.5 17 0.00038 30.1 5.0 49 120-173 131-179 (184)
63 PF13936 HTH_38: Helix-turn-he 61.4 8.6 0.00019 25.1 2.5 40 119-163 3-42 (44)
64 TIGR02985 Sig70_bacteroi1 RNA 61.2 18 0.00039 28.7 4.9 46 121-171 114-159 (161)
65 TIGR02989 Sig-70_gvs1 RNA poly 60.9 17 0.00037 29.2 4.7 46 120-170 111-156 (159)
66 smart00421 HTH_LUXR helix_turn 60.5 21 0.00046 23.0 4.4 42 121-168 4-45 (58)
67 TIGR03879 near_KaiC_dom probab 60.2 3.6 7.9E-05 30.4 0.5 38 130-167 21-58 (73)
68 PRK05602 RNA polymerase sigma 59.9 20 0.00044 29.8 5.2 49 121-174 129-177 (186)
69 TIGR02999 Sig-70_X6 RNA polyme 59.4 20 0.00043 29.6 5.0 46 121-171 135-180 (183)
70 PRK09648 RNA polymerase sigma 59.0 20 0.00043 29.9 5.0 47 120-171 139-185 (189)
71 TIGR02948 SigW_bacill RNA poly 58.9 18 0.00038 29.9 4.6 48 120-172 136-183 (187)
72 PF10668 Phage_terminase: Phag 58.8 5.9 0.00013 28.2 1.4 21 143-163 24-44 (60)
73 PRK09639 RNA polymerase sigma 58.7 27 0.00058 28.2 5.6 47 121-173 113-159 (166)
74 TIGR02959 SigZ RNA polymerase 57.8 25 0.00054 29.0 5.3 50 120-174 100-149 (170)
75 TIGR02939 RpoE_Sigma70 RNA pol 57.5 16 0.00036 30.2 4.2 31 142-172 155-185 (190)
76 PRK12515 RNA polymerase sigma 57.2 27 0.00058 29.2 5.5 50 120-174 131-180 (189)
77 PRK09413 IS2 repressor TnpA; R 56.4 26 0.00056 27.8 4.9 41 118-163 10-51 (121)
78 PRK10072 putative transcriptio 56.2 13 0.00028 28.8 3.1 40 121-167 33-72 (96)
79 PRK12530 RNA polymerase sigma 56.1 28 0.00061 29.3 5.4 47 121-172 135-181 (189)
80 PRK09047 RNA polymerase factor 56.1 26 0.00056 28.1 5.0 48 120-172 106-153 (161)
81 TIGR02983 SigE-fam_strep RNA p 56.0 23 0.0005 28.6 4.7 47 121-172 111-157 (162)
82 PRK06930 positive control sigm 55.7 29 0.00063 29.4 5.4 50 120-174 114-163 (170)
83 PRK07037 extracytoplasmic-func 55.1 27 0.00059 28.2 5.0 47 121-172 110-156 (163)
84 PRK12537 RNA polymerase sigma 55.1 27 0.00059 29.0 5.1 46 121-171 134-179 (182)
85 PRK09637 RNA polymerase sigma 54.9 24 0.00052 29.6 4.8 48 121-173 107-154 (181)
86 PF09607 BrkDBD: Brinker DNA-b 54.8 25 0.00054 24.9 4.0 44 118-163 3-47 (58)
87 PRK12529 RNA polymerase sigma 54.7 26 0.00057 29.1 5.0 48 120-172 127-174 (178)
88 PRK12541 RNA polymerase sigma 53.9 23 0.0005 28.7 4.4 47 120-171 112-158 (161)
89 PRK12538 RNA polymerase sigma 53.6 26 0.00055 31.0 4.9 32 143-174 189-220 (233)
90 cd04761 HTH_MerR-SF Helix-Turn 53.4 9.3 0.0002 24.6 1.6 22 144-165 3-24 (49)
91 TIGR02952 Sig70_famx2 RNA poly 53.2 29 0.00062 28.1 4.9 46 121-171 123-168 (170)
92 PRK12546 RNA polymerase sigma 52.6 26 0.00056 29.7 4.6 49 121-174 114-162 (188)
93 PRK12536 RNA polymerase sigma 52.5 30 0.00065 28.7 5.0 30 143-172 147-176 (181)
94 TIGR02954 Sig70_famx3 RNA poly 52.1 31 0.00066 28.2 4.9 46 121-171 120-165 (169)
95 PRK12524 RNA polymerase sigma 51.6 35 0.00075 28.8 5.3 49 121-174 137-185 (196)
96 PRK12523 RNA polymerase sigma 51.4 33 0.00071 28.2 5.0 47 121-172 120-166 (172)
97 PRK12543 RNA polymerase sigma 50.7 42 0.00091 27.8 5.6 50 121-175 118-167 (179)
98 PRK09645 RNA polymerase sigma 50.5 35 0.00077 27.8 5.1 47 121-172 119-165 (173)
99 PRK12532 RNA polymerase sigma 50.2 38 0.00083 28.4 5.3 49 121-174 137-185 (195)
100 PRK06986 fliA flagellar biosyn 50.0 29 0.00064 30.3 4.7 47 121-172 185-231 (236)
101 PRK12547 RNA polymerase sigma 50.0 35 0.00076 27.8 4.9 47 121-172 113-159 (164)
102 TIGR00721 tfx DNA-binding prot 49.8 50 0.0011 27.3 5.7 48 118-171 4-51 (137)
103 PRK12539 RNA polymerase sigma 49.6 37 0.0008 28.3 5.1 48 120-172 131-178 (184)
104 PF13443 HTH_26: Cro/C1-type H 49.3 11 0.00023 25.8 1.5 27 143-169 12-38 (63)
105 PRK13919 putative RNA polymera 48.8 38 0.00083 28.0 5.1 46 121-171 136-181 (186)
106 PRK06811 RNA polymerase factor 48.6 36 0.00077 28.5 4.8 49 120-173 131-179 (189)
107 PF13518 HTH_28: Helix-turn-he 48.5 14 0.00031 24.0 1.9 24 143-166 14-37 (52)
108 PF00424 REV: REV protein (ant 48.2 32 0.0007 26.5 4.0 37 127-177 15-51 (91)
109 PRK09647 RNA polymerase sigma 48.0 45 0.00097 28.6 5.5 31 143-173 156-186 (203)
110 cd06170 LuxR_C_like C-terminal 47.7 44 0.00096 21.5 4.3 37 122-164 2-38 (57)
111 PF02796 HTH_7: Helix-turn-hel 47.2 29 0.00063 22.6 3.2 38 120-162 5-42 (45)
112 PRK12516 RNA polymerase sigma 47.0 46 0.001 28.0 5.3 49 121-174 117-165 (187)
113 TIGR02943 Sig70_famx1 RNA poly 46.9 54 0.0012 27.5 5.7 49 121-174 132-180 (188)
114 PRK09480 slmA division inhibit 46.5 22 0.00047 29.3 3.2 41 126-167 16-56 (194)
115 PRK12520 RNA polymerase sigma 45.5 54 0.0012 27.4 5.5 49 121-174 132-180 (191)
116 PRK12531 RNA polymerase sigma 45.4 48 0.001 27.8 5.2 47 121-172 142-188 (194)
117 TIGR03001 Sig-70_gmx1 RNA poly 45.4 50 0.0011 29.4 5.5 49 121-174 162-210 (244)
118 PF13384 HTH_23: Homeodomain-l 45.3 15 0.00032 24.0 1.6 23 142-164 18-40 (50)
119 PRK09649 RNA polymerase sigma 45.1 39 0.00085 28.3 4.6 46 121-171 131-176 (185)
120 TIGR02479 FliA_WhiG RNA polyme 44.6 43 0.00094 28.9 4.9 47 120-171 175-221 (224)
121 PRK10403 transcriptional regul 44.1 28 0.0006 28.3 3.4 46 120-171 153-198 (215)
122 PRK10360 DNA-binding transcrip 43.9 29 0.00063 28.1 3.5 45 120-170 137-181 (196)
123 PRK12545 RNA polymerase sigma 43.7 61 0.0013 27.5 5.6 48 121-173 140-187 (201)
124 PRK12525 RNA polymerase sigma 43.5 51 0.0011 26.9 5.0 47 120-171 118-164 (168)
125 PRK12533 RNA polymerase sigma 43.5 42 0.0009 29.3 4.6 48 121-173 135-182 (216)
126 smart00027 EH Eps15 homology d 43.4 42 0.00091 25.1 4.1 44 120-163 3-51 (96)
127 PRK12528 RNA polymerase sigma 42.9 49 0.0011 26.7 4.7 44 121-169 114-157 (161)
128 PRK08583 RNA polymerase sigma 42.9 47 0.001 29.4 5.0 48 120-172 205-252 (257)
129 PRK12511 RNA polymerase sigma 42.8 58 0.0012 27.3 5.3 50 120-174 111-160 (182)
130 PRK11923 algU RNA polymerase s 42.6 61 0.0013 27.0 5.4 34 141-174 154-187 (193)
131 PRK12518 RNA polymerase sigma 42.6 27 0.00057 28.6 3.1 34 140-173 135-168 (175)
132 PRK09651 RNA polymerase sigma 42.4 44 0.00096 27.5 4.4 31 142-172 136-166 (172)
133 cd04762 HTH_MerR-trunc Helix-T 42.3 18 0.00039 22.6 1.6 24 144-167 3-26 (49)
134 PRK12535 RNA polymerase sigma 42.0 53 0.0011 27.9 4.9 49 121-174 134-182 (196)
135 PRK09641 RNA polymerase sigma 41.8 51 0.0011 27.1 4.7 31 142-172 153-183 (187)
136 TIGR02947 SigH_actino RNA poly 41.8 26 0.00057 29.3 3.0 34 141-174 147-180 (193)
137 PRK12542 RNA polymerase sigma 41.7 53 0.0012 27.2 4.9 47 121-172 123-169 (185)
138 PRK12544 RNA polymerase sigma 41.7 66 0.0014 27.7 5.5 48 121-173 149-196 (206)
139 PRK05657 RNA polymerase sigma 41.1 45 0.00098 31.1 4.7 53 120-173 262-314 (325)
140 PF08280 HTH_Mga: M protein tr 40.7 38 0.00083 23.3 3.2 36 124-163 6-41 (59)
141 PRK12522 RNA polymerase sigma 40.6 66 0.0014 26.3 5.2 30 143-172 137-166 (173)
142 TIGR02980 SigBFG RNA polymeras 40.3 56 0.0012 28.2 4.9 47 120-171 178-224 (227)
143 PRK07670 RNA polymerase sigma 40.1 54 0.0012 29.0 4.8 46 121-171 202-247 (251)
144 PRK06288 RNA polymerase sigma 40.0 69 0.0015 28.6 5.6 49 120-173 212-260 (268)
145 TIGR02941 Sigma_B RNA polymera 39.4 54 0.0012 29.0 4.8 47 120-171 205-251 (255)
146 COG2944 Predicted transcriptio 39.2 37 0.00079 26.9 3.2 40 121-167 44-83 (104)
147 PRK09415 RNA polymerase factor 39.1 52 0.0011 27.3 4.4 47 120-171 127-173 (179)
148 PRK15369 two component system 38.9 59 0.0013 26.0 4.6 45 120-170 149-193 (211)
149 PF07638 Sigma70_ECF: ECF sigm 38.4 64 0.0014 27.2 4.9 29 143-171 153-181 (185)
150 PRK12513 RNA polymerase sigma 38.4 28 0.00062 29.1 2.7 34 140-173 154-187 (194)
151 COG4367 Uncharacterized protei 38.2 37 0.00081 26.2 3.0 39 121-159 3-41 (97)
152 PRK10651 transcriptional regul 38.1 55 0.0012 26.6 4.3 46 120-171 155-200 (216)
153 PRK08301 sporulation sigma fac 37.8 56 0.0012 28.4 4.5 51 121-172 179-229 (234)
154 PRK07408 RNA polymerase sigma 37.5 63 0.0014 28.8 4.9 48 120-172 203-250 (256)
155 PRK08295 RNA polymerase factor 37.4 74 0.0016 26.7 5.1 31 142-172 171-201 (208)
156 PF06056 Terminase_5: Putative 37.2 11 0.00024 26.4 0.0 26 143-170 15-40 (58)
157 PRK10100 DNA-binding transcrip 37.0 50 0.0011 28.8 4.1 46 120-171 155-200 (216)
158 PF13411 MerR_1: MerR HTH fami 36.9 23 0.0005 24.5 1.6 20 144-163 3-22 (69)
159 TIGR02859 spore_sigH RNA polym 36.2 22 0.00047 29.7 1.6 32 140-171 164-195 (198)
160 TIGR03020 EpsA transcriptional 36.1 50 0.0011 29.8 4.0 50 118-173 188-237 (247)
161 PRK12527 RNA polymerase sigma 36.1 91 0.002 25.0 5.3 47 121-172 106-152 (159)
162 PRK09643 RNA polymerase sigma 36.0 1E+02 0.0022 25.9 5.7 46 121-171 135-180 (192)
163 PRK12540 RNA polymerase sigma 35.9 74 0.0016 26.6 4.9 48 121-173 112-159 (182)
164 PRK09935 transcriptional regul 35.7 46 0.00099 27.0 3.5 46 119-170 148-193 (210)
165 PRK12517 RNA polymerase sigma 35.6 95 0.0021 26.0 5.5 50 121-175 129-178 (188)
166 TIGR02950 SigM_subfam RNA poly 35.5 34 0.00074 27.2 2.6 33 139-171 119-151 (154)
167 PRK07122 RNA polymerase sigma 35.3 65 0.0014 29.0 4.7 47 120-171 215-261 (264)
168 TIGR02957 SigX4 RNA polymerase 35.1 67 0.0015 29.0 4.7 47 121-172 109-155 (281)
169 PRK09636 RNA polymerase sigma 34.8 69 0.0015 28.9 4.8 47 121-172 116-162 (293)
170 cd01392 HTH_LacI Helix-turn-he 34.7 17 0.00036 23.8 0.5 21 146-166 2-22 (52)
171 PF12824 MRP-L20: Mitochondria 34.6 1.1E+02 0.0023 26.1 5.5 47 117-165 82-128 (164)
172 TIGR03541 reg_near_HchA LuxR f 34.6 56 0.0012 28.7 4.0 51 118-174 169-219 (232)
173 cd04763 HTH_MlrA-like Helix-Tu 34.3 27 0.00059 24.4 1.7 21 144-164 3-23 (68)
174 PF01381 HTH_3: Helix-turn-hel 34.3 24 0.00052 23.2 1.3 23 144-166 12-34 (55)
175 PRK11922 RNA polymerase sigma 34.1 49 0.0011 28.8 3.6 37 138-174 162-198 (231)
176 cd04764 HTH_MlrA-like_sg1 Heli 33.9 29 0.00064 24.1 1.8 21 144-164 3-23 (67)
177 PRK09640 RNA polymerase sigma 33.6 48 0.001 27.7 3.3 32 142-173 151-182 (188)
178 PF00376 MerR: MerR family reg 33.5 29 0.00063 22.1 1.5 19 144-162 2-20 (38)
179 PRK12534 RNA polymerase sigma 33.1 1E+02 0.0022 25.5 5.2 46 121-171 138-183 (187)
180 PF13551 HTH_29: Winged helix- 32.7 1E+02 0.0022 23.0 4.7 46 118-163 55-109 (112)
181 PRK06424 transcription factor; 32.3 40 0.00088 28.0 2.6 24 144-167 100-123 (144)
182 PF13730 HTH_36: Helix-turn-he 31.7 48 0.001 21.9 2.5 43 121-164 3-48 (55)
183 smart00595 MADF subfamily of S 31.3 65 0.0014 23.5 3.4 34 145-178 31-64 (89)
184 PRK09638 RNA polymerase sigma 31.3 46 0.00099 27.2 2.8 33 139-171 140-172 (176)
185 TIGR01764 excise DNA binding d 31.2 31 0.00068 21.6 1.4 25 144-168 4-28 (49)
186 TIGR02960 SigX5 RNA polymerase 31.1 80 0.0017 28.7 4.6 47 121-172 143-189 (324)
187 cd01104 HTH_MlrA-CarA Helix-Tu 30.8 35 0.00076 23.5 1.7 20 144-163 3-22 (68)
188 KOG0773|consensus 30.8 52 0.0011 30.6 3.3 41 134-174 117-157 (342)
189 PRK05803 sporulation sigma fac 30.7 1.1E+02 0.0024 26.6 5.3 51 121-172 176-226 (233)
190 TIGR02393 RpoD_Cterm RNA polym 30.6 99 0.0022 27.0 5.0 52 120-172 176-227 (238)
191 PRK05911 RNA polymerase sigma 30.3 99 0.0022 27.6 5.0 48 120-172 205-252 (257)
192 TIGR03070 couple_hipB transcri 29.9 31 0.00067 22.5 1.3 23 144-166 18-40 (58)
193 PRK08215 sporulation sigma fac 29.7 1E+02 0.0022 27.4 4.9 47 120-171 209-255 (258)
194 PF01710 HTH_Tnp_IS630: Transp 29.6 80 0.0017 24.9 3.8 31 128-163 10-40 (119)
195 TIGR02885 spore_sigF RNA polym 28.9 1.1E+02 0.0023 26.5 4.8 44 120-168 183-226 (231)
196 PF13565 HTH_32: Homeodomain-l 28.5 2.1E+02 0.0045 20.0 5.9 32 122-153 32-64 (77)
197 cd00093 HTH_XRE Helix-turn-hel 28.3 36 0.00077 21.0 1.3 23 144-166 15-37 (58)
198 TIGR02392 rpoH_proteo alternat 28.3 93 0.002 27.9 4.4 50 120-172 218-267 (270)
199 cd00131 PAX Paired Box domain 27.7 2E+02 0.0044 23.0 5.9 45 121-165 76-127 (128)
200 PRK06704 RNA polymerase factor 27.6 1.1E+02 0.0024 27.1 4.7 31 143-173 134-164 (228)
201 COG1595 RpoE DNA-directed RNA 27.5 63 0.0014 26.8 3.0 32 143-174 145-176 (182)
202 TIGR02984 Sig-70_plancto1 RNA 26.8 1.3E+02 0.0028 24.6 4.8 46 121-171 141-186 (189)
203 TIGR02846 spore_sigmaK RNA pol 26.8 1.4E+02 0.003 25.9 5.2 51 120-171 174-224 (227)
204 PRK05572 sporulation sigma fac 26.8 1.2E+02 0.0026 26.8 4.9 47 120-171 202-248 (252)
205 PTZ00183 centrin; Provisional 26.3 1.7E+02 0.0037 22.9 5.3 42 112-153 2-48 (158)
206 PRK11511 DNA-binding transcrip 25.9 84 0.0018 24.9 3.3 26 140-165 24-49 (127)
207 PF12728 HTH_17: Helix-turn-he 25.9 43 0.00093 21.9 1.4 24 144-167 4-27 (51)
208 PRK07500 rpoH2 RNA polymerase 25.8 1E+02 0.0022 28.1 4.3 51 120-173 227-277 (289)
209 PHA02955 hypothetical protein; 24.9 80 0.0017 28.1 3.2 45 123-167 60-105 (213)
210 TIGR02394 rpoS_proteo RNA poly 24.8 1.4E+02 0.003 27.0 4.9 53 120-173 222-274 (285)
211 PRK09975 DNA-binding transcrip 24.8 58 0.0012 27.4 2.3 41 126-167 17-57 (213)
212 TIGR02607 antidote_HigA addict 24.7 43 0.00094 23.7 1.3 23 144-166 21-43 (78)
213 PRK09958 DNA-binding transcrip 24.6 1.2E+02 0.0025 24.6 4.1 44 120-169 143-186 (204)
214 PRK09390 fixJ response regulat 24.4 1.1E+02 0.0024 24.2 3.9 46 121-172 142-187 (202)
215 PRK08241 RNA polymerase factor 24.1 1E+02 0.0023 28.3 4.1 29 143-171 171-199 (339)
216 PRK15411 rcsA colanic acid cap 23.9 1.2E+02 0.0027 26.0 4.2 45 120-170 137-181 (207)
217 PF04936 DUF658: Protein of un 23.7 37 0.00079 29.1 0.8 33 142-174 15-47 (186)
218 PRK10840 transcriptional regul 23.5 1.4E+02 0.003 25.1 4.4 43 120-168 150-192 (216)
219 PRK11552 putative DNA-binding 23.5 78 0.0017 27.4 3.0 44 125-170 18-61 (225)
220 PRK13870 transcriptional regul 23.4 1.4E+02 0.003 26.4 4.6 27 145-171 192-218 (234)
221 TIGR02835 spore_sigmaE RNA pol 23.1 77 0.0017 27.7 2.9 53 120-173 178-230 (234)
222 PHA01976 helix-turn-helix prot 23.1 49 0.0011 22.7 1.3 23 144-166 18-40 (67)
223 PF08279 HTH_11: HTH domain; 23.0 1.1E+02 0.0023 20.2 3.0 36 125-163 2-37 (55)
224 KOG3755|consensus 21.7 55 0.0012 33.5 1.8 62 110-171 643-708 (769)
225 PRK09483 response regulator; P 21.5 1.6E+02 0.0034 24.1 4.4 45 119-169 147-191 (217)
226 PF05263 DUF722: Protein of un 21.5 1.3E+02 0.0028 24.6 3.7 22 145-166 103-124 (130)
227 smart00530 HTH_XRE Helix-turn- 21.3 57 0.0012 19.8 1.3 24 144-167 13-36 (56)
228 COG2963 Transposase and inacti 21.2 2.1E+02 0.0046 21.9 4.8 42 118-163 5-47 (116)
229 PF04539 Sigma70_r3: Sigma-70 21.1 1.1E+02 0.0024 21.6 2.9 21 143-163 22-42 (78)
230 PRK10430 DNA-binding transcrip 21.1 1.2E+02 0.0026 26.0 3.7 45 120-165 158-202 (239)
231 COG1905 NuoE NADH:ubiquinone o 20.7 1.4E+02 0.0029 25.4 3.7 37 123-159 25-61 (160)
232 PF13412 HTH_24: Winged helix- 20.6 2.1E+02 0.0047 18.2 4.0 37 122-162 2-38 (48)
233 smart00422 HTH_MERR helix_turn 20.4 65 0.0014 22.1 1.5 20 144-163 3-22 (70)
234 PF05703 Auxin_canalis: Auxin 20.3 1.4E+02 0.0031 27.0 4.0 17 154-170 99-115 (242)
235 PRK10188 DNA-binding transcrip 20.3 1.8E+02 0.004 25.7 4.7 47 119-171 178-224 (240)
236 PRK15008 HTH-type transcriptio 20.0 1.4E+02 0.003 25.4 3.7 45 126-171 24-68 (212)
No 1
>KOG0484|consensus
Probab=99.84 E-value=3.8e-21 Score=149.27 Aligned_cols=70 Identities=71% Similarity=1.075 Sum_probs=65.7
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK 178 (256)
Q Consensus 109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~ 178 (256)
..++|+||.||+|+..||.+||+.|...+||++..|++||..+.|++.+|||||||||+|.||+++...-
T Consensus 12 ~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 12 TEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 3468899999999999999999999999999999999999999999999999999999999999986643
No 2
>KOG2251|consensus
Probab=99.82 E-value=3.8e-20 Score=160.77 Aligned_cols=68 Identities=65% Similarity=0.995 Sum_probs=65.1
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
...||+||.||+|+..|+++||..|.+++||+...|++||.+|+|.+.+|+|||+|||+|+|+++++.
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 55689999999999999999999999999999999999999999999999999999999999988865
No 3
>KOG0488|consensus
Probab=99.81 E-value=3.5e-19 Score=164.27 Aligned_cols=72 Identities=44% Similarity=0.701 Sum_probs=65.7
Q ss_pred cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704 108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ 179 (256)
Q Consensus 108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~ 179 (256)
....+|+||.||.||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+||||+.....+.
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~ 237 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGEL 237 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhcc
Confidence 344588889999999999999999999999999999999999999999999999999999999987764443
No 4
>KOG0489|consensus
Probab=99.80 E-value=8.8e-20 Score=164.85 Aligned_cols=68 Identities=46% Similarity=0.762 Sum_probs=63.7
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ 179 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~ 179 (256)
.+.||.||.||..|+.+||+.|..|+|+++..|.|||..|+|+|+|||||||||||||||.++.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 46789999999999999999999999999999999999999999999999999999999988766544
No 5
>KOG0842|consensus
Probab=99.80 E-value=3.7e-19 Score=162.68 Aligned_cols=78 Identities=45% Similarity=0.599 Sum_probs=69.5
Q ss_pred cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcCCcccCC
Q psy2704 108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQPQELFS 185 (256)
Q Consensus 108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~~~~~~~ 185 (256)
.++.+++||.|..|+..|+.+||+.|..++|++..||++||..|+|++.||||||||||-|+||+++...........
T Consensus 147 ~t~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~~~ 224 (307)
T KOG0842|consen 147 QTGKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLLAS 224 (307)
T ss_pred ccccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccCCC
Confidence 345678888899999999999999999999999999999999999999999999999999999998877665544443
No 6
>KOG0850|consensus
Probab=99.78 E-value=1e-18 Score=152.68 Aligned_cols=71 Identities=41% Similarity=0.650 Sum_probs=65.6
Q ss_pred ccCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704 107 QQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS 177 (256)
Q Consensus 107 ~~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~ 177 (256)
...+.+|.||.||.|+.-||..|.++|++++|+...||.+||..|||+..||||||||||.|.||..+...
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence 34566788888999999999999999999999999999999999999999999999999999999888443
No 7
>KOG0487|consensus
Probab=99.76 E-value=2.2e-18 Score=157.68 Aligned_cols=73 Identities=33% Similarity=0.479 Sum_probs=65.5
Q ss_pred ccCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704 107 QQTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ 179 (256)
Q Consensus 107 ~~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~ 179 (256)
.....+..||||--+|+.|+.+||+.|..|.|++++.|.||++.|+|+++||||||||||+|.||..+....+
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 3344577888899999999999999999999999999999999999999999999999999999988755444
No 8
>KOG0491|consensus
Probab=99.76 E-value=2e-18 Score=144.08 Aligned_cols=138 Identities=25% Similarity=0.272 Sum_probs=105.5
Q ss_pred CCCCCCCCCCCCCCCCCCCccccccccCCCCCCCCcccCCCCCCCCCCCCCCC---CCCCCCCCCCCCCCCccCCCCCCC
Q psy2704 39 QNGDPLLSGFTLPISQMPPVIVTTLQQSCSANFQPVMKYNPSTSPQVSPSSPP---TLCFSPTPTPESPPTQQTGKRKQR 115 (256)
Q Consensus 39 ~~~~p~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~s~~~s~s~~~---~~~~s~~~~~~~~~~~~~~~~k~r 115 (256)
....+...|.+.+++.++++-++.+..+...+.+..|...-..++..+....- ..++...-...+-.......-++|
T Consensus 22 ~~pq~~gcGaeq~~psl~~sp~t~pptpt~gp~pss~lll~a~sp~~~hk~~~~~~kgv~p~lalglgn~~~~~~~~~r~ 101 (194)
T KOG0491|consen 22 SSPQPVGCGAEQNYPSLQMSPATMPPTPTVGPLPSSMLLLIADSPDSSHKLLLASPKGVQPTLALGLGNKKTARLHCRRR 101 (194)
T ss_pred cCCcccCcCcccCCCccccCCCCCCCCCCCCCCccccceeeccCCcccccccccCCCccchhHhhhcccchhhhHHHHhh
Confidence 34456777999999999999999999999999888888888887777663110 000000000000011112234567
Q ss_pred CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
+.|++|+..|+..||+.|+..+|.+..+|.|||..|+|++.|||.||||||+|.||+++..
T Consensus 102 K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 102 KARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred hhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 7899999999999999999999999999999999999999999999999999999987653
No 9
>KOG0494|consensus
Probab=99.74 E-value=2.5e-18 Score=152.45 Aligned_cols=66 Identities=61% Similarity=1.036 Sum_probs=61.1
Q ss_pred CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK 178 (256)
Q Consensus 113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~ 178 (256)
|+|+.||.||..|+++||+.|+..+||+...|+.||..+.|.|.+|+|||||||+||||.++.+..
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 444449999999999999999999999999999999999999999999999999999999987653
No 10
>KOG0848|consensus
Probab=99.72 E-value=3.7e-18 Score=151.89 Aligned_cols=68 Identities=40% Similarity=0.673 Sum_probs=63.1
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS 177 (256)
Q Consensus 110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~ 177 (256)
+.|.+-|.|.++|..|+.+||++|..++|+++..+.|||..|||+|+||||||||||+|+||..+.+.
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 44556677999999999999999999999999999999999999999999999999999999888774
No 11
>KOG0843|consensus
Probab=99.71 E-value=9.3e-18 Score=141.90 Aligned_cols=65 Identities=38% Similarity=0.582 Sum_probs=61.5
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
.+.||.||.|+.+|+..||..|+.++|....+|++||+.|+|++.||||||||||.|.||.+...
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37889999999999999999999999999999999999999999999999999999999977653
No 12
>KOG0485|consensus
Probab=99.69 E-value=5.3e-17 Score=140.91 Aligned_cols=67 Identities=39% Similarity=0.657 Sum_probs=62.4
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
+..++||.||+|+..|+..||..|+..+|++..+|..||++|.|+|.||||||||||.||||+-...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad 166 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAAD 166 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhh
Confidence 4567888899999999999999999999999999999999999999999999999999999976543
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.68 E-value=6.1e-17 Score=113.09 Aligned_cols=57 Identities=49% Similarity=0.697 Sum_probs=55.1
Q ss_pred CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
||.|+.|+.+|+.+|+.+|..++||+..+++.||..|||+..+|++||+|||+++||
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 577999999999999999999999999999999999999999999999999999986
No 14
>KOG0492|consensus
Probab=99.66 E-value=1.3e-16 Score=137.71 Aligned_cols=68 Identities=37% Similarity=0.626 Sum_probs=62.1
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhcC
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVSKQ 179 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~~ 179 (256)
+..|+.||.||..||..||+.|+..+|.++.+|.+++..|.|++.||||||||||+|.||.+...-+.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 44567799999999999999999999999999999999999999999999999999999987765444
No 15
>KOG0844|consensus
Probab=99.62 E-value=3.2e-16 Score=141.85 Aligned_cols=67 Identities=39% Similarity=0.625 Sum_probs=62.6
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175 (256)
Q Consensus 109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~ 175 (256)
.....-||.||.||.+|+..||+.|-+..|.++..|.|||..|+|.|..|||||||||+|+||++..
T Consensus 176 sa~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 176 SADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred CccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3456788999999999999999999999999999999999999999999999999999999998754
No 16
>KOG0486|consensus
Probab=99.61 E-value=3.8e-16 Score=141.83 Aligned_cols=66 Identities=58% Similarity=0.943 Sum_probs=63.0
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS 177 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~ 177 (256)
+|+||.||.|+..|+.+||..|++++||+...|++||...+|+|.+|+|||+|||+||||+++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 488999999999999999999999999999999999999999999999999999999999987654
No 17
>KOG0493|consensus
Probab=99.58 E-value=2e-15 Score=134.26 Aligned_cols=60 Identities=38% Similarity=0.658 Sum_probs=56.9
Q ss_pred CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
||.||.|+.+||..|+..|+.|+|++.+.|++||.+|+|.|.||||||||+|+|.||...
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 577999999999999999999999999999999999999999999999999999998543
No 18
>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=2.7e-15 Score=106.07 Aligned_cols=53 Identities=25% Similarity=0.341 Sum_probs=50.8
Q ss_pred CCCCccccCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCccchhhhhhhhhh
Q psy2704 114 QRRYRTTFSNFQLEELERAFHKTHY----PDVFFREELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 114 ~rR~Rt~ft~~Ql~~Le~~F~~~~y----Ps~~~r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
+||.||.||.+|+..||..|+.++| |+..++++||..|||++.+|+|||||.+
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 3788999999999999999999999 9999999999999999999999999965
No 19
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.55 E-value=8.5e-15 Score=102.06 Aligned_cols=57 Identities=54% Similarity=0.817 Sum_probs=54.0
Q ss_pred CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+.|..|+..|+.+|+.+|..++||+..+++.||..+||++.+|++||+|||.+.|+.
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 557889999999999999999999999999999999999999999999999998863
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.55 E-value=7.1e-15 Score=101.78 Aligned_cols=56 Identities=59% Similarity=0.960 Sum_probs=52.4
Q ss_pred CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
++.|+.|+.+|+.+|++.|..++||+..++..||..+||+..+|++||+|||++.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35577899999999999999999999999999999999999999999999999864
No 21
>KOG3802|consensus
Probab=99.55 E-value=2e-15 Score=141.15 Aligned_cols=63 Identities=29% Similarity=0.389 Sum_probs=60.0
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.|+||+||.|+...+..||++|.+|+.|+.+|+.+||.+|+|.+.+|+|||||||+|.||...
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 478888999999999999999999999999999999999999999999999999999998665
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.49 E-value=3.7e-14 Score=119.11 Aligned_cols=68 Identities=34% Similarity=0.515 Sum_probs=60.7
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS 177 (256)
Q Consensus 110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~ 177 (256)
+.+..+++|++.+.+|+.+|++.|+.++||+...|..|+..|+|+++.|||||||||++.|+......
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 33456667778889999999999999999999999999999999999999999999999998776543
No 23
>KOG0483|consensus
Probab=99.47 E-value=2.3e-14 Score=124.46 Aligned_cols=56 Identities=30% Similarity=0.593 Sum_probs=53.0
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
+.+|+.+|...||+.|+.+.+....++..||+.|||..+||.|||||||||||.++
T Consensus 54 k~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 54 KRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 44599999999999999999999999999999999999999999999999999865
No 24
>KOG0847|consensus
Probab=99.39 E-value=1.7e-13 Score=119.35 Aligned_cols=65 Identities=42% Similarity=0.741 Sum_probs=59.7
Q ss_pred CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175 (256)
Q Consensus 111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~ 175 (256)
..+++..|.+|+..|+..||+.|+..+|+-..+|.+||..+||++.+|+|||||||.||||+...
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 35666678899999999999999999999999999999999999999999999999999997543
No 25
>KOG4577|consensus
Probab=99.37 E-value=1.5e-12 Score=117.46 Aligned_cols=67 Identities=40% Similarity=0.568 Sum_probs=61.6
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 110 GKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
+....||.||+++..||+.|+..|+..+.|.+..|+.|+..+||.-++|||||||||+|+||.++..
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 3445678899999999999999999999999999999999999999999999999999999987643
No 26
>KOG0490|consensus
Probab=99.36 E-value=2.9e-13 Score=118.34 Aligned_cols=64 Identities=56% Similarity=0.706 Sum_probs=61.5
Q ss_pred CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
..++||.|+.|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||+|||++++
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 5688999999999999999999999999999999999999999999999999999999999875
No 27
>KOG0849|consensus
Probab=99.24 E-value=3e-11 Score=113.77 Aligned_cols=68 Identities=56% Similarity=0.836 Sum_probs=63.5
Q ss_pred cCCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704 108 QTGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175 (256)
Q Consensus 108 ~~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~ 175 (256)
...+++.||.|++|+..|+..||+.|++++||+...|++||.++++++..|+|||+|||+|+||....
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 44567888889999999999999999999999999999999999999999999999999999998754
No 28
>KOG1168|consensus
Probab=99.07 E-value=4.5e-11 Score=108.04 Aligned_cols=63 Identities=27% Similarity=0.408 Sum_probs=58.3
Q ss_pred CCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
..+||+||.+-.-+...||.+|..++.|+.+.+..||++|+|.+.+|+|||||+|+|.||...
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 356788999999999999999999999999999999999999999999999999999988553
No 29
>KOG0775|consensus
Probab=99.00 E-value=2.1e-09 Score=96.63 Aligned_cols=52 Identities=31% Similarity=0.425 Sum_probs=47.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
|...-..+|.++|..++||+..++.+||+.+||+..||-+||+|||+|+|-.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 5556678999999999999999999999999999999999999999999943
No 30
>KOG0774|consensus
Probab=98.97 E-value=1.5e-09 Score=97.03 Aligned_cols=63 Identities=33% Similarity=0.505 Sum_probs=57.3
Q ss_pred CCCCccccCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 114 QRRYRTTFSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 114 ~rR~Rt~ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
.||+|..|++.-.++|..+| ..++||+.+++++||+++|++..||..||.|+|-++||.....
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 57788999999999999999 4788999999999999999999999999999999999865443
No 31
>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=98.42 E-value=1.8e-07 Score=61.38 Aligned_cols=34 Identities=32% Similarity=0.579 Sum_probs=29.0
Q ss_pred hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 135 KTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 135 ~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
.++||+.+++++||.++||+..||..||-|.|.|
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 5789999999999999999999999999999875
No 32
>KOG2252|consensus
Probab=98.20 E-value=1.9e-06 Score=84.15 Aligned_cols=57 Identities=21% Similarity=0.395 Sum_probs=53.3
Q ss_pred CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169 (256)
Q Consensus 113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~ 169 (256)
+.||.|.+|+..|+..|..+|+.+++|+.+..+.|+.+|||....|.+||-|-|.|.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 356779999999999999999999999999999999999999999999999988764
No 33
>KOG0490|consensus
Probab=98.20 E-value=1.5e-06 Score=75.90 Aligned_cols=66 Identities=52% Similarity=0.704 Sum_probs=61.1
Q ss_pred CCCCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 109 TGKRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 109 ~~~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
....+.++.|+.|...|+..|+..|..+.+|+...++.|+..+|+.+..|++||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 345677888999999999999999999999999999999999999999999999999999998765
No 34
>KOG1146|consensus
Probab=97.73 E-value=6e-05 Score=80.01 Aligned_cols=64 Identities=34% Similarity=0.467 Sum_probs=59.1
Q ss_pred CCCCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 111 KRKQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 111 ~~k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.-.+|+.|+.++..||..|...|....|+..++.+-|...+++..+.|++||||-|+|.||...
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3456778999999999999999999999999999999999999999999999999999988665
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.02 E-value=0.00055 Score=48.06 Aligned_cols=43 Identities=21% Similarity=0.299 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
+..|+++|...+++...+...|+.+.+|+..||+.||--|+.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 4569999999999999999999999999999999999766543
No 36
>KOG0773|consensus
Probab=96.39 E-value=0.0024 Score=59.67 Aligned_cols=60 Identities=22% Similarity=0.248 Sum_probs=49.8
Q ss_pred CCCCccccCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 114 QRRYRTTFSNFQLEELERAFH---KTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 114 ~rR~Rt~ft~~Ql~~Le~~F~---~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++|.+..+......+|+.++. ..+||+..++..||.++||+..||.+||-|.|-|..+-.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 445566788899999998753 346999999999999999999999999999998765533
No 37
>KOG3623|consensus
Probab=95.91 E-value=0.0092 Score=60.71 Aligned_cols=49 Identities=20% Similarity=0.272 Sum_probs=45.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+.+|..+|..|..|+.++...+|.+.||..+.|+.||++++++.++.++
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~r 616 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVER 616 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhcc
Confidence 7789999999999999999999999999999999999999999887664
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.09 E-value=0.055 Score=37.33 Aligned_cols=47 Identities=13% Similarity=0.266 Sum_probs=35.2
Q ss_pred CCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhh
Q psy2704 115 RRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 115 rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
||+|..+|-++...+-..++... ....||..+|++..+|..|..|+.
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 46788899988877777787765 577899999999999999999853
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=86.33 E-value=1.8 Score=28.75 Aligned_cols=46 Identities=17% Similarity=0.250 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.++..+..+|...|... ..-.++|..+|++...|+.+...-..|-|
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 36778889999998333 34678999999999999988876555544
No 40
>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=81.12 E-value=2.9 Score=26.69 Aligned_cols=44 Identities=16% Similarity=0.174 Sum_probs=32.4
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
.++..+..++...|... ....++|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35667777777776433 246778999999999999998765544
No 41
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=79.85 E-value=4.7 Score=33.47 Aligned_cols=52 Identities=17% Similarity=0.168 Sum_probs=41.1
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhh
Q psy2704 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLV 176 (256)
Q Consensus 119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~ 176 (256)
..++..|..+|...+ .. ....++|..||++...|+.|.++.+.|.|+.....
T Consensus 5 ~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~tl 56 (141)
T PRK03975 5 SFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKARETL 56 (141)
T ss_pred cCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 467888999998743 22 23568999999999999999999888888776654
No 42
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=78.91 E-value=4.2 Score=27.19 Aligned_cols=43 Identities=19% Similarity=0.199 Sum_probs=28.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
++..+..++...|.. .....++|..+|+++..|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 455666666665533 3467889999999999999999755443
No 43
>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=74.10 E-value=6.5 Score=26.83 Aligned_cols=45 Identities=18% Similarity=0.167 Sum_probs=34.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.||..++.+|.....-. ...++|..+|++++.|+.+.++=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 47888888888776533 4788999999999999999887776654
No 44
>KOG3755|consensus
Probab=72.27 E-value=1.5 Score=44.37 Aligned_cols=47 Identities=19% Similarity=0.110 Sum_probs=32.6
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHhC-------CccchhhhhhhhhhHHHHHHHH
Q psy2704 128 ELERAFHKTHYPDVFFREELALRID-------LTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 128 ~Le~~F~~~~yPs~~~r~~LA~~lg-------Ls~~qVqvWFQNRRaK~rk~~~ 174 (256)
+-+.+|.+++.+..-...+.-..+. ...+.|+.||+|||.++++.+-
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 3355677777777665555444333 4567899999999999998653
No 45
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=71.47 E-value=9.3 Score=21.59 Aligned_cols=37 Identities=19% Similarity=0.266 Sum_probs=26.0
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhh
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWF 162 (256)
++.++...+...|... + ...++|..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 5566666666666532 2 46688999999998888874
No 46
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=71.33 E-value=8.6 Score=32.47 Aligned_cols=49 Identities=16% Similarity=0.190 Sum_probs=35.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..+|...|..+ ....++|..||++...|+++...-|.+.|+.-
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 35666666666554333 34678999999999999999987777766643
No 47
>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=71.32 E-value=2.5 Score=30.12 Aligned_cols=45 Identities=16% Similarity=0.154 Sum_probs=28.4
Q ss_pred CCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhh
Q psy2704 116 RYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 116 R~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQN 164 (256)
++|..|+.++...+-..+... .....++|..+||+...+..|-+-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHH
Confidence 456789998866666555222 246788999999999999999753
No 48
>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=70.31 E-value=7.6 Score=26.85 Aligned_cols=40 Identities=25% Similarity=0.336 Sum_probs=31.7
Q ss_pred cCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCccchhhh
Q psy2704 121 FSNFQLEELERAFHKTHY--PDVFFREELALRIDLTEARVQV 160 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~y--Ps~~~r~~LA~~lgLs~~qVqv 160 (256)
+|..|..+|...|+..-| |-.....+||..||++...|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 478899999999976643 5556778999999999976543
No 49
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=68.06 E-value=11 Score=32.23 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++..+..++...|..+ ...+++|..+|+++..|+++...-|.+.|+..
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555556665444222 34688999999999999999877777666644
No 50
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=67.63 E-value=11 Score=30.67 Aligned_cols=48 Identities=13% Similarity=0.031 Sum_probs=34.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.+++.+..++...|... ....++|..+|+++..|+.|...-|.|.|+.
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 36666777776654322 2467899999999999999998666666654
No 51
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=67.44 E-value=11 Score=30.25 Aligned_cols=47 Identities=17% Similarity=0.137 Sum_probs=33.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.+++.+..++...|..+ ....++|..+|+++..|+.|...-|.|.|+
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 35566666666555333 247889999999999999998766665554
No 52
>KOG1146|consensus
Probab=67.05 E-value=8.5 Score=42.34 Aligned_cols=61 Identities=23% Similarity=0.324 Sum_probs=54.8
Q ss_pred CCCCCccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 113 KQRRYRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 113 k~rR~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
+-++-|...-.+++..|-++|-.+.-|+...+..|......+.+++.+||+|-|.|.|+..
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 4456678888899999999999999999999999999999999999999999999988765
No 53
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=66.58 E-value=10 Score=33.06 Aligned_cols=52 Identities=25% Similarity=0.316 Sum_probs=40.7
Q ss_pred ccCHHHHHHHHHHHhhCC--CCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTH--YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~--yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.+|..|+.+|...|...= ||-.....+||++||+++.. +|..=||+..|-..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~Kl~~ 208 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERKLIE 208 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHHHHH
Confidence 699999999999997654 46666779999999999965 56666777655433
No 54
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.06 E-value=16 Score=29.73 Aligned_cols=49 Identities=14% Similarity=0.065 Sum_probs=33.8
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
++..+..++...|-. ....+++|..+|+++..|++|.+.-|.+.|+.-+
T Consensus 109 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 109 LPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 455555555543322 2246889999999999999999877777766543
No 55
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=65.04 E-value=10 Score=31.73 Aligned_cols=47 Identities=21% Similarity=0.224 Sum_probs=32.8
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...| .......++|..+|++...|+.|++.-|.+.|+.
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3444555554443 2233568899999999999999998777776664
No 56
>PRK04217 hypothetical protein; Provisional
Probab=65.00 E-value=16 Score=29.11 Aligned_cols=49 Identities=16% Similarity=0.078 Sum_probs=36.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++.+|..++...|.... ...+||+.+|++...|+..++.-|.+.|..-
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~L 90 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQML 90 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 367778777777764432 5678999999999999999987777665543
No 57
>PRK00118 putative DNA-binding protein; Validated
Probab=64.16 E-value=20 Score=28.24 Aligned_cols=49 Identities=12% Similarity=0.113 Sum_probs=35.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
++..|..++...|... ....+||..+|++...|..|...-|.+.|+...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~ 66 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEE 66 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555666666655443 246789999999999999999887777776543
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=63.83 E-value=18 Score=29.23 Aligned_cols=48 Identities=15% Similarity=0.065 Sum_probs=32.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++..+..++...|.. .....++|..+|++...|+.|...-|.|.|+.-
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l 173 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLRECL 173 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 444444455444322 234578999999999999999987777766543
No 59
>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=62.96 E-value=15 Score=28.31 Aligned_cols=46 Identities=17% Similarity=0.195 Sum_probs=31.8
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..++...|-. .....++|..+|+++..|+.|.+.-+.|.|+
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 455555555544322 2346789999999999999998876666554
No 60
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=62.71 E-value=17 Score=29.96 Aligned_cols=47 Identities=21% Similarity=0.331 Sum_probs=32.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|-.. ...+++|..+|+++..|++++..-|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 4445555555554222 2468899999999999999988766666553
No 61
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=62.13 E-value=18 Score=29.28 Aligned_cols=47 Identities=13% Similarity=0.104 Sum_probs=32.4
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|... ...+++|..+|+++..|++++..-|.+.|+.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555544322 2357899999999999999998766666654
No 62
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=61.46 E-value=17 Score=30.09 Aligned_cols=49 Identities=16% Similarity=0.096 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..++...|... ...++||..+|++...|+.++..-|.+.|+.-
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 35666666666654333 24678999999999999999987777766543
No 63
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=61.41 E-value=8.6 Score=25.14 Aligned_cols=40 Identities=13% Similarity=0.173 Sum_probs=21.4
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
..+|.+|...++..+... .-..+||..||.+...|..|.+
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 457788888888886543 3466799999999999988875
No 64
>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=61.16 E-value=18 Score=28.67 Aligned_cols=46 Identities=11% Similarity=0.018 Sum_probs=30.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..++...|.. .....++|..+|+++..|+.+...-|.|.|+
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 445555555554432 2246789999999999999888766555553
No 65
>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=60.85 E-value=17 Score=29.15 Aligned_cols=46 Identities=20% Similarity=0.138 Sum_probs=32.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.++..+..++...|.. ....+++|..+|++...|+++...-|.+.|
T Consensus 111 ~L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 111 KLPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred HCCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4566666666664432 235788999999999999988765555544
No 66
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=60.47 E-value=21 Score=22.96 Aligned_cols=42 Identities=21% Similarity=0.241 Sum_probs=29.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
++..+..++...+ .. ....++|..+|++...|+.|.+.-+.|
T Consensus 4 l~~~e~~i~~~~~-~g-----~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 4 LTPREREVLRLLA-EG-----LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5667777775543 22 246789999999999999988754433
No 67
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=60.24 E-value=3.6 Score=30.42 Aligned_cols=38 Identities=18% Similarity=0.065 Sum_probs=27.2
Q ss_pred HHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 130 ERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 130 e~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
+..|....|-......+||..+|+++..|+.|+.+...
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~~~ 58 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKGETK 58 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcCcc
Confidence 33444444444456789999999999999999975443
No 68
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=59.85 E-value=20 Score=29.77 Aligned_cols=49 Identities=16% Similarity=0.157 Sum_probs=33.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
++..+..++...|... ....++|..+|++...|+.+...-|.+.|+.-.
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555543222 246789999999999999999877777666443
No 69
>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=59.37 E-value=20 Score=29.59 Aligned_cols=46 Identities=22% Similarity=0.136 Sum_probs=33.4
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...+..++...|... ...+++|..+|+++..|++..+.-|.+.|+
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 5556666666655333 246789999999999999999877766655
No 70
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=58.99 E-value=20 Score=29.92 Aligned_cols=47 Identities=26% Similarity=0.099 Sum_probs=33.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.+...|..++...|... ...+++|..+|++...|+.+...-|.+.|+
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45666666666654333 347889999999999999988765555554
No 71
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=58.89 E-value=18 Score=29.89 Aligned_cols=48 Identities=17% Similarity=0.158 Sum_probs=33.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..+++..|. .....+++|..+|++...|+++++.-|.+.|+.
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345555555555432 223467899999999999999998777766654
No 72
>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=58.79 E-value=5.9 Score=28.22 Aligned_cols=21 Identities=14% Similarity=0.449 Sum_probs=18.0
Q ss_pred HHHHHHHHhCCccchhhhhhh
Q psy2704 143 FREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQ 163 (256)
...+||.+||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 456789999999999999954
No 73
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=58.69 E-value=27 Score=28.23 Aligned_cols=47 Identities=19% Similarity=0.229 Sum_probs=34.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++..+..+|...| .. ....+||..+|++...|+.+...-|.+.|+.-
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5556666666665 22 24678999999999999999977666666643
No 74
>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=57.80 E-value=25 Score=29.00 Aligned_cols=50 Identities=14% Similarity=0.146 Sum_probs=35.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.++..+..+|...|... ...+++|..+|+++..|+++.+.-|.+.|+.-.
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 45666666666655333 246889999999999999998776666666443
No 75
>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=57.51 E-value=16 Score=30.17 Aligned_cols=31 Identities=16% Similarity=0.112 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
..-.++|..+|+++..|+++...-|.+.|+.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999987666665554
No 76
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=57.19 E-value=27 Score=29.17 Aligned_cols=50 Identities=18% Similarity=0.143 Sum_probs=36.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.++..+..+|...|... ....++|..+|++...|++-+..-|.+.|+.-+
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666666654332 246789999999999999988877777766543
No 77
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=56.37 E-value=26 Score=27.77 Aligned_cols=41 Identities=10% Similarity=0.163 Sum_probs=27.3
Q ss_pred ccccCHHHHH-HHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 118 RTTFSNFQLE-ELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 118 Rt~ft~~Ql~-~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
|..|+.++.. ++...+. +.+ ...++|..+|++...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 3446776644 3333343 332 366789999999999999964
No 78
>PRK10072 putative transcriptional regulator; Provisional
Probab=56.23 E-value=13 Score=28.76 Aligned_cols=40 Identities=20% Similarity=0.223 Sum_probs=29.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
.+...+..|...... ...+||..+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 355556666443222 2678999999999999999998775
No 79
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=56.09 E-value=28 Score=29.26 Aligned_cols=47 Identities=11% Similarity=0.096 Sum_probs=33.6
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|-.. ...+++|..+|+++..|+++...-|.+.|+.
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4556666666654332 2467899999999999999998666666654
No 80
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=56.09 E-value=26 Score=28.12 Aligned_cols=48 Identities=15% Similarity=0.093 Sum_probs=32.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..++.-.|-.. ....++|..||++...|++....-|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35556666666544322 2367899999999999999887666655543
No 81
>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=55.98 E-value=23 Score=28.55 Aligned_cols=47 Identities=11% Similarity=0.123 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|... ...+++|..+|++...|+++...-|.+.|+.
T Consensus 111 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRYYED-----LSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHHHhc-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4455666665554222 2467899999999999999988777776654
No 82
>PRK06930 positive control sigma-like factor; Validated
Probab=55.69 E-value=29 Score=29.41 Aligned_cols=50 Identities=14% Similarity=0.074 Sum_probs=36.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.++..+..++...|... ..-.++|..+|++...|+.+...-|.|.++.-.
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 36666666666654333 246789999999999999999988777776543
No 83
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=55.14 E-value=27 Score=28.17 Aligned_cols=47 Identities=11% Similarity=0.053 Sum_probs=32.2
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+++.+..++...|... ...+++|+.+|++...|+...+.-|.+.|+.
T Consensus 110 L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 110 LPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555665544322 2467899999999999999877666666553
No 84
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=55.08 E-value=27 Score=29.00 Aligned_cols=46 Identities=15% Similarity=0.247 Sum_probs=31.4
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..++...|..+ ...+++|..+|++...|++|...-|.+.|+
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 4445555555544322 246789999999999999998866666554
No 85
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=54.91 E-value=24 Score=29.59 Aligned_cols=48 Identities=17% Similarity=0.140 Sum_probs=32.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++..+..++...|-. ....+++|..+|++...|+..+..-|.+.|+.-
T Consensus 107 L~~~~r~i~~l~~~~-----g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 107 LPEKYAEALRLTELE-----GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 455555555554322 234688999999999999999886666666543
No 86
>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=54.76 E-value=25 Score=24.90 Aligned_cols=44 Identities=16% Similarity=0.214 Sum_probs=22.8
Q ss_pred ccccCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 118 RTTFSNFQ-LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 118 Rt~ft~~Q-l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
|..|+... |.+++.+...+. --..+ ..-|.++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~-RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQ-RAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-H-HHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhH-HHHHHHhCccHHHHHHHHH
Confidence 44566644 555555554332 11122 3359999999999999975
No 87
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=54.66 E-value=26 Score=29.08 Aligned_cols=48 Identities=10% Similarity=0.083 Sum_probs=35.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.+...|..++.-.|... ...+++|..||+++..|+....+-+.+++..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 35666666666654332 2467899999999999999998777777553
No 88
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=53.87 E-value=23 Score=28.66 Aligned_cols=47 Identities=17% Similarity=0.073 Sum_probs=33.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..|..++.-.|-.+ ....++|..+|++...|+++...-|.+.|+
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 35566666666554322 246789999999999999988766666554
No 89
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=53.58 E-value=26 Score=30.96 Aligned_cols=32 Identities=25% Similarity=0.252 Sum_probs=26.5
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
..++||..||+++..|+++.+.-|.|.|+.-.
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777776543
No 90
>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=53.37 E-value=9.3 Score=24.61 Aligned_cols=22 Identities=14% Similarity=0.090 Sum_probs=18.7
Q ss_pred HHHHHHHhCCccchhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNR 165 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNR 165 (256)
..++|+.+|++...|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999997543
No 91
>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=53.18 E-value=29 Score=28.06 Aligned_cols=46 Identities=17% Similarity=0.117 Sum_probs=30.4
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..+|...|-.. ....++|..||+++..|+.....-|.+.|+
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555543322 346789999999999999877655555443
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=52.59 E-value=26 Score=29.69 Aligned_cols=49 Identities=20% Similarity=0.060 Sum_probs=33.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
++..+..++.-.|. .....+++|..||++...|++++..-|.+.|+.-.
T Consensus 114 Lp~~~r~v~~L~~~-----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 114 LPDEQREALILVGA-----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 44555555554432 22346789999999999999999877777766443
No 93
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=52.45 E-value=30 Score=28.73 Aligned_cols=30 Identities=20% Similarity=0.089 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
..+++|..+|++...|++....-|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 468899999999999999998777776653
No 94
>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=52.11 E-value=31 Score=28.15 Aligned_cols=46 Identities=13% Similarity=0.191 Sum_probs=31.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...+..++...|... ....++|..||++...|+++...-|.+.|+
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555556665554333 246789999999999999888766666555
No 95
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=51.65 E-value=35 Score=28.78 Aligned_cols=49 Identities=8% Similarity=-0.012 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+++.+..++.-.|.. ....++||..+|++...|++++..-|.+.|+.-.
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 185 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLTARGKRALAALLA 185 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 455555555544332 2236789999999999999999877777666443
No 96
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=51.42 E-value=33 Score=28.16 Aligned_cols=47 Identities=13% Similarity=0.082 Sum_probs=32.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+...+..++.-.|-.. ..-.++|..+|++...|+++..+-|.+++..
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4445555555443222 2467899999999999999998777777654
No 97
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=50.66 E-value=42 Score=27.77 Aligned_cols=50 Identities=14% Similarity=0.205 Sum_probs=34.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~ 175 (256)
++..+..++...|... ....++|..+|+++..|++....-|.+.|+.-..
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4444554554443222 2467899999999999999998888888775443
No 98
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=50.51 E-value=35 Score=27.83 Aligned_cols=47 Identities=15% Similarity=0.191 Sum_probs=32.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+...+..+|...|-.. ...+++|..||+++..|+.....-|.+.|+.
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5566666666654332 2367899999999999999887666555553
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=50.23 E-value=38 Score=28.39 Aligned_cols=49 Identities=8% Similarity=0.064 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+...+..++...|... ...+++|..+|++...|+.+...-|.+.|+.-.
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 185 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQCLQ 185 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555433222 246789999999999999999877777776543
No 100
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=50.02 E-value=29 Score=30.30 Aligned_cols=47 Identities=13% Similarity=0.182 Sum_probs=34.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+...+..++...|... ....++|..+|++...|+.+.+.-|.+.|+.
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555566665555322 3468899999999999999998888777764
No 101
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=49.95 E-value=35 Score=27.80 Aligned_cols=47 Identities=15% Similarity=0.044 Sum_probs=32.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|... ...+++|..+|++...|+++...-|.+.|+.
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5555666555544322 3467899999999999999988666665543
No 102
>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=49.76 E-value=50 Score=27.26 Aligned_cols=48 Identities=23% Similarity=0.201 Sum_probs=37.5
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.+.++..|+.+|+..+ .. ...+++|..+|++...|+.|-+.-|.|.|+
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 4568888999998742 22 146789999999999999998877777765
No 103
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=49.58 E-value=37 Score=28.26 Aligned_cols=48 Identities=13% Similarity=0.016 Sum_probs=33.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..+++-.|-. .....++|..+|++...|+.+...-|.+.|+.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566666666654432 23467899999999999999987666666553
No 104
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=49.28 E-value=11 Score=25.82 Aligned_cols=27 Identities=7% Similarity=0.190 Sum_probs=18.5
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKW 169 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~ 169 (256)
...+||+.+|++...|..||.++..+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 467899999999999999999884443
No 105
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=48.82 E-value=38 Score=27.98 Aligned_cols=46 Identities=11% Similarity=0.138 Sum_probs=31.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..+|...|-.. ..-+++|..+|++...|+++.+.-|.+.|+
T Consensus 136 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 136 LSPEERRVIEVLYYQG-----YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5555666665544222 246789999999999999888765555544
No 106
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=48.55 E-value=36 Score=28.53 Aligned_cols=49 Identities=20% Similarity=0.252 Sum_probs=33.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.+++.+..++...|-.. ...+++|..+|++...|++..+.-|.+.|++.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 35566666666544322 24678999999999999988776666655543
No 107
>PF13518 HTH_28: Helix-turn-helix domain
Probab=48.52 E-value=14 Score=24.03 Aligned_cols=24 Identities=21% Similarity=0.403 Sum_probs=19.9
Q ss_pred HHHHHHHHhCCccchhhhhhhhhh
Q psy2704 143 FREELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
...++|..+|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 356799999999999999997543
No 108
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=48.16 E-value=32 Score=26.52 Aligned_cols=37 Identities=22% Similarity=0.474 Sum_probs=20.7
Q ss_pred HHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHhhh
Q psy2704 127 EELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKLVS 177 (256)
Q Consensus 127 ~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~ 177 (256)
.+..-.|+.|+||...-... | =+|||.+||+.+.+..
T Consensus 15 RiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHH
Confidence 34445578899997542111 1 1699999999887654
No 109
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=47.99 E-value=45 Score=28.64 Aligned_cols=31 Identities=19% Similarity=0.207 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
...++|..||++...|+++...-|.+.|+.-
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999987666666544
No 110
>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=47.65 E-value=44 Score=21.52 Aligned_cols=37 Identities=19% Similarity=0.144 Sum_probs=25.6
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhh
Q psy2704 122 SNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 122 t~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQN 164 (256)
+..+..++...+ .. ....++|..++++...|+.|...
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 344555555433 22 25678899999999999998863
No 111
>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=47.19 E-value=29 Score=22.58 Aligned_cols=38 Identities=18% Similarity=0.331 Sum_probs=26.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhh
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWF 162 (256)
.++.++.+.+.+.+... ....+||+.+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 35666677777777655 247789999999999988766
No 112
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=47.02 E-value=46 Score=28.00 Aligned_cols=49 Identities=14% Similarity=0.045 Sum_probs=33.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+...+..++...|... ..-.++|..||+++..|+++...-|.+.|+.-+
T Consensus 117 Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 117 LPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555544322 236789999999999999999877777666544
No 113
>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=46.92 E-value=54 Score=27.53 Aligned_cols=49 Identities=10% Similarity=0.104 Sum_probs=34.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+...+..++...|... ...++||..+|++...|++....-|.+.|+.-.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555666665554333 246889999999999999988776666666443
No 114
>PRK09480 slmA division inhibitor protein; Provisional
Probab=46.53 E-value=22 Score=29.34 Aligned_cols=41 Identities=20% Similarity=0.301 Sum_probs=32.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
+......|..++. .......||++.|++...+-.+|.|+..
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3444445655556 7788999999999999999999999773
No 115
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=45.51 E-value=54 Score=27.38 Aligned_cols=49 Identities=12% Similarity=0.054 Sum_probs=34.2
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
++..+..++...|-.. ....++|..+|+++..|++....-|.+.|+.-.
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555544322 236789999999999999998877777666544
No 116
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=45.43 E-value=48 Score=27.83 Aligned_cols=47 Identities=15% Similarity=0.200 Sum_probs=32.0
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+...+..++...|... ..-+++|..+|++...|++.+..-|.+.|+.
T Consensus 142 Lp~~~r~v~~l~~~eg-----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 142 LPKAQRDVLQAVYLEE-----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 4555666666544322 2467899999999999988876666555543
No 117
>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=45.40 E-value=50 Score=29.42 Aligned_cols=49 Identities=12% Similarity=0.236 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+...+..++.-.|... ...+++|..+|+++..|+++...-|.+.|+.-+
T Consensus 162 Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 162 LSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444443322 246789999999999999999888877776543
No 118
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=45.32 E-value=15 Score=23.99 Aligned_cols=23 Identities=22% Similarity=0.499 Sum_probs=17.5
Q ss_pred HHHHHHHHHhCCccchhhhhhhh
Q psy2704 142 FFREELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQN 164 (256)
....++|+.||++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 35778999999999999999864
No 119
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=45.14 E-value=39 Score=28.28 Aligned_cols=46 Identities=11% Similarity=-0.056 Sum_probs=30.6
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...|..++.-.|... ...++||..+|+++..|+++...-|.+.|+
T Consensus 131 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 131 LTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4444555554443222 246789999999999999988766665554
No 120
>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=44.55 E-value=43 Score=28.93 Aligned_cols=47 Identities=21% Similarity=0.187 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..+|...|... ...+++|..+|++...|+.+.+.-+.+.|+
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 35677777777766433 246889999999999999988766665554
No 121
>PRK10403 transcriptional regulator NarP; Provisional
Probab=44.15 E-value=28 Score=28.26 Aligned_cols=46 Identities=17% Similarity=0.255 Sum_probs=36.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..+|+..... ..+.+||..++++++.|++..+|=|.|-..
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 5788888888765432 346788999999999999999887777544
No 122
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=43.86 E-value=29 Score=28.11 Aligned_cols=45 Identities=18% Similarity=0.146 Sum_probs=35.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.++..+..+|+-.+.. + .+++||..++++++.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g--~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG--M----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5788888888776543 2 5788999999999999998887776643
No 123
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=43.66 E-value=61 Score=27.50 Aligned_cols=48 Identities=13% Similarity=0.088 Sum_probs=33.0
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
+...+..++.-.|... ....++|..+|+++..|++....-|.+.|+.-
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4455555555543222 24678999999999999999887776666644
No 124
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=43.53 E-value=51 Score=26.94 Aligned_cols=47 Identities=9% Similarity=0.043 Sum_probs=32.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++.-.|-.. ..-+++|..||++...|+.+..+-+.+++.
T Consensus 118 ~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 118 GLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35555656665544332 246789999999999999988776666654
No 125
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=43.46 E-value=42 Score=29.28 Aligned_cols=48 Identities=15% Similarity=-0.014 Sum_probs=33.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
+...+..++...|... ...+++|..||+++..|+++...-|.+.|+.-
T Consensus 135 Lp~~~R~v~~L~y~eg-----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 135 LPVEYREVLVLRELED-----MSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CCHHHHhHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4455555555544322 24678999999999999999887666666644
No 126
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=43.35 E-value=42 Score=25.09 Aligned_cols=44 Identities=11% Similarity=0.086 Sum_probs=35.0
Q ss_pred ccCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 120 TFSNFQLEELERAFHK-----THYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~-----~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
.++.+|+..|...|.. +.+.+..+..++-..+|+++..|+.+|.
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 3678899999999853 4578888888877778999888888875
No 127
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=42.89 E-value=49 Score=26.69 Aligned_cols=44 Identities=11% Similarity=0.104 Sum_probs=30.4
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~ 169 (256)
++..|..++...|-.. ..-.++|..+|++...|+++...-+.++
T Consensus 114 L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra~~~~ 157 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKAAMRC 157 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5555666665554333 2467899999999999999887555444
No 128
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=42.88 E-value=47 Score=29.38 Aligned_cols=48 Identities=15% Similarity=0.213 Sum_probs=35.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..+|...|... ....++|..+|++...|+.|...-|.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 36667777777766332 2357899999999999999987666666543
No 129
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=42.84 E-value=58 Score=27.34 Aligned_cols=50 Identities=16% Similarity=0.084 Sum_probs=34.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.++..+..++...|-.. ...+++|..+|++...|+++...-|.+.|+...
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 35666666666654332 246789999999999999998766666555443
No 130
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=42.62 E-value=61 Score=26.97 Aligned_cols=34 Identities=15% Similarity=0.063 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 141 VFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 141 ~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
....+++|..+|+++..|++..+.-|.+-|+.-+
T Consensus 154 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 154 GLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3446889999999999999998877777776544
No 131
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=42.61 E-value=27 Score=28.60 Aligned_cols=34 Identities=18% Similarity=0.176 Sum_probs=27.4
Q ss_pred CHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 140 DVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 140 s~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.....+++|..+|++...|++.+..-|.+.|+.-
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345788999999999999999987777777654
No 132
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.35 E-value=44 Score=27.47 Aligned_cols=31 Identities=10% Similarity=0.141 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
...++||..+|++...|+++...-+.+++..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~~ 166 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKATEHCLLF 166 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999997666666553
No 133
>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=42.32 E-value=18 Score=22.64 Aligned_cols=24 Identities=13% Similarity=0.361 Sum_probs=20.3
Q ss_pred HHHHHHHhCCccchhhhhhhhhhH
Q psy2704 144 REELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
..++|+.||++...|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 468899999999999999876554
No 134
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=41.97 E-value=53 Score=27.94 Aligned_cols=49 Identities=16% Similarity=0.045 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+...+..++...|-.. ...+++|..+|++...|+++...-|.+.|+.-.
T Consensus 134 Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 134 LPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 4455555554444322 246789999999999999998766666665443
No 135
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=41.83 E-value=51 Score=27.09 Aligned_cols=31 Identities=26% Similarity=0.319 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
..-+++|..+|++...|+++...-|.|.|+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3468899999999999998887777666653
No 136
>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=41.82 E-value=26 Score=29.33 Aligned_cols=34 Identities=24% Similarity=0.168 Sum_probs=27.9
Q ss_pred HHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 141 VFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 141 ~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.....+||..||++...|+++...-|.+.|+.-.
T Consensus 147 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 147 GFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3456889999999999999999887777776554
No 137
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=41.73 E-value=53 Score=27.24 Aligned_cols=47 Identities=15% Similarity=0.219 Sum_probs=31.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|... ...+++|..+|++...|++....-|.+.|+.
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4455555555543222 2467899999999999999887666666553
No 138
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=41.68 E-value=66 Score=27.66 Aligned_cols=48 Identities=13% Similarity=0.095 Sum_probs=34.2
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
++..+..++...|-.. ....++|..+|++...|+++.+.-|.+.|+.-
T Consensus 149 L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 149 LPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4555656665554332 23578999999999999999887777766654
No 139
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=41.09 E-value=45 Score=31.09 Aligned_cols=53 Identities=25% Similarity=0.164 Sum_probs=40.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..+|...|... |......++||..+|++...|+.+...-+.|.|+.-
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 47778888888877332 223345789999999999999999987777776644
No 140
>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=40.70 E-value=38 Score=23.31 Aligned_cols=36 Identities=22% Similarity=0.297 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 124 FQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 124 ~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
.|+..|+-.|. +...+ ..+||..+|++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~---~~ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWIT---LKELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBB---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCc---HHHHHHHHCCCHHHHHHHHH
Confidence 47888888888 55554 44899999999999886554
No 141
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=40.56 E-value=66 Score=26.29 Aligned_cols=30 Identities=10% Similarity=0.193 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.-+++|..+|++...|+++...-|.+.|+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999999987666666554
No 142
>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=40.33 E-value=56 Score=28.19 Aligned_cols=47 Identities=17% Similarity=0.215 Sum_probs=34.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++...|... ....++|..+|++...|+.|...=+.|.|+
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 46777777777766432 246789999999999999998765555554
No 143
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=40.07 E-value=54 Score=29.01 Aligned_cols=46 Identities=13% Similarity=0.174 Sum_probs=32.8
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...+..++...|... ....++|..+|++...|+.++..-|.+.|+
T Consensus 202 L~~~~r~vl~l~~~~~-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYKEE-----LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555666666655322 246889999999999999998766666554
No 144
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=40.02 E-value=69 Score=28.65 Aligned_cols=49 Identities=14% Similarity=0.155 Sum_probs=35.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.+...+..+|...|... ....++|..+|++...|+.....-+.+.|+.-
T Consensus 212 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35666666776666433 24678999999999999988877777766654
No 145
>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=39.38 E-value=54 Score=28.98 Aligned_cols=47 Identities=13% Similarity=0.184 Sum_probs=34.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++...|.... ...++|..+|++...|+.+...-+.|.|+
T Consensus 205 ~L~~~~r~ii~l~~~~g~-----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL-----SQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 466777777777764332 35789999999999999988766666554
No 146
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=39.23 E-value=37 Score=26.86 Aligned_cols=40 Identities=15% Similarity=0.321 Sum_probs=33.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
++..++..+.+.+... ...+|..||++...|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 7788888888877544 457899999999999999999874
No 147
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=39.11 E-value=52 Score=27.27 Aligned_cols=47 Identities=13% Similarity=0.108 Sum_probs=32.1
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++...|-.. ...+++|..+|++...|+.+...-|.+.|+
T Consensus 127 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE-----LSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35555655655543222 246789999999999999988766666554
No 148
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=38.90 E-value=59 Score=25.97 Aligned_cols=45 Identities=13% Similarity=0.144 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.++..+..+|+- +..+ + ...++|+.++++++.|+.|.+|=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 478888888876 4333 2 2578999999999999999988776653
No 149
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=38.45 E-value=64 Score=27.18 Aligned_cols=29 Identities=31% Similarity=0.396 Sum_probs=24.1
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
..+++|..+|++++.|+..++.=|.+.++
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56889999999999999988877766554
No 150
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=38.35 E-value=28 Score=29.11 Aligned_cols=34 Identities=21% Similarity=0.107 Sum_probs=26.5
Q ss_pred CHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 140 DVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 140 s~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.....+++|..+|++...|+++...-|.+.|+.-
T Consensus 154 ~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 154 GDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345788999999999999988877676666543
No 151
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.23 E-value=37 Score=26.15 Aligned_cols=39 Identities=15% Similarity=0.186 Sum_probs=27.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhh
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQ 159 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVq 159 (256)
++++|...-...|+.+--.+.-..+++|..||+++..|+
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 455666665666655555555668899999999987654
No 152
>PRK10651 transcriptional regulator NarL; Provisional
Probab=38.15 E-value=55 Score=26.57 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=35.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+.++|+-..+. + ...++|+.++++++.|++..+|=|.|-.-
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 4889999888775532 1 35678999999999999999988777543
No 153
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=37.76 E-value=56 Score=28.38 Aligned_cols=51 Identities=12% Similarity=0.100 Sum_probs=34.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|... +......+++|..+|++...|+.+...-|.+.|+.
T Consensus 179 Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 179 LSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5566666666655210 02223467899999999999999887766666654
No 154
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=37.47 E-value=63 Score=28.79 Aligned_cols=48 Identities=19% Similarity=0.206 Sum_probs=34.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.+...+..+|...|... ....++|..+|++...|+.+...-+.|.|+.
T Consensus 203 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFLHD-----LTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35666667777766432 3568899999999999999987666665553
No 155
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=37.40 E-value=74 Score=26.70 Aligned_cols=31 Identities=16% Similarity=0.087 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
..-.++|..+|++...|++.+..-|.+.|+.
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998887766666654
No 156
>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=37.25 E-value=11 Score=26.37 Aligned_cols=26 Identities=27% Similarity=0.521 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
...+||..||++...|..|-+ |.+|.
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 467899999999999999975 44443
No 157
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=37.00 E-value=50 Score=28.84 Aligned_cols=46 Identities=17% Similarity=0.077 Sum_probs=36.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.+|+.++++|+...+- ..-.++|+.|+++++.|+.+..+-..|..-
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4888999999887652 235688999999999999999887777654
No 158
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=36.86 E-value=23 Score=24.55 Aligned_cols=20 Identities=10% Similarity=0.215 Sum_probs=17.6
Q ss_pred HHHHHHHhCCccchhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQ 163 (256)
..++|+.+|++...|+.|=+
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 46899999999999999954
No 159
>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=36.17 E-value=22 Score=29.73 Aligned_cols=32 Identities=19% Similarity=0.123 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 140 DVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 140 s~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
......++|..+|++...|++++..-|.+.|+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999888765555544
No 160
>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=36.14 E-value=50 Score=29.79 Aligned_cols=50 Identities=16% Similarity=0.069 Sum_probs=38.1
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
...++..+.++|+-..+ . ....++|..||+++..|+.+.+|=+.|.+-..
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 34688889999986542 2 23678999999999999999998877765443
No 161
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=36.08 E-value=91 Score=25.02 Aligned_cols=47 Identities=9% Similarity=0.065 Sum_probs=31.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|-.. ...+++|..+|+++..|++....-|.+.|+.
T Consensus 106 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 106 LPPACRDSFLLRKLEG-----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4445555554443222 2467899999999999998887666665554
No 162
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=35.97 E-value=1e+02 Score=25.92 Aligned_cols=46 Identities=15% Similarity=0.095 Sum_probs=28.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...+..+|+..|... ....+||..+|++...|++=...-|.+.|+
T Consensus 135 Lp~~~r~i~~l~~~~g-----~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 135 LPVEQRAALVAVDMQG-----YSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455555555544322 246789999999999987644433333333
No 163
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=35.93 E-value=74 Score=26.62 Aligned_cols=48 Identities=17% Similarity=0.012 Sum_probs=31.9
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
+...+..++...|.. ....+++|..||+++..|++....-|.+.|+.-
T Consensus 112 Lp~~~R~v~~L~~~~-----g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 112 LPQDQREALILVGAS-----GFSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 445555555554422 234678999999999999998876555555543
No 164
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=35.73 E-value=46 Score=27.03 Aligned_cols=46 Identities=22% Similarity=0.156 Sum_probs=35.3
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
..++..+..+|+..++. ..++++|..++++.+.|+++.++=|.|-.
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 34788888888754433 35788999999999999999987777643
No 165
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=35.58 E-value=95 Score=26.04 Aligned_cols=50 Identities=20% Similarity=0.133 Sum_probs=33.7
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHHh
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEKL 175 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~ 175 (256)
+...+..++...|... ...+++|..||+++..|+++...-|.+.|+.-+.
T Consensus 129 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (188)
T PRK12517 129 LDPEYREPLLLQVIGG-----FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEK 178 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555554443222 2467899999999999999988777766665543
No 166
>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=35.48 E-value=34 Score=27.16 Aligned_cols=33 Identities=24% Similarity=0.255 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 139 PDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 139 Ps~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
......+++|..+|+++..|+++...-|.|.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344467899999999999999998766666554
No 167
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=35.31 E-value=65 Score=28.97 Aligned_cols=47 Identities=15% Similarity=0.261 Sum_probs=34.9
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..+|...|... ....++|..+|++...|+.+...-+.|.|+
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 35666777777766432 346889999999999999998776666655
No 168
>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=35.11 E-value=67 Score=28.97 Aligned_cols=47 Identities=15% Similarity=0.083 Sum_probs=32.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+++.|..++.-.|-.. ..-.++|..+|+++..|+.+++.-|.+.|+.
T Consensus 109 L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 109 LSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4555555554443222 2357899999999999999998777776653
No 169
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=34.83 E-value=69 Score=28.95 Aligned_cols=47 Identities=13% Similarity=-0.003 Sum_probs=32.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
+++.|..++.-.|-.. ...+++|..+|+++..|+...+.-|.+.|+.
T Consensus 116 L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 116 LSPLERAAFLLHDVFG-----VPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4455555554443222 2367899999999999999998777666653
No 170
>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=34.72 E-value=17 Score=23.81 Aligned_cols=21 Identities=14% Similarity=0.191 Sum_probs=19.3
Q ss_pred HHHHHhCCccchhhhhhhhhh
Q psy2704 146 ELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 146 ~LA~~lgLs~~qVqvWFQNRR 166 (256)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999984
No 171
>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=34.62 E-value=1.1e+02 Score=26.09 Aligned_cols=47 Identities=15% Similarity=0.224 Sum_probs=37.0
Q ss_pred CccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhh
Q psy2704 117 YRTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNR 165 (256)
Q Consensus 117 ~Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNR 165 (256)
++..++.+++.++.+.-..+ |....+..||+++|++..-|.+=..--
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~ 128 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAP 128 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCC
Confidence 34689999999998886555 677889999999999988776655433
No 172
>TIGR03541 reg_near_HchA LuxR family transcriptional regulatory, chaperone HchA-associated. Members of this protein family belong to the LuxR transcriptional regulator family, and contain both autoinducer binding (pfam03472) and transcriptional regulator (pfam00196) domains. Members, however, occur only in a few members of the Gammaproteobacteria that have the chaperone/aminopeptidase HchA, and are always encoded by the adjacent gene.
Probab=34.61 E-value=56 Score=28.69 Aligned_cols=51 Identities=16% Similarity=0.120 Sum_probs=37.5
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
...++..++++|.-... . ..-.++|..||++++.|+.+.+|=+.|.+-..+
T Consensus 169 ~~~Lt~re~evl~~~a~-G-----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~ 219 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL-G-----RRQADIAAILGISERTVENHLRSARRKLGVATT 219 (232)
T ss_pred hccCCHHHHHHHHHHHC-C-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCH
Confidence 34577888888776431 1 245788999999999999999988877665433
No 173
>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=34.32 E-value=27 Score=24.37 Aligned_cols=21 Identities=19% Similarity=0.344 Sum_probs=18.3
Q ss_pred HHHHHHHhCCccchhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQN 164 (256)
..++|+.+|++...++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468899999999999999753
No 174
>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=34.27 E-value=24 Score=23.24 Aligned_cols=23 Identities=17% Similarity=0.367 Sum_probs=19.6
Q ss_pred HHHHHHHhCCccchhhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
..+||..+|++...|..|..++|
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 47899999999999999998865
No 175
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=34.06 E-value=49 Score=28.82 Aligned_cols=37 Identities=22% Similarity=0.200 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 138 YPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 138 yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
|......+++|..+|++...|++....-|.|.|+.-.
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3344567899999999999999988877777777543
No 176
>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=33.91 E-value=29 Score=24.08 Aligned_cols=21 Identities=10% Similarity=0.151 Sum_probs=18.4
Q ss_pred HHHHHHHhCCccchhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQN 164 (256)
..++|+.+|++...++.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999764
No 177
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=33.63 E-value=48 Score=27.66 Aligned_cols=32 Identities=13% Similarity=0.133 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
...+++|..+|++...|+++...-|.+.|+.-
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 35689999999999999999987777666643
No 178
>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=33.46 E-value=29 Score=22.05 Aligned_cols=19 Identities=11% Similarity=0.135 Sum_probs=15.5
Q ss_pred HHHHHHHhCCccchhhhhh
Q psy2704 144 REELALRIDLTEARVQVWF 162 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWF 162 (256)
+.++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 4578999999999999885
No 179
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=33.10 E-value=1e+02 Score=25.49 Aligned_cols=46 Identities=28% Similarity=0.356 Sum_probs=29.6
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+...+..++...|. ....-+++|..||++...|++....-|.+.|+
T Consensus 138 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 138 LEPPRSELIRTAFF-----EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 44555555555442 22346789999999999988776655544443
No 180
>PF13551 HTH_29: Winged helix-turn helix
Probab=32.70 E-value=1e+02 Score=22.96 Aligned_cols=46 Identities=17% Similarity=0.137 Sum_probs=30.0
Q ss_pred ccccCHHHHHHHHHHHhhCC-----CCCHHHHHH-H-HHH--hCCccchhhhhhh
Q psy2704 118 RTTFSNFQLEELERAFHKTH-----YPDVFFREE-L-ALR--IDLTEARVQVWFQ 163 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~-----yPs~~~r~~-L-A~~--lgLs~~qVqvWFQ 163 (256)
+..++.++...|.+.+..++ ..+.....+ | ... +.++...|..|++
T Consensus 55 ~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 55 RKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33389999999999998765 234444433 3 222 2577777887775
No 181
>PRK06424 transcription factor; Provisional
Probab=32.34 E-value=40 Score=27.98 Aligned_cols=24 Identities=13% Similarity=0.029 Sum_probs=21.4
Q ss_pred HHHHHHHhCCccchhhhhhhhhhH
Q psy2704 144 REELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
.++||..+|++...|.-|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999988875
No 182
>PF13730 HTH_36: Helix-turn-helix domain
Probab=31.74 E-value=48 Score=21.93 Aligned_cols=43 Identities=16% Similarity=-0.040 Sum_probs=27.3
Q ss_pred cCHHHHHHHHHHH---hhCCCCCHHHHHHHHHHhCCccchhhhhhhh
Q psy2704 121 FSNFQLEELERAF---HKTHYPDVFFREELALRIDLTEARVQVWFQN 164 (256)
Q Consensus 121 ft~~Ql~~Le~~F---~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQN 164 (256)
++..+..++-..+ ..+.. ...-.+.||..+|++.+.|+.+.+.
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 3444444444433 22333 4445788999999999999988754
No 183
>smart00595 MADF subfamily of SANT domain.
Probab=31.34 E-value=65 Score=23.45 Aligned_cols=34 Identities=24% Similarity=0.424 Sum_probs=29.1
Q ss_pred HHHHHHhCCccchhhhhhhhhhHHHHHHHHhhhc
Q psy2704 145 EELALRIDLTEARVQVWFQNRRAKWRKQEKLVSK 178 (256)
Q Consensus 145 ~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~~~~~ 178 (256)
.+||..+|.+...|+.-++|=|.++++..+....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999987665543
No 184
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=31.31 E-value=46 Score=27.20 Aligned_cols=33 Identities=21% Similarity=0.224 Sum_probs=26.1
Q ss_pred CCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 139 PDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 139 Ps~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
......++||..+|++...|+.+...-|.+.|+
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 334557899999999999999988766666665
No 185
>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=31.20 E-value=31 Score=21.65 Aligned_cols=25 Identities=16% Similarity=0.114 Sum_probs=20.2
Q ss_pred HHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 144 REELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
..++|+.||++...|..|.++.+..
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~i~ 28 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGELP 28 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCCCC
Confidence 5678999999999999998665433
No 186
>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=31.08 E-value=80 Score=28.68 Aligned_cols=47 Identities=19% Similarity=0.003 Sum_probs=31.2
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..|..++.-.|... ..-.+||..||+++..|+.....-|.+.|+.
T Consensus 143 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 143 LPPRQRAVLLLRDVLG-----WRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred CCHHHhhHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 4445555554443222 2357899999999999999887666665554
No 187
>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=30.85 E-value=35 Score=23.51 Aligned_cols=20 Identities=10% Similarity=0.228 Sum_probs=17.8
Q ss_pred HHHHHHHhCCccchhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQ 163 (256)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46889999999999999985
No 188
>KOG0773|consensus
Probab=30.80 E-value=52 Score=30.62 Aligned_cols=41 Identities=32% Similarity=0.495 Sum_probs=35.5
Q ss_pred hhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 134 HKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 134 ~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
+.+.|++..+...++...+|+..+|.+||-|.|.+.++..+
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~ 157 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELK 157 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccC
Confidence 46789999999999999999999999999999888776443
No 189
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=30.74 E-value=1.1e+02 Score=26.56 Aligned_cols=51 Identities=14% Similarity=0.083 Sum_probs=32.3
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..++...|.... ......+++|..+|++...|+.+-..-|.|.|+.
T Consensus 176 Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 176 LDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred CCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55566666666552110 1223477899999999999988855445555543
No 190
>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=30.64 E-value=99 Score=27.04 Aligned_cols=52 Identities=15% Similarity=0.116 Sum_probs=38.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..+|...|....+ ......++|..+|++...|+.+.+.-+.|.|..
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 4667777888887733222 223478899999999999999988777777764
No 191
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=30.27 E-value=99 Score=27.58 Aligned_cols=48 Identities=13% Similarity=0.173 Sum_probs=34.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.+.+.+..+|...|... ....+||..+|++...|+.+...-+.|.|+.
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 35566666776666332 3468899999999999998887666665553
No 192
>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=29.92 E-value=31 Score=22.52 Aligned_cols=23 Identities=9% Similarity=-0.057 Sum_probs=20.5
Q ss_pred HHHHHHHhCCccchhhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999998775
No 193
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=29.74 E-value=1e+02 Score=27.39 Aligned_cols=47 Identities=19% Similarity=0.154 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..+++..|... ....++|..+|++...|+.+-.+-+.|.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57778888888887433 246789999999999998776654444443
No 194
>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=29.59 E-value=80 Score=24.86 Aligned_cols=31 Identities=19% Similarity=0.270 Sum_probs=23.2
Q ss_pred HHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 128 ELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 128 ~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
..-..|+... -+.++|..++++...|..||+
T Consensus 10 rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 10 RVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3334555433 456789999999999999998
No 195
>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=28.94 E-value=1.1e+02 Score=26.53 Aligned_cols=44 Identities=11% Similarity=0.096 Sum_probs=31.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
.++..+..++...|... ....++|..+|++...|+.+-..=..|
T Consensus 183 ~L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~~ 226 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEKKVLKK 226 (231)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46677777777766432 357889999999999888766543333
No 196
>PF13565 HTH_32: Homeodomain-like domain
Probab=28.47 E-value=2.1e+02 Score=19.98 Aligned_cols=32 Identities=13% Similarity=-0.094 Sum_probs=23.6
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHH-HHHHhCC
Q psy2704 122 SNFQLEELERAFHKTHYPDVFFREE-LALRIDL 153 (256)
Q Consensus 122 t~~Ql~~Le~~F~~~~yPs~~~r~~-LA~~lgL 153 (256)
+.++...|.+.+..++..+..+..+ |+..+|+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGI 64 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC
Confidence 6777788889988887777776655 5666664
No 197
>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=28.31 E-value=36 Score=20.98 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=19.8
Q ss_pred HHHHHHHhCCccchhhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
...+|..+|++...|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999998764
No 198
>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=28.25 E-value=93 Score=27.91 Aligned_cols=50 Identities=16% Similarity=0.183 Sum_probs=37.2
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
.++..+..+|...|... ......++|..+|++...|+.+.++-..|.|+.
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 46777888888877321 123457899999999999999888777777653
No 199
>cd00131 PAX Paired Box domain
Probab=27.68 E-value=2e+02 Score=23.00 Aligned_cols=45 Identities=7% Similarity=-0.006 Sum_probs=29.5
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-------ccchhhhhhhhh
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDL-------TEARVQVWFQNR 165 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgL-------s~~qVqvWFQNR 165 (256)
.+..+...++.....++..+..+..++...-|+ +...|-.||+++
T Consensus 76 ~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 76 ATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 455666667776778887777766554223355 778888887753
No 200
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=27.57 E-value=1.1e+02 Score=27.07 Aligned_cols=31 Identities=13% Similarity=0.152 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
...++|+.+|+++..|+++...-|.+.|+.-
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999886666666543
No 201
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=27.46 E-value=63 Score=26.83 Aligned_cols=32 Identities=25% Similarity=0.285 Sum_probs=27.0
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
.-.++|..+|++...|+.|...-|.+.|+...
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35789999999999999999988888777554
No 202
>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=26.83 E-value=1.3e+02 Score=24.56 Aligned_cols=46 Identities=20% Similarity=0.156 Sum_probs=30.6
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
++..+..++...|. ......++|..||++...|+.=...-|.+.|+
T Consensus 141 L~~~~r~vi~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 141 LPEDYREVILLRHL-----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55666666655442 23356789999999999998766555555443
No 203
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=26.82 E-value=1.4e+02 Score=25.89 Aligned_cols=51 Identities=14% Similarity=0.037 Sum_probs=32.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++...|....+ .....+++|..+|++...|+.+...-|.|.|+
T Consensus 174 ~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4666677777776531100 11246789999999999998776544554443
No 204
>PRK05572 sporulation sigma factor SigF; Validated
Probab=26.81 E-value=1.2e+02 Score=26.76 Aligned_cols=47 Identities=11% Similarity=0.104 Sum_probs=34.5
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++..+..++...|..+ ....+||..+|++...|+.+-..-..|.|+
T Consensus 202 ~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 47777778887777433 346889999999999998877655555543
No 205
>PTZ00183 centrin; Provisional
Probab=26.26 E-value=1.7e+02 Score=22.88 Aligned_cols=42 Identities=21% Similarity=0.173 Sum_probs=32.3
Q ss_pred CCCCCCccccCHHHHHHHHHHHh-----hCCCCCHHHHHHHHHHhCC
Q psy2704 112 RKQRRYRTTFSNFQLEELERAFH-----KTHYPDVFFREELALRIDL 153 (256)
Q Consensus 112 ~k~rR~Rt~ft~~Ql~~Le~~F~-----~~~yPs~~~r~~LA~~lgL 153 (256)
+|++-.+..++..++..++..|. .+.+.+..+...+...+|+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 2 RKRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 35555678899999999999985 3557888888777777764
No 206
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=25.89 E-value=84 Score=24.89 Aligned_cols=26 Identities=15% Similarity=0.188 Sum_probs=21.7
Q ss_pred CHHHHHHHHHHhCCccchhhhhhhhh
Q psy2704 140 DVFFREELALRIDLTEARVQVWFQNR 165 (256)
Q Consensus 140 s~~~r~~LA~~lgLs~~qVqvWFQNR 165 (256)
.....++||..+|++++.+..+|+..
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34567899999999999999888765
No 207
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.86 E-value=43 Score=21.90 Aligned_cols=24 Identities=17% Similarity=0.356 Sum_probs=19.8
Q ss_pred HHHHHHHhCCccchhhhhhhhhhH
Q psy2704 144 REELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
..++|+.||++...|..|.++..-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876544
No 208
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=25.75 E-value=1e+02 Score=28.09 Aligned_cols=51 Identities=18% Similarity=0.117 Sum_probs=38.0
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..+|...|. |-......+||..+|++...|+.+-..-+.|.|+.-
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 477778888888773 112335688999999999999998877777766543
No 209
>PHA02955 hypothetical protein; Provisional
Probab=24.92 E-value=80 Score=28.06 Aligned_cols=45 Identities=13% Similarity=-0.006 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 123 NFQLEELERAFHKT-HYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 123 ~~Ql~~Le~~F~~~-~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
..++..|-+.|... .-...++|.+++++||+.-..|..||.+.-.
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~ 105 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQ 105 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhh
Confidence 34666676766544 4677889999999999999888999987443
No 210
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=24.77 E-value=1.4e+02 Score=26.97 Aligned_cols=53 Identities=26% Similarity=0.165 Sum_probs=36.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..+|...|... |.....-.+||..||++...|+.+...-|.|.|+.-
T Consensus 222 ~Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 46677777777766111 122234678999999999999999887666666543
No 211
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=24.76 E-value=58 Score=27.38 Aligned_cols=41 Identities=15% Similarity=0.181 Sum_probs=31.8
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhH
Q psy2704 126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
++.-.+.|....|-. ....+||+..|++...+-.+|.++-.
T Consensus 17 l~aa~~lf~~~G~~~-~ti~~Ia~~agvsk~t~Y~~F~sKe~ 57 (213)
T PRK09975 17 IETAIAQFALRGVSN-TTLNDIADAANVTRGAIYWHFENKTQ 57 (213)
T ss_pred HHHHHHHHHHcCccc-CCHHHHHHHcCCCHHHHHHHcCCHHH
Confidence 444555677776654 34778999999999999999999876
No 212
>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=24.68 E-value=43 Score=23.66 Aligned_cols=23 Identities=17% Similarity=0.263 Sum_probs=20.3
Q ss_pred HHHHHHHhCCccchhhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
..+||+.+|++...|..|+.++|
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998765
No 213
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=24.60 E-value=1.2e+02 Score=24.64 Aligned_cols=44 Identities=9% Similarity=0.148 Sum_probs=35.4
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~ 169 (256)
.++..+.++|+..+... .+++||..++++++.|++.-++=|.|.
T Consensus 143 ~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl 186 (204)
T PRK09958 143 SLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKL 186 (204)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 48888888888887543 377899999999999998877766664
No 214
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=24.43 E-value=1.1e+02 Score=24.19 Aligned_cols=46 Identities=15% Similarity=0.173 Sum_probs=31.1
Q ss_pred cCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHH
Q psy2704 121 FSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQ 172 (256)
Q Consensus 121 ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~ 172 (256)
++..+..+|+..+... .-+++|..+|+++..|+++-++=|.|.+..
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~ 187 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAG 187 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHccc
Confidence 5555556665433221 245689999999999999888877775543
No 215
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=24.13 E-value=1e+02 Score=28.25 Aligned_cols=29 Identities=28% Similarity=0.209 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 143 FREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
...+||..||+++..|+.....-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 46789999999999999988766666555
No 216
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=23.86 E-value=1.2e+02 Score=25.95 Aligned_cols=45 Identities=11% Similarity=0.058 Sum_probs=33.7
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
.+|+.++++|.-.-+-. .-.++|++|+++++.|+.-..|=..|..
T Consensus 137 ~LT~RE~eVL~lla~G~------snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMAGQ------GTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 48999999997764322 3578999999999999987765555443
No 217
>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=23.67 E-value=37 Score=29.11 Aligned_cols=33 Identities=30% Similarity=0.407 Sum_probs=28.7
Q ss_pred HHHHHHHHHhCCccchhhhhhhhhhHHHHHHHH
Q psy2704 142 FFREELALRIDLTEARVQVWFQNRRAKWRKQEK 174 (256)
Q Consensus 142 ~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~~ 174 (256)
..+.+|+..++++..+|-+|.+|-+...|+...
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 467899999999999999999999988776554
No 218
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=23.48 E-value=1.4e+02 Score=25.09 Aligned_cols=43 Identities=14% Similarity=0.041 Sum_probs=32.8
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAK 168 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK 168 (256)
.+|+.++++|....+-. .-.++|+.|+++++.|+.-.+|=..|
T Consensus 150 ~Lt~rE~evl~~~~~G~------s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 150 RLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred cCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 48999999998876432 36789999999999999866554433
No 219
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=23.45 E-value=78 Score=27.44 Aligned_cols=44 Identities=9% Similarity=0.120 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHH
Q psy2704 125 QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWR 170 (256)
Q Consensus 125 Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~r 170 (256)
-+..-...|....|- ....+||+..|+++..|..+|.|+..=+.
T Consensus 18 Il~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 18 LIAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 345555668888877 57889999999999999999999877543
No 220
>PRK13870 transcriptional regulator TraR; Provisional
Probab=23.37 E-value=1.4e+02 Score=26.36 Aligned_cols=27 Identities=19% Similarity=0.166 Sum_probs=23.1
Q ss_pred HHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 145 EELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 145 ~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
.++|..||++++.|+.-.+|=|.|.--
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KLga 218 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRFDV 218 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCC
Confidence 578999999999999999998877543
No 221
>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=23.12 E-value=77 Score=27.67 Aligned_cols=53 Identities=9% Similarity=0.066 Sum_probs=34.3
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHHHH
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRKQE 173 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk~~ 173 (256)
.++..+..++...|.... .......++|..+|++...|+++.+.-|.+.|+.-
T Consensus 178 ~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l 230 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKEI 230 (234)
T ss_pred hCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 355666666665542100 11234678999999999999998876666666543
No 222
>PHA01976 helix-turn-helix protein
Probab=23.07 E-value=49 Score=22.71 Aligned_cols=23 Identities=17% Similarity=0.261 Sum_probs=20.1
Q ss_pred HHHHHHHhCCccchhhhhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRR 166 (256)
..+||..+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56799999999999999997765
No 223
>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=22.96 E-value=1.1e+02 Score=20.16 Aligned_cols=36 Identities=14% Similarity=0.099 Sum_probs=23.3
Q ss_pred HHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhh
Q psy2704 125 QLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 125 Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQ 163 (256)
|..+|+..+....+. ...+||..|+++.+.|+.-..
T Consensus 2 ~~~il~~L~~~~~~i---t~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPI---TAKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSB---EHHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCc---CHHHHHHHhCCCHHHHHHHHH
Confidence 345555555555543 456899999999998875443
No 224
>KOG3755|consensus
Probab=21.69 E-value=55 Score=33.54 Aligned_cols=62 Identities=26% Similarity=0.333 Sum_probs=51.1
Q ss_pred CCCCCCCCccccCHHHHHHHHHHHhh-CCCCCHHH---HHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 110 GKRKQRRYRTTFSNFQLEELERAFHK-THYPDVFF---REELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 110 ~~~k~rR~Rt~ft~~Ql~~Le~~F~~-~~yPs~~~---r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
....+.|+|+.+..+-+..|..+-.. .-||+... ..-|...+++.++.+--.|||.|...+.
T Consensus 643 ~n~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 643 KNWHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred HhccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 34456778999999999999887644 44888887 8889999999999999999999987553
No 225
>PRK09483 response regulator; Provisional
Probab=21.52 E-value=1.6e+02 Score=24.09 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=32.6
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHH
Q psy2704 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKW 169 (256)
Q Consensus 119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~ 169 (256)
..+|..+.++|+... ..+ .-.++|..++++++.|+.--+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~----~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQ----KVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCC----CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 458999999996543 222 234899999999999998776655553
No 226
>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=21.48 E-value=1.3e+02 Score=24.61 Aligned_cols=22 Identities=14% Similarity=0.409 Sum_probs=17.6
Q ss_pred HHHHHHhCCccchhhhhhhhhh
Q psy2704 145 EELALRIDLTEARVQVWFQNRR 166 (256)
Q Consensus 145 ~~LA~~lgLs~~qVqvWFQNRR 166 (256)
..+|..+++++++++-|++.=+
T Consensus 103 ~~IA~~l~i~erta~r~~~~fK 124 (130)
T PF05263_consen 103 YQIAQKLHISERTARRWRDRFK 124 (130)
T ss_pred HHHHHHhCccHHHHHHHHHHHH
Confidence 5679999999999988876433
No 227
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=21.31 E-value=57 Score=19.80 Aligned_cols=24 Identities=21% Similarity=0.347 Sum_probs=20.0
Q ss_pred HHHHHHHhCCccchhhhhhhhhhH
Q psy2704 144 REELALRIDLTEARVQVWFQNRRA 167 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQNRRa 167 (256)
...+|+.+|++...|..|-.+++.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~~ 36 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKRK 36 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 557899999999999999877643
No 228
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.21 E-value=2.1e+02 Score=21.92 Aligned_cols=42 Identities=14% Similarity=0.131 Sum_probs=31.3
Q ss_pred ccccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-ccchhhhhhh
Q psy2704 118 RTTFSNFQLEELERAFHKTHYPDVFFREELALRIDL-TEARVQVWFQ 163 (256)
Q Consensus 118 Rt~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgL-s~~qVqvWFQ 163 (256)
|..|+.+....+-+.+....+ ...++|+.+|+ ...++..|-+
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 667888887666666555444 57889999996 9888887764
No 229
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=21.11 E-value=1.1e+02 Score=21.61 Aligned_cols=21 Identities=24% Similarity=0.322 Sum_probs=16.2
Q ss_pred HHHHHHHHhCCccchhhhhhh
Q psy2704 143 FREELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 143 ~r~~LA~~lgLs~~qVqvWFQ 163 (256)
..++||..|||+...|+..++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 467899999999999886653
No 230
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=21.11 E-value=1.2e+02 Score=26.03 Aligned_cols=45 Identities=13% Similarity=0.127 Sum_probs=32.6
Q ss_pred ccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhh
Q psy2704 120 TFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNR 165 (256)
Q Consensus 120 ~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNR 165 (256)
.++..++.+|......+ +-....-+++|..+++++..|+..+++=
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 36777777776655433 3334456889999999999999988765
No 231
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.71 E-value=1.4e+02 Score=25.45 Aligned_cols=37 Identities=22% Similarity=0.083 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhh
Q psy2704 123 NFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQ 159 (256)
Q Consensus 123 ~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVq 159 (256)
..-+..|...++...|.....++.+|..||++...|.
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 3467888899988899999999999999999988764
No 232
>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=20.64 E-value=2.1e+02 Score=18.18 Aligned_cols=37 Identities=16% Similarity=0.177 Sum_probs=23.8
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhh
Q psy2704 122 SNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWF 162 (256)
Q Consensus 122 t~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWF 162 (256)
+..+..+|+..++ ++.. .+.+||..+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 3456677766665 3333 46789999999998876544
No 233
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.38 E-value=65 Score=22.13 Aligned_cols=20 Identities=10% Similarity=0.071 Sum_probs=17.2
Q ss_pred HHHHHHHhCCccchhhhhhh
Q psy2704 144 REELALRIDLTEARVQVWFQ 163 (256)
Q Consensus 144 r~~LA~~lgLs~~qVqvWFQ 163 (256)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999954
No 234
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=20.34 E-value=1.4e+02 Score=27.00 Aligned_cols=17 Identities=18% Similarity=0.536 Sum_probs=13.2
Q ss_pred ccchhhhhhhhhhHHHH
Q psy2704 154 TEARVQVWFQNRRAKWR 170 (256)
Q Consensus 154 s~~qVqvWFQNRRaK~r 170 (256)
.-..|..||+.|+.|.|
T Consensus 99 ~~~~i~~w~~~~~~kkk 115 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKK 115 (242)
T ss_pred ccchHHHHHHHHHHHHH
Confidence 45679999999988643
No 235
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=20.33 E-value=1.8e+02 Score=25.66 Aligned_cols=47 Identities=21% Similarity=0.249 Sum_probs=32.0
Q ss_pred cccCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 119 TTFSNFQLEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 119 t~ft~~Ql~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
..+|..++++|.-..+- ..-.++|..|+++++.|+.-.+|=+.|..-
T Consensus 178 ~~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~KL~~ 224 (240)
T PRK10188 178 MNFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKKFNA 224 (240)
T ss_pred CCCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 34666666666544221 124678999999999999988887776543
No 236
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=20.00 E-value=1.4e+02 Score=25.36 Aligned_cols=45 Identities=13% Similarity=0.205 Sum_probs=33.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCccchhhhhhhhhhHHHHH
Q psy2704 126 LEELERAFHKTHYPDVFFREELALRIDLTEARVQVWFQNRRAKWRK 171 (256)
Q Consensus 126 l~~Le~~F~~~~yPs~~~r~~LA~~lgLs~~qVqvWFQNRRaK~rk 171 (256)
+..-...|....|-. ....+||+..|++...|-..|.|+..=...
T Consensus 24 L~AA~~lf~e~Gy~~-~s~~dIA~~aGvs~gtiY~hF~sKe~L~~a 68 (212)
T PRK15008 24 LSAALDTFSQFGFHG-TRLEQIAELAGVSKTNLLYYFPSKEALYIA 68 (212)
T ss_pred HHHHHHHHHHhCccc-CCHHHHHHHhCcCHHHHHHHCCCHHHHHHH
Confidence 444445577777654 346789999999999999999998774443
Done!