Query psy15100
Match_columns 165
No_of_seqs 213 out of 1290
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 20:38:53 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy15100.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/15100hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.8 4E-21 8.6E-26 158.8 6.9 74 26-99 159-232 (309)
2 KOG0850|consensus 99.8 2.8E-20 6E-25 145.4 8.8 69 33-101 116-184 (245)
3 KOG0842|consensus 99.8 2E-20 4.3E-25 153.1 7.9 70 36-105 150-219 (307)
4 KOG0489|consensus 99.8 3.2E-20 6.9E-25 150.5 7.5 70 35-104 155-224 (261)
5 KOG0487|consensus 99.8 4.3E-20 9.3E-25 151.2 4.3 68 32-99 228-295 (308)
6 KOG0485|consensus 99.8 5.7E-19 1.2E-23 137.0 8.7 64 36-99 101-164 (268)
7 KOG0484|consensus 99.8 1.8E-19 3.9E-24 125.0 4.9 64 36-99 14-77 (125)
8 KOG2251|consensus 99.8 4.6E-19 9.9E-24 137.9 5.1 66 34-99 32-97 (228)
9 KOG0843|consensus 99.8 7.3E-19 1.6E-23 132.9 4.8 63 38-100 101-163 (197)
10 PF00046 Homeobox: Homeobox do 99.7 1.8E-18 4E-23 109.0 5.4 57 40-96 1-57 (57)
11 KOG0848|consensus 99.7 1E-18 2.3E-23 139.2 2.7 63 39-101 199-261 (317)
12 KOG0492|consensus 99.7 2.3E-18 4.9E-23 132.8 4.4 62 38-99 143-204 (246)
13 KOG0494|consensus 99.7 1.4E-17 2.9E-22 132.4 7.2 61 39-99 141-201 (332)
14 KOG0493|consensus 99.7 1E-17 2.2E-22 133.2 6.5 65 35-99 242-306 (342)
15 KOG0491|consensus 99.7 1E-17 2.2E-22 125.1 3.1 66 36-101 97-162 (194)
16 KOG3802|consensus 99.7 1.1E-16 2.4E-21 133.9 7.8 62 38-99 293-354 (398)
17 smart00389 HOX Homeodomain. DN 99.7 2.3E-16 5E-21 98.7 5.6 56 40-95 1-56 (56)
18 cd00086 homeodomain Homeodomai 99.6 3.1E-16 6.8E-21 98.9 6.1 57 41-97 2-58 (59)
19 TIGR01565 homeo_ZF_HD homeobox 99.6 2.9E-16 6.3E-21 99.4 5.3 53 39-91 1-57 (58)
20 KOG0844|consensus 99.6 5.1E-16 1.1E-20 125.9 6.4 71 36-106 178-248 (408)
21 KOG0486|consensus 99.6 2.3E-16 4.9E-21 128.3 3.8 64 37-100 110-173 (351)
22 COG5576 Homeodomain-containing 99.6 1.5E-15 3.2E-20 114.3 5.9 67 34-100 46-112 (156)
23 KOG0483|consensus 99.6 1.3E-15 2.7E-20 118.5 4.0 60 39-98 50-109 (198)
24 KOG4577|consensus 99.5 5.4E-14 1.2E-18 113.5 4.7 65 35-99 163-227 (383)
25 KOG0847|consensus 99.5 3.6E-14 7.9E-19 110.6 3.5 63 37-99 165-227 (288)
26 KOG0490|consensus 99.3 8.6E-13 1.9E-17 104.2 2.9 64 36-99 57-120 (235)
27 KOG0849|consensus 99.3 1.4E-11 3.1E-16 103.9 8.2 71 28-98 165-235 (354)
28 KOG0775|consensus 99.2 6.5E-11 1.4E-15 95.1 8.2 53 46-98 183-235 (304)
29 KOG1168|consensus 99.2 7.9E-12 1.7E-16 101.1 1.3 64 36-99 306-369 (385)
30 KOG0774|consensus 99.1 5.5E-10 1.2E-14 89.3 7.7 58 40-97 189-249 (334)
31 KOG2252|consensus 98.8 1.9E-08 4.1E-13 87.7 8.9 66 30-95 411-476 (558)
32 PF05920 Homeobox_KN: Homeobox 98.7 8.3E-09 1.8E-13 60.6 2.2 34 60-93 7-40 (40)
33 KOG0490|consensus 98.2 1.1E-06 2.4E-11 69.2 4.1 66 34-99 148-213 (235)
34 KOG1146|consensus 98.0 1.6E-05 3.5E-10 75.5 7.2 63 37-99 901-963 (1406)
35 PF11569 Homez: Homeodomain le 97.6 5.1E-05 1.1E-09 47.4 2.3 43 51-93 10-52 (56)
36 KOG0773|consensus 97.2 0.00042 9E-09 58.2 3.9 58 39-96 239-299 (342)
37 KOG3623|consensus 96.7 0.0034 7.4E-08 57.2 5.9 49 51-99 568-616 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.0 0.019 4.2E-07 35.4 4.6 46 40-90 1-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 90.5 0.48 1E-05 28.2 3.5 46 45-95 4-49 (50)
40 cd06171 Sigma70_r4 Sigma70, re 87.8 0.96 2.1E-05 26.1 3.5 44 45-93 10-53 (55)
41 PF01527 HTH_Tnp_1: Transposas 85.9 0.89 1.9E-05 29.2 2.8 44 41-88 2-45 (76)
42 cd00569 HTH_Hin_like Helix-tur 85.5 2.6 5.7E-05 21.6 4.3 38 45-87 5-42 (42)
43 PF08281 Sigma70_r4_2: Sigma-7 85.5 1.5 3.2E-05 26.3 3.5 42 46-92 11-52 (54)
44 PF04967 HTH_10: HTH DNA bindi 84.6 1.8 4E-05 26.6 3.6 42 46-87 1-44 (53)
45 PRK03975 tfx putative transcri 84.0 2.3 4.9E-05 31.6 4.5 50 43-98 4-53 (141)
46 PF00196 GerE: Bacterial regul 80.1 2.9 6.2E-05 25.6 3.3 44 45-94 3-46 (58)
47 PF09607 BrkDBD: Brinker DNA-b 78.8 5.2 0.00011 25.1 4.1 43 44-88 4-47 (58)
48 PF15063 TC1: Thyroid cancer p 78.7 4.1 8.8E-05 27.0 3.7 38 44-81 32-69 (79)
49 PF10668 Phage_terminase: Phag 78.4 1.5 3.3E-05 27.8 1.6 19 69-87 25-43 (60)
50 PRK09646 RNA polymerase sigma 77.4 4.2 9.1E-05 30.9 4.2 31 68-98 160-190 (194)
51 PRK04217 hypothetical protein; 77.1 5.1 0.00011 28.5 4.2 50 43-97 40-89 (110)
52 KOG3755|consensus 76.2 0.73 1.6E-05 41.7 -0.4 48 55-102 708-762 (769)
53 PRK06759 RNA polymerase factor 75.8 5 0.00011 28.9 4.1 46 46-96 107-152 (154)
54 TIGR03879 near_KaiC_dom probab 74.6 1.4 3E-05 29.1 0.7 34 56-89 22-55 (73)
55 PF13936 HTH_38: Helix-turn-he 74.0 3.3 7.2E-05 24.1 2.2 40 44-88 3-42 (44)
56 PRK12512 RNA polymerase sigma 73.5 6.7 0.00015 29.3 4.4 32 68-99 149-180 (184)
57 PRK09642 RNA polymerase sigma 73.1 5.8 0.00013 28.9 3.9 31 69-99 125-155 (160)
58 PRK12526 RNA polymerase sigma 73.1 6 0.00013 30.5 4.1 31 68-98 171-201 (206)
59 smart00421 HTH_LUXR helix_turn 72.8 9 0.00019 22.2 4.1 41 45-91 3-43 (58)
60 PRK09652 RNA polymerase sigma 72.3 6.3 0.00014 28.9 3.9 47 46-97 129-175 (182)
61 PRK11924 RNA polymerase sigma 71.1 6.9 0.00015 28.6 3.9 30 68-97 143-172 (179)
62 KOG1146|consensus 70.7 9.2 0.0002 37.9 5.4 61 38-98 704-764 (1406)
63 PRK12514 RNA polymerase sigma 70.5 8.4 0.00018 28.6 4.3 30 68-97 147-176 (179)
64 cd04761 HTH_MerR-SF Helix-Turn 70.5 3.7 8.1E-05 23.7 1.9 22 69-90 3-24 (49)
65 PF08280 HTH_Mga: M protein tr 69.5 8.1 0.00018 23.9 3.4 37 48-88 5-41 (59)
66 PRK00118 putative DNA-binding 69.5 9.9 0.00021 26.7 4.1 47 46-97 18-64 (104)
67 TIGR02989 Sig-70_gvs1 RNA poly 69.3 8.5 0.00018 27.8 4.0 28 68-95 129-156 (159)
68 PRK12519 RNA polymerase sigma 69.0 6.4 0.00014 29.7 3.4 31 67-97 158-188 (194)
69 TIGR02937 sigma70-ECF RNA poly 68.9 8.5 0.00018 26.8 3.9 29 68-96 128-156 (158)
70 PRK09413 IS2 repressor TnpA; R 68.9 9.8 0.00021 27.0 4.1 42 43-88 10-51 (121)
71 TIGR02959 SigZ RNA polymerase 68.2 9.3 0.0002 28.3 4.1 31 68-98 118-148 (170)
72 COG4367 Uncharacterized protei 68.1 8.3 0.00018 26.4 3.3 40 46-85 3-42 (97)
73 PF13518 HTH_28: Helix-turn-he 68.0 4.4 9.5E-05 23.7 1.9 21 69-89 15-35 (52)
74 PRK09648 RNA polymerase sigma 67.6 9.5 0.00021 28.6 4.1 30 68-97 157-186 (189)
75 TIGR02999 Sig-70_X6 RNA polyme 67.3 9.9 0.00021 28.3 4.1 29 69-97 153-181 (183)
76 PRK12541 RNA polymerase sigma 67.2 9.4 0.0002 27.8 3.9 30 68-97 130-159 (161)
77 TIGR02985 Sig70_bacteroi1 RNA 67.1 11 0.00023 27.0 4.1 29 68-96 131-159 (161)
78 PRK10072 putative transcriptio 65.9 5 0.00011 27.8 2.0 24 69-92 49-72 (96)
79 PRK09644 RNA polymerase sigma 65.8 10 0.00022 27.8 3.9 30 68-97 126-155 (165)
80 TIGR02939 RpoE_Sigma70 RNA pol 65.5 7.9 0.00017 28.9 3.3 32 67-98 155-186 (190)
81 PRK12515 RNA polymerase sigma 65.2 11 0.00025 28.2 4.1 32 68-99 149-180 (189)
82 PRK12523 RNA polymerase sigma 65.1 14 0.00031 27.3 4.6 33 68-100 137-169 (172)
83 PF13384 HTH_23: Homeodomain-l 65.1 5.3 0.00012 23.4 1.8 23 67-89 18-40 (50)
84 PRK05602 RNA polymerase sigma 65.0 10 0.00022 28.4 3.8 31 69-99 147-177 (186)
85 COG3413 Predicted DNA binding 64.7 9.4 0.0002 29.8 3.7 49 45-95 155-205 (215)
86 PRK12530 RNA polymerase sigma 64.6 11 0.00025 28.4 4.1 29 69-97 153-181 (189)
87 smart00027 EH Eps15 homology d 64.2 19 0.0004 24.2 4.7 44 45-88 3-51 (96)
88 PRK12537 RNA polymerase sigma 64.2 13 0.00028 27.8 4.3 29 68-96 151-179 (182)
89 TIGR02948 SigW_bacill RNA poly 64.0 10 0.00023 28.1 3.7 31 67-97 153-183 (187)
90 PRK09047 RNA polymerase factor 63.6 14 0.0003 26.7 4.2 29 69-97 125-153 (161)
91 TIGR00721 tfx DNA-binding prot 63.2 18 0.00039 26.7 4.6 48 43-96 4-51 (137)
92 TIGR02983 SigE-fam_strep RNA p 63.0 13 0.00028 27.0 4.0 31 68-98 128-158 (162)
93 PRK09637 RNA polymerase sigma 62.7 13 0.00028 28.0 4.0 31 68-98 124-154 (181)
94 PRK12536 RNA polymerase sigma 62.6 14 0.0003 27.6 4.2 31 68-98 147-177 (181)
95 PRK12529 RNA polymerase sigma 62.3 18 0.00038 27.0 4.7 29 69-97 146-174 (178)
96 PRK09639 RNA polymerase sigma 62.1 14 0.0003 26.9 4.0 30 68-97 129-158 (166)
97 PRK09645 RNA polymerase sigma 61.9 16 0.00034 26.9 4.3 30 69-98 137-166 (173)
98 PRK06930 positive control sigm 61.9 14 0.00031 28.0 4.1 48 45-97 114-161 (170)
99 PRK12546 RNA polymerase sigma 61.8 12 0.00026 28.4 3.7 31 68-98 131-161 (188)
100 cd04762 HTH_MerR-trunc Helix-T 61.4 7.9 0.00017 21.8 2.1 24 69-92 3-26 (49)
101 PF06056 Terminase_5: Putative 61.3 7 0.00015 24.4 1.9 26 69-96 16-41 (58)
102 PF13443 HTH_26: Cro/C1-type H 60.8 6.8 0.00015 24.0 1.8 24 68-91 12-35 (63)
103 cd06170 LuxR_C_like C-terminal 60.6 21 0.00045 20.7 4.0 36 47-88 2-37 (57)
104 PRK12538 RNA polymerase sigma 60.4 12 0.00026 29.7 3.6 31 68-98 189-219 (233)
105 PF02796 HTH_7: Helix-turn-hel 60.2 16 0.00034 21.2 3.2 37 46-87 6-42 (45)
106 PRK07037 extracytoplasmic-func 60.2 17 0.00037 26.4 4.2 29 69-97 128-156 (163)
107 TIGR02954 Sig70_famx3 RNA poly 59.5 17 0.00037 26.6 4.1 30 68-97 137-166 (169)
108 PRK12547 RNA polymerase sigma 59.5 17 0.00036 26.7 4.1 30 68-97 130-159 (164)
109 PRK13919 putative RNA polymera 59.3 18 0.00039 26.9 4.3 30 68-97 153-182 (186)
110 PRK09480 slmA division inhibit 58.9 11 0.00023 28.1 3.0 39 52-91 17-55 (194)
111 PRK12543 RNA polymerase sigma 58.7 17 0.00038 27.0 4.1 30 68-97 135-164 (179)
112 PRK09649 RNA polymerase sigma 58.6 20 0.00044 26.9 4.4 28 69-96 149-176 (185)
113 PRK12533 RNA polymerase sigma 58.5 16 0.00034 28.6 3.9 33 68-100 152-184 (216)
114 PHA02955 hypothetical protein; 58.4 15 0.00032 29.2 3.6 46 48-93 60-106 (213)
115 PF00376 MerR: MerR family reg 58.1 8.4 0.00018 21.8 1.7 20 69-88 2-21 (38)
116 PRK12524 RNA polymerase sigma 58.0 18 0.00038 27.5 4.0 30 69-98 155-184 (196)
117 TIGR02952 Sig70_famx2 RNA poly 57.9 19 0.0004 26.2 4.1 29 68-96 140-168 (170)
118 PRK12532 RNA polymerase sigma 57.4 18 0.00038 27.4 4.0 30 69-98 155-184 (195)
119 PRK06986 fliA flagellar biosyn 57.2 16 0.00034 28.7 3.8 30 68-97 202-231 (236)
120 PRK12539 RNA polymerase sigma 57.1 19 0.00042 26.9 4.1 30 68-97 149-178 (184)
121 PRK12516 RNA polymerase sigma 55.8 20 0.00044 27.1 4.1 31 69-99 135-165 (187)
122 PRK06811 RNA polymerase factor 55.4 23 0.00049 26.7 4.3 31 68-98 149-179 (189)
123 TIGR02943 Sig70_famx1 RNA poly 55.4 22 0.00047 26.9 4.1 30 68-97 149-178 (188)
124 cd01392 HTH_LacI Helix-turn-he 55.3 7.3 0.00016 22.8 1.2 21 71-91 2-22 (52)
125 PF13411 MerR_1: MerR HTH fami 55.3 9.7 0.00021 23.7 1.9 21 69-89 3-23 (69)
126 KOG0773|consensus 53.9 16 0.00034 30.6 3.4 41 58-98 116-156 (342)
127 PRK08583 RNA polymerase sigma 53.4 23 0.0005 28.1 4.2 48 46-98 206-253 (257)
128 PF01381 HTH_3: Helix-turn-hel 53.4 12 0.00025 22.2 1.9 23 69-91 12-34 (55)
129 PRK09647 RNA polymerase sigma 53.4 24 0.00052 27.2 4.1 29 69-97 157-185 (203)
130 cd04763 HTH_MlrA-like Helix-Tu 53.0 11 0.00024 23.6 1.9 21 69-89 3-23 (68)
131 PRK12531 RNA polymerase sigma 52.9 25 0.00054 26.6 4.2 30 68-97 159-188 (194)
132 COG2944 Predicted transcriptio 52.9 19 0.00042 25.3 3.2 40 46-92 44-83 (104)
133 PHA03308 transcriptional regul 52.5 18 0.0004 34.0 3.7 17 37-53 1292-1308(1463)
134 PF13551 HTH_29: Winged helix- 52.3 68 0.0015 21.4 6.0 45 44-88 56-109 (112)
135 PRK12520 RNA polymerase sigma 52.3 25 0.00055 26.4 4.1 30 69-98 150-179 (191)
136 PRK10403 transcriptional regul 52.0 15 0.00033 26.9 2.8 45 44-94 152-196 (215)
137 TIGR02479 FliA_WhiG RNA polyme 51.9 24 0.00052 27.4 4.0 46 46-96 176-221 (224)
138 PRK12545 RNA polymerase sigma 51.3 27 0.00058 26.7 4.1 31 68-98 157-187 (201)
139 cd04764 HTH_MlrA-like_sg1 Heli 51.2 12 0.00027 23.3 1.8 21 69-89 3-23 (67)
140 PF08279 HTH_11: HTH domain; 51.0 23 0.0005 21.0 3.0 36 50-88 2-37 (55)
141 TIGR01764 excise DNA binding d 51.0 15 0.00031 20.8 2.0 23 69-91 4-26 (49)
142 PRK10100 DNA-binding transcrip 50.3 23 0.0005 27.7 3.6 45 45-95 155-199 (216)
143 PRK12511 RNA polymerase sigma 50.2 28 0.0006 26.2 4.0 32 68-99 129-160 (182)
144 PRK09651 RNA polymerase sigma 50.1 21 0.00046 26.4 3.3 29 68-96 137-165 (172)
145 PRK12544 RNA polymerase sigma 50.1 29 0.00063 26.8 4.1 29 69-97 167-195 (206)
146 TIGR03001 Sig-70_gmx1 RNA poly 49.8 28 0.0006 27.8 4.1 29 69-97 180-208 (244)
147 PRK12528 RNA polymerase sigma 49.7 30 0.00066 25.1 4.0 25 69-93 132-156 (161)
148 PRK12542 RNA polymerase sigma 49.6 29 0.00063 25.9 4.0 30 69-98 141-170 (185)
149 PRK12535 RNA polymerase sigma 49.4 39 0.00084 25.8 4.7 31 69-99 152-182 (196)
150 TIGR03070 couple_hipB transcri 49.3 15 0.00033 21.5 2.0 23 69-91 18-40 (58)
151 cd01104 HTH_MlrA-CarA Helix-Tu 49.3 13 0.00029 23.0 1.8 20 69-88 3-22 (68)
152 PRK09641 RNA polymerase sigma 49.3 28 0.00061 25.8 3.9 30 68-97 154-183 (187)
153 TIGR02980 SigBFG RNA polymeras 49.2 29 0.00064 26.9 4.1 47 45-96 178-224 (227)
154 TIGR03020 EpsA transcriptional 49.1 24 0.00053 28.4 3.7 48 43-96 188-235 (247)
155 cd00131 PAX Paired Box domain 49.0 97 0.0021 22.2 6.6 46 45-90 75-127 (128)
156 PRK12522 RNA polymerase sigma 48.9 31 0.00067 25.4 4.0 29 69-97 138-166 (173)
157 TIGR02947 SigH_actino RNA poly 48.7 14 0.00029 27.9 2.1 33 66-98 147-179 (193)
158 PRK11923 algU RNA polymerase s 48.5 28 0.00061 26.1 3.8 30 68-97 156-185 (193)
159 PRK10651 transcriptional regul 48.5 28 0.00061 25.5 3.8 45 45-95 155-199 (216)
160 PRK15369 two component system 48.3 34 0.00073 24.7 4.2 44 45-94 149-192 (211)
161 PRK10360 DNA-binding transcrip 48.0 20 0.00043 26.2 2.8 44 45-94 137-180 (196)
162 PRK12525 RNA polymerase sigma 47.8 35 0.00075 25.1 4.2 28 69-96 137-164 (168)
163 TIGR02859 spore_sigH RNA polym 47.8 34 0.00074 25.6 4.2 32 65-96 164-195 (198)
164 PRK07670 RNA polymerase sigma 47.4 30 0.00065 27.5 4.0 47 46-97 202-248 (251)
165 cd00093 HTH_XRE Helix-turn-hel 47.2 18 0.00038 20.2 2.0 23 69-91 15-37 (58)
166 PRK08295 RNA polymerase factor 47.0 35 0.00076 25.8 4.2 32 67-98 171-202 (208)
167 TIGR02957 SigX4 RNA polymerase 46.8 34 0.00074 27.7 4.3 29 69-97 127-155 (281)
168 TIGR02941 Sigma_B RNA polymera 46.6 30 0.00065 27.5 3.8 46 46-96 206-251 (255)
169 PRK12513 RNA polymerase sigma 46.5 13 0.00029 28.0 1.7 34 65-98 154-187 (194)
170 PRK07408 RNA polymerase sigma 46.4 34 0.00074 27.4 4.2 48 46-98 204-251 (256)
171 PF12728 HTH_17: Helix-turn-he 46.3 18 0.00039 21.2 2.0 24 69-92 4-27 (51)
172 PF04936 DUF658: Protein of un 46.1 15 0.00032 28.1 1.8 32 67-98 15-46 (186)
173 PRK12540 RNA polymerase sigma 46.1 35 0.00075 25.7 4.0 32 68-99 129-160 (182)
174 PRK12518 RNA polymerase sigma 46.0 14 0.00029 27.3 1.7 35 65-99 135-169 (175)
175 PRK09636 RNA polymerase sigma 45.8 37 0.0008 27.6 4.3 30 69-98 134-163 (293)
176 TIGR03541 reg_near_HchA LuxR f 45.5 30 0.00065 27.2 3.7 47 44-96 170-216 (232)
177 COG1905 NuoE NADH:ubiquinone o 45.1 39 0.00085 25.6 4.0 36 48-83 25-60 (160)
178 PF13412 HTH_24: Winged helix- 45.0 40 0.00087 19.4 3.3 38 47-88 2-39 (48)
179 PRK05657 RNA polymerase sigma 44.9 30 0.00065 28.9 3.7 53 45-98 262-314 (325)
180 COG2963 Transposase and inacti 44.4 56 0.0012 22.6 4.6 42 43-88 5-47 (116)
181 PF07638 Sigma70_ECF: ECF sigm 44.3 40 0.00087 25.5 4.1 30 68-97 153-182 (185)
182 PRK12527 RNA polymerase sigma 44.2 43 0.00094 24.2 4.1 29 69-97 124-152 (159)
183 PRK08301 sporulation sigma fac 44.0 31 0.00066 27.0 3.5 30 68-97 200-229 (234)
184 PRK09935 transcriptional regul 42.9 26 0.00057 25.7 2.8 45 44-94 148-192 (210)
185 TIGR02960 SigX5 RNA polymerase 42.9 38 0.00081 27.7 4.0 31 69-99 161-191 (324)
186 PRK06288 RNA polymerase sigma 42.8 41 0.00088 27.0 4.1 47 46-97 213-259 (268)
187 PHA01976 helix-turn-helix prot 42.3 22 0.00048 21.9 2.0 23 69-91 18-40 (67)
188 PF13730 HTH_36: Helix-turn-he 42.3 22 0.00049 21.0 2.0 42 46-88 3-47 (55)
189 PRK09415 RNA polymerase factor 42.2 38 0.00082 25.2 3.6 28 69-96 146-173 (179)
190 PRK09643 RNA polymerase sigma 41.0 48 0.001 25.0 4.1 30 68-97 152-181 (192)
191 KOG3623|consensus 41.0 29 0.00062 32.7 3.2 54 44-97 631-684 (1007)
192 PRK05988 formate dehydrogenase 41.0 52 0.0011 24.6 4.2 36 49-84 24-59 (156)
193 PRK12534 RNA polymerase sigma 40.8 53 0.0012 24.4 4.3 29 68-96 155-183 (187)
194 PRK11511 DNA-binding transcrip 40.8 37 0.0008 24.1 3.2 25 66-90 25-49 (127)
195 TIGR02607 antidote_HigA addict 40.7 23 0.00051 22.4 2.0 23 69-91 21-43 (78)
196 TIGR02950 SigM_subfam RNA poly 40.6 21 0.00046 25.5 1.9 33 64-96 119-151 (154)
197 PRK06424 transcription factor; 39.7 45 0.00097 24.7 3.6 24 69-92 100-123 (144)
198 PRK07122 RNA polymerase sigma 39.5 43 0.00093 27.0 3.7 47 46-97 216-262 (264)
199 PRK11922 RNA polymerase sigma 39.3 24 0.00053 27.6 2.2 36 63-98 162-197 (231)
200 PRK07539 NADH dehydrogenase su 38.2 60 0.0013 24.1 4.1 35 50-84 24-58 (154)
201 TIGR02393 RpoD_Cterm RNA polym 37.8 46 0.001 26.2 3.6 52 45-97 176-227 (238)
202 TIGR02835 spore_sigmaE RNA pol 37.6 59 0.0013 25.5 4.2 30 68-97 200-229 (234)
203 smart00530 HTH_XRE Helix-turn- 37.3 31 0.00067 18.9 2.0 23 69-91 13-35 (56)
204 PRK12517 RNA polymerase sigma 36.9 62 0.0014 24.4 4.1 30 68-97 146-175 (188)
205 PF05263 DUF722: Protein of un 36.9 59 0.0013 23.8 3.7 40 46-88 82-121 (130)
206 PF01710 HTH_Tnp_IS630: Transp 36.7 64 0.0014 22.7 3.9 37 47-88 4-40 (119)
207 PRK10840 transcriptional regul 36.4 57 0.0012 24.7 3.9 41 45-91 150-190 (216)
208 PF01257 2Fe-2S_thioredx: Thio 36.4 53 0.0012 24.1 3.5 35 50-84 15-49 (145)
209 TIGR02885 spore_sigF RNA polym 36.1 61 0.0013 25.2 4.1 44 45-93 183-226 (231)
210 PRK07571 bidirectional hydroge 36.0 71 0.0015 24.3 4.2 35 50-84 38-72 (169)
211 TIGR01958 nuoE_fam NADH-quinon 36.0 69 0.0015 23.5 4.1 36 49-84 17-52 (148)
212 PRK15411 rcsA colanic acid cap 35.7 58 0.0013 25.1 3.9 43 45-93 137-179 (207)
213 PRK13870 transcriptional regul 35.3 67 0.0014 25.5 4.2 25 70-94 192-216 (234)
214 smart00422 HTH_MERR helix_turn 35.1 30 0.00064 21.4 1.8 20 69-88 3-22 (70)
215 cd01106 HTH_TipAL-Mta Helix-Tu 35.1 31 0.00067 23.5 2.0 22 69-90 3-24 (103)
216 PRK05803 sporulation sigma fac 35.1 55 0.0012 25.6 3.7 31 67-97 196-226 (233)
217 PRK10188 DNA-binding transcrip 34.9 73 0.0016 25.3 4.4 45 45-95 179-223 (240)
218 PRK09726 antitoxin HipB; Provi 34.9 1.1E+02 0.0023 20.2 4.6 23 69-91 28-50 (88)
219 PRK11552 putative DNA-binding 34.8 40 0.00088 26.2 2.8 41 51-93 19-59 (225)
220 PRK08215 sporulation sigma fac 34.7 63 0.0014 25.7 4.0 47 45-96 209-255 (258)
221 PRK05911 RNA polymerase sigma 34.6 66 0.0014 25.8 4.1 47 46-97 206-252 (257)
222 PRK05572 sporulation sigma fac 34.4 63 0.0014 25.6 4.0 47 45-96 202-248 (252)
223 TIGR01557 myb_SHAQKYF myb-like 34.2 1E+02 0.0023 19.0 4.1 49 41-89 1-52 (57)
224 TIGR02846 spore_sigmaK RNA pol 34.1 69 0.0015 24.9 4.1 50 46-96 175-224 (227)
225 TIGR02392 rpoH_proteo alternat 34.0 51 0.0011 26.5 3.4 50 45-97 218-267 (270)
226 PRK10430 DNA-binding transcrip 34.0 55 0.0012 25.3 3.5 45 45-90 158-202 (239)
227 PF13309 HTH_22: HTH domain 33.8 87 0.0019 19.6 3.8 41 46-86 21-62 (64)
228 KOG3755|consensus 33.8 33 0.00071 31.5 2.3 60 37-96 645-708 (769)
229 PRK06704 RNA polymerase factor 33.7 60 0.0013 25.8 3.7 30 69-98 135-164 (228)
230 PF08671 SinI: Anti-repressor 33.6 51 0.0011 17.8 2.2 20 69-88 8-27 (30)
231 PRK09638 RNA polymerase sigma 33.4 33 0.00071 25.2 2.0 34 64-97 140-173 (176)
232 PF01726 LexA_DNA_bind: LexA D 33.4 83 0.0018 19.9 3.6 40 46-87 4-47 (65)
233 TIGR02984 Sig-70_plancto1 RNA 33.4 77 0.0017 23.3 4.1 29 68-96 158-186 (189)
234 PF13542 HTH_Tnp_ISL3: Helix-t 33.1 37 0.0008 19.8 1.9 20 69-88 30-49 (52)
235 PF07022 Phage_CI_repr: Bacter 33.1 26 0.00057 22.0 1.2 21 69-89 15-36 (66)
236 PRK09975 DNA-binding transcrip 32.6 33 0.00072 25.9 2.0 41 51-92 17-57 (213)
237 PF13560 HTH_31: Helix-turn-he 32.5 38 0.00082 20.8 1.9 25 68-92 16-40 (64)
238 PRK09640 RNA polymerase sigma 32.3 33 0.00072 25.7 1.9 31 67-97 151-181 (188)
239 PF00424 REV: REV protein (ant 31.9 32 0.00069 23.6 1.5 35 51-99 14-48 (91)
240 PRK09958 DNA-binding transcrip 31.4 65 0.0014 23.5 3.4 44 45-94 143-186 (204)
241 PRK08241 RNA polymerase factor 31.2 60 0.0013 26.8 3.4 29 68-96 171-199 (339)
242 PRK11475 DNA-binding transcrip 30.6 81 0.0018 24.5 3.9 43 45-93 134-176 (207)
243 PRK14996 TetR family transcrip 30.5 66 0.0014 23.9 3.3 41 51-92 14-54 (192)
244 cd01105 HTH_GlnR-like Helix-Tu 30.5 38 0.00082 22.5 1.8 19 69-87 4-22 (88)
245 PRK13890 conjugal transfer pro 30.4 40 0.00086 24.0 1.9 23 69-91 21-43 (120)
246 COG1595 RpoE DNA-directed RNA 30.2 38 0.00083 25.2 1.9 31 69-99 146-176 (182)
247 PRK09706 transcriptional repre 30.2 41 0.00088 24.1 2.0 24 69-92 21-44 (135)
248 PF00249 Myb_DNA-binding: Myb- 30.1 1.1E+02 0.0025 17.5 3.8 43 43-88 1-45 (48)
249 PF00440 TetR_N: Bacterial reg 30.1 41 0.00089 19.4 1.7 35 56-91 7-41 (47)
250 PRK10878 hypothetical protein; 29.9 1.1E+02 0.0025 19.8 3.9 44 50-93 3-48 (72)
251 cd04774 HTH_YfmP Helix-Turn-He 29.8 42 0.00091 22.8 1.9 21 69-89 3-23 (96)
252 PRK09483 response regulator; P 29.7 84 0.0018 23.2 3.8 44 44-93 147-190 (217)
253 PRK07500 rpoH2 RNA polymerase 29.3 65 0.0014 26.4 3.3 50 45-97 227-276 (289)
254 TIGR02394 rpoS_proteo RNA poly 28.9 91 0.002 25.3 4.1 52 46-98 223-274 (285)
255 PF08452 DNAP_B_exo_N: DNA pol 28.8 18 0.00039 18.0 -0.0 9 84-92 6-14 (22)
256 PF14549 P22_Cro: DNA-binding 28.8 44 0.00095 21.0 1.7 18 69-86 12-29 (60)
257 PF14229 DUF4332: Domain of un 28.5 55 0.0012 23.3 2.4 25 63-87 26-50 (122)
258 TIGR03629 arch_S13P archaeal r 28.4 65 0.0014 23.9 2.8 14 46-59 52-65 (144)
259 cd04766 HTH_HspR Helix-Turn-He 28.3 44 0.00095 22.3 1.8 21 69-89 4-24 (91)
260 PF10078 DUF2316: Uncharacteri 28.1 41 0.00088 23.0 1.6 38 46-87 3-44 (89)
261 PF12844 HTH_19: Helix-turn-he 27.9 51 0.0011 20.0 1.9 24 68-91 14-37 (64)
262 PF03444 HrcA_DNA-bdg: Winged 27.9 1.6E+02 0.0034 19.6 4.3 40 46-87 2-44 (78)
263 cd04779 HTH_MerR-like_sg4 Heli 27.4 46 0.001 24.2 1.9 23 69-91 3-25 (134)
264 PF12200 DUF3597: Domain of un 27.3 62 0.0013 23.6 2.5 31 63-93 82-117 (127)
265 PF12114 Period_C: Period prot 27.2 1.1E+02 0.0025 23.9 4.1 31 51-89 126-156 (195)
266 PF07954 DUF1689: Protein of u 26.9 84 0.0018 23.6 3.2 25 53-77 3-27 (152)
267 PF13565 HTH_32: Homeodomain-l 26.8 1.7E+02 0.0036 18.3 6.3 40 47-86 32-76 (77)
268 PF01047 MarR: MarR family; I 26.5 85 0.0018 18.6 2.7 39 46-88 1-39 (59)
269 PRK09635 sigI RNA polymerase s 26.5 1E+02 0.0022 25.2 4.0 29 69-97 137-165 (290)
270 cd04768 HTH_BmrR-like Helix-Tu 26.4 53 0.0011 22.2 1.9 22 69-90 3-24 (96)
271 PTZ00183 centrin; Provisional 26.3 2.3E+02 0.0051 19.8 5.9 41 38-78 3-48 (158)
272 COG2197 CitB Response regulato 26.2 1.1E+02 0.0023 23.8 3.9 41 44-90 147-187 (211)
273 cd04780 HTH_MerR-like_sg5 Heli 26.1 50 0.0011 22.4 1.8 20 69-88 3-22 (95)
274 PF12244 DUF3606: Protein of u 26.0 67 0.0014 19.8 2.2 18 67-84 21-38 (57)
275 PF04297 UPF0122: Putative hel 25.9 74 0.0016 22.2 2.6 42 45-91 17-58 (101)
276 cd04773 HTH_TioE_rpt2 Second H 25.9 54 0.0012 22.7 2.0 21 69-89 3-23 (108)
277 PRK09390 fixJ response regulat 25.9 96 0.0021 22.1 3.4 44 46-95 142-185 (202)
278 PRK15008 HTH-type transcriptio 25.6 86 0.0019 23.9 3.2 41 51-92 24-64 (212)
279 smart00354 HTH_LACI helix_turn 25.1 62 0.0013 20.4 2.0 23 69-91 3-25 (70)
280 PF12802 MarR_2: MarR family; 25.1 74 0.0016 18.9 2.3 38 46-85 3-40 (62)
281 TIGR03826 YvyF flagellar opero 24.8 1E+02 0.0022 22.7 3.3 48 46-93 20-73 (137)
282 PF04539 Sigma70_r3: Sigma-70 24.5 54 0.0012 20.8 1.6 20 69-88 23-42 (78)
283 TIGR03830 CxxCG_CxxCG_HTH puta 24.4 86 0.0019 21.7 2.8 22 70-91 82-103 (127)
284 PF07037 DUF1323: Putative tra 24.2 53 0.0011 23.7 1.6 20 69-88 3-22 (122)
285 TIGR01636 phage_rinA phage tra 24.1 1.2E+02 0.0025 21.9 3.5 38 46-86 83-120 (134)
286 PF06971 Put_DNA-bind_N: Putat 24.0 51 0.0011 19.9 1.3 17 69-85 31-47 (50)
287 cd04782 HTH_BltR Helix-Turn-He 23.5 63 0.0014 21.8 1.9 21 69-89 3-23 (97)
288 PRK08359 transcription factor; 23.4 1.4E+02 0.003 23.0 3.9 25 69-93 101-125 (176)
289 PRK10668 DNA-binding transcrip 23.3 52 0.0011 24.9 1.6 42 50-92 16-57 (215)
290 PRK06596 RNA polymerase factor 23.3 1E+02 0.0022 25.2 3.3 49 45-96 230-278 (284)
291 PF08880 QLQ: QLQ; InterPro: 23.2 81 0.0018 17.8 2.0 13 45-57 2-14 (37)
292 cd08315 Death_TRAILR_DR4_DR5 D 23.2 96 0.0021 21.2 2.8 34 51-84 3-37 (96)
293 PF13404 HTH_AsnC-type: AsnC-t 23.1 55 0.0012 18.8 1.3 16 69-84 20-35 (42)
294 cd04767 HTH_HspR-like_MBC Heli 23.0 65 0.0014 23.1 1.9 22 69-90 4-25 (120)
295 PRK15451 tRNA cmo(5)U34 methyl 23.0 1.9E+02 0.0041 22.8 4.8 43 46-90 190-233 (247)
296 PRK00215 LexA repressor; Valid 22.8 92 0.002 23.8 2.9 42 46-89 2-47 (205)
297 cd01279 HTH_HspR-like Helix-Tu 22.8 67 0.0015 21.8 1.9 21 69-89 4-24 (98)
298 cd04775 HTH_Cfa-like Helix-Tur 22.5 64 0.0014 22.0 1.8 21 69-89 4-24 (102)
299 cd00592 HTH_MerR-like Helix-Tu 22.4 70 0.0015 21.4 1.9 21 69-89 3-23 (100)
300 cd04765 HTH_MlrA-like_sg2 Heli 22.3 65 0.0014 22.0 1.8 21 69-89 3-23 (99)
301 PF08784 RPA_C: Replication pr 22.2 57 0.0012 22.1 1.5 42 45-86 44-85 (102)
302 PHA03273 envelope glycoprotein 21.9 19 0.00041 31.9 -1.2 23 73-96 113-135 (486)
303 cd04788 HTH_NolA-AlbR Helix-Tu 21.8 72 0.0015 21.5 1.9 21 69-89 3-23 (96)
304 smart00595 MADF subfamily of S 21.7 73 0.0016 20.7 1.9 30 70-99 31-60 (89)
305 PF05703 Auxin_canalis: Auxin 21.7 74 0.0016 25.8 2.2 18 79-96 99-116 (242)
306 cd01109 HTH_YyaN Helix-Turn-He 21.6 69 0.0015 22.2 1.8 20 69-88 3-22 (113)
307 PF09862 DUF2089: Protein of u 21.5 1.9E+02 0.0042 20.6 4.1 38 45-87 33-70 (113)
308 TIGR02054 MerD mercuric resist 21.5 69 0.0015 22.9 1.8 21 69-89 6-26 (120)
309 PF00325 Crp: Bacterial regula 21.4 69 0.0015 17.5 1.4 20 68-87 4-23 (32)
310 PF08765 Mor: Mor transcriptio 21.4 60 0.0013 22.5 1.5 26 68-93 74-99 (108)
311 PF14771 DUF4476: Domain of un 21.4 2.4E+02 0.0053 18.7 4.5 40 43-82 19-58 (95)
312 TIGR03613 RutR pyrimidine util 21.4 96 0.0021 23.1 2.7 39 52-91 15-53 (202)
313 PF13022 HTH_Tnp_1_2: Helix-tu 21.2 1.1E+02 0.0023 22.8 2.7 23 66-88 34-56 (142)
314 PF06163 DUF977: Bacterial pro 20.9 1.2E+02 0.0025 22.2 2.9 42 45-89 4-49 (127)
315 cd04789 HTH_Cfa Helix-Turn-Hel 20.6 75 0.0016 21.7 1.8 22 69-90 4-25 (102)
316 cd01111 HTH_MerD Helix-Turn-He 20.0 78 0.0017 22.0 1.8 21 69-89 3-23 (107)
No 1
>KOG0488|consensus
Probab=99.84 E-value=4e-21 Score=158.76 Aligned_cols=74 Identities=46% Similarity=0.775 Sum_probs=67.8
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 26 NRGRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 26 ~~~~~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..........++|.||.|++||..||..||+.|++.+|++..+|++||..|||++.||++||||||+||||+..
T Consensus 159 ~~~~~~~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 159 QTNHPYQRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred ccCCCcccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 33555556677999999999999999999999999999999999999999999999999999999999999754
No 2
>KOG0850|consensus
Probab=99.82 E-value=2.8e-20 Score=145.37 Aligned_cols=69 Identities=45% Similarity=0.640 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100 33 TQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101 (165)
Q Consensus 33 ~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~ 101 (165)
..+.||.||.||.|+..||..|++.|++++|+...||.+||..|||+..||||||||||.|.||..+.+
T Consensus 116 Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 116 NGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 446788999999999999999999999999999999999999999999999999999999999987643
No 3
>KOG0842|consensus
Probab=99.82 E-value=2e-20 Score=153.10 Aligned_cols=70 Identities=44% Similarity=0.596 Sum_probs=64.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNS 105 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~ 105 (165)
.+++||.|..|+..|+-+||+.|.+++|++..||+.||..|+|+++||||||||||-|+||++.+...+.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 5678888999999999999999999999999999999999999999999999999999999887554443
No 4
>KOG0489|consensus
Probab=99.81 E-value=3.2e-20 Score=150.49 Aligned_cols=70 Identities=44% Similarity=0.719 Sum_probs=64.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCC
Q psy15100 35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVN 104 (165)
Q Consensus 35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~ 104 (165)
...+.||.|+.||..|+.+||+.|..|+|++...|.+||..|+|+|+||||||||||+||||..+.....
T Consensus 155 ~~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 155 TGGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred ccCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 3456889999999999999999999999999999999999999999999999999999999988765544
No 5
>KOG0487|consensus
Probab=99.79 E-value=4.3e-20 Score=151.21 Aligned_cols=68 Identities=41% Similarity=0.575 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 32 NTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 32 ~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
+-...+..||||.-+|+.|+.+||+.|..|.|++.+.|.+|++.|+|+++||+|||||||+|+||..+
T Consensus 228 ~~~~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 228 NASSARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 44556788999999999999999999999999999999999999999999999999999999999875
No 6
>KOG0485|consensus
Probab=99.78 E-value=5.7e-19 Score=137.05 Aligned_cols=64 Identities=52% Similarity=0.788 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..++||.|++|+..|+..||..|+..+|++..||..||+.|.|+|.||||||||||.||||+..
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 4478889999999999999999999999999999999999999999999999999999999854
No 7
>KOG0484|consensus
Probab=99.78 E-value=1.8e-19 Score=125.02 Aligned_cols=64 Identities=39% Similarity=0.639 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
.+|.++-|+.|+..||.+||+.|.+..||++-.|++||.++.|++..|+|||||||+|.||+++
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3567788999999999999999999999999999999999999999999999999999999865
No 8
>KOG2251|consensus
Probab=99.76 E-value=4.6e-19 Score=137.87 Aligned_cols=66 Identities=39% Similarity=0.641 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..++|.||+||.|+..|+++||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 678999999999999999999999999999999999999999999999999999999999998765
No 9
>KOG0843|consensus
Probab=99.75 E-value=7.3e-19 Score=132.88 Aligned_cols=63 Identities=51% Similarity=0.685 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100 38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100 (165)
Q Consensus 38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~ 100 (165)
+.||.||.|+.+||..||..|+.+.|..-.||++||..|+|++.||+|||||||.|.||.+..
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 788899999999999999999999999999999999999999999999999999999997654
No 10
>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=99.75 E-value=1.8e-18 Score=109.03 Aligned_cols=57 Identities=53% Similarity=0.609 Sum_probs=55.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
|++|+.|+.+|+.+|+..|..++||+..+++.||.+|||+..+|++||+|||.++||
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 578899999999999999999999999999999999999999999999999999986
No 11
>KOG0848|consensus
Probab=99.73 E-value=1e-18 Score=139.16 Aligned_cols=63 Identities=41% Similarity=0.619 Sum_probs=58.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100 39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101 (165)
Q Consensus 39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~ 101 (165)
+-|-|.++|+.|+.+||+.|..++|+++..+.+||..|||+|+||||||||||+|+||..+..
T Consensus 199 kDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 199 KDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 345588999999999999999999999999999999999999999999999999999976544
No 12
>KOG0492|consensus
Probab=99.73 E-value=2.3e-18 Score=132.84 Aligned_cols=62 Identities=53% Similarity=0.811 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..||+|+.||..||..||+.|.+.+|.+++||.+++..|.|++.||+|||||||+|.||.++
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 36788999999999999999999999999999999999999999999999999999999764
No 13
>KOG0494|consensus
Probab=99.72 E-value=1.4e-17 Score=132.40 Aligned_cols=61 Identities=39% Similarity=0.602 Sum_probs=57.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
+|.-||.||..|++.||+.|++..||+...|+.||.+++|.|..|+|||||||+||||.++
T Consensus 141 RRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 141 RRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 3334999999999999999999999999999999999999999999999999999999875
No 14
>KOG0493|consensus
Probab=99.72 E-value=1e-17 Score=133.19 Aligned_cols=65 Identities=46% Similarity=0.715 Sum_probs=60.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..+..||+|+.|+.+||+.|+..|+.|+|++...|.+||.+|+|.+.||+|||||+|+|.||-..
T Consensus 242 ~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 242 SSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred ccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 34456788999999999999999999999999999999999999999999999999999998753
No 15
>KOG0491|consensus
Probab=99.69 E-value=1e-17 Score=125.07 Aligned_cols=66 Identities=48% Similarity=0.648 Sum_probs=61.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGM 101 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~ 101 (165)
..+++|.|++|+..|+..||+.|+..+|.+..|+.+||..|+|+++||+.||||||+|.||+.+..
T Consensus 97 ~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 97 HCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 345678899999999999999999999999999999999999999999999999999999987643
No 16
>KOG3802|consensus
Probab=99.67 E-value=1.1e-16 Score=133.93 Aligned_cols=62 Identities=29% Similarity=0.369 Sum_probs=60.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
++||+||.|....+..||++|.+|+.|+.+|+..||.+|+|.+++|+|||||||.|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 78899999999999999999999999999999999999999999999999999999999887
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=2.3e-16 Score=98.74 Aligned_cols=56 Identities=52% Similarity=0.769 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
++.|+.|+.+|+.+|+..|..+.||+..++..||..+||+..+|++||+|||.+.+
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 35678899999999999999999999999999999999999999999999998864
No 18
>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=99.65 E-value=3.1e-16 Score=98.88 Aligned_cols=57 Identities=53% Similarity=0.693 Sum_probs=54.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+.|..|+.+|+.+||..|..++||+..+++.||.++||++.+|++||+|||.+.++.
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 567889999999999999999999999999999999999999999999999998864
No 19
>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=99.64 E-value=2.9e-16 Score=99.35 Aligned_cols=53 Identities=17% Similarity=0.245 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 39 DLVPESAFTYEQLVALENKFKTTRY----LSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 39 ~~~~R~~~s~~Ql~~Le~~F~~~~~----p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
++|.||.|+.+|+..||..|+.++| |+..++++||..|||++.+|++||||.+
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 20
>KOG0844|consensus
Probab=99.63 E-value=5.1e-16 Score=125.92 Aligned_cols=71 Identities=41% Similarity=0.554 Sum_probs=64.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCCCCCCCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPGMDVNSP 106 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~~~~~~~ 106 (165)
...-||-|+.||.+|+..||+.|-+..|.+...|.+||..|+|.|..||+||||||+|+||+.-.+....+
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhp 248 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHP 248 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCC
Confidence 34557789999999999999999999999999999999999999999999999999999999876666554
No 21
>KOG0486|consensus
Probab=99.62 E-value=2.3e-16 Score=128.28 Aligned_cols=64 Identities=38% Similarity=0.694 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100 37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100 (165)
Q Consensus 37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~ 100 (165)
+|+||.|+.|+..||.+||..|++++||+...|++||..++|++..|++||+|||+||||+++.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN 173 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERN 173 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhh
Confidence 4678889999999999999999999999999999999999999999999999999999998763
No 22
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.59 E-value=1.5e-15 Score=114.27 Aligned_cols=67 Identities=37% Similarity=0.548 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100 34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100 (165)
Q Consensus 34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~ 100 (165)
......+++|.+.+.+|+.+|+..|+.++||+..+|..|+..|+|+++.|+|||||||++.|+....
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3445677788899999999999999999999999999999999999999999999999999987664
No 23
>KOG0483|consensus
Probab=99.58 E-value=1.3e-15 Score=118.46 Aligned_cols=60 Identities=35% Similarity=0.568 Sum_probs=55.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 39 DLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 39 ~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...++.+|+.+|+..||..|+.+.+....++..||++|||.++||.|||||||+|||.++
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 445567799999999999999999999999999999999999999999999999999865
No 24
>KOG4577|consensus
Probab=99.46 E-value=5.4e-14 Score=113.47 Aligned_cols=65 Identities=28% Similarity=0.391 Sum_probs=60.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 35 TPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 35 ~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
.....||+|+.++..||+.|+..|+..+.|....|++|+.++||.-+.|+|||||||+|+||.++
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 34557889999999999999999999999999999999999999999999999999999998754
No 25
>KOG0847|consensus
Probab=99.46 E-value=3.6e-14 Score=110.61 Aligned_cols=63 Identities=46% Similarity=0.795 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
.+++..|-.|+..|+..||..|+..+|+-.+++.+||..+|+++.+|+|||||||.||||+..
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 455666788999999999999999999999999999999999999999999999999999754
No 26
>KOG0490|consensus
Probab=99.31 E-value=8.6e-13 Score=104.16 Aligned_cols=64 Identities=34% Similarity=0.438 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..++++.|+.|+..|+++||+.|+...||+...++.||..+++++..|++||||||+||+++.+
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 4577889999999999999999999999999999999999999999999999999999999874
No 27
>KOG0849|consensus
Probab=99.27 E-value=1.4e-11 Score=103.87 Aligned_cols=71 Identities=35% Similarity=0.591 Sum_probs=64.1
Q ss_pred CCCCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 28 GRSPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 28 ~~~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.........++.++.|+.|+..|++.||+.|+.++||++..|++||.+++|++..|++||+|||++++|..
T Consensus 165 ~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 165 EEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33444555667778899999999999999999999999999999999999999999999999999999987
No 28
>KOG0775|consensus
Probab=99.20 E-value=6.5e-11 Score=95.08 Aligned_cols=53 Identities=32% Similarity=0.399 Sum_probs=48.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
|...-..+|.++|..++||+..++.+||+.+||+..||-+||+|||+++|-..
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 44445789999999999999999999999999999999999999999999543
No 29
>KOG1168|consensus
Probab=99.16 E-value=7.9e-12 Score=101.12 Aligned_cols=64 Identities=23% Similarity=0.280 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 36 PSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 36 ~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..++||+|+.+-.-+...||.+|...+.|+.+.+..||++|.|.+..|++||||.|+|.||...
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4578889999999999999999999999999999999999999999999999999999999653
No 30
>KOG0774|consensus
Probab=99.06 E-value=5.5e-10 Score=89.33 Aligned_cols=58 Identities=28% Similarity=0.399 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 40 LVPESAFTYEQLVALENKFK---TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 40 ~~~R~~~s~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+|+|..|++.-.++|.++|- .++||+.+++++||+++|++..||.+||.|+|-+.||.
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 57788899999999999995 67899999999999999999999999999999999884
No 31
>KOG2252|consensus
Probab=98.82 E-value=1.9e-08 Score=87.72 Aligned_cols=66 Identities=23% Similarity=0.213 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 30 SPNTQTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 30 ~~~~~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.+....--..||.|.+|+..|++.|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|.|.+
T Consensus 411 ep~~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 411 EPTDDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCCccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 333444556778899999999999999999999999999999999999999999999999887753
No 32
>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=98.71 E-value=8.3e-09 Score=60.56 Aligned_cols=34 Identities=32% Similarity=0.482 Sum_probs=28.8
Q ss_pred hcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 60 TTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 60 ~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.++||+.+|+++|+.++||+..||..||-|.|.+
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 4789999999999999999999999999998864
No 33
>KOG0490|consensus
Probab=98.24 E-value=1.1e-06 Score=69.20 Aligned_cols=66 Identities=33% Similarity=0.512 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 34 QTPSEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 34 ~~~~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
....+.++.|+.+...|+..|+..|....+|+...++.|+..+|+.+..|++||+|+|.+.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 344567788999999999999999999999999999999999999999999999999999998765
No 34
>KOG1146|consensus
Probab=98.00 E-value=1.6e-05 Score=75.54 Aligned_cols=63 Identities=22% Similarity=0.259 Sum_probs=58.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 37 SEDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 37 ~~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
-.++..|+.++..||.+|..+|+...++..++.+.|...+++..+.|++||||-|.|.|+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 346778999999999999999999999999999999999999999999999999999998765
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.57 E-value=5.1e-05 Score=47.42 Aligned_cols=43 Identities=21% Similarity=0.318 Sum_probs=31.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
+..|+..|...+++...+...|..+.+|+..||+.||-.|+.+
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 4669999999999999999999999999999999999765443
No 36
>KOG0773|consensus
Probab=97.17 E-value=0.00042 Score=58.21 Aligned_cols=58 Identities=29% Similarity=0.349 Sum_probs=49.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 39 DLVPESAFTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 39 ~~~~R~~~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++++..+......+|+.+... .+||+..++..|+.++||+..||.+||-|.|.+..+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 5556668999999999988443 469999999999999999999999999999887554
No 37
>KOG3623|consensus
Probab=96.71 E-value=0.0034 Score=57.22 Aligned_cols=49 Identities=18% Similarity=0.199 Sum_probs=46.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
+.+|..+|..|..|..++...|+.+.||..+.|+.||+++++++...++
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 7899999999999999999999999999999999999999999888764
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=95.98 E-value=0.019 Score=35.35 Aligned_cols=46 Identities=11% Similarity=0.271 Sum_probs=35.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100 40 LVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 40 ~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNR 90 (165)
+++|..+|-++...+-..++... ....||.++|+...+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46788899999888878887776 47789999999999999999884
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=90.46 E-value=0.48 Score=28.22 Aligned_cols=46 Identities=9% Similarity=0.116 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.+++.+..+|...|..+ ..-.++|..+|++...|+.+...-..|-|
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 46788999999999322 34678899999999999998765554443
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=87.81 E-value=0.96 Score=26.08 Aligned_cols=44 Identities=11% Similarity=0.111 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.++..+..+++..|..+ ....++|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 36777888888777433 245678999999999999998754443
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=85.87 E-value=0.89 Score=29.19 Aligned_cols=44 Identities=7% Similarity=0.092 Sum_probs=28.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 41 VPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
++|..|+.++...+-..+... ......||.++||+...|..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence 456789999877766665222 24677899999999999999964
No 42
>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=85.49 E-value=2.6 Score=21.65 Aligned_cols=38 Identities=13% Similarity=0.157 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
.++.++...+...|... . ...+++..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35666666666666533 2 45678899999999988884
No 43
>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=85.46 E-value=1.5 Score=26.33 Aligned_cols=42 Identities=17% Similarity=0.156 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
+++.+..++...|..+ ....++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4566666666655433 35778999999999999999975443
No 44
>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=84.57 E-value=1.8 Score=26.64 Aligned_cols=42 Identities=17% Similarity=0.153 Sum_probs=33.4
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRY--LSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~--p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
+|+.|+++|...|+..=| |-.....+||.+||++...|..-.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 578899999999986543 666677899999999998765544
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=84.05 E-value=2.3 Score=31.60 Aligned_cols=50 Identities=20% Similarity=0.125 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+++.|+.+|+..+ .. ....+||..||++...|..|.++.+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568999999998843 22 23567899999999999999998777766643
No 46
>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=80.13 E-value=2.9 Score=25.57 Aligned_cols=44 Identities=20% Similarity=0.149 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
.||..++++|.-...-. ...++|..+++++..|+.+..+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 47888999887776543 367899999999999999988766554
No 47
>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=78.77 E-value=5.2 Score=25.15 Aligned_cols=43 Identities=23% Similarity=0.287 Sum_probs=22.7
Q ss_pred CCCCHHH-HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 44 SAFTYEQ-LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 44 ~~~s~~Q-l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
..|+... |.+++..+..+. --...|. .|.++|+.+++|+-|-+
T Consensus 4 rsy~~~FKL~Vv~~a~~~~n-c~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNN-CKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHHH-TT-TTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHHHccc-hhhhHHH-HHHHhCccHHHHHHHHH
Confidence 3455544 445554443333 2223333 49999999999999975
No 48
>PF15063 TC1: Thyroid cancer protein 1
Probab=78.68 E-value=4.1 Score=27.03 Aligned_cols=38 Identities=16% Similarity=0.150 Sum_probs=31.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCch
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTET 81 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~ 81 (165)
..|....+..|.+.|+...=...+||.+|.-.+.-...
T Consensus 32 NIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~e 69 (79)
T PF15063_consen 32 NIFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDPE 69 (79)
T ss_pred hhhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCHH
Confidence 35888889999999999999999999998766655544
No 49
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=78.45 E-value=1.5 Score=27.78 Aligned_cols=19 Identities=21% Similarity=0.489 Sum_probs=16.8
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WF 87 (165)
-.+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4568999999999999994
No 50
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=77.37 E-value=4.2 Score=30.91 Aligned_cols=31 Identities=13% Similarity=0.076 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..||++...|+.+...-|.+.|+..
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 4567899999999999999987777766653
No 51
>PRK04217 hypothetical protein; Provisional
Probab=77.09 E-value=5.1 Score=28.45 Aligned_cols=50 Identities=16% Similarity=0.061 Sum_probs=39.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
=..++.+|+.++...|...- ...+||+.+|++...|+..+..-+.+.+..
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35688999988877765443 467799999999999999988777766654
No 52
>KOG3755|consensus
Probab=76.21 E-value=0.73 Score=41.70 Aligned_cols=48 Identities=21% Similarity=0.203 Sum_probs=32.3
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhC-------CCchhhhhhhhcchhhhhhhCCCCC
Q psy15100 55 ENKFKTTRYLSVCERLNLALSLS-------LTETQVKIWFQNRRTKWKKQNPGMD 102 (165)
Q Consensus 55 e~~F~~~~~p~~~~r~~La~~lg-------l~~~qV~~WFqNRR~k~kr~~~~~~ 102 (165)
+.+|..+..+......+.-.++. ...+.|+.||+|||.++++.+-..+
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~~d 762 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMSYD 762 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhccCC
Confidence 44555666666665555444433 3557899999999999999865433
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=75.82 E-value=5 Score=28.92 Aligned_cols=46 Identities=15% Similarity=0.143 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
+++.+..++...|-.+ ....+||..+|++...|+.|...-+.+.|+
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 3444445544443322 346789999999999999998765555443
No 54
>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=74.60 E-value=1.4 Score=29.06 Aligned_cols=34 Identities=18% Similarity=0.056 Sum_probs=25.4
Q ss_pred HHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100 56 NKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 56 ~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN 89 (165)
..|....+.......+||..+|+++..|+.|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3454444444445788999999999999999975
No 55
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=73.96 E-value=3.3 Score=24.14 Aligned_cols=40 Identities=15% Similarity=0.101 Sum_probs=21.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
..++.++...++..++.. .-..+||..||.+...|..|.+
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 357888888888886533 3456799999999999988864
No 56
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=73.54 E-value=6.7 Score=29.30 Aligned_cols=32 Identities=16% Similarity=0.122 Sum_probs=26.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
.-.+||..||++...|+.++..-|.+.|+...
T Consensus 149 s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 149 SIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 35678999999999999999887777776543
No 57
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=73.13 E-value=5.8 Score=28.88 Aligned_cols=31 Identities=19% Similarity=0.127 Sum_probs=25.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..+||..+|+++..|+..+..-|.+.|+..+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999877777766543
No 58
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=73.06 E-value=6 Score=30.46 Aligned_cols=31 Identities=26% Similarity=0.147 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|+++..|+.+...-+.+.++..
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766654
No 59
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=72.85 E-value=9 Score=22.23 Aligned_cols=41 Identities=20% Similarity=0.139 Sum_probs=29.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
.++..+..++...+. . ....++|..+|++...|..|.+.-+
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 367778887766432 2 2457889999999999999987433
No 60
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=72.25 E-value=6.3 Score=28.95 Aligned_cols=47 Identities=11% Similarity=-0.024 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+++.+..+|...|-. .....+||..+|++...|+.|...-+.+.|+.
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 445555555444322 22355789999999999999998666665554
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=71.07 E-value=6.9 Score=28.63 Aligned_cols=30 Identities=17% Similarity=0.122 Sum_probs=24.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.|...-|.+.|+.
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356899999999999999998766666553
No 62
>KOG1146|consensus
Probab=70.72 E-value=9.2 Score=37.87 Aligned_cols=61 Identities=16% Similarity=0.199 Sum_probs=54.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 38 EDLVPESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 38 ~~~~~R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..+..|..+-.+++.+|-.+|-.+.-|+...+..|......+.+++.+||+|-|.+.++..
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 3445567777899999999999999999999999999999999999999999999988765
No 63
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=70.55 E-value=8.4 Score=28.64 Aligned_cols=30 Identities=13% Similarity=0.233 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|+++..|+++...-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 356799999999999999998777766654
No 64
>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=70.51 E-value=3.7 Score=23.72 Aligned_cols=22 Identities=9% Similarity=0.024 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcc
Q psy15100 69 RLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNR 90 (165)
..++|+.+|++...|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997654
No 65
>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=69.53 E-value=8.1 Score=23.86 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=28.7
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 48 YEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 48 ~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
..|+..|+-.++ +...+.. +||..+|++++.|+.-..
T Consensus 5 ~rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 5 KRQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 357888998898 7777654 789999999999887654
No 66
>PRK00118 putative DNA-binding protein; Validated
Probab=69.52 E-value=9.9 Score=26.70 Aligned_cols=47 Identities=11% Similarity=-0.002 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
++..|..++...|..+. ...+||..+|++...|..|...-|.+.|+.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56667777766655433 356789999999999999998777766653
No 67
>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=69.29 E-value=8.5 Score=27.81 Aligned_cols=28 Identities=21% Similarity=0.105 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
...+||..+|++...|+.+...-|.+.|
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4667899999999999999875555544
No 68
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=68.96 E-value=6.4 Score=29.71 Aligned_cols=31 Identities=16% Similarity=0.107 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
....+||..+|++...|+.|+..-|.+.|+.
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999998766666653
No 69
>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=68.86 E-value=8.5 Score=26.83 Aligned_cols=29 Identities=21% Similarity=0.237 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..+|+++..|+.|...-+.|.|+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999998866665544
No 70
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=68.85 E-value=9.8 Score=27.02 Aligned_cols=42 Identities=12% Similarity=0.109 Sum_probs=28.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
|..|+.++....-.....+.. ...++|.++||+...|..|.+
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 456888875544333333332 356789999999999999953
No 71
>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=68.18 E-value=9.3 Score=28.35 Aligned_cols=31 Identities=26% Similarity=0.219 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|+++..|+.+...-|.+.++..
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987777666654
No 72
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=68.12 E-value=8.3 Score=26.40 Aligned_cols=40 Identities=18% Similarity=0.156 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKI 85 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~ 85 (165)
+.++|+..-.+.|+.+--.+....+++|.+|++++..|+.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 5677877777777777666667788899999999876653
No 73
>PF13518 HTH_28: Helix-turn-helix domain
Probab=67.96 E-value=4.4 Score=23.74 Aligned_cols=21 Identities=14% Similarity=0.389 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|.++||+..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 556899999999999999864
No 74
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=67.60 E-value=9.5 Score=28.65 Aligned_cols=30 Identities=10% Similarity=0.071 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|++...|+.+...-|.+-|+.
T Consensus 157 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 157 SAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466799999999999999987666665543
No 75
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=67.33 E-value=9.9 Score=28.25 Aligned_cols=29 Identities=14% Similarity=0.041 Sum_probs=23.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..||+++..|++....-|.+.|+.
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998767666553
No 76
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=67.24 E-value=9.4 Score=27.83 Aligned_cols=30 Identities=23% Similarity=0.167 Sum_probs=23.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-|.+-|+.
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 356789999999999999988666665543
No 77
>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=67.06 E-value=11 Score=27.05 Aligned_cols=29 Identities=14% Similarity=0.180 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..+|+++..|+.+...-|.|.|+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999998765555543
No 78
>PRK10072 putative transcriptional regulator; Provisional
Probab=65.94 E-value=5 Score=27.76 Aligned_cols=24 Identities=25% Similarity=0.278 Sum_probs=21.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcchh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
..+||..+|++...|..|.+.+|.
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 567899999999999999987764
No 79
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=65.81 E-value=10 Score=27.77 Aligned_cols=30 Identities=20% Similarity=0.078 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|+++..|+.|.+.-|.+.|+.
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998777776664
No 80
>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=65.53 E-value=7.9 Score=28.88 Aligned_cols=32 Identities=9% Similarity=-0.043 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..-.+||..+|++...|+++...-|.+-|+..
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 34568999999999999999987666666553
No 81
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=65.21 E-value=11 Score=28.25 Aligned_cols=32 Identities=16% Similarity=0.091 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
...+||..+|++...|++-+..-|.+.|+...
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999877777776543
No 82
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=65.13 E-value=14 Score=27.26 Aligned_cols=33 Identities=12% Similarity=0.148 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~ 100 (165)
.-.+||..+|++...|+.+..+-+.+.+....+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~~l~~ 169 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYIALYG 169 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhcC
Confidence 356789999999999999998877777765443
No 83
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=65.12 E-value=5.3 Score=23.37 Aligned_cols=23 Identities=17% Similarity=0.348 Sum_probs=17.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhc
Q psy15100 67 CERLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqN 89 (165)
....++|..||++...|..|.+.
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 34677899999999999999753
No 84
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=65.03 E-value=10 Score=28.45 Aligned_cols=31 Identities=10% Similarity=0.172 Sum_probs=25.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..+||..+|++...|+.+...-|.+.|+...
T Consensus 147 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999877777776543
No 85
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=64.74 E-value=9.4 Score=29.78 Aligned_cols=49 Identities=24% Similarity=0.266 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhcC--CCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 45 AFTYEQLVALENKFKTTR--YLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~--~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.+|..|+++|...|...= +|-.....+||++||+++..+. ..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~--ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLS--EHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH--HHHHHHHHH
Confidence 599999999999998653 4777778899999999997544 444455443
No 86
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=64.63 E-value=11 Score=28.41 Aligned_cols=29 Identities=3% Similarity=0.148 Sum_probs=23.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..+|+++..|+.+...-|.+.|+.
T Consensus 153 ~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 153 SEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999998666666553
No 87
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=64.24 E-value=19 Score=24.20 Aligned_cols=44 Identities=16% Similarity=0.195 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 45 AFTYEQLVALENKFKT-----TRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~-----~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
.++.+|+..|...|.. +.+.+..+..++-..+|+++..|..+|.
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 4688899999999864 3478888888877778999998888885
No 88
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=64.18 E-value=13 Score=27.79 Aligned_cols=29 Identities=17% Similarity=0.307 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..+|++...|+.|...-+.+.|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 35678999999999999998866655554
No 89
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=63.97 E-value=10 Score=28.12 Aligned_cols=31 Identities=23% Similarity=0.198 Sum_probs=24.9
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+++|..+|++...|+++++.-|.+.|..
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999998767666654
No 90
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=63.59 E-value=14 Score=26.74 Aligned_cols=29 Identities=17% Similarity=0.116 Sum_probs=23.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..||++...|++....-|.+.|+.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999988666666654
No 91
>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=63.17 E-value=18 Score=26.70 Aligned_cols=48 Identities=19% Similarity=0.138 Sum_probs=37.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.+.++..|+.+|+-.+ ..+ ...+||..+|++...|..|-..-+.+-++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KGL----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999998842 221 46788999999999999998877766665
No 92
>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=63.03 E-value=13 Score=27.01 Aligned_cols=31 Identities=13% Similarity=0.143 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|++...|+.+...-|.+-|+..
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 158 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRELL 158 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 3567899999999999999987777766653
No 93
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=62.67 E-value=13 Score=28.03 Aligned_cols=31 Identities=26% Similarity=0.213 Sum_probs=25.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|++...|+..+..-|.+.|+..
T Consensus 124 ~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (181)
T PRK09637 124 SQKEIAEKLGLSLSGAKSRVQRGRVKLKELL 154 (181)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999987776666543
No 94
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=62.55 E-value=14 Score=27.58 Aligned_cols=31 Identities=16% Similarity=0.074 Sum_probs=25.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..||++...|++....-|.+.|+..
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~l 177 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAKI 177 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 4567899999999999999988777777654
No 95
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=62.32 E-value=18 Score=27.04 Aligned_cols=29 Identities=14% Similarity=0.187 Sum_probs=24.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.++||..||+++..|+.....-+.+++..
T Consensus 146 ~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 146 QKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 56789999999999999998777776654
No 96
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=62.10 E-value=14 Score=26.95 Aligned_cols=30 Identities=20% Similarity=0.297 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-|.+.|+.
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999997766666654
No 97
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=61.85 E-value=16 Score=26.92 Aligned_cols=30 Identities=17% Similarity=0.134 Sum_probs=24.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.++||..||+++..|+.....-|.+.|+..
T Consensus 137 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 166 (173)
T PRK09645 137 TAQIAADLGIPEGTVKSRLHYALRALRLAL 166 (173)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 567899999999999999876666666654
No 98
>PRK06930 positive control sigma-like factor; Validated
Probab=61.85 E-value=14 Score=28.01 Aligned_cols=48 Identities=13% Similarity=0.034 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.+++.+..+|...|.... .-.+||..+|++...|+.+...-+.|.++.
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355666666655443222 356789999999999999998777776654
No 99
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=61.75 E-value=12 Score=28.43 Aligned_cols=31 Identities=13% Similarity=-0.034 Sum_probs=25.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...++|..||++...|++++..-|.+.|+..
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777777653
No 100
>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=61.45 E-value=7.9 Score=21.81 Aligned_cols=24 Identities=13% Similarity=0.318 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCchhhhhhhhcchh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
..++|..||++...|..|.++..-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876543
No 101
>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=61.28 E-value=7 Score=24.39 Aligned_cols=26 Identities=27% Similarity=0.519 Sum_probs=20.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
..+||..|||....|..|-+ |.+|..
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 56789999999999999965 444443
No 102
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=60.80 E-value=6.8 Score=23.99 Aligned_cols=24 Identities=8% Similarity=0.192 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcch
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
....||+.+|++...|..|+.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 456799999999999999998773
No 103
>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=60.62 E-value=21 Score=20.70 Aligned_cols=36 Identities=19% Similarity=0.096 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 47 s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
+..+..++...+ +. ....++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455666665543 22 2467789999999999999986
No 104
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=60.35 E-value=12 Score=29.66 Aligned_cols=31 Identities=13% Similarity=0.114 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..||+++..|+.+...-|.+.|+..
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777776654
No 105
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=60.23 E-value=16 Score=21.21 Aligned_cols=37 Identities=11% Similarity=0.248 Sum_probs=25.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
++.++.+.+.+.+... ....+||+.+|++...|.-++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5665666666666654 246789999999999998776
No 106
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=60.17 E-value=17 Score=26.40 Aligned_cols=29 Identities=17% Similarity=0.256 Sum_probs=23.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++|..+|++...|+.....-+.+.|+.
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999987666666654
No 107
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=59.49 E-value=17 Score=26.64 Aligned_cols=30 Identities=23% Similarity=0.259 Sum_probs=23.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...++|..||++...|+.+...-|.+.|+.
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999987666665553
No 108
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=59.46 E-value=17 Score=26.69 Aligned_cols=30 Identities=10% Similarity=0.027 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|++...|+.+...-|.+.|..
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 366789999999999999998766666554
No 109
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=59.34 E-value=18 Score=26.94 Aligned_cols=30 Identities=17% Similarity=0.082 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-|.+.|+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999987666665554
No 110
>PRK09480 slmA division inhibitor protein; Provisional
Probab=58.92 E-value=11 Score=28.09 Aligned_cols=39 Identities=15% Similarity=0.184 Sum_probs=30.7
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 52 ~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
+.....|..+.. .......||++.|++...+-.+|.|+-
T Consensus 17 ~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~ 55 (194)
T PRK09480 17 QALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKA 55 (194)
T ss_pred HHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHH
Confidence 333444555555 777889999999999999999999975
No 111
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=58.73 E-value=17 Score=27.01 Aligned_cols=30 Identities=17% Similarity=0.171 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.....-|.+.|+.
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 164 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQK 164 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355789999999999999998877777764
No 112
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=58.62 E-value=20 Score=26.94 Aligned_cols=28 Identities=7% Similarity=-0.047 Sum_probs=23.2
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++||..+|++...|+.+...-|.+.|+
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5678999999999999999766666665
No 113
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=58.52 E-value=16 Score=28.62 Aligned_cols=33 Identities=12% Similarity=0.040 Sum_probs=26.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNPG 100 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~~ 100 (165)
..++||..||+++..|+.+...-|.+.++...+
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l~~ 184 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALLGG 184 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHcc
Confidence 356789999999999999998777777776543
No 114
>PHA02955 hypothetical protein; Provisional
Probab=58.38 E-value=15 Score=29.18 Aligned_cols=46 Identities=11% Similarity=0.030 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 48 YEQLVALENKFKTT-RYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 48 ~~Ql~~Le~~F~~~-~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
..++..|-+.|.+. .-...+|+.+++++||+....|..||.+.-.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 34666666666555 56788999999999999998889999875444
No 115
>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=58.10 E-value=8.4 Score=21.82 Aligned_cols=20 Identities=10% Similarity=0.112 Sum_probs=16.0
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
+.++|+.+|++.+.|+.|=+
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 35789999999999999953
No 116
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=57.99 E-value=18 Score=27.47 Aligned_cols=30 Identities=7% Similarity=-0.022 Sum_probs=24.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
-++||..||++...|+.++..-|.+.|+..
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 557899999999999999987777776654
No 117
>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=57.87 E-value=19 Score=26.23 Aligned_cols=29 Identities=28% Similarity=0.129 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..||+++..|+....--|.+.|+
T Consensus 140 s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 140 PIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678999999999999988655555444
No 118
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=57.41 E-value=18 Score=27.35 Aligned_cols=30 Identities=3% Similarity=0.047 Sum_probs=24.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..+||..+|++...|+.+...-|.+.|+..
T Consensus 155 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 155 SDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999987777766643
No 119
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=57.24 E-value=16 Score=28.71 Aligned_cols=30 Identities=10% Similarity=0.184 Sum_probs=25.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-+.+.|+.
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999998877777664
No 120
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=57.14 E-value=19 Score=26.90 Aligned_cols=30 Identities=13% Similarity=0.075 Sum_probs=24.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..||++...|+.+...-|.+.|+.
T Consensus 149 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 149 SVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 466789999999999999998766666654
No 121
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=55.77 E-value=20 Score=27.09 Aligned_cols=31 Identities=10% Similarity=-0.045 Sum_probs=25.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
-.+||..||+++..|+.+...-|.+.|+...
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5578999999999999999877777776543
No 122
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=55.42 E-value=23 Score=26.69 Aligned_cols=31 Identities=23% Similarity=0.291 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|++...|+...+.-|.+.|++.
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 3567899999999999999886666666554
No 123
>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=55.37 E-value=22 Score=26.90 Aligned_cols=30 Identities=10% Similarity=0.207 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|++...|+.....-|.+.|+.
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988766666654
No 124
>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=55.34 E-value=7.3 Score=22.82 Aligned_cols=21 Identities=10% Similarity=0.175 Sum_probs=19.0
Q ss_pred HHHHHhCCCchhhhhhhhcch
Q psy15100 71 NLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 71 ~La~~lgl~~~qV~~WFqNRR 91 (165)
+||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999873
No 125
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=55.31 E-value=9.7 Score=23.70 Aligned_cols=21 Identities=10% Similarity=0.184 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999643
No 126
>KOG0773|consensus
Probab=53.92 E-value=16 Score=30.61 Aligned_cols=41 Identities=39% Similarity=0.524 Sum_probs=35.4
Q ss_pred HHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 58 FKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 58 F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
-+.+.|++..+...|+...+|+..+|.+||-|-|.+.+...
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~ 156 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKEL 156 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhcc
Confidence 35688999999999999999999999999999888866643
No 127
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=53.41 E-value=23 Score=28.15 Aligned_cols=48 Identities=8% Similarity=0.115 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
++..+..+|...|-.. ....+||..+|++...|+.|...-+.|.|+..
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l 253 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREAA 253 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5555566665555322 23578899999999999999887676666543
No 128
>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=53.40 E-value=12 Score=22.17 Aligned_cols=23 Identities=17% Similarity=0.265 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||..+|++...|..|..+++
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 36799999999999999998854
No 129
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=53.36 E-value=24 Score=27.20 Aligned_cols=29 Identities=14% Similarity=0.186 Sum_probs=23.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..||++...|+.+...-|.+.++.
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998766666654
No 130
>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=52.98 E-value=11 Score=23.59 Aligned_cols=21 Identities=14% Similarity=0.260 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999753
No 131
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=52.94 E-value=25 Score=26.56 Aligned_cols=30 Identities=13% Similarity=0.088 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.-++||..||++...|+.....-|.+.|+.
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999887766666654
No 132
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=52.86 E-value=19 Score=25.31 Aligned_cols=40 Identities=20% Similarity=0.363 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
++..++..+.+.+... ...+|..||++...|+.|=|+|+.
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 6677777776665433 356789999999999999888754
No 133
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=52.51 E-value=18 Score=34.03 Aligned_cols=17 Identities=6% Similarity=-0.076 Sum_probs=12.7
Q ss_pred CCCCCCCCCCCHHHHHH
Q psy15100 37 SEDLVPESAFTYEQLVA 53 (165)
Q Consensus 37 ~~~~~~R~~~s~~Ql~~ 53 (165)
..+||.|..+..+|...
T Consensus 1292 ~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1292 GGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CccccCCCCCChHHhhh
Confidence 34667788899988766
No 134
>PF13551 HTH_29: Winged helix-turn helix
Probab=52.33 E-value=68 Score=21.43 Aligned_cols=45 Identities=11% Similarity=0.146 Sum_probs=30.3
Q ss_pred CCCCHHHHHHHHHHHHhcCC-----CCHHHHHH-H-HHHh--CCCchhhhhhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRY-----LSVCERLN-L-ALSL--SLTETQVKIWFQ 88 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~-----p~~~~r~~-L-a~~l--gl~~~qV~~WFq 88 (165)
..++.++.+.|.+.+..++. .+..+..+ | .... .++...|..|++
T Consensus 56 ~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 56 KRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33899999999999998762 33444433 3 2222 477778888875
No 135
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=52.29 E-value=25 Score=26.37 Aligned_cols=30 Identities=13% Similarity=0.181 Sum_probs=24.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..+||..+|+++..|++....-|.+.|+..
T Consensus 150 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 150 TEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999987777766653
No 136
>PRK10403 transcriptional regulator NarP; Provisional
Probab=51.95 E-value=15 Score=26.93 Aligned_cols=45 Identities=24% Similarity=0.256 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
..++..+.++|+...+. ....+||..++++++.|+...+|=+.|-
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 35899999998765532 3356789999999999999998766664
No 137
>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=51.90 E-value=24 Score=27.39 Aligned_cols=46 Identities=15% Similarity=0.153 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
++..+..+|...|... ....+||..+|++...|+.+...-+.+.|+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4555566666555322 235789999999999999998766665554
No 138
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=51.28 E-value=27 Score=26.69 Aligned_cols=31 Identities=19% Similarity=0.264 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
...+||..+|++...|++....-|.+-|+..
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999887777766644
No 139
>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=51.19 E-value=12 Score=23.27 Aligned_cols=21 Identities=0% Similarity=0.088 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999754
No 140
>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=50.99 E-value=23 Score=20.98 Aligned_cols=36 Identities=14% Similarity=0.145 Sum_probs=24.3
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 50 Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
|..+|+..++.+.+.+ ..+||.+|+++.+.|+.-..
T Consensus 2 ~~~il~~L~~~~~~it---~~eLa~~l~vS~rTi~~~i~ 37 (55)
T PF08279_consen 2 QKQILKLLLESKEPIT---AKELAEELGVSRRTIRRDIK 37 (55)
T ss_dssp HHHHHHHHHHTTTSBE---HHHHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHcCCCcC---HHHHHHHhCCCHHHHHHHHH
Confidence 4566666656666544 56789999999998876543
No 141
>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=50.97 E-value=15 Score=20.79 Aligned_cols=23 Identities=13% Similarity=0.034 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..++|..||++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 46788999999999999986654
No 142
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=50.31 E-value=23 Score=27.74 Aligned_cols=45 Identities=22% Similarity=0.088 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.+++.++++|+-..+- + .-.+||..|++++..|+.+..|-..|..
T Consensus 155 ~Lt~rE~~Vl~l~~~G--~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 155 LLTHREKEILNKLRIG--A----SNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCCHHHHHHHHHHHcC--C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4899999999888762 2 2467899999999999999987666644
No 143
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=50.23 E-value=28 Score=26.24 Aligned_cols=32 Identities=9% Similarity=0.015 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
...+||..+|++...|+.+...-|.+.|+...
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999998766666665443
No 144
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=50.12 E-value=21 Score=26.40 Aligned_cols=29 Identities=14% Similarity=0.135 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
..++||..+|++...|+++...-+.+++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999998755555443
No 145
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=50.09 E-value=29 Score=26.79 Aligned_cols=29 Identities=7% Similarity=0.234 Sum_probs=24.3
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..+|++...|+.....-|.+.|+.
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999998777776664
No 146
>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=49.77 E-value=28 Score=27.83 Aligned_cols=29 Identities=10% Similarity=0.248 Sum_probs=24.5
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.++||..+|++...|+.+...-|.+.|+.
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~ 208 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARERLLER 208 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999998777766654
No 147
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=49.69 E-value=30 Score=25.07 Aligned_cols=25 Identities=16% Similarity=0.242 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
-.+||..+|++...|+.+...-+.+
T Consensus 132 ~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 132 YGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5578999999999999998754444
No 148
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=49.57 E-value=29 Score=25.91 Aligned_cols=30 Identities=17% Similarity=0.277 Sum_probs=24.2
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.++||..+|++...|+.....-|.+.++..
T Consensus 141 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 141 YQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 567899999999999999887666666543
No 149
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=49.36 E-value=39 Score=25.77 Aligned_cols=31 Identities=6% Similarity=-0.033 Sum_probs=25.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..+||..+|++...|+.+...-|.+.|+...
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 5678999999999999999877777776543
No 150
>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=49.30 E-value=15 Score=21.51 Aligned_cols=23 Identities=9% Similarity=-0.062 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999997664
No 151
>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=49.30 E-value=13 Score=22.96 Aligned_cols=20 Identities=10% Similarity=0.172 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
..++|+.+|++...|+.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999975
No 152
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=49.26 E-value=28 Score=25.76 Aligned_cols=30 Identities=23% Similarity=0.221 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.-+++|..+|++...|+.....-|.+.|+.
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999988766666654
No 153
>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=49.18 E-value=29 Score=26.88 Aligned_cols=47 Identities=15% Similarity=0.137 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++..+..+|...|.. .....+||..+|++...|+.|...-+.+.|+
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3666666666665532 2246789999999999999998755555443
No 154
>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=49.14 E-value=24 Score=28.44 Aligned_cols=48 Identities=17% Similarity=0.025 Sum_probs=36.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...++..+.++|+-.. .. ....+||..|++++..|+.+.+|=+.|...
T Consensus 188 ~~~LT~RE~evl~l~a--~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v 235 (247)
T TIGR03020 188 AGLITAREAEILAWVR--DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDV 235 (247)
T ss_pred ccCCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCC
Confidence 3468999999998654 22 235678999999999999999887666543
No 155
>cd00131 PAX Paired Box domain
Probab=48.98 E-value=97 Score=22.20 Aligned_cols=46 Identities=13% Similarity=0.044 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC-------Cchhhhhhhhcc
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSL-------TETQVKIWFQNR 90 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl-------~~~qV~~WFqNR 90 (165)
..+..+...|+...+.++..+..|..++...-|+ +...|-.||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4566677777777788888877777654334455 777888887653
No 156
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=48.92 E-value=31 Score=25.39 Aligned_cols=29 Identities=10% Similarity=0.160 Sum_probs=23.2
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
-+++|..+|++...|+.....-|.+-|+.
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 138 YKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999988666665543
No 157
>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=48.74 E-value=14 Score=27.94 Aligned_cols=33 Identities=15% Similarity=0.043 Sum_probs=26.9
Q ss_pred HHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 66 VCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 66 ~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.....+||..||++...|+++...-|.+.|+..
T Consensus 147 g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 147 GFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344678999999999999999987777777654
No 158
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=48.47 E-value=28 Score=26.06 Aligned_cols=30 Identities=13% Similarity=0.060 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|+++..|+.....-|.+-|+.
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 185 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAIDKA 185 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988767666654
No 159
>PRK10651 transcriptional regulator NarL; Provisional
Probab=48.46 E-value=28 Score=25.51 Aligned_cols=45 Identities=22% Similarity=0.166 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.++..+.++|+-..+. + ...++|.++++++..|++..+|=+.|-.
T Consensus 155 ~Lt~rE~~vl~~l~~g--~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~ 199 (216)
T PRK10651 155 QLTPRERDILKLIAQG--L----PNKMIARRLDITESTVKVHVKHMLKKMK 199 (216)
T ss_pred cCCHHHHHHHHHHHcC--C----CHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 3899999999775532 1 2566788999999999999988776643
No 160
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=48.34 E-value=34 Score=24.73 Aligned_cols=44 Identities=20% Similarity=0.150 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
.++..+.++|+- +..+ + ...++|..+++++..|+.+.+|=+.|-
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl 192 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKL 192 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 488888888876 3332 2 256789999999999999998766554
No 161
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=47.98 E-value=20 Score=26.22 Aligned_cols=44 Identities=18% Similarity=0.117 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
.++..+.++|+-..+. ..+++||..++++++.|++..++=|.|-
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 5888888888776643 2577889999999999999988766653
No 162
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=47.84 E-value=35 Score=25.06 Aligned_cols=28 Identities=4% Similarity=0.096 Sum_probs=22.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
-++||..||++...|+.+..+-+.+++.
T Consensus 137 ~~EIA~~l~is~~tV~~~l~ra~~~~~~ 164 (168)
T PRK12525 137 YVEIGERLGVSLSRIHQYMVEAFKCCYQ 164 (168)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999998776666554
No 163
>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=47.80 E-value=34 Score=25.60 Aligned_cols=32 Identities=16% Similarity=0.072 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 65 SVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 65 ~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
......+||..+|++...|++++..-|.+.|+
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 33445679999999999999998766666554
No 164
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=47.39 E-value=30 Score=27.47 Aligned_cols=47 Identities=13% Similarity=0.142 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+...+..+|...|. ......+||..+|++...|+.++..-+.+.|+.
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34444445544432 222356789999999999999998766666543
No 165
>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=47.21 E-value=18 Score=20.16 Aligned_cols=23 Identities=17% Similarity=0.241 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
...+|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999988753
No 166
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=47.04 E-value=35 Score=25.78 Aligned_cols=32 Identities=16% Similarity=0.036 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..-.+||..+|++...|++.+..-|.+.|+..
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44567899999999999998887777766643
No 167
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=46.77 E-value=34 Score=27.70 Aligned_cols=29 Identities=10% Similarity=0.119 Sum_probs=23.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
-.+||..||+++..|+..++.-|.+.|..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999998777666654
No 168
>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=46.64 E-value=30 Score=27.48 Aligned_cols=46 Identities=11% Similarity=0.147 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
++..+..+|...|.... ...+||..+|++...|+.+...-+.+.|+
T Consensus 206 L~~~~r~ii~l~~~~g~-----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEENL-----SQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55666666666654332 34689999999999999998766666554
No 169
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=46.48 E-value=13 Score=27.98 Aligned_cols=34 Identities=18% Similarity=0.048 Sum_probs=26.7
Q ss_pred CHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 65 SVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 65 ~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
......+||..+|++...|+.+...-|.+.|+..
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 3344678999999999999999887777766653
No 170
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=46.45 E-value=34 Score=27.38 Aligned_cols=48 Identities=17% Similarity=0.048 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
+...+..+|...|.. .....+||..+|++...|+.+...-+.|.|+..
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 455555566555533 234578999999999999999887666666543
No 171
>PF12728 HTH_17: Helix-turn-helix domain
Probab=46.33 E-value=18 Score=21.15 Aligned_cols=24 Identities=17% Similarity=0.295 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcchh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
..++|..||++...|..|.++..-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 457889999999999999866543
No 172
>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=46.08 E-value=15 Score=28.06 Aligned_cols=32 Identities=19% Similarity=0.308 Sum_probs=27.5
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..+.+|+..++++..+|-.|..|-+...+...
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 35778999999999999999999988877654
No 173
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=46.08 E-value=35 Score=25.67 Aligned_cols=32 Identities=13% Similarity=-0.048 Sum_probs=25.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
..++||..||++...|+.....-|.+.|+...
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999877777666544
No 174
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=46.04 E-value=14 Score=27.28 Aligned_cols=35 Identities=17% Similarity=0.069 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 65 SVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 65 ~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
....-++||..+|++...|+..+..-|.+.|+...
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 33346789999999999999999887777776543
No 175
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=45.76 E-value=37 Score=27.60 Aligned_cols=30 Identities=10% Similarity=0.056 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.++||..+|+++..|+...+.-|.+.|+..
T Consensus 134 ~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~ 163 (293)
T PRK09636 134 FDEIASTLGRSPAACRQLASRARKHVRAAR 163 (293)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 457899999999999999987666666543
No 176
>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=45.51 E-value=30 Score=27.24 Aligned_cols=47 Identities=15% Similarity=0.133 Sum_probs=34.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
..++..++++|.-..+ . ..-.+||..||+++..|+.+..|=+.|.+.
T Consensus 170 ~~Lt~re~evl~~~a~--G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 170 GVLSEREREVLAWTAL--G----RRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred ccCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 3578888888866431 1 235678899999999999999987777553
No 177
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=45.12 E-value=39 Score=25.59 Aligned_cols=36 Identities=14% Similarity=0.051 Sum_probs=31.7
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhh
Q psy15100 48 YEQLVALENKFKTTRYLSVCERLNLALSLSLTETQV 83 (165)
Q Consensus 48 ~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV 83 (165)
..-+..|...+++..|......+.+|..|||+...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 445788889999999999999999999999998765
No 178
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=45.00 E-value=40 Score=19.36 Aligned_cols=38 Identities=16% Similarity=0.170 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 47 s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
+..+..+|...++ ++.. ...+||..+|++...|..-++
T Consensus 2 ~~~~~~Il~~l~~-~~~~---t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPRI---TQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp -HHHHHHHHHHHH-CTTS----HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCCC---CHHHHHHHhCCCHHHHHHHHH
Confidence 4567788877666 4433 466789999999998876553
No 179
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=44.86 E-value=30 Score=28.92 Aligned_cols=53 Identities=13% Similarity=0.114 Sum_probs=38.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
.++..+..+|+..|-... ......++||..+|++...|+.+...-+.|.|+..
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 466677777776663222 23345678999999999999999988777777654
No 180
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.44 E-value=56 Score=22.58 Aligned_cols=42 Identities=12% Similarity=0.115 Sum_probs=32.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC-Cchhhhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSL-TETQVKIWFQ 88 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl-~~~qV~~WFq 88 (165)
|..|+.+....+-+.+....+ ...+||.++|+ ...++..|-+
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 677999987776666665554 57789999996 9999998864
No 181
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=44.27 E-value=40 Score=25.47 Aligned_cols=30 Identities=17% Similarity=0.270 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..+|++++.|+..++.-|.+.++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999998888777555543
No 182
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=44.18 E-value=43 Score=24.16 Aligned_cols=29 Identities=14% Similarity=0.184 Sum_probs=23.0
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..+||..+|++...|+.....-+.+.++.
T Consensus 124 ~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 124 HQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999887666665554
No 183
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=43.95 E-value=31 Score=26.96 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-|.+-|+.
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999987666666654
No 184
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=42.88 E-value=26 Score=25.69 Aligned_cols=45 Identities=16% Similarity=0.107 Sum_probs=34.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
..++..+..+|+...+. ..+++||.+++++.+.|+.+.++=|.|-
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl 192 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKL 192 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 34788888888754433 4478899999999999999988766663
No 185
>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=42.85 E-value=38 Score=27.70 Aligned_cols=31 Identities=19% Similarity=0.182 Sum_probs=25.2
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
-.+||..||+++..|+.....-|.+.|+...
T Consensus 161 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 161 AAETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 4678999999999999999877777666544
No 186
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=42.82 E-value=41 Score=27.02 Aligned_cols=47 Identities=9% Similarity=0.069 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+...+..+|...|... ....+||..+|++...|+.....-+.+.|+.
T Consensus 213 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5555555565555332 2357789999999999998887766665554
No 187
>PHA01976 helix-turn-helix protein
Probab=42.35 E-value=22 Score=21.89 Aligned_cols=23 Identities=9% Similarity=0.120 Sum_probs=19.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||..+|++...|..|...++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46799999999999999987654
No 188
>PF13730 HTH_36: Helix-turn-helix domain
Probab=42.33 E-value=22 Score=21.03 Aligned_cols=42 Identities=10% Similarity=-0.032 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHh---cCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 46 FTYEQLVALENKFKT---TRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~---~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
++..++.++-..+.. +.. ...-...||..+|++.+.|+.+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455565555555432 223 333577899999999999998875
No 189
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=42.23 E-value=38 Score=25.18 Aligned_cols=28 Identities=21% Similarity=0.211 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
..++|..+|++...|+.+...-|.+.|+
T Consensus 146 ~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 146 IKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5678999999999999998866666554
No 190
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=41.03 E-value=48 Score=25.00 Aligned_cols=30 Identities=20% Similarity=0.159 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.=...-|.+.|+.
T Consensus 152 s~~EIA~~lg~s~~tV~~rl~rar~~Lr~~ 181 (192)
T PRK09643 152 SVADAARMLGVAEGTVKSRCARGRARLAEL 181 (192)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999986665555555554
No 191
>KOG3623|consensus
Probab=41.01 E-value=29 Score=32.69 Aligned_cols=54 Identities=19% Similarity=0.137 Sum_probs=40.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+....++-..|...|+.+-.+...+--.++..|...+..|.+||++|+...+..
T Consensus 631 sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 631 SPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred CCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 445555566677778777766666666666678888889999999998887764
No 192
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=40.95 E-value=52 Score=24.60 Aligned_cols=36 Identities=19% Similarity=0.145 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhh
Q psy15100 49 EQLVALENKFKTTRYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 49 ~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
.-+.+|...=+...|.+.+....||..|||+..+|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 346667666677789999999999999999998764
No 193
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=40.82 E-value=53 Score=24.38 Aligned_cols=29 Identities=24% Similarity=0.231 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.-++||..||++...|+.....-|.+-|.
T Consensus 155 s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 155 TYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45678999999999999887765555544
No 194
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.80 E-value=37 Score=24.11 Aligned_cols=25 Identities=4% Similarity=0.015 Sum_probs=20.6
Q ss_pred HHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100 66 VCERLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 66 ~~~r~~La~~lgl~~~qV~~WFqNR 90 (165)
....++||..+||+.+.+..+|+.-
T Consensus 25 ~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 25 PLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3557889999999999998888753
No 195
>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=40.71 E-value=23 Score=22.42 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=19.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||+.+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45799999999999999997664
No 196
>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=40.65 E-value=21 Score=25.52 Aligned_cols=33 Identities=24% Similarity=0.190 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 64 LSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 64 p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
......++||..+|+++..|+++...-|.+.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344456789999999999999998866666554
No 197
>PRK06424 transcription factor; Provisional
Probab=39.73 E-value=45 Score=24.74 Aligned_cols=24 Identities=8% Similarity=-0.021 Sum_probs=20.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcchh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
.++||..+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 457999999999999999987764
No 198
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=39.51 E-value=43 Score=27.03 Aligned_cols=47 Identities=11% Similarity=0.171 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
++..+..+|...|.. .....+||..+|++...|+.+...-+.+.|+.
T Consensus 216 L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 216 LPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred CCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 455555566655532 23457899999999999999987666665553
No 199
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=39.33 E-value=24 Score=27.59 Aligned_cols=36 Identities=19% Similarity=0.155 Sum_probs=28.4
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 63 YLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 63 ~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
|.......+||..+|++...|+.....-|.|.|+..
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 344455678999999999999999887777777754
No 200
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=38.17 E-value=60 Score=24.06 Aligned_cols=35 Identities=14% Similarity=0.054 Sum_probs=28.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhh
Q psy15100 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 50 Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
-+.+|...=+...|.+.+....+|..+||+..+|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 45666666667789999999999999999998764
No 201
>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=37.78 E-value=46 Score=26.15 Aligned_cols=52 Identities=8% Similarity=0.043 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.++..+..+|...|....+ ......+||..+|++...|+.+...-+.|.|..
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 3566667777776632222 223467889999999999999988766666653
No 202
>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=37.62 E-value=59 Score=25.47 Aligned_cols=30 Identities=13% Similarity=0.144 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...+||..+|++...|+.+...-+.+.|+.
T Consensus 200 s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 200 TQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999987666666654
No 203
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=37.30 E-value=31 Score=18.88 Aligned_cols=23 Identities=17% Similarity=0.222 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
...||..+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999987653
No 204
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=36.90 E-value=62 Score=24.36 Aligned_cols=30 Identities=20% Similarity=0.199 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
..++||..||+++..|+++...-|.+.++.
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEA 175 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999987666665554
No 205
>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=36.87 E-value=59 Score=23.77 Aligned_cols=40 Identities=13% Similarity=0.258 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
+..+...+++..|..-...++ ..+|.++++++++++-|++
T Consensus 82 l~de~k~Ii~lry~~r~~~TW---~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTW---YQIAQKLHISERTARRWRD 121 (130)
T ss_pred hCHHHHHHHHHHHcccccchH---HHHHHHhCccHHHHHHHHH
Confidence 344444555555544433333 3578889999999988865
No 206
>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=36.73 E-value=64 Score=22.68 Aligned_cols=37 Identities=8% Similarity=0.159 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 47 TYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 47 s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
+.+-....-..++... -+.++|..++++...|..||+
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3344444445555433 356678999999999999998
No 207
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=36.41 E-value=57 Score=24.67 Aligned_cols=41 Identities=7% Similarity=-0.098 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
.+|+.++++|.-..+-. .-.+||.+|+++++.|+.-.+|=.
T Consensus 150 ~Lt~rE~evl~~~~~G~------s~~eIA~~l~iS~~TV~~h~~~i~ 190 (216)
T PRK10840 150 RLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAM 190 (216)
T ss_pred cCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 48999999998775332 256789999999999998765533
No 208
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=36.38 E-value=53 Score=24.05 Aligned_cols=35 Identities=17% Similarity=0.144 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhh
Q psy15100 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 50 Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
-+.+|...=+...|.+.+....+|..|||+..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 35667666667789999999999999999998764
No 209
>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=36.06 E-value=61 Score=25.18 Aligned_cols=44 Identities=11% Similarity=0.062 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.++..+..+|...|..+ ....+||..+|++...|..+-..-..|
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 35666666666665432 347789999999999998886543333
No 210
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=36.01 E-value=71 Score=24.30 Aligned_cols=35 Identities=23% Similarity=0.141 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhh
Q psy15100 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 50 Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
-+.+|...=+...|.+.+..+.+|..|||+..+|.
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 35555555566789999999999999999997654
No 211
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=36.01 E-value=69 Score=23.54 Aligned_cols=36 Identities=14% Similarity=0.022 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhh
Q psy15100 49 EQLVALENKFKTTRYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 49 ~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
.-+.+|...=+...|.+.+..+.+|..|||+..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345666666566789999999999999999997754
No 212
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.75 E-value=58 Score=25.08 Aligned_cols=43 Identities=9% Similarity=0.058 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.+|+.++++|.-.-+ .+. -.+||.+|+++++.|+.-..|=..|
T Consensus 137 ~LT~RE~eVL~lla~--G~s----nkeIA~~L~iS~~TVk~h~~~I~~K 179 (207)
T PRK15411 137 SLSRTESSMLRMWMA--GQG----TIQISDQMNIKAKTVSSHKGNIKRK 179 (207)
T ss_pred cCCHHHHHHHHHHHc--CCC----HHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 389999999976643 222 4678999999999999887654444
No 213
>PRK13870 transcriptional regulator TraR; Provisional
Probab=35.34 E-value=67 Score=25.45 Aligned_cols=25 Identities=8% Similarity=0.136 Sum_probs=21.6
Q ss_pred HHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 70 LNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 70 ~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
.+||..||++++.|+.-.+|=+.|-
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 3688999999999999999877774
No 214
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=35.12 E-value=30 Score=21.36 Aligned_cols=20 Identities=5% Similarity=0.002 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 215
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=35.11 E-value=31 Score=23.55 Aligned_cols=22 Identities=5% Similarity=-0.088 Sum_probs=18.7
Q ss_pred HHHHHHHhCCCchhhhhhhhcc
Q psy15100 69 RLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNR 90 (165)
..++|+.+||+...|+.|..+-
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIG 24 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999998653
No 216
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=35.07 E-value=55 Score=25.59 Aligned_cols=31 Identities=16% Similarity=0.099 Sum_probs=23.0
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...++||..+|++...|+.+-..-+.+.|+.
T Consensus 196 ~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 196 KTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999865545555543
No 217
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=34.91 E-value=73 Score=25.31 Aligned_cols=45 Identities=20% Similarity=0.260 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
.+|..++++|.-..+- ..-.+||..|+++++.|+.-.+|=+.|-.
T Consensus 179 ~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~KL~ 223 (240)
T PRK10188 179 NFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKKFN 223 (240)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 4666666666544221 12356899999999999999888776643
No 218
>PRK09726 antitoxin HipB; Provisional
Probab=34.90 E-value=1.1e+02 Score=20.20 Aligned_cols=23 Identities=13% Similarity=0.241 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||..+|++...|..|..+++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 56789999999999999987653
No 219
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=34.82 E-value=40 Score=26.24 Aligned_cols=41 Identities=10% Similarity=0.150 Sum_probs=33.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
++.-...|....|- .....||+..|+++..|..+|.||..=
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L 59 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDL 59 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 44445568888877 568889999999999999999997553
No 220
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=34.68 E-value=63 Score=25.71 Aligned_cols=47 Identities=13% Similarity=0.175 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++..+..+|+..|..+ ....+||..+|++...|...-.+-..|-|+
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 47777778888877432 236789999999999999887655555443
No 221
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=34.59 E-value=66 Score=25.76 Aligned_cols=47 Identities=9% Similarity=0.040 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
+...+..+|...|.. .....+||..+|++...|+.+...-+.+.|+.
T Consensus 206 L~~~er~vi~l~y~e-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 206 LEEKERKVMALYYYE-----ELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555555566555532 22357899999999999999887666655553
No 222
>PRK05572 sporulation sigma factor SigF; Validated
Probab=34.40 E-value=63 Score=25.60 Aligned_cols=47 Identities=11% Similarity=0.091 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++..+..+|...|..+ ....+||..+|++...|..+-..-..|.|+
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 47777777777776432 346789999999999999887665555554
No 223
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=34.20 E-value=1e+02 Score=18.97 Aligned_cols=49 Identities=18% Similarity=0.078 Sum_probs=29.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCH---HHHHHHHHHhCCCchhhhhhhhc
Q psy15100 41 VPESAFTYEQLVALENKFKTTRYLSV---CERLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 41 ~~R~~~s~~Ql~~Le~~F~~~~~p~~---~~r~~La~~lgl~~~qV~~WFqN 89 (165)
|+|...|.+.-..+...++.-...+. ..+.++-...+|+..||+.=.|-
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QK 52 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQK 52 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHH
Confidence 35667777776666666666665444 44444433446677888765553
No 224
>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=34.14 E-value=69 Score=24.94 Aligned_cols=50 Identities=12% Similarity=0.020 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
++..+..+|...|-... ......++||..+|++...|+.+...-+.+-|+
T Consensus 175 L~~~~r~il~l~y~~~~-~e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 175 LDGREREVIEMRYGLGD-GRRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred CCHHHHHHHHHHHcCCC-CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44444555554442110 012246788999999999998886544555443
No 225
>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=34.03 E-value=51 Score=26.54 Aligned_cols=50 Identities=12% Similarity=0.122 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.++..+..+|...|... ......+||..+|++...|+....+-..|.|+.
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 36677777777777321 122357899999999999999988777776654
No 226
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=34.01 E-value=55 Score=25.35 Aligned_cols=45 Identities=11% Similarity=0.031 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNR 90 (165)
.++..++.+|......+ +-....-.+||.++++++..|+..+.+=
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 37788877776665433 2233346789999999999999998753
No 227
>PF13309 HTH_22: HTH domain
Probab=33.84 E-value=87 Score=19.62 Aligned_cols=41 Identities=12% Similarity=0.139 Sum_probs=29.2
Q ss_pred CCHHH-HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhh
Q psy15100 46 FTYEQ-LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIW 86 (165)
Q Consensus 46 ~s~~Q-l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~W 86 (165)
++.++ +++++..++..-|--......+|..||++...|-.+
T Consensus 21 l~~~~k~~iV~~L~~~G~F~lKgav~~vA~~L~iS~~TVY~Y 62 (64)
T PF13309_consen 21 LSKEEKKEIVRQLYEKGIFLLKGAVEYVAEKLGISRATVYRY 62 (64)
T ss_pred CCHHHHHHHHHHHHHCCCcccCcHHHHHHHHHCCCHHHHHHH
Confidence 44444 455566666666777777888999999999887654
No 228
>KOG3755|consensus
Probab=33.78 E-value=33 Score=31.53 Aligned_cols=60 Identities=20% Similarity=0.181 Sum_probs=50.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhc-CCCCHHH---HHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 37 SEDLVPESAFTYEQLVALENKFKTT-RYLSVCE---RLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 37 ~~~~~~R~~~s~~Ql~~Le~~F~~~-~~p~~~~---r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
..++++|+.+..+.+.+|..+-..- -||+.+. ...|...+++.++.+...|+|.|...+.
T Consensus 645 ~~~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 645 WHKPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred ccCccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 3477889999999999998886544 4888888 8889999999999999999999887553
No 229
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=33.69 E-value=60 Score=25.77 Aligned_cols=30 Identities=23% Similarity=0.212 Sum_probs=24.5
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
..+||..+|+++..|+.+...-|.+-|+..
T Consensus 135 ~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 135 IADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999987777666654
No 230
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=33.55 E-value=51 Score=17.80 Aligned_cols=20 Identities=10% Similarity=0.270 Sum_probs=14.3
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
...-|...||+..+|+..+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34459999999999998874
No 231
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=33.42 E-value=33 Score=25.21 Aligned_cols=34 Identities=18% Similarity=0.133 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 64 LSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 64 p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
......++||..+|++...|+.+...-|.+.++.
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 3344567899999999999999987766666654
No 232
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=33.40 E-value=83 Score=19.86 Aligned_cols=40 Identities=23% Similarity=0.207 Sum_probs=24.7
Q ss_pred CCHHHHHHHHHH---HHhcCCCCHHHHHHHHHHhCCC-chhhhhhh
Q psy15100 46 FTYEQLVALENK---FKTTRYLSVCERLNLALSLSLT-ETQVKIWF 87 (165)
Q Consensus 46 ~s~~Ql~~Le~~---F~~~~~p~~~~r~~La~~lgl~-~~qV~~WF 87 (165)
+|..|.++|+-. .+.+.||. ...+|+..+|+. ...|..-.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 677787777654 55677764 567889999997 66665544
No 233
>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=33.40 E-value=77 Score=23.32 Aligned_cols=29 Identities=10% Similarity=0.164 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..||++...|+.=...-|.+.|+
T Consensus 158 s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 158 SFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999777665655554
No 234
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=33.10 E-value=37 Score=19.76 Aligned_cols=20 Identities=20% Similarity=0.232 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
...+|..+|++...|+.+|.
T Consensus 30 ~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56789999999999999885
No 235
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=33.06 E-value=26 Score=22.01 Aligned_cols=21 Identities=19% Similarity=0.400 Sum_probs=14.5
Q ss_pred HHHHHHHhCCCchhhh-hhhhc
Q psy15100 69 RLNLALSLSLTETQVK-IWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~-~WFqN 89 (165)
..+||..||++...|. .|...
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCcCHHHhhHHHHhC
Confidence 4578888888888888 88753
No 236
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=32.63 E-value=33 Score=25.93 Aligned_cols=41 Identities=12% Similarity=0.131 Sum_probs=30.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
++...+.|....|-. ....+||++.|++...+-.+|.++-.
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 444455576766644 34678899999999999999998754
No 237
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=32.46 E-value=38 Score=20.78 Aligned_cols=25 Identities=24% Similarity=0.283 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
...++|..+|++...|..|-.+++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4567899999999999999988874
No 238
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=32.27 E-value=33 Score=25.67 Aligned_cols=31 Identities=13% Similarity=0.179 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 67 CERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
...++||..+|++...|+++...-|.+.|+.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999988666665553
No 239
>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=31.86 E-value=32 Score=23.63 Aligned_cols=35 Identities=17% Similarity=0.329 Sum_probs=18.4
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
+.+..-.|+.|+||..+-... ==.|||.+||+++.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~--------------aRRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ--------------ARRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH--------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc--------------cccchhhhHHHHHH
Confidence 344555688999987442111 11588888887654
No 240
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=31.42 E-value=65 Score=23.53 Aligned_cols=44 Identities=7% Similarity=0.166 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKW 94 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~ 94 (165)
.++..+.++|+-.++.. .+++|+..++++++.|+..-.+=|.|-
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 48999999998887543 367889999999999998877655553
No 241
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=31.20 E-value=60 Score=26.79 Aligned_cols=29 Identities=17% Similarity=0.123 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
...+||..||++...|+.....-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 35678999999999999998766666555
No 242
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=30.56 E-value=81 Score=24.46 Aligned_cols=43 Identities=12% Similarity=-0.034 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.+|+.++++|+-..+-.. -.+||.+|+++++.|+.--.|=..|
T Consensus 134 ~LT~RE~eVL~ll~~G~s------nkeIA~~L~iS~~TV~~h~~~I~~K 176 (207)
T PRK11475 134 MLSPTEREILRFMSRGYS------MPQIAEQLERNIKTIRAHKFNVMSK 176 (207)
T ss_pred CCCHHHHHHHHHHHCCCC------HHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 489999999987764322 4678999999999999876554333
No 243
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=30.48 E-value=66 Score=23.93 Aligned_cols=41 Identities=15% Similarity=0.077 Sum_probs=31.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
++.-...|.++.|-. .....||+..|++...|-.+|.||..
T Consensus 14 l~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~ 54 (192)
T PRK14996 14 LQAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGE 54 (192)
T ss_pred HHHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHH
Confidence 444455677777743 45778999999999999999998755
No 244
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.46 E-value=38 Score=22.54 Aligned_cols=19 Identities=11% Similarity=0.200 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WF 87 (165)
..++|+.+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999994
No 245
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=30.40 E-value=40 Score=24.00 Aligned_cols=23 Identities=4% Similarity=-0.010 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
+++||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56799999999999999999875
No 246
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=30.19 E-value=38 Score=25.24 Aligned_cols=31 Identities=23% Similarity=0.207 Sum_probs=26.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
-.++|..+|++...|+.|...-|.+.++...
T Consensus 146 ~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 146 YEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4578999999999999999988888777654
No 247
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=30.16 E-value=41 Score=24.10 Aligned_cols=24 Identities=13% Similarity=0.374 Sum_probs=20.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcchh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 467899999999999999988753
No 248
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=30.11 E-value=1.1e+02 Score=17.48 Aligned_cols=43 Identities=19% Similarity=0.097 Sum_probs=26.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhC--CCchhhhhhhh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLS--LTETQVKIWFQ 88 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lg--l~~~qV~~WFq 88 (165)
|..+|.++...|.+.+.....-... .||..++ -+..+|+.=|+
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W~---~Ia~~~~~~Rt~~qc~~~~~ 45 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNWK---KIAKRMPGGRTAKQCRSRYQ 45 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHHH---HHHHHHSSSSTHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHHH---HHHHHcCCCCCHHHHHHHHH
Confidence 4568999999999998877655333 4455554 55566665444
No 249
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=30.07 E-value=41 Score=19.37 Aligned_cols=35 Identities=11% Similarity=0.227 Sum_probs=24.5
Q ss_pred HHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 56 NKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 56 ~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
+.|....|-. .....|++++|++...+-..|.|+-
T Consensus 7 ~l~~~~G~~~-~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 7 ELFAEKGYEA-VSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHTTT-SSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHhCHHh-CCHHHHHHHHccchhhHHHHcCCHH
Confidence 3444444333 2356789999999999999998853
No 250
>PRK10878 hypothetical protein; Provisional
Probab=29.85 E-value=1.1e+02 Score=19.84 Aligned_cols=44 Identities=20% Similarity=0.187 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 50 QLVALENKFKTTRY--LSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 50 Ql~~Le~~F~~~~~--p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.+++|-..|-...| .+.+++......|.+....+-.||-++..-
T Consensus 3 ElDlll~~F~~~~~~~l~~~e~~~Fe~LL~~~D~dL~~W~~g~~~p 48 (72)
T PRK10878 3 ELDISIMPFFEHEYDSLSDDEKRIFIRLLECDDPDLFNWLMNHGKP 48 (72)
T ss_pred hHHHHHHHHHHHHHhhCCHHHHHHHHHHHcCCCHHHHHHHhCCCCC
Confidence 35666666666654 788888889999999999999999876443
No 251
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=29.78 E-value=42 Score=22.81 Aligned_cols=21 Identities=24% Similarity=0.194 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.++|+.+|++...|+.|.+.
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 252
>PRK09483 response regulator; Provisional
Probab=29.71 E-value=84 Score=23.18 Aligned_cols=44 Identities=11% Similarity=0.036 Sum_probs=31.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
..+|..++++|+-.. ..+. -.+||..|+++++.|+...+|=+.|
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~----~~~Ia~~l~is~~TV~~~~~~i~~K 190 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQK----VNEISEQLNLSPKTVNSYRYRMFSK 190 (217)
T ss_pred cccCHHHHHHHHHHH--CCCC----HHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 358999999996543 2222 2378999999999999877665544
No 253
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=29.27 E-value=65 Score=26.37 Aligned_cols=50 Identities=10% Similarity=0.066 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
.++..+..+|...|- +-......+||..+|++...|+.+-..-+.|.|..
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~ 276 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRA 276 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467777777777663 11233467899999999999999987766666654
No 254
>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=28.92 E-value=91 Score=25.26 Aligned_cols=52 Identities=15% Similarity=0.086 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhhhC
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKKQN 98 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr~~ 98 (165)
++..+..+|.-.|... +.....-.+||..||++...|+.+...-+.+.|+..
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 5555555665554111 122234677899999999999999987777776653
No 255
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=28.81 E-value=18 Score=18.01 Aligned_cols=9 Identities=33% Similarity=0.833 Sum_probs=6.8
Q ss_pred hhhhhcchh
Q psy15100 84 KIWFQNRRT 92 (165)
Q Consensus 84 ~~WFqNRR~ 92 (165)
-+||.||..
T Consensus 6 iNWFE~~ge 14 (22)
T PF08452_consen 6 INWFESRGE 14 (22)
T ss_pred eehhhhCCc
Confidence 479998764
No 256
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=28.80 E-value=44 Score=20.96 Aligned_cols=18 Identities=28% Similarity=0.527 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCchhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIW 86 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~W 86 (165)
...||+.||++...|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357999999999999999
No 257
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=28.48 E-value=55 Score=23.34 Aligned_cols=25 Identities=24% Similarity=0.279 Sum_probs=21.8
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 63 YLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 63 ~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
-.+...|.+||..+|++.+.|..|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 4567778889999999999999994
No 258
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=28.44 E-value=65 Score=23.91 Aligned_cols=14 Identities=21% Similarity=0.344 Sum_probs=7.6
Q ss_pred CCHHHHHHHHHHHH
Q psy15100 46 FTYEQLVALENKFK 59 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~ 59 (165)
++.+|+..|+...+
T Consensus 52 Lt~~qi~~l~~~i~ 65 (144)
T TIGR03629 52 LDDEEIEKLEEAVE 65 (144)
T ss_pred CCHHHHHHHHHHHH
Confidence 55555555555443
No 259
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.26 E-value=44 Score=22.26 Aligned_cols=21 Identities=5% Similarity=-0.062 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|..+|++...|+.|-+.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999753
No 260
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=28.11 E-value=41 Score=23.00 Aligned_cols=38 Identities=16% Similarity=0.172 Sum_probs=25.1
Q ss_pred CCHHHH----HHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 46 FTYEQL----VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 46 ~s~~Ql----~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
++++|. .+|.+.|+...+. .+.+|..|+++...|..=+
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~ls----~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSGLS----LEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcCCC----HHHHHHHhCCCHHHHHHHH
Confidence 445553 4677777776643 5667888888887765444
No 261
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=27.91 E-value=51 Score=19.98 Aligned_cols=24 Identities=17% Similarity=0.275 Sum_probs=19.3
Q ss_pred HHHHHHHHhCCCchhhhhhhhcch
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 356789999999999999998866
No 262
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=27.89 E-value=1.6e+02 Score=19.61 Aligned_cols=40 Identities=15% Similarity=0.028 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHH---HHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 46 FTYEQLVALENK---FKTTRYLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 46 ~s~~Ql~~Le~~---F~~~~~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
++..|.++|... |....-|-.. ..||+.++++...|++=.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVgS--k~ia~~l~~s~aTIRN~M 44 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVGS--KTIAEELGRSPATIRNEM 44 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcCH--HHHHHHHCCChHHHHHHH
Confidence 466677776665 6666554433 456778999988886543
No 263
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=27.43 E-value=46 Score=24.24 Aligned_cols=23 Identities=9% Similarity=-0.011 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
+.++|+.+|++.+.|+.|.+.-.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~GL 25 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLGL 25 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999997543
No 264
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=27.27 E-value=62 Score=23.59 Aligned_cols=31 Identities=26% Similarity=0.426 Sum_probs=20.4
Q ss_pred CCCHHHHHHHHHHhCCCc-----hhhhhhhhcchhh
Q psy15100 63 YLSVCERLNLALSLSLTE-----TQVKIWFQNRRTK 93 (165)
Q Consensus 63 ~p~~~~r~~La~~lgl~~-----~qV~~WFqNRR~k 93 (165)
-.+...|.+||.+||++. .+..+|....-.+
T Consensus 82 DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~ 117 (127)
T PF12200_consen 82 DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQ 117 (127)
T ss_dssp --SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHH
Confidence 367789999999999887 3678898754443
No 265
>PF12114 Period_C: Period protein 2/3C-terminal region; InterPro: IPR022728 This domain is found in eukaryotes and is typically between 164 to 200 amino acids in length. Sequences represented by this entry are found C-terminal to PF08447 from PFAM.
Probab=27.16 E-value=1.1e+02 Score=23.88 Aligned_cols=31 Identities=29% Similarity=0.312 Sum_probs=22.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN 89 (165)
++.|+..=+..+.....++++|+ +|..|.+.
T Consensus 126 ~ekLk~mq~~QP~fs~~Qk~EL~--------qvh~wiq~ 156 (195)
T PF12114_consen 126 REKLKSMQKQQPRFSNEQKEELA--------QVHPWIQS 156 (195)
T ss_pred HHHHHHHHhhCCcchHHHHHHHH--------HhhHHHHc
Confidence 45555555567788888888886 67888864
No 266
>PF07954 DUF1689: Protein of unknown function (DUF1689) ; InterPro: IPR012470 Family of fungal proteins with unknown function. A member of this family has been found to localise in the mitochondria [].
Probab=26.87 E-value=84 Score=23.60 Aligned_cols=25 Identities=28% Similarity=0.321 Sum_probs=21.8
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhC
Q psy15100 53 ALENKFKTTRYLSVCERLNLALSLS 77 (165)
Q Consensus 53 ~Le~~F~~~~~p~~~~r~~La~~lg 77 (165)
.+-++|+.+..++.++|.+|+..+.
T Consensus 3 ~av~FYEaD~~L~~~DR~eL~~~~q 27 (152)
T PF07954_consen 3 AAVEFYEADQKLDHEDRLELAKDLQ 27 (152)
T ss_pred HHHHHHHhhccCCHHHHHHHHHHHH
Confidence 4567899999999999999998884
No 267
>PF13565 HTH_32: Homeodomain-like domain
Probab=26.84 E-value=1.7e+02 Score=18.28 Aligned_cols=40 Identities=13% Similarity=0.003 Sum_probs=27.0
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHH-HHHHhCC----Cchhhhhh
Q psy15100 47 TYEQLVALENKFKTTRYLSVCERLN-LALSLSL----TETQVKIW 86 (165)
Q Consensus 47 s~~Ql~~Le~~F~~~~~p~~~~r~~-La~~lgl----~~~qV~~W 86 (165)
+.++.+.|.+.+..++..+..+..+ |..++|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 6777788888888887666666644 6666664 44445443
No 268
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=26.48 E-value=85 Score=18.55 Aligned_cols=39 Identities=18% Similarity=0.231 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFq 88 (165)
++..|..+|...++... . ...+||..++++...|..+..
T Consensus 1 lt~~q~~iL~~l~~~~~-~---~~~~la~~~~~~~~~~t~~i~ 39 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG-I---TQSELAEKLGISRSTVTRIIK 39 (59)
T ss_dssp STHHHHHHHHHHHHHSS-E---EHHHHHHHHTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC-C---CHHHHHHHHCCChhHHHHHHH
Confidence 46778889988887666 2 234889999999988877654
No 269
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=26.47 E-value=1e+02 Score=25.22 Aligned_cols=29 Identities=10% Similarity=0.141 Sum_probs=23.1
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTKWKKQ 97 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k~kr~ 97 (165)
-.+||..||+++..|+...+.-|.+.+..
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 45689999999999999998666665553
No 270
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.40 E-value=53 Score=22.19 Aligned_cols=22 Identities=5% Similarity=-0.105 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcc
Q psy15100 69 RLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNR 90 (165)
+.++|+.+|++...++.|.+..
T Consensus 3 i~eva~~~gvs~~tLRyye~~G 24 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999998653
No 271
>PTZ00183 centrin; Provisional
Probab=26.26 E-value=2.3e+02 Score=19.80 Aligned_cols=41 Identities=15% Similarity=0.089 Sum_probs=30.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCC
Q psy15100 38 EDLVPESAFTYEQLVALENKFKT-----TRYLSVCERLNLALSLSL 78 (165)
Q Consensus 38 ~~~~~R~~~s~~Ql~~Le~~F~~-----~~~p~~~~r~~La~~lgl 78 (165)
+.+-.+..++..++..|+..|.. +.+.+..+...+...+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 3 KRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 33445667999999999999863 457888888777777764
No 272
>COG2197 CitB Response regulator containing a CheY-like receiver domain and an HTH DNA-binding domain [Signal transduction mechanisms / Transcription]
Probab=26.20 E-value=1.1e+02 Score=23.77 Aligned_cols=41 Identities=24% Similarity=0.185 Sum_probs=30.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100 44 SAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 44 ~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNR 90 (165)
..+|..++++|.-.-+ .+. -.+||.+|+++++.|++.-.|=
T Consensus 147 ~~LT~RE~eVL~lla~--G~s----nkeIA~~L~iS~~TVk~h~~~i 187 (211)
T COG2197 147 ELLTPRELEVLRLLAE--GLS----NKEIAEELNLSEKTVKTHVSNI 187 (211)
T ss_pred CCCCHHHHHHHHHHHC--CCC----HHHHHHHHCCCHhHHHHHHHHH
Confidence 4689999999866532 222 3568999999999999887663
No 273
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.06 E-value=50 Score=22.40 Aligned_cols=20 Identities=10% Similarity=0.225 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
+.+||+.+|++.+.|+.|=+
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999965
No 274
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=26.04 E-value=67 Score=19.81 Aligned_cols=18 Identities=28% Similarity=0.267 Sum_probs=12.2
Q ss_pred HHHHHHHHHhCCCchhhh
Q psy15100 67 CERLNLALSLSLTETQVK 84 (165)
Q Consensus 67 ~~r~~La~~lgl~~~qV~ 84 (165)
.+...++++||+++.+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 455667777777777665
No 275
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=25.93 E-value=74 Score=22.21 Aligned_cols=42 Identities=17% Similarity=0.091 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
.+|..|..+|+-.|..+- -..+||..+|++..-|.-|.+.-+
T Consensus 17 LLT~kQ~~~l~lyy~eDl-----SlsEIAe~~~iSRqaV~d~ikr~~ 58 (101)
T PF04297_consen 17 LLTEKQREILELYYEEDL-----SLSEIAEELGISRQAVYDSIKRAE 58 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccCC-----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 478889999987766543 466889999999999999987433
No 276
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=25.91 E-value=54 Score=22.67 Aligned_cols=21 Identities=19% Similarity=0.300 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...|+.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999764
No 277
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=25.86 E-value=96 Score=22.11 Aligned_cols=44 Identities=14% Similarity=0.175 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWK 95 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~k 95 (165)
++..+..+|+..+... .-.++|..+++++..|+++-.+=|.|-+
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~ 185 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQ 185 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHc
Confidence 4455555555333211 2455788999999999988877666643
No 278
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=25.62 E-value=86 Score=23.90 Aligned_cols=41 Identities=15% Similarity=0.237 Sum_probs=30.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 51 LVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 51 l~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
++.-...|....|-.. ....||+..|++...|...|.|+..
T Consensus 24 L~AA~~lf~e~Gy~~~-s~~dIA~~aGvs~gtiY~hF~sKe~ 64 (212)
T PRK15008 24 LSAALDTFSQFGFHGT-RLEQIAELAGVSKTNLLYYFPSKEA 64 (212)
T ss_pred HHHHHHHHHHhCcccC-CHHHHHHHhCcCHHHHHHHCCCHHH
Confidence 3334445777776543 3667899999999999999999754
No 279
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=25.09 E-value=62 Score=20.40 Aligned_cols=23 Identities=9% Similarity=0.043 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCchhhhhhhhcch
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR 91 (165)
..+||+.+|++...|-.++.+++
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~~ 25 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGNG 25 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCCC
Confidence 45789999999999999998764
No 280
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=25.07 E-value=74 Score=18.93 Aligned_cols=38 Identities=18% Similarity=0.118 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKI 85 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~ 85 (165)
++..|..+|...+..... .....+|+..++++...|..
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 678889999888776653 12456789999999877654
No 281
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=24.75 E-value=1e+02 Score=22.67 Aligned_cols=48 Identities=8% Similarity=0.054 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHhcC-----CCC-HHHHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 46 FTYEQLVALENKFKTTR-----YLS-VCERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~-----~p~-~~~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
+-+.-....|+.|+.-. +|. .....+|+..+|+++.+|..|...-|-.
T Consensus 20 iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 20 VCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred cCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 44455556666665322 232 2346788999999999999999766654
No 282
>PF04539 Sigma70_r3: Sigma-70 region 3; InterPro: IPR007624 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 3 forms a discrete compact three helical domain within the sigma-factor. Region is not normally involved in the recognition of promoter DNA, but in some specific bacterial promoters containing an extended -10 promoter element, residues within region 3 play an important role. Region 3 primarily is involved in binding the core RNA polymerase in the holoenzyme [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 1L0O_C 1KU2_B 1RP3_C 1SC5_A 1TTY_A 2BE5_F 2A6E_F 2CW0_F 2A69_P 2A6H_P ....
Probab=24.51 E-value=54 Score=20.79 Aligned_cols=20 Identities=20% Similarity=0.272 Sum_probs=16.2
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
.++||..|||+...|+..++
T Consensus 23 ~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 23 DEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHcccHHHHHHHHH
Confidence 56789999999999997774
No 283
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=24.38 E-value=86 Score=21.75 Aligned_cols=22 Identities=9% Similarity=-0.139 Sum_probs=16.6
Q ss_pred HHHHHHhCCCchhhhhhhhcch
Q psy15100 70 LNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 70 ~~La~~lgl~~~qV~~WFqNRR 91 (165)
.+||..+|++...|..|-..+.
T Consensus 82 ~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 82 REAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHhCCCHHHHHHHHCCCC
Confidence 4578888888888888876554
No 284
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=24.16 E-value=53 Score=23.74 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
-++||..+|++...|.-|..
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 36899999999999999985
No 285
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=24.10 E-value=1.2e+02 Score=21.88 Aligned_cols=38 Identities=16% Similarity=0.159 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhh
Q psy15100 46 FTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIW 86 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~W 86 (165)
++.++..+++..|...... .-..||..+|+++..|..|
T Consensus 83 Ld~~er~II~~rY~~~~~~---t~~~Ia~~l~iS~~t~~r~ 120 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRPL---TLVGLAQQLFISKSTAYRL 120 (134)
T ss_pred CCHHHHHHHHHHHccCCCC---CHHHHHHHhCCCHHHHHHH
Confidence 5566666776666433322 3567888899999887755
No 286
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=24.00 E-value=51 Score=19.90 Aligned_cols=17 Identities=35% Similarity=0.399 Sum_probs=13.2
Q ss_pred HHHHHHHhCCCchhhhh
Q psy15100 69 RLNLALSLSLTETQVKI 85 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~ 85 (165)
-.+||..+|++..||+-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 35789999999999874
No 287
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.50 E-value=63 Score=21.84 Aligned_cols=21 Identities=5% Similarity=-0.069 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.++|+.+||+...++.|.+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKI 23 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999764
No 288
>PRK08359 transcription factor; Validated
Probab=23.37 E-value=1.4e+02 Score=22.95 Aligned_cols=25 Identities=8% Similarity=0.061 Sum_probs=20.5
Q ss_pred HHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
.++||..+|++...|..|=.+++.-
T Consensus 101 QeeLA~~lgvs~stI~~iE~G~~~P 125 (176)
T PRK08359 101 YEELSHEVGLSVNDLRRIAHGEYEP 125 (176)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCcCC
Confidence 4578999999999999998777643
No 289
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=23.33 E-value=52 Score=24.92 Aligned_cols=42 Identities=17% Similarity=0.151 Sum_probs=32.3
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchh
Q psy15100 50 QLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRT 92 (165)
Q Consensus 50 Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~ 92 (165)
-++.-...|.+..|-.. ....||++.|+++.-+-.+|.||-.
T Consensus 16 Il~AA~~lf~e~G~~~~-t~~~Ia~~agvs~~tlY~~F~sKe~ 57 (215)
T PRK10668 16 ILDAALRLFSQQGVSAT-SLADIAKAAGVTRGAIYWHFKNKSD 57 (215)
T ss_pred HHHHHHHHHHHcCcccC-CHHHHHHHhCCChHHHHHHCCCHHH
Confidence 35555666888887553 3677899999999999999998744
No 290
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=23.27 E-value=1e+02 Score=25.17 Aligned_cols=49 Identities=14% Similarity=0.125 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcchhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
.++..+..+|...|..+ ......+||..+|++...|+.+-..-..|-|+
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666777766322 22335689999999999999886655555444
No 291
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=23.22 E-value=81 Score=17.80 Aligned_cols=13 Identities=38% Similarity=0.450 Sum_probs=11.1
Q ss_pred CCCHHHHHHHHHH
Q psy15100 45 AFTYEQLVALENK 57 (165)
Q Consensus 45 ~~s~~Ql~~Le~~ 57 (165)
.||..|+..|+.-
T Consensus 2 ~FT~~Ql~~L~~Q 14 (37)
T PF08880_consen 2 PFTPAQLQELRAQ 14 (37)
T ss_pred CCCHHHHHHHHHH
Confidence 5899999999875
No 292
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=23.22 E-value=96 Score=21.18 Aligned_cols=34 Identities=18% Similarity=0.222 Sum_probs=23.2
Q ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHHhCCCchhhh
Q psy15100 51 LVALENKFKTT-RYLSVCERLNLALSLSLTETQVK 84 (165)
Q Consensus 51 l~~Le~~F~~~-~~p~~~~r~~La~~lgl~~~qV~ 84 (165)
.+.|...|..- ......+=..|+..|||++..|.
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~ 37 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEID 37 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHH
Confidence 35667777543 34445566679999999998765
No 293
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=23.15 E-value=55 Score=18.76 Aligned_cols=16 Identities=38% Similarity=0.476 Sum_probs=12.5
Q ss_pred HHHHHHHhCCCchhhh
Q psy15100 69 RLNLALSLSLTETQVK 84 (165)
Q Consensus 69 r~~La~~lgl~~~qV~ 84 (165)
-.+||..+||++..|.
T Consensus 20 ~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 20 YAELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHCcCHHHHH
Confidence 4678999999998875
No 294
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=23.01 E-value=65 Score=23.15 Aligned_cols=22 Identities=18% Similarity=0.268 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCchhhhhhhhcc
Q psy15100 69 RLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNR 90 (165)
..++|+.+|++...++.|.+..
T Consensus 4 I~eVA~~~GVs~~TLR~wE~~G 25 (120)
T cd04767 4 IGVVAELLNIHPETLRIWERHG 25 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999998653
No 295
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=22.98 E-value=1.9e+02 Score=22.75 Aligned_cols=43 Identities=12% Similarity=0.177 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHHHhcCCC-CHHHHHHHHHHhCCCchhhhhhhhcc
Q psy15100 46 FTYEQLVALENKFKTTRYL-SVCERLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~~~~~p-~~~~r~~La~~lgl~~~qV~~WFqNR 90 (165)
++..++......++..-.| +.++..+|.++.|.. .|.+|||+-
T Consensus 190 ~s~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~--~v~~~~~~~ 233 (247)
T PRK15451 190 YSELEISQKRSMLENVMLTDSVETHKARLHKAGFE--HSELWFQCF 233 (247)
T ss_pred CCHHHHHHHHHHHHhhcccCCHHHHHHHHHHcCch--hHHHHHHHH
Confidence 5555554444444443333 666667777777755 688888764
No 296
>PRK00215 LexA repressor; Validated
Probab=22.78 E-value=92 Score=23.76 Aligned_cols=42 Identities=24% Similarity=0.193 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCC-Cchhhhhhhhc
Q psy15100 46 FTYEQLVALENKFK---TTRYLSVCERLNLALSLSL-TETQVKIWFQN 89 (165)
Q Consensus 46 ~s~~Ql~~Le~~F~---~~~~p~~~~r~~La~~lgl-~~~qV~~WFqN 89 (165)
+|..|..+|+...+ .+.++ ....+||..+|+ +...|..+.+.
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~ 47 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKA 47 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHH
Confidence 57788888887763 33332 235678999999 88888887753
No 297
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.75 E-value=67 Score=21.81 Aligned_cols=21 Identities=10% Similarity=0.029 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...++.|.++
T Consensus 4 i~eva~~~gVs~~tLR~ye~~ 24 (98)
T cd01279 4 ISVAAELLGIHPQTLRVYDRL 24 (98)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999654
No 298
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.53 E-value=64 Score=22.02 Aligned_cols=21 Identities=0% Similarity=0.001 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.++|+.+|++...++.|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999753
No 299
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.42 E-value=70 Score=21.39 Aligned_cols=21 Identities=10% Similarity=0.101 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|..+|++...|+.|-+.
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~ 23 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEK 23 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999653
No 300
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=22.32 E-value=65 Score=22.00 Aligned_cols=21 Identities=19% Similarity=0.238 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
..++|+.+|++...++.|-++
T Consensus 3 i~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 3 IGEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHHCcCHHHHHHHHHH
Confidence 357899999999999999754
No 301
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=22.19 E-value=57 Score=22.07 Aligned_cols=42 Identities=14% Similarity=0.000 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIW 86 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~W 86 (165)
.++..+..+|+-+=+.+....-..+.+|+++|+|++.+|+.=
T Consensus 44 ~~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~a 85 (102)
T PF08784_consen 44 GLSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRKA 85 (102)
T ss_dssp -S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHHH
T ss_pred CCCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHHH
Confidence 366777777755443344555566788999999999988743
No 302
>PHA03273 envelope glycoprotein C; Provisional
Probab=21.86 E-value=19 Score=31.87 Aligned_cols=23 Identities=17% Similarity=0.511 Sum_probs=15.5
Q ss_pred HHHhCCCchhhhhhhhcchhhhhh
Q psy15100 73 ALSLSLTETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 73 a~~lgl~~~qV~~WFqNRR~k~kr 96 (165)
....++++-.+++||+ +|.+.+.
T Consensus 113 ~~~~~~~~~RLeiWf~-~r~rf~~ 135 (486)
T PHA03273 113 SVGVNYSEYRLEIYLN-QRTPFSG 135 (486)
T ss_pred cCCCCCcceEEEEEEc-ccccccc
Confidence 3445666778999998 5666433
No 303
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.81 E-value=72 Score=21.52 Aligned_cols=21 Identities=14% Similarity=-0.017 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.++|+.+|++.+.++.|-+.
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 304
>smart00595 MADF subfamily of SANT domain.
Probab=21.70 E-value=73 Score=20.71 Aligned_cols=30 Identities=20% Similarity=0.351 Sum_probs=24.9
Q ss_pred HHHHHHhCCCchhhhhhhhcchhhhhhhCC
Q psy15100 70 LNLALSLSLTETQVKIWFQNRRTKWKKQNP 99 (165)
Q Consensus 70 ~~La~~lgl~~~qV~~WFqNRR~k~kr~~~ 99 (165)
.+||.++|.+...|+.-+.|=|.+.++..+
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~ 60 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELK 60 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 458999999999999999998888777543
No 305
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=21.65 E-value=74 Score=25.77 Aligned_cols=18 Identities=22% Similarity=0.540 Sum_probs=13.7
Q ss_pred Cchhhhhhhhcchhhhhh
Q psy15100 79 TETQVKIWFQNRRTKWKK 96 (165)
Q Consensus 79 ~~~qV~~WFqNRR~k~kr 96 (165)
....|..||+.++.|.|-
T Consensus 99 ~~~~i~~w~~~~~~kkke 116 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKE 116 (242)
T ss_pred ccchHHHHHHHHHHHHHH
Confidence 466899999998886443
No 306
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.61 E-value=69 Score=22.17 Aligned_cols=20 Identities=10% Similarity=0.135 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCchhhhhhhh
Q psy15100 69 RLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFq 88 (165)
+.++|+.+|++.+.|+.|-+
T Consensus 3 i~e~a~~~gvs~~tlr~ye~ 22 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEK 22 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 307
>PF09862 DUF2089: Protein of unknown function (DUF2089); InterPro: IPR018658 This family consists of various hypothetical prokaryotic proteins.
Probab=21.54 E-value=1.9e+02 Score=20.55 Aligned_cols=38 Identities=16% Similarity=0.136 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhh
Q psy15100 45 AFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WF 87 (165)
.++.+|+.-++.+..... -..++++.+|+++-.|+.=+
T Consensus 33 ~L~~E~~~Fi~~Fi~~rG-----nlKe~e~~lgiSYPTvR~rL 70 (113)
T PF09862_consen 33 RLSPEQLEFIKLFIKNRG-----NLKEMEKELGISYPTVRNRL 70 (113)
T ss_pred cCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCcHHHHHHH
Confidence 478888888877765443 35567778888887776544
No 308
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=21.47 E-value=69 Score=22.88 Aligned_cols=21 Identities=14% Similarity=0.094 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.+||..+||+.+.|+.|-+.
T Consensus 6 I~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 6 ISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 678999999999999999653
No 309
>PF00325 Crp: Bacterial regulatory proteins, crp family; InterPro: IPR001808 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. This family groups together a range of proteins, including anr, crp, clp, cysR, fixK, flp, fnr, fnrN, hlyX and ntcA [, ]. Within this family, the HTH motif is situated towards the C terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 2OZ6_A 1CGP_B 2GZW_C 1O3T_B 3ROU_A 2CGP_A 3RDI_A 1I5Z_A 3IYD_H 3FWE_B ....
Probab=21.44 E-value=69 Score=17.48 Aligned_cols=20 Identities=30% Similarity=0.285 Sum_probs=14.6
Q ss_pred HHHHHHHHhCCCchhhhhhh
Q psy15100 68 ERLNLALSLSLTETQVKIWF 87 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WF 87 (165)
.+++||..+|++...|--=|
T Consensus 4 tr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHH
Confidence 46889999999998876544
No 310
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=21.43 E-value=60 Score=22.47 Aligned_cols=26 Identities=23% Similarity=0.241 Sum_probs=16.5
Q ss_pred HHHHHHHHhCCCchhhhhhhhcchhh
Q psy15100 68 ERLNLALSLSLTETQVKIWFQNRRTK 93 (165)
Q Consensus 68 ~r~~La~~lgl~~~qV~~WFqNRR~k 93 (165)
...+||.+.||++++|..=....+.+
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 36789999999999887666544333
No 311
>PF14771 DUF4476: Domain of unknown function (DUF4476)
Probab=21.38 E-value=2.4e+02 Score=18.69 Aligned_cols=40 Identities=18% Similarity=0.277 Sum_probs=25.0
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCchh
Q psy15100 43 ESAFTYEQLVALENKFKTTRYLSVCERLNLALSLSLTETQ 82 (165)
Q Consensus 43 R~~~s~~Ql~~Le~~F~~~~~p~~~~r~~La~~lgl~~~q 82 (165)
+..|...++..|+.....+...+..+...|...+..+...
T Consensus 19 ~~~fd~dkl~~l~~~~~~~~~~T~~Qv~~il~~f~fd~~k 58 (95)
T PF14771_consen 19 KESFDSDKLKVLEAAAKTNNCFTCAQVKQILSLFSFDNDK 58 (95)
T ss_pred cCCCcHHHHHHHHHHHhcCCceeHHHHHHHHHHcCCCHHH
Confidence 3457777777777776664446666666666666554443
No 312
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=21.35 E-value=96 Score=23.11 Aligned_cols=39 Identities=13% Similarity=0.197 Sum_probs=28.7
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhCCCchhhhhhhhcch
Q psy15100 52 VALENKFKTTRYLSVCERLNLALSLSLTETQVKIWFQNRR 91 (165)
Q Consensus 52 ~~Le~~F~~~~~p~~~~r~~La~~lgl~~~qV~~WFqNRR 91 (165)
+.-...|.+..|-. .....||+..|++...|-..|.|+-
T Consensus 15 ~aA~~lf~e~G~~~-~s~~~IA~~agvs~~~lY~hF~sKe 53 (202)
T TIGR03613 15 SAALDTFSRFGFHG-TSLEQIAELAGVSKTNLLYYFPSKD 53 (202)
T ss_pred HHHHHHHHHhCccc-CCHHHHHHHhCCCHHHHHHHcCCHH
Confidence 33344566676544 3367789999999999999999863
No 313
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=21.16 E-value=1.1e+02 Score=22.84 Aligned_cols=23 Identities=13% Similarity=0.276 Sum_probs=17.4
Q ss_pred HHHHHHHHHHhCCCchhhhhhhh
Q psy15100 66 VCERLNLALSLSLTETQVKIWFQ 88 (165)
Q Consensus 66 ~~~r~~La~~lgl~~~qV~~WFq 88 (165)
.....+||.++|++...+-.|-+
T Consensus 34 r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 34 RRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp -S-HHHHHHHHTS-HHHHHHHHH
T ss_pred cchHHHHHHHhCCCHHHHHHHHh
Confidence 34567899999999999999973
No 314
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.90 E-value=1.2e+02 Score=22.16 Aligned_cols=42 Identities=17% Similarity=0.258 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHHH----HhcCCCCHHHHHHHHHHhCCCchhhhhhhhc
Q psy15100 45 AFTYEQLVALENKF----KTTRYLSVCERLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 45 ~~s~~Ql~~Le~~F----~~~~~p~~~~r~~La~~lgl~~~qV~~WFqN 89 (165)
.||++|...|...- .++...+ ..+|...+|++...|+..|.+
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiT---i~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRIT---IKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCcc---HHHHHHHHCCCHHHHHHHHHH
Confidence 58888887776552 2333444 445666777777777666643
No 315
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.61 E-value=75 Score=21.72 Aligned_cols=22 Identities=9% Similarity=0.036 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCchhhhhhhhcc
Q psy15100 69 RLNLALSLSLTETQVKIWFQNR 90 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqNR 90 (165)
..++|+.+|++...++.|-+.-
T Consensus 4 i~eva~~~gvs~~tlR~ye~~G 25 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKLG 25 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4678999999999999997643
No 316
>cd01111 HTH_MerD Helix-Turn-Helix DNA binding domain of the MerD transcription regulator. Helix-turn-helix (HTH) transcription regulator MerD. The putative secondary regulator of mercury resistance (mer) operons, MerD, has been shown to down-regulate the expression of this operon in gram-negative bacteria. It binds to the same operator DNA as MerR that activates transcription of the operon in the presence of mercury ions. The MerD protein shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily, which promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are conserved and contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules such as metal ions, drugs,
Probab=20.03 E-value=78 Score=21.95 Aligned_cols=21 Identities=19% Similarity=0.202 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCchhhhhhhhc
Q psy15100 69 RLNLALSLSLTETQVKIWFQN 89 (165)
Q Consensus 69 r~~La~~lgl~~~qV~~WFqN 89 (165)
+.++|+.+||+...|+.|-+.
T Consensus 3 Ige~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
Done!