Query psy4877
Match_columns 120
No_of_seqs 129 out of 1542
Neff 8.5
Searched_HMMs 46136
Date Fri Aug 16 20:05:24 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy4877.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/4877hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.8 6.6E-20 1.4E-24 114.3 8.4 64 3-71 18-81 (125)
2 KOG2251|consensus 99.7 3.3E-17 7.1E-22 114.5 7.2 63 2-69 37-99 (228)
3 KOG0489|consensus 99.7 1.5E-17 3.2E-22 121.0 2.8 63 4-71 161-223 (261)
4 KOG0488|consensus 99.7 3.7E-17 8E-22 121.2 4.2 62 4-70 174-235 (309)
5 KOG0842|consensus 99.7 5.2E-17 1.1E-21 119.3 4.3 65 4-73 155-219 (307)
6 KOG0848|consensus 99.6 3.3E-16 7.2E-21 112.2 6.9 59 6-69 203-261 (317)
7 KOG0492|consensus 99.6 3E-16 6.5E-21 108.8 6.1 61 5-70 147-207 (246)
8 KOG0494|consensus 99.6 1.4E-16 2.9E-21 113.8 3.7 58 6-68 145-202 (332)
9 KOG0843|consensus 99.6 4E-16 8.7E-21 106.1 4.9 60 5-69 105-164 (197)
10 KOG0487|consensus 99.6 2.8E-16 6E-21 115.6 3.9 62 3-69 236-297 (308)
11 KOG0485|consensus 99.6 9.1E-15 2E-19 102.2 8.4 61 6-71 108-168 (268)
12 PF00046 Homeobox: Homeobox do 99.6 3.2E-15 7E-20 85.0 4.5 55 5-64 3-57 (57)
13 KOG0850|consensus 99.5 1.3E-14 2.9E-19 102.0 6.8 61 5-70 125-185 (245)
14 KOG0491|consensus 99.5 5E-15 1.1E-19 99.5 3.2 63 3-70 101-163 (194)
15 KOG0493|consensus 99.5 8.4E-15 1.8E-19 104.9 3.1 71 5-80 249-319 (342)
16 KOG0844|consensus 99.4 3.1E-14 6.7E-19 103.9 2.1 55 6-65 185-239 (408)
17 KOG0483|consensus 99.4 7.9E-14 1.7E-18 97.3 2.9 56 5-65 53-108 (198)
18 cd00086 homeodomain Homeodomai 99.4 2.5E-13 5.3E-18 77.4 4.0 55 5-64 3-57 (59)
19 KOG0486|consensus 99.4 3.4E-13 7.5E-18 98.7 5.3 65 3-72 113-177 (351)
20 smart00389 HOX Homeodomain. DN 99.4 2E-13 4.4E-18 77.1 3.2 53 5-62 3-55 (56)
21 COG5576 Homeodomain-containing 99.4 3.3E-13 7.1E-18 91.3 4.2 61 3-68 52-112 (156)
22 KOG0490|consensus 99.4 1.1E-13 2.4E-18 98.4 1.9 66 2-67 92-213 (235)
23 KOG4577|consensus 99.4 2.4E-13 5.3E-18 98.6 2.9 58 6-68 171-228 (383)
24 TIGR01565 homeo_ZF_HD homeobox 99.3 1.8E-12 4E-17 73.8 3.9 50 5-59 4-57 (58)
25 KOG0775|consensus 99.2 1.1E-11 2.3E-16 89.5 5.2 40 28-67 197-236 (304)
26 KOG0488|consensus 99.2 4.4E-12 9.5E-17 94.3 1.4 30 1-30 203-232 (309)
27 KOG0489|consensus 99.2 6.6E-12 1.4E-16 91.5 1.6 34 1-34 190-223 (261)
28 KOG0490|consensus 99.2 8.3E-12 1.8E-16 88.7 2.0 59 4-67 62-120 (235)
29 KOG0847|consensus 99.2 1.6E-11 3.4E-16 86.3 2.8 59 8-71 173-231 (288)
30 KOG3802|consensus 99.1 2.2E-11 4.7E-16 91.8 2.7 59 3-66 295-353 (398)
31 KOG0849|consensus 99.1 1.7E-10 3.6E-15 87.4 5.2 58 6-68 180-237 (354)
32 KOG0494|consensus 99.1 5.5E-11 1.2E-15 85.3 1.9 37 3-39 174-210 (332)
33 KOG0484|consensus 99.0 9.6E-11 2.1E-15 73.4 1.3 29 2-30 49-77 (125)
34 KOG0848|consensus 98.9 4.7E-10 1E-14 80.9 1.4 29 2-30 231-259 (317)
35 KOG0487|consensus 98.9 2.2E-10 4.9E-15 84.6 -0.3 30 1-30 266-295 (308)
36 PF05920 Homeobox_KN: Homeobox 98.9 1.1E-09 2.4E-14 57.9 2.2 34 28-61 7-40 (40)
37 KOG0843|consensus 98.8 8E-10 1.7E-14 75.5 1.2 28 2-29 134-161 (197)
38 KOG0774|consensus 98.8 2.2E-08 4.8E-13 72.2 7.1 60 6-70 192-254 (334)
39 KOG0483|consensus 98.7 2.3E-09 5.1E-14 75.0 0.9 39 2-40 82-121 (198)
40 KOG0485|consensus 98.7 5.2E-09 1.1E-13 73.6 1.3 27 2-28 136-162 (268)
41 KOG0847|consensus 98.7 6E-09 1.3E-13 73.4 1.4 28 1-28 198-225 (288)
42 KOG2251|consensus 98.6 1.1E-08 2.5E-13 71.9 0.3 29 2-30 69-97 (228)
43 KOG0850|consensus 98.5 2.2E-08 4.8E-13 70.9 1.2 30 1-30 153-182 (245)
44 KOG0491|consensus 98.5 4E-08 8.7E-13 66.4 1.2 30 1-30 131-160 (194)
45 PF00046 Homeobox: Homeobox do 98.5 7.5E-08 1.6E-12 54.3 2.2 26 2-27 32-57 (57)
46 KOG1168|consensus 98.5 2.5E-08 5.4E-13 72.9 0.1 38 28-65 330-367 (385)
47 KOG0844|consensus 98.3 8.2E-08 1.8E-12 70.7 -0.3 26 2-27 213-238 (408)
48 KOG0842|consensus 98.2 1.3E-07 2.8E-12 70.0 -1.2 27 2-28 185-211 (307)
49 KOG0492|consensus 98.2 2.8E-07 6.1E-12 64.5 0.2 27 2-28 176-202 (246)
50 cd00086 homeodomain Homeodomai 98.2 9.3E-07 2E-11 49.8 2.1 26 2-27 32-57 (59)
51 KOG0493|consensus 98.2 6.3E-07 1.4E-11 64.8 1.7 26 2-27 278-303 (342)
52 COG5576 Homeodomain-containing 98.2 3.5E-07 7.6E-12 62.0 -0.0 59 2-61 83-146 (156)
53 smart00389 HOX Homeodomain. DN 98.1 1.8E-06 3.8E-11 48.3 1.7 24 2-25 32-55 (56)
54 KOG4577|consensus 97.9 2.7E-06 5.8E-11 62.4 0.7 26 2-27 199-224 (383)
55 TIGR01565 homeo_ZF_HD homeobox 97.8 2.2E-06 4.9E-11 48.8 -0.7 19 2-20 37-55 (58)
56 KOG0486|consensus 97.8 4.6E-06 9.9E-11 61.7 0.3 29 2-30 144-172 (351)
57 KOG1146|consensus 97.8 2E-05 4.3E-10 67.4 3.4 61 2-67 903-963 (1406)
58 KOG0849|consensus 97.5 4E-05 8.7E-10 58.3 1.8 32 2-33 208-239 (354)
59 KOG0773|consensus 97.4 5.2E-05 1.1E-09 57.2 1.1 56 8-69 245-304 (342)
60 PF05920 Homeobox_KN: Homeobox 97.4 0.00013 2.8E-09 38.4 1.9 22 2-23 18-39 (40)
61 KOG2252|consensus 97.4 0.00023 4.9E-09 56.4 4.0 52 6-62 424-475 (558)
62 KOG3802|consensus 96.8 8.6E-05 1.9E-09 56.7 -3.2 29 2-30 326-354 (398)
63 KOG0775|consensus 96.3 0.0017 3.6E-08 47.6 1.1 21 2-22 208-228 (304)
64 PF11569 Homez: Homeodomain le 95.4 0.014 2.9E-07 32.9 2.1 31 29-59 20-50 (56)
65 PF01381 HTH_3: Helix-turn-hel 94.3 0.072 1.6E-06 29.1 3.2 40 2-49 14-53 (55)
66 PHA01976 helix-turn-helix prot 94.2 0.075 1.6E-06 30.3 3.2 40 2-49 20-59 (67)
67 PF13443 HTH_26: Cro/C1-type H 93.6 0.091 2E-06 29.5 2.8 43 2-51 15-57 (63)
68 TIGR02607 antidote_HigA addict 93.5 0.1 2.2E-06 30.6 2.9 39 2-48 23-61 (78)
69 KOG3623|consensus 93.2 0.06 1.3E-06 44.6 2.2 62 3-64 589-683 (1007)
70 TIGR03070 couple_hipB transcri 93.2 0.12 2.6E-06 28.1 2.8 37 2-46 20-56 (58)
71 PF13560 HTH_31: Helix-turn-he 93.1 0.15 3.3E-06 28.9 3.3 44 2-52 19-62 (64)
72 PF11569 Homez: Homeodomain le 93.1 0.06 1.3E-06 30.3 1.4 21 2-22 30-50 (56)
73 PF12844 HTH_19: Helix-turn-he 93.0 0.16 3.4E-06 28.7 3.2 43 2-52 17-59 (64)
74 KOG3623|consensus 92.8 0.11 2.4E-06 43.2 3.0 38 28-65 577-614 (1007)
75 TIGR00270 conserved hypothetic 91.9 0.22 4.7E-06 33.8 3.2 41 2-50 87-127 (154)
76 PF07022 Phage_CI_repr: Bacter 91.7 0.23 4.9E-06 28.6 2.8 38 2-48 17-55 (66)
77 PRK06424 transcription factor; 91.6 0.21 4.5E-06 33.5 2.8 39 2-48 102-140 (144)
78 PRK13890 conjugal transfer pro 91.4 0.27 5.8E-06 31.8 3.1 42 2-51 23-64 (120)
79 smart00530 HTH_XRE Helix-turn- 91.2 0.32 6.9E-06 25.1 2.9 39 2-48 15-53 (56)
80 PRK09726 antitoxin HipB; Provi 90.8 0.29 6.4E-06 29.7 2.8 23 36-58 27-49 (88)
81 PRK10072 putative transcriptio 90.6 0.37 8E-06 30.1 3.1 24 36-59 48-71 (96)
82 cd00093 HTH_XRE Helix-turn-hel 90.1 0.47 1E-05 24.6 3.0 39 2-48 17-55 (58)
83 PRK08359 transcription factor; 90.0 0.35 7.7E-06 33.5 2.9 39 2-48 103-141 (176)
84 PHA01083 hypothetical protein 89.6 0.41 8.9E-06 32.2 2.9 44 2-52 21-64 (149)
85 PRK09706 transcriptional repre 88.9 0.58 1.3E-05 30.6 3.2 39 2-48 23-61 (135)
86 TIGR02612 mob_myst_A mobile my 88.8 0.39 8.4E-06 32.4 2.3 42 2-49 43-84 (150)
87 cd01392 HTH_LacI Helix-turn-he 87.8 0.81 1.7E-05 24.5 2.9 39 2-48 2-43 (52)
88 KOG1168|consensus 87.4 0.048 1E-06 40.6 -2.9 26 2-27 341-366 (385)
89 PRK09943 DNA-binding transcrip 86.9 0.82 1.8E-05 31.4 3.2 41 2-50 25-65 (185)
90 TIGR02684 dnstrm_HI1420 probab 86.9 0.81 1.8E-05 28.1 2.8 39 2-48 48-86 (89)
91 TIGR03879 near_KaiC_dom probab 85.7 0.69 1.5E-05 27.4 1.9 46 3-57 9-55 (73)
92 KOG3755|consensus 83.4 0.96 2.1E-05 37.0 2.4 63 3-65 684-757 (769)
93 PRK08154 anaerobic benzoate ca 82.2 1.6 3.5E-05 32.6 3.1 42 2-51 46-87 (309)
94 PRK02866 cyanate hydratase; Va 82.1 2.2 4.7E-05 28.8 3.4 41 2-50 23-63 (147)
95 PF10668 Phage_terminase: Phag 82.1 0.86 1.9E-05 26.0 1.2 16 2-17 27-42 (60)
96 PF10668 Phage_terminase: Phag 81.9 0.83 1.8E-05 26.0 1.1 20 36-55 24-43 (60)
97 KOG0774|consensus 81.2 2.2 4.8E-05 31.5 3.4 25 2-26 223-247 (334)
98 COG2944 Predicted transcriptio 80.0 1.5 3.3E-05 27.8 2.0 18 4-21 64-81 (104)
99 PRK03975 tfx putative transcri 78.1 3.6 7.7E-05 27.5 3.4 50 5-65 3-52 (141)
100 PF13413 HTH_25: Helix-turn-he 77.4 4.1 9E-05 23.1 3.1 44 2-51 15-62 (62)
101 TIGR00673 cynS cyanate hydrata 77.4 3.7 8E-05 27.8 3.3 41 2-50 26-66 (150)
102 PF08281 Sigma70_r4_2: Sigma-7 76.9 3.8 8.3E-05 22.0 2.8 29 31-59 23-51 (54)
103 PF04545 Sigma70_r4: Sigma-70, 75.4 5.6 0.00012 21.1 3.2 41 8-58 4-44 (50)
104 PF13518 HTH_28: Helix-turn-he 74.9 2.8 6.1E-05 22.2 1.9 21 2-22 17-37 (52)
105 PF04218 CENP-B_N: CENP-B N-te 73.4 1.9 4E-05 23.7 0.9 26 34-59 22-47 (53)
106 PF00196 GerE: Bacterial regul 72.0 6.3 0.00014 21.6 3.0 44 8-62 3-46 (58)
107 cd06171 Sigma70_r4 Sigma70, re 71.6 3.9 8.5E-05 21.0 2.0 21 2-22 31-51 (55)
108 PF06056 Terminase_5: Putative 71.4 1.9 4E-05 24.3 0.6 32 31-64 10-41 (58)
109 cd04761 HTH_MerR-SF Helix-Turn 71.3 2.9 6.4E-05 21.8 1.4 20 2-21 5-24 (49)
110 COG1813 Predicted transcriptio 69.5 6 0.00013 27.2 2.9 37 2-46 97-133 (165)
111 COG1476 Predicted transcriptio 68.8 9.5 0.00021 22.3 3.3 40 2-49 19-58 (68)
112 PF13411 MerR_1: MerR HTH fami 68.7 4.1 8.8E-05 23.0 1.7 22 2-23 5-26 (69)
113 KOG1146|consensus 68.5 2.6 5.7E-05 37.5 1.2 25 3-27 936-960 (1406)
114 PHA00542 putative Cro-like pro 68.0 7.1 0.00015 23.3 2.7 24 35-58 32-55 (82)
115 PRK04140 hypothetical protein; 67.5 6 0.00013 30.0 2.9 39 2-48 144-182 (317)
116 KOG0044|consensus 66.7 4.7 0.0001 28.4 2.0 31 2-38 16-46 (193)
117 PRK10072 putative transcriptio 65.6 3.6 7.9E-05 25.6 1.2 19 2-20 51-69 (96)
118 TIGR00721 tfx DNA-binding prot 64.0 12 0.00027 24.8 3.5 50 4-64 2-51 (137)
119 PRK09646 RNA polymerase sigma 63.7 9.2 0.0002 26.2 3.0 34 31-64 155-188 (194)
120 KOG0773|consensus 63.3 1.8 3.8E-05 32.7 -0.7 22 2-23 274-295 (342)
121 PRK12526 RNA polymerase sigma 61.8 9.4 0.0002 26.5 2.8 35 31-65 166-200 (206)
122 PRK06759 RNA polymerase factor 61.7 9.9 0.00022 24.7 2.8 33 31-63 119-151 (154)
123 cd04763 HTH_MlrA-like Helix-Tu 60.9 6.3 0.00014 22.3 1.5 19 2-20 5-23 (68)
124 PF13384 HTH_23: Homeodomain-l 58.9 6.2 0.00014 20.7 1.2 20 2-21 22-41 (50)
125 PF04967 HTH_10: HTH DNA bindi 58.9 18 0.00039 19.9 3.1 42 9-53 1-42 (53)
126 PF01978 TrmB: Sugar-specific 56.8 7.4 0.00016 22.0 1.4 40 6-54 3-42 (68)
127 PF08671 SinI: Anti-repressor 56.5 6.5 0.00014 19.2 0.9 17 2-18 10-26 (30)
128 PRK10856 cytoskeletal protein 56.4 14 0.00031 28.1 3.1 21 2-22 32-52 (331)
129 TIGR03830 CxxCG_CxxCG_HTH puta 55.7 15 0.00031 23.3 2.7 24 36-59 80-103 (127)
130 PF06971 Put_DNA-bind_N: Putat 55.4 5.5 0.00012 21.8 0.6 14 2-15 33-46 (50)
131 cd08311 Death_p75NR Death doma 55.2 8.6 0.00019 22.9 1.5 17 2-18 20-36 (77)
132 smart00342 HTH_ARAC helix_turn 55.0 14 0.00031 20.8 2.4 20 2-21 6-25 (84)
133 TIGR02985 Sig70_bacteroi1 RNA 55.0 15 0.00032 23.7 2.7 34 31-64 126-159 (161)
134 cd01104 HTH_MlrA-CarA Helix-Tu 54.7 9.3 0.0002 21.4 1.5 19 2-20 5-23 (68)
135 PRK12515 RNA polymerase sigma 54.5 21 0.00046 24.1 3.6 35 31-65 144-178 (189)
136 PF00376 MerR: MerR family reg 54.5 9.5 0.00021 19.4 1.4 19 2-20 4-22 (38)
137 PRK12519 RNA polymerase sigma 54.4 13 0.00028 25.2 2.5 34 31-64 154-187 (194)
138 TIGR02999 Sig-70_X6 RNA polyme 54.3 18 0.00038 24.2 3.1 34 31-64 147-180 (183)
139 cd04764 HTH_MlrA-like_sg1 Heli 54.1 9.9 0.00021 21.4 1.6 19 2-20 5-23 (67)
140 PRK04217 hypothetical protein; 53.8 26 0.00055 22.4 3.6 47 8-64 42-88 (110)
141 PF11212 DUF2999: Protein of u 53.6 23 0.00049 21.0 3.0 41 3-52 7-47 (82)
142 PRK06930 positive control sigm 53.5 24 0.00052 24.1 3.7 34 32-65 128-161 (170)
143 PRK09652 RNA polymerase sigma 53.4 18 0.0004 23.8 3.1 34 31-64 141-174 (182)
144 PRK03975 tfx putative transcri 52.3 14 0.0003 24.7 2.3 26 2-27 26-51 (141)
145 cd04762 HTH_MerR-trunc Helix-T 52.3 11 0.00024 19.0 1.5 21 2-22 5-25 (49)
146 PF12728 HTH_17: Helix-turn-he 52.2 6 0.00013 21.0 0.4 19 2-20 6-24 (51)
147 smart00482 POLAc DNA polymeras 51.8 15 0.00033 25.8 2.5 27 3-35 88-114 (206)
148 PRK11924 RNA polymerase sigma 51.8 25 0.00054 23.1 3.5 35 31-65 138-172 (179)
149 PF05269 Phage_CII: Bacterioph 51.8 26 0.00055 21.7 3.2 43 12-64 11-53 (91)
150 PRK12518 RNA polymerase sigma 51.6 12 0.00026 24.9 1.9 36 30-65 132-167 (175)
151 TIGR02937 sigma70-ECF RNA poly 51.6 19 0.00042 22.6 2.9 33 32-64 124-156 (158)
152 PRK12514 RNA polymerase sigma 51.5 19 0.00041 24.1 2.9 34 31-64 142-175 (179)
153 PRK09648 RNA polymerase sigma 51.1 21 0.00045 24.1 3.1 34 31-64 152-185 (189)
154 PRK09642 RNA polymerase sigma 51.1 25 0.00053 23.0 3.4 35 31-65 119-153 (160)
155 smart00421 HTH_LUXR helix_turn 50.7 25 0.00055 18.2 2.9 23 35-57 19-41 (58)
156 PF04760 IF2_N: Translation in 50.7 19 0.0004 19.5 2.3 44 2-45 8-52 (54)
157 PRK12535 RNA polymerase sigma 50.3 23 0.00049 24.4 3.2 38 31-68 146-183 (196)
158 PRK09644 RNA polymerase sigma 49.7 26 0.00057 23.1 3.4 35 31-65 121-155 (165)
159 PRK11923 algU RNA polymerase s 49.4 26 0.00057 23.7 3.4 36 31-66 151-186 (193)
160 PRK09047 RNA polymerase factor 49.4 29 0.00063 22.5 3.5 34 31-64 119-152 (161)
161 cd08306 Death_FADD Fas-associa 49.3 14 0.00031 22.3 1.8 19 2-20 18-36 (86)
162 PF01710 HTH_Tnp_IS630: Transp 49.2 15 0.00032 23.5 2.0 51 2-53 23-90 (119)
163 PF10453 NUFIP1: Nuclear fragi 49.1 25 0.00055 19.6 2.7 23 10-38 19-41 (56)
164 PF13404 HTH_AsnC-type: AsnC-t 49.0 8.9 0.00019 19.9 0.7 14 2-15 22-35 (42)
165 PF12824 MRP-L20: Mitochondria 48.7 82 0.0018 21.5 5.6 50 5-61 82-131 (164)
166 TIGR02939 RpoE_Sigma70 RNA pol 48.2 24 0.00051 23.7 3.0 35 31-65 151-185 (190)
167 PRK12543 RNA polymerase sigma 47.7 40 0.00086 22.6 4.0 37 31-67 130-166 (179)
168 PF04539 Sigma70_r3: Sigma-70 47.5 13 0.00028 21.5 1.4 19 2-20 25-43 (78)
169 PF07638 Sigma70_ECF: ECF sigm 47.2 24 0.00053 24.1 2.9 34 31-64 148-181 (185)
170 TIGR02989 Sig-70_gvs1 RNA poly 47.2 24 0.00053 22.9 2.9 32 31-62 124-155 (159)
171 PRK12536 RNA polymerase sigma 47.1 25 0.00053 23.7 2.9 34 31-64 142-175 (181)
172 TIGR03001 Sig-70_gmx1 RNA poly 47.0 52 0.0011 23.7 4.7 40 31-70 174-213 (244)
173 TIGR02983 SigE-fam_strep RNA p 46.9 24 0.00053 23.0 2.9 34 31-64 123-156 (162)
174 PRK12512 RNA polymerase sigma 46.3 26 0.00055 23.5 2.9 35 31-65 144-178 (184)
175 PRK09639 RNA polymerase sigma 46.3 41 0.0009 22.0 3.9 35 30-65 124-158 (166)
176 PF00165 HTH_AraC: Bacterial r 45.8 16 0.00035 18.5 1.5 20 2-21 13-32 (42)
177 TIGR02948 SigW_bacill RNA poly 45.6 27 0.00058 23.4 2.9 34 31-64 149-182 (187)
178 PRK06811 RNA polymerase factor 44.6 26 0.00056 23.8 2.8 34 31-64 144-177 (189)
179 PRK12530 RNA polymerase sigma 44.5 42 0.00091 22.8 3.8 35 31-65 147-181 (189)
180 smart00422 HTH_MERR helix_turn 44.3 16 0.00034 20.4 1.4 19 2-20 5-23 (70)
181 PRK12538 RNA polymerase sigma 44.0 40 0.00086 24.0 3.7 36 31-66 184-219 (233)
182 cd01670 Death Death Domain: a 44.0 19 0.0004 20.7 1.7 20 2-21 15-34 (79)
183 PRK12546 RNA polymerase sigma 43.9 27 0.00059 23.9 2.8 35 31-65 126-160 (188)
184 cd08313 Death_TNFR1 Death doma 43.8 16 0.00034 21.9 1.4 19 2-20 16-34 (80)
185 TIGR03020 EpsA transcriptional 43.7 27 0.00058 25.5 2.8 45 8-63 190-234 (247)
186 PRK09637 RNA polymerase sigma 43.5 31 0.00067 23.4 3.0 34 31-64 119-152 (181)
187 TIGR03541 reg_near_HchA LuxR f 43.0 28 0.0006 24.8 2.8 46 8-64 171-216 (232)
188 TIGR02950 SigM_subfam RNA poly 42.5 17 0.00036 23.5 1.5 35 30-64 117-151 (154)
189 PRK00118 putative DNA-binding 42.5 38 0.00082 21.4 3.0 33 33-65 32-64 (104)
190 PRK09647 RNA polymerase sigma 42.4 42 0.0009 23.3 3.6 35 31-65 151-185 (203)
191 TIGR02954 Sig70_famx3 RNA poly 42.3 30 0.00066 22.8 2.8 34 31-64 132-165 (169)
192 PRK12522 RNA polymerase sigma 42.2 40 0.00086 22.4 3.4 35 31-65 132-166 (173)
193 TIGR02959 SigZ RNA polymerase 42.1 43 0.00093 22.3 3.5 34 31-64 113-146 (170)
194 PRK12529 RNA polymerase sigma 42.0 35 0.00075 22.9 3.0 34 31-64 140-173 (178)
195 PRK12520 RNA polymerase sigma 42.0 51 0.0011 22.3 3.9 37 31-67 144-180 (191)
196 PRK12543 RNA polymerase sigma 41.1 22 0.00047 23.9 1.9 26 2-27 138-163 (179)
197 PRK12532 RNA polymerase sigma 40.8 46 0.001 22.6 3.6 36 31-66 149-184 (195)
198 PRK05602 RNA polymerase sigma 40.1 43 0.00093 22.5 3.3 35 31-65 141-175 (186)
199 cd08804 Death_ank2 Death domai 40.0 17 0.00036 21.9 1.1 19 2-20 20-38 (84)
200 COG3413 Predicted DNA binding 40.0 40 0.00087 23.6 3.2 43 8-53 155-197 (215)
201 smart00354 HTH_LACI helix_turn 39.7 42 0.0009 19.1 2.7 19 2-20 5-23 (70)
202 PRK12523 RNA polymerase sigma 39.5 38 0.00081 22.5 2.9 34 31-64 132-165 (172)
203 TIGR02947 SigH_actino RNA poly 39.4 34 0.00073 23.2 2.7 36 31-66 144-179 (193)
204 TIGR01764 excise DNA binding d 39.0 24 0.00052 17.8 1.5 19 2-20 6-24 (49)
205 cd08317 Death_ank Death domain 38.9 25 0.00054 20.9 1.7 18 2-19 20-37 (84)
206 PRK12524 RNA polymerase sigma 38.8 45 0.00097 22.7 3.2 34 31-64 149-182 (196)
207 cd08777 Death_RIP1 Death Domai 38.7 25 0.00054 21.3 1.7 17 2-18 18-34 (86)
208 PRK15411 rcsA colanic acid cap 38.5 24 0.00052 24.6 1.9 41 9-60 138-178 (207)
209 TIGR03001 Sig-70_gmx1 RNA poly 38.4 46 0.001 24.0 3.3 43 2-51 182-224 (244)
210 COG4977 Transcriptional regula 38.4 43 0.00094 25.6 3.3 20 2-21 241-260 (328)
211 PRK12547 RNA polymerase sigma 38.2 44 0.00095 22.0 3.0 34 31-64 125-158 (164)
212 cd04774 HTH_YfmP Helix-Turn-He 38.1 22 0.00048 21.8 1.4 58 2-59 5-71 (96)
213 PRK12516 RNA polymerase sigma 38.0 56 0.0012 22.2 3.6 35 31-65 129-163 (187)
214 cd08318 Death_NMPP84 Death dom 38.0 19 0.0004 21.7 1.1 17 2-18 23-39 (86)
215 PRK06986 fliA flagellar biosyn 37.9 50 0.0011 23.3 3.4 35 31-65 197-231 (236)
216 PRK12531 RNA polymerase sigma 37.7 49 0.0011 22.5 3.3 34 31-64 154-187 (194)
217 cd08638 DNA_pol_A_theta DNA po 37.7 33 0.00072 26.4 2.6 28 3-36 214-241 (373)
218 PF12802 MarR_2: MarR family; 37.3 45 0.00097 17.9 2.6 38 7-52 1-39 (62)
219 cd06170 LuxR_C_like C-terminal 36.7 37 0.00081 17.6 2.1 19 2-20 20-38 (57)
220 PRK12513 RNA polymerase sigma 36.7 32 0.0007 23.3 2.3 35 31-65 152-186 (194)
221 PRK12533 RNA polymerase sigma 36.6 71 0.0015 22.5 4.0 35 31-65 147-181 (216)
222 PRK13919 putative RNA polymera 36.5 49 0.0011 22.2 3.1 34 31-64 148-181 (186)
223 PRK10100 DNA-binding transcrip 36.4 40 0.00086 23.8 2.7 44 9-63 156-199 (216)
224 cd08640 DNA_pol_A_plastid_like 36.1 38 0.00083 26.2 2.7 29 2-36 215-243 (371)
225 PRK11511 DNA-binding transcrip 35.9 26 0.00057 22.4 1.6 20 2-21 30-49 (127)
226 PF08280 HTH_Mga: M protein tr 35.9 20 0.00044 19.8 0.9 19 2-20 24-42 (59)
227 PRK12537 RNA polymerase sigma 35.8 46 0.001 22.3 2.9 33 31-63 146-178 (182)
228 PF12833 HTH_18: Helix-turn-he 35.7 30 0.00065 19.8 1.7 19 3-21 1-19 (81)
229 PRK12542 RNA polymerase sigma 35.5 47 0.001 22.3 2.9 34 31-64 135-168 (185)
230 cd01105 HTH_GlnR-like Helix-Tu 35.3 26 0.00057 21.0 1.5 20 2-21 6-25 (88)
231 PRK12545 RNA polymerase sigma 35.3 69 0.0015 22.0 3.8 35 31-65 152-186 (201)
232 cd08319 Death_RAIDD Death doma 35.2 30 0.00066 20.8 1.7 19 2-20 18-36 (83)
233 PF13412 HTH_24: Winged helix- 35.2 29 0.00063 18.0 1.5 19 2-20 22-40 (48)
234 PF09607 BrkDBD: Brinker DNA-b 35.1 30 0.00066 19.5 1.5 17 4-20 32-48 (58)
235 PRK08295 RNA polymerase factor 35.1 35 0.00075 23.3 2.2 34 31-64 167-200 (208)
236 TIGR02947 SigH_actino RNA poly 35.0 35 0.00076 23.1 2.2 25 2-26 152-176 (193)
237 smart00351 PAX Paired Box doma 35.0 33 0.00072 22.1 2.0 22 2-23 38-59 (125)
238 COG3655 Predicted transcriptio 34.9 53 0.0012 19.4 2.6 16 2-17 20-35 (73)
239 PRK09649 RNA polymerase sigma 34.8 44 0.00095 22.6 2.7 34 31-64 143-176 (185)
240 TIGR02943 Sig70_famx1 RNA poly 34.8 71 0.0015 21.7 3.7 35 31-65 144-178 (188)
241 PRK12541 RNA polymerase sigma 34.7 41 0.0009 22.0 2.5 34 31-64 125-158 (161)
242 PRK13870 transcriptional regul 34.5 44 0.00095 23.9 2.7 44 8-62 173-216 (234)
243 PRK10188 DNA-binding transcrip 34.5 48 0.001 23.8 2.9 45 7-62 178-222 (240)
244 PRK12528 RNA polymerase sigma 34.1 51 0.0011 21.5 2.8 29 31-59 126-154 (161)
245 PF00531 Death: Death domain; 34.0 32 0.00069 19.8 1.7 19 2-20 17-35 (83)
246 TIGR02952 Sig70_famx2 RNA poly 33.5 62 0.0013 21.1 3.2 32 31-62 135-166 (170)
247 PRK07037 extracytoplasmic-func 33.5 64 0.0014 21.0 3.3 34 31-64 122-155 (163)
248 PF04814 HNF-1_N: Hepatocyte n 33.2 62 0.0013 22.6 3.1 24 37-61 134-157 (180)
249 PF13551 HTH_29: Winged helix- 33.1 36 0.00077 20.6 1.8 22 2-23 17-38 (112)
250 PRK12517 RNA polymerase sigma 33.1 93 0.002 21.1 4.1 37 31-67 141-177 (188)
251 COG1595 RpoE DNA-directed RNA 33.0 64 0.0014 21.6 3.3 35 31-65 140-174 (182)
252 cd04767 HTH_HspR-like_MBC Heli 32.9 29 0.00063 22.5 1.4 21 2-22 6-26 (120)
253 COG1356 tfx Transcriptional re 32.8 27 0.00058 23.1 1.2 51 3-66 3-53 (143)
254 cd04790 HTH_Cfa-like_unk Helix 32.7 62 0.0013 22.1 3.1 42 2-51 123-164 (172)
255 PRK07408 RNA polymerase sigma 32.5 64 0.0014 23.3 3.3 34 31-64 216-249 (256)
256 PRK09651 RNA polymerase sigma 32.3 56 0.0012 21.7 2.9 33 31-63 132-164 (172)
257 PRK09413 IS2 repressor TnpA; R 32.2 36 0.00078 21.7 1.8 22 2-23 34-55 (121)
258 PRK09641 RNA polymerase sigma 32.2 51 0.0011 21.9 2.7 34 31-64 149-182 (187)
259 PRK12544 RNA polymerase sigma 32.0 88 0.0019 21.7 3.9 36 31-66 161-196 (206)
260 PF13744 HTH_37: Helix-turn-he 31.8 61 0.0013 18.9 2.6 17 2-18 36-52 (80)
261 cd04780 HTH_MerR-like_sg5 Heli 31.8 33 0.00071 21.0 1.5 56 2-57 5-70 (95)
262 TIGR02859 spore_sigH RNA polym 31.7 27 0.00058 23.6 1.2 33 31-63 162-194 (198)
263 PF04936 DUF658: Protein of un 31.7 19 0.00041 24.8 0.4 37 35-71 15-51 (186)
264 PRK12527 RNA polymerase sigma 31.6 82 0.0018 20.4 3.5 34 31-64 118-151 (159)
265 PF00356 LacI: Bacterial regul 31.6 85 0.0018 16.6 2.9 19 2-20 4-22 (46)
266 PRK10403 transcriptional regul 31.5 53 0.0012 21.6 2.7 28 35-62 169-196 (215)
267 PF07813 LTXXQ: LTXXQ motif fa 31.4 35 0.00076 20.3 1.6 21 2-22 8-28 (100)
268 cd04766 HTH_HspR Helix-Turn-He 31.4 34 0.00073 20.6 1.5 54 2-55 6-68 (91)
269 PRK12525 RNA polymerase sigma 31.2 59 0.0013 21.5 2.8 33 31-63 131-163 (168)
270 PF13730 HTH_36: Helix-turn-he 30.9 89 0.0019 16.4 3.1 20 36-55 27-46 (55)
271 PF00476 DNA_pol_A: DNA polyme 30.8 39 0.00084 26.1 2.0 31 2-38 228-258 (383)
272 COG1513 CynS Cyanate lyase [In 30.8 89 0.0019 20.8 3.4 42 2-51 26-67 (151)
273 PF07037 DUF1323: Putative tra 30.2 37 0.0008 22.1 1.5 24 2-27 5-28 (122)
274 PRK09640 RNA polymerase sigma 30.0 42 0.00092 22.7 2.0 34 31-64 147-180 (188)
275 cd08637 DNA_pol_A_pol_I_C Poly 29.9 55 0.0012 25.3 2.7 28 3-36 225-252 (377)
276 cd08803 Death_ank3 Death domai 29.9 37 0.0008 20.5 1.5 16 2-17 20-35 (84)
277 PRK09638 RNA polymerase sigma 29.6 34 0.00074 22.6 1.4 35 30-64 138-172 (176)
278 smart00005 DEATH DEATH domain, 29.6 44 0.00095 19.5 1.8 19 2-20 22-40 (88)
279 PRK09415 RNA polymerase factor 29.6 57 0.0012 21.8 2.5 34 31-64 140-173 (179)
280 PRK11922 RNA polymerase sigma 29.5 46 0.001 23.4 2.1 37 30-66 161-197 (231)
281 PRK09645 RNA polymerase sigma 29.5 70 0.0015 21.1 2.9 34 31-64 131-164 (173)
282 PF01527 HTH_Tnp_1: Transposas 29.4 45 0.00097 18.9 1.7 21 2-22 28-48 (76)
283 PRK08583 RNA polymerase sigma 29.2 75 0.0016 22.7 3.2 34 31-64 218-251 (257)
284 cd04775 HTH_Cfa-like Helix-Tur 29.1 38 0.00083 20.9 1.5 57 2-58 6-70 (102)
285 TIGR02479 FliA_WhiG RNA polyme 28.9 79 0.0017 22.1 3.3 34 31-64 188-221 (224)
286 cd04773 HTH_TioE_rpt2 Second H 28.9 38 0.00082 21.2 1.4 56 2-57 5-69 (108)
287 PF08279 HTH_11: HTH domain; 28.8 32 0.00069 18.3 0.9 15 2-16 20-34 (55)
288 cd00592 HTH_MerR-like Helix-Tu 28.6 39 0.00086 20.4 1.5 59 2-60 5-71 (100)
289 KOG2252|consensus 28.5 35 0.00075 27.9 1.4 24 2-25 452-475 (558)
290 PF08452 DNAP_B_exo_N: DNA pol 28.4 18 0.0004 16.1 -0.1 8 53-60 7-14 (22)
291 PF00325 Crp: Bacterial regula 28.3 61 0.0013 15.9 1.8 21 2-22 7-27 (32)
292 cd01798 parkin_N amino-termina 28.2 40 0.00087 19.0 1.4 26 35-60 23-48 (70)
293 TIGR02984 Sig-70_plancto1 RNA 28.0 80 0.0017 21.0 3.1 33 31-63 153-185 (189)
294 PRK12511 RNA polymerase sigma 28.0 93 0.002 21.0 3.4 34 31-64 124-157 (182)
295 cd01796 DDI1_N DNA damage indu 27.8 41 0.00089 19.2 1.4 27 35-61 24-50 (71)
296 COG1427 Predicted periplasmic 27.8 51 0.0011 24.3 2.1 21 2-22 203-223 (252)
297 PF13542 HTH_Tnp_ISL3: Helix-t 27.8 53 0.0011 17.1 1.7 17 3-19 33-49 (52)
298 cd01106 HTH_TipAL-Mta Helix-Tu 27.7 42 0.0009 20.6 1.5 58 2-59 5-71 (103)
299 PRK08301 sporulation sigma fac 27.7 52 0.0011 23.1 2.1 33 32-64 196-228 (234)
300 cd00569 HTH_Hin_like Helix-tur 27.6 42 0.00092 14.9 1.2 20 36-55 23-42 (42)
301 PRK12538 RNA polymerase sigma 27.5 54 0.0012 23.4 2.2 25 2-26 192-216 (233)
302 cd01279 HTH_HspR-like Helix-Tu 27.5 41 0.0009 20.6 1.4 56 2-57 6-70 (98)
303 PF14229 DUF4332: Domain of un 27.5 42 0.00091 21.6 1.5 25 31-55 26-50 (122)
304 cd04768 HTH_BmrR-like Helix-Tu 27.4 42 0.00091 20.4 1.4 58 2-59 5-71 (96)
305 PHA00675 hypothetical protein 27.3 1.1E+02 0.0024 18.3 3.1 37 7-53 21-58 (78)
306 PRK09935 transcriptional regul 27.1 75 0.0016 20.9 2.8 28 34-61 164-191 (210)
307 TIGR02054 MerD mercuric resist 27.1 43 0.00093 21.6 1.5 54 2-55 8-70 (120)
308 PRK06704 RNA polymerase factor 26.8 85 0.0018 22.5 3.1 33 33-65 131-163 (228)
309 PRK12539 RNA polymerase sigma 26.8 90 0.002 20.9 3.1 34 31-64 144-177 (184)
310 COG4367 Uncharacterized protei 26.7 1.3E+02 0.0028 18.6 3.4 39 9-52 3-41 (97)
311 cd04789 HTH_Cfa Helix-Turn-Hel 26.6 46 0.00099 20.5 1.5 57 2-58 6-70 (102)
312 PRK10651 transcriptional regul 26.6 73 0.0016 21.0 2.7 43 9-62 156-198 (216)
313 cd04765 HTH_MlrA-like_sg2 Heli 26.5 47 0.001 20.5 1.5 59 2-60 5-73 (99)
314 TIGR02835 spore_sigmaE RNA pol 26.4 99 0.0021 21.8 3.4 31 34-64 198-228 (234)
315 cd08779 Death_PIDD Death Domai 26.3 49 0.0011 19.9 1.5 19 2-20 18-36 (86)
316 PRK12540 RNA polymerase sigma 26.1 1E+02 0.0022 20.8 3.3 34 31-64 124-157 (182)
317 PRK07670 RNA polymerase sigma 25.9 1E+02 0.0022 22.0 3.4 34 31-64 214-247 (251)
318 PTZ00044 ubiquitin; Provisiona 25.9 46 0.00099 18.9 1.3 28 34-61 24-51 (76)
319 TIGR02980 SigBFG RNA polymeras 25.9 96 0.0021 21.6 3.2 33 31-63 191-223 (227)
320 PF12244 DUF3606: Protein of u 25.8 39 0.00084 18.8 1.0 14 3-16 26-39 (57)
321 PF13936 HTH_38: Helix-turn-he 25.8 56 0.0012 16.9 1.5 22 34-55 20-41 (44)
322 cd08315 Death_TRAILR_DR4_DR5 D 25.5 43 0.00093 20.7 1.2 19 2-20 24-42 (96)
323 cd01803 Ubiquitin Ubiquitin. U 25.4 46 0.001 18.7 1.3 25 34-58 24-48 (76)
324 cd04782 HTH_BltR Helix-Turn-He 25.4 50 0.0011 20.1 1.5 57 2-58 5-70 (97)
325 PF01476 LysM: LysM domain; I 25.4 51 0.0011 16.4 1.4 15 3-17 12-26 (44)
326 TIGR02941 Sigma_B RNA polymera 25.2 97 0.0021 22.1 3.2 33 32-64 219-251 (255)
327 PF14549 P22_Cro: DNA-binding 25.0 44 0.00095 18.9 1.1 18 37-54 12-29 (60)
328 PRK07122 RNA polymerase sigma 24.9 1.1E+02 0.0023 22.3 3.4 34 31-64 228-261 (264)
329 cd01793 Fubi Fubi ubiquitin-li 24.7 47 0.001 19.0 1.2 27 35-61 23-49 (74)
330 PRK10219 DNA-binding transcrip 24.7 56 0.0012 19.9 1.6 20 2-21 26-45 (107)
331 cd01111 HTH_MerD Helix-Turn-He 24.5 52 0.0011 20.6 1.5 19 2-20 5-23 (107)
332 PRK06288 RNA polymerase sigma 24.4 1.2E+02 0.0027 21.9 3.6 35 31-65 225-259 (268)
333 PF06400 Alpha-2-MRAP_N: Alpha 24.4 1E+02 0.0022 20.0 2.8 27 4-41 52-78 (120)
334 cd01797 NIRF_N amino-terminal 24.3 50 0.0011 19.3 1.3 29 34-62 26-54 (78)
335 cd02413 40S_S3_KH K homology R 24.1 37 0.00081 20.2 0.7 22 35-56 54-75 (81)
336 cd04788 HTH_NolA-AlbR Helix-Tu 23.9 55 0.0012 19.9 1.5 57 2-58 5-70 (96)
337 TIGR03826 YvyF flagellar opero 23.8 49 0.0011 22.0 1.3 22 2-23 51-72 (137)
338 cd08784 Death_DRs Death Domain 23.8 50 0.0011 19.4 1.2 19 2-20 16-34 (79)
339 PRK14584 hmsS hemin storage sy 23.5 39 0.00085 22.9 0.8 30 30-59 94-123 (153)
340 TIGR02589 cas_Csd2 CRISPR-asso 23.4 61 0.0013 24.3 1.9 20 2-21 188-207 (284)
341 PF01726 LexA_DNA_bind: LexA D 23.3 1.3E+02 0.0027 17.1 2.8 39 8-52 3-44 (65)
342 TIGR02393 RpoD_Cterm RNA polym 23.2 1.5E+02 0.0033 20.9 3.9 33 33-65 195-227 (238)
343 PF02082 Rrf2: Transcriptional 23.1 59 0.0013 19.1 1.5 21 2-22 30-50 (83)
344 TIGR02957 SigX4 RNA polymerase 23.0 1.4E+02 0.0031 21.7 3.7 30 35-64 125-154 (281)
345 PRK05657 RNA polymerase sigma 22.7 1.3E+02 0.0029 22.7 3.6 34 32-65 280-313 (325)
346 PF05344 DUF746: Domain of Unk 22.4 65 0.0014 18.6 1.4 22 2-23 18-39 (65)
347 COG1396 HipB Predicted transcr 22.4 1.4E+02 0.0031 16.2 3.1 41 2-49 19-59 (120)
348 PRK05911 RNA polymerase sigma 22.1 1.5E+02 0.0032 21.4 3.7 34 31-64 218-251 (257)
349 PF15076 DUF4543: Domain of un 22.1 1.8E+02 0.0038 16.9 3.3 39 9-47 9-47 (75)
350 smart00595 MADF subfamily of S 21.9 1.4E+02 0.003 17.4 3.0 35 36-70 29-63 (89)
351 cd01807 GDX_N ubiquitin-like d 21.7 61 0.0013 18.4 1.3 27 35-61 25-51 (74)
352 cd01110 HTH_SoxR Helix-Turn-He 21.4 63 0.0014 21.2 1.5 55 2-56 6-68 (139)
353 cd01769 UBL Ubiquitin-like dom 21.3 66 0.0014 17.4 1.4 25 34-58 21-45 (69)
354 PRK11475 DNA-binding transcrip 21.2 1.2E+02 0.0025 21.3 2.9 36 8-54 134-169 (207)
355 PRK09636 RNA polymerase sigma 21.1 1.1E+02 0.0023 22.5 2.7 34 31-64 128-161 (293)
356 PF04703 FaeA: FaeA-like prote 21.0 72 0.0016 18.1 1.5 19 2-20 20-38 (62)
357 TIGR02044 CueR Cu(I)-responsiv 21.0 64 0.0014 20.6 1.4 55 2-56 5-68 (127)
358 PRK05657 RNA polymerase sigma 20.9 85 0.0018 23.7 2.2 22 2-23 287-308 (325)
359 PF08765 Mor: Mor transcriptio 20.8 60 0.0013 20.3 1.2 22 34-55 72-93 (108)
360 PF13743 Thioredoxin_5: Thiore 20.8 1.1E+02 0.0023 20.9 2.5 33 29-61 98-130 (176)
361 PRK10840 transcriptional regul 20.7 97 0.0021 21.1 2.4 22 34-55 165-186 (216)
362 cd01282 HTH_MerR-like_sg3 Heli 20.5 71 0.0015 20.0 1.5 55 2-56 5-67 (112)
363 PF05930 Phage_AlpA: Prophage 20.5 63 0.0014 17.1 1.1 19 2-20 8-26 (51)
364 COG5484 Uncharacterized conser 20.4 51 0.0011 24.4 0.9 32 30-63 15-46 (279)
365 PF00440 TetR_N: Bacterial reg 20.4 67 0.0015 16.5 1.2 26 35-60 17-42 (47)
366 COG0789 SoxR Predicted transcr 20.2 74 0.0016 19.8 1.6 21 2-22 5-25 (124)
367 COG3636 Predicted transcriptio 20.1 1.4E+02 0.003 18.8 2.7 39 2-48 54-92 (100)
368 cd01794 DC_UbP_C dendritic cel 20.1 71 0.0015 18.2 1.3 27 35-61 23-49 (70)
No 1
>KOG0484|consensus
Probab=99.82 E-value=6.6e-20 Score=114.33 Aligned_cols=64 Identities=28% Similarity=0.433 Sum_probs=57.8
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~ 71 (120)
..-|+.||..||+.++..|- ++|||++..|++||.++.|+|.+|||||||||||.|++.+....
T Consensus 18 RRIRTTFTS~QLkELErvF~-----ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~ 81 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFA-----ETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIA 81 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHH-----hhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34578999999999998887 69999999999999999999999999999999999998776554
No 2
>KOG2251|consensus
Probab=99.71 E-value=3.3e-17 Score=114.49 Aligned_cols=63 Identities=29% Similarity=0.400 Sum_probs=58.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~ 69 (120)
+..+||.|+-.|+.|++-.|. +++|||...|++||.+++|.+.+|||||+|||+|+|+++...
T Consensus 37 qRRERTtFtr~QlevLe~LF~-----kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFA-----KTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cccccceecHHHHHHHHHHHH-----hhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 356899999999999888887 699999999999999999999999999999999999987765
No 3
>KOG0489|consensus
Probab=99.68 E-value=1.5e-17 Score=121.04 Aligned_cols=63 Identities=43% Similarity=0.651 Sum_probs=56.8
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~ 71 (120)
..|+.||..|+..++..|- .|+|.+...|.|||..|.|+|+||+|||||||+||||..+....
T Consensus 161 R~RtayT~~QllELEkEFh-----fN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 161 RRRTAFTRYQLLELEKEFH-----FNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCcccchhhhhhhhhhhc-----cccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 4688999999999999888 69999999999999999999999999999999999996554443
No 4
>KOG0488|consensus
Probab=99.67 E-value=3.7e-17 Score=121.21 Aligned_cols=62 Identities=44% Similarity=0.638 Sum_probs=57.0
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
..|+-||+.||+.++..|. +++|.+..+|.+||+.+||+..||++||||||+|||++.....
T Consensus 174 ksRTaFT~~Ql~~LEkrF~-----~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 174 KSRTAFSDHQLFELEKRFE-----KQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred cchhhhhHHHHHHHHHHHH-----HhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 4688999999999998888 5999999999999999999999999999999999999877644
No 5
>KOG0842|consensus
Probab=99.67 E-value=5.2e-17 Score=119.33 Aligned_cols=65 Identities=34% Similarity=0.461 Sum_probs=57.0
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHHh
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMV 73 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~~ 73 (120)
.-|+=|+..||=++++.|+ +++|++..+|++||..|.|+++||+|||||||-|.||+..++....
T Consensus 155 KrRVLFSqAQV~ELERRFr-----qQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 155 KRRVLFSQAQVYELERRFR-----QQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccchhHHHHHHHHHH-----hhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 4467788888888888777 7999999999999999999999999999999999999877766543
No 6
>KOG0848|consensus
Probab=99.65 E-value=3.3e-16 Score=112.19 Aligned_cols=59 Identities=32% Similarity=0.489 Sum_probs=49.2
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~ 69 (120)
|+-+|+.|-=.++.+|- ..+|.++..+.|||.-|||+|+||+|||||||||+||..+.+
T Consensus 203 RvVYTDhQRLELEKEfh-----~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFH-----TSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred eEEecchhhhhhhhhhc-----cccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 34456655555566665 589999999999999999999999999999999999987766
No 7
>KOG0492|consensus
Probab=99.65 E-value=3e-16 Score=108.84 Aligned_cols=61 Identities=39% Similarity=0.548 Sum_probs=56.0
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
=||-||..||..++.+|| +.+|.++.+|.+++..+.|+++||+|||||||||.||.+....
T Consensus 147 PRtPFTtqQLlaLErkfr-----ekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 147 PRTPFTTQQLLALERKFR-----EKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCHHHHHHHHHHHh-----HhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 378899999999999998 6899999999999999999999999999999999999766544
No 8
>KOG0494|consensus
Probab=99.64 E-value=1.4e-16 Score=113.84 Aligned_cols=58 Identities=31% Similarity=0.453 Sum_probs=53.5
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~ 68 (120)
||.||+.|+..++..|. +-+|||...|+-||.+++|.|.+||||||||||||||..+.
T Consensus 145 RTiFT~~Qle~LEkaFk-----eaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFK-----EAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cchhhHHHHHHHHHHHh-----hccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 78999999988887776 79999999999999999999999999999999999997554
No 9
>KOG0843|consensus
Probab=99.63 E-value=4e-16 Score=106.05 Aligned_cols=60 Identities=32% Similarity=0.443 Sum_probs=54.7
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~ 69 (120)
.||-|+.+|+..++-.|. .++|....+|++||+.|+|++.||+|||||||.|.||.....
T Consensus 105 ~RT~ft~~Ql~~LE~~F~-----~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 105 IRTAFTPEQLLKLEHAFE-----GNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cccccCHHHHHHHHHHHh-----cCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 478999999999888887 599999999999999999999999999999999999975553
No 10
>KOG0487|consensus
Probab=99.62 E-value=2.8e-16 Score=115.56 Aligned_cols=62 Identities=40% Similarity=0.463 Sum_probs=56.7
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~ 69 (120)
.++|.-+|..|+..++.+|. .|.|.+...|.||++.|+|+|+||+|||||||+|.||..++.
T Consensus 236 RKKRcPYTK~QtlELEkEFl-----fN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 236 RKKRCPYTKHQTLELEKEFL-----FNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred ccccCCchHHHHHHHHHHHH-----HHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 35778899999999999998 599999999999999999999999999999999999987633
No 11
>KOG0485|consensus
Probab=99.58 E-value=9.1e-15 Score=102.18 Aligned_cols=61 Identities=39% Similarity=0.635 Sum_probs=54.0
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~ 71 (120)
||-|+..||.-++-.|. ..+|.+..+|.-||+++.|+|+||+|||||||.||||+......
T Consensus 108 RTvFSraQV~qLEs~Fe-----~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~e 168 (268)
T KOG0485|consen 108 RTVFSRAQVFQLESTFE-----LKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLE 168 (268)
T ss_pred hhhhhHHHHHHHHHHHH-----HHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhh
Confidence 56789999988888887 47899999999999999999999999999999999998554443
No 12
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.57 E-value=3.2e-15 Score=85.04 Aligned_cols=55 Identities=45% Similarity=0.544 Sum_probs=51.2
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.++.|+++|++++..-|. .++||+..++++||..+||+..+|++||+|+|+++|+
T Consensus 3 ~r~~~t~~q~~~L~~~f~-----~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 3 KRTRFTKEQLKVLEEYFQ-----ENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSHHHHHHHHHHHH-----HSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHHH-----HhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999888887 4999999999999999999999999999999999886
No 13
>KOG0850|consensus
Probab=99.55 E-value=1.3e-14 Score=102.00 Aligned_cols=61 Identities=33% Similarity=0.507 Sum_probs=52.4
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
-||=++.-||+.+-+.|. +++|.-..+|.+||+.|||+.+||+|||||||.|.||+.++..
T Consensus 125 PRTIYSS~QLqaL~rRFQ-----kTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~ 185 (245)
T KOG0850|consen 125 PRTIYSSLQLQALNRRFQ-----QTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGS 185 (245)
T ss_pred CcccccHHHHHHHHHHHh-----hcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCC
Confidence 356677888888766665 5899999999999999999999999999999999999877433
No 14
>KOG0491|consensus
Probab=99.53 E-value=5e-15 Score=99.46 Aligned_cols=63 Identities=37% Similarity=0.507 Sum_probs=53.8
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
...|+-|.+.|+.++...|. .++|.+..+|.|||..++|+++||+.||||||+|+||+.+...
T Consensus 101 ~K~Rtvfs~~ql~~l~~rFe-----~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 101 RKARTVFSDPQLSGLEKRFE-----RQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhcccccCccccccHHHHh-----hhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 34567777777777766665 4899999999999999999999999999999999999877665
No 15
>KOG0493|consensus
Probab=99.51 E-value=8.4e-15 Score=104.85 Aligned_cols=71 Identities=35% Similarity=0.504 Sum_probs=57.9
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHHhhcCCCCC
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKMVAHNRPTG 80 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~~~~~~~~~ 80 (120)
-||-||.+||+.+-..|+ +|+|.+...|.+||.+|+|+|.||+|||||+|+|.||....+.......+..+
T Consensus 249 PRTAFtaeQL~RLK~EF~-----enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqg 319 (342)
T KOG0493|consen 249 PRTAFTAEQLQRLKAEFQ-----ENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQG 319 (342)
T ss_pred ccccccHHHHHHHHHHHh-----hhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccc
Confidence 368899999999888877 49999999999999999999999999999999999995444333333333333
No 16
>KOG0844|consensus
Probab=99.44 E-value=3.1e-14 Score=103.91 Aligned_cols=55 Identities=44% Similarity=0.599 Sum_probs=49.6
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
||-||.+||-.++.+| +++.|-+...|.|||..++|+|+.|+|||||||+|+|||
T Consensus 185 RTAFTReQIaRLEKEF-----yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQ 239 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEF-----YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQ 239 (408)
T ss_pred HhhhhHHHHHHHHHHH-----HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhh
Confidence 6789999996666555 469999999999999999999999999999999999997
No 17
>KOG0483|consensus
Probab=99.42 E-value=7.9e-14 Score=97.34 Aligned_cols=56 Identities=36% Similarity=0.552 Sum_probs=52.1
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
++.+|+.+|+..++..|. .++|..-..+..||..+||.++||.||||||||+||..
T Consensus 53 kk~Rlt~eQ~~~LE~~F~-----~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~k 108 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSFE-----SEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTK 108 (198)
T ss_pred ccccccHHHHHHhHHhhc-----cccccChHHHHHHHHhhCCChhHHHHHHhhccccccch
Confidence 567899999999998887 59999999999999999999999999999999999975
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=99.41 E-value=2.5e-13 Score=77.37 Aligned_cols=55 Identities=42% Similarity=0.543 Sum_probs=49.2
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.+..++++++.++...|. .++||+..++.+||..+||++.+|++||+|+|++.++
T Consensus 3 ~r~~~~~~~~~~Le~~f~-----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 3 KRTRFTPEQLEELEKEFE-----KNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCcCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 456789999888777776 3999999999999999999999999999999999876
No 19
>KOG0486|consensus
Probab=99.40 E-value=3.4e-13 Score=98.65 Aligned_cols=65 Identities=28% Similarity=0.502 Sum_probs=55.5
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLKM 72 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~~ 72 (120)
..+|+-|+..|+|.++--|+ +|+||+...|+|||--++|+|.+|.|||+|||+||||.++.....
T Consensus 113 rrQrthFtSqqlqele~tF~-----rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae 177 (351)
T KOG0486|consen 113 RRQRTHFTSQQLQELEATFQ-----RNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAE 177 (351)
T ss_pred hhhhhhhHHHHHHHHHHHHh-----hccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHH
Confidence 46788899999888555544 399999999999999999999999999999999999977665533
No 20
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.40 E-value=2e-13 Score=77.10 Aligned_cols=53 Identities=40% Similarity=0.610 Sum_probs=48.0
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
.++.++.+++.++.+.+. .++||+..++.+||..+||+..+|++||+|+|++.
T Consensus 3 ~r~~~~~~~~~~L~~~f~-----~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 3 KRTSFTPEQLEELEKEFQ-----KNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCcCCHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 356789999999888877 49999999999999999999999999999999875
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.39 E-value=3.3e-13 Score=91.28 Aligned_cols=61 Identities=33% Similarity=0.444 Sum_probs=56.0
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~ 68 (120)
...++..+..|+-|+.+.|. .++||+...|.+|+..++|+++-|||||||+|++.|+....
T Consensus 52 ~~~r~R~t~~Q~~vL~~~F~-----i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 52 KSKRRRTTDEQLMVLEREFE-----INPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cccceechHHHHHHHHHHhc-----cCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 46788999999999999998 59999999999999999999999999999999999986444
No 22
>KOG0490|consensus
Probab=99.39 E-value=1.1e-13 Score=98.37 Aligned_cols=66 Identities=36% Similarity=0.558 Sum_probs=58.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcc----------------------------------------------------
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD---------------------------------------------------- 29 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~---------------------------------------------------- 29 (120)
+||.+++++|.+|||||||||+||+++.
T Consensus 92 ~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 171 (235)
T KOG0490|consen 92 CLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPSNKKPRRPRTTFTENQLEVLETV 171 (235)
T ss_pred HHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCCccccCCCccccccchhHhhhhc
Confidence 5899999999999999999999999633
Q ss_pred ----cccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 30 ----KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 30 ----~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
.+|+...+++|+..+|+++..|++||+|+|++.++...
T Consensus 172 ~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 172 FRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 35567889999999999999999999999999998544
No 23
>KOG4577|consensus
Probab=99.37 E-value=2.4e-13 Score=98.62 Aligned_cols=58 Identities=29% Similarity=0.294 Sum_probs=51.8
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~ 68 (120)
||.+|..||+++-+.+.+ ...|-...|++|+..+||..++|||||||||||.||..++
T Consensus 171 RTTItAKqLETLK~AYn~-----SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 171 RTTITAKQLETLKQAYNT-----SPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred cceeeHHHHHHHHHHhcC-----CCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 678899999998888764 6789999999999999999999999999999999987543
No 24
>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=99.32 E-value=1.8e-12 Score=73.81 Aligned_cols=50 Identities=14% Similarity=0.171 Sum_probs=46.3
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccc----cchhHHHHHhhhhcchhhhhhccccchh
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKY----LSVSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~y----p~~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
.||.||.+|++.....+. .+.| |+...+++||..+||++.+|+|||||-+
T Consensus 4 ~RT~Ft~~Q~~~Le~~fe-----~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 4 RRTKFTAEQKEKMRDFAE-----KLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCHHHHHHHHHHHH-----HcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 589999999999888887 4899 9999999999999999999999999964
No 25
>KOG0775|consensus
Probab=99.25 E-value=1.1e-11 Score=89.45 Aligned_cols=40 Identities=33% Similarity=0.523 Sum_probs=36.9
Q ss_pred cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
++.||+..++.+||+.+||+..||-+||+|||+++|....
T Consensus 197 ~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 197 QNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred cCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 3999999999999999999999999999999999995433
No 26
>KOG0488|consensus
Probab=99.20 E-value=4.4e-12 Score=94.26 Aligned_cols=30 Identities=60% Similarity=1.004 Sum_probs=27.8
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
|+||++||||+.||++||||||||||++.-
T Consensus 203 ~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 203 IELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred HHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 689999999999999999999999998743
No 27
>KOG0489|consensus
Probab=99.18 E-value=6.6e-12 Score=91.51 Aligned_cols=34 Identities=59% Similarity=0.882 Sum_probs=30.2
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhcccccch
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV 34 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~ 34 (120)
||+|..|+|+|.||++|||||||||||+++-...
T Consensus 190 iEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 190 IEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred HHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 6899999999999999999999999998774443
No 28
>KOG0490|consensus
Probab=99.18 E-value=8.3e-12 Score=88.74 Aligned_cols=59 Identities=25% Similarity=0.262 Sum_probs=53.7
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
-.+++|+..|++.+...|. .+|||+...|+.||..+.++|..|+|||||+|+||+++..
T Consensus 62 r~rt~~~~~ql~~ler~f~-----~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 62 CARCKFTISQLDELERAFE-----KVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccCCCCCcCHHHHHHHhhc-----CCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 3578899999999888887 4899999999999999999999999999999999999764
No 29
>KOG0847|consensus
Probab=99.17 E-value=1.6e-11 Score=86.28 Aligned_cols=59 Identities=42% Similarity=0.669 Sum_probs=49.0
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~ 71 (120)
.|+-.||+.....+. +.+|+-..+|.+||..+|+++.+|+|||||||.||||.......
T Consensus 173 Tf~g~qi~~le~~fe-----qtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEma 231 (288)
T KOG0847|consen 173 TFTGHQIYQLERKFE-----QTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMA 231 (288)
T ss_pred Cccchhhhhhhhhhh-----hhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchh
Confidence 355667766665555 69999999999999999999999999999999999997554443
No 30
>KOG3802|consensus
Probab=99.14 E-value=2.2e-11 Score=91.83 Aligned_cols=59 Identities=17% Similarity=0.166 Sum_probs=49.5
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
..+||.|.....-.++..|. .|..|+..++.+||.+|+|...+|+|||||||+|.||..
T Consensus 295 RKKRTSie~~vr~aLE~~F~-----~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 295 RKKRTSIEVNVRGALEKHFL-----KNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccceeHHHHHHHHHHHH-----hCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 35677777666556666665 499999999999999999999999999999999999943
No 31
>KOG0849|consensus
Probab=99.08 E-value=1.7e-10 Score=87.39 Aligned_cols=58 Identities=28% Similarity=0.490 Sum_probs=51.8
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~ 68 (120)
||.|+..|+..+...|. .++||++..|++||.++++++..|+|||+|||++++++...
T Consensus 180 rtsft~~Q~~~le~~f~-----rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 180 RTSFSPSQLEALEECFQ-----RTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccchHHHHHHHhc-----CCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 57799999988777666 48899999999999999999999999999999999997644
No 32
>KOG0494|consensus
Probab=99.06 E-value=5.5e-11 Score=85.35 Aligned_cols=37 Identities=41% Similarity=0.679 Sum_probs=32.4
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRME 39 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~ 39 (120)
||.+|.|+|++||||||||||||||.++......++.
T Consensus 174 la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ma 210 (332)
T KOG0494|consen 174 LADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMA 210 (332)
T ss_pred HhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhh
Confidence 7889999999999999999999999888766665554
No 33
>KOG0484|consensus
Probab=99.01 E-value=9.6e-11 Score=73.42 Aligned_cols=29 Identities=38% Similarity=0.846 Sum_probs=26.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
|||.++-|||.+|||||||||||.+|+.+
T Consensus 49 EiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 49 EIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 79999999999999999999999998754
No 34
>KOG0848|consensus
Probab=98.89 E-value=4.7e-10 Score=80.85 Aligned_cols=29 Identities=52% Similarity=0.766 Sum_probs=26.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
|||.-|||+|+||++||||||||-||.++
T Consensus 231 ELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 231 ELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred HHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 89999999999999999999998887755
No 35
>KOG0487|consensus
Probab=98.89 E-value=2.2e-10 Score=84.56 Aligned_cols=30 Identities=63% Similarity=0.923 Sum_probs=27.8
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
.|||..|+|||.||++||||||+|.||.++
T Consensus 266 ~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 266 LELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred HHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 389999999999999999999999999864
No 36
>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=98.88 E-value=1.1e-09 Score=57.90 Aligned_cols=34 Identities=35% Similarity=0.572 Sum_probs=29.1
Q ss_pred cccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
.+.||+..++++||..+||+..||..||-|.|.+
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 4899999999999999999999999999999864
No 37
>KOG0843|consensus
Probab=98.85 E-value=8e-10 Score=75.52 Aligned_cols=28 Identities=54% Similarity=0.894 Sum_probs=25.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD 29 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~ 29 (120)
+||+.|+|+|.||+|||||||+|-||..
T Consensus 134 ~LA~~L~LsetQVkvWFQNRRtk~kr~~ 161 (197)
T KOG0843|consen 134 QLAQSLSLSETQVKVWFQNRRTKHKRMQ 161 (197)
T ss_pred HHHHHcCCChhHhhhhhhhhhHHHHHHH
Confidence 6999999999999999999999888753
No 38
>KOG0774|consensus
Probab=98.79 E-value=2.2e-08 Score=72.16 Aligned_cols=60 Identities=27% Similarity=0.490 Sum_probs=48.8
Q ss_pred ccCCCH---HHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 6 LLNLTE---VQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 6 ~~~~~~---~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
|-+|+. +-|+.||-..+ .|.||+...+++||.+++++..||..||.|.|-+.+|......
T Consensus 192 RRNFsK~aTeiLneyF~~h~-----~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ 254 (334)
T KOG0774|consen 192 RRNFSKQATEILNEYFYSHL-----SNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQ 254 (334)
T ss_pred hcccchhHHHHHHHHHHHhc-----CCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhh
Confidence 335544 55666776665 6999999999999999999999999999999999998654443
No 39
>KOG0483|consensus
Probab=98.75 E-value=2.3e-09 Score=74.99 Aligned_cols=39 Identities=38% Similarity=0.609 Sum_probs=29.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcc-cccchhHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVD-KYLSVSKRMEL 40 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~-~yp~~~~r~~L 40 (120)
.||+.+||...||.||||||||||+..+ -+.....+..+
T Consensus 82 ~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~ 121 (198)
T KOG0483|consen 82 KLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQL 121 (198)
T ss_pred HHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHH
Confidence 6999999999999999999999998732 23334444443
No 40
>KOG0485|consensus
Probab=98.69 E-value=5.2e-09 Score=73.58 Aligned_cols=27 Identities=59% Similarity=0.986 Sum_probs=25.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV 28 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~ 28 (120)
-||+.|-|||.||++||||||.|||++
T Consensus 136 ~LA~sLqLTETQVKIWFQNRRnKwKRq 162 (268)
T KOG0485|consen 136 GLAASLQLTETQVKIWFQNRRNKWKRQ 162 (268)
T ss_pred HHHHhhhhhhhhhhhhhhhhhHHHHHH
Confidence 389999999999999999999999976
No 41
>KOG0847|consensus
Probab=98.69 E-value=6e-09 Score=73.39 Aligned_cols=28 Identities=57% Similarity=1.016 Sum_probs=25.9
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYV 28 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~ 28 (120)
.|||..+|++|.||+|||||||+||||+
T Consensus 198 a~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 198 AQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred HHhhccccccHHHHHHHHhcchhhhhhh
Confidence 3788999999999999999999999984
No 42
>KOG2251|consensus
Probab=98.58 E-value=1.1e-08 Score=71.91 Aligned_cols=29 Identities=41% Similarity=0.754 Sum_probs=27.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
|||.+|+|+|.+|||||.|||||++++.+
T Consensus 69 elAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 69 ELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred HHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 79999999999999999999999998655
No 43
>KOG0850|consensus
Probab=98.55 E-value=2.2e-08 Score=70.85 Aligned_cols=30 Identities=53% Similarity=0.872 Sum_probs=26.7
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
+|||+-||||.+||++||||||-|.||.-+
T Consensus 153 AeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 153 AELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred HHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 489999999999999999999988887543
No 44
>KOG0491|consensus
Probab=98.50 E-value=4e-08 Score=66.42 Aligned_cols=30 Identities=53% Similarity=0.832 Sum_probs=27.0
Q ss_pred CcchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 1 MELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 1 ~~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
+|||..++|++.||++||||||+|-+|+.+
T Consensus 131 ~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 131 QELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 489999999999999999999999888643
No 45
>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=98.49 E-value=7.5e-08 Score=54.34 Aligned_cols=26 Identities=65% Similarity=0.872 Sum_probs=24.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
+||+.+||+..+|++||+|+|+|.++
T Consensus 32 ~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 32 ELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp HHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred cccccccccccccccCHHHhHHHhCc
Confidence 69999999999999999999998774
No 46
>KOG1168|consensus
Probab=98.49 E-value=2.5e-08 Score=72.88 Aligned_cols=38 Identities=29% Similarity=0.436 Sum_probs=35.5
Q ss_pred cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
++..|+.+....||+++.|...+|.|||||+|+|-||.
T Consensus 330 vQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 330 VQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 57889999999999999999999999999999998883
No 47
>KOG0844|consensus
Probab=98.34 E-value=8.2e-08 Score=70.68 Aligned_cols=26 Identities=62% Similarity=0.842 Sum_probs=25.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
|||+.|+|+|..|+|||||||+|-|+
T Consensus 213 ELAAaLNLPEtTIKVWFQNRRMKDKR 238 (408)
T KOG0844|consen 213 ELAAALNLPETTIKVWFQNRRMKDKR 238 (408)
T ss_pred hHHHhhCCCcceeehhhhhchhhhhh
Confidence 89999999999999999999999887
No 48
>KOG0842|consensus
Probab=98.23 E-value=1.3e-07 Score=70.02 Aligned_cols=27 Identities=52% Similarity=0.704 Sum_probs=25.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV 28 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~ 28 (120)
+||.-|+||++||++||||||=|.||+
T Consensus 185 ~LA~~LrLT~TQVKIWFQNrRYK~KR~ 211 (307)
T KOG0842|consen 185 HLASSLRLTPTQVKIWFQNRRYKTKRQ 211 (307)
T ss_pred HHHHhcCCCchheeeeeecchhhhhhh
Confidence 699999999999999999999888875
No 49
>KOG0492|consensus
Probab=98.22 E-value=2.8e-07 Score=64.51 Aligned_cols=27 Identities=59% Similarity=0.860 Sum_probs=23.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV 28 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~ 28 (120)
|++.-+.|||.||++||||||||-||.
T Consensus 176 efSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 176 EFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred hhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 567778999999999999999977643
No 50
>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=98.20 E-value=9.3e-07 Score=49.82 Aligned_cols=26 Identities=65% Similarity=0.917 Sum_probs=23.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
+||+.+|+++.+|+.||+|+|++.++
T Consensus 32 ~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 32 ELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 68999999999999999999986653
No 51
>KOG0493|consensus
Probab=98.20 E-value=6.3e-07 Score=64.80 Aligned_cols=26 Identities=58% Similarity=0.851 Sum_probs=25.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
+||.+|||.|.||++||||.|+|.+|
T Consensus 278 ~La~ELgLNEsQIKIWFQNKRAKiKK 303 (342)
T KOG0493|consen 278 ELAQELGLNESQIKIWFQNKRAKIKK 303 (342)
T ss_pred HHHHHhCcCHHHhhHHhhhhhhhhhh
Confidence 69999999999999999999999998
No 52
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=98.17 E-value=3.5e-07 Score=61.99 Aligned_cols=59 Identities=29% Similarity=0.354 Sum_probs=45.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc-----ccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK-----YLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~-----yp~~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
+|+..+++++.-||+||||+|++.++..+ ++.. +-..++....+.-..+-+||.+...+
T Consensus 83 ~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~~~~-e~~~~~~~~~~~~~~~~~~~~~~~s~ 146 (156)
T COG5576 83 KLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQRPGE-EEADLAKIGSLSTGQISIIETLEFSR 146 (156)
T ss_pred HHHHhcCCChhhhhhhhchHHHHHHHhcccchhccccc-ccccccccccccccchhhHHhhhccc
Confidence 68999999999999999999999988554 3333 44556777777777888888665433
No 53
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=98.08 E-value=1.8e-06 Score=48.29 Aligned_cols=24 Identities=63% Similarity=1.135 Sum_probs=22.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW 25 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~ 25 (120)
+||+.+|++..+|+.||+|+|++.
T Consensus 32 ~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 32 ELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred HHHHHHCcCHHHHHHhHHHHhhcc
Confidence 699999999999999999999753
No 54
>KOG4577|consensus
Probab=97.93 E-value=2.7e-06 Score=62.40 Aligned_cols=26 Identities=42% Similarity=0.583 Sum_probs=24.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
||+.+|||.-..|||||||||||.++
T Consensus 199 QLsseTGLDMRVVQVWFQNRRAKEKR 224 (383)
T KOG4577|consen 199 QLSSETGLDMRVVQVWFQNRRAKEKR 224 (383)
T ss_pred HhhhccCcceeehhhhhhhhhHHHHh
Confidence 68999999999999999999998876
No 55
>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=97.85 E-value=2.2e-06 Score=48.76 Aligned_cols=19 Identities=26% Similarity=0.594 Sum_probs=18.4
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||..|||++.+|+|||||
T Consensus 37 ~la~~lgl~~~vvKVWfqN 55 (58)
T TIGR01565 37 EFCEEIGVTRKVFKVWMHN 55 (58)
T ss_pred HHHHHhCCCHHHeeeeccc
Confidence 6899999999999999999
No 56
>KOG0486|consensus
Probab=97.82 E-value=4.6e-06 Score=61.72 Aligned_cols=29 Identities=41% Similarity=0.953 Sum_probs=26.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
|+|-.++|||.+|.|||.|||+||||.++
T Consensus 144 EIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 144 EIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred HHHhhccccchhhhhhcccchhhhhhhhh
Confidence 78999999999999999999999998655
No 57
>KOG1146|consensus
Probab=97.78 E-value=2e-05 Score=67.38 Aligned_cols=61 Identities=21% Similarity=0.244 Sum_probs=56.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
++|.+|-+++.||+..++=|++ ..||...+.|.|...+++..++|+|||||-|+|.++...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~-----q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEA-----QRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhh-----ccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4789999999999999999884 899999999999999999999999999999999998654
No 58
>KOG0849|consensus
Probab=97.54 E-value=4e-05 Score=58.33 Aligned_cols=32 Identities=41% Similarity=0.750 Sum_probs=28.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLS 33 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~ 33 (120)
+||.+++++|.+|+|||+|+|+||+|+..+.+
T Consensus 208 ~La~~i~l~e~riqvwf~nrra~~rr~~~~~s 239 (354)
T KOG0849|consen 208 TLAKETGLPEPRVQVWFQNRRAKWRRQHRDCS 239 (354)
T ss_pred HHhhhccCCchHHHHHHhhhhhhhhhcccccc
Confidence 68999999999999999999999998765433
No 59
>KOG0773|consensus
Probab=97.42 E-value=5.2e-05 Score=57.22 Aligned_cols=56 Identities=23% Similarity=0.413 Sum_probs=47.9
Q ss_pred CCCHHHHHH----HHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHH
Q psy4877 8 NLTEVQIKT----WFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASK 69 (120)
Q Consensus 8 ~~~~~~~q~----~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~ 69 (120)
+|++.-+.+ ||+++. ..||+...+..||.++||+..+|-+||-|.|-+.-+.....
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~------~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLL------HPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCHHHHHHHHHHHHHhcc------CCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 888887777 777775 78999999999999999999999999999998877654433
No 60
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=97.37 E-value=0.00013 Score=38.41 Aligned_cols=22 Identities=45% Similarity=0.726 Sum_probs=19.5
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
+||+.+|++..||..||-|.|.
T Consensus 18 ~L~~~tgls~~Qi~~WF~NaRr 39 (40)
T PF05920_consen 18 ELAKQTGLSRKQISNWFINARR 39 (40)
T ss_dssp HHHHHHTS-HHHHHHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHHHhHc
Confidence 6999999999999999999875
No 61
>KOG2252|consensus
Probab=97.36 E-value=0.00023 Score=56.36 Aligned_cols=52 Identities=25% Similarity=0.243 Sum_probs=43.3
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
|+-||+.|-..+.--|+ +++||+....+.|+.+|+|..+.|.+||-|-|-+.
T Consensus 424 RlVfTd~QkrTL~aiFk-----e~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 424 RLVFTDIQKRTLQAIFK-----ENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred eeeecHHHHHHHHHHHh-----cCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 66788866655444444 49999999999999999999999999999988774
No 62
>KOG3802|consensus
Probab=96.77 E-value=8.6e-05 Score=56.66 Aligned_cols=29 Identities=31% Similarity=0.580 Sum_probs=27.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDK 30 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~ 30 (120)
+||+.|+|..+.|.|||.|||-|.||.+.
T Consensus 326 ~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 326 HIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHHHhccccceEEEEeeccccccccCCC
Confidence 68999999999999999999998888877
No 63
>KOG0775|consensus
Probab=96.30 E-value=0.0017 Score=47.60 Aligned_cols=21 Identities=48% Similarity=0.855 Sum_probs=20.4
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
|||+.||||..||-.||.|||
T Consensus 208 eLA~aTgLt~tQVsNWFKNRR 228 (304)
T KOG0775|consen 208 ELAEATGLTITQVSNWFKNRR 228 (304)
T ss_pred HHHHHhCCchhhhhhhhhhhh
Confidence 799999999999999999998
No 64
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.42 E-value=0.014 Score=32.89 Aligned_cols=31 Identities=26% Similarity=0.404 Sum_probs=21.6
Q ss_pred ccccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 29 ~~yp~~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
.+++....-..|..+++|+..+|+.||-.+.
T Consensus 20 h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 20 HKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp T----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred cCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 5677778888999999999999999996554
No 65
>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=94.26 E-value=0.072 Score=29.07 Aligned_cols=40 Identities=18% Similarity=0.236 Sum_probs=32.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV 49 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~ 49 (120)
+||+.+|++...|..|+.+ ...|+...-..||..+|++..
T Consensus 14 ~la~~~gis~~~i~~~~~g--------~~~~~~~~~~~ia~~l~~~~~ 53 (55)
T PF01381_consen 14 ELAEKLGISRSTISRIENG--------KRNPSLDTLKKIAKALGVSPE 53 (55)
T ss_dssp HHHHHHTS-HHHHHHHHTT--------SSTSBHHHHHHHHHHHTSEHH
T ss_pred HHHHHhCCCcchhHHHhcC--------CCCCCHHHHHHHHHHHCCCHH
Confidence 6888999999999988888 457888888888998888763
No 66
>PHA01976 helix-turn-helix protein
Probab=94.20 E-value=0.075 Score=30.31 Aligned_cols=40 Identities=18% Similarity=0.208 Sum_probs=32.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV 49 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~ 49 (120)
+||+++|++...|..|+.. ...|+...-..||..++++..
T Consensus 20 ~lA~~~gvs~~~v~~~e~g--------~~~p~~~~l~~ia~~l~v~~~ 59 (67)
T PHA01976 20 ELSRRAGVRHSLIYDFEAD--------KRLPNLKTLLRLADALGVTLD 59 (67)
T ss_pred HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHHCcCHH
Confidence 6888888888888888877 346788888888888888774
No 67
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=93.57 E-value=0.091 Score=29.54 Aligned_cols=43 Identities=12% Similarity=0.242 Sum_probs=25.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
+||+++|++...|..|+.+. ...++...-..||..++++...+
T Consensus 15 ~La~~~gis~~tl~~~~~~~-------~~~~~~~~l~~ia~~l~~~~~el 57 (63)
T PF13443_consen 15 DLARKTGISRSTLSRILNGK-------PSNPSLDTLEKIAKALNCSPEEL 57 (63)
T ss_dssp HHHHHHT--HHHHHHHHTTT------------HHHHHHHHHHHT--HHHC
T ss_pred HHHHHHCcCHHHHHHHHhcc-------cccccHHHHHHHHHHcCCCHHHH
Confidence 57778888888888777763 24666777777787777776554
No 68
>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=93.46 E-value=0.1 Score=30.63 Aligned_cols=39 Identities=15% Similarity=0.275 Sum_probs=32.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+++|++...|..|+.. ...++......|+..++++.
T Consensus 23 ~lA~~~gis~~tis~~~~g--------~~~~~~~~~~~l~~~l~v~~ 61 (78)
T TIGR02607 23 ALAKALGVSRSTLSRIVNG--------RRGITADMALRLAKALGTSP 61 (78)
T ss_pred HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHcCCCH
Confidence 6888999999999888877 34677788888999998876
No 69
>KOG3623|consensus
Probab=93.24 E-value=0.06 Score=44.64 Aligned_cols=62 Identities=15% Similarity=0.253 Sum_probs=42.6
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccch---------------------------------hHHHHHhhhhcchhh
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV---------------------------------SKRMELSKLLNLTEV 49 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~---------------------------------~~r~~La~~~~l~~~ 49 (120)
+|..+|++-+.|++||++++++-...++-|+. .+-.-++.++...+.
T Consensus 589 ia~qvglp~~vvk~wfE~~~a~e~sv~rsps~psg~~p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~p 668 (1007)
T KOG3623|consen 589 IAQQVGLPFAVVKAWFEDEEAEEMSVERSPSQPSGERPVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPP 668 (1007)
T ss_pred HHHHhcccHHHHHHHHHhhhhhhhhhccCccCCCCCCCccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCc
Confidence 57788999999999999999988764433321 000012333455667
Q ss_pred hhhccccchhHHHHH
Q psy4877 50 QIKTWFQNRRTKWKK 64 (120)
Q Consensus 50 ~vqvWFqNrRak~rr 64 (120)
+++|||++|+..-+.
T Consensus 669 v~ev~dhsrsstpsp 683 (1007)
T KOG3623|consen 669 VVEVWDHSRSSTPSP 683 (1007)
T ss_pred chhhcccCCCCCCCC
Confidence 789999999887665
No 70
>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=93.18 E-value=0.12 Score=28.10 Aligned_cols=37 Identities=16% Similarity=0.200 Sum_probs=18.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNL 46 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l 46 (120)
+||+++|++...|..|+..+ ..|+......++..+|+
T Consensus 20 ~lA~~~gvs~~~vs~~e~g~--------~~~~~~~~~~i~~~lgv 56 (58)
T TIGR03070 20 DLADLAGVGLRFIRDVENGK--------PTVRLDKVLRVLDALGL 56 (58)
T ss_pred HHHHHhCCCHHHHHHHHCCC--------CCCCHHHHHHHHHHcCC
Confidence 35555555555555555442 23444444555554443
No 71
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=93.11 E-value=0.15 Score=28.88 Aligned_cols=44 Identities=16% Similarity=0.184 Sum_probs=30.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq 52 (120)
++|+++|++...|.-|+..++ ..|+...-..|+..++++...+.
T Consensus 19 ~lA~~~g~s~s~v~~iE~G~~-------~~p~~~~l~~l~~~l~~~~~~~~ 62 (64)
T PF13560_consen 19 QLADRLGVSQSTVSRIERGRR-------PRPSPDTLQRLARALGVPPDERA 62 (64)
T ss_dssp HHHHHHTS-HHHHHHHHTTSS-------SS-BHHHHHHHHHHTT--HHHHH
T ss_pred HHHHHHCcCHHHHHHHHCCCC-------CCCCHHHHHHHHHHHCcCHHHHc
Confidence 578888888888888888843 14788888888888888876554
No 72
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=93.11 E-value=0.06 Score=30.29 Aligned_cols=21 Identities=29% Similarity=0.601 Sum_probs=16.8
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
+|..+++|+..||..||-.++
T Consensus 30 ~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 30 ELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp HHHHHTT--HHHHHHHHHHHS
T ss_pred HHHHHHCCCHHHHHHHHHHhc
Confidence 578899999999999999874
No 73
>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=92.99 E-value=0.16 Score=28.66 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=32.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq 52 (120)
++|+.+|++...|.-|+.+ ...|+......||..++++...+-
T Consensus 17 ~~a~~~~i~~~~i~~~e~g--------~~~~~~~~l~~i~~~~~v~~~~l~ 59 (64)
T PF12844_consen 17 DLAEKLGISRSTISKIENG--------KRKPSVSTLKKIAEALGVSLDELF 59 (64)
T ss_dssp HHHHHHTS-HHHHHHHHTT--------SS--BHHHHHHHHHHHTS-HHHHC
T ss_pred HHHHHHCcCHHHHHHHHCC--------CcCCCHHHHHHHHHHhCCCHHHHh
Confidence 5788999999999999998 347888888999999999886543
No 74
>KOG3623|consensus
Probab=92.77 E-value=0.11 Score=43.18 Aligned_cols=38 Identities=13% Similarity=0.284 Sum_probs=34.9
Q ss_pred cccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 28 VDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 28 ~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
.|..|+..+-..+|...||+...|++||++++++....
T Consensus 577 ln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv 614 (1007)
T KOG3623|consen 577 LNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSV 614 (1007)
T ss_pred hcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhh
Confidence 38899999999999999999999999999999997764
No 75
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=91.88 E-value=0.22 Score=33.77 Aligned_cols=41 Identities=22% Similarity=0.143 Sum_probs=28.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ 50 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~ 50 (120)
+||+++|++...|..|+.+ ...|+......||..++++...
T Consensus 87 eLA~~lgvs~s~IsriE~G--------~~~Ps~~~l~kLa~~Lgvsl~e 127 (154)
T TIGR00270 87 QLAKKIQEKESLIKKIENA--------EIEPEPKVVEKLEKLLKIKLRE 127 (154)
T ss_pred HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence 5677777777777777766 4567777777777777766643
No 76
>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=91.73 E-value=0.23 Score=28.60 Aligned_cols=38 Identities=11% Similarity=0.237 Sum_probs=23.3
Q ss_pred cchhccCCCHHHHH-HHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIK-TWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q-~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+.+|++..-|. .|... +..| ...-..+|..+|++.
T Consensus 17 ~lA~~lgis~st~s~~~~~r--------~~~P-~~~l~~ia~~~gvsl 55 (66)
T PF07022_consen 17 ELAERLGISKSTLSNNWKKR--------GSIP-AEWLIKIALETGVSL 55 (66)
T ss_dssp HHHCCTT--HHHHH-HHHHS--------SS---HHHHHHHHHHH---H
T ss_pred HHHHHhCcCHHHhhHHHHhC--------CCCC-HHHHHHHHHHHCcCH
Confidence 68888888888887 66654 6777 667777788888776
No 77
>PRK06424 transcription factor; Provisional
Probab=91.59 E-value=0.21 Score=33.53 Aligned_cols=39 Identities=18% Similarity=0.181 Sum_probs=23.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
|||+++|++...|..|+.. ...|+......||..+|++.
T Consensus 102 eLA~~iGvs~stIskiE~G--------~~~Ps~~~l~kLa~~Lgvsl 140 (144)
T PRK06424 102 DLAAKIFERKNVIASIERG--------DLLPDIKTARKLEKILGITL 140 (144)
T ss_pred HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCC
Confidence 4666666666666666666 33556666666666665543
No 78
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=91.36 E-value=0.27 Score=31.82 Aligned_cols=42 Identities=12% Similarity=0.045 Sum_probs=35.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
|||+++|++...+.-|++++ ..|+...-..||..++++...+
T Consensus 23 eLA~~~Gis~~~is~iE~g~--------~~ps~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 23 ELSERSGVSISFLSDLTTGK--------ANPSLKVMEAIADALETPLPLL 64 (120)
T ss_pred HHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCCCHHHH
Confidence 68999999999999999884 4688999999999999887533
No 79
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=91.22 E-value=0.32 Score=25.15 Aligned_cols=39 Identities=18% Similarity=0.221 Sum_probs=24.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+.+|++...|..|..+ ...++......++..+|++.
T Consensus 15 ~la~~~~i~~~~i~~~~~~--------~~~~~~~~~~~i~~~~~~~~ 53 (56)
T smart00530 15 ELAEKLGVSRSTLSRIENG--------KRKPSLETLKKLAKALGVSL 53 (56)
T ss_pred HHHHHhCCCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCh
Confidence 4666777777777666655 23445555666666666654
No 80
>PRK09726 antitoxin HipB; Provisional
Probab=90.78 E-value=0.29 Score=29.69 Aligned_cols=23 Identities=22% Similarity=0.375 Sum_probs=14.6
Q ss_pred HHHHHhhhhcchhhhhhccccch
Q psy4877 36 KRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWFqNr 58 (120)
..++||..+|++...|..|..++
T Consensus 27 tq~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 27 TQSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred CHHHHHHHHCcCHHHHHHHHCCC
Confidence 35566666666666666666554
No 81
>PRK10072 putative transcriptional regulator; Provisional
Probab=90.63 E-value=0.37 Score=30.09 Aligned_cols=24 Identities=21% Similarity=0.455 Sum_probs=14.5
Q ss_pred HHHHHhhhhcchhhhhhccccchh
Q psy4877 36 KRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
...+||..+|++...|..|...+|
T Consensus 48 TQ~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 48 KIDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 355566666666666666665554
No 82
>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=90.05 E-value=0.47 Score=24.63 Aligned_cols=39 Identities=21% Similarity=0.233 Sum_probs=19.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
++|..+|++...|..|+.+ ...++......++..++++.
T Consensus 17 ~~a~~~~~~~~~v~~~~~g--------~~~~~~~~~~~i~~~~~~~~ 55 (58)
T cd00093 17 ELAEKLGVSRSTISRIENG--------KRNPSLETLEKLAKALGVSL 55 (58)
T ss_pred HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCh
Confidence 3455555555555555554 22444444445555555443
No 83
>PRK08359 transcription factor; Validated
Probab=89.96 E-value=0.35 Score=33.49 Aligned_cols=39 Identities=13% Similarity=0.219 Sum_probs=28.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
|||+.+|++...|..|+.+ ...|+......||..++++.
T Consensus 103 eLA~~lgvs~stI~~iE~G--------~~~Ps~~~l~kLak~l~VsL 141 (176)
T PRK08359 103 ELSHEVGLSVNDLRRIAHG--------EYEPTIKEAKKLERYFKIKL 141 (176)
T ss_pred HHHHHhCCCHHHHHHHHCC--------CcCCCHHHHHHHHHHhCCcc
Confidence 5777778877777777777 34677777777777777763
No 84
>PHA01083 hypothetical protein
Probab=89.62 E-value=0.41 Score=32.19 Aligned_cols=44 Identities=11% Similarity=0.123 Sum_probs=36.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq 52 (120)
+||+++|++...|..|-... .+|.+..+-..||+.+|++...+-
T Consensus 21 qLA~~LGVs~q~IS~~R~G~-------r~~i~de~A~~LAe~aGiDp~eal 64 (149)
T PHA01083 21 QIAHDLGVSPQKISKMRTGV-------RTYISDEEAIFLAESAGIDPEIAL 64 (149)
T ss_pred HHHHHhCCCHHHHHHHHcCC-------CCCCCHHHHHHHHHHhCCCHHHHH
Confidence 69999999999998876661 358999999999999999975443
No 85
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=88.86 E-value=0.58 Score=30.59 Aligned_cols=39 Identities=21% Similarity=0.348 Sum_probs=21.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+++|++...|..|+.+. ..|+...-..||..+|++.
T Consensus 23 ~lA~~~gvs~~~is~~E~g~--------~~p~~~~l~~la~~l~vs~ 61 (135)
T PRK09706 23 SLAKAVKVSHVSISQWERDE--------TEPTGKNLFALAKALQCSP 61 (135)
T ss_pred HHHHHhCCCHHHHHHHHcCC--------CCCCHHHHHHHHHHHCcCH
Confidence 45555666666665555552 2455555555555555554
No 86
>TIGR02612 mob_myst_A mobile mystery protein A. Members of this protein family are found in mobization-related contexts more often than not, including within a CRISPR-associated gene region in Geobacter sulfurreducens PCA, and on plasmids in Agrobacterium tumefaciens and Coxiella burnetii, always together with mobile mystery protein B, a member of the Fic protein family (pfam02661). This protein is encoded by the upstream member of the gene pair and belongs to a family of helix-turn-helix DNA binding proteins (pfam01381).
Probab=88.79 E-value=0.39 Score=32.43 Aligned_cols=42 Identities=14% Similarity=0.146 Sum_probs=34.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV 49 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~ 49 (120)
|||+++|++...|..|+.+.. +..|+...-..||..+|++..
T Consensus 43 eLAerlGVS~~tIs~iE~G~~------~~~psl~~L~kIA~aLgv~~~ 84 (150)
T TIGR02612 43 QLAGRLGVTPQRVEALEKSEL------SGTVTLKTLRAAAEALDCTFV 84 (150)
T ss_pred HHHHHhCCCHHHHHHHHcCCC------CCCCCHHHHHHHHHHcCCCHH
Confidence 789999999999999998842 334778888899999998873
No 87
>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=87.83 E-value=0.81 Score=24.46 Aligned_cols=39 Identities=8% Similarity=0.211 Sum_probs=26.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHH---HHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKR---MELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r---~~La~~~~l~~ 48 (120)
+||+++|++...|..|+.+. ..++...+ .+++..+|...
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~--------~~vs~~~~~~i~~~~~~l~~~~ 43 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK--------PRVSEETRERVLAAAEELGYRP 43 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC--------CCCCHHHHHHHHHHHHHhCCCC
Confidence 68999999999999988884 23333333 34567766544
No 88
>KOG1168|consensus
Probab=87.43 E-value=0.048 Score=40.55 Aligned_cols=26 Identities=31% Similarity=0.607 Sum_probs=21.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
-+|+++-|....|.|||.|.|-|-+|
T Consensus 341 aIAekLDLKKNVVRVWFCNQRQKQKR 366 (385)
T KOG1168|consen 341 AIAEKLDLKKNVVRVWFCNQRQKQKR 366 (385)
T ss_pred HHHHhhhhhhceEEEEeeccHHHHHH
Confidence 37899999999999999999865443
No 89
>PRK09943 DNA-binding transcriptional repressor PuuR; Provisional
Probab=86.93 E-value=0.82 Score=31.41 Aligned_cols=41 Identities=24% Similarity=0.206 Sum_probs=35.9
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ 50 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~ 50 (120)
+||+++|++...|..|++. ...|+...-..||..++++...
T Consensus 25 elA~~~gis~~~is~~E~g--------~~~p~~~~l~~ia~~l~v~~~~ 65 (185)
T PRK09943 25 RAAELSGLTHSAISTIEQD--------KVSPAISTLQKLLKVYGLSLSE 65 (185)
T ss_pred HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence 6899999999999999988 4588899999999999998754
No 90
>TIGR02684 dnstrm_HI1420 probable addiction module antidote protein. gene pairs, when found on the bacterial chromosome, are located often with prophage regions, but also both in integrated plasmid regions and in housekeeping gene regions. Analysis suggests that the gene pair may serve as an addiction module.
Probab=86.86 E-value=0.81 Score=28.09 Aligned_cols=39 Identities=13% Similarity=0.181 Sum_probs=23.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+++|++...|-.|+.+ ...|+...-..++..+|++-
T Consensus 48 qLAe~~GIs~stLs~iE~g--------~~~Ps~~tL~kI~~aLgi~l 86 (89)
T TIGR02684 48 QLARKTGLSRESLYKALSG--------KGNPTFDTILKVTKALGLKL 86 (89)
T ss_pred HHHHHHCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHcCCce
Confidence 3566666666666666655 34566666666666666543
No 91
>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=85.70 E-value=0.69 Score=27.44 Aligned_cols=46 Identities=15% Similarity=0.124 Sum_probs=31.6
Q ss_pred chhcc-CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccc
Q psy4877 3 LSKLL-NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQN 57 (120)
Q Consensus 3 la~~~-~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqN 57 (120)
||+++ .+++..-++ |.=.| |-......++|..+|+++..|+.|+.+
T Consensus 9 ~~~~l~~l~~~~r~a-f~L~R--------~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 9 LAERLTWVDSLAEAA-AALAR--------EEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHhcCCHHHHHH-HHHHH--------HHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 67777 444443333 33322 334667889999999999999999864
No 92
>KOG3755|consensus
Probab=83.44 E-value=0.96 Score=37.02 Aligned_cols=63 Identities=27% Similarity=0.333 Sum_probs=40.2
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhh----cccccchhHHHHHhhhh-------cchhhhhhccccchhHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKY----VDKYLSVSKRMELSKLL-------NLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~----~~~yp~~~~r~~La~~~-------~l~~~~vqvWFqNrRak~rr~ 65 (120)
|+.-+.++...+..-|||.+.-.+. .++-++.....+.-... .....-|+-||+|||+++++.
T Consensus 684 LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~ 757 (769)
T KOG3755|consen 684 LSAQLDLPKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRL 757 (769)
T ss_pred hhhhhcccHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhh
Confidence 5667788888888888887764433 33444443333322222 224467889999999999884
No 93
>PRK08154 anaerobic benzoate catabolism transcriptional regulator; Reviewed
Probab=82.24 E-value=1.6 Score=32.58 Aligned_cols=42 Identities=10% Similarity=0.090 Sum_probs=36.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
+||+++|++...|..|+.. ...|+...-..||..+|++...+
T Consensus 46 ~lA~~~gvs~~~i~~~E~g--------~~~ps~~~l~~ia~~l~v~~~~l 87 (309)
T PRK08154 46 VLAQASGVSERYLAQLESG--------QGNVSILLLRRVARALGCSLADL 87 (309)
T ss_pred HHHHHHCcCHHHHHHHHCC--------CCCCCHHHHHHHHHHhCCCHHHH
Confidence 6899999999999999999 45789999999999999886433
No 94
>PRK02866 cyanate hydratase; Validated
Probab=82.13 E-value=2.2 Score=28.77 Aligned_cols=41 Identities=20% Similarity=0.324 Sum_probs=30.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ 50 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~ 50 (120)
+||+.+|+++.-+-.+|.. ++.++...-+.|+..++|++..
T Consensus 23 ~IA~~iG~S~v~vaaa~lG--------Q~~ls~e~A~kla~~LgL~~~~ 63 (147)
T PRK02866 23 DIAEAIGLSEVWVTAALLG--------QMTLPAEEAEKVAELLGLDEDA 63 (147)
T ss_pred HHHHHhCCCHHHHHHHHhC--------CCCCCHHHHHHHHHHhCCCHHH
Confidence 5777788888777777776 5566777777778888887753
No 95
>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=82.08 E-value=0.86 Score=26.01 Aligned_cols=16 Identities=25% Similarity=0.771 Sum_probs=8.9
Q ss_pred cchhccCCCHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTW 17 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~ 17 (120)
++|++||+++.+|..|
T Consensus 27 dIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 27 DIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHCCCHHHHHHH
Confidence 3555556665555544
No 96
>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=81.85 E-value=0.83 Score=26.05 Aligned_cols=20 Identities=25% Similarity=0.556 Sum_probs=17.5
Q ss_pred HHHHHhhhhcchhhhhhccc
Q psy4877 36 KRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWF 55 (120)
.-.+||..+|+++.+|..|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45678999999999999985
No 97
>KOG0774|consensus
Probab=81.22 E-value=2.2 Score=31.51 Aligned_cols=25 Identities=44% Similarity=0.829 Sum_probs=21.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~ 26 (120)
|||+.-|++..||..||-|.|-+.+
T Consensus 223 eLAkqCnItvsQvsnwfgnkrIryk 247 (334)
T KOG0774|consen 223 ELAKQCNITVSQVSNWFGNKRIRYK 247 (334)
T ss_pred HHHHHcCceehhhccccccceeehh
Confidence 7999999999999999999884443
No 98
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=79.99 E-value=1.5 Score=27.78 Aligned_cols=18 Identities=22% Similarity=0.604 Sum_probs=9.5
Q ss_pred hhccCCCHHHHHHHHhhh
Q psy4877 4 SKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~ 21 (120)
|..+|.+..-|+.|+|+|
T Consensus 64 A~~L~vs~~Tv~~WEqGr 81 (104)
T COG2944 64 ARYLGVSVSTVRKWEQGR 81 (104)
T ss_pred HHHHCCCHHHHHHHHcCC
Confidence 444555555555555553
No 99
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=78.11 E-value=3.6 Score=27.52 Aligned_cols=50 Identities=20% Similarity=0.174 Sum_probs=39.2
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
....|++.|.+++.- +. ......++|..+|++...|..|-.+-+.+.++.
T Consensus 3 ~~~~Lt~rqreVL~l-r~----------~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 3 MESFLTERQIEVLRL-RE----------RGLTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred cccCCCHHHHHHHHH-HH----------cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999998644 21 256678999999999999999998877777764
No 100
>PF13413 HTH_25: Helix-turn-helix domain; PDB: 2WUS_R 3FYM_A.
Probab=77.45 E-value=4.1 Score=23.10 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=28.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccch-hHHH---HHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSV-SKRM---ELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~-~~r~---~La~~~~l~~~~v 51 (120)
++|..|+++...|+.++.+.- +.+|+. ..+. ..|..+||+...|
T Consensus 15 ~va~~t~I~~~~l~aiE~~~~------~~lp~~~y~rg~lr~Ya~~Lgld~~~l 62 (62)
T PF13413_consen 15 DVAEETKISVSYLEAIENGDF------DSLPSPVYARGYLRKYARFLGLDPDEL 62 (62)
T ss_dssp HHHHHCS--HHHHHHHHCT-G------CCSSSHHHHHHHHHHHHHHTT--HHHH
T ss_pred HHHHHhCCCHHHHHHHHCcCh------hhCCcHHHHHHHHHHHHHHhCcCcccC
Confidence 578899999999999988864 666654 3333 3488888887654
No 101
>TIGR00673 cynS cyanate hydratase. Alternate names include cyanate lyase, cyanase and cyanate hydrolase.
Probab=77.42 E-value=3.7 Score=27.75 Aligned_cols=41 Identities=17% Similarity=0.177 Sum_probs=32.7
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQ 50 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~ 50 (120)
+||+.+|+++.=+-..|.. ++.++...-+.|++.++|+...
T Consensus 26 ~IAe~iG~sevwvaaa~lG--------Q~~ls~e~A~kla~lLgL~~e~ 66 (150)
T TIGR00673 26 DIADGLGLAEVFVAAALYG--------QAAAPADEARLVGAKLDLDEDS 66 (150)
T ss_pred HHHHHHCCCHHHHHHHHhC--------CCCCCHHHHHHHHHHhCcCHHH
Confidence 5788888888877777776 5677888888889999998754
No 102
>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=76.89 E-value=3.8 Score=22.01 Aligned_cols=29 Identities=21% Similarity=0.439 Sum_probs=20.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
|.....-.++|..+|+++..|+.|...-|
T Consensus 23 ~~~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 23 YFQGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp HTS---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred HHHCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55677888999999999999999886433
No 103
>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=75.39 E-value=5.6 Score=21.07 Aligned_cols=41 Identities=10% Similarity=0.153 Sum_probs=26.8
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccch
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNr 58 (120)
.|++.+-++.... |-....-.++|..+|++...|..+...-
T Consensus 4 ~L~~~er~vi~~~----------y~~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLR----------YFEGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHH----------HTST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHH----------hcCCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 4666666664433 3334567889999999999988766433
No 104
>PF13518 HTH_28: Helix-turn-helix domain
Probab=74.87 E-value=2.8 Score=22.16 Aligned_cols=21 Identities=14% Similarity=0.544 Sum_probs=17.4
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
++|+++|++..+|..|.+.++
T Consensus 17 ~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 17 EIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHCCCHhHHHHHHHHHH
Confidence 578888888888888888876
No 105
>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=73.41 E-value=1.9 Score=23.73 Aligned_cols=26 Identities=8% Similarity=0.299 Sum_probs=20.0
Q ss_pred hhHHHHHhhhhcchhhhhhccccchh
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
.....+||..+|++.++|..|..|+.
T Consensus 22 g~s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 22 GESKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp TT-HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHhHH
Confidence 45788899999999999999998864
No 106
>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=72.02 E-value=6.3 Score=21.59 Aligned_cols=44 Identities=18% Similarity=0.169 Sum_probs=30.1
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
.||+.++++..--.. +....++|..+++++..|.....+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~-----------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ-----------GMSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHT-----------TS-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHh-----------cCCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 477777777433322 56788899999999999998776555543
No 107
>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=71.59 E-value=3.9 Score=21.05 Aligned_cols=21 Identities=10% Similarity=0.390 Sum_probs=12.2
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
++|+.+|++...|..|....+
T Consensus 31 ~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 31 EIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred HHHHHHCcCHHHHHHHHHHHH
Confidence 456666666666666555443
No 108
>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=71.36 E-value=1.9 Score=24.32 Aligned_cols=32 Identities=25% Similarity=0.516 Sum_probs=25.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.......++|..+|++...|..|-+ |.+|..
T Consensus 10 Y~~G~~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 10 YLQGWSIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred HHcCCCHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 55567788999999999999999974 555544
No 109
>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=71.27 E-value=2.9 Score=21.77 Aligned_cols=20 Identities=20% Similarity=0.306 Sum_probs=16.7
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
|+|+.+|++...|.-|.++-
T Consensus 5 e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 5 ELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHCcCHHHHHHHHHCC
Confidence 67888999999998887764
No 110
>COG1813 Predicted transcription factor, homolog of eukaryotic MBF1 [Transcription]
Probab=69.46 E-value=6 Score=27.17 Aligned_cols=37 Identities=19% Similarity=0.197 Sum_probs=20.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNL 46 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l 46 (120)
+||++++..+.-|..|++.+ --|+......|.+.+|+
T Consensus 97 dLA~ki~ek~svI~~iE~g~--------~~P~~~~akkLEk~LgI 133 (165)
T COG1813 97 DLAAKLKEKVSVIRRIERGE--------ATPNIKVAKKLEKLLGI 133 (165)
T ss_pred HHHHHhcccHHHHHHHHhcc--------cCccHHHHHHHHHHhCc
Confidence 45666666666666666552 34555555555555543
No 111
>COG1476 Predicted transcriptional regulators [Transcription]
Probab=68.80 E-value=9.5 Score=22.29 Aligned_cols=40 Identities=18% Similarity=0.217 Sum_probs=29.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV 49 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~ 49 (120)
+||+.+|++...+-.|+.+ .--|+...-..+|..++++..
T Consensus 19 elA~~vgVsRQTi~~iEkg--------ky~Psl~La~kia~~f~~~ie 58 (68)
T COG1476 19 ELAKLVGVSRQTIIAIEKG--------KYNPSLELALKIARVFGKTIE 58 (68)
T ss_pred HHHHHcCcCHHHHHHHHcC--------CCCchHHHHHHHHHHhCCCHH
Confidence 6888888888888777777 335777777778888775543
No 112
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=68.74 E-value=4.1 Score=22.98 Aligned_cols=22 Identities=18% Similarity=0.329 Sum_probs=19.3
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
|+|+.+|++...|..|.....-
T Consensus 5 eva~~~gvs~~tlr~y~~~gll 26 (69)
T PF13411_consen 5 EVAKLLGVSPSTLRYYEREGLL 26 (69)
T ss_dssp HHHHHTTTTHHHHHHHHHTTSS
T ss_pred HHHHHHCcCHHHHHHHHHhcCc
Confidence 6899999999999999887653
No 113
>KOG1146|consensus
Probab=68.47 E-value=2.6 Score=37.47 Aligned_cols=25 Identities=40% Similarity=0.627 Sum_probs=22.4
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
|.+.++++...|+|||||-|.|.++
T Consensus 936 l~~~~~~~~~~i~vw~qna~~~s~k 960 (1406)
T KOG1146|consen 936 LEEPIGLPKRVIQVWFQNARAKSKK 960 (1406)
T ss_pred hcccccCCcchhHHhhhhhhhhhhh
Confidence 4567899999999999999999988
No 114
>PHA00542 putative Cro-like protein
Probab=68.00 E-value=7.1 Score=23.31 Aligned_cols=24 Identities=8% Similarity=0.209 Sum_probs=17.1
Q ss_pred hHHHHHhhhhcchhhhhhccccch
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNr 58 (120)
....+||..+|++...|.-|..++
T Consensus 32 lTq~elA~~lgIs~~tIsr~e~g~ 55 (82)
T PHA00542 32 WSQEQIADATDVSQPTICRIYSGR 55 (82)
T ss_pred CCHHHHHHHHCcCHHHHHHHHcCC
Confidence 345667777888887777777655
No 115
>PRK04140 hypothetical protein; Provisional
Probab=67.52 E-value=6 Score=29.96 Aligned_cols=39 Identities=18% Similarity=0.293 Sum_probs=29.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
+||+.+|++...|..|+.+ ...|+...-..||..+|++.
T Consensus 144 eLA~~lGVSr~tIskyE~G--------~~~Ps~e~~~kLa~~Lgv~l 182 (317)
T PRK04140 144 ELASELGVSRRTISKYENG--------GMNASIEVAIKLEEILDVPL 182 (317)
T ss_pred HHHHHhCCCHHHHHHHHcC--------CCCCCHHHHHHHHHHhCCCh
Confidence 5778888888888888887 34677777777887777653
No 116
>KOG0044|consensus
Probab=66.75 E-value=4.7 Score=28.37 Aligned_cols=31 Identities=13% Similarity=0.375 Sum_probs=25.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRM 38 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~ 38 (120)
+|.+.+.|++..|+.|+.++. +-+|++..-.
T Consensus 16 ~l~~~t~f~~~ei~~~Yr~Fk------~~cP~G~~~~ 46 (193)
T KOG0044|consen 16 QLVQQTKFSKKEIQQWYRGFK------NECPSGRLTL 46 (193)
T ss_pred HHHHhcCCCHHHHHHHHHHhc------ccCCCCccCH
Confidence 466789999999999999997 6777775433
No 117
>PRK10072 putative transcriptional regulator; Provisional
Probab=65.56 E-value=3.6 Score=25.60 Aligned_cols=19 Identities=16% Similarity=0.565 Sum_probs=12.1
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||+.+|++...|..|++.
T Consensus 51 elA~~lGvS~~TVs~WE~G 69 (96)
T PRK10072 51 DFARVLGVSVAMVKEWESR 69 (96)
T ss_pred HHHHHhCCCHHHHHHHHcC
Confidence 4666666666666666655
No 118
>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=64.02 E-value=12 Score=24.81 Aligned_cols=50 Identities=28% Similarity=0.180 Sum_probs=38.0
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
++...|++.|.++..- +. ......++|..+|++...|..+-..-+.+-++
T Consensus 2 ~~~~~Lte~qr~VL~L-r~----------~GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 2 SKKTFLTERQIKVLEL-RE----------KGLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CccCCCCHHHHHHHHH-HH----------cCCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4677899999988543 21 24578899999999999999988766666554
No 119
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=63.72 E-value=9.2 Score=26.17 Aligned_cols=34 Identities=15% Similarity=0.181 Sum_probs=27.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|+++...-|.+.++
T Consensus 155 ~~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 155 YYGGLTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred HHcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 4556778899999999999999988766666555
No 120
>KOG0773|consensus
Probab=63.30 E-value=1.8 Score=32.73 Aligned_cols=22 Identities=36% Similarity=0.629 Sum_probs=20.2
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
.||+.|||+.-||..||-|.|.
T Consensus 274 ~La~~TGLs~~Qv~NWFINaR~ 295 (342)
T KOG0773|consen 274 MLAKQTGLSRPQVSNWFINARV 295 (342)
T ss_pred ccchhcCCCcccCCchhhhccc
Confidence 5999999999999999999874
No 121
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.81 E-value=9.4 Score=26.49 Aligned_cols=35 Identities=23% Similarity=0.260 Sum_probs=28.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|+++..|.++..+-+.+.++.
T Consensus 166 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 166 YFQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55667788999999999999999887666665554
No 122
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=61.68 E-value=9.9 Score=24.67 Aligned_cols=33 Identities=12% Similarity=0.144 Sum_probs=25.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|.....-.++|..+|+++..|..+...-+.+-|
T Consensus 119 ~~~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 119 FFVGKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 555677889999999999999998865444443
No 123
>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=60.88 E-value=6.3 Score=22.29 Aligned_cols=19 Identities=16% Similarity=0.443 Sum_probs=17.3
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|++.
T Consensus 5 e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 5 EVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHCcCHHHHHHHHHh
Confidence 7899999999999999875
No 124
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=58.95 E-value=6.2 Score=20.74 Aligned_cols=20 Identities=20% Similarity=0.527 Sum_probs=9.6
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
++|+.+|++...|..|...+
T Consensus 22 ~ia~~lgvs~~Tv~~w~kr~ 41 (50)
T PF13384_consen 22 EIAKRLGVSRSTVYRWIKRY 41 (50)
T ss_dssp HHHHHHTS-HHHHHHHHT--
T ss_pred HHHHHHCcCHHHHHHHHHHc
Confidence 34555566666665555544
No 125
>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=58.88 E-value=18 Score=19.94 Aligned_cols=42 Identities=14% Similarity=0.071 Sum_probs=28.8
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhc
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKT 53 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqv 53 (120)
||+.|.+++......-.+ .+|-...-.+||..+|++..-+.-
T Consensus 1 LT~~Q~e~L~~A~~~GYf---d~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYF---DVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCC---CCCCcCCHHHHHHHhCCCHHHHHH
Confidence 678888887777652111 135556778899999999876654
No 126
>PF01978 TrmB: Sugar-specific transcriptional regulator TrmB; InterPro: IPR002831 TrmB, is a protein of 38,800 apparent molecular weight, that is involved in the maltose-specific regulation of the trehalose/maltose ABC transport operon in Thermococcus litoralis. TrmB has been shown to be a maltose-specific repressor, and this inhibition is counteracted by maltose and trehalose. TrmB binds maltose and trehalose half-maximally at 20 uM and 0.5 mM sugar concentration, respectively []. Other members of this family are annotated as either transcriptional regulators or hypothetical proteins. ; PDB: 2D1H_A 3QPH_A 1SFX_A.
Probab=56.81 E-value=7.4 Score=22.00 Aligned_cols=40 Identities=15% Similarity=0.262 Sum_probs=28.7
Q ss_pred ccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhcc
Q psy4877 6 LLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTW 54 (120)
Q Consensus 6 ~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvW 54 (120)
.+||++.+.+++.---. + ....-.+||..+|++...|..-
T Consensus 3 ~~gLs~~E~~vy~~Ll~------~---~~~t~~eIa~~l~i~~~~v~~~ 42 (68)
T PF01978_consen 3 VLGLSENEAKVYLALLK------N---GPATAEEIAEELGISRSTVYRA 42 (68)
T ss_dssp HHCHHHHHHHHHHHHHH------H---CHEEHHHHHHHHTSSHHHHHHH
T ss_pred cCCcCHHHHHHHHHHHH------c---CCCCHHHHHHHHCcCHHHHHHH
Confidence 78999999999654421 1 1355677999999999877643
No 127
>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=56.55 E-value=6.5 Score=19.17 Aligned_cols=17 Identities=18% Similarity=0.333 Sum_probs=10.9
Q ss_pred cchhccCCCHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWF 18 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~f 18 (120)
.-|..+|++.++|...+
T Consensus 10 ~eA~~~Gls~eeir~FL 26 (30)
T PF08671_consen 10 KEAKESGLSKEEIREFL 26 (30)
T ss_dssp HHHHHTT--HHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHH
Confidence 45788888888887644
No 128
>PRK10856 cytoskeletal protein RodZ; Provisional
Probab=56.37 E-value=14 Score=28.09 Aligned_cols=21 Identities=10% Similarity=0.183 Sum_probs=18.7
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
+||++++++...|+.|+.+..
T Consensus 32 ~vA~~l~l~~~~I~~iE~g~~ 52 (331)
T PRK10856 32 AVAERLCLKVSTVRDIEEDKA 52 (331)
T ss_pred HHHHHHCCCHHHHHHHHCCCC
Confidence 689999999999999999864
No 129
>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=55.69 E-value=15 Score=23.29 Aligned_cols=24 Identities=13% Similarity=0.066 Sum_probs=15.7
Q ss_pred HHHHHhhhhcchhhhhhccccchh
Q psy4877 36 KRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
...+||..+|++...|.-|-....
T Consensus 80 tq~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 80 SQREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 345677777777777777765554
No 130
>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=55.36 E-value=5.5 Score=21.78 Aligned_cols=14 Identities=36% Similarity=0.631 Sum_probs=9.9
Q ss_pred cchhccCCCHHHHH
Q psy4877 2 ELSKLLNLTEVQIK 15 (120)
Q Consensus 2 ~la~~~~~~~~~~q 15 (120)
|||+.+|++..||.
T Consensus 33 ~La~~~gi~~~qVR 46 (50)
T PF06971_consen 33 ELAEALGITPAQVR 46 (50)
T ss_dssp HHHHHHTS-HHHHH
T ss_pred HHHHHHCCCHHHhc
Confidence 57888888888774
No 131
>cd08311 Death_p75NR Death domain of p75 Neurotophin Receptor. Death Domain (DD) found in p75 neurotrophin receptor (p75NTR, NGFR, TNFRSF16). p75NTR binds members of the neurotrophin (NT) family including nerve growth factor (NGF), brain-derived neurotrophic factor (BDNF), and NT3, among others. It contains an NT-binding extracellular region that bears four cysteine-rich repeats, a transmembrane domain, and an intracellular DD. p75NTR plays roles in the immune, vascular, and nervous systems, and has been shown to promote cell death or survival, and to induce neurite outgrowth or collapse depending on its ligands and co-receptors. In general, 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 adaptor
Probab=55.22 E-value=8.6 Score=22.88 Aligned_cols=17 Identities=24% Similarity=0.231 Sum_probs=15.0
Q ss_pred cchhccCCCHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWF 18 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~f 18 (120)
.||.++||++..|+.+-
T Consensus 20 ~LA~~LG~~~~~I~~i~ 36 (77)
T cd08311 20 SLAGELGYEDEAIDTFG 36 (77)
T ss_pred HHHHHcCCCHHHHHHHH
Confidence 68999999999998854
No 132
>smart00342 HTH_ARAC helix_turn_helix, arabinose operon control protein.
Probab=55.02 E-value=14 Score=20.79 Aligned_cols=20 Identities=15% Similarity=0.473 Sum_probs=16.4
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
+||+.+|++...+...|...
T Consensus 6 ~la~~~~~s~~~l~~~f~~~ 25 (84)
T smart00342 6 DLAEALGMSPRHLQRLFKKE 25 (84)
T ss_pred HHHHHhCCCHHHHHHHHHHH
Confidence 68999999999998877653
No 133
>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=55.01 E-value=15 Score=23.73 Aligned_cols=34 Identities=9% Similarity=0.124 Sum_probs=25.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.......++|..+|+++..|..+...-+.+.++
T Consensus 126 ~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 126 RFEGKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4456678889999999999999887655555443
No 134
>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=54.74 E-value=9.3 Score=21.36 Aligned_cols=19 Identities=11% Similarity=0.471 Sum_probs=17.1
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|.+.
T Consensus 5 eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 5 AVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHCcCHHHHHHHHHh
Confidence 6899999999999999874
No 135
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=54.52 E-value=21 Score=24.14 Aligned_cols=35 Identities=20% Similarity=0.288 Sum_probs=27.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|++...|++-...-|.+.++.
T Consensus 144 ~~~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 178 (189)
T PRK12515 144 YYHEKSVEEVGEIVGIPESTVKTRMFYARKKLAEL 178 (189)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44556778899999999999999887666666654
No 136
>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=54.50 E-value=9.5 Score=19.38 Aligned_cols=19 Identities=21% Similarity=0.441 Sum_probs=14.4
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|...
T Consensus 4 e~A~~~gvs~~tlR~ye~~ 22 (38)
T PF00376_consen 4 EVAKLLGVSPRTLRYYERE 22 (38)
T ss_dssp HHHHHHTS-HHHHHHHHHT
T ss_pred HHHHHHCCCHHHHHHHHHC
Confidence 6788888888888887765
No 137
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=54.44 E-value=13 Score=25.24 Aligned_cols=34 Identities=18% Similarity=0.194 Sum_probs=28.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|+++..|.+++..-|.+.++
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5566778899999999999999999766666555
No 138
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=54.30 E-value=18 Score=24.25 Aligned_cols=34 Identities=12% Similarity=0.168 Sum_probs=26.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|++....-|.+-++
T Consensus 147 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 147 FFAGLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4445677889999999999999988765555544
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=54.08 E-value=9.9 Score=21.36 Aligned_cols=19 Identities=11% Similarity=0.359 Sum_probs=17.4
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|.++
T Consensus 5 evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 5 EVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHCcCHHHHHHHHHh
Confidence 6899999999999999876
No 140
>PRK04217 hypothetical protein; Provisional
Probab=53.76 E-value=26 Score=22.39 Aligned_cols=47 Identities=11% Similarity=0.006 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.|++++.+++...+ -......++|+.+|++...|...+..-+.+.+.
T Consensus 42 ~Lt~eereai~l~~----------~eGlS~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 42 FMTYEEFEALRLVD----------YEGLTQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred cCCHHHHHHHHHHH----------HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35666666543332 224467889999999999999887655555444
No 141
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=53.62 E-value=23 Score=21.00 Aligned_cols=41 Identities=20% Similarity=0.260 Sum_probs=26.2
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq 52 (120)
+-+.-++++++|...||... +|. ..-+-+-.++|++...+|
T Consensus 7 ~LKehnvsd~qi~elFq~lT-----~NP----l~AMa~i~qLGip~eKLQ 47 (82)
T PF11212_consen 7 ILKEHNVSDEQINELFQALT-----QNP----LAAMATIQQLGIPQEKLQ 47 (82)
T ss_pred HHHHcCCCHHHHHHHHHHHh-----hCH----HHHHHHHHHcCCCHHHHH
Confidence 44667899999999999975 333 222333455666665544
No 142
>PRK06930 positive control sigma-like factor; Validated
Probab=53.54 E-value=24 Score=24.12 Aligned_cols=34 Identities=15% Similarity=0.183 Sum_probs=27.3
Q ss_pred cchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 32 p~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
-....-.++|..+|++...|+.+..+-+.+.++.
T Consensus 128 ~eg~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~ 161 (170)
T PRK06930 128 GYGLSYSEIADYLNIKKSTVQSMIERAEKKIARQ 161 (170)
T ss_pred HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3456678899999999999999998777776664
No 143
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=53.40 E-value=18 Score=23.84 Aligned_cols=34 Identities=6% Similarity=0.082 Sum_probs=26.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|+++..|..|...-+.+.++
T Consensus 141 ~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 141 EIEGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3445667889999999999999998765555554
No 144
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=52.33 E-value=14 Score=24.67 Aligned_cols=26 Identities=12% Similarity=0.252 Sum_probs=22.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
|+|+.+|++...|..|...-+.|.++
T Consensus 26 EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 26 EIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999999987765554
No 145
>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=52.26 E-value=11 Score=19.04 Aligned_cols=21 Identities=19% Similarity=0.613 Sum_probs=16.8
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
|+|+.+|++...|..|..+-.
T Consensus 5 e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 5 EAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHCcCHHHHHHHHHcCC
Confidence 678888999998888877643
No 146
>PF12728 HTH_17: Helix-turn-helix domain
Probab=52.20 E-value=6 Score=20.99 Aligned_cols=19 Identities=21% Similarity=0.615 Sum_probs=14.1
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|.|+-+|++...|..|-..
T Consensus 6 e~a~~l~is~~tv~~~~~~ 24 (51)
T PF12728_consen 6 EAAELLGISRSTVYRWIRQ 24 (51)
T ss_pred HHHHHHCcCHHHHHHHHHc
Confidence 5677788888888777655
No 147
>smart00482 POLAc DNA polymerase A domain.
Probab=51.82 E-value=15 Score=25.77 Aligned_cols=27 Identities=19% Similarity=0.331 Sum_probs=20.5
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchh
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVS 35 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~ 35 (120)
||+.+|+++++.+....+++ +.||...
T Consensus 88 la~~lg~s~~ea~~~~~~f~------~~~p~v~ 114 (206)
T smart00482 88 LAEQLGISEAEAKELIKAYF------ARFPGVK 114 (206)
T ss_pred HHHHcCCCHHHHHHHHHHHH------HHCccHH
Confidence 67888888888888777776 5666553
No 148
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=51.78 E-value=25 Score=23.10 Aligned_cols=35 Identities=14% Similarity=0.253 Sum_probs=27.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|++...|..|...-|.+.|+.
T Consensus 138 ~~~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 138 YVEGLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556678999999999999999987666666653
No 149
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=51.76 E-value=26 Score=21.68 Aligned_cols=43 Identities=16% Similarity=0.229 Sum_probs=29.0
Q ss_pred HHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 12 VQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 12 ~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.+++.+.-++-+ ..-...+|...|+++++|.-|..+-+.++-.
T Consensus 11 r~iEs~iL~rlA----------~~gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 11 RRIESEILNRLA----------SVGQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHHHH----------HHHHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHH----------HHhhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 456666666554 4456678999999999999986554444433
No 150
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=51.63 E-value=12 Score=24.92 Aligned_cols=36 Identities=19% Similarity=0.240 Sum_probs=29.2
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
+|-....-+++|..+|+++..|++.+..-|.+.++.
T Consensus 132 ~~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~ 167 (175)
T PRK12518 132 HDLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKF 167 (175)
T ss_pred hHhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356666788999999999999999987777776664
No 151
>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=51.58 E-value=19 Score=22.56 Aligned_cols=33 Identities=18% Similarity=0.301 Sum_probs=25.3
Q ss_pred cchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 32 p~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
-....-.++|..+|+++..|..+...-+.|.++
T Consensus 124 ~~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 124 LEGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 345667789999999999999988765555443
No 152
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=51.52 E-value=19 Score=24.09 Aligned_cols=34 Identities=21% Similarity=0.362 Sum_probs=27.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|+++..|.++...-|.+.|+
T Consensus 142 ~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 142 YLEGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred HHcCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 4556678899999999999999988766666554
No 153
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=51.10 E-value=21 Score=24.14 Aligned_cols=34 Identities=6% Similarity=-0.027 Sum_probs=26.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|..+...-+.+-|+
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 152 VVVGLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556778899999999999999987655555444
No 154
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=51.09 E-value=25 Score=22.99 Aligned_cols=35 Identities=17% Similarity=0.152 Sum_probs=27.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|+++..|++....-|.+-|+.
T Consensus 119 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 119 YLEEKSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44456677899999999999999887666665553
No 155
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=50.70 E-value=25 Score=18.16 Aligned_cols=23 Identities=26% Similarity=0.407 Sum_probs=18.9
Q ss_pred hHHHHHhhhhcchhhhhhccccc
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQN 57 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqN 57 (120)
....++|..++++...|..|...
T Consensus 19 ~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 19 LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 45688999999999999887753
No 156
>PF04760 IF2_N: Translation initiation factor IF-2, N-terminal region; InterPro: IPR006847 This region is found in the N-terminal half of translation initiation factor IF-2. It is found in two copies in IF-2 alpha isoforms, and in only one copy in the N-terminally truncated beta and gamma isoforms []. Its function is unknown.; GO: 0003743 translation initiation factor activity, 0006413 translational initiation; PDB: 1ND9_A.
Probab=50.66 E-value=19 Score=19.46 Aligned_cols=44 Identities=18% Similarity=0.203 Sum_probs=22.5
Q ss_pred cchhccCCCHHHHH-HHHhhhHhhhhhcccccchhHHHHHhhhhc
Q psy4877 2 ELSKLLNLTEVQIK-TWFQNRRTKWKYVDKYLSVSKRMELSKLLN 45 (120)
Q Consensus 2 ~la~~~~~~~~~~q-~~fq~~r~k~~~~~~yp~~~~r~~La~~~~ 45 (120)
|||+.+|++..+|- .+|+..--.-...+...+......|+..++
T Consensus 8 elAk~l~v~~~~ii~~l~~~~Gi~~~~~~~~ld~e~~~~i~~~~~ 52 (54)
T PF04760_consen 8 ELAKELGVPSKEIIKKLFKELGIMVKSINSSLDEEEAELIAEEFG 52 (54)
T ss_dssp HHHHHHSSSHHHHHHHH-HHHTS---SSSS-EETTGGGHHHHHH-
T ss_pred HHHHHHCcCHHHHHHHHHHhCCcCcCCCCCcCCHHHHHHHHHHhC
Confidence 79999999996554 444522111122345555555555555543
No 157
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=50.32 E-value=23 Score=24.43 Aligned_cols=38 Identities=13% Similarity=0.066 Sum_probs=28.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLAS 68 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~ 68 (120)
|-....-.++|..+|++...|.++...-|.+.|+....
T Consensus 146 ~~~g~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~~ 183 (196)
T PRK12535 146 QVLGYTYEEAAKIADVRVGTIRSRVARARADLIAATAT 183 (196)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhcc
Confidence 44456678899999999999999887666666654333
No 158
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=49.75 E-value=26 Score=23.06 Aligned_cols=35 Identities=17% Similarity=0.114 Sum_probs=27.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|......+++|..+|+++..|.++...-|.+.++.
T Consensus 121 ~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~ 155 (165)
T PRK09644 121 DVHELTYEEAASVLDLKLNTYKSHLFRGRKRLKAL 155 (165)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556788899999999999999987666666553
No 159
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=49.44 E-value=26 Score=23.67 Aligned_cols=36 Identities=8% Similarity=0.093 Sum_probs=28.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
|.....-.++|..+|+++..|.+....-|.+-|+..
T Consensus 151 ~~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 151 EFDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 555667788999999999999998876666666643
No 160
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=49.38 E-value=29 Score=22.54 Aligned_cols=34 Identities=18% Similarity=0.145 Sum_probs=25.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|+++..|++....-|.+.|.
T Consensus 119 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 119 YWEDMDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred HHhcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445667889999999999999877655555444
No 161
>cd08306 Death_FADD Fas-associated Death Domain protein-protein interaction domain. Death domain (DD) found in FAS-associated via death domain (FADD). FADD is a component of the death-inducing signaling complex (DISC) and serves as an adaptor in the signaling pathway of death receptor proteins. It modulates apoptosis as well as non-apoptotic processes such as cell cycle progression, survival, innate immune signaling, and hematopoiesis. FADD contains an N-terminal DED and a C-terminal DD. Its DD interacts with the DD of the activated death receptor, FAS, and its DED recruits the initiator caspases, caspase-8 and -10, to the DISC complex via a homotypic interaction with the N-terminal DED of the caspase. 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),
Probab=49.27 E-value=14 Score=22.27 Aligned_cols=19 Identities=26% Similarity=0.427 Sum_probs=16.3
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||.++||++.+|.....+
T Consensus 18 ~laR~LGlse~~Id~i~~~ 36 (86)
T cd08306 18 KLARKLGLSETKIESIEEA 36 (86)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 6899999999999886655
No 162
>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=49.16 E-value=15 Score=23.45 Aligned_cols=51 Identities=20% Similarity=0.294 Sum_probs=32.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhh--------h---------cccccchhHHHHHhhhhcchhhhhhc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWK--------Y---------VDKYLSVSKRMELSKLLNLTEVQIKT 53 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~--------~---------~~~yp~~~~r~~La~~~~l~~~~vqv 53 (120)
+.|++.+++...|..|+..+++-.. + ...+|+.... |||..+|++...|-.
T Consensus 23 eaa~~F~VS~~Tv~~W~k~~~~G~~~~k~r~~~Kid~~~L~~~v~~~pd~tl~-Ela~~l~Vs~~ti~~ 90 (119)
T PF01710_consen 23 EAAKRFGVSRNTVYRWLKRKETGDLEPKPRGRKKIDRDELKALVEENPDATLR-ELAERLGVSPSTIWR 90 (119)
T ss_pred HHHHHhCcHHHHHHHHHHhcccccccccccccccccHHHHHHHHHHCCCcCHH-HHHHHcCCCHHHHHH
Confidence 5678889999999999984443111 1 1225555544 578888877665544
No 163
>PF10453 NUFIP1: Nuclear fragile X mental retardation-interacting protein 1 (NUFIP1); InterPro: IPR019496 Nuclear fragile X mental retardation-interacting protein 1 (Nufip1) has been implicated in the assembly of the large subunit of the ribosome [] and in telomere maintenance []. It is known to bind RNA [] and is phosphorylated upon DNA damage []. This entry represents a conserved domain found within Nufip1. Some proteins containing this region also contain a CCCH zinc finger.
Probab=49.12 E-value=25 Score=19.64 Aligned_cols=23 Identities=26% Similarity=0.534 Sum_probs=19.0
Q ss_pred CHHHHHHHHhhhHhhhhhcccccchhHHH
Q psy4877 10 TEVQIKTWFQNRRTKWKYVDKYLSVSKRM 38 (120)
Q Consensus 10 ~~~~~q~~fq~~r~k~~~~~~yp~~~~r~ 38 (120)
|++.|+.|-..|| ..||+....+
T Consensus 19 t~eeI~~W~eERr------k~~PT~~~i~ 41 (56)
T PF10453_consen 19 TPEEIAKWIEERR------KNYPTKANIE 41 (56)
T ss_pred CHHHHHHHHHHHH------HcCCcHHHHH
Confidence 7899999999998 6888876543
No 164
>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=48.96 E-value=8.9 Score=19.95 Aligned_cols=14 Identities=36% Similarity=0.605 Sum_probs=9.4
Q ss_pred cchhccCCCHHHHH
Q psy4877 2 ELSKLLNLTEVQIK 15 (120)
Q Consensus 2 ~la~~~~~~~~~~q 15 (120)
+||+.+|+++..|.
T Consensus 22 ~la~~lglS~~~v~ 35 (42)
T PF13404_consen 22 ELAEELGLSESTVR 35 (42)
T ss_dssp HHHHHHTS-HHHHH
T ss_pred HHHHHHCcCHHHHH
Confidence 57777888877664
No 165
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=48.72 E-value=82 Score=21.53 Aligned_cols=50 Identities=20% Similarity=0.131 Sum_probs=37.3
Q ss_pred hccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 5 KLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 5 ~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
....|++++|+..-+=| ..=|..-.+..||++.|++..-|.+-..--..+
T Consensus 82 k~y~Lt~e~i~Eir~LR-------~~DP~~wTr~~LAkkF~~S~~fV~~v~~~~~e~ 131 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLR-------AEDPEKWTRKKLAKKFNCSPLFVSMVAPAPKEK 131 (164)
T ss_pred ccccCCHHHHHHHHHHH-------HcCchHhhHHHHHHHhCCCHHHHHHhcCCCHHH
Confidence 34679999999866665 345677889999999999998887655444433
No 166
>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=48.20 E-value=24 Score=23.70 Aligned_cols=35 Identities=6% Similarity=0.080 Sum_probs=27.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|+++..|.++...-|.+-|+.
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 55667788999999999999999886666655553
No 167
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=47.70 E-value=40 Score=22.59 Aligned_cols=37 Identities=19% Similarity=0.286 Sum_probs=30.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
|.....-.++|..+|+++..|++....-+.+.|+...
T Consensus 130 ~~e~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 166 (179)
T PRK12543 130 YLHDYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQ 166 (179)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555677889999999999999988888888777543
No 168
>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=47.52 E-value=13 Score=21.49 Aligned_cols=19 Identities=16% Similarity=0.386 Sum_probs=14.7
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|||+.+|++.++|...++-
T Consensus 25 EiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 25 EIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHcccHHHHHHHHHh
Confidence 6889999999998876654
No 169
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=47.24 E-value=24 Score=24.07 Aligned_cols=34 Identities=12% Similarity=0.281 Sum_probs=26.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-.+..-+++|..+|+++..|+..+..=|++.++
T Consensus 148 ~~~Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 148 FFEGLSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3446788999999999999999877665655444
No 170
>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=47.24 E-value=24 Score=22.86 Aligned_cols=32 Identities=16% Similarity=0.092 Sum_probs=24.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
|.....-+++|..+|++...|.++...-|.+-
T Consensus 124 ~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 124 YQRGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 55567788999999999999998765444443
No 171
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=47.07 E-value=25 Score=23.68 Aligned_cols=34 Identities=18% Similarity=0.098 Sum_probs=27.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|+++..|++....-|.+.++
T Consensus 142 ~~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 142 KLEGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556778889999999999999988776766665
No 172
>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=47.03 E-value=52 Score=23.71 Aligned_cols=40 Identities=8% Similarity=0.285 Sum_probs=30.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
|-....-+++|..+|+++..|+++...-|.+-++......
T Consensus 174 ~~eg~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 174 FVDGLSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445667889999999999999999877777776544433
No 173
>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=46.94 E-value=24 Score=23.02 Aligned_cols=34 Identities=9% Similarity=0.230 Sum_probs=26.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|+++-..-|.+.++
T Consensus 123 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 123 YYEDLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred HHhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4445677889999999999999988766666555
No 174
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=46.35 E-value=26 Score=23.55 Aligned_cols=35 Identities=9% Similarity=0.070 Sum_probs=28.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-+++|..+|++...|..++..-|.+.+..
T Consensus 144 ~~~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 144 SVEGASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45567788999999999999999887666666553
No 175
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=46.25 E-value=41 Score=21.96 Aligned_cols=35 Identities=20% Similarity=0.339 Sum_probs=27.9
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
.| ....-.++|..+|+++..|..+...-+.+.|+.
T Consensus 124 ~~-~g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~ 158 (166)
T PRK09639 124 RF-SGYSYKEIAEALGIKESSVGTTLARAKKKFRKI 158 (166)
T ss_pred HH-cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35 677888999999999999999886666665553
No 176
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=45.76 E-value=16 Score=18.47 Aligned_cols=20 Identities=5% Similarity=0.262 Sum_probs=14.1
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
++|+.+||++.-+...|++.
T Consensus 13 ~iA~~~g~S~~~f~r~Fk~~ 32 (42)
T PF00165_consen 13 DIAEQAGFSPSYFSRLFKKE 32 (42)
T ss_dssp HHHHHHTS-HHHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHHH
Confidence 57888888888777777663
No 177
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=45.64 E-value=27 Score=23.37 Aligned_cols=34 Identities=26% Similarity=0.375 Sum_probs=27.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|+++..|.+++..-|.+-+.
T Consensus 149 ~~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 149 YMEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5556778889999999999999998766666554
No 178
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=44.57 E-value=26 Score=23.77 Aligned_cols=34 Identities=35% Similarity=0.403 Sum_probs=25.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|......+++|..+|++...|.+..+.-|.+-++
T Consensus 144 ~~~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 144 YLLGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445677899999999999999877655555444
No 179
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=44.49 E-value=42 Score=22.79 Aligned_cols=35 Identities=3% Similarity=0.027 Sum_probs=26.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|+++..|+++...-|.+.|+.
T Consensus 147 ~~~g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 147 EYLELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44456678899999999999999987556555553
No 180
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=44.34 E-value=16 Score=20.41 Aligned_cols=19 Identities=16% Similarity=0.261 Sum_probs=16.5
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|...
T Consensus 5 eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 5 EVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred HHHHHHCcCHHHHHHHHHC
Confidence 6889999999999998654
No 181
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=44.05 E-value=40 Score=24.04 Aligned_cols=36 Identities=14% Similarity=0.308 Sum_probs=28.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
|.....-.++|..+|+++..|++....-|.+.|+..
T Consensus 184 ~~eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 184 YHENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 455667788999999999999998877777766643
No 182
>cd01670 Death Death Domain: a protein-protein interaction domain. Death Domains (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. Structural analysis of DD-DD complexes show that the domains interact with each other in many different ways. DD-containing proteins serve as adaptors in signaling pathways and they can recruit other proteins into signaling complexes. In mammals, they are prominent components of the programmed cell death (apoptosis) pathway and are found in a number of other signaling pathways. In invertebrates, they are involved in transcriptional regulation of zygotic patterning genes in insect embryogenesis, and are components of the ToII/NF-kappaB pathway, a conserved innate immune pathway in a
Probab=43.95 E-value=19 Score=20.71 Aligned_cols=20 Identities=20% Similarity=0.350 Sum_probs=16.9
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
+||.++||++.+|+.+..+.
T Consensus 15 ~la~~Lgl~~~~I~~i~~~~ 34 (79)
T cd01670 15 KLARKLGLSDGEIDQIEEDN 34 (79)
T ss_pred HHHHHhCCCHHHHHHHHHhC
Confidence 58999999999999876664
No 183
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=43.93 E-value=27 Score=23.89 Aligned_cols=35 Identities=11% Similarity=0.018 Sum_probs=27.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|++...|+++...-|.+.|+.
T Consensus 126 ~~~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~ 160 (188)
T PRK12546 126 GASGFSYEEAAEMCGVAVGTVKSRANRARARLAEL 160 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44566778899999999999999987666665553
No 184
>cd08313 Death_TNFR1 Death domain of Tumor Necrosis Factor Receptor 1. Death Domain (DD) found in tumor necrosis factor receptor-1 (TNFR-1). TNFR-1 has many names including TNFRSF1A, CD120a, p55, p60, and TNFR60. It activates two major intracellular signaling pathways that lead to the activation of the transcription factor NF-kB and the induction of cell death. Upon binding of its ligand TNF, TNFR-1 trimerizes which leads to the recruitment of an adaptor protein named TNFR-associated death domain protein (TRADD) through a DD/DD interaction. Mutations in the TNFRSF1A gene causes TNFR-associated periodic syndrome (TRAPS), a rare disorder characterized recurrent fever, myalgia, abdominal pain, conjunctivitis and skin eruptions. 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 a
Probab=43.84 E-value=16 Score=21.95 Aligned_cols=19 Identities=21% Similarity=0.288 Sum_probs=15.4
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
++|.++||+|.+|+....+
T Consensus 16 ~~~R~LGlse~~Id~ie~~ 34 (80)
T cd08313 16 EFVRRLGLSDNEIERVELD 34 (80)
T ss_pred HHHHHcCCCHHHHHHHHHh
Confidence 5789999999999875544
No 185
>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=43.74 E-value=27 Score=25.45 Aligned_cols=45 Identities=16% Similarity=0.176 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
.||+.+.+++.--.. .....++|..+++++..|+....|=+.|..
T Consensus 190 ~LT~RE~evl~l~a~-----------G~s~~eIA~~L~IS~~TVk~hl~~i~~KL~ 234 (247)
T TIGR03020 190 LITAREAEILAWVRD-----------GKTNEEIAAILGISSLTVKNHLQHIFKKLD 234 (247)
T ss_pred CCCHHHHHHHHHHHC-----------CCCHHHHHHHHCcCHHHHHHHHHHHHHHhC
Confidence 688888888554322 466788999999999999998877666644
No 186
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=43.47 E-value=31 Score=23.37 Aligned_cols=34 Identities=26% Similarity=0.237 Sum_probs=26.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|+..+..-|.+.++
T Consensus 119 ~~~g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 119 ELEGLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4456678889999999999999988655555554
No 187
>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=43.01 E-value=28 Score=24.77 Aligned_cols=46 Identities=13% Similarity=0.210 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.||+.+.++++.--. ...-.++|..++++++.|+.+..|=+.|..-
T Consensus 171 ~Lt~re~evl~~~a~-----------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~ 216 (232)
T TIGR03541 171 VLSEREREVLAWTAL-----------GRRQADIAAILGISERTVENHLRSARRKLGV 216 (232)
T ss_pred cCCHHHHHHHHHHHC-----------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCC
Confidence 577777777555321 4567789999999999999988877666543
No 188
>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=42.53 E-value=17 Score=23.52 Aligned_cols=35 Identities=26% Similarity=0.326 Sum_probs=27.0
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
.|.....-+++|..+|+++..|.++...-|.+.++
T Consensus 117 ~~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 117 REFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35667788899999999999999987655555443
No 189
>PRK00118 putative DNA-binding protein; Validated
Probab=42.48 E-value=38 Score=21.39 Aligned_cols=33 Identities=6% Similarity=0.018 Sum_probs=25.8
Q ss_pred chhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 33 SVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 33 ~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
....-.++|..+|++...|..|...-|.+.+..
T Consensus 32 eg~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 32 DDYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356677899999999999999987666666553
No 190
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=42.39 E-value=42 Score=23.30 Aligned_cols=35 Identities=9% Similarity=0.116 Sum_probs=27.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|+++..|.++...-|.+.++.
T Consensus 151 ~~~g~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 151 DIEGLSYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556778899999999999999887666665553
No 191
>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=42.34 E-value=30 Score=22.81 Aligned_cols=34 Identities=26% Similarity=0.363 Sum_probs=25.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|+++..|.+....-|.+-++
T Consensus 132 ~~~g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 132 YYHDLTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4446678889999999999999877655555444
No 192
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=42.21 E-value=40 Score=22.37 Aligned_cols=35 Identities=17% Similarity=0.294 Sum_probs=26.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-+++|..+|+++..|.+....-|.+-++.
T Consensus 132 ~~~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 132 YYEQYSYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 45556678899999999999999886555555543
No 193
>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=42.12 E-value=43 Score=22.28 Aligned_cols=34 Identities=26% Similarity=0.242 Sum_probs=26.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|+++..|.++...-|.+.+.
T Consensus 113 ~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 146 (170)
T TIGR02959 113 ELEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKE 146 (170)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4456778889999999999999987655555554
No 194
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=42.03 E-value=35 Score=22.94 Aligned_cols=34 Identities=12% Similarity=0.210 Sum_probs=26.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|++...+-+.+.+.
T Consensus 140 ~~~g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 140 TLDGMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445677889999999999999988755555543
No 195
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=41.96 E-value=51 Score=22.27 Aligned_cols=37 Identities=14% Similarity=0.108 Sum_probs=27.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
|.....-.++|..+|+++..|.+....-|.+.++...
T Consensus 144 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 144 EWLELETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4445667889999999999999988766666555433
No 196
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=41.06 E-value=22 Score=23.92 Aligned_cols=26 Identities=19% Similarity=0.303 Sum_probs=20.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
|+|+.+|+++.-|++....-+.+.++
T Consensus 138 EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 138 EIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 78999999999999977776655544
No 197
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=40.83 E-value=46 Score=22.56 Aligned_cols=36 Identities=11% Similarity=0.145 Sum_probs=28.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
|-....-+++|..+|++...|.+....-|.+.|+..
T Consensus 149 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 149 EILGFSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 445566788999999999999998876666666643
No 198
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=40.12 E-value=43 Score=22.51 Aligned_cols=35 Identities=11% Similarity=0.278 Sum_probs=27.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|++...|..+...-|.+.++.
T Consensus 141 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 141 YYQGLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred HhcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 44566778899999999999999887666665553
No 199
>cd08804 Death_ank2 Death domain of Ankyrin-2. Death Domain (DD) of Ankyrin-2 (ANK-2) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-2, also called ankyrin-B (for broadly expressed), is required for proper function of the Na/Ca ion exchanger-1 in cardiomyocytes, and is thought to function in linking integral membrane proteins to the underlying cytoskeleton. Human ANK-2 is associated with "Ankyrin-B syndrome", an atypical arrythmia disorder with risk of sudden cardiac death. It also plays key roles in the brain and striated muscle. Loss of ANK-2 is associated with significant nervous system defects and sarcomere disorganization. In general, 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
Probab=40.03 E-value=17 Score=21.88 Aligned_cols=19 Identities=37% Similarity=0.392 Sum_probs=15.2
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||.++||++..|.....+
T Consensus 20 ~LAr~Lg~se~dI~~i~~~ 38 (84)
T cd08804 20 ELARELDFTEEQIHQIRIE 38 (84)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 6899999999999774433
No 200
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.02 E-value=40 Score=23.65 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhc
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKT 53 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqv 53 (120)
.||+.|++++-..+.+=.+ -||-...-.+||+.+|++..-+.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYF---d~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYF---DYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCC---CCCccCCHHHHHHHhCCCHHHHHH
Confidence 6999999998877752111 145556667889999999976654
No 201
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=39.72 E-value=42 Score=19.10 Aligned_cols=19 Identities=5% Similarity=0.345 Sum_probs=12.6
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||+++|++...|.-++.+
T Consensus 5 ~iA~~~gvS~~TVSr~ln~ 23 (70)
T smart00354 5 DVARLAGVSKATVSRVLNG 23 (70)
T ss_pred HHHHHHCCCHHHHHHHHCC
Confidence 4667777777777666655
No 202
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=39.50 E-value=38 Score=22.51 Aligned_cols=34 Identities=9% Similarity=0.148 Sum_probs=26.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-.++|..+|+++..|+++..+-+.+.+.
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 132 RLDGMGHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455677889999999999999988655555544
No 203
>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=39.43 E-value=34 Score=23.21 Aligned_cols=36 Identities=14% Similarity=0.181 Sum_probs=28.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
|.....-.++|..+|+++..|+++...-|.+.++..
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 555667888999999999999999876666666643
No 204
>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=39.00 E-value=24 Score=17.82 Aligned_cols=19 Identities=11% Similarity=0.246 Sum_probs=15.9
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|.|+.+|++...|..|...
T Consensus 6 e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 6 EAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHCCCHHHHHHHHHc
Confidence 6788899999999888765
No 205
>cd08317 Death_ank Death domain associated with Ankyrins. Death Domain (DD) associated with Ankyrins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. Ankyrins function as adaptor proteins and they interact, through ANK repeats, with structurally diverse membrane proteins, including ion channels/pumps, calcium release channels, and cell adhesion molecules. They play critical roles in the proper expression and membrane localization of these proteins. In mammals, this family includes ankyrin-R for restricted (or ANK1), ankyrin-B for broadly expressed (or ANK2) and ankyrin-G for general or giant (or ANK3). They are expressed in different combinations in many tissues and play non-overlapping functions. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-associati
Probab=38.87 E-value=25 Score=20.90 Aligned_cols=18 Identities=22% Similarity=0.313 Sum_probs=15.0
Q ss_pred cchhccCCCHHHHHHHHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQ 19 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq 19 (120)
+||.++||++..|...-.
T Consensus 20 ~LAr~Lg~~~~dI~~i~~ 37 (84)
T cd08317 20 QLARELGVSETDIDLIKA 37 (84)
T ss_pred HHHHHcCCCHHHHHHHHH
Confidence 689999999999988443
No 206
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=38.76 E-value=45 Score=22.74 Aligned_cols=34 Identities=3% Similarity=0.080 Sum_probs=26.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|+++...-|.+.++
T Consensus 149 ~~~g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~ 182 (196)
T PRK12524 149 HIEGLSNPEIAEVMEIGVEAVESLTARGKRALAA 182 (196)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455668889999999999999998755555555
No 207
>cd08777 Death_RIP1 Death Domain of Receptor-Interacting Protein 1. Death domain (DD) found in Receptor-Interacting Protein 1 (RIP1) and related proteins. RIP kinases serve as essential sensors of cellular stress. Vertebrates contain several types containing a homologous N-terminal kinase domain and varying C-terminal domains. RIP1 harbors a C-terminal DD, which binds death receptors (DRs) including TNF receptor 1, Fas, TNF-related apoptosis-inducing ligand receptor 1 (TRAILR1), and TRAILR2. It also interacts with other DD-containing adaptor proteins such as TRADD and FADD. RIP1 plays a crucial role in determining a cell's fate, between survival or death, following exposure to stress signals. It is important in the signaling of NF-kappaB and MAPKs, and it links DR-associated signaling to reactive oxygen species (ROS) production. Abnormal RIP1 function may result in ROS accumulation affecting inflammatory responses, innate immunity, stress responses, and cell survival. In general, DDs ar
Probab=38.71 E-value=25 Score=21.26 Aligned_cols=17 Identities=24% Similarity=0.249 Sum_probs=14.8
Q ss_pred cchhccCCCHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWF 18 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~f 18 (120)
+||.++||++..|....
T Consensus 18 ~lar~LG~s~~eI~~ie 34 (86)
T cd08777 18 RCARKLGFTESEIEEID 34 (86)
T ss_pred HHHHHcCCCHHHHHHHH
Confidence 68999999999998854
No 208
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=38.50 E-value=24 Score=24.58 Aligned_cols=41 Identities=10% Similarity=0.093 Sum_probs=28.1
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhH
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRT 60 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRa 60 (120)
||+.+.+|+---- .+..-+++|.+++++++.|+.-..|=-.
T Consensus 138 LT~RE~eVL~lla-----------~G~snkeIA~~L~iS~~TVk~h~~~I~~ 178 (207)
T PRK15411 138 LSRTESSMLRMWM-----------AGQGTIQISDQMNIKAKTVSSHKGNIKR 178 (207)
T ss_pred CCHHHHHHHHHHH-----------cCCCHHHHHHHcCCCHHHHHHHHHHHHH
Confidence 7787777744332 2566788899999999888876544333
No 209
>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=38.44 E-value=46 Score=23.97 Aligned_cols=43 Identities=14% Similarity=0.373 Sum_probs=29.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
|+|+.+|+++..|+++...=+.+.+ ...+.+++..+++....+
T Consensus 182 EIA~~Lgis~~TVk~rl~RAr~~Lr-------~~l~~~~~~~~~~~~~~~ 224 (244)
T TIGR03001 182 RIGAMYQVHRSTVSRWVAQARERLL-------ERTRRRLAERLKLSSPEL 224 (244)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHH-------HHHHHHHHHhcCCCcccH
Confidence 7899999999999997776654444 234555666666555443
No 210
>COG4977 Transcriptional regulator containing an amidase domain and an AraC-type DNA-binding HTH domain [Transcription]
Probab=38.38 E-value=43 Score=25.56 Aligned_cols=20 Identities=25% Similarity=0.410 Sum_probs=12.2
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
+||+++|+++.+++-.|+..
T Consensus 241 ~LA~~~~~S~R~leRlF~~~ 260 (328)
T COG4977 241 ELADRAGLSRRQLERLFRAE 260 (328)
T ss_pred HHHHHhCCCHHHHHHHHHHH
Confidence 46666666666666655554
No 211
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=38.18 E-value=44 Score=22.02 Aligned_cols=34 Identities=12% Similarity=0.022 Sum_probs=26.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|+++...-|.+-+.
T Consensus 125 ~~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 125 GASGFSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4556778889999999999999988655555443
No 212
>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=38.06 E-value=22 Score=21.82 Aligned_cols=58 Identities=16% Similarity=0.157 Sum_probs=34.3
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh-cccc--cchhHHHH-----Hhhh-hcchhhhhhccccchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY-VDKY--LSVSKRME-----LSKL-LNLTEVQIKTWFQNRR 59 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~-~~~y--p~~~~r~~-----La~~-~~l~~~~vqvWFqNrR 59 (120)
|+|+.+|++...|.-|++.-...-.+ .+.| -+...-.. .... +|++-..++......+
T Consensus 5 e~a~~~gvs~~tLR~ye~~Gll~p~r~~~g~R~Y~~~dv~~l~~I~~L~~~~G~~l~ei~~~l~~~~ 71 (96)
T cd04774 5 EVAKRLGLTKRTLKYYEEIGLVSPERSEGRYRLYSEEDLKRLERILRLREVLGFSLQEVTHFLERPL 71 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCEEECHHHHHHHHHHHHHHHHcCCCHHHHHHHHhccc
Confidence 68999999999999998764432111 1111 11111111 1344 7888888887665544
No 213
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=38.04 E-value=56 Score=22.22 Aligned_cols=35 Identities=14% Similarity=0.023 Sum_probs=26.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|+++..|++....-|.+.++.
T Consensus 129 ~~~g~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~ 163 (187)
T PRK12516 129 GASGFAYEEAAEICGCAVGTIKSRVNRARQRLQEI 163 (187)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34456677899999999999999887666655553
No 214
>cd08318 Death_NMPP84 Death domain of Nuclear Matrix Protein P84. Death domain (DD) found in the Nuclear Matrix Protein P84 (also known as HPR1 or THOC1). HPR1/p84 resides in the nuclear matrix and is part of the THO complex, also called TREX (transcription/export) complex, which functions in mRNP biogenesis at the interface between transcription and export of mRNA from the nucleus. Mice lacking THOC1 have abnormal testis development and are sterile. In general, 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=37.99 E-value=19 Score=21.72 Aligned_cols=17 Identities=18% Similarity=0.288 Sum_probs=14.3
Q ss_pred cchhccCCCHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWF 18 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~f 18 (120)
+||.++||++..|+...
T Consensus 23 ~Lar~LGls~~dI~~i~ 39 (86)
T cd08318 23 TLAPHLEMKDKEIRAIE 39 (86)
T ss_pred HHHHHcCCCHHHHHHHH
Confidence 68999999999997743
No 215
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=37.88 E-value=50 Score=23.33 Aligned_cols=35 Identities=11% Similarity=0.237 Sum_probs=27.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|++...|+.+...-+.+.|+.
T Consensus 197 ~~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 197 YQEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556778899999999999999987777666653
No 216
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=37.70 E-value=49 Score=22.48 Aligned_cols=34 Identities=12% Similarity=0.261 Sum_probs=25.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|++...|++-...-|.+.++
T Consensus 154 ~~eg~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 154 YLEELPHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred HHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999998877555555444
No 217
>cd08638 DNA_pol_A_theta DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis and in somatic hypermutation. DNA polymerase theta is a low-fidelity family A enzyme implicated in translesion synthesis (TLS) and in somatic hypermutation (SHM). DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Pol theta is an exception among family A polymerases and generates processive single base substitutions. Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondri
Probab=37.66 E-value=33 Score=26.42 Aligned_cols=28 Identities=21% Similarity=0.459 Sum_probs=22.5
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSK 36 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~ 36 (120)
||+.+|++.++.+.+..++. ..||....
T Consensus 214 La~~l~~s~~eA~~~i~~f~------~~~p~v~~ 241 (373)
T cd08638 214 LAEQLGVSEEEAKQFIESFK------NAYPGVRR 241 (373)
T ss_pred HHHHhCCCHHHHHHHHHHHH------HHCccHHH
Confidence 78889999999988888887 67776643
No 218
>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=37.32 E-value=45 Score=17.95 Aligned_cols=38 Identities=21% Similarity=0.260 Sum_probs=26.6
Q ss_pred cCCCHHHHHHHHhhhHhhhhhcccccch-hHHHHHhhhhcchhhhhh
Q psy4877 7 LNLTEVQIKTWFQNRRTKWKYVDKYLSV-SKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 7 ~~~~~~~~q~~fq~~r~k~~~~~~yp~~-~~r~~La~~~~l~~~~vq 52 (120)
.||+..|..+++--.. ++.. ....+||..++++...|.
T Consensus 1 ~glt~~q~~vL~~l~~--------~~~~~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 1 LGLTPSQFRVLMALAR--------HPGEELTQSELAERLGISKSTVS 39 (62)
T ss_dssp TTSTHHHHHHHHHHHH--------STTSGEEHHHHHHHHTS-HHHHH
T ss_pred CccCHHHHHHHHHHHH--------CCCCCcCHHHHHHHHCcCHHHHH
Confidence 4788888888776643 3433 467889999999886654
No 219
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=36.70 E-value=37 Score=17.56 Aligned_cols=19 Identities=32% Similarity=0.644 Sum_probs=13.0
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|..+...
T Consensus 20 eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 20 EIADILGISEKTVKTHLRN 38 (57)
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 5677777777777665543
No 220
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=36.70 E-value=32 Score=23.29 Aligned_cols=35 Identities=14% Similarity=0.131 Sum_probs=27.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-+++|..+|++...|.++...-|.+-|+.
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55667788999999999999998876666665553
No 221
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=36.63 E-value=71 Score=22.48 Aligned_cols=35 Identities=9% Similarity=0.084 Sum_probs=27.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-+++|..+|+++..|.+....-|.+.++.
T Consensus 147 y~eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 147 ELEDMSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45566778899999999999999887666665554
No 222
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.47 E-value=49 Score=22.15 Aligned_cols=34 Identities=24% Similarity=0.244 Sum_probs=25.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|.++...-|.+-+.
T Consensus 148 ~~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 148 YYQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455677889999999999999877655555443
No 223
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=36.41 E-value=40 Score=23.80 Aligned_cols=44 Identities=23% Similarity=0.158 Sum_probs=31.2
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
||+.+.+++.--.. ...-.++|..+++++..|+.+..|-..|..
T Consensus 156 Lt~rE~~Vl~l~~~-----------G~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~ 199 (216)
T PRK10100 156 LTHREKEILNKLRI-----------GASNNEIARSLFISENTVKTHLYNLFKKIA 199 (216)
T ss_pred CCHHHHHHHHHHHc-----------CCCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 67777777443321 455678999999999999998876655543
No 224
>cd08640 DNA_pol_A_plastid_like DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. DNA polymerase A type from plastids of higher plants possibly involve in DNA replication or in the repair of errors occurring during replication. Family A polymerase functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I ,mitochondrial polymerase delta, and several bacteriphage polymerases including
Probab=36.14 E-value=38 Score=26.21 Aligned_cols=29 Identities=10% Similarity=-0.010 Sum_probs=23.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSK 36 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~ 36 (120)
-||+.+|++.+..+....+++ +.||....
T Consensus 215 ~La~~lgis~~eA~~~i~~f~------~~fP~v~~ 243 (371)
T cd08640 215 GLAKDWKVKLKEAERTVDAWY------SDRPEVEQ 243 (371)
T ss_pred HHHHHcCCCHHHHHHHHHHHH------HHCccHHH
Confidence 378899999999988888887 67877743
No 225
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=35.89 E-value=26 Score=22.42 Aligned_cols=20 Identities=10% Similarity=0.278 Sum_probs=17.8
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
+||+.+|+++..++-+|...
T Consensus 30 ~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 30 KVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred HHHHHHCcCHHHHHHHHHHH
Confidence 68999999999999988875
No 226
>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=35.88 E-value=20 Score=19.79 Aligned_cols=19 Identities=42% Similarity=0.503 Sum_probs=13.2
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|||+.+|+++..|+....+
T Consensus 24 ela~~l~~S~rti~~~i~~ 42 (59)
T PF08280_consen 24 ELAKKLNISERTIKNDINE 42 (59)
T ss_dssp HHHHHCTS-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHHH
Confidence 6788888888888764444
No 227
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=35.82 E-value=46 Score=22.33 Aligned_cols=33 Identities=15% Similarity=0.346 Sum_probs=24.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|-....-+++|..+|+++..|.++...-+.+.|
T Consensus 146 ~~~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 146 YVDGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHcCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 444566788999999999999998765444443
No 228
>PF12833 HTH_18: Helix-turn-helix domain; PDB: 2K9S_A 3LSG_C 3OIO_A 1D5Y_B 3GBG_A 3OOU_A 1BL0_A 1XS9_A 3MN2_B 3MKL_B ....
Probab=35.68 E-value=30 Score=19.84 Aligned_cols=19 Identities=21% Similarity=0.387 Sum_probs=15.3
Q ss_pred chhccCCCHHHHHHHHhhh
Q psy4877 3 LSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~ 21 (120)
||+.+|+++..|+..|...
T Consensus 1 lA~~~~~s~~~l~~~f~~~ 19 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKKE 19 (81)
T ss_dssp HHHHCTS-HHHHHHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHHH
Confidence 6889999999999887774
No 229
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=35.50 E-value=47 Score=22.34 Aligned_cols=34 Identities=18% Similarity=0.337 Sum_probs=26.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|++....-|.+.++
T Consensus 135 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 135 VFYNLTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555677889999999999999987655655554
No 230
>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=35.32 E-value=26 Score=21.00 Aligned_cols=20 Identities=30% Similarity=0.547 Sum_probs=17.2
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
|+|+.+|++...|.-|...-
T Consensus 6 evA~~~gvs~~tLR~ye~~G 25 (88)
T cd01105 6 EVSKLTGVSPRQLRYWEEKG 25 (88)
T ss_pred HHHHHHCcCHHHHHHHHHCC
Confidence 68999999999999996653
No 231
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=35.26 E-value=69 Score=21.98 Aligned_cols=35 Identities=14% Similarity=0.079 Sum_probs=26.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|+++..|++....-|.+-|+.
T Consensus 152 ~~eg~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 186 (201)
T PRK12545 152 EFLDFEIDDICTELTLTANHCSVLLYRARTRLRTC 186 (201)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44556678899999999999999876555555553
No 232
>cd08319 Death_RAIDD Death domain of RIP-associated ICH-1 homologous protein with a death domain. Death domain (DD) of RAIDD (RIP-associated ICH-1 homologous protein with a death domain), also known as CRADD (Caspase and RIP adaptor). RAIDD is an adaptor protein that together with the p53-inducible protein PIDD and caspase-2, forms the PIDDosome complex, which is required for caspase-2 activation and plays a role in mediating stress-induced apoptosis. RAIDD contains an N-terminal Caspase Activation and Recruitment Domain (CARD), which interacts with the caspase-2 CARD, and a C-terminal DD, which interacts with the DD of PIDD. In general, 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, DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other pr
Probab=35.24 E-value=30 Score=20.83 Aligned_cols=19 Identities=21% Similarity=0.190 Sum_probs=15.7
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
.||..+||++.+|..+..+
T Consensus 18 ~Lar~Lgls~~~I~~i~~~ 36 (83)
T cd08319 18 QVLLDLGLSQTDIYRCKEN 36 (83)
T ss_pred HHHHHcCCCHHHHHHHHHh
Confidence 4788999999999886655
No 233
>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=35.17 E-value=29 Score=17.95 Aligned_cols=19 Identities=16% Similarity=0.492 Sum_probs=12.7
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|||+++|++...|....+.
T Consensus 22 ela~~~~is~~tv~~~l~~ 40 (48)
T PF13412_consen 22 ELAEKLGISRSTVNRYLKK 40 (48)
T ss_dssp HHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHhCCCHHHHHHHHHH
Confidence 6788888888777654443
No 234
>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=35.13 E-value=30 Score=19.52 Aligned_cols=17 Identities=18% Similarity=0.608 Sum_probs=10.7
Q ss_pred hhccCCCHHHHHHHHhh
Q psy4877 4 SKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~ 20 (120)
|.+.|+.+.+|+.|.+-
T Consensus 32 arkf~V~r~~Vr~W~kq 48 (58)
T PF09607_consen 32 ARKFNVSRRQVRKWRKQ 48 (58)
T ss_dssp HHHTTS-HHHHHHHHTT
T ss_pred HHHhCccHHHHHHHHHH
Confidence 45567777777777655
No 235
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=35.09 E-value=35 Score=23.31 Aligned_cols=34 Identities=26% Similarity=0.276 Sum_probs=26.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-.++|..+|++...|++-...-|.+.++
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999999877655555554
No 236
>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=35.04 E-value=35 Score=23.15 Aligned_cols=25 Identities=8% Similarity=0.267 Sum_probs=19.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~ 26 (120)
|+|+.+|+++..|++....-+.+.+
T Consensus 152 EIA~~lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 152 EIAEIMGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred HHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 7899999999999997776554333
No 237
>smart00351 PAX Paired Box domain.
Probab=35.00 E-value=33 Score=22.07 Aligned_cols=22 Identities=9% Similarity=0.125 Sum_probs=19.5
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
++|+++|++...|..|.+.++.
T Consensus 38 ~iA~~~gvs~~tV~kwi~r~~~ 59 (125)
T smart00351 38 DISRQLCVSHGCVSKILGRYYE 59 (125)
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999999988763
No 238
>COG3655 Predicted transcriptional regulator [Transcription]
Probab=34.88 E-value=53 Score=19.43 Aligned_cols=16 Identities=19% Similarity=0.478 Sum_probs=9.7
Q ss_pred cchhccCCCHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTW 17 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~ 17 (120)
+||+.+|+++..+.+.
T Consensus 20 eLa~~igis~~~ls~l 35 (73)
T COG3655 20 ELAEAIGISEANLSKL 35 (73)
T ss_pred HHHHHHcccHHHHHHH
Confidence 4666666666666553
No 239
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=34.82 E-value=44 Score=22.63 Aligned_cols=34 Identities=9% Similarity=-0.037 Sum_probs=24.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|++....-|.+.++
T Consensus 143 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 143 QLLGLSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4445667889999999999999987544444433
No 240
>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=34.81 E-value=71 Score=21.67 Aligned_cols=35 Identities=9% Similarity=0.044 Sum_probs=27.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-+++|..+|++...|++....-|.+-++.
T Consensus 144 ~~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 144 EVLGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred HHhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 55567788899999999999998776656555554
No 241
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=34.73 E-value=41 Score=21.95 Aligned_cols=34 Identities=15% Similarity=0.107 Sum_probs=25.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|+++...-|.+-++
T Consensus 125 ~~~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 125 DYYGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3445667889999999999999988655555443
No 242
>PRK13870 transcriptional regulator TraR; Provisional
Probab=34.46 E-value=44 Score=23.92 Aligned_cols=44 Identities=5% Similarity=-0.043 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
.||.++++++...-. +-.-.++|..+|++++.|.--.+|=+.|-
T Consensus 173 ~LT~RE~E~L~W~A~-----------GKT~~EIa~ILgISe~TV~~Hl~na~~KL 216 (234)
T PRK13870 173 WLDPKEATYLRWIAV-----------GKTMEEIADVEGVKYNSVRVKLREAMKRF 216 (234)
T ss_pred CCCHHHHHHHHHHHc-----------CCCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 355555555444322 34456789999999999998887776663
No 243
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=34.46 E-value=48 Score=23.77 Aligned_cols=45 Identities=13% Similarity=0.216 Sum_probs=31.2
Q ss_pred cCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 7 LNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 7 ~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
..||+.+++++..--. ...-.++|..+++++..|..-..|=+.|.
T Consensus 178 ~~LT~rE~evl~~~a~-----------G~t~~eIa~~l~is~~TV~~h~~~~~~KL 222 (240)
T PRK10188 178 MNFSKREKEILKWTAE-----------GKTSAEIAMILSISENTVNFHQKNMQKKF 222 (240)
T ss_pred CCCCHHHHHHHHHHHc-----------CCCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 3567777777554432 45567789999999999988766655553
No 244
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=34.05 E-value=51 Score=21.52 Aligned_cols=29 Identities=10% Similarity=0.141 Sum_probs=22.4
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
|.....-+++|..+|++...|+++...-+
T Consensus 126 ~~~g~s~~EIA~~l~is~~tV~~~l~ra~ 154 (161)
T PRK12528 126 QVDGLGYGEIATELGISLATVKRYLNKAA 154 (161)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 44556778899999999999998775433
No 245
>PF00531 Death: Death domain; InterPro: IPR000488 The death domain (DD) is a homotypic protein interaction module composed of a bundle of six alpha-helices. DD is related in sequence and structure to the death effector domain (DED, see IPR001875 from INTERPRO) and the caspase recruitment domain (CARD, see IPR001315 from INTERPRO), which work in similar pathways and show similar interaction properties []. DD bind each other forming oligomers. Mammals have numerous and diverse DD-containing proteins []. Within these proteins, the DD domains can be found in combination with other domains, including: CARDs, DEDs, ankyrin repeats (IPR002110 from INTERPRO), caspase-like folds, kinase domains, leucine zippers (IPR002158 from INTERPRO), leucine-rich repeats (LRR) (IPR001611 from INTERPRO), TIR domains (IPR000157 from INTERPRO), and ZU5 domains (IPR000906 from INTERPRO) []. Some DD-containing proteins are involved in the regulation of apoptosis and inflammation through their activation of caspases and NF-kappaB, which typically involves interactions with TNF (tumour necrosis factor) cytokine receptors [, ]. In humans, eight of the over 30 known TNF receptors contain DD in their cytoplasmic tails; several of these TNF receptors use caspase activation as a signalling mechanism. The DD mediates self-association of these receptors, thus giving the signal to downstream events that lead to apoptosis. Other DD-containing proteins, such as ankyrin, MyD88 and pelle, are probably not directly involved in cell death signalling. DD-containing proteins also have links to innate immunity, communicating with Toll family receptors through bipartite adapter proteins such as MyD88 [].; GO: 0005515 protein binding, 0007165 signal transduction; PDB: 3OQ9_L 3EZQ_F 1E41_A 1E3Y_A 2GF5_A 2OF5_L 3EWV_E 3G5B_A 3MOP_L 2A9I_A ....
Probab=34.03 E-value=32 Score=19.77 Aligned_cols=19 Identities=26% Similarity=0.403 Sum_probs=15.1
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
.||..+||++.+|+.+-..
T Consensus 17 ~La~~Lg~~~~~i~~i~~~ 35 (83)
T PF00531_consen 17 RLARKLGLSESEIENIEEE 35 (83)
T ss_dssp HHHHHTTS-HHHHHHHHHH
T ss_pred HHHHHhCcCHHHHHHHHHh
Confidence 5899999999999886664
No 246
>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=33.51 E-value=62 Score=21.12 Aligned_cols=32 Identities=19% Similarity=0.101 Sum_probs=23.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
|.....-.++|..+|+++..|.+...--|.+.
T Consensus 135 ~~~g~s~~eIA~~l~is~~tv~~~l~ra~~~L 166 (170)
T TIGR02952 135 FGQNLPIAEVARILGKTEGAVKILQFRAIKKL 166 (170)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45566778899999999999998664334333
No 247
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=33.49 E-value=64 Score=20.99 Aligned_cols=34 Identities=9% Similarity=0.191 Sum_probs=25.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-......++|..+|++...|......-+.+.++
T Consensus 122 ~~~~~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 122 RLHGETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445668889999999999999876544444444
No 248
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=33.24 E-value=62 Score=22.59 Aligned_cols=24 Identities=13% Similarity=0.339 Sum_probs=16.3
Q ss_pred HHHHhhhhcchhhhhhccccchhHH
Q psy4877 37 RMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 37 r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..+++..+||+...|.-|+ |+-.-
T Consensus 134 Q~~V~q~TGisQS~lSq~L-~kGt~ 157 (180)
T PF04814_consen 134 QREVVQVTGISQSHLSQHL-NKGTP 157 (180)
T ss_dssp CHHHHHHHT--HHHHHHHH-CTB--
T ss_pred HHHHHHHhhhhHHHHHHHH-HcCCC
Confidence 4457999999999999997 65433
No 249
>PF13551 HTH_29: Winged helix-turn helix
Probab=33.07 E-value=36 Score=20.63 Aligned_cols=22 Identities=18% Similarity=0.557 Sum_probs=18.8
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
++|+.+|++...|..|...++.
T Consensus 17 ~ia~~lg~s~~Tv~r~~~~~~~ 38 (112)
T PF13551_consen 17 EIARRLGISRRTVYRWLKRYRE 38 (112)
T ss_pred HHHHHHCcCHHHHHHHHHHHHc
Confidence 5788999999999999888763
No 250
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=33.07 E-value=93 Score=21.12 Aligned_cols=37 Identities=19% Similarity=0.274 Sum_probs=28.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLA 67 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~ 67 (120)
|-....-+++|..+|+++..|.++...-|.+.++...
T Consensus 141 ~~~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 141 VIGGFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999999988666666555443
No 251
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=33.03 E-value=64 Score=21.65 Aligned_cols=35 Identities=23% Similarity=0.391 Sum_probs=28.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|.....-.++|..+|++...|+.+...-|.+.++.
T Consensus 140 ~~~gls~~EIA~~l~i~~~tVks~l~ra~~~l~~~ 174 (182)
T COG1595 140 YLEGLSYEEIAEILGISVGTVKSRLHRARKKLREQ 174 (182)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556678899999999999999998777776664
No 252
>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=32.86 E-value=29 Score=22.47 Aligned_cols=21 Identities=19% Similarity=0.458 Sum_probs=18.2
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
|+|+.+|++...|..|++.-.
T Consensus 6 eVA~~~GVs~~TLR~wE~~GL 26 (120)
T cd04767 6 VVAELLNIHPETLRIWERHGL 26 (120)
T ss_pred HHHHHHCcCHHHHHHHHHCCC
Confidence 689999999999999987643
No 253
>COG1356 tfx Transcriptional regulator [DNA replication, recombination and repair]
Probab=32.77 E-value=27 Score=23.10 Aligned_cols=51 Identities=20% Similarity=0.181 Sum_probs=34.9
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
+++++=|||.||+|+--..+ +....++|..++-+..-|.. -.|||+.....
T Consensus 3 ~~~dtflte~qikvl~lRek-----------G~tQ~eIA~~L~TTraNvSa--IEkrA~enIek 53 (143)
T COG1356 3 TAMDTFLTEQQIKVLVLREK-----------GLTQSEIARILKTTRANVSA--IEKRALENIEK 53 (143)
T ss_pred cchhceeehhheeeeehhhc-----------cccHHHHHHHHccchhhHHH--HHHHHHHHHHH
Confidence 57888999999999433221 56678889988887765553 35666665543
No 254
>cd04790 HTH_Cfa-like_unk Helix-Turn-Helix DNA binding domain of putative Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulator; conserved, Cfa-like, unknown proteins (~172 a.a.). The N-terminal domain of these proteins appears to be related to the HTH domain of Cfa, a cyclopropane fatty acid synthase. These Cfa-like proteins have a unique C-terminal domain with conserved histidines (motif HXXFX7HXXF). Based on sequence similarity of the N-terminal domains, 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 domain
Probab=32.74 E-value=62 Score=22.06 Aligned_cols=42 Identities=17% Similarity=0.275 Sum_probs=31.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
+|.+.+|+++..+..|-+.|. ..-|+.+ .+.-..+|+++..+
T Consensus 123 ~l~~~~g~~~~~m~~wh~~fe------~~~p~~h--~~~l~~~g~~~~~~ 164 (172)
T cd04790 123 AILKAAGMDEADMRRWHIEFE------KMEPEAH--QEFLQSLGIPEDEI 164 (172)
T ss_pred HHHHHcCCChHHHHHHHHHHH------HhCcHHH--HHHHHHcCCCHHHH
Confidence 466778999999999999987 5666665 34557778887654
No 255
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=32.45 E-value=64 Score=23.27 Aligned_cols=34 Identities=18% Similarity=0.257 Sum_probs=26.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|..+...-+.|.|+
T Consensus 216 y~~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 216 FLHDLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred HHCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4456678899999999999999988655555554
No 256
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=32.35 E-value=56 Score=21.72 Aligned_cols=33 Identities=12% Similarity=0.134 Sum_probs=25.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|.....-+++|..+|++...|+++...-+.+.+
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 555677889999999999999998754444443
No 257
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=32.24 E-value=36 Score=21.67 Aligned_cols=22 Identities=9% Similarity=0.226 Sum_probs=19.5
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
++|.++|++...|-.|-+.++.
T Consensus 34 evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 34 LVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred HHHHHHCcCHHHHHHHHHHHhh
Confidence 6899999999999999888763
No 258
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=32.18 E-value=51 Score=21.94 Aligned_cols=34 Identities=26% Similarity=0.375 Sum_probs=26.3
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|++...|.+....-|.+.++
T Consensus 149 ~~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 149 YIEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred HhhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999998877666665554
No 259
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=32.03 E-value=88 Score=21.71 Aligned_cols=36 Identities=11% Similarity=0.181 Sum_probs=27.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
|-....-.++|..+|++...|.+....-|.+-|+..
T Consensus 161 ~~~g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 161 EFIELETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 344555688999999999999998876666666643
No 260
>PF13744 HTH_37: Helix-turn-helix domain; PDB: 2A6C_B 2O38_A.
Probab=31.83 E-value=61 Score=18.94 Aligned_cols=17 Identities=18% Similarity=0.319 Sum_probs=7.5
Q ss_pred cchhccCCCHHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTWF 18 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~f 18 (120)
++|+++|++..+|....
T Consensus 36 e~A~~lgisq~~vS~l~ 52 (80)
T PF13744_consen 36 ELAERLGISQPRVSRLE 52 (80)
T ss_dssp HHHHHHTS-HHHHHHHH
T ss_pred HHHHHHCCChhHHHHHH
Confidence 34445555554444433
No 261
>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=31.77 E-value=33 Score=21.00 Aligned_cols=56 Identities=23% Similarity=0.185 Sum_probs=33.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh--hhcc--cccchhH--HHHH---hh-hhcchhhhhhccccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW--KYVD--KYLSVSK--RMEL---SK-LLNLTEVQIKTWFQN 57 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~--~~~~--~yp~~~~--r~~L---a~-~~~l~~~~vqvWFqN 57 (120)
|+|+.+|++...|.-|...---.- +..+ ++-+... +-.+ .. .+|++-..|+..+..
T Consensus 5 eva~~~gvs~~tlR~Ye~~GLl~p~~r~~~g~r~Y~~~dv~~l~~I~~L~~~~G~~l~~I~~~l~~ 70 (95)
T cd04780 5 ELSKRSGVSVATIKYYLREGLLPEGRRLAPNQAEYSEAHVERLRLIRALQQEGGLPISQIKEVLDA 70 (95)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCCeecCHHHHHHHHHHHHHHHHcCCCHHHHHHHHHh
Confidence 789999999999999887643221 1011 1111111 1111 23 378888888887765
No 262
>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=31.70 E-value=27 Score=23.62 Aligned_cols=33 Identities=24% Similarity=0.200 Sum_probs=25.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|-....-.++|..+|++...|.+.+..-|.+-+
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~ 194 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLE 194 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556677788999999999999987765454443
No 263
>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=31.69 E-value=19 Score=24.83 Aligned_cols=37 Identities=14% Similarity=0.306 Sum_probs=29.9
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHHHHHHHHHHHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKLK 71 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~~ 71 (120)
-...+|+.-++++..+|-+|-.|-+...++..+.+..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yKhA 51 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYKHA 51 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccchhhHH
Confidence 3577899999999999999999998887775554443
No 264
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=31.64 E-value=82 Score=20.44 Aligned_cols=34 Identities=9% Similarity=0.131 Sum_probs=24.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-.....+++|..+|+++..|.+....-+.+.+.
T Consensus 118 ~~~~~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~ 151 (159)
T PRK12527 118 KLEGLSHQQIAEHLGISRSLVEKHIVNAMKHCRV 151 (159)
T ss_pred HHcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4455677889999999999999877644444444
No 265
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=31.57 E-value=85 Score=16.55 Aligned_cols=19 Identities=0% Similarity=0.225 Sum_probs=9.8
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
++|+..|++...|.-.+-+
T Consensus 4 dIA~~agvS~~TVSr~ln~ 22 (46)
T PF00356_consen 4 DIAREAGVSKSTVSRVLNG 22 (46)
T ss_dssp HHHHHHTSSHHHHHHHHTT
T ss_pred HHHHHHCcCHHHHHHHHhC
Confidence 3455555555555544444
No 266
>PRK10403 transcriptional regulator NarP; Provisional
Probab=31.52 E-value=53 Score=21.63 Aligned_cols=28 Identities=21% Similarity=0.338 Sum_probs=22.2
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
..++++|..++++++.|.+...|=+.|-
T Consensus 169 ~s~~~ia~~l~~s~~tv~~~~~~i~~kl 196 (215)
T PRK10403 169 LSNKQIASVLNISEQTVKVHIRNLLRKL 196 (215)
T ss_pred CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 5577899999999999988776665553
No 267
>PF07813 LTXXQ: LTXXQ motif family protein; InterPro: IPR012899 This five residue motif is found in a number of bacterial proteins bearing similarity to the protein CpxP (P32158 from SWISSPROT). This is a periplasmic protein that aids in combating extracytoplasmic protein-mediated toxicity, and may also be involved in the response to alkaline pH []. Another member of this family, Spy (P77754 from SWISSPROT) is also a periplasmic protein that may be involved in the response to stress []. The homology between CpxP and Spy may indicate that these two proteins are functionally related []. The motif is found repeated twice in many members of this entry. ; GO: 0042597 periplasmic space; PDB: 3ITF_B 3QZC_B 3OEO_D 3O39_A.
Probab=31.45 E-value=35 Score=20.31 Aligned_cols=21 Identities=38% Similarity=0.517 Sum_probs=14.6
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
.|...|+||++|.+.|..=+.
T Consensus 8 ~l~~~L~LT~eQ~~~~~~i~~ 28 (100)
T PF07813_consen 8 RLKEELNLTDEQKAKWRAIRQ 28 (100)
T ss_dssp STTTTS--THHHHHHHHHHHH
T ss_pred HHHhhCCCCHHHHHHHHHHHH
Confidence 467899999999998765544
No 268
>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=31.42 E-value=34 Score=20.56 Aligned_cols=54 Identities=9% Similarity=0.086 Sum_probs=31.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhc-c--c-ccch-----hHHHHHhhhhcchhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV-D--K-YLSV-----SKRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~-~--~-yp~~-----~~r~~La~~~~l~~~~vqvWF 55 (120)
++|+.+|++...|.-|.+.-.-+-.+. + . |... .....|...+|++...|+.-+
T Consensus 6 e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 6 VAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred HHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 689999999999999987644332111 1 1 2221 112223344788887776554
No 269
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=31.17 E-value=59 Score=21.47 Aligned_cols=33 Identities=12% Similarity=0.086 Sum_probs=24.7
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|-....-+++|..+|+++..|+.+..+-+.+.+
T Consensus 131 ~~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 131 QLEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 444566788999999999999987755555544
No 270
>PF13730 HTH_36: Helix-turn-helix domain
Probab=30.86 E-value=89 Score=16.44 Aligned_cols=20 Identities=15% Similarity=0.197 Sum_probs=16.7
Q ss_pred HHHHHhhhhcchhhhhhccc
Q psy4877 36 KRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWF 55 (120)
-.+.||..+|++.+.|+.+.
T Consensus 27 S~~~la~~~g~s~~Tv~~~i 46 (55)
T PF13730_consen 27 SQETLAKDLGVSRRTVQRAI 46 (55)
T ss_pred CHHHHHHHHCcCHHHHHHHH
Confidence 47789999999998888665
No 271
>PF00476 DNA_pol_A: DNA polymerase family A; InterPro: IPR001098 Synonym(s): DNA nucleotidyltransferase (DNA-directed) DNA-directed DNA polymerases(2.7.7.7 from EC) are the key enzymes catalysing the accurate replication of DNA. They require either a small RNA molecule or a protein as a primer for the de novo synthesis of a DNA chain. A number of polymerases belong to this family [, , ].; GO: 0003677 DNA binding, 0003887 DNA-directed DNA polymerase activity, 0006260 DNA replication; PDB: 1TKD_A 1TK5_A 2AJQ_F 1T8E_A 1T7P_A 1SKR_A 1X9W_A 1TK8_A 1TK0_A 1SL2_A ....
Probab=30.83 E-value=39 Score=26.06 Aligned_cols=31 Identities=23% Similarity=0.299 Sum_probs=24.7
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRM 38 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~ 38 (120)
-||+.+|+++++.+.+.+++. +.||....-.
T Consensus 228 ~la~~l~~s~~eA~~~~~~f~------~~~p~v~~~~ 258 (383)
T PF00476_consen 228 GLAEQLGISEEEAKELIDAFF------EAFPGVKKWM 258 (383)
T ss_dssp HHHHHHTSCHHHHHHHHHHHH------HHSHHHHHHH
T ss_pred HHHHHccCCHHHHHHHHHHHH------HhCchHHHHH
Confidence 378899999999999998887 6788764433
No 272
>COG1513 CynS Cyanate lyase [Inorganic ion transport and metabolism]
Probab=30.77 E-value=89 Score=20.79 Aligned_cols=42 Identities=24% Similarity=0.294 Sum_probs=27.7
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQI 51 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~v 51 (120)
+|+..+|+.+.-+-..|=. +.-.+..+-+.+++.++|++.-|
T Consensus 26 Dl~~~lG~~ev~vaa~~yg--------qa~~~~~ear~v~e~L~L~~~~v 67 (151)
T COG1513 26 DLADGLGLAEVFVAAALYG--------QAALPADEARAVGEALDLDEDAI 67 (151)
T ss_pred HHHhhcCccHHHHHHHHHh--------hccCCHHHHHHHHHHhCCCHHHH
Confidence 4666777777777665555 33444556666788888888544
No 273
>PF07037 DUF1323: Putative transcription regulator (DUF1323); InterPro: IPR010749 This family consists of several hypothetical Enterobacterial proteins of around 120 residues in length. The function of this family is unknown.
Probab=30.17 E-value=37 Score=22.11 Aligned_cols=24 Identities=29% Similarity=0.680 Sum_probs=19.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY 27 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~ 27 (120)
|||+.||++.-.|..|-.. -.|+.
T Consensus 5 ELA~~tG~srQTINrWvRk--egW~T 28 (122)
T PF07037_consen 5 ELAELTGYSRQTINRWVRK--EGWKT 28 (122)
T ss_pred HHHHHhCccHHHHHHHHHh--cCcee
Confidence 7999999999999999765 34553
No 274
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=30.04 E-value=42 Score=22.66 Aligned_cols=34 Identities=9% Similarity=0.241 Sum_probs=26.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|.++...-+.+-|+
T Consensus 147 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 147 FVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455677889999999999999988766665555
No 275
>cd08637 DNA_pol_A_pol_I_C Polymerase I functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. Family A polymerase (polymerase I) functions primarily to fill DNA gaps that arise during DNA repair, recombination and replication. DNA-dependent DNA polymerases can be classified in six main groups based upon phylogenetic relationships with E. coli polymerase I (classA), E. coli polymerase II (class B), E.coli polymerase III (class C), euryarchaaeota polymerase II (class D), human polymerase beta (class x), E. coli UmuC/DinB and eukaryotic RAP 30/Xeroderma pigmentosum variant (class Y). Family A polymerase are found primarily in organisms related to prokaryotes and include prokaryotic DNA polymerase I (pol I) ,mitochondrial polymerase delta, and several bacteriphage polymerases including those from odd-numbered phage (T3, T5, and T7). Prokaryotic Pol Is have two functional domains located on the same polypeptide; a 5'-3' polymerase and 5'-3' exonuc
Probab=29.94 E-value=55 Score=25.26 Aligned_cols=28 Identities=21% Similarity=0.380 Sum_probs=21.9
Q ss_pred chhccCCCHHHHHHHHhhhHhhhhhcccccchhH
Q psy4877 3 LSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSK 36 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~ 36 (120)
||+.+|+++++.+.+..+++ ..||....
T Consensus 225 la~~lg~s~~eA~~~~~~f~------~~~p~v~~ 252 (377)
T cd08637 225 LSQQLGISRKEAKEYIDRYF------ARYPGVKE 252 (377)
T ss_pred HHHHcCCCHHHHHHHHHHHH------HHCccHHH
Confidence 67888999988888888887 56777643
No 276
>cd08803 Death_ank3 Death domain of Ankyrin-3. Death Domain (DD) of the human protein ankyrin-3 (ANK-3) and related proteins. Ankyrins are modular proteins comprising three conserved domains, an N-terminal membrane-binding domain containing ANK repeats, a spectrin-binding domain and a C-terminal DD. ANK-3, also called anykyrin-G (for general or giant), is found in neurons and at least one splice variant has been shown to be essential for propagation of action potentials as a binding partner to neurofascin and voltage-gated sodium channels. It is required for maintaining axo-dendritic polarity, and may be a genetic risk factor associated with bipolar disorder. ANK-3 may also play roles in other cell types. Mutations affecting ANK-3 pathways for Na channel localization are associated with Brugada syndrome, a potentially fata arrythmia. In general, DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by se
Probab=29.93 E-value=37 Score=20.46 Aligned_cols=16 Identities=31% Similarity=0.414 Sum_probs=14.1
Q ss_pred cchhccCCCHHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKTW 17 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~ 17 (120)
+||..+||++..|...
T Consensus 20 ~LA~eLg~s~~dI~~i 35 (84)
T cd08803 20 ELARELNFSVDEINQI 35 (84)
T ss_pred HHHHHcCCCHHHHHHH
Confidence 6899999999999774
No 277
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=29.61 E-value=34 Score=22.65 Aligned_cols=35 Identities=23% Similarity=0.257 Sum_probs=26.6
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
+|.....-+++|..+|++...|..+...-|.+.++
T Consensus 138 ~~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 138 KHYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 35566778899999999999998877655555444
No 278
>smart00005 DEATH DEATH domain, found in proteins involved in cell death (apoptosis). Alpha-helical domain present in a variety of proteins with apoptotic functions. Some (but not all) of these domains form homotypic and heterotypic dimers.
Probab=29.57 E-value=44 Score=19.55 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=15.3
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||.++||++..|...-.+
T Consensus 22 ~la~~Lg~~~~~i~~i~~~ 40 (88)
T smart00005 22 ELARKLGLSEADIDQIRTE 40 (88)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5899999999998775544
No 279
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=29.56 E-value=57 Score=21.83 Aligned_cols=34 Identities=21% Similarity=0.303 Sum_probs=26.1
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|++...|..+...-|.+.+.
T Consensus 140 ~~~g~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 140 YYEELSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999999987655555444
No 280
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=29.51 E-value=46 Score=23.45 Aligned_cols=37 Identities=22% Similarity=0.267 Sum_probs=29.3
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQL 66 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~~ 66 (120)
+|.....-+++|..+|++...|.+....-|.+.|+..
T Consensus 161 ~~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 161 RVVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred ehhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3666778889999999999999988766666666643
No 281
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=29.49 E-value=70 Score=21.08 Aligned_cols=34 Identities=12% Similarity=0.134 Sum_probs=25.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|+.....-|.+.|+
T Consensus 131 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 131 YYRGWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4445667889999999999999877544544444
No 282
>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=29.38 E-value=45 Score=18.86 Aligned_cols=21 Identities=14% Similarity=0.428 Sum_probs=17.1
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
++|.++|++...|-.|-..++
T Consensus 28 ~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 28 EVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp HHHHHHTS-HHHHHHHHHHHH
T ss_pred eeecccccccccccHHHHHHh
Confidence 578899999999999988875
No 283
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=29.18 E-value=75 Score=22.73 Aligned_cols=34 Identities=9% Similarity=0.240 Sum_probs=25.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|..|...-+.+-|+
T Consensus 218 ~~~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 218 FIENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred HhCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455667889999999999999987655555444
No 284
>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=29.15 E-value=38 Score=20.86 Aligned_cols=57 Identities=7% Similarity=0.000 Sum_probs=34.8
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh-hhccc--ccchhHHHH-----Hhhhhcchhhhhhccccch
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW-KYVDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~-~~~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFqNr 58 (120)
|+|+.+|++...|.-|.+.---.- +..+- +-+...-.. ....+|++-..|...+...
T Consensus 6 eva~~~gvs~~tLR~ye~~Gll~~~r~~~g~R~Y~~~dl~~l~~I~~l~~~G~~l~ei~~~~~~~ 70 (102)
T cd04775 6 QMSRKFGVSRSTLLYYESIGLIPSARSEANYRLYSEADLSRLEKIVFLQAGGLPLEEIAGCLAQP 70 (102)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCCCCCCeeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC
Confidence 689999999999999887633211 11121 122221111 2477788888888776554
No 285
>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=28.94 E-value=79 Score=22.06 Aligned_cols=34 Identities=21% Similarity=0.299 Sum_probs=24.9
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|++...|..+...-+.+-|+
T Consensus 188 y~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 188 YYEELNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred HhCCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4445567889999999999998877654544443
No 286
>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=28.85 E-value=38 Score=21.17 Aligned_cols=56 Identities=18% Similarity=0.160 Sum_probs=34.7
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh--cc--cccchhHHHH-----Hhhhhcchhhhhhccccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY--VD--KYLSVSKRME-----LSKLLNLTEVQIKTWFQN 57 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~--~~--~yp~~~~r~~-----La~~~~l~~~~vqvWFqN 57 (120)
|+|+.+|++...|.-|.+.-.-.-.+ .+ +|-+...-.. ....+|++-..|+.++..
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~~~~~g~R~Y~~~dl~~l~~I~~lr~~G~~l~~I~~~l~~ 69 (108)
T cd04773 5 ELAHLLGVPPSTLRHWEKEGLLSPDREPETGYRVYDPSDVRDARLIHLLRRGGYLLEQIATVVEQ 69 (108)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCceeeCHHHHHHHHHHHHHHHCCCCHHHHHHHHHH
Confidence 68999999999999998865432211 11 1122222222 246678888888877653
No 287
>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=28.77 E-value=32 Score=18.29 Aligned_cols=15 Identities=27% Similarity=0.439 Sum_probs=9.8
Q ss_pred cchhccCCCHHHHHH
Q psy4877 2 ELSKLLNLTEVQIKT 16 (120)
Q Consensus 2 ~la~~~~~~~~~~q~ 16 (120)
|||+.+|+++..|..
T Consensus 20 eLa~~l~vS~rTi~~ 34 (55)
T PF08279_consen 20 ELAEELGVSRRTIRR 34 (55)
T ss_dssp HHHHHCTS-HHHHHH
T ss_pred HHHHHhCCCHHHHHH
Confidence 577777777777644
No 288
>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=28.64 E-value=39 Score=20.41 Aligned_cols=59 Identities=15% Similarity=0.142 Sum_probs=33.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhc---ccccchhHHHH-----HhhhhcchhhhhhccccchhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYV---DKYLSVSKRME-----LSKLLNLTEVQIKTWFQNRRT 60 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~---~~yp~~~~r~~-----La~~~~l~~~~vqvWFqNrRa 60 (120)
|+|+.+|++...|.-|.+.-.-.-.+. ..+-+...-.. -....|++...|...+.....
T Consensus 5 eva~~~gi~~~tlr~~~~~Gll~~~~~~~g~r~y~~~dv~~l~~i~~l~~~g~~~~~i~~~l~~~~~ 71 (100)
T cd00592 5 EVAKLLGVSVRTLRYYEEKGLLPPERSENGYRLYSEEDLERLRLIRRLRELGLSLKEIRELLDARDE 71 (100)
T ss_pred HHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCcccCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcccc
Confidence 689999999999999977644321110 01111111111 123378888887766655443
No 289
>KOG2252|consensus
Probab=28.47 E-value=35 Score=27.89 Aligned_cols=24 Identities=29% Similarity=0.430 Sum_probs=21.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW 25 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~ 25 (120)
+|+..|||.-..|..||-|.|.|.
T Consensus 452 tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 452 TISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred HHHHHhCCcHHHHHHHHHhhhhhc
Confidence 688999999999999999988654
No 290
>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=28.40 E-value=18 Score=16.12 Aligned_cols=8 Identities=38% Similarity=1.161 Sum_probs=5.9
Q ss_pred ccccchhH
Q psy4877 53 TWFQNRRT 60 (120)
Q Consensus 53 vWFqNrRa 60 (120)
+||-|+..
T Consensus 7 NWFE~~ge 14 (22)
T PF08452_consen 7 NWFESRGE 14 (22)
T ss_pred ehhhhCCc
Confidence 69988763
No 291
>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=28.31 E-value=61 Score=15.88 Aligned_cols=21 Identities=14% Similarity=0.322 Sum_probs=14.1
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
+||..+|++.+-|--.+...+
T Consensus 7 diA~~lG~t~ETVSR~l~~l~ 27 (32)
T PF00325_consen 7 DIADYLGLTRETVSRILKKLE 27 (32)
T ss_dssp HHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHhCCcHHHHHHHHHHHH
Confidence 578888888888766555543
No 292
>cd01798 parkin_N amino-terminal ubiquitin-like of parkin protein. parkin_N parkin protein is a RING-type E3 ubiquitin ligase with an amino-terminal ubiquitin-like (Ubl) domain and an RBR signature consisting of two RING finger domains separated by an IBR/DRIL domain. Naturally occurring mutations in parkin are thought to cause the disease AR_JP (autosomal-recessive juvenile parkinsonism). Parkin binds the Rpn10 subunit of 26S proteasomes through its Ubl domain.
Probab=28.23 E-value=40 Score=18.98 Aligned_cols=26 Identities=12% Similarity=0.175 Sum_probs=21.8
Q ss_pred hHHHHHhhhhcchhhhhhccccchhH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRT 60 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRa 60 (120)
..+..++...|++..++..+|.++.-
T Consensus 23 ~lK~~i~~~~gi~~~~q~Li~~G~~L 48 (70)
T cd01798 23 QLKEVVAKRQGVPPDQLRVIFAGKEL 48 (70)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCeEC
Confidence 56777899999999999999987763
No 293
>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=28.03 E-value=80 Score=20.98 Aligned_cols=33 Identities=9% Similarity=0.094 Sum_probs=24.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|.....-.++|..+|++...|.+=...-|.+.|
T Consensus 153 ~~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr 185 (189)
T TIGR02984 153 HLEGLSFAEVAERMDRSEGAVSMLWVRGLARLR 185 (189)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 556677888999999999999875554444444
No 294
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.97 E-value=93 Score=21.05 Aligned_cols=34 Identities=9% Similarity=0.065 Sum_probs=25.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-+++|..+|+++..|.++...-|.+-++
T Consensus 124 ~~eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 124 AIEGLSYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred HHcCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 4456678889999999999999987655555444
No 295
>cd01796 DDI1_N DNA damage inducible protein 1 ubiquitin-like domain. DDI1_N DDI1 (DNA damage inducible protein 1) has an amino-terminal ubiquitin-like domain, an retroviral protease-like (RVP-like) domain, and a UBA (ubiquitin-associated) domain. This CD represents the amino-terminal ubiquitin-like domain of DDI1.
Probab=27.84 E-value=41 Score=19.19 Aligned_cols=27 Identities=7% Similarity=0.003 Sum_probs=21.8
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..+..++...|++..+..+||..+--.
T Consensus 24 ~lK~~I~~~~gip~~~q~Li~~Gk~L~ 50 (71)
T cd01796 24 NFKALCEAESGIPASQQQLIYNGRELV 50 (71)
T ss_pred HHHHHHHHHhCCCHHHeEEEECCeEcc
Confidence 567778899999999999999766443
No 296
>COG1427 Predicted periplasmic solute-binding protein [General function prediction only]
Probab=27.83 E-value=51 Score=24.27 Aligned_cols=21 Identities=29% Similarity=0.521 Sum_probs=17.1
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
++|+++|++..-++.+|.+.+
T Consensus 203 ~~a~~lglp~~~~~eYy~~~~ 223 (252)
T COG1427 203 EAAKRLGLPRSDVEEYYTNIR 223 (252)
T ss_pred HHHHHcCCCHHHHHHHHHHhe
Confidence 467888888888888888865
No 297
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=27.80 E-value=53 Score=17.13 Aligned_cols=17 Identities=12% Similarity=0.333 Sum_probs=9.4
Q ss_pred chhccCCCHHHHHHHHh
Q psy4877 3 LSKLLNLTEVQIKTWFQ 19 (120)
Q Consensus 3 la~~~~~~~~~~q~~fq 19 (120)
+|+.+|++...|.-+|.
T Consensus 33 vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 33 VARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHCCCHHHHHHHHH
Confidence 45555666665555543
No 298
>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=27.69 E-value=42 Score=20.63 Aligned_cols=58 Identities=14% Similarity=0.103 Sum_probs=36.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh--hhc--ccccchhHHHH-----Hhhhhcchhhhhhccccchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW--KYV--DKYLSVSKRME-----LSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~--~~~--~~yp~~~~r~~-----La~~~~l~~~~vqvWFqNrR 59 (120)
|+|+.+|++...|.-|+..-...- +.. .++-+...... ....+|++-..|+.++....
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~~~~~~~~g~R~y~~~di~~l~~i~~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 5 EVAKLTGVSVRTLHYYDEIGLLKPSRRTENGYRLYTEEDLERLQQILFLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHHcCc
Confidence 689999999999999877633211 111 12222222222 24667999999998887764
No 299
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=27.68 E-value=52 Score=23.13 Aligned_cols=33 Identities=15% Similarity=0.169 Sum_probs=25.1
Q ss_pred cchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 32 p~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
-....-+++|..+|+++..|+.+...-+.+-|+
T Consensus 196 ~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 196 GEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345567889999999999999877655555554
No 300
>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=27.63 E-value=42 Score=14.88 Aligned_cols=20 Identities=10% Similarity=0.320 Sum_probs=15.5
Q ss_pred HHHHHhhhhcchhhhhhccc
Q psy4877 36 KRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWF 55 (120)
...++|..++++...|..|.
T Consensus 23 s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 23 SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CHHHHHHHHCCCHHHHHHhC
Confidence 56678889999888877663
No 301
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.52 E-value=54 Score=23.35 Aligned_cols=25 Identities=12% Similarity=0.412 Sum_probs=19.7
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWK 26 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~ 26 (120)
|+|+.+|+++..|++....-+.|.+
T Consensus 192 EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 192 EIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred HHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 7899999999999997766554444
No 302
>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=27.49 E-value=41 Score=20.61 Aligned_cols=56 Identities=13% Similarity=0.013 Sum_probs=32.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh---cccccchhHHH------HHhhhhcchhhhhhccccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY---VDKYLSVSKRM------ELSKLLNLTEVQIKTWFQN 57 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~---~~~yp~~~~r~------~La~~~~l~~~~vqvWFqN 57 (120)
|+|+.+|++...|.-|.+.-.-.-.+ -.+|-+...-. .|....|++-..|+..+..
T Consensus 6 eva~~~gVs~~tLR~ye~~Gli~p~r~~~g~R~Ys~~dv~~l~~I~~L~~~~G~~l~~i~~~l~l 70 (98)
T cd01279 6 VAAELLGIHPQTLRVYDRLGLVSPARTNGGGRRYSNNDLELLRQVQRLSQDEGFNLAGIKRIIEL 70 (98)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeeECHHHHHHHHHHHHHHHHCCCCHHHHHHHHHh
Confidence 68999999999999997764322111 11122222111 2233478888888866543
No 303
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.47 E-value=42 Score=21.58 Aligned_cols=25 Identities=24% Similarity=0.323 Sum_probs=21.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccc
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWF 55 (120)
-.+...|.+||.++|+++..|.-|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 4556778889999999999999884
No 304
>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=27.44 E-value=42 Score=20.43 Aligned_cols=58 Identities=16% Similarity=0.175 Sum_probs=37.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh--ccc--ccchhHHHH-----Hhhhhcchhhhhhccccchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY--VDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~--~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFqNrR 59 (120)
|+|+.+|++...|.-|++.-.-.-.+ .+. |-+...-.. ....+|++-..|+-.+.+.-
T Consensus 5 eva~~~gvs~~tLRyye~~Gll~p~~~~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~~I~~~l~~~~ 71 (96)
T cd04768 5 EFAKLAGVSIRTLRHYDDIGLFKPAKIAENGYRYYSYAQLYQLQFILFLRELGFSLAEIKELLDTEM 71 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCCCCeeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcCc
Confidence 68999999999999999874332211 122 222222222 35778999988888776643
No 305
>PHA00675 hypothetical protein
Probab=27.34 E-value=1.1e+02 Score=18.32 Aligned_cols=37 Identities=11% Similarity=0.059 Sum_probs=26.1
Q ss_pred cCCCHHHHHHHHhhh-HhhhhhcccccchhHHHHHhhhhcchhhhhhc
Q psy4877 7 LNLTEVQIKTWFQNR-RTKWKYVDKYLSVSKRMELSKLLNLTEVQIKT 53 (120)
Q Consensus 7 ~~~~~~~~q~~fq~~-r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqv 53 (120)
-.|++.+|+..+.-+ +. ...-..||.++|++..-|+.
T Consensus 21 AKLt~~qV~~IR~l~~r~----------G~s~~~IA~~fGVsrstV~~ 58 (78)
T PHA00675 21 AKLTDAEVERIRELHEVE----------GMSYAVLAEKFEQSKGAIAK 58 (78)
T ss_pred cccCHHHHHHHHHHHHhc----------CccHHHHHHHhCCCHHHHHH
Confidence 368888888766554 31 33455789999999987763
No 306
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=27.13 E-value=75 Score=20.94 Aligned_cols=28 Identities=18% Similarity=0.089 Sum_probs=22.4
Q ss_pred hhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
...++++|..++++.+.|+++-.+=|.|
T Consensus 164 g~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 164 GLSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3668889999999999999877665555
No 307
>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=27.06 E-value=43 Score=21.58 Aligned_cols=54 Identities=4% Similarity=-0.013 Sum_probs=31.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh--ccc---ccch-hHHHH---Hhhhhcchhhhhhccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY--VDK---YLSV-SKRME---LSKLLNLTEVQIKTWF 55 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~--~~~---yp~~-~~r~~---La~~~~l~~~~vqvWF 55 (120)
|||+++|++...|.-|.+.=-..-.+ .+- |... ..+-. .+..+|++-..|+..+
T Consensus 8 elA~~~gvs~~tlR~Ye~~GLL~p~~r~~~gyR~Y~~~~l~rL~~I~~lr~~G~~L~eI~~ll 70 (120)
T TIGR02054 8 RLAEDAGVSVHVVRDYLLRGLLHPVRRTTSGYGIFDDASLQRLRFVRAAFEAGIGLGELARLC 70 (120)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCeeCCHHHHHHHHHHHHHHHcCCCHHHHHHHH
Confidence 78999999999999988764322111 111 2111 11222 2466788777776543
No 308
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=26.82 E-value=85 Score=22.47 Aligned_cols=33 Identities=15% Similarity=0.177 Sum_probs=25.4
Q ss_pred chhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 33 SVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 33 ~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
....-.++|..+|+++..|+++...-|.+-+..
T Consensus 131 eg~S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 131 FQYSIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred hCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999886666665553
No 309
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=26.80 E-value=90 Score=20.92 Aligned_cols=34 Identities=12% Similarity=0.004 Sum_probs=26.8
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|+.+...-+.+.++
T Consensus 144 ~~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 144 KLEGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred HHcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4556778889999999999999988665655554
No 310
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.72 E-value=1.3e+02 Score=18.59 Aligned_cols=39 Identities=26% Similarity=0.202 Sum_probs=23.3
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhh
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIK 52 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vq 52 (120)
|..+|++.=-+..++ |--.+....+++|..++.++..|+
T Consensus 3 Ln~eq~~~Tk~elqa-----n~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 3 LNPEQKQRTKQELQA-----NFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCHHHHHHHHHHHHH-----hhhhccccHHHHHHHhCCCHHHHH
Confidence 445555443333332 334455677888999998886655
No 311
>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=26.64 E-value=46 Score=20.55 Aligned_cols=57 Identities=9% Similarity=0.016 Sum_probs=34.0
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh-ccc---ccch----hHHHHHhhhhcchhhhhhccccch
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY-VDK---YLSV----SKRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~-~~~---yp~~----~~r~~La~~~~l~~~~vqvWFqNr 58 (120)
|+|+.+|++...|.-|.+.-.-.-.+ .+- |... .........+|++-..|+-.+.+.
T Consensus 6 eva~~~gvs~~tlR~ye~~Gll~~~r~~~g~R~Y~~~~l~~l~~I~~l~~~G~~l~ei~~~l~~~ 70 (102)
T cd04789 6 ELAEKAGISRSTLLYYEKLGLITGTRNANGYRLYPDSDLQRLLLIQQLQAGGLSLKECLACLQGK 70 (102)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeeCCHHHHHHHHHHHHHHHCCCCHHHHHHHHcCC
Confidence 68999999999999888764332111 111 1111 111123567788888887766543
No 312
>PRK10651 transcriptional regulator NarL; Provisional
Probab=26.64 E-value=73 Score=21.02 Aligned_cols=43 Identities=16% Similarity=0.084 Sum_probs=29.3
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
||+.+.++..--- ....-+++|..+++++..|.+..+|=+.|-
T Consensus 156 Lt~rE~~vl~~l~-----------~g~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 156 LTPRERDILKLIA-----------QGLPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred CCHHHHHHHHHHH-----------cCCCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 6777766643221 123567789999999999998887666654
No 313
>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=26.48 E-value=47 Score=20.45 Aligned_cols=59 Identities=15% Similarity=0.089 Sum_probs=34.4
Q ss_pred cchhccCCCHHHHHHHHhhhH-hhhhh---cccccchhHHH------HHhhhhcchhhhhhccccchhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR-TKWKY---VDKYLSVSKRM------ELSKLLNLTEVQIKTWFQNRRT 60 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r-~k~~~---~~~yp~~~~r~------~La~~~~l~~~~vqvWFqNrRa 60 (120)
|+|+.+|++...|.-|.++.- -.-.+ -.++-+..... .|.+..|++-..|+.+..+...
T Consensus 5 EvA~~~gVs~~tLR~ye~~~gli~p~r~~~g~R~Yt~~di~~l~~I~~llr~~G~~l~~i~~~l~~~~~ 73 (99)
T cd04765 5 EVAEILGLPPHVLRYWETEFPQLKPVKRAGGRRYYRPKDVELLLLIKHLLYEKGYTIEGAKQALKEDGA 73 (99)
T ss_pred HHHHHHCcCHHHHHHHHHHcCCCCCcCCCCCCeeeCHHHHHHHHHHHHHHHHCCCCHHHHHHHHHhccc
Confidence 689999999999999987621 11101 01111111111 1235678888888877765433
No 314
>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=26.42 E-value=99 Score=21.83 Aligned_cols=31 Identities=16% Similarity=0.227 Sum_probs=24.0
Q ss_pred hhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
...-.++|..+|++...|.++...-+.+.|+
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4567889999999999998877655555544
No 315
>cd08779 Death_PIDD Death Domain of p53-induced protein with a death domain. Death domain (DD) found in PIDD (p53-induced protein with a death domain) and similar proteins. PIDD is a component of the PIDDosome complex, which is an oligomeric caspase-activating complex involved in caspase-2 activation and plays a role in mediating stress-induced apoptosis. The PIDDosome complex is composed of three components, PIDD, RAIDD and caspase-2, which interact through their DDs and DD-like domains. The DD of PIDD interacts with the DD of RAIDD, which also contains a Caspase Activation and Recruitment Domain (CARD) that interacts with the caspase-2 CARD. Autoproteolysis of PIDD determines the downstream signaling event, between pro-survival NF-kB or pro-death caspase-2 activation. In general, 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
Probab=26.29 E-value=49 Score=19.90 Aligned_cols=19 Identities=16% Similarity=0.128 Sum_probs=15.9
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||..+||++..|.....+
T Consensus 18 ~lar~LGlse~~Id~Ie~~ 36 (86)
T cd08779 18 AIGLHLGLSYRELQRIKYN 36 (86)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5889999999999886555
No 316
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=26.11 E-value=1e+02 Score=20.79 Aligned_cols=34 Identities=15% Similarity=0.012 Sum_probs=25.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|++....-|.+-++
T Consensus 124 ~~~g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~ 157 (182)
T PRK12540 124 GASGFSYEDAAAICGCAVGTIKSRVNRARSKLSA 157 (182)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4456677889999999999999877544444443
No 317
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=25.92 E-value=1e+02 Score=22.05 Aligned_cols=34 Identities=26% Similarity=0.297 Sum_probs=25.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-.++|..+|+++..|...+..-+.+-|.
T Consensus 214 ~~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 214 YKEELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455667889999999999999888655555443
No 318
>PTZ00044 ubiquitin; Provisional
Probab=25.88 E-value=46 Score=18.93 Aligned_cols=28 Identities=14% Similarity=0.237 Sum_probs=22.6
Q ss_pred hhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
...+..|+...|++...++.||..+...
T Consensus 24 ~~lK~~i~~~~gi~~~~q~L~~~g~~L~ 51 (76)
T PTZ00044 24 QQVKMALQEKEGIDVKQIRLIYSGKQMS 51 (76)
T ss_pred HHHHHHHHHHHCCCHHHeEEEECCEEcc
Confidence 3567778999999999999999877643
No 319
>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=25.86 E-value=96 Score=21.61 Aligned_cols=33 Identities=9% Similarity=0.335 Sum_probs=25.0
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
|.....-.++|..+|++...|..|...-+.+.+
T Consensus 191 y~~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr 223 (227)
T TIGR02980 191 FFEDKTQSEIAERLGISQMHVSRLLRRALKKLR 223 (227)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 445567888999999999999998764444443
No 320
>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=25.83 E-value=39 Score=18.78 Aligned_cols=14 Identities=29% Similarity=0.427 Sum_probs=10.9
Q ss_pred chhccCCCHHHHHH
Q psy4877 3 LSKLLNLTEVQIKT 16 (120)
Q Consensus 3 la~~~~~~~~~~q~ 16 (120)
.|+++|+|++||..
T Consensus 26 wa~~~gvt~~~L~~ 39 (57)
T PF12244_consen 26 WAKRFGVTEEQLRE 39 (57)
T ss_pred HHHHHCcCHHHHHH
Confidence 46788899888865
No 321
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=25.76 E-value=56 Score=16.85 Aligned_cols=22 Identities=14% Similarity=0.057 Sum_probs=13.4
Q ss_pred hhHHHHHhhhhcchhhhhhccc
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWF 55 (120)
.....+||..+|.+...|..+.
T Consensus 20 G~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 20 GMSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---HHHHHHHTT--HHHHHHHH
T ss_pred CCCHHHHHHHHCcCcHHHHHHH
Confidence 4556679999999998887654
No 322
>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=25.48 E-value=43 Score=20.66 Aligned_cols=19 Identities=32% Similarity=0.323 Sum_probs=15.4
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||.++||++..|....-+
T Consensus 24 ~laR~LGLse~~I~~i~~~ 42 (96)
T cd08315 24 RLMRQLGLSENEIDVAKAN 42 (96)
T ss_pred HHHHHcCCCHHHHHHHHHH
Confidence 5889999999999885544
No 323
>cd01803 Ubiquitin Ubiquitin. Ubiquitin (includes Ubq/RPL40e and Ubq/RPS27a fusions as well as homopolymeric multiubiquitin protein chains)
Probab=25.42 E-value=46 Score=18.71 Aligned_cols=25 Identities=8% Similarity=0.126 Sum_probs=20.6
Q ss_pred hhHHHHHhhhhcchhhhhhccccch
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNr 58 (120)
...+..|+..++++...++.||.++
T Consensus 24 ~~lK~~i~~~~g~~~~~q~L~~~g~ 48 (76)
T cd01803 24 ENVKAKIQDKEGIPPDQQRLIFAGK 48 (76)
T ss_pred HHHHHHHHHHhCCCHHHeEEEECCE
Confidence 4677788999999999999998654
No 324
>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=25.42 E-value=50 Score=20.14 Aligned_cols=57 Identities=21% Similarity=0.251 Sum_probs=34.5
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh--hhccc--ccchhHHHH-----Hhhhhcchhhhhhccccch
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW--KYVDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~--~~~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFqNr 58 (120)
|+|+.+|++...|.-|++.=...- +..+. +-+...-.. ....+|++-..|+.-+.+.
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~~~~~gyR~Y~~~~~~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (97)
T cd04782 5 EFAKLCGISKQTLFHYDKIGLFKPEIVKENGYRYYTLEQFEQLDIILLLKELGISLKEIKDYLDNR 70 (97)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCCCCCccCCHHHHHHHHHHHHHHHcCCCHHHHHHHHhcC
Confidence 689999999999999877533211 11121 222222222 2567788888888666544
No 325
>PF01476 LysM: LysM domain; InterPro: IPR018392 This domain is about 40 residues long and is found in a variety of enzymes involved in bacterial cell wall degradation []. This domain may have a general peptidoglycan binding function.; GO: 0016998 cell wall macromolecule catabolic process; PDB: 2DJP_A 3ZQD_A 1Y7M_B 4A52_A 2L9Y_A 1E0G_A.
Probab=25.42 E-value=51 Score=16.40 Aligned_cols=15 Identities=7% Similarity=0.160 Sum_probs=9.9
Q ss_pred chhccCCCHHHHHHH
Q psy4877 3 LSKLLNLTEVQIKTW 17 (120)
Q Consensus 3 la~~~~~~~~~~q~~ 17 (120)
||.+.|++..+|..|
T Consensus 12 IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 12 IAKRYGISVDELMEL 26 (44)
T ss_dssp HHHHTTS-HHHHHHH
T ss_pred HHhhhhhhHhHHHHh
Confidence 677777777777654
No 326
>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=25.23 E-value=97 Score=22.14 Aligned_cols=33 Identities=12% Similarity=0.159 Sum_probs=24.1
Q ss_pred cchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 32 p~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
-....-.++|..+|++...|+.+...-+.+-|+
T Consensus 219 ~~g~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 219 EENLSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 334556889999999999998877655554443
No 327
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=25.02 E-value=44 Score=18.85 Aligned_cols=18 Identities=22% Similarity=0.580 Sum_probs=15.2
Q ss_pred HHHHhhhhcchhhhhhcc
Q psy4877 37 RMELSKLLNLTEVQIKTW 54 (120)
Q Consensus 37 r~~La~~~~l~~~~vqvW 54 (120)
...||+.+|++..-|.-|
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 347899999999999999
No 328
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=24.91 E-value=1.1e+02 Score=22.30 Aligned_cols=34 Identities=0% Similarity=0.294 Sum_probs=25.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|..+...-+.+.|+
T Consensus 228 y~~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 228 FFESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred hcCCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4455667899999999999999887655555444
No 329
>cd01793 Fubi Fubi ubiquitin-like protein. Fubi is a ubiquitin-like protein encoded by the fau gene which has an N-terminal ubiquitin-like domain (also referred to as FUBI) fused to the ribosomal protein S30. Fubi is thought to be a tumor suppressor protein and the FUBI domain may act as a substitute or an inhibitor of ubiquitin or one of ubiquitin's close relatives UCRP, FAT10, and Nedd8.
Probab=24.72 E-value=47 Score=18.96 Aligned_cols=27 Identities=4% Similarity=-0.026 Sum_probs=22.3
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..+..++...|++..+...+|.++.-.
T Consensus 23 ~lK~~i~~~~gip~~~q~Li~~Gk~L~ 49 (74)
T cd01793 23 DIKAHVAGLEGIDVEDQVLLLAGVPLE 49 (74)
T ss_pred HHHHHHHhhhCCCHHHEEEEECCeECC
Confidence 567778899999999999999877644
No 330
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=24.67 E-value=56 Score=19.93 Aligned_cols=20 Identities=10% Similarity=0.150 Sum_probs=16.3
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
+||+.+|++...++..|...
T Consensus 26 ~lA~~~~~S~~~l~r~f~~~ 45 (107)
T PRK10219 26 VVAKKSGYSKWYLQRMFRTV 45 (107)
T ss_pred HHHHHHCCCHHHHHHHHHHH
Confidence 68889999999998877664
No 331
>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=24.53 E-value=52 Score=20.57 Aligned_cols=19 Identities=5% Similarity=0.142 Sum_probs=16.9
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++...|.-|+..
T Consensus 5 e~A~~~gvs~~tlR~ye~~ 23 (107)
T cd01111 5 QLALDAGVSVHIVRDYLLR 23 (107)
T ss_pred HHHHHHCcCHHHHHHHHHC
Confidence 6899999999999998765
No 332
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.43 E-value=1.2e+02 Score=21.86 Aligned_cols=35 Identities=20% Similarity=0.277 Sum_probs=26.2
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
|-....-.++|..+|++...|.....+-+.+-|+.
T Consensus 225 ~~~~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 225 YYEDLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred HHcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44456678899999999999988776655555554
No 333
>PF06400 Alpha-2-MRAP_N: Alpha-2-macroglobulin RAP, N-terminal domain; InterPro: IPR009066 The alpha-2-macroglobulin receptor-associated protein (RAP) is a glycoprotein that binds to the alpha-2-macroglobulin receptor, as well as to other members of the low density lipoprotein receptor family (IPR002172 from INTERPRO). RAP acts to inhibit the binding of all know ligands for these receptors, and may prevent receptor aggregation and degradation in the endoplasmic reticulum, thereby acting as a molecular chaperone []. RAP may be under the regulatory control of calmodulin, since it is able to bind calmodulin and be phosphorylated by calmodulin-dependent kinase II (IPR002048 from INTERPRO). RAP is comprised of three domains. Both domains 1 and 3 are involved in binding to the alpha-2-macroglobulin receptor, while domain 1 is also involved in inhibiting the binding of activated alpha-2-macroglobulin (IPR001599 from INTERPRO). Structural studies have revealed the RAP domain 1 to be comprised of a partly opened bundle of three helices, the first one being shorter than the other two.; PDB: 1NRE_A 2P03_A 1OV2_A 1LRE_A 2FYL_A 1OP1_A 2P01_A.
Probab=24.37 E-value=1e+02 Score=20.04 Aligned_cols=27 Identities=26% Similarity=0.572 Sum_probs=17.9
Q ss_pred hhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHh
Q psy4877 4 SKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELS 41 (120)
Q Consensus 4 a~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La 41 (120)
|.|+.|++..++.+|..-. ++++++|+
T Consensus 52 A~r~~Ls~~kLk~L~~dLK-----------i~dkeEl~ 78 (120)
T PF06400_consen 52 AQRLRLSEVKLKSLYSDLK-----------IHDKEELA 78 (120)
T ss_dssp HHHHT--HHHHHHHHHHHH-----------HHHHHHHH
T ss_pred HHHccCChHHHHHHHHHHH-----------HhHHHHHH
Confidence 5667788888888777755 56777765
No 334
>cd01797 NIRF_N amino-terminal ubiquitin-like domain of Np95 and NIRF. NIRF_N This CD represents the amino-terminal ubiquitin-like domain of a family of nuclear proteins that includes Np95 and NIRF (Np95/ICBP90-like RING finger) protein. Both Np95 and NIRF have a domain architecture consisting of a ubiquitin-like domain, a PHD finger, a YDG/SRA domain, Rb-binding motifs and a RING finger domain. Both Np95 and NIRF are ubiquitin ligases that ubiquitinate PCNP (PEST-containing nuclear proteins). While Np95 is capable of binding histones, NIRF is involved in cell cycle regulation.
Probab=24.34 E-value=50 Score=19.33 Aligned_cols=29 Identities=10% Similarity=0.240 Sum_probs=23.5
Q ss_pred hhHHHHHhhhhcchhhhhhccccchhHHH
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNRRTKW 62 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNrRak~ 62 (120)
...+..++...|++..+.+.||.++..++
T Consensus 26 ~~lK~~i~~~~gi~~~~QrLi~~Gk~L~D 54 (78)
T cd01797 26 EELREKIQELFNVEPECQRLFYRGKQMED 54 (78)
T ss_pred HHHHHHHHHHhCCCHHHeEEEeCCEECCC
Confidence 35677788899999999999998776553
No 335
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=24.09 E-value=37 Score=20.25 Aligned_cols=22 Identities=14% Similarity=0.178 Sum_probs=18.3
Q ss_pred hHHHHHhhhhcchhhhhhcccc
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQ 56 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFq 56 (120)
..+..|...++|..-++.||+.
T Consensus 54 ~L~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 54 ELTSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHHHhCCCCCeEEEEEE
Confidence 4566688889999999999985
No 336
>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=23.92 E-value=55 Score=19.88 Aligned_cols=57 Identities=9% Similarity=-0.001 Sum_probs=35.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh--hhccc--ccchhHHHH-----Hhhhhcchhhhhhccccch
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW--KYVDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~--~~~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFqNr 58 (120)
|+|+.+|++...|.-|+..-...- +..+- +-+...-.. ....+|++-..|+..+.+.
T Consensus 5 eva~~~gvs~~tlR~ye~~Gll~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~~l~eI~~~l~~~ 70 (96)
T cd04788 5 ELARRTGLSVRTLHHYDHIGLLSPSQRTEGGHRLYDRADIRRLHQIIALRRLGFSLREIGRALDGP 70 (96)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCccCCCCceeeCHHHHHHHHHHHHHHHcCCCHHHHHHHHhCC
Confidence 689999999999999987544321 11122 112222221 2467788888888777543
No 337
>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=23.79 E-value=49 Score=21.98 Aligned_cols=22 Identities=18% Similarity=0.273 Sum_probs=18.8
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
|+++.||+++.+|..|-..=|.
T Consensus 51 eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 51 EIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred HHHHHHCcCHHHHHHHHHcCCe
Confidence 6899999999999998887553
No 338
>cd08784 Death_DRs Death Domain of Death Receptors. Death domain (DD) found in death receptor proteins. Death receptors are members of the tumor necrosis factor (TNF) receptor superfamily, characterized by having a cytoplasmic DD. Known members of the family are Fas (CD95/APO-1), TNF-receptor 1 (TNFR1/TNFRSF1A/p55/CD120a), TNF-related apoptosis-inducing ligand receptor 1 (TRAIL-R1 /DR4), and receptor 2 (TRAIL-R2/DR5/APO-2/KILLER), as well as Death Receptor 3 (DR3/APO-3/TRAMP/WSL-1/LARD). They are involved in apoptosis signaling pathways. 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=23.75 E-value=50 Score=19.45 Aligned_cols=19 Identities=21% Similarity=0.223 Sum_probs=15.5
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
+||.++||++..|....-+
T Consensus 16 ~laR~LGls~~~I~~ie~~ 34 (79)
T cd08784 16 RFFRKLGLSDNEIKVAELD 34 (79)
T ss_pred HHHHHcCCCHHHHHHHHHc
Confidence 5788999999999886544
No 339
>PRK14584 hmsS hemin storage system protein; Provisional
Probab=23.50 E-value=39 Score=22.93 Aligned_cols=30 Identities=13% Similarity=-0.055 Sum_probs=22.9
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchh
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRR 59 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrR 59 (120)
..+....-+++|+.+++++..++.|-+++.
T Consensus 94 ~~~~~l~~dElA~sF~l~~e~i~qLr~~ki 123 (153)
T PRK14584 94 GHRPDLDDDELASSFALSPELIAQLKSGSC 123 (153)
T ss_pred CCCCCCChHHHHHHcCCCHHHHHHHHhCCe
Confidence 345566788999999999998887765443
No 340
>TIGR02589 cas_Csd2 CRISPR-associated protein, Csd2 family. This model represents one of two closely related CRISPR-associated proteins that belong to the larger family of TIGR01595. Members are the Csd2 protein of the Dvulg subtype of CRISPR/cas system. CRISPR stands for Clustered Regularly Interspaced Short Palindromic Repeats. The related model is TIGR02590, the Csh2 protein of the Hmari CRISPR subtype.
Probab=23.39 E-value=61 Score=24.28 Aligned_cols=20 Identities=10% Similarity=0.135 Sum_probs=16.6
Q ss_pred cchhccCCCHHHHHHHHhhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNR 21 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~ 21 (120)
.||+++||+|+-++.+.+.-
T Consensus 188 ~~A~~Tg~SeeDlell~~AL 207 (284)
T TIGR02589 188 QLAEKTGFSDEDLELIKQAL 207 (284)
T ss_pred hhHhhcCCCHHHHHHHHHHH
Confidence 58999999999999866553
No 341
>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=23.27 E-value=1.3e+02 Score=17.09 Aligned_cols=39 Identities=21% Similarity=0.218 Sum_probs=20.6
Q ss_pred CCCHHHHHHHH--hhhHhhhhhcccccchhHHHHHhhhhcch-hhhhh
Q psy4877 8 NLTEVQIKTWF--QNRRTKWKYVDKYLSVSKRMELSKLLNLT-EVQIK 52 (120)
Q Consensus 8 ~~~~~~~q~~f--q~~r~k~~~~~~yp~~~~r~~La~~~~l~-~~~vq 52 (120)
.||+.|.+++. .++-. ++-|| ....+||..+|+. ...|+
T Consensus 3 ~LT~rQ~~vL~~I~~~~~----~~G~~--Pt~rEIa~~~g~~S~~tv~ 44 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIE----ENGYP--PTVREIAEALGLKSTSTVQ 44 (65)
T ss_dssp ---HHHHHHHHHHHHHHH----HHSS-----HHHHHHHHTSSSHHHHH
T ss_pred CCCHHHHHHHHHHHHHHH----HcCCC--CCHHHHHHHhCCCChHHHH
Confidence 57888888843 23221 23444 5678899999997 54444
No 342
>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=23.18 E-value=1.5e+02 Score=20.93 Aligned_cols=33 Identities=18% Similarity=0.150 Sum_probs=26.0
Q ss_pred chhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 33 SVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 33 ~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
....-.++|..+|++...|......-..|.|..
T Consensus 195 ~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 195 RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 345678899999999999998887666666654
No 343
>PF02082 Rrf2: Transcriptional regulator; InterPro: IPR000944 The following uncharacterised bacterial proteins have been shown to be evolutionary related, Desulfovibrio vulgaris protein Rrf2; Escherichia coli hypothetical proteins yfhP and yjeB; Bacillus subtilis hypothetical proteins yhdE, yrzC and ywgB; Mycobacterium tuberculosis hypothetical protein Rv1287; and Synechocystis sp. (strain PCC 6803) hypothetical protein slr0846. These are small proteins of 12 to 18kDa which seem to contain a signal sequence, and may represent a family of probable transcriptional regulators.; PDB: 3T8T_A 3T8R_A 3K69_A 3LWF_C 1XD7_A 2Y75_E 1YLF_C.
Probab=23.12 E-value=59 Score=19.06 Aligned_cols=21 Identities=14% Similarity=0.347 Sum_probs=15.7
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
|||+++++++..|...++.-.
T Consensus 30 eiA~~~~i~~~~l~kil~~L~ 50 (83)
T PF02082_consen 30 EIAERLGISPSYLRKILQKLK 50 (83)
T ss_dssp HHHHHHTS-HHHHHHHHHHHH
T ss_pred HHHHHHCcCHHHHHHHHHHHh
Confidence 689999999988887766643
No 344
>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=22.95 E-value=1.4e+02 Score=21.73 Aligned_cols=30 Identities=10% Similarity=0.174 Sum_probs=15.7
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
..-.++|..+|+++..|+..+..-|.+-+.
T Consensus 125 ~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 125 YPYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 334555555555555555555544444443
No 345
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=22.68 E-value=1.3e+02 Score=22.65 Aligned_cols=34 Identities=6% Similarity=0.142 Sum_probs=26.7
Q ss_pred cchhHHHHHhhhhcchhhhhhccccchhHHHHHH
Q psy4877 32 LSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKKQ 65 (120)
Q Consensus 32 p~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr~ 65 (120)
-....-+++|..+|++...|+.+...-+.+-|+.
T Consensus 280 ~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~ 313 (325)
T PRK05657 280 YEAATLEDVAREIGLTRERVRQIQVEALRRLREI 313 (325)
T ss_pred CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3456778999999999999999887666665553
No 346
>PF05344 DUF746: Domain of Unknown Function (DUF746); InterPro: IPR008008 This is a short conserved region found in some transposons.
Probab=22.39 E-value=65 Score=18.63 Aligned_cols=22 Identities=14% Similarity=0.303 Sum_probs=18.1
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
|.|+.+|..+.-|..|-..+|.
T Consensus 18 ~Aa~~lG~~~~~v~~wv~~fR~ 39 (65)
T PF05344_consen 18 QAADRLGTDPGTVRRWVRMFRQ 39 (65)
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 5688888888888888888774
No 347
>COG1396 HipB Predicted transcriptional regulators [Transcription]
Probab=22.36 E-value=1.4e+02 Score=16.19 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=24.4
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEV 49 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~ 49 (120)
++|.++|++...+..|..... . .|+......++..+++...
T Consensus 19 ~~a~~~~~~~~~~~~~e~~~~------~-~~~~~~~~~~~~~~~~~~~ 59 (120)
T COG1396 19 ELAERLGVSRSTISRIERGRS------E-SPSLELLARLAAALGVSLD 59 (120)
T ss_pred HHHHHhCCCHHHHHHHHcCCC------C-CCCHHHHHHHHHHHCCCHH
Confidence 466677776666666666642 1 5666666666665554443
No 348
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=22.08 E-value=1.5e+02 Score=21.40 Aligned_cols=34 Identities=18% Similarity=0.259 Sum_probs=24.6
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|.....-.++|..+|++...|..+...-+.+-|+
T Consensus 218 y~e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 218 YYEELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred HhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3445667889999999999999876544444444
No 349
>PF15076 DUF4543: Domain of unknown function (DUF4543)
Probab=22.07 E-value=1.8e+02 Score=16.94 Aligned_cols=39 Identities=26% Similarity=0.235 Sum_probs=27.8
Q ss_pred CCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcch
Q psy4877 9 LTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLT 47 (120)
Q Consensus 9 ~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~ 47 (120)
++|.+.+-+.+.+|--+-++--+|+...|+.+..-+.|.
T Consensus 9 l~Ek~AKqlLRsrR~dr~~K~GfpdepmrE~ml~l~~Le 47 (75)
T PF15076_consen 9 LTEKQAKQLLRSRRQDRPRKPGFPDEPMREYMLHLQALE 47 (75)
T ss_pred ccHHHHHHHHHHHHhcCCCCCCCCcchHHHHHHHHHHHH
Confidence 678888877877775444455689999999876555443
No 350
>smart00595 MADF subfamily of SANT domain.
Probab=21.89 E-value=1.4e+02 Score=17.38 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=26.9
Q ss_pred HHHHHhhhhcchhhhhhccccchhHHHHHHHHHHH
Q psy4877 36 KRMELSKLLNLTEVQIKTWFQNRRTKWKKQLASKL 70 (120)
Q Consensus 36 ~r~~La~~~~l~~~~vqvWFqNrRak~rr~~~~~~ 70 (120)
.=.+||..+|.+...++.-+.|=|...++......
T Consensus 29 aW~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~ 63 (89)
T smart00595 29 AWEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQ 63 (89)
T ss_pred HHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33457899999999999988999988888644433
No 351
>cd01807 GDX_N ubiquitin-like domain of GDX. GDX contains an N-terminal ubiquitin-like domain as well as an uncharacterized c-terminal domain. The function of GDX is unknown.
Probab=21.72 E-value=61 Score=18.43 Aligned_cols=27 Identities=22% Similarity=0.290 Sum_probs=22.2
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..++.++...|++..+...+|..+...
T Consensus 25 ~lK~~i~~~~gi~~~~q~L~~~G~~L~ 51 (74)
T cd01807 25 TLKKLVSEHLNVPEEQQRLLFKGKALA 51 (74)
T ss_pred HHHHHHHHHHCCCHHHeEEEECCEECC
Confidence 567788999999999999999876644
No 352
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=21.42 E-value=63 Score=21.21 Aligned_cols=55 Identities=11% Similarity=0.020 Sum_probs=32.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh-ccc--ccchhHHHH-----Hhhhhcchhhhhhcccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY-VDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQ 56 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~-~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFq 56 (120)
|+|+.+|++...|.-|++.=.-.-.+ .+- +-+...-.. ....+|++-..|+-.+.
T Consensus 6 EvA~~~Gvs~~tLRyYE~~GLl~p~r~~~g~R~Y~~~dl~~l~~I~~lr~~G~sl~eI~~~l~ 68 (139)
T cd01110 6 EVAKRSGVAVSALHFYEQKGLIASWRNAGNQRRYPRDVLRRIAFIKVAQRLGLSLAEIAEALA 68 (139)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCcCCCCCeEECHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 78999999999999988764221111 111 111111111 24667888887776554
No 353
>cd01769 UBL Ubiquitin-like domain of UBL. UBLs function by remodeling the surface of their target proteins, changing their target's half-life, enzymatic activity, protein-protein interactions, subcellular localization or other properties. At least 10 different ubiquitin-like modifications exist in mammals, and attachment of different ubls to a target leads to different biological consequences. Ubl-conjugation cascades are initiated by activating enzymes, which also coordinate the ubls with their downstream pathways.
Probab=21.30 E-value=66 Score=17.39 Aligned_cols=25 Identities=4% Similarity=0.113 Sum_probs=19.8
Q ss_pred hhHHHHHhhhhcchhhhhhccccch
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWFQNR 58 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWFqNr 58 (120)
...++.++..+|++...+..+|.++
T Consensus 21 ~~lK~~i~~~~~~~~~~~~l~~~g~ 45 (69)
T cd01769 21 AELKAKIAAKEGVPPEQQRLIYAGK 45 (69)
T ss_pred HHHHHHHHHHHCcChHHEEEEECCc
Confidence 3567778888999999888888653
No 354
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=21.21 E-value=1.2e+02 Score=21.28 Aligned_cols=36 Identities=11% Similarity=0.001 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchhhhhhcc
Q psy4877 8 NLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTEVQIKTW 54 (120)
Q Consensus 8 ~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~~~vqvW 54 (120)
.||..+.+|+.---+ +..-.++|.+++++++.|+.-
T Consensus 134 ~LT~RE~eVL~ll~~-----------G~snkeIA~~L~iS~~TV~~h 169 (207)
T PRK11475 134 MLSPTEREILRFMSR-----------GYSMPQIAEQLERNIKTIRAH 169 (207)
T ss_pred CCCHHHHHHHHHHHC-----------CCCHHHHHHHHCCCHHHHHHH
Confidence 467777777443322 556678999999999998873
No 355
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=21.09 E-value=1.1e+02 Score=22.48 Aligned_cols=34 Identities=9% Similarity=-0.016 Sum_probs=25.5
Q ss_pred ccchhHHHHHhhhhcchhhhhhccccchhHHHHH
Q psy4877 31 YLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWKK 64 (120)
Q Consensus 31 yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~rr 64 (120)
|-....-+++|..+|+++..|+.....-|.+-++
T Consensus 128 ~~~g~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~ 161 (293)
T PRK09636 128 DVFGVPFDEIASTLGRSPAACRQLASRARKHVRA 161 (293)
T ss_pred HHhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3444567788999999999999888766666555
No 356
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=21.01 E-value=72 Score=18.10 Aligned_cols=19 Identities=21% Similarity=0.426 Sum_probs=13.2
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+|+.+|++..++.-|...
T Consensus 20 eiA~~~gls~~~aR~yL~~ 38 (62)
T PF04703_consen 20 EIADALGLSIYQARYYLEK 38 (62)
T ss_dssp HHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHhCCCHHHHHHHHHH
Confidence 6788888888888665544
No 357
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=20.96 E-value=64 Score=20.65 Aligned_cols=55 Identities=13% Similarity=0.145 Sum_probs=34.2
Q ss_pred cchhccCCCHHHHHHHHhhhHhhh--hhcccc--cchhHHHH-----Hhhhhcchhhhhhcccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKW--KYVDKY--LSVSKRME-----LSKLLNLTEVQIKTWFQ 56 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~--~~~~~y--p~~~~r~~-----La~~~~l~~~~vqvWFq 56 (120)
|+|+++|++...|.-|++.---.- +..+-| =+...... .++.+|++-..|+..+.
T Consensus 5 e~a~~~gvs~~tlRyYe~~GLl~p~~r~~~gyR~Y~~~~l~~l~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 5 QVAKLTGLSSKMIRYYEEKGLIPPPLRSEGGYRTYTQQHLDELRLISRARQVGFSLEECKELLN 68 (127)
T ss_pred HHHHHHCcCHHHHHHHHHCCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHCCCCHHHHHHHHH
Confidence 689999999999999887654322 111221 11111111 36778888888887663
No 358
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.92 E-value=85 Score=23.69 Aligned_cols=22 Identities=9% Similarity=0.199 Sum_probs=18.3
Q ss_pred cchhccCCCHHHHHHHHhhhHh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRT 23 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~ 23 (120)
|+|+.+|++...|+.+...-+.
T Consensus 287 EIA~~Lgis~~tV~~~~~rAl~ 308 (325)
T PRK05657 287 DVAREIGLTRERVRQIQVEALR 308 (325)
T ss_pred HHHHHHCcCHHHHHHHHHHHHH
Confidence 6899999999999997766553
No 359
>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=20.80 E-value=60 Score=20.25 Aligned_cols=22 Identities=27% Similarity=0.196 Sum_probs=14.6
Q ss_pred hhHHHHHhhhhcchhhhhhccc
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWF 55 (120)
.....+||.+.|||++.|..=.
T Consensus 72 G~n~~eLA~kyglS~r~I~~Ii 93 (108)
T PF08765_consen 72 GMNVRELARKYGLSERQIYRII 93 (108)
T ss_dssp SS-HHHHHHHHT--HHHHHHHH
T ss_pred CCCHHHHHHHHCcCHHHHHHHH
Confidence 4457899999999998876433
No 360
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=20.75 E-value=1.1e+02 Score=20.87 Aligned_cols=33 Identities=18% Similarity=0.211 Sum_probs=23.1
Q ss_pred ccccchhHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 29 DKYLSVSKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 29 ~~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..|-+...-.++|+.+||+.......|...-++
T Consensus 98 ~~~s~~~~l~~iA~~~gLD~~~F~~d~~S~~~~ 130 (176)
T PF13743_consen 98 KNYSDEELLLEIAEELGLDVEMFKEDLHSDEAK 130 (176)
T ss_dssp --TTSHHHHHHHHHHTT--HHHHHHHHTSHHHH
T ss_pred CCCCHHHHHHHHHHHhCCCHHHHHHHHhChHHH
Confidence 345555888899999999999999888655555
No 361
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=20.70 E-value=97 Score=21.11 Aligned_cols=22 Identities=23% Similarity=0.004 Sum_probs=17.5
Q ss_pred hhHHHHHhhhhcchhhhhhccc
Q psy4877 34 VSKRMELSKLLNLTEVQIKTWF 55 (120)
Q Consensus 34 ~~~r~~La~~~~l~~~~vqvWF 55 (120)
+..-.++|..++++++.|+.--
T Consensus 165 G~s~~eIA~~l~iS~~TV~~h~ 186 (216)
T PRK10840 165 GFLVTEIAKKLNRSIKTISSQK 186 (216)
T ss_pred CCCHHHHHHHHCCCHHHHHHHH
Confidence 4566778999999999998743
No 362
>cd01282 HTH_MerR-like_sg3 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 3). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.50 E-value=71 Score=20.00 Aligned_cols=55 Identities=9% Similarity=-0.001 Sum_probs=32.1
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhh-ccc--ccchhHHHH-----Hhhhhcchhhhhhcccc
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKY-VDK--YLSVSKRME-----LSKLLNLTEVQIKTWFQ 56 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~-~~~--yp~~~~r~~-----La~~~~l~~~~vqvWFq 56 (120)
|+|+.+|++...|.-|++.=.-+-.+ .+- |=+...-.. ....+|++-..|+-.+.
T Consensus 5 eva~~~gvs~~tlR~Ye~~GLl~p~r~~~g~R~Y~~~~~~~l~~I~~lr~~G~sl~eI~~~l~ 67 (112)
T cd01282 5 ELAARTGVSVRSLRYYEEQGLLVPERSANGYRDYDEAAVDRVRQIRRLLAAGLTLEEIREFLP 67 (112)
T ss_pred HHHHHHCCCHHHHHHHHHCCCCCCCcCCCCCeecCHHHHHHHHHHHHHHHcCCCHHHHHHHHH
Confidence 68999999999999988753322111 111 111111111 24667888877775543
No 363
>PF05930 Phage_AlpA: Prophage CP4-57 regulatory protein (AlpA); InterPro: IPR010260 This entry is represents phage P4, Orf88. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. In Escherichia coli phage P4 Orf 88 is similar to AlpA of the CP4-57 cryptic prophage []. AlpA acts as a positive transcriptional regulator of slpA, a gene linked to alpA and necessary for suppression of lon mutants [, ]. The sequence of slpA suggests that it encodes an integrase gene closely related to phage P4 int and that both alpA and slpA are part of a cryptic P4-like prophage. Increase in alpA expression increases SlpA synthesis. Increased SlpA leads, in turn, to the excision and loss of the cryptic prophage. ; PDB: 1Z4H_A.
Probab=20.47 E-value=63 Score=17.13 Aligned_cols=19 Identities=21% Similarity=0.431 Sum_probs=13.7
Q ss_pred cchhccCCCHHHHHHHHhh
Q psy4877 2 ELSKLLNLTEVQIKTWFQN 20 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~ 20 (120)
|+++.+|++...+-.|..+
T Consensus 8 ev~~~~g~s~~ti~~~~k~ 26 (51)
T PF05930_consen 8 EVAELLGVSRSTIYRLIKD 26 (51)
T ss_dssp HHHHHHSS-HHHHHHHHHH
T ss_pred HHHHHHCCCHHHHHHHHhc
Confidence 5678889988888776664
No 364
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=20.43 E-value=51 Score=24.42 Aligned_cols=32 Identities=31% Similarity=0.628 Sum_probs=25.7
Q ss_pred cccchhHHHHHhhhhcchhhhhhccccchhHHHH
Q psy4877 30 KYLSVSKRMELSKLLNLTEVQIKTWFQNRRTKWK 63 (120)
Q Consensus 30 ~yp~~~~r~~La~~~~l~~~~vqvWFqNrRak~r 63 (120)
.|...-.-.+||.++|++..+|..|- ||-.|.
T Consensus 15 ~yl~gmk~~dIAeklGvspntiksWK--rr~gWs 46 (279)
T COG5484 15 DYLKGMKLKDIAEKLGVSPNTIKSWK--RRDGWS 46 (279)
T ss_pred HHHhhccHHHHHHHhCCChHHHHHHH--HhcCCC
Confidence 45556566789999999999999997 577774
No 365
>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=20.42 E-value=67 Score=16.54 Aligned_cols=26 Identities=4% Similarity=0.202 Sum_probs=20.3
Q ss_pred hHHHHHhhhhcchhhhhhccccchhH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRT 60 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRa 60 (120)
....++|++.|++...+---|.|+-+
T Consensus 17 ~s~~~Ia~~~gvs~~~~y~~f~~k~~ 42 (47)
T PF00440_consen 17 VSIRDIARRAGVSKGSFYRYFPSKDD 42 (47)
T ss_dssp SSHHHHHHHHTSCHHHHHHHCSSHHH
T ss_pred CCHHHHHHHHccchhhHHHHcCCHHH
Confidence 34567899999999988888887644
No 366
>COG0789 SoxR Predicted transcriptional regulators [Transcription]
Probab=20.23 E-value=74 Score=19.84 Aligned_cols=21 Identities=14% Similarity=0.237 Sum_probs=17.8
Q ss_pred cchhccCCCHHHHHHHHhhhH
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRR 22 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r 22 (120)
|+|+.+|++...|.=|...--
T Consensus 5 eva~~~gvs~~tLRyYE~~GL 25 (124)
T COG0789 5 EVAKLTGVSVRTLRFYERKGL 25 (124)
T ss_pred HHHHHhCCCHHHHHHHHHcCC
Confidence 689999999999999887644
No 367
>COG3636 Predicted transcriptional regulator [Transcription]
Probab=20.12 E-value=1.4e+02 Score=18.76 Aligned_cols=39 Identities=10% Similarity=0.095 Sum_probs=25.6
Q ss_pred cchhccCCCHHHHHHHHhhhHhhhhhcccccchhHHHHHhhhhcchh
Q psy4877 2 ELSKLLNLTEVQIKTWFQNRRTKWKYVDKYLSVSKRMELSKLLNLTE 48 (120)
Q Consensus 2 ~la~~~~~~~~~~q~~fq~~r~k~~~~~~yp~~~~r~~La~~~~l~~ 48 (120)
++|++.|++.+.|-.=+.. +-.|+......+.+.+|+--
T Consensus 54 qvA~~aGlsRe~LYkaLS~--------~GNPtf~Til~V~kAlG~rl 92 (100)
T COG3636 54 QVARKAGLSREGLYKALSP--------GGNPTFDTILAVLKALGLRL 92 (100)
T ss_pred HHHHHhCccHHHHHHHhCC--------CCCCcHHHHHHHHHHcCcee
Confidence 5788888888877443333 55666666666666666543
No 368
>cd01794 DC_UbP_C dendritic cell derived ubiquitin-like protein. DC_UbP (dendritic cell derived ubiquitin-like protein) is a ubiquitin-like protein from human dendritic cells that is expressed in the mitochondrion. The ubiquitin-like domain of this protein is found at the C-terminus and lacks the canonical gly-gly motif of ubiquitin required for ubiquitinization. DC_UbP is expressed in tumor cells but not in normal human adult tissue suggesting a role for DC_UbP in tumorogenesis.
Probab=20.08 E-value=71 Score=18.24 Aligned_cols=27 Identities=7% Similarity=0.101 Sum_probs=21.2
Q ss_pred hHHHHHhhhhcchhhhhhccccchhHH
Q psy4877 35 SKRMELSKLLNLTEVQIKTWFQNRRTK 61 (120)
Q Consensus 35 ~~r~~La~~~~l~~~~vqvWFqNrRak 61 (120)
..+..++...|++..+...||..+-..
T Consensus 23 ~lK~~I~~~~gi~~~~q~Li~~G~~L~ 49 (70)
T cd01794 23 QLKKQLQAAEGVDPCCQRWFFSGKLLT 49 (70)
T ss_pred HHHHHHHHHhCCCHHHeEEEECCeECC
Confidence 456778888899999999999776544
Done!