Query psy8536
Match_columns 186
No_of_seqs 242 out of 1286
Neff 9.1
Searched_HMMs 46136
Date Fri Aug 16 21:25:10 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy8536.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/8536hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0484|consensus 99.9 3E-22 6.5E-27 131.0 4.6 66 2-67 14-79 (125)
2 KOG0850|consensus 99.8 6.6E-20 1.4E-24 136.5 6.4 72 1-72 118-189 (245)
3 KOG2251|consensus 99.8 7.8E-20 1.7E-24 135.5 5.2 66 2-67 34-99 (228)
4 KOG0488|consensus 99.8 2E-19 4.4E-24 143.2 7.5 74 2-75 169-242 (309)
5 KOG0494|consensus 99.8 1.8E-19 3.9E-24 136.1 6.0 66 2-67 137-203 (332)
6 KOG0843|consensus 99.8 8.6E-19 1.9E-23 125.9 6.5 64 4-67 101-164 (197)
7 PF00046 Homeobox: Homeobox do 99.8 1.9E-18 4.1E-23 105.0 7.1 57 6-62 1-57 (57)
8 KOG0489|consensus 99.8 6.4E-19 1.4E-23 138.1 5.7 68 3-70 157-224 (261)
9 KOG0487|consensus 99.7 6.6E-19 1.4E-23 138.3 4.3 65 3-67 233-297 (308)
10 KOG0848|consensus 99.7 7.5E-19 1.6E-23 133.3 4.0 68 1-68 195-262 (317)
11 KOG0842|consensus 99.7 4.8E-18 1E-22 133.4 3.7 71 2-72 150-220 (307)
12 KOG0492|consensus 99.7 1.9E-17 4.1E-22 121.5 6.2 69 1-69 140-208 (246)
13 TIGR01565 homeo_ZF_HD homeobox 99.7 2.7E-17 5.8E-22 98.7 4.2 53 5-57 1-57 (58)
14 KOG0485|consensus 99.7 1.3E-16 2.9E-21 117.8 8.2 68 4-71 103-170 (268)
15 KOG0493|consensus 99.7 6.1E-17 1.3E-21 122.6 5.6 61 5-65 246-306 (342)
16 smart00389 HOX Homeodomain. DN 99.7 4.1E-16 8.8E-21 94.3 6.5 54 7-60 2-55 (56)
17 cd00086 homeodomain Homeodomai 99.6 8.5E-16 1.8E-20 93.8 7.4 56 7-62 2-57 (59)
18 COG5576 Homeodomain-containing 99.6 6.2E-16 1.4E-20 111.5 6.4 69 3-71 49-117 (156)
19 KOG0486|consensus 99.6 2.1E-16 4.5E-21 122.7 4.2 76 2-77 109-184 (351)
20 KOG0483|consensus 99.6 2.9E-16 6.3E-21 116.9 3.9 81 6-86 51-131 (198)
21 KOG0491|consensus 99.6 5.7E-16 1.2E-20 109.8 3.2 64 5-68 100-163 (194)
22 KOG0490|consensus 99.6 7E-16 1.5E-20 119.2 2.5 63 3-65 58-120 (235)
23 KOG0844|consensus 99.5 2.1E-15 4.6E-20 116.7 1.7 71 5-75 181-251 (408)
24 KOG3802|consensus 99.5 1.7E-15 3.7E-20 121.6 1.1 62 4-65 293-354 (398)
25 KOG4577|consensus 99.5 5E-14 1.1E-18 108.3 5.0 63 4-66 166-228 (383)
26 KOG0849|consensus 99.3 2.3E-12 5E-17 105.1 5.0 65 2-66 173-237 (354)
27 KOG0847|consensus 99.3 2.1E-12 4.6E-17 95.8 4.3 63 5-67 167-229 (288)
28 KOG0848|consensus 99.1 2.1E-11 4.5E-16 93.1 1.7 28 159-186 193-220 (317)
29 KOG0489|consensus 99.1 5E-11 1.1E-15 93.6 2.7 36 151-186 138-180 (261)
30 KOG1168|consensus 99.0 5.7E-11 1.2E-15 91.7 0.0 62 4-65 308-369 (385)
31 KOG0774|consensus 99.0 3.8E-10 8.2E-15 86.0 4.2 61 5-65 188-251 (334)
32 KOG0775|consensus 99.0 7.3E-10 1.6E-14 85.1 4.9 49 14-62 185-233 (304)
33 PF05920 Homeobox_KN: Homeobox 98.8 4.7E-09 1E-13 58.4 3.9 34 26-59 7-40 (40)
34 KOG2252|consensus 98.6 1.1E-07 2.3E-12 79.9 6.5 57 4-60 419-475 (558)
35 KOG0844|consensus 98.4 2.5E-07 5.5E-12 72.3 3.4 55 74-131 205-259 (408)
36 KOG0484|consensus 98.4 6.1E-08 1.3E-12 64.0 -0.2 56 61-116 26-83 (125)
37 KOG0490|consensus 98.3 7.1E-07 1.5E-11 68.9 4.5 63 3-65 151-213 (235)
38 KOG0487|consensus 98.0 2.8E-06 6E-11 67.5 1.8 24 163-186 233-256 (308)
39 KOG0850|consensus 98.0 1.2E-05 2.6E-10 60.8 4.5 39 85-123 157-195 (245)
40 KOG1146|consensus 97.8 2.4E-05 5.3E-10 71.8 4.0 61 5-65 903-963 (1406)
41 KOG0488|consensus 97.6 3.7E-05 8E-10 61.8 2.8 24 163-186 170-193 (309)
42 TIGR01565 homeo_ZF_HD homeobox 97.5 6E-05 1.3E-09 45.3 2.0 21 165-185 1-21 (58)
43 KOG0494|consensus 97.5 4.8E-05 1E-09 58.5 1.9 24 162-185 138-161 (332)
44 PF11569 Homez: Homeodomain le 97.4 0.00026 5.7E-09 41.9 3.9 40 17-56 10-49 (56)
45 KOG2251|consensus 97.4 6.8E-05 1.5E-09 56.5 1.7 53 60-112 45-99 (228)
46 KOG0842|consensus 97.1 0.00037 8.1E-09 55.6 2.5 31 84-114 187-217 (307)
47 KOG0485|consensus 96.9 0.00052 1.1E-08 51.6 1.9 30 84-113 138-167 (268)
48 KOG0773|consensus 96.8 0.00077 1.7E-08 55.2 2.6 58 5-62 239-299 (342)
49 KOG0491|consensus 96.6 0.00069 1.5E-08 48.8 0.7 27 87-113 137-163 (194)
50 COG5576 Homeodomain-containing 96.6 0.0012 2.6E-08 47.9 1.8 44 68-111 67-112 (156)
51 KOG0843|consensus 96.5 0.0016 3.5E-08 47.7 2.1 22 164-185 101-122 (197)
52 KOG3623|consensus 96.1 0.011 2.4E-07 52.0 5.4 48 17-64 568-615 (1007)
53 KOG0483|consensus 96.1 0.00059 1.3E-08 51.3 -2.2 23 88-110 88-110 (198)
54 KOG4577|consensus 96.0 0.0017 3.6E-08 51.0 -0.3 17 93-109 210-226 (383)
55 PF04218 CENP-B_N: CENP-B N-te 95.9 0.025 5.3E-07 33.3 4.7 47 6-57 1-47 (53)
56 KOG0486|consensus 95.4 0.016 3.4E-07 46.2 3.2 51 63-113 123-175 (351)
57 PF00046 Homeobox: Homeobox do 95.3 0.013 2.9E-07 34.7 2.0 20 166-185 1-20 (57)
58 KOG0847|consensus 95.0 0.0037 8.1E-08 47.2 -1.2 24 89-112 206-229 (288)
59 KOG0492|consensus 94.9 0.021 4.6E-07 42.9 2.4 23 163-185 142-164 (246)
60 KOG0493|consensus 94.7 0.019 4E-07 44.6 1.9 22 164-185 245-266 (342)
61 KOG0849|consensus 92.4 0.1 2.2E-06 43.1 2.5 25 161-185 172-196 (354)
62 KOG0775|consensus 92.2 0.21 4.5E-06 39.2 3.8 29 82-110 208-236 (304)
63 smart00389 HOX Homeodomain. DN 92.0 0.12 2.6E-06 30.2 1.9 20 166-185 1-20 (56)
64 PF04967 HTH_10: HTH DNA bindi 91.5 0.42 9.2E-06 28.1 3.8 40 12-51 1-42 (53)
65 PF01527 HTH_Tnp_1: Transposas 88.7 0.72 1.6E-05 28.7 3.5 44 7-54 2-45 (76)
66 PF04545 Sigma70_r4: Sigma-70, 88.7 2.4 5.2E-05 24.1 5.5 41 11-56 4-44 (50)
67 cd00086 homeodomain Homeodomai 87.4 0.47 1E-05 27.8 1.9 19 167-185 2-20 (59)
68 PF10668 Phage_terminase: Phag 85.7 0.79 1.7E-05 27.7 2.2 21 33-53 23-43 (60)
69 cd06171 Sigma70_r4 Sigma70, re 82.1 3.5 7.6E-05 22.9 4.0 42 11-57 10-51 (55)
70 COG3413 Predicted DNA binding 80.3 2.8 6.1E-05 31.9 4.0 41 11-51 155-197 (215)
71 KOG3802|consensus 79.5 3.6 7.7E-05 34.3 4.4 43 68-110 310-354 (398)
72 PF09607 BrkDBD: Brinker DNA-b 78.2 8.2 0.00018 23.1 4.6 45 9-54 3-47 (58)
73 cd00569 HTH_Hin_like Helix-tur 76.4 7.7 0.00017 19.2 4.9 38 10-52 4-41 (42)
74 KOG1168|consensus 76.4 3.3 7.2E-05 33.0 3.3 25 92-116 351-375 (385)
75 PRK04217 hypothetical protein; 76.1 18 0.00038 24.7 6.4 49 10-63 41-89 (110)
76 PF08281 Sigma70_r4_2: Sigma-7 76.0 12 0.00027 21.3 5.5 41 12-57 11-51 (54)
77 PRK09413 IS2 repressor TnpA; R 75.3 11 0.00023 26.0 5.4 45 7-55 8-52 (121)
78 TIGR03879 near_KaiC_dom probab 74.3 2.1 4.5E-05 27.0 1.4 36 20-55 20-55 (73)
79 KOG3755|consensus 73.8 0.94 2E-05 39.5 -0.3 103 5-109 647-758 (769)
80 PF13936 HTH_38: Helix-turn-he 71.7 9.9 0.00021 21.1 3.7 40 10-54 3-42 (44)
81 PF06056 Terminase_5: Putative 71.2 4.3 9.2E-05 24.2 2.2 22 33-54 14-35 (58)
82 PRK03975 tfx putative transcri 71.2 24 0.00053 25.1 6.4 51 9-65 4-54 (141)
83 cd04761 HTH_MerR-SF Helix-Turn 67.1 7.2 0.00016 21.6 2.6 20 35-54 3-22 (49)
84 PF08280 HTH_Mga: M protein tr 65.8 12 0.00025 22.2 3.4 35 15-53 6-40 (59)
85 PF13518 HTH_28: Helix-turn-he 63.7 11 0.00025 21.1 3.0 24 34-57 14-37 (52)
86 PRK09642 RNA polymerase sigma 62.8 38 0.00083 23.9 6.3 32 33-64 123-154 (160)
87 COG4367 Uncharacterized protei 62.6 17 0.00037 23.6 3.8 40 11-50 2-41 (97)
88 PF00196 GerE: Bacterial regul 62.1 22 0.00049 20.6 4.2 43 11-59 3-45 (58)
89 KOG2252|consensus 61.2 7 0.00015 33.9 2.4 24 162-185 417-440 (558)
90 PRK12526 RNA polymerase sigma 61.1 37 0.00081 25.4 6.2 35 30-64 167-201 (206)
91 PF08880 QLQ: QLQ; InterPro: 61.0 6.2 0.00013 21.3 1.4 12 171-182 2-13 (37)
92 PF00376 MerR: MerR family reg 59.7 9.3 0.0002 20.6 2.0 18 36-53 3-20 (38)
93 PF13384 HTH_23: Homeodomain-l 58.5 10 0.00022 21.2 2.2 24 32-55 17-40 (50)
94 PF13551 HTH_29: Winged helix- 58.4 49 0.0011 21.6 6.0 48 7-54 53-109 (112)
95 PRK10072 putative transcriptio 58.4 8.6 0.00019 25.5 2.0 39 13-58 34-72 (96)
96 PF13411 MerR_1: MerR HTH fami 58.1 10 0.00022 22.8 2.2 19 35-53 3-21 (69)
97 smart00027 EH Eps15 homology d 58.0 45 0.00097 21.6 5.5 43 12-54 4-51 (96)
98 PRK00118 putative DNA-binding 57.9 55 0.0012 22.0 6.6 48 11-63 17-64 (104)
99 PRK12514 RNA polymerase sigma 56.1 26 0.00057 25.3 4.6 30 33-62 146-175 (179)
100 smart00421 HTH_LUXR helix_turn 55.9 34 0.00074 19.0 5.3 39 11-55 3-41 (58)
101 PRK09652 RNA polymerase sigma 55.5 58 0.0013 23.2 6.4 46 12-62 129-174 (182)
102 PRK06759 RNA polymerase factor 55.5 45 0.00098 23.3 5.6 43 12-59 107-149 (154)
103 PF13443 HTH_26: Cro/C1-type H 55.0 13 0.00027 22.0 2.2 26 34-59 12-37 (63)
104 PRK09646 RNA polymerase sigma 54.9 46 0.00099 24.5 5.8 31 33-63 159-189 (194)
105 PRK06930 positive control sigm 54.4 66 0.0014 23.6 6.4 50 11-65 114-163 (170)
106 PRK09644 RNA polymerase sigma 52.7 70 0.0015 22.7 6.3 33 32-64 124-156 (165)
107 cd04762 HTH_MerR-trunc Helix-T 52.6 19 0.00041 19.4 2.7 22 35-56 3-24 (49)
108 PRK12512 RNA polymerase sigma 52.5 60 0.0013 23.5 6.0 32 32-63 147-178 (184)
109 PRK12543 RNA polymerase sigma 52.2 88 0.0019 22.6 6.9 36 32-67 133-168 (179)
110 PF02796 HTH_7: Helix-turn-hel 52.2 37 0.00081 18.7 3.8 39 10-53 4-42 (45)
111 PF01726 LexA_DNA_bind: LexA D 51.9 38 0.00082 20.6 4.0 39 11-51 3-45 (65)
112 TIGR02937 sigma70-ECF RNA poly 51.6 42 0.00092 22.8 4.9 45 12-61 111-155 (158)
113 PRK09639 RNA polymerase sigma 51.5 71 0.0015 22.6 6.2 32 33-64 128-159 (166)
114 PF08279 HTH_11: HTH domain; 51.4 23 0.0005 20.2 3.0 34 17-53 3-36 (55)
115 cd04763 HTH_MlrA-like Helix-Tu 50.7 17 0.00037 21.9 2.4 20 35-54 3-22 (68)
116 PRK11924 RNA polymerase sigma 50.4 50 0.0011 23.5 5.3 32 32-63 141-172 (179)
117 PRK12515 RNA polymerase sigma 50.0 85 0.0018 22.9 6.5 33 33-65 148-180 (189)
118 cd04764 HTH_MlrA-like_sg1 Heli 49.6 21 0.00045 21.4 2.6 20 35-54 3-22 (67)
119 TIGR02999 Sig-70_X6 RNA polyme 49.6 76 0.0016 22.9 6.2 30 33-62 151-180 (183)
120 PRK09648 RNA polymerase sigma 48.1 69 0.0015 23.3 5.8 29 33-61 156-184 (189)
121 cd01392 HTH_LacI Helix-turn-he 47.9 13 0.00029 20.8 1.5 20 37-56 2-21 (52)
122 cd06170 LuxR_C_like C-terminal 47.7 49 0.0011 18.4 4.5 36 13-54 2-37 (57)
123 PRK12538 RNA polymerase sigma 47.5 82 0.0018 24.2 6.3 35 31-65 186-220 (233)
124 KOG1146|consensus 46.8 27 0.00057 33.9 3.9 59 6-64 706-764 (1406)
125 PRK12519 RNA polymerase sigma 46.7 77 0.0017 23.2 5.8 35 29-63 154-188 (194)
126 PRK05602 RNA polymerase sigma 46.4 88 0.0019 22.7 6.1 33 32-64 144-176 (186)
127 KOG0774|consensus 46.3 15 0.00033 28.9 2.0 27 84-110 225-251 (334)
128 PRK12530 RNA polymerase sigma 46.2 1.1E+02 0.0023 22.5 6.5 31 33-63 151-181 (189)
129 PRK06986 fliA flagellar biosyn 46.1 59 0.0013 24.9 5.3 46 13-63 186-231 (236)
130 TIGR02959 SigZ RNA polymerase 45.8 1.1E+02 0.0024 21.9 6.5 32 33-64 117-148 (170)
131 PF01381 HTH_3: Helix-turn-hel 45.2 17 0.00037 20.6 1.7 24 34-57 11-34 (55)
132 PRK08301 sporulation sigma fac 44.5 87 0.0019 23.8 6.0 33 31-63 197-229 (234)
133 PRK11511 DNA-binding transcrip 44.4 37 0.0008 23.4 3.6 28 29-56 22-49 (127)
134 PRK05988 formate dehydrogenase 44.3 53 0.0012 23.8 4.5 36 15-50 24-59 (156)
135 PF13412 HTH_24: Winged helix- 44.0 56 0.0012 18.0 4.6 37 13-53 2-38 (48)
136 COG2963 Transposase and inacti 43.2 77 0.0017 21.2 5.0 42 9-54 5-47 (116)
137 PRK12518 RNA polymerase sigma 43.0 48 0.001 23.8 4.2 36 29-64 133-168 (175)
138 cd01104 HTH_MlrA-CarA Helix-Tu 42.8 32 0.0007 20.4 2.8 20 35-54 3-22 (68)
139 COG1905 NuoE NADH:ubiquinone o 42.5 53 0.0012 24.0 4.2 37 14-50 25-61 (160)
140 TIGR02989 Sig-70_gvs1 RNA poly 42.3 1E+02 0.0022 21.5 5.7 29 30-58 125-153 (159)
141 TIGR02985 Sig70_bacteroi1 RNA 41.8 68 0.0015 22.2 4.8 28 32-59 129-156 (161)
142 PRK09047 RNA polymerase factor 41.4 1.2E+02 0.0026 21.1 6.5 30 33-62 123-152 (161)
143 PRK10403 transcriptional regul 41.1 66 0.0014 23.1 4.8 43 11-59 153-195 (215)
144 TIGR02948 SigW_bacill RNA poly 41.1 75 0.0016 22.9 5.0 33 30-62 150-182 (187)
145 PRK09480 slmA division inhibit 41.0 30 0.00066 25.1 2.9 40 18-58 14-56 (194)
146 TIGR01958 nuoE_fam NADH-quinon 40.5 64 0.0014 23.0 4.4 36 15-50 17-52 (148)
147 PRK07037 extracytoplasmic-func 40.5 1.3E+02 0.0028 21.2 6.3 30 33-62 126-155 (163)
148 COG5484 Uncharacterized conser 40.3 24 0.00051 27.8 2.2 22 33-54 20-41 (279)
149 TIGR03070 couple_hipB transcri 40.0 23 0.0005 20.0 1.7 23 35-57 18-40 (58)
150 PF13730 HTH_36: Helix-turn-he 39.7 54 0.0012 18.6 3.3 42 12-54 3-47 (55)
151 PRK12524 RNA polymerase sigma 39.7 1.4E+02 0.0031 21.9 6.4 32 32-63 152-183 (196)
152 smart00422 HTH_MERR helix_turn 39.6 29 0.00063 20.7 2.2 19 35-53 3-21 (70)
153 TIGR02939 RpoE_Sigma70 RNA pol 39.6 1E+02 0.0022 22.3 5.5 34 29-62 151-184 (190)
154 PF14229 DUF4332: Domain of un 39.6 40 0.00087 23.2 3.1 26 28-53 25-50 (122)
155 PF07037 DUF1323: Putative tra 39.6 27 0.00059 24.1 2.2 20 35-54 3-22 (122)
156 TIGR03001 Sig-70_gmx1 RNA poly 39.4 1.5E+02 0.0032 23.0 6.6 36 33-68 178-213 (244)
157 PRK07539 NADH dehydrogenase su 39.1 69 0.0015 23.0 4.4 36 16-51 24-59 (154)
158 TIGR02393 RpoD_Cterm RNA polym 39.1 1.3E+02 0.0027 23.1 6.1 52 11-63 176-227 (238)
159 PRK12516 RNA polymerase sigma 39.1 1.5E+02 0.0033 21.7 6.4 33 33-65 133-165 (187)
160 TIGR02947 SigH_actino RNA poly 38.9 84 0.0018 23.0 5.0 37 29-65 144-180 (193)
161 PF12728 HTH_17: Helix-turn-he 38.9 37 0.00079 19.0 2.4 22 35-56 4-25 (51)
162 PRK12529 RNA polymerase sigma 38.9 1.3E+02 0.0029 21.6 6.1 28 33-60 144-171 (178)
163 PRK10360 DNA-binding transcrip 38.7 78 0.0017 22.6 4.8 43 11-59 137-179 (196)
164 TIGR02954 Sig70_famx3 RNA poly 38.5 1.2E+02 0.0026 21.5 5.7 29 33-61 136-164 (169)
165 PRK09637 RNA polymerase sigma 38.5 1.5E+02 0.0033 21.5 6.3 32 32-63 122-153 (181)
166 cd08318 Death_NMPP84 Death dom 38.3 38 0.00083 21.7 2.7 34 11-51 4-37 (86)
167 KOG3755|consensus 38.3 37 0.00081 30.1 3.2 44 21-64 708-758 (769)
168 PRK05657 RNA polymerase sigma 38.2 1.2E+02 0.0027 24.6 6.2 53 11-64 262-314 (325)
169 PHA02955 hypothetical protein; 38.1 34 0.00074 26.1 2.7 44 14-57 60-104 (213)
170 cd08315 Death_TRAILR_DR4_DR5 D 38.1 50 0.0011 21.8 3.2 35 17-51 3-38 (96)
171 PRK07571 bidirectional hydroge 38.1 75 0.0016 23.4 4.5 34 17-50 39-72 (169)
172 PRK09645 RNA polymerase sigma 38.1 1.5E+02 0.0032 21.1 6.1 30 33-62 135-164 (173)
173 PF10078 DUF2316: Uncharacteri 38.0 31 0.00066 22.6 2.1 36 12-51 3-42 (89)
174 TIGR01764 excise DNA binding d 37.9 40 0.00087 18.2 2.5 21 35-55 4-24 (49)
175 PF03444 HrcA_DNA-bdg: Winged 37.7 98 0.0021 19.7 4.3 38 12-51 2-42 (78)
176 PRK08583 RNA polymerase sigma 37.5 90 0.002 24.2 5.2 46 12-62 206-251 (257)
177 PRK12541 RNA polymerase sigma 37.5 1.2E+02 0.0026 21.3 5.5 28 33-60 129-156 (161)
178 TIGR02983 SigE-fam_strep RNA p 37.4 96 0.0021 21.8 5.0 31 32-62 126-156 (162)
179 PRK12532 RNA polymerase sigma 37.3 1.6E+02 0.0036 21.5 6.4 32 33-64 153-184 (195)
180 PRK12537 RNA polymerase sigma 37.1 1.4E+02 0.0031 21.5 6.0 30 31-60 148-177 (182)
181 PRK06811 RNA polymerase factor 36.6 1.1E+02 0.0025 22.2 5.4 45 12-61 132-176 (189)
182 PRK13919 putative RNA polymera 36.5 1.4E+02 0.0031 21.5 5.9 30 32-61 151-180 (186)
183 PF12200 DUF3597: Domain of un 36.0 79 0.0017 22.1 4.0 30 29-58 82-116 (127)
184 TIGR02479 FliA_WhiG RNA polyme 35.9 1.4E+02 0.0031 22.5 6.0 45 12-61 176-220 (224)
185 TIGR00721 tfx DNA-binding prot 35.8 1.6E+02 0.0035 20.9 6.6 48 9-62 4-51 (137)
186 PRK07408 RNA polymerase sigma 35.6 95 0.0021 24.2 5.0 47 12-63 204-250 (256)
187 PF13404 HTH_AsnC-type: AsnC-t 35.3 35 0.00075 18.7 1.8 18 33-50 18-35 (42)
188 cd00131 PAX Paired Box domain 35.2 1.5E+02 0.0033 20.5 7.3 47 10-56 74-127 (128)
189 PRK12546 RNA polymerase sigma 35.2 1.6E+02 0.0034 21.7 5.9 33 32-64 129-161 (188)
190 PRK07670 RNA polymerase sigma 34.9 1E+02 0.0022 23.8 5.1 44 13-61 203-246 (251)
191 TIGR02941 Sigma_B RNA polymera 34.5 1.4E+02 0.0031 23.0 5.9 45 12-61 206-250 (255)
192 PF01257 2Fe-2S_thioredx: Thio 34.4 69 0.0015 22.7 3.7 36 16-51 15-50 (145)
193 TIGR02952 Sig70_famx2 RNA poly 33.6 1.5E+02 0.0033 20.8 5.6 23 32-54 138-160 (170)
194 PRK12539 RNA polymerase sigma 33.3 1.9E+02 0.0041 20.9 6.2 31 32-62 147-177 (184)
195 PF06971 Put_DNA-bind_N: Putat 33.3 38 0.00083 19.5 1.8 19 32-50 28-46 (50)
196 TIGR02607 antidote_HigA addict 33.0 39 0.00085 20.7 2.0 23 35-57 21-43 (78)
197 PRK06288 RNA polymerase sigma 32.6 1.3E+02 0.0029 23.5 5.5 48 12-64 213-260 (268)
198 TIGR02950 SigM_subfam RNA poly 32.3 86 0.0019 21.8 4.0 33 29-61 118-150 (154)
199 PRK12545 RNA polymerase sigma 32.2 2.1E+02 0.0045 21.2 6.6 33 32-64 155-187 (201)
200 TIGR03541 reg_near_HchA LuxR f 32.2 1E+02 0.0022 23.6 4.6 47 9-61 169-215 (232)
201 PRK12520 RNA polymerase sigma 32.1 2E+02 0.0043 20.9 6.6 32 33-64 148-179 (191)
202 PRK05803 sporulation sigma fac 32.1 1.8E+02 0.004 22.1 6.1 24 31-54 194-217 (233)
203 PRK12547 RNA polymerase sigma 32.1 1.8E+02 0.004 20.5 6.2 30 32-61 128-157 (164)
204 PRK09649 RNA polymerase sigma 31.9 1.7E+02 0.0037 21.3 5.6 27 33-59 147-173 (185)
205 PRK12536 RNA polymerase sigma 31.4 2E+02 0.0044 20.7 6.2 32 31-62 144-175 (181)
206 TIGR02980 SigBFG RNA polymeras 31.3 1.4E+02 0.003 22.6 5.2 43 12-59 179-221 (227)
207 cd01105 HTH_GlnR-like Helix-Tu 31.3 46 0.001 21.3 2.2 19 35-53 4-22 (88)
208 PRK12513 RNA polymerase sigma 31.2 1E+02 0.0022 22.5 4.4 35 29-63 152-186 (194)
209 PF00325 Crp: Bacterial regula 31.2 48 0.001 17.2 1.8 20 34-53 4-23 (32)
210 PHA01976 helix-turn-helix prot 31.2 44 0.00096 19.8 2.0 24 34-57 17-40 (67)
211 PF12824 MRP-L20: Mitochondria 31.2 2.1E+02 0.0046 20.9 6.3 44 8-53 82-125 (164)
212 TIGR02392 rpoH_proteo alternat 31.1 1.5E+02 0.0032 23.3 5.5 49 11-62 218-266 (270)
213 PRK12542 RNA polymerase sigma 31.0 2E+02 0.0043 20.8 5.9 30 33-62 139-168 (185)
214 cd01106 HTH_TipAL-Mta Helix-Tu 31.0 51 0.0011 21.7 2.5 21 35-55 3-23 (103)
215 TIGR02943 Sig70_famx1 RNA poly 31.0 2.1E+02 0.0046 20.8 6.7 33 31-63 146-178 (188)
216 PRK15369 two component system 30.9 1.7E+02 0.0036 20.7 5.5 44 10-59 148-191 (211)
217 PRK07500 rpoH2 RNA polymerase 30.8 1.7E+02 0.0037 23.3 5.9 49 11-62 227-275 (289)
218 PRK12533 RNA polymerase sigma 30.8 1.8E+02 0.0038 22.1 5.7 34 31-64 149-182 (216)
219 PRK11923 algU RNA polymerase s 30.5 1.1E+02 0.0023 22.4 4.4 35 30-64 152-186 (193)
220 PRK08295 RNA polymerase factor 30.3 1E+02 0.0022 22.7 4.3 34 29-62 167-200 (208)
221 PF13542 HTH_Tnp_ISL3: Helix-t 30.3 73 0.0016 17.7 2.8 21 34-54 29-49 (52)
222 PRK12522 RNA polymerase sigma 30.3 1.1E+02 0.0025 21.8 4.4 32 31-62 134-165 (173)
223 PRK09935 transcriptional regul 30.1 1.3E+02 0.0027 21.6 4.7 43 11-59 149-191 (210)
224 cd00093 HTH_XRE Helix-turn-hel 30.1 59 0.0013 17.3 2.4 22 35-56 15-36 (58)
225 KOG0773|consensus 30.0 80 0.0017 25.8 3.9 38 25-62 117-154 (342)
226 PRK12511 RNA polymerase sigma 30.0 2.2E+02 0.0048 20.7 6.3 31 33-63 128-158 (182)
227 PF13022 HTH_Tnp_1_2: Helix-tu 29.7 88 0.0019 22.3 3.5 24 31-54 33-56 (142)
228 PRK12531 RNA polymerase sigma 29.6 2.3E+02 0.0049 20.7 6.3 30 32-61 157-186 (194)
229 PF12802 MarR_2: MarR family; 29.0 87 0.0019 18.0 3.0 37 12-50 3-39 (62)
230 PF08452 DNAP_B_exo_N: DNA pol 28.9 22 0.00047 16.6 0.2 11 92-102 3-13 (22)
231 PRK09640 RNA polymerase sigma 28.9 1.2E+02 0.0027 22.0 4.5 34 29-62 147-180 (188)
232 TIGR02394 rpoS_proteo RNA poly 28.5 2.9E+02 0.0063 21.8 6.8 52 12-64 223-274 (285)
233 PF07022 Phage_CI_repr: Bacter 28.5 35 0.00076 20.6 1.2 23 34-56 14-37 (66)
234 COG2944 Predicted transcriptio 28.4 99 0.0021 20.9 3.4 41 12-59 44-84 (104)
235 PRK09647 RNA polymerase sigma 28.3 2.5E+02 0.0055 20.9 6.6 30 33-62 155-184 (203)
236 PRK07122 RNA polymerase sigma 28.3 1.5E+02 0.0033 23.2 5.1 45 12-61 216-260 (264)
237 PRK12523 RNA polymerase sigma 28.2 2.2E+02 0.0048 20.2 6.2 29 33-61 136-164 (172)
238 cd04766 HTH_HspR Helix-Turn-He 28.2 52 0.0011 21.2 2.0 20 35-54 4-23 (91)
239 PRK09641 RNA polymerase sigma 28.0 1.8E+02 0.004 20.8 5.3 33 30-62 150-182 (187)
240 PRK09651 RNA polymerase sigma 27.4 2.3E+02 0.0051 20.2 5.8 29 29-57 132-160 (172)
241 PF05269 Phage_CII: Bacterioph 27.3 1.3E+02 0.0029 19.7 3.8 31 33-63 24-54 (91)
242 PF07638 Sigma70_ECF: ECF sigm 27.0 1.1E+02 0.0024 22.4 3.9 30 32-61 151-180 (185)
243 PF12244 DUF3606: Protein of u 26.9 85 0.0018 18.5 2.6 19 32-50 20-38 (57)
244 PRK12528 RNA polymerase sigma 26.8 2.3E+02 0.0049 19.9 5.8 23 33-55 130-152 (161)
245 TIGR03826 YvyF flagellar opero 26.7 1.1E+02 0.0025 21.6 3.7 28 32-59 46-73 (137)
246 PRK12535 RNA polymerase sigma 26.4 2.7E+02 0.0058 20.5 6.1 31 33-63 150-180 (196)
247 PRK06596 RNA polymerase factor 26.3 2.3E+02 0.0049 22.5 5.8 41 11-54 230-270 (284)
248 PRK09415 RNA polymerase factor 26.2 2.5E+02 0.0055 20.2 5.8 29 33-61 144-172 (179)
249 cd04780 HTH_MerR-like_sg5 Heli 26.2 59 0.0013 21.3 2.1 20 35-54 3-22 (95)
250 TIGR03629 arch_S13P archaeal r 26.0 65 0.0014 23.1 2.4 16 11-26 51-66 (144)
251 TIGR02859 spore_sigH RNA polym 26.0 71 0.0015 23.3 2.7 31 29-59 162-192 (198)
252 smart00530 HTH_XRE Helix-turn- 25.9 82 0.0018 16.5 2.5 22 35-56 13-34 (56)
253 PRK05911 RNA polymerase sigma 25.8 2.1E+02 0.0045 22.3 5.4 46 12-62 206-251 (257)
254 PRK11552 putative DNA-binding 25.6 94 0.002 23.6 3.4 37 22-60 24-60 (225)
255 cd04774 HTH_YfmP Helix-Turn-He 25.5 83 0.0018 20.6 2.7 20 35-54 3-22 (96)
256 cd04779 HTH_MerR-like_sg4 Heli 25.5 67 0.0014 22.6 2.3 21 35-55 3-23 (134)
257 smart00595 MADF subfamily of S 25.1 1.8E+02 0.0039 18.2 4.7 35 35-69 30-64 (89)
258 PRK12534 RNA polymerase sigma 25.1 1.8E+02 0.004 20.9 4.8 25 31-55 152-176 (187)
259 PF14549 P22_Cro: DNA-binding 25.0 68 0.0015 19.2 2.0 18 35-52 12-29 (60)
260 TIGR02835 spore_sigmaE RNA pol 24.9 1.2E+02 0.0026 23.1 3.9 31 32-62 198-228 (234)
261 PF00165 HTH_AraC: Bacterial r 24.9 1.1E+02 0.0024 16.2 2.7 26 29-54 5-30 (42)
262 COG1595 RpoE DNA-directed RNA 24.9 1.5E+02 0.0032 21.5 4.2 33 33-65 144-176 (182)
263 PRK12544 RNA polymerase sigma 24.8 3E+02 0.0065 20.5 6.6 32 33-64 165-196 (206)
264 PF06569 DUF1128: Protein of u 24.3 1.8E+02 0.0039 18.2 3.8 34 10-43 31-67 (71)
265 PF01476 LysM: LysM domain; I 24.2 96 0.0021 16.4 2.4 20 33-52 7-26 (44)
266 PRK13890 conjugal transfer pro 24.1 70 0.0015 21.9 2.2 24 34-57 20-43 (120)
267 PRK10651 transcriptional regul 24.1 1.9E+02 0.0041 20.7 4.8 44 11-60 155-198 (216)
268 cd04768 HTH_BmrR-like Helix-Tu 24.0 79 0.0017 20.6 2.4 20 35-54 3-22 (96)
269 TIGR03020 EpsA transcriptional 24.0 1.9E+02 0.0042 22.6 4.9 46 9-60 188-233 (247)
270 cd04775 HTH_Cfa-like Helix-Tur 24.0 68 0.0015 21.2 2.1 20 35-54 4-23 (102)
271 TIGR01636 phage_rinA phage tra 23.9 1.8E+02 0.0038 20.3 4.3 38 12-52 83-120 (134)
272 PRK05572 sporulation sigma fac 23.9 2.4E+02 0.0053 21.7 5.5 44 11-59 202-245 (252)
273 PRK15183 Vi polysaccharide bio 23.9 68 0.0015 21.7 2.0 36 11-46 95-130 (143)
274 cd04788 HTH_NolA-AlbR Helix-Tu 23.8 70 0.0015 20.8 2.1 20 35-54 3-22 (96)
275 TIGR02984 Sig-70_plancto1 RNA 23.8 2.5E+02 0.0054 20.1 5.3 29 31-59 155-183 (189)
276 PF07471 Phage_Nu1: Phage DNA 23.7 74 0.0016 23.3 2.3 21 35-55 5-25 (164)
277 PRK08215 sporulation sigma fac 23.7 2.2E+02 0.0047 22.1 5.2 40 11-55 209-248 (258)
278 PRK09706 transcriptional repre 23.6 64 0.0014 22.4 2.0 23 35-57 21-43 (135)
279 PF12833 HTH_18: Helix-turn-he 23.6 78 0.0017 19.4 2.2 18 38-55 1-18 (81)
280 PF06163 DUF977: Bacterial pro 23.6 1.7E+02 0.0036 20.5 3.9 45 10-54 3-48 (127)
281 PRK13558 bacterio-opsin activa 23.4 1.1E+02 0.0023 27.3 3.8 41 10-50 606-648 (665)
282 PF00424 REV: REV protein (ant 23.4 1.8E+02 0.004 19.1 3.9 34 19-67 16-50 (91)
283 cd04789 HTH_Cfa Helix-Turn-Hel 23.4 71 0.0015 21.1 2.1 20 35-54 4-23 (102)
284 PF04936 DUF658: Protein of un 23.3 70 0.0015 23.4 2.1 31 33-63 15-45 (186)
285 PF03672 UPF0154: Uncharacteri 23.3 1.9E+02 0.0041 17.7 4.5 33 18-50 20-54 (64)
286 PF04539 Sigma70_r3: Sigma-70 23.1 93 0.002 19.0 2.5 21 33-53 21-41 (78)
287 cd04782 HTH_BltR Helix-Turn-He 23.0 85 0.0018 20.5 2.4 20 35-54 3-22 (97)
288 PF13560 HTH_31: Helix-turn-he 22.7 68 0.0015 18.9 1.7 26 33-58 15-40 (64)
289 PRK10430 DNA-binding transcrip 22.6 1.8E+02 0.0039 21.9 4.5 43 11-54 158-200 (239)
290 PF01325 Fe_dep_repress: Iron 22.5 56 0.0012 19.4 1.3 41 13-53 3-43 (60)
291 TIGR01557 myb_SHAQKYF myb-like 22.5 1.8E+02 0.0039 17.1 5.2 52 7-58 1-55 (57)
292 PRK15411 rcsA colanic acid cap 22.5 67 0.0014 24.1 2.0 39 11-55 137-175 (207)
293 PRK14996 TetR family transcrip 22.4 1.1E+02 0.0025 22.1 3.3 39 20-59 17-55 (192)
294 PRK12525 RNA polymerase sigma 22.3 2.9E+02 0.0063 19.5 5.8 27 33-59 135-161 (168)
295 PTZ00183 centrin; Provisional 22.1 2.7E+02 0.0059 19.1 5.5 42 3-44 2-48 (158)
296 cd00592 HTH_MerR-like Helix-Tu 22.0 86 0.0019 20.3 2.3 20 35-54 3-22 (100)
297 PRK11922 RNA polymerase sigma 22.0 1.8E+02 0.0039 22.1 4.4 37 29-65 162-198 (231)
298 TIGR02846 spore_sigmaK RNA pol 21.8 3.2E+02 0.007 20.6 5.7 26 33-58 195-220 (227)
299 cd04765 HTH_MlrA-like_sg2 Heli 21.8 97 0.0021 20.4 2.5 19 36-54 4-22 (99)
300 PF01710 HTH_Tnp_IS630: Transp 21.7 86 0.0019 21.3 2.3 38 12-54 3-40 (119)
301 PRK00215 LexA repressor; Valid 21.6 1.5E+02 0.0032 22.1 3.7 41 12-54 2-46 (205)
302 cd08313 Death_TNFR1 Death doma 21.5 1.2E+02 0.0027 19.3 2.8 20 32-51 11-30 (80)
303 PF08784 RPA_C: Replication pr 21.5 1E+02 0.0023 20.1 2.6 40 12-51 45-84 (102)
304 PRK10100 DNA-binding transcrip 21.5 1.9E+02 0.0042 21.9 4.4 43 11-59 155-197 (216)
305 cd04773 HTH_TioE_rpt2 Second H 21.3 89 0.0019 20.9 2.2 20 35-54 3-22 (108)
306 PF05263 DUF722: Protein of un 21.3 2.4E+02 0.0052 19.8 4.4 40 12-54 82-121 (130)
307 cd01111 HTH_MerD Helix-Turn-He 21.3 83 0.0018 21.1 2.1 20 35-54 3-22 (107)
308 PRK09958 DNA-binding transcrip 21.2 2.8E+02 0.006 19.8 5.1 43 11-59 143-185 (204)
309 PF10945 DUF2629: Protein of u 21.1 1.3E+02 0.0028 16.9 2.4 29 14-42 3-33 (44)
310 PF13613 HTH_Tnp_4: Helix-turn 21.0 95 0.0021 17.7 2.0 21 34-54 21-41 (53)
311 PF11212 DUF2999: Protein of u 20.9 2.3E+02 0.0049 17.8 4.6 38 10-51 11-48 (82)
312 PF12844 HTH_19: Helix-turn-he 20.8 78 0.0017 18.4 1.7 24 34-57 14-37 (64)
313 PRK09638 RNA polymerase sigma 20.6 1.8E+02 0.004 20.6 4.0 33 29-61 139-171 (176)
314 TIGR02054 MerD mercuric resist 20.6 1E+02 0.0022 21.2 2.4 21 34-54 5-25 (120)
315 cd01109 HTH_YyaN Helix-Turn-He 20.6 86 0.0019 21.0 2.1 19 35-53 3-21 (113)
316 cd08306 Death_FADD Fas-associa 20.4 82 0.0018 20.2 1.8 20 35-54 16-35 (86)
317 cd01107 HTH_BmrR Helix-Turn-He 20.2 89 0.0019 20.8 2.1 20 35-54 3-22 (108)
No 1
>KOG0484|consensus
Probab=99.86 E-value=3e-22 Score=131.00 Aligned_cols=66 Identities=38% Similarity=0.610 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
.+|+||.||.||+.|+.+||..|.+++|||+-.|++||.++.|++.+|+|||||||+|.+++.+-.
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a 79 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAA 79 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHH
Confidence 578999999999999999999999999999999999999999999999999999999999876643
No 2
>KOG0850|consensus
Probab=99.80 E-value=6.6e-20 Score=136.49 Aligned_cols=72 Identities=43% Similarity=0.645 Sum_probs=66.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536 1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVI 72 (186)
Q Consensus 1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~ 72 (186)
|.||.||.||.|+..||..|+..|+.+.|.-..+|.+||..|||+..||+|||||||.|.||..+..+....
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e 189 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVE 189 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcCCCccc
Confidence 678999999999999999999999999999999999999999999999999999999999998875444333
No 3
>KOG2251|consensus
Probab=99.79 E-value=7.8e-20 Score=135.50 Aligned_cols=66 Identities=35% Similarity=0.568 Sum_probs=63.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
+||.||.||.|+..|+++||+.|.++.|||+..|++||.+|+|.+.+|+|||.|||+|+++++...
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 589999999999999999999999999999999999999999999999999999999999887754
No 4
>KOG0488|consensus
Probab=99.79 E-value=2e-19 Score=143.20 Aligned_cols=74 Identities=41% Similarity=0.692 Sum_probs=67.0
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCC
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDP 75 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~ 75 (186)
+||+|+.||.||..|+..||+.|+...|.+..+|++||..|||+..||++||||||+|||++.....+......
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~~~~~~~ 242 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGELLYQAG 242 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhccccccc
Confidence 57888999999999999999999999999999999999999999999999999999999999887554444333
No 5
>KOG0494|consensus
Probab=99.78 E-value=1.8e-19 Score=136.12 Aligned_cols=66 Identities=36% Similarity=0.587 Sum_probs=59.9
Q ss_pred CCCCCCC-CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 2 TRTKDKY-RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 2 ~~~~rr~-r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
++++||. ||+||..|++.||+.|++.+|||...|+.||.++.|.|.+|+|||||||+||++.++.-
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 3444454 99999999999999999999999999999999999999999999999999999976643
No 6
>KOG0843|consensus
Probab=99.77 E-value=8.6e-19 Score=125.93 Aligned_cols=64 Identities=38% Similarity=0.658 Sum_probs=61.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
+-+|.||.||.+|+..||..|+.|+|-...+|+.||+.|+|++.||+|||||||.|.|+...+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 6788999999999999999999999999999999999999999999999999999999987765
No 7
>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=99.77 E-value=1.9e-18 Score=105.03 Aligned_cols=57 Identities=46% Similarity=0.701 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
||+|+.||.+|+.+|++.|..++||+..+++.||..+||+..+|.+||+|+|.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578899999999999999999999999999999999999999999999999999875
No 8
>KOG0489|consensus
Probab=99.76 E-value=6.4e-19 Score=138.06 Aligned_cols=68 Identities=46% Similarity=0.774 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhh
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEV 70 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~ 70 (186)
.+.||.||.||..|+.+||+.|..|.|.+...|.+||..|+|+|+||+|||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 35688999999999999999999999999999999999999999999999999999999876654433
No 9
>KOG0487|consensus
Probab=99.75 E-value=6.6e-19 Score=138.32 Aligned_cols=65 Identities=52% Similarity=0.818 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
+..||||.-||+.|+.+||+.|.-|.|++.+.|.+|++.|+|+++||+|||||||+|+||..++.
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 67889999999999999999999999999999999999999999999999999999999988643
No 10
>KOG0848|consensus
Probab=99.75 E-value=7.5e-19 Score=133.33 Aligned_cols=68 Identities=85% Similarity=1.219 Sum_probs=64.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536 1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68 (186)
Q Consensus 1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~ 68 (186)
|+|++-|-|.+||+.|+-+||+.|..+.|+++..+.+||..|||+|+||+|||||||+|++|..++..
T Consensus 195 KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 195 KTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred eeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 67888889999999999999999999999999999999999999999999999999999999877653
No 11
>KOG0842|consensus
Probab=99.71 E-value=4.8e-18 Score=133.43 Aligned_cols=71 Identities=44% Similarity=0.688 Sum_probs=65.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhc
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVI 72 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~ 72 (186)
.+++||.|..||..|+-+||+.|....|.+..+|++||..|+|++.||+|||||||=|.||+.++......
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 46788889999999999999999999999999999999999999999999999999999998887654443
No 12
>KOG0492|consensus
Probab=99.71 E-value=1.9e-17 Score=121.48 Aligned_cols=69 Identities=43% Similarity=0.696 Sum_probs=63.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhh
Q psy8536 1 KTRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69 (186)
Q Consensus 1 ~~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~ 69 (186)
|-+..|+.||-||..|+..||..|....|.++.+|.+++..|.|++.||+|||||||+|.|+.+..+.+
T Consensus 140 Khk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~E 208 (246)
T KOG0492|consen 140 KHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELE 208 (246)
T ss_pred ccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHH
Confidence 345678889999999999999999999999999999999999999999999999999999987765443
No 13
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.69 E-value=2.7e-17 Score=98.73 Aligned_cols=53 Identities=15% Similarity=0.389 Sum_probs=50.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRY----ITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~----p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
+||.||.||.+|++.|+..|..++| ||..++++||..|||++.+|+|||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999953
No 14
>KOG0485|consensus
Probab=99.68 E-value=1.3e-16 Score=117.85 Aligned_cols=68 Identities=46% Similarity=0.665 Sum_probs=62.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhh
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVV 71 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~ 71 (186)
++||.||+|+..|+..||..|+...|.+..+|..||.+|.|+|.||+|||||||.|||++-....+..
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~ 170 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA 170 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence 56788999999999999999999999999999999999999999999999999999999876554443
No 15
>KOG0493|consensus
Probab=99.67 E-value=6.1e-17 Score=122.62 Aligned_cols=61 Identities=44% Similarity=0.746 Sum_probs=57.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
-+|.||.||.+||..|++.|+.|.|.+...|++||.+|||.+.||+|||||+|+|.|+..-
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 3578999999999999999999999999999999999999999999999999999987543
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=4.1e-16 Score=94.26 Aligned_cols=54 Identities=54% Similarity=0.785 Sum_probs=51.6
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
+.|+.|+.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|+|.+.
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKW 55 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhcc
Confidence 567889999999999999999999999999999999999999999999999875
No 17
>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=99.64 E-value=8.5e-16 Score=93.77 Aligned_cols=56 Identities=52% Similarity=0.796 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
+.|..|+..|+.+|+++|..++||+..++..||..+||++.+|+.||+|+|.+.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 56789999999999999999999999999999999999999999999999999775
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.63 E-value=6.2e-16 Score=111.47 Aligned_cols=69 Identities=32% Similarity=0.485 Sum_probs=62.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhh
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVV 71 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~ 71 (186)
...+++|++.|.+|+.+|+..|..|+||+...|..|+..|||+++-|+|||||+|++.++.........
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~~~~ 117 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKVEQR 117 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccchhcc
Confidence 456788999999999999999999999999999999999999999999999999999998776544433
No 19
>KOG0486|consensus
Probab=99.63 E-value=2.1e-16 Score=122.69 Aligned_cols=76 Identities=32% Similarity=0.503 Sum_probs=67.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCCCc
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSK 77 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~~~ 77 (186)
..|+||.|+.||..|+.+||.+|+++.|||...|++||..++|++.+|.+||.|||+||++.+........+....
T Consensus 109 i~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f~ 184 (351)
T KOG0486|consen 109 ISKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGFG 184 (351)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCCc
Confidence 3488999999999999999999999999999999999999999999999999999999999887766444444443
No 20
>KOG0483|consensus
Probab=99.62 E-value=2.9e-16 Score=116.94 Aligned_cols=81 Identities=31% Similarity=0.432 Sum_probs=72.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCCCcccccchhh
Q psy8536 6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKV 85 (186)
Q Consensus 6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 85 (186)
.+++.+||.+|+..||..|+.+.+.....+..||..|||.++||.||||||||+||..+.+.+...++.....+...+..
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~~ 130 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSENDR 130 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhhH
Confidence 45567999999999999999999999999999999999999999999999999999999998888888887777766554
Q ss_pred h
Q psy8536 86 M 86 (186)
Q Consensus 86 ~ 86 (186)
.
T Consensus 131 L 131 (198)
T KOG0483|consen 131 L 131 (198)
T ss_pred H
Confidence 3
No 21
>KOG0491|consensus
Probab=99.59 E-value=5.7e-16 Score=109.80 Aligned_cols=64 Identities=50% Similarity=0.761 Sum_probs=60.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~ 68 (186)
+++-|++|+..|+..|++.|+...|.+-.+|.+||..|+|++.||+.||||||+|.|+.++...
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 4567999999999999999999999999999999999999999999999999999999877654
No 22
>KOG0490|consensus
Probab=99.57 E-value=7e-16 Score=119.24 Aligned_cols=63 Identities=35% Similarity=0.411 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
.++|+.|+.|+..|+++|+.+|+.++|||...++.||..+++++..|++||||+|++++++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 467889999999999999999999999999999999999999999999999999999998763
No 23
>KOG0844|consensus
Probab=99.53 E-value=2.1e-15 Score=116.67 Aligned_cols=71 Identities=38% Similarity=0.628 Sum_probs=64.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhhhhccCC
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKREEVVIKDP 75 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~~~~~~~ 75 (186)
-||.||.||.+||..||+.|-...|-+...|.+||..|+|.|..|+|||||||+|+|++..-........+
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhpaDP 251 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHPADP 251 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCCCCh
Confidence 36789999999999999999999999999999999999999999999999999999998887665555443
No 24
>KOG3802|consensus
Probab=99.53 E-value=1.7e-15 Score=121.59 Aligned_cols=62 Identities=34% Similarity=0.429 Sum_probs=58.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
++||+||.|+...+..||++|..|+.|+..++..||++|+|...+|+|||||||.|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 67889999999999999999999999999999999999999999999999999999997543
No 25
>KOG4577|consensus
Probab=99.47 E-value=5e-14 Score=108.33 Aligned_cols=63 Identities=30% Similarity=0.490 Sum_probs=59.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~ 66 (186)
..+|+||.||..|++.|+.+|...+.|....|++|+.++||..+.|+|||||||+|+|+..+.
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 357899999999999999999999999999999999999999999999999999999987654
No 26
>KOG0849|consensus
Probab=99.30 E-value=2.3e-12 Score=105.05 Aligned_cols=65 Identities=38% Similarity=0.577 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHh
Q psy8536 2 TRTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKK 66 (186)
Q Consensus 2 ~~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~ 66 (186)
.++.+|.|+.|+..|++.|++.|..++||++..|+.||.++|+++..|++||+|+|+++++....
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 36778889999999999999999999999999999999999999999999999999999987743
No 27
>KOG0847|consensus
Probab=99.30 E-value=2.1e-12 Score=95.84 Aligned_cols=63 Identities=37% Similarity=0.662 Sum_probs=57.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
++--|-.|+-.|+..|+..|+...|+-..++.+||..+|+.+.+|+|||||||.||+++..-+
T Consensus 167 rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 167 RKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred ccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 334467899999999999999999999999999999999999999999999999999876533
No 28
>KOG0848|consensus
Probab=99.11 E-value=2.1e-11 Score=93.13 Aligned_cols=28 Identities=82% Similarity=1.159 Sum_probs=25.9
Q ss_pred cccCCCCCccccccchHHHHHHhhhhcC
Q psy8536 159 TRKTRTKDKYRVVYSDQQRLELEKEFHY 186 (186)
Q Consensus 159 ~~~~~~~~~~r~~~~~~q~~~l~~~f~~ 186 (186)
++++|+++++|++|||+|+||||||||+
T Consensus 193 ~~KtRTkDKYRvVYTDhQRLELEKEfh~ 220 (317)
T KOG0848|consen 193 NVKTRTKDKYRVVYTDHQRLELEKEFHT 220 (317)
T ss_pred CceeecccceeEEecchhhhhhhhhhcc
Confidence 5578999999999999999999999996
No 29
>KOG0489|consensus
Probab=99.08 E-value=5e-11 Score=93.62 Aligned_cols=36 Identities=33% Similarity=0.469 Sum_probs=29.4
Q ss_pred Ccccccccc-------ccCCCCCccccccchHHHHHHhhhhcC
Q psy8536 151 TSYILDIDT-------RKTRTKDKYRVVYSDQQRLELEKEFHY 186 (186)
Q Consensus 151 ~~~~~~~~~-------~~~~~~~~~r~~~~~~q~~~l~~~f~~ 186 (186)
..|+|+... +.+++.||.||+||++||+||||||||
T Consensus 138 ~~~p~~~~~~~~~~~~~~~~~~kR~RtayT~~QllELEkEFhf 180 (261)
T KOG0489|consen 138 QIYPWMKSTANYLSSSETGGKSKRRRTAFTRYQLLELEKEFHF 180 (261)
T ss_pred ccccchhhhhcccccccccCCCCCCCcccchhhhhhhhhhhcc
Confidence 466666543 335678999999999999999999997
No 30
>KOG1168|consensus
Probab=99.00 E-value=5.7e-11 Score=91.74 Aligned_cols=62 Identities=24% Similarity=0.416 Sum_probs=58.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
.++|+||.+-.-....||++|...+.|+.+....||++|.|....|+|||||+|.|.|+...
T Consensus 308 ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 308 EKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 46788999999999999999999999999999999999999999999999999999998544
No 31
>KOG0774|consensus
Probab=99.00 E-value=3.8e-10 Score=86.05 Aligned_cols=61 Identities=28% Similarity=0.398 Sum_probs=56.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 5 KDKYRVVYSDQQRLELEKEFH---YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
.||+|..|+..-.++|+++|. .++||+.+.+++||.++|++..||..||.|+|-+.++..-
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 478899999999999999996 7899999999999999999999999999999999887543
No 32
>KOG0775|consensus
Probab=98.97 E-value=7.3e-10 Score=85.07 Aligned_cols=49 Identities=37% Similarity=0.596 Sum_probs=45.5
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 14 DQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 14 ~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
+.-+.+|+++|..|+||+..++.+||+.+||+..||-.||.|||.++|-
T Consensus 185 ekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 185 EKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred HhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 3446799999999999999999999999999999999999999999983
No 33
>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=98.84 E-value=4.7e-09 Score=58.43 Aligned_cols=34 Identities=38% Similarity=0.632 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 26 YSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 26 ~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|||+..+++.||..+||+..||..||-|.|.+
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4799999999999999999999999999999864
No 34
>KOG2252|consensus
Probab=98.59 E-value=1.1e-07 Score=79.86 Aligned_cols=57 Identities=23% Similarity=0.339 Sum_probs=53.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 4 TKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 4 ~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
..+|.|.+||..|+..|.++|+.+++|+.+..+.|+.+|||....|..||-|-|.+.
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 356779999999999999999999999999999999999999999999999998885
No 35
>KOG0844|consensus
Probab=98.39 E-value=2.5e-07 Score=72.31 Aligned_cols=55 Identities=24% Similarity=0.267 Sum_probs=42.7
Q ss_pred CCCcccccchhhhhhcccceeeeeeeehhhhhhhhhhhcccccccCCCcccccccccc
Q psy8536 74 DPSKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKDLFLSNKVM 131 (186)
Q Consensus 74 ~~~~~~~~~~~~~~~~~~~riq~WFqNrRak~~~~~~~~~~~~~~~p~~~~~~~~~~~ 131 (186)
..+.....+...+.++..+.|.|||||||+|+++|.-...++...+|. ||..|-.
T Consensus 205 YVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPhpaDPa---fytymm~ 259 (408)
T KOG0844|consen 205 YVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPHPADPA---FYTYMMN 259 (408)
T ss_pred cccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCCCCChH---HHHHHHH
Confidence 344555677778888999999999999999999998877777766665 6666654
No 36
>KOG0484|consensus
Probab=98.38 E-value=6.1e-08 Score=64.01 Aligned_cols=56 Identities=32% Similarity=0.466 Sum_probs=44.2
Q ss_pred HHHHHhhhhhhccCCCcccccchhhhhhccc--ceeeeeeeehhhhhhhhhhhccccc
Q psy8536 61 RKQLKKREEVVIKDPSKDLFLSNKVMYTYLV--FQVKIWFQNRRAKERKQLKKREEVV 116 (186)
Q Consensus 61 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~--~riq~WFqNrRak~~~~~~~~~~~~ 116 (186)
.-+.++.+..+.-.++.++......+..+.+ .+||||||||||+.++|+......+
T Consensus 26 S~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~ 83 (125)
T KOG0484|consen 26 SAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM 83 (125)
T ss_pred HHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence 3456677888888899999887776665554 5999999999999999988765543
No 37
>KOG0490|consensus
Probab=98.31 E-value=7.1e-07 Score=68.86 Aligned_cols=63 Identities=35% Similarity=0.557 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
.+.++.|+.++..|+..|...|..+++|+...++.|+..+|+++..|++||+|+|.+.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 456778999999999999999999999999999999999999999999999999999987655
No 38
>KOG0487|consensus
Probab=97.99 E-value=2.8e-06 Score=67.54 Aligned_cols=24 Identities=50% Similarity=0.733 Sum_probs=20.7
Q ss_pred CCCCccccccchHHHHHHhhhhcC
Q psy8536 163 RTKDKYRVVYSDQQRLELEKEFHY 186 (186)
Q Consensus 163 ~~~~~~r~~~~~~q~~~l~~~f~~ 186 (186)
+..|+.|.-||.+||+||||||-|
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlf 256 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLF 256 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHH
Confidence 455666999999999999999975
No 39
>KOG0850|consensus
Probab=97.95 E-value=1.2e-05 Score=60.77 Aligned_cols=39 Identities=44% Similarity=0.523 Sum_probs=29.7
Q ss_pred hhhhcccceeeeeeeehhhhhhhhhhhcccccccCCCcc
Q psy8536 85 VMYTYLVFQVKIWFQNRRAKERKQLKKREEVVIKDPSKD 123 (186)
Q Consensus 85 ~~~~~~~~riq~WFqNrRak~~~~~~~~~~~~~~~p~~~ 123 (186)
...++..++|.|||||||+|.++..+.+.....-+|...
T Consensus 157 AsLGLTQTQVKIWFQNrRSK~KKl~k~g~~~~e~~p~~~ 195 (245)
T KOG0850|consen 157 ASLGLTQTQVKIWFQNRRSKFKKLKKQGSGPVEGDPSAS 195 (245)
T ss_pred HHhCCchhHhhhhhhhhHHHHHHHHhcCCCccccCcccC
Confidence 334455579999999999999999997777666555543
No 40
>KOG1146|consensus
Probab=97.76 E-value=2.4e-05 Score=71.85 Aligned_cols=61 Identities=31% Similarity=0.482 Sum_probs=57.2
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 5 KDKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
+|..|+.+++.|+.+|...|....||...+.+.|...+++..+.|++||||-|++.++...
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4567999999999999999999999999999999999999999999999999999988655
No 41
>KOG0488|consensus
Probab=97.62 E-value=3.7e-05 Score=61.83 Aligned_cols=24 Identities=42% Similarity=0.654 Sum_probs=22.1
Q ss_pred CCCCccccccchHHHHHHhhhhcC
Q psy8536 163 RTKDKYRVVYSDQQRLELEKEFHY 186 (186)
Q Consensus 163 ~~~~~~r~~~~~~q~~~l~~~f~~ 186 (186)
+++|+.||+||+.||.||||.|++
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~ 193 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEK 193 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHH
Confidence 678889999999999999999984
No 42
>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=97.52 E-value=6e-05 Score=45.30 Aligned_cols=21 Identities=14% Similarity=0.276 Sum_probs=19.4
Q ss_pred CCccccccchHHHHHHhhhhc
Q psy8536 165 KDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 165 ~~~~r~~~~~~q~~~l~~~f~ 185 (186)
+||.||.||.+|+.+||++|+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe 21 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAE 21 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHH
Confidence 378899999999999999996
No 43
>KOG0494|consensus
Probab=97.51 E-value=4.8e-05 Score=58.51 Aligned_cols=24 Identities=29% Similarity=0.610 Sum_probs=20.9
Q ss_pred CCCCCccccccchHHHHHHhhhhc
Q psy8536 162 TRTKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 162 ~~~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
.+++|++||.||.||+.||||.|.
T Consensus 138 k~kRRh~RTiFT~~Qle~LEkaFk 161 (332)
T KOG0494|consen 138 KKKRRHFRTIFTSYQLEELEKAFK 161 (332)
T ss_pred ccccccccchhhHHHHHHHHHHHh
Confidence 346777899999999999999994
No 44
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.43 E-value=0.00026 Score=41.88 Aligned_cols=40 Identities=25% Similarity=0.362 Sum_probs=30.5
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhh
Q psy8536 17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnr 56 (186)
+..|+..|....++...+...|+.+.||+..||+.||-.+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~ 49 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAER 49 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHH
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHh
Confidence 4569999999999999999999999999999999999654
No 45
>KOG2251|consensus
Probab=97.42 E-value=6.8e-05 Score=56.47 Aligned_cols=53 Identities=34% Similarity=0.567 Sum_probs=38.2
Q ss_pred HHHHHHhhhhhhccCCCcccccchh--hhhhcccceeeeeeeehhhhhhhhhhhc
Q psy8536 60 ERKQLKKREEVVIKDPSKDLFLSNK--VMYTYLVFQVKIWFQNRRAKERKQLKKR 112 (186)
Q Consensus 60 ~~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~~~riq~WFqNrRak~~~~~~~~ 112 (186)
.+++....+..+.+..+.|+..... ...++.+++|+|||.|||||++.+.+..
T Consensus 45 tr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 45 TRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred cHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 3445555566666666777766555 4456667999999999999999887753
No 46
>KOG0842|consensus
Probab=97.06 E-value=0.00037 Score=55.55 Aligned_cols=31 Identities=42% Similarity=0.572 Sum_probs=23.5
Q ss_pred hhhhhcccceeeeeeeehhhhhhhhhhhccc
Q psy8536 84 KVMYTYLVFQVKIWFQNRRAKERKQLKKREE 114 (186)
Q Consensus 84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~~~ 114 (186)
....++..++|.|||||+|.|.+++......
T Consensus 187 A~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~ 217 (307)
T KOG0842|consen 187 ASSLRLTPTQVKIWFQNRRYKTKRQQKDKAL 217 (307)
T ss_pred HHhcCCCchheeeeeecchhhhhhhhhhhhh
Confidence 3445566689999999999998887665433
No 47
>KOG0485|consensus
Probab=96.90 E-value=0.00052 Score=51.62 Aligned_cols=30 Identities=40% Similarity=0.513 Sum_probs=23.4
Q ss_pred hhhhhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536 84 KVMYTYLVFQVKIWFQNRRAKERKQLKKRE 113 (186)
Q Consensus 84 ~~~~~~~~~riq~WFqNrRak~~~~~~~~~ 113 (186)
.....+..++|.|||||||.||+++.....
T Consensus 138 A~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 138 AASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred HHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 344456678999999999999999866543
No 48
>KOG0773|consensus
Probab=96.83 E-value=0.00077 Score=55.17 Aligned_cols=58 Identities=28% Similarity=0.255 Sum_probs=49.5
Q ss_pred CCCCCCCCCHHHHHHHHHHH-h--hcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 5 KDKYRVVYSDQQRLELEKEF-H--YSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f-~--~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..|++..+......+|+.+. . ..+||+..++..||.++||+..||.+||-|.|.+.-+
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~ 299 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWK 299 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCC
Confidence 44556789999999999884 3 3579999999999999999999999999999988554
No 49
>KOG0491|consensus
Probab=96.63 E-value=0.00069 Score=48.83 Aligned_cols=27 Identities=44% Similarity=0.698 Sum_probs=22.1
Q ss_pred hhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536 87 YTYLVFQVKIWFQNRRAKERKQLKKRE 113 (186)
Q Consensus 87 ~~~~~~riq~WFqNrRak~~~~~~~~~ 113 (186)
.++...+|..||||+|+|++++..+..
T Consensus 137 L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 137 LSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 344446999999999999999988775
No 50
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=96.58 E-value=0.0012 Score=47.87 Aligned_cols=44 Identities=30% Similarity=0.418 Sum_probs=27.0
Q ss_pred hhhhccCCCcccccch--hhhhhcccceeeeeeeehhhhhhhhhhh
Q psy8536 68 EEVVIKDPSKDLFLSN--KVMYTYLVFQVKIWFQNRRAKERKQLKK 111 (186)
Q Consensus 68 ~~~~~~~~~~~~~~~~--~~~~~~~~~riq~WFqNrRak~~~~~~~ 111 (186)
+..+...+..+....- ....+...-.||+||||+|++.++....
T Consensus 67 ~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 67 EREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred HHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3444455554444332 3333444569999999999998775443
No 51
>KOG0843|consensus
Probab=96.52 E-value=0.0016 Score=47.66 Aligned_cols=22 Identities=27% Similarity=0.537 Sum_probs=20.8
Q ss_pred CCCccccccchHHHHHHhhhhc
Q psy8536 164 TKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 164 ~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
..||.||+||..||+.||.+|.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~ 122 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFE 122 (197)
T ss_pred CCCccccccCHHHHHHHHHHHh
Confidence 6899999999999999999996
No 52
>KOG3623|consensus
Probab=96.13 E-value=0.011 Score=52.01 Aligned_cols=48 Identities=21% Similarity=0.309 Sum_probs=44.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
+.+|++.|..|..|+..+...+|...||+...|+.||++.++......
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999877654
No 53
>KOG0483|consensus
Probab=96.09 E-value=0.00059 Score=51.31 Aligned_cols=23 Identities=39% Similarity=0.575 Sum_probs=17.4
Q ss_pred hcccceeeeeeeehhhhhhhhhh
Q psy8536 88 TYLVFQVKIWFQNRRAKERKQLK 110 (186)
Q Consensus 88 ~~~~~riq~WFqNrRak~~~~~~ 110 (186)
++..-+|.||||||||+|+...-
T Consensus 88 gL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 88 GLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred CCChhHHHHHHhhccccccchhh
Confidence 33345999999999999876443
No 54
>KOG4577|consensus
Probab=95.95 E-value=0.0017 Score=50.97 Aligned_cols=17 Identities=59% Similarity=1.068 Sum_probs=14.0
Q ss_pred eeeeeeeehhhhhhhhh
Q psy8536 93 QVKIWFQNRRAKERKQL 109 (186)
Q Consensus 93 riq~WFqNrRak~~~~~ 109 (186)
-|||||||||||.++..
T Consensus 210 VVQVWFQNRRAKEKRLK 226 (383)
T KOG4577|consen 210 VVQVWFQNRRAKEKRLK 226 (383)
T ss_pred ehhhhhhhhhHHHHhhh
Confidence 68999999999966543
No 55
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.92 E-value=0.025 Score=33.33 Aligned_cols=47 Identities=21% Similarity=0.376 Sum_probs=35.8
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
+|+|..+|-++...+-..++... ...+||.++|++..+|..|..|+-
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46789999999888888887666 578899999999999999998753
No 56
>KOG0486|consensus
Probab=95.42 E-value=0.016 Score=46.21 Aligned_cols=51 Identities=27% Similarity=0.475 Sum_probs=34.6
Q ss_pred HHHhhhhhhccCCCcccccchhhh--hhcccceeeeeeeehhhhhhhhhhhcc
Q psy8536 63 QLKKREEVVIKDPSKDLFLSNKVM--YTYLVFQVKIWFQNRRAKERKQLKKRE 113 (186)
Q Consensus 63 ~~~~~~~~~~~~~~~~~~~~~~~~--~~~~~~riq~WFqNrRak~~~~~~~~~ 113 (186)
+..+.+..+...-+.+.....+.+ .++.+-+|.+||.||||+|++.+.+..
T Consensus 123 qlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 123 QLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred HHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 344445555555555554444433 345556999999999999999998877
No 57
>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=95.27 E-value=0.013 Score=34.69 Aligned_cols=20 Identities=25% Similarity=0.391 Sum_probs=18.3
Q ss_pred CccccccchHHHHHHhhhhc
Q psy8536 166 DKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 166 ~~~r~~~~~~q~~~l~~~f~ 185 (186)
|+.|+.||.+|+..||..|.
T Consensus 1 kr~r~~~t~~q~~~L~~~f~ 20 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQ 20 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHH
Confidence 56799999999999999995
No 58
>KOG0847|consensus
Probab=95.04 E-value=0.0037 Score=47.17 Aligned_cols=24 Identities=50% Similarity=0.693 Sum_probs=19.5
Q ss_pred cccceeeeeeeehhhhhhhhhhhc
Q psy8536 89 YLVFQVKIWFQNRRAKERKQLKKR 112 (186)
Q Consensus 89 ~~~~riq~WFqNrRak~~~~~~~~ 112 (186)
...++|.|||||||-||++.+...
T Consensus 206 mteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 206 MTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred ccHHHHHHHHhcchhhhhhhhccc
Confidence 345799999999999999976543
No 59
>KOG0492|consensus
Probab=94.86 E-value=0.021 Score=42.86 Aligned_cols=23 Identities=35% Similarity=0.569 Sum_probs=20.4
Q ss_pred CCCCccccccchHHHHHHhhhhc
Q psy8536 163 RTKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 163 ~~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
...|+.||.||..||+.||+.|+
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfr 164 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFR 164 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHh
Confidence 34678899999999999999996
No 60
>KOG0493|consensus
Probab=94.74 E-value=0.019 Score=44.62 Aligned_cols=22 Identities=23% Similarity=0.454 Sum_probs=20.0
Q ss_pred CCCccccccchHHHHHHhhhhc
Q psy8536 164 TKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 164 ~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
+.||.||+||.+||..|..||.
T Consensus 245 eeKRPRTAFtaeQL~RLK~EF~ 266 (342)
T KOG0493|consen 245 EEKRPRTAFTAEQLQRLKAEFQ 266 (342)
T ss_pred hhcCccccccHHHHHHHHHHHh
Confidence 3578999999999999999996
No 61
>KOG0849|consensus
Probab=92.39 E-value=0.1 Score=43.10 Aligned_cols=25 Identities=28% Similarity=0.316 Sum_probs=22.4
Q ss_pred cCCCCCccccccchHHHHHHhhhhc
Q psy8536 161 KTRTKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 161 ~~~~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
-+++.+|.||+||..|+.+||++|+
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~ 196 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQ 196 (354)
T ss_pred ccccccccccccccchHHHHHHHhc
Confidence 3577888899999999999999997
No 62
>KOG0775|consensus
Probab=92.19 E-value=0.21 Score=39.24 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=22.4
Q ss_pred chhhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536 82 SNKVMYTYLVFQVKIWFQNRRAKERKQLK 110 (186)
Q Consensus 82 ~~~~~~~~~~~riq~WFqNrRak~~~~~~ 110 (186)
+...++.+..++|..||.|||.+++....
T Consensus 208 eLA~aTgLt~tQVsNWFKNRRQRDRa~~a 236 (304)
T KOG0775|consen 208 ELAEATGLTITQVSNWFKNRRQRDRAAAA 236 (304)
T ss_pred HHHHHhCCchhhhhhhhhhhhhhhhhccc
Confidence 34466677778999999999999985444
No 63
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=91.99 E-value=0.12 Score=30.19 Aligned_cols=20 Identities=40% Similarity=0.592 Sum_probs=17.6
Q ss_pred CccccccchHHHHHHhhhhc
Q psy8536 166 DKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 166 ~~~r~~~~~~q~~~l~~~f~ 185 (186)
++.|+.||.+|+..||..|.
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~ 20 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQ 20 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHH
Confidence 35688999999999999996
No 64
>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=91.53 E-value=0.42 Score=28.08 Aligned_cols=40 Identities=28% Similarity=0.302 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHcCCChhHHHH
Q psy8536 12 YSDQQRLELEKEFHYSR--YITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~--~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
+|+.|.++|..++...= +|-...-.+||.++|++...+..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 58899999999987443 47788889999999999887654
No 65
>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=88.67 E-value=0.72 Score=28.69 Aligned_cols=44 Identities=25% Similarity=0.363 Sum_probs=29.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
++|..||.++...+-..+... .....++|.++||+...|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHH
Confidence 457899999888776666222 36788899999999999999974
No 66
>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=88.66 E-value=2.4 Score=24.09 Aligned_cols=41 Identities=17% Similarity=0.218 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhh
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnr 56 (186)
.+++.+..+|...|.. ...-.++|..+|++...|..+...-
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 4788899999999932 2456788999999999999876543
No 67
>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=87.40 E-value=0.47 Score=27.83 Aligned_cols=19 Identities=42% Similarity=0.597 Sum_probs=17.2
Q ss_pred ccccccchHHHHHHhhhhc
Q psy8536 167 KYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 167 ~~r~~~~~~q~~~l~~~f~ 185 (186)
+.|+.|+..|+..||+.|+
T Consensus 2 ~~r~~~~~~~~~~Le~~f~ 20 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFE 20 (59)
T ss_pred CCCCcCCHHHHHHHHHHHH
Confidence 4588999999999999996
No 68
>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=85.75 E-value=0.79 Score=27.66 Aligned_cols=21 Identities=29% Similarity=0.624 Sum_probs=18.0
Q ss_pred HHHHHHHHHcCCChhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WF 53 (186)
-.-.+||.+||+++.+|..|=
T Consensus 23 i~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 23 IKLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred ccHHHHHHHHCCCHHHHHHHh
Confidence 345678999999999999995
No 69
>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=82.10 E-value=3.5 Score=22.90 Aligned_cols=42 Identities=19% Similarity=0.230 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
.++..+..++...|... ..-.++|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45777788887776422 3567789999999999999986543
No 70
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=80.26 E-value=2.8 Score=31.92 Aligned_cols=41 Identities=22% Similarity=0.238 Sum_probs=34.6
Q ss_pred CCCHHHHHHHHHHHhh--cCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 11 VYSDQQRLELEKEFHY--SRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~--~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
-+|+.|+++|..+|.. =.+|-...-.+||+++|++...+.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 5999999999999973 4467788889999999999887653
No 71
>KOG3802|consensus
Probab=79.50 E-value=3.6 Score=34.26 Aligned_cols=43 Identities=26% Similarity=0.394 Sum_probs=25.9
Q ss_pred hhhhccCCCcccccchhhhhhc--ccceeeeeeeehhhhhhhhhh
Q psy8536 68 EEVVIKDPSKDLFLSNKVMYTY--LVFQVKIWFQNRRAKERKQLK 110 (186)
Q Consensus 68 ~~~~~~~~~~~~~~~~~~~~~~--~~~riq~WFqNrRak~~~~~~ 110 (186)
+..+.+.+-...-.+...+..+ ..--|.|||=|||.|.++...
T Consensus 310 E~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 310 EKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred HHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 4444444444443333333332 234799999999999887655
No 72
>PF09607 BrkDBD: Brinker DNA-binding domain; InterPro: IPR018586 This DNA-binding domain is the first approx. 100 residues of the N-terminal end of Brinker. The structure of this domain in complex with DNA consists of four alpha-helices that contain a helix-turn-helix DNA recognition motif specific for GC-rich DNA. The Brinker nuclear repressor is a major element of the Drosophila Decapentaplegic morphogen signalling pathway []. ; PDB: 2GLO_A.
Probab=78.21 E-value=8.2 Score=23.07 Aligned_cols=45 Identities=22% Similarity=0.336 Sum_probs=22.0
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
|..|+....-..-..|..+..--...|. -|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4456654433333333333222223344 49999999999999974
No 73
>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=76.42 E-value=7.7 Score=19.18 Aligned_cols=38 Identities=21% Similarity=0.190 Sum_probs=27.4
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIW 52 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~W 52 (186)
..++.++...+...+... . ...++|..+|++...|..|
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 446777777776666532 2 5667899999999888877
No 74
>KOG1168|consensus
Probab=76.36 E-value=3.3 Score=33.00 Aligned_cols=25 Identities=28% Similarity=0.634 Sum_probs=18.8
Q ss_pred ceeeeeeeehhhhhhhhhhhccccc
Q psy8536 92 FQVKIWFQNRRAKERKQLKKREEVV 116 (186)
Q Consensus 92 ~riq~WFqNrRak~~~~~~~~~~~~ 116 (186)
.-|.|||=|+|.|.++........+
T Consensus 351 NVVRVWFCNQRQKQKRm~~Sa~~~m 375 (385)
T KOG1168|consen 351 NVVRVWFCNQRQKQKRMKRSATAVM 375 (385)
T ss_pred ceEEEEeeccHHHHHHhhhhhceee
Confidence 5799999999999888655444333
No 75
>PRK04217 hypothetical protein; Provisional
Probab=76.11 E-value=18 Score=24.68 Aligned_cols=49 Identities=14% Similarity=0.054 Sum_probs=36.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..++.+|++++...|...- ...+||+.+|++...|......-+.+-+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4678889888877765433 667899999999999998887655555443
No 76
>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=76.02 E-value=12 Score=21.31 Aligned_cols=41 Identities=29% Similarity=0.329 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
+++.+..++.-.|. ....-.++|..+|+++..|+.|...-+
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45556666655443 345678899999999999999986444
No 77
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=75.30 E-value=11 Score=25.99 Aligned_cols=45 Identities=13% Similarity=0.234 Sum_probs=31.3
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
++|..||.++....-.....+. ....++|.++|++...|..|-+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 4467788887654433333333 34567899999999999999753
No 78
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=74.28 E-value=2.1 Score=26.96 Aligned_cols=36 Identities=22% Similarity=0.278 Sum_probs=28.2
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 20 LEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 20 L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
.+..|..+.|-......+||..+|+++..|+.|+.+
T Consensus 20 ~r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 20 AEAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 345566666656677889999999999999999853
No 79
>KOG3755|consensus
Probab=73.84 E-value=0.94 Score=39.54 Aligned_cols=103 Identities=20% Similarity=0.256 Sum_probs=66.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHh-hcCCCCHHH---HHHHHHHcCCChhHHHHHHHhhHHHHHHHHH----hhhh-hhccCC
Q psy8536 5 KDKYRVVYSDQQRLELEKEFH-YSRYITIRR---KAELANSLGLSERQVKIWFQNRRAKERKQLK----KREE-VVIKDP 75 (186)
Q Consensus 5 ~rr~r~~~t~~q~~~L~~~f~-~~~~p~~~~---r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~----~~~~-~~~~~~ 75 (186)
+.+.|+.+..+-+.+|..+-. ..-||+... ...|+..+.++.+-|.--|+|.|.-.+..-. .... .....-
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYk 726 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYK 726 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecchhheecccCchhHHHHHhh
Confidence 456788899999999988754 445899888 8899999999999999999999876442211 0000 000000
Q ss_pred Ccccccchhhhhhcccceeeeeeeehhhhhhhhh
Q psy8536 76 SKDLFLSNKVMYTYLVFQVKIWFQNRRAKERKQL 109 (186)
Q Consensus 76 ~~~~~~~~~~~~~~~~~riq~WFqNrRak~~~~~ 109 (186)
...+. ...-..+..-.++.||.|+|++..+-.
T Consensus 727 ee~~~--~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 727 EEELL--MPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred HHhhc--chhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 00000 011112233478999999999877643
No 80
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.72 E-value=9.9 Score=21.08 Aligned_cols=40 Identities=20% Similarity=0.162 Sum_probs=20.5
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
..+|.+++..++..... .....+||..+|.+...|..+-.
T Consensus 3 ~~Lt~~eR~~I~~l~~~-----G~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQ-----GMSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHc-----CCCHHHHHHHHCcCcHHHHHHHh
Confidence 56788888888877653 34566799999999999887653
No 81
>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=71.24 E-value=4.3 Score=24.25 Aligned_cols=22 Identities=27% Similarity=0.454 Sum_probs=18.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFq 54 (186)
-...++|+.||++...|..|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3456899999999999999974
No 82
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=71.18 E-value=24 Score=25.14 Aligned_cols=51 Identities=20% Similarity=0.120 Sum_probs=39.4
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
...+|+.|+.+|.. +. ......++|..+|++...|..|-.+-+.+.++...
T Consensus 4 ~~~Lt~rqreVL~l-r~-----~GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRL-RE-----RGLTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHH-HH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999977 32 22456789999999999999999877766655444
No 83
>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=67.09 E-value=7.2 Score=21.62 Aligned_cols=20 Identities=25% Similarity=0.355 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|..|-+
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~ 22 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYER 22 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 84
>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=65.79 E-value=12 Score=22.20 Aligned_cols=35 Identities=37% Similarity=0.477 Sum_probs=26.0
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 15 QQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 15 ~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
.|+..|+-.+. +...+.. +||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 47788888888 6555444 89999999999988543
No 85
>PF13518 HTH_28: Helix-turn-helix domain
Probab=63.74 E-value=11 Score=21.07 Aligned_cols=24 Identities=29% Similarity=0.548 Sum_probs=19.7
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
...++|.++|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 456689999999999999986433
No 86
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=62.82 E-value=38 Score=23.90 Aligned_cols=32 Identities=16% Similarity=0.150 Sum_probs=24.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|..+|+++..|+.....-|.+-+...
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 123 KSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34568899999999999998876666655544
No 87
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=62.60 E-value=17 Score=23.63 Aligned_cols=40 Identities=15% Similarity=0.215 Sum_probs=27.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
.++++|+..-...|+.+--.+....+++|..||+++-.|.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3566777655555555444455778899999999986655
No 88
>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=62.09 E-value=22 Score=20.63 Aligned_cols=43 Identities=23% Similarity=0.200 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|..++.+|.....- ....++|..+|++++.|..+..+=+.|
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~K 45 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKK 45 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHH
Confidence 5788888888766553 456789999999999999888765555
No 89
>KOG2252|consensus
Probab=61.15 E-value=7 Score=33.94 Aligned_cols=24 Identities=29% Similarity=0.425 Sum_probs=20.8
Q ss_pred CCCCCccccccchHHHHHHhhhhc
Q psy8536 162 TRTKDKYRVVYSDQQRLELEKEFH 185 (186)
Q Consensus 162 ~~~~~~~r~~~~~~q~~~l~~~f~ 185 (186)
+-..|+.|.+||++|..-|-+.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFk 440 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFK 440 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHh
Confidence 446778899999999999999985
No 90
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=61.14 E-value=37 Score=25.36 Aligned_cols=35 Identities=23% Similarity=0.187 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 30 ITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 30 p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
.....-.++|..+|+++..|+.+...-+.+-++..
T Consensus 167 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 167 FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33455678999999999999988866555555443
No 91
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=61.05 E-value=6.2 Score=21.28 Aligned_cols=12 Identities=25% Similarity=0.290 Sum_probs=10.7
Q ss_pred ccchHHHHHHhh
Q psy8536 171 VYSDQQRLELEK 182 (186)
Q Consensus 171 ~~~~~q~~~l~~ 182 (186)
.||..|+.|||.
T Consensus 2 ~FT~~Ql~~L~~ 13 (37)
T PF08880_consen 2 PFTPAQLQELRA 13 (37)
T ss_pred CCCHHHHHHHHH
Confidence 599999999985
No 92
>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=59.73 E-value=9.3 Score=20.57 Aligned_cols=18 Identities=33% Similarity=0.552 Sum_probs=15.0
Q ss_pred HHHHHHcCCChhHHHHHH
Q psy8536 36 AELANSLGLSERQVKIWF 53 (186)
Q Consensus 36 ~~la~~~~l~~~~v~~WF 53 (186)
.++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999999985
No 93
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=58.50 E-value=10 Score=21.24 Aligned_cols=24 Identities=29% Similarity=0.433 Sum_probs=17.7
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
.....++|..+|++...|..|...
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 356678899999999999999753
No 94
>PF13551 HTH_29: Winged helix-turn helix
Probab=58.41 E-value=49 Score=21.60 Aligned_cols=48 Identities=21% Similarity=0.248 Sum_probs=30.6
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHHc--CCChhHHHHHHH
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRY-----ITIRRKAE-L-ANSL--GLSERQVKIWFQ 54 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~-----p~~~~r~~-l-a~~~--~l~~~~v~~WFq 54 (186)
+.+..+++++...|.+.+..++. .+.....+ | .... .++...|..|+.
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 33444999999999999997763 22232222 3 2222 467888887774
No 95
>PRK10072 putative transcriptional regulator; Provisional
Probab=58.41 E-value=8.6 Score=25.51 Aligned_cols=39 Identities=28% Similarity=0.284 Sum_probs=27.7
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRA 58 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~ 58 (186)
+...+..|...-.. ...+||..+|++...|..|...+|.
T Consensus 34 ~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 34 SFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred ChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 44445555443332 3678899999999999999987764
No 96
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=58.10 E-value=10 Score=22.82 Aligned_cols=19 Identities=26% Similarity=0.385 Sum_probs=16.7
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWF 53 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WF 53 (186)
..++|+.+|++...|+.|=
T Consensus 3 i~eva~~~gvs~~tlr~y~ 21 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYE 21 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999995
No 97
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=58.05 E-value=45 Score=21.57 Aligned_cols=43 Identities=14% Similarity=0.171 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHY-----SRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~-----~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
++.+|+..|...|.. +.+.+..+...+-..+|+++..|...|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678899999999864 3467777777777778998888887763
No 98
>PRK00118 putative DNA-binding protein; Validated
Probab=57.90 E-value=55 Score=22.02 Aligned_cols=48 Identities=15% Similarity=0.120 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
.++..|..++...|... ..-.++|+.+|++...|..|...-+.+.+..
T Consensus 17 ~L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 17 LLTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 35667777776665543 3456799999999999999987666665543
No 99
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=56.13 E-value=26 Score=25.32 Aligned_cols=30 Identities=20% Similarity=0.314 Sum_probs=23.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-+++|..+|+++..|+.+...-|.+-++
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 456789999999999999888655555443
No 100
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=55.91 E-value=34 Score=18.99 Aligned_cols=39 Identities=28% Similarity=0.345 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
.++..+..++...+. . ....++|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 467788887765432 1 35588999999999999988763
No 101
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=55.51 E-value=58 Score=23.19 Aligned_cols=46 Identities=15% Similarity=0.086 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
+++.+..+|...|- ....-.++|..+|++...|..|...-+.+-++
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 44555555554432 23345688999999999999998755554444
No 102
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.48 E-value=45 Score=23.26 Aligned_cols=43 Identities=14% Similarity=0.215 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
+++.+..++...|- ....-.++|..+|++...|..+...-+.+
T Consensus 107 L~~~~r~ii~l~~~-----~~~s~~EIA~~l~is~~tV~~~~~ra~~~ 149 (154)
T PRK06759 107 LDEKEKYIIFERFF-----VGKTMGEIALETEMTYYQVRWIYRQALEK 149 (154)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34445555544443 23457889999999999999988644443
No 103
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=54.97 E-value=13 Score=21.97 Aligned_cols=26 Identities=15% Similarity=0.327 Sum_probs=18.5
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
...+||+.+|++...|..|+.++...
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~ 37 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSN 37 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT---
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccc
Confidence 56789999999999999999877433
No 104
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=54.91 E-value=46 Score=24.52 Aligned_cols=31 Identities=19% Similarity=0.160 Sum_probs=23.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..-.++|+.+|++...|+.+...-|.+-+..
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 4567889999999999999886555554443
No 105
>PRK06930 positive control sigma-like factor; Validated
Probab=54.43 E-value=66 Score=23.59 Aligned_cols=50 Identities=16% Similarity=0.209 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
.+++.+..++...|.. ...-.++|..+|++...|+.+...-+.+-+....
T Consensus 114 ~L~~rer~V~~L~~~e-----g~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGY-----GLSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3555555655554322 2345678999999999999999877666665444
No 106
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=52.73 E-value=70 Score=22.71 Aligned_cols=33 Identities=21% Similarity=0.106 Sum_probs=25.1
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
.....++|..+|+++..|+.|...-|.+-++..
T Consensus 124 g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 124 ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999876666655543
No 107
>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=52.63 E-value=19 Score=19.44 Aligned_cols=22 Identities=27% Similarity=0.531 Sum_probs=18.6
Q ss_pred HHHHHHHcCCChhHHHHHHHhh
Q psy8536 35 KAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnr 56 (186)
..++|..+|++...|..|-++.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4678999999999999998643
No 108
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=52.47 E-value=60 Score=23.53 Aligned_cols=32 Identities=22% Similarity=0.149 Sum_probs=24.8
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
...-.+||..+|++...|..+...-+.+-+..
T Consensus 147 g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 147 GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999887666665543
No 109
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=52.19 E-value=88 Score=22.61 Aligned_cols=36 Identities=19% Similarity=0.119 Sum_probs=27.8
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
...-.++|+.+|+++..|+.....-+.+-++.....
T Consensus 133 ~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 133 DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999998887777766655444
No 110
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=52.17 E-value=37 Score=18.71 Aligned_cols=39 Identities=23% Similarity=0.279 Sum_probs=26.9
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
..++.++.+.+...+... ....++|+.+|++...|.-++
T Consensus 4 ~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 456776677666666644 457789999999999887665
No 111
>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=51.92 E-value=38 Score=20.59 Aligned_cols=39 Identities=26% Similarity=0.294 Sum_probs=25.1
Q ss_pred CCCHHHHHHHHHH---HhhcCCCCHHHHHHHHHHcCCC-hhHHHH
Q psy8536 11 VYSDQQRLELEKE---FHYSRYITIRRKAELANSLGLS-ERQVKI 51 (186)
Q Consensus 11 ~~t~~q~~~L~~~---f~~~~~p~~~~r~~la~~~~l~-~~~v~~ 51 (186)
.+|+-|.++|+-. ...+.|| ....+||+.+|+. ...|..
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~--Pt~rEIa~~~g~~S~~tv~~ 45 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYP--PTVREIAEALGLKSTSTVQR 45 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCC--CCHHHHHHHhCCCChHHHHH
Confidence 4677888877654 4567787 4778899999996 777664
No 112
>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=51.61 E-value=42 Score=22.79 Aligned_cols=45 Identities=27% Similarity=0.270 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
++..+..++...|- ....-.++|..+|+++..|..+...-+.+-+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44555555544432 2345668999999999999988865544433
No 113
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=51.49 E-value=71 Score=22.57 Aligned_cols=32 Identities=28% Similarity=0.321 Sum_probs=24.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|..+|++...|..+...-+.+.+...
T Consensus 128 ~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 128 YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999998866666655543
No 114
>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=51.37 E-value=23 Score=20.18 Aligned_cols=34 Identities=24% Similarity=0.229 Sum_probs=21.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
..+|...+....+ ....+||..+|++.+.|..-.
T Consensus 3 ~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 3 KQILKLLLESKEP---ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHH
Confidence 3445444444443 567789999999999887533
No 115
>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=50.73 E-value=17 Score=21.93 Aligned_cols=20 Identities=20% Similarity=0.391 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 116
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=50.40 E-value=50 Score=23.47 Aligned_cols=32 Identities=25% Similarity=0.186 Sum_probs=24.7
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
...-.++|..+|++...|..|...-+.+.++.
T Consensus 141 ~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 141 GLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34557899999999999999987666555543
No 117
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=49.96 E-value=85 Score=22.88 Aligned_cols=33 Identities=27% Similarity=0.336 Sum_probs=24.6
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
..-.++|+.+|++...|+.-...-|.+.+....
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 148 KSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999887666665555433
No 118
>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=49.62 E-value=21 Score=21.41 Aligned_cols=20 Identities=10% Similarity=0.335 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|-+
T Consensus 3 i~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999975
No 119
>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=49.58 E-value=76 Score=22.87 Aligned_cols=30 Identities=30% Similarity=0.224 Sum_probs=22.6
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-.++|+.+|+++..|+.....-|.+-++
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 151 LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999888655555443
No 120
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=48.11 E-value=69 Score=23.34 Aligned_cols=29 Identities=21% Similarity=0.217 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
..-.++|..+|++...|+.+...-+.+-+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45778999999999999988754444433
No 121
>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=47.94 E-value=13 Score=20.83 Aligned_cols=20 Identities=20% Similarity=0.343 Sum_probs=18.6
Q ss_pred HHHHHcCCChhHHHHHHHhh
Q psy8536 37 ELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 37 ~la~~~~l~~~~v~~WFqnr 56 (186)
+||+.+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 58999999999999999887
No 122
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=47.65 E-value=49 Score=18.38 Aligned_cols=36 Identities=28% Similarity=0.368 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
+..+..++...+ . .....++|..+|++...|..|..
T Consensus 2 ~~~e~~i~~~~~--~----~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--E----GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHH
Confidence 455666665433 2 23667889999999999999885
No 123
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=47.54 E-value=82 Score=24.22 Aligned_cols=35 Identities=17% Similarity=0.230 Sum_probs=26.4
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
....-.++|..+|+++..|+.....-|.+-++...
T Consensus 186 eg~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 186 ENMSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 33456789999999999999988766666655443
No 124
>KOG1146|consensus
Probab=46.78 E-value=27 Score=33.89 Aligned_cols=59 Identities=15% Similarity=0.292 Sum_probs=53.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 6 DKYRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 6 rr~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
+..+..+-.++..+|-++|..+..|+...+..|.-..+...+++.+||.|-+.+.++..
T Consensus 706 ~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34567777799999999999999999999999999999999999999999999988755
No 125
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=46.72 E-value=77 Score=23.17 Aligned_cols=35 Identities=26% Similarity=0.254 Sum_probs=26.4
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
|.....-.++|..+|++...|..|...-+.+-++.
T Consensus 154 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 154 YYEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred hhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34455677899999999999999997655555543
No 126
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=46.38 E-value=88 Score=22.71 Aligned_cols=33 Identities=21% Similarity=0.160 Sum_probs=24.7
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
...-.++|..+|++...|..+...-|.+-++..
T Consensus 144 g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 144 GLSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 345578899999999999998866565555443
No 127
>KOG0774|consensus
Probab=46.35 E-value=15 Score=28.93 Aligned_cols=27 Identities=30% Similarity=0.468 Sum_probs=20.2
Q ss_pred hhhhhcccceeeeeeeehhhhhhhhhh
Q psy8536 84 KVMYTYLVFQVKIWFQNRRAKERKQLK 110 (186)
Q Consensus 84 ~~~~~~~~~riq~WFqNrRak~~~~~~ 110 (186)
...-++.+++|..||.|.|-+..+...
T Consensus 225 AkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 225 AKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HHHcCceehhhccccccceeehhhhhh
Confidence 344467778999999999988665443
No 128
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=46.24 E-value=1.1e+02 Score=22.48 Aligned_cols=31 Identities=6% Similarity=0.145 Sum_probs=23.7
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..-.++|..+|+++..|+.+...-|.+-+..
T Consensus 151 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 151 LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999999986555554443
No 129
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=46.08 E-value=59 Score=24.88 Aligned_cols=46 Identities=20% Similarity=0.243 Sum_probs=31.8
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
+..+..++...| .....-.++|..+|++...|+.+...-+.+-+..
T Consensus 186 ~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 186 PEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444444444 3334668899999999999999987766666553
No 130
>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=45.79 E-value=1.1e+02 Score=21.91 Aligned_cols=32 Identities=34% Similarity=0.361 Sum_probs=24.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|..+|+++..|+.+-..-|.+.+...
T Consensus 117 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 117 LSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45678899999999999988865555555443
No 131
>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=45.20 E-value=17 Score=20.61 Aligned_cols=24 Identities=29% Similarity=0.436 Sum_probs=19.0
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
...+||+.+|++...|..|..+.+
T Consensus 11 s~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 11 SQKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHhCCCcchhHHHhcCCC
Confidence 347899999999999999997644
No 132
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=44.50 E-value=87 Score=23.83 Aligned_cols=33 Identities=18% Similarity=0.255 Sum_probs=24.5
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
....-.++|..+|++...|+.+...-+.+-++.
T Consensus 197 eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 197 EEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345577889999999999998876555554443
No 133
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=44.41 E-value=37 Score=23.38 Aligned_cols=28 Identities=11% Similarity=0.164 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhh
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnr 56 (186)
+-......+||..+|+++..+..+|...
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3345677899999999999999999755
No 134
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=44.33 E-value=53 Score=23.76 Aligned_cols=36 Identities=19% Similarity=0.104 Sum_probs=29.8
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 15 QQRLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 15 ~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
.-+.+|...=....|.+......+|+.+|++..+|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 345666666667789999999999999999998876
No 135
>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=43.99 E-value=56 Score=17.97 Aligned_cols=37 Identities=27% Similarity=0.311 Sum_probs=24.6
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
+..+..+|..... ++. ....+||+.+|++...|..-.
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHH
Confidence 4566777866666 332 667789999999998887544
No 136
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.18 E-value=77 Score=21.22 Aligned_cols=42 Identities=26% Similarity=0.335 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGL-SERQVKIWFQ 54 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l-~~~~v~~WFq 54 (186)
|..||.+....+-+.+....+ ...++|+++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 788999988766666555553 67789999996 9999998874
No 137
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=42.96 E-value=48 Score=23.76 Aligned_cols=36 Identities=25% Similarity=0.182 Sum_probs=27.8
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
|.....-+++|..+|++...|+..+..-|.+-++..
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 445556788999999999999999876666665544
No 138
>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=42.78 E-value=32 Score=20.43 Aligned_cols=20 Identities=20% Similarity=0.414 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...+..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999984
No 139
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=42.54 E-value=53 Score=23.98 Aligned_cols=37 Identities=16% Similarity=0.127 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 14 DQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 14 ~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
+.-+.+|...+....|.+......+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4557788888998899999999999999999987764
No 140
>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=42.33 E-value=1e+02 Score=21.54 Aligned_cols=29 Identities=21% Similarity=0.071 Sum_probs=21.2
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHHhhHH
Q psy8536 30 ITIRRKAELANSLGLSERQVKIWFQNRRA 58 (186)
Q Consensus 30 p~~~~r~~la~~~~l~~~~v~~WFqnrr~ 58 (186)
.....-.++|+.+|++...|..+...-|.
T Consensus 125 ~~g~~~~eIA~~l~is~~tv~~~l~Rar~ 153 (159)
T TIGR02989 125 QRGVSLTALAEQLGRTVNAVYKALSRLRV 153 (159)
T ss_pred hcCCCHHHHHHHhCCCHHHHHHHHHHHHH
Confidence 33455678899999999999987643333
No 141
>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=41.76 E-value=68 Score=22.24 Aligned_cols=28 Identities=21% Similarity=0.298 Sum_probs=20.7
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.....++|..+|+++..|..+...-+.+
T Consensus 129 ~~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 129 GKSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 3456678999999999999877544433
No 142
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.38 E-value=1.2e+02 Score=21.15 Aligned_cols=30 Identities=30% Similarity=0.222 Sum_probs=22.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-.++|..+|++...|+.....-+.+-+.
T Consensus 123 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 123 MDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999877654444443
No 143
>PRK10403 transcriptional regulator NarP; Provisional
Probab=41.14 E-value=66 Score=23.10 Aligned_cols=43 Identities=23% Similarity=0.258 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|..+.++|...... ....+||+.+|++++.|+....|=+.|
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~k 195 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRK 195 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHH
Confidence 5788888888755432 456789999999999999888766655
No 144
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=41.09 E-value=75 Score=22.91 Aligned_cols=33 Identities=24% Similarity=0.216 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 30 ITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 30 p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
.....-.++|..+|++...|..+...-|.+-+.
T Consensus 150 ~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 150 MEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344566789999999999999988655555443
No 145
>PRK09480 slmA division inhibitor protein; Provisional
Probab=40.96 E-value=30 Score=25.11 Aligned_cols=40 Identities=20% Similarity=0.165 Sum_probs=32.3
Q ss_pred HHHHHH---HhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHH
Q psy8536 18 LELEKE---FHYSRYITIRRKAELANSLGLSERQVKIWFQNRRA 58 (186)
Q Consensus 18 ~~L~~~---f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~ 58 (186)
.+|++. |...+. +......||...|++...+-.+|.|+-.
T Consensus 14 ~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 14 QILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 444443 555556 8899999999999999999999999864
No 146
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=40.53 E-value=64 Score=22.97 Aligned_cols=36 Identities=19% Similarity=0.093 Sum_probs=29.0
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 15 QQRLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 15 ~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
.-+.+|...=....|.+......+|+.+||+..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 445566666566679999999999999999998876
No 147
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=40.52 E-value=1.3e+02 Score=21.15 Aligned_cols=30 Identities=23% Similarity=0.376 Sum_probs=22.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
....++|+.+|++...|+.....-+.+.++
T Consensus 126 ~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 126 ETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346788999999999999876544444443
No 148
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=40.26 E-value=24 Score=27.80 Aligned_cols=22 Identities=27% Similarity=0.587 Sum_probs=18.7
Q ss_pred HHHHHHHHHcCCChhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFq 54 (186)
---.+||+++|+++.+|+.|=+
T Consensus 20 mk~~dIAeklGvspntiksWKr 41 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKR 41 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHH
Confidence 3456799999999999999974
No 149
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=39.99 E-value=23 Score=20.03 Aligned_cols=23 Identities=22% Similarity=0.268 Sum_probs=19.8
Q ss_pred HHHHHHHcCCChhHHHHHHHhhH
Q psy8536 35 KAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnrr 57 (186)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999986653
No 150
>PF13730 HTH_36: Helix-turn-helix domain
Probab=39.75 E-value=54 Score=18.55 Aligned_cols=42 Identities=24% Similarity=0.233 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHY---SRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~---~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
++..++.++-..... +.. .......||..+|++.+.|+.+..
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 455555555544332 222 334678899999999999987764
No 151
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=39.65 E-value=1.4e+02 Score=21.87 Aligned_cols=32 Identities=9% Similarity=0.020 Sum_probs=24.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
...-.++|+.+|++...|+.+...-|.+-+..
T Consensus 152 g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 152 GLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999997555555543
No 152
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=39.64 E-value=29 Score=20.71 Aligned_cols=19 Identities=26% Similarity=0.371 Sum_probs=16.6
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWF 53 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WF 53 (186)
..++|+.+|++...|..|-
T Consensus 3 ~~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999996
No 153
>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=39.62 E-value=1e+02 Score=22.29 Aligned_cols=34 Identities=9% Similarity=-0.036 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
|.....-.++|..+|+++..|+.+...-|.+-+.
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3444556789999999999999888555544443
No 154
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=39.59 E-value=40 Score=23.24 Aligned_cols=26 Identities=35% Similarity=0.442 Sum_probs=22.9
Q ss_pred CCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 28 RYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 28 ~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
.-++...|.+||..+|++.+.|..|-
T Consensus 25 ~~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 25 AGDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred cCCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 34667899999999999999999995
No 155
>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=39.56 E-value=27 Score=24.12 Aligned_cols=20 Identities=30% Similarity=0.582 Sum_probs=18.0
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
-++||..+|++...|.-|-.
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 37899999999999999984
No 156
>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=39.43 E-value=1.5e+02 Score=23.03 Aligned_cols=36 Identities=11% Similarity=0.234 Sum_probs=28.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhh
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQLKKRE 68 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~ 68 (186)
..-.++|..+|++...|+.+...-|.+-++......
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~ 213 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRL 213 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999999877777666554443
No 157
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=39.12 E-value=69 Score=23.00 Aligned_cols=36 Identities=14% Similarity=0.093 Sum_probs=28.9
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 16 QRLELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 16 q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
-+.+|...=....|.+......+|+.+|++..+|.-
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~~ 59 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVEE 59 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 345565555667899999999999999999988763
No 158
>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=39.10 E-value=1.3e+02 Score=23.12 Aligned_cols=52 Identities=10% Similarity=0.133 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
.++..+..+|...|....+ ......++|..+|++...|......-..+-+..
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 3566777777777754332 334678899999999999998887666665543
No 159
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=39.08 E-value=1.5e+02 Score=21.67 Aligned_cols=33 Identities=18% Similarity=0.143 Sum_probs=24.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
..-.++|+.+|+++..|+.....-|.+-++...
T Consensus 133 ~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 133 FAYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 445688999999999999988766666555443
No 160
>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=38.87 E-value=84 Score=23.01 Aligned_cols=37 Identities=24% Similarity=0.174 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
|.....-.++|..+|+++..|+.+...-|.+-++...
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444567789999999999999998766666665443
No 161
>PF12728 HTH_17: Helix-turn-helix domain
Probab=38.86 E-value=37 Score=19.01 Aligned_cols=22 Identities=32% Similarity=0.495 Sum_probs=18.3
Q ss_pred HHHHHHHcCCChhHHHHHHHhh
Q psy8536 35 KAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnr 56 (186)
..++|+.||++...|..|-...
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4678999999999999998543
No 162
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=38.86 E-value=1.3e+02 Score=21.63 Aligned_cols=28 Identities=14% Similarity=0.268 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
..-.++|..+|+++..|+.....-+.+.
T Consensus 144 ~s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 144 MKQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3457889999999999998876444443
No 163
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=38.73 E-value=78 Score=22.58 Aligned_cols=43 Identities=28% Similarity=0.247 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|..+.++|+-.... ...++||..++++++.|....++=+.|
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~K 179 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEK 179 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5778888888766543 368889999999999999888766555
No 164
>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=38.53 E-value=1.2e+02 Score=21.54 Aligned_cols=29 Identities=21% Similarity=0.248 Sum_probs=21.3
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
..-.++|+.+|++...|..+...-|.+-+
T Consensus 136 ~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 136 LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45678899999999999987754444433
No 165
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=38.48 E-value=1.5e+02 Score=21.48 Aligned_cols=32 Identities=31% Similarity=0.276 Sum_probs=24.0
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
...-.++|..+|++...|+..+..-|.+.++.
T Consensus 122 g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (181)
T PRK09637 122 GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKEL 153 (181)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34567889999999999998886555555443
No 166
>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=38.29 E-value=38 Score=21.73 Aligned_cols=34 Identities=12% Similarity=0.163 Sum_probs=23.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
..|.+|+..+-. ..... =..||..||+++..|..
T Consensus 4 ~~t~~~l~~ia~------~iG~~-Wk~Lar~LGls~~dI~~ 37 (86)
T cd08318 4 PVTGEQITVFAN------KLGED-WKTLAPHLEMKDKEIRA 37 (86)
T ss_pred CCCHHHHHHHHH------HHhhh-HHHHHHHcCCCHHHHHH
Confidence 467777777742 22223 34489999999988865
No 167
>KOG3755|consensus
Probab=38.27 E-value=37 Score=30.14 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=33.4
Q ss_pred HHHHhhcCCCCHHHHHHHHHHcCCC-------hhHHHHHHHhhHHHHHHHH
Q psy8536 21 EKEFHYSRYITIRRKAELANSLGLS-------ERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 21 ~~~f~~~~~p~~~~r~~la~~~~l~-------~~~v~~WFqnrr~~~~~~~ 64 (186)
+.+|..+..+......+.-++..|. .+-|+.||.|||.++++..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 5567788888888777776666543 4678999999999988744
No 168
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=38.19 E-value=1.2e+02 Score=24.62 Aligned_cols=53 Identities=21% Similarity=0.261 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
.++..|..+|...|.... ......++||..+|++...|+.+...-+.+-++..
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 456777777877764332 34466788999999999999999876666665544
No 169
>PHA02955 hypothetical protein; Provisional
Probab=38.14 E-value=34 Score=26.12 Aligned_cols=44 Identities=11% Similarity=0.104 Sum_probs=34.4
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 14 DQQRLELEKEFHYS-RYITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 14 ~~q~~~L~~~f~~~-~~p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
..++..|-+.|.+. .-.+..++.+++.++|+....|..||.+.-
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~ 104 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDL 104 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchh
Confidence 45677777777665 567789999999999999877788886543
No 170
>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=38.10 E-value=50 Score=21.78 Aligned_cols=35 Identities=23% Similarity=0.396 Sum_probs=24.7
Q ss_pred HHHHHHHHhhc-CCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 17 RLELEKEFHYS-RYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 17 ~~~L~~~f~~~-~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
.+.|..+|..- .......=..||+.|||++..|..
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 45677777643 334455666799999999988774
No 171
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=38.08 E-value=75 Score=23.38 Aligned_cols=34 Identities=21% Similarity=0.060 Sum_probs=27.1
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 17 RLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 17 ~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
+.+|...=....|.+....+.+|+.+||+...|.
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 4455555456679999999999999999988776
No 172
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=38.07 E-value=1.5e+02 Score=21.12 Aligned_cols=30 Identities=27% Similarity=0.282 Sum_probs=21.9
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-.++|+.+|+++..|+.....-+.+-++
T Consensus 135 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 135 WSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345788999999999999877544444443
No 173
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=38.01 E-value=31 Score=22.59 Aligned_cols=36 Identities=28% Similarity=0.388 Sum_probs=26.6
Q ss_pred CCHHHHH----HHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 12 YSDQQRL----ELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 12 ~t~~q~~----~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
++.+|.. +|++.|.... ...+.+|..||++...|..
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~----ls~~~ia~dL~~s~~~le~ 42 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSG----LSLEQIAADLGTSPEHLEQ 42 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHH
Confidence 4555554 6777788777 4567889999999888764
No 174
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=37.87 E-value=40 Score=18.16 Aligned_cols=21 Identities=29% Similarity=0.302 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHHh
Q psy8536 35 KAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqn 55 (186)
..++|+.+|++...|..|-.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 467899999999999999853
No 175
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=37.66 E-value=98 Score=19.70 Aligned_cols=38 Identities=18% Similarity=0.181 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHH---HhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 12 YSDQQRLELEKE---FHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 12 ~t~~q~~~L~~~---f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
+|.-|..+|.+. |....-| .--..||+.++++...|+.
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~P--VgSk~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEP--VGSKTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCC--cCHHHHHHHHCCChHHHHH
Confidence 577788888776 5555555 4456778899999888764
No 176
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=37.55 E-value=90 Score=24.18 Aligned_cols=46 Identities=22% Similarity=0.244 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
++..+..+|.-.|- ....-.++|..+|++...|..|...-+.+-+.
T Consensus 206 L~~~~r~vl~l~~~-----~g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 206 LSDREKSIIQCTFI-----ENLSQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CCHHHHHHHHHHHh-----CCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555556655543 23345889999999999999888655555443
No 177
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=37.54 E-value=1.2e+02 Score=21.32 Aligned_cols=28 Identities=32% Similarity=0.314 Sum_probs=20.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
..-.++|..+|++...|+.+...-|.+-
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~Rar~~L 156 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELHRGRKET 156 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4557789999999999998875444443
No 178
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=37.43 E-value=96 Score=21.79 Aligned_cols=31 Identities=29% Similarity=0.314 Sum_probs=23.0
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
...-.++|..+|++...|+.+-..-+.+-++
T Consensus 126 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 126 DLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3456788999999999999887655555443
No 179
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=37.26 E-value=1.6e+02 Score=21.45 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=24.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|+.+|++...|+.....-|.+-++..
T Consensus 153 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 153 FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44578999999999999998876665555543
No 180
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=37.13 E-value=1.4e+02 Score=21.49 Aligned_cols=30 Identities=27% Similarity=0.315 Sum_probs=22.1
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
....-.++|+.+|++...|+.+-..-+.+-
T Consensus 148 ~~~s~~eIA~~lgis~~tV~~~l~ra~~~L 177 (182)
T PRK12537 148 DGCSHAEIAQRLGAPLGTVKAWIKRSLKAL 177 (182)
T ss_pred cCCCHHHHHHHHCCChhhHHHHHHHHHHHH
Confidence 334567889999999999998876444443
No 181
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=36.64 E-value=1.1e+02 Score=22.23 Aligned_cols=45 Identities=18% Similarity=0.244 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
+++.+..++.-.|- ......++|+.+|++...|......-|.+-+
T Consensus 132 L~~~~r~i~~l~~~-----~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 132 LEKLDREIFIRRYL-----LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred CCHHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34444444443332 2345678899999999999877654444433
No 182
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=36.53 E-value=1.4e+02 Score=21.45 Aligned_cols=30 Identities=20% Similarity=0.128 Sum_probs=21.2
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
...-.++|+.+|++...|..+...-|.+-+
T Consensus 151 ~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 151 GYTHREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 344567899999999999987754444433
No 183
>PF12200 DUF3597: Domain of unknown function (DUF3597); InterPro: IPR022016 This family of proteins is found in bacteria, eukaryotes and viruses. Proteins in this family are typically between 126 and 281 amino acids in length. The function of this domain is unknown. The structure of this domain has been found to contain five helices with a long flexible loop between helices one and two. ; PDB: 2GQB_A.
Probab=35.95 E-value=79 Score=22.11 Aligned_cols=30 Identities=23% Similarity=0.513 Sum_probs=19.9
Q ss_pred CCCHHHHHHHHHHcCCCh-----hHHHHHHHhhHH
Q psy8536 29 YITIRRKAELANSLGLSE-----RQVKIWFQNRRA 58 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~-----~~v~~WFqnrr~ 58 (186)
-.+...|.+||.+||++. .+..+|.-..-+
T Consensus 82 DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm 116 (127)
T PF12200_consen 82 DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVM 116 (127)
T ss_dssp --SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence 457899999999999875 577788854433
No 184
>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=35.92 E-value=1.4e+02 Score=22.47 Aligned_cols=45 Identities=24% Similarity=0.257 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
++..+..+|...|.. .....++|..+|++...|+.+...-+.+-+
T Consensus 176 L~~~~r~il~l~y~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYE-----ELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 455566666665532 235688999999999999988754444433
No 185
>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=35.80 E-value=1.6e+02 Score=20.88 Aligned_cols=48 Identities=17% Similarity=0.120 Sum_probs=37.2
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
.+.+|..|+.+|.-. . . .....++|..+|++...|..+-..-+.+-+.
T Consensus 4 ~~~Lte~qr~VL~Lr-~-~----GlTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELR-E-K----GLSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHH-H-c----CCCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 467899999999774 2 2 2367889999999999999888766666554
No 186
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=35.61 E-value=95 Score=24.19 Aligned_cols=47 Identities=23% Similarity=0.190 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
++..+..+|...|. ....-.++|..+|++...|..+...-+.+-+..
T Consensus 204 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 204 LEERTREVLEFVFL-----HDLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred CCHHHHHHHHHHHH-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 44555555555553 345678899999999999999886555554443
No 187
>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=35.31 E-value=35 Score=18.73 Aligned_cols=18 Identities=61% Similarity=0.781 Sum_probs=13.3
Q ss_pred HHHHHHHHHcCCChhHHH
Q psy8536 33 RRKAELANSLGLSERQVK 50 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~ 50 (186)
..-.+||+.+||++..|.
T Consensus 18 ~s~~~la~~lglS~~~v~ 35 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVR 35 (42)
T ss_dssp S-HHHHHHHHTS-HHHHH
T ss_pred ccHHHHHHHHCcCHHHHH
Confidence 445679999999998876
No 188
>cd00131 PAX Paired Box domain
Probab=35.24 E-value=1.5e+02 Score=20.49 Aligned_cols=47 Identities=11% Similarity=-0.013 Sum_probs=31.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCC-------ChhHHHHHHHhh
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGL-------SERQVKIWFQNR 56 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l-------~~~~v~~WFqnr 56 (186)
...+..+...++..-..++..+..+..++...-|+ +...|..|++++
T Consensus 74 r~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 74 RVATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred CcCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 35566777777776777877776666554224466 888888888653
No 189
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=35.18 E-value=1.6e+02 Score=21.69 Aligned_cols=33 Identities=24% Similarity=0.110 Sum_probs=25.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
...-.++|..+|++...|+.+...-|.+-++..
T Consensus 129 g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 129 GFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999999976666655443
No 190
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=34.90 E-value=1e+02 Score=23.81 Aligned_cols=44 Identities=16% Similarity=0.167 Sum_probs=29.4
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
++.+..++...| .....-.++|..+|++...|+.....-+.+-+
T Consensus 203 ~~~~r~vl~l~~-----~~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr 246 (251)
T PRK07670 203 SEKEQLVISLFY-----KEELTLTEIGQVLNLSTSRISQIHSKALFKLK 246 (251)
T ss_pred CHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 444555555444 23345688999999999999988865555444
No 191
>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=34.52 E-value=1.4e+02 Score=23.04 Aligned_cols=45 Identities=18% Similarity=0.240 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
+++.+..+|...|... ..-.++|..+|++...|+.+...-+.+-+
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr 250 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLK 250 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4556666666665322 34578999999999999988765444433
No 192
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=34.44 E-value=69 Score=22.74 Aligned_cols=36 Identities=22% Similarity=0.150 Sum_probs=26.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 16 QRLELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 16 q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
-+.+|...=....|.+......+|+.+||+..+|.-
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~~ 50 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVYG 50 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHHH
Confidence 355666665667799999999999999999988773
No 193
>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=33.62 E-value=1.5e+02 Score=20.83 Aligned_cols=23 Identities=39% Similarity=0.260 Sum_probs=18.0
Q ss_pred HHHHHHHHHHcCCChhHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFq 54 (186)
...-.++|..+|+++..|+....
T Consensus 138 g~s~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 138 NLPIAEVARILGKTEGAVKILQF 160 (170)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHH
Confidence 34567789999999999987664
No 194
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.32 E-value=1.9e+02 Score=20.94 Aligned_cols=31 Identities=26% Similarity=0.129 Sum_probs=23.2
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
...-.++|..+|++...|+.+...-+.+-++
T Consensus 147 g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 147 GLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4556788999999999999888555544443
No 195
>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=33.25 E-value=38 Score=19.51 Aligned_cols=19 Identities=37% Similarity=0.525 Sum_probs=14.2
Q ss_pred HHHHHHHHHHcCCChhHHH
Q psy8536 32 IRRKAELANSLGLSERQVK 50 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~ 50 (186)
...-.+||+.+|++..||+
T Consensus 28 ~vSS~~La~~~gi~~~qVR 46 (50)
T PF06971_consen 28 RVSSQELAEALGITPAQVR 46 (50)
T ss_dssp EE-HHHHHHHHTS-HHHHH
T ss_pred eECHHHHHHHHCCCHHHhc
Confidence 3455789999999999986
No 196
>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=32.97 E-value=39 Score=20.68 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=19.7
Q ss_pred HHHHHHHcCCChhHHHHHHHhhH
Q psy8536 35 KAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnrr 57 (186)
..+||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999996654
No 197
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=32.63 E-value=1.3e+02 Score=23.47 Aligned_cols=48 Identities=15% Similarity=0.172 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
+++.+..+|...|.. ...-.++|..+|++...|......-+.+-+...
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 455555566555532 345688999999999999987765555555443
No 198
>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=32.31 E-value=86 Score=21.76 Aligned_cols=33 Identities=24% Similarity=0.121 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
|.....-.++|..+|+++..|..+..--|.+-+
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455667888999999999999988754444433
No 199
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=32.25 E-value=2.1e+02 Score=21.16 Aligned_cols=33 Identities=15% Similarity=0.221 Sum_probs=24.6
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
...-.++|..+|+++..|+.....-|.+-+...
T Consensus 155 g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 155 DFEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 345678899999999999988765555555443
No 200
>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=32.23 E-value=1e+02 Score=23.63 Aligned_cols=47 Identities=34% Similarity=0.365 Sum_probs=36.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
...+|..++++|.-.. ....-.++|..+|++++.|+.+..|=+.|-.
T Consensus 169 ~~~Lt~re~evl~~~a------~G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~ 215 (232)
T TIGR03541 169 AGVLSEREREVLAWTA------LGRRQADIAAILGISERTVENHLRSARRKLG 215 (232)
T ss_pred hccCCHHHHHHHHHHH------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHC
Confidence 3468889999887753 2356678899999999999999987766643
No 201
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=32.14 E-value=2e+02 Score=20.90 Aligned_cols=32 Identities=16% Similarity=0.255 Sum_probs=24.1
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|..+|+++..|+.....-|.+-+...
T Consensus 148 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 148 LETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999998765555554433
No 202
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=32.14 E-value=1.8e+02 Score=22.08 Aligned_cols=24 Identities=25% Similarity=0.314 Sum_probs=19.3
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
....-+++|..+|++...|..+-.
T Consensus 194 e~~S~~EIA~~lgis~~tV~~~~~ 217 (233)
T PRK05803 194 KEKTQREIAKALGISRSYVSRIEK 217 (233)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 345678899999999999987743
No 203
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=32.10 E-value=1.8e+02 Score=20.50 Aligned_cols=30 Identities=13% Similarity=0.028 Sum_probs=22.6
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
...-.++|+.+|+++..|+.+...-|.+-+
T Consensus 128 g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 128 GFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 345678899999999999988865554443
No 204
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=31.88 E-value=1.7e+02 Score=21.30 Aligned_cols=27 Identities=15% Similarity=0.096 Sum_probs=20.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
..-.++|..+|+++..|+.....-|.+
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~ 173 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDA 173 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 445788999999999999887544443
No 205
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=31.39 E-value=2e+02 Score=20.70 Aligned_cols=32 Identities=28% Similarity=0.128 Sum_probs=24.1
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
....-.++|..+|++...|+.....-|.+-+.
T Consensus 144 ~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 144 EGLSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33456788999999999999988665555554
No 206
>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=31.30 E-value=1.4e+02 Score=22.57 Aligned_cols=43 Identities=23% Similarity=0.344 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
+++.+..+|...|. ....-.++|+.+|++...|..|...-+.+
T Consensus 179 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~ 221 (227)
T TIGR02980 179 LPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKK 221 (227)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45555556655543 23467789999999999999887544433
No 207
>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=31.27 E-value=46 Score=21.35 Aligned_cols=19 Identities=32% Similarity=0.595 Sum_probs=16.7
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWF 53 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WF 53 (186)
..++|+.+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999994
No 208
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=31.24 E-value=1e+02 Score=22.50 Aligned_cols=35 Identities=23% Similarity=0.120 Sum_probs=25.9
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
|.....-.++|..+|++...|..+...-|.+-+..
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44556678899999999999998776555554443
No 209
>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=31.22 E-value=48 Score=17.17 Aligned_cols=20 Identities=25% Similarity=0.479 Sum_probs=14.2
Q ss_pred HHHHHHHHcCCChhHHHHHH
Q psy8536 34 RKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WF 53 (186)
.+++||..+|++...|-.=+
T Consensus 4 tr~diA~~lG~t~ETVSR~l 23 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRIL 23 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHH
Confidence 57899999999987776433
No 210
>PHA01976 helix-turn-helix protein
Probab=31.20 E-value=44 Score=19.77 Aligned_cols=24 Identities=17% Similarity=0.285 Sum_probs=19.9
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
...+||..+|++...|..|-...+
T Consensus 17 t~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 17 SAPELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred CHHHHHHHhCCCHHHHHHHHcCCC
Confidence 457899999999999999986543
No 211
>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=31.16 E-value=2.1e+02 Score=20.92 Aligned_cols=44 Identities=11% Similarity=0.019 Sum_probs=36.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 8 YRVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 8 ~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
+...+|.+++.++...-..++ ..-.+..||+++|++.--|.+=-
T Consensus 82 k~y~Lt~e~i~Eir~LR~~DP--~~wTr~~LAkkF~~S~~fV~~v~ 125 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAEDP--EKWTRKKLAKKFNCSPLFVSMVA 125 (164)
T ss_pred ccccCCHHHHHHHHHHHHcCc--hHhhHHHHHHHhCCCHHHHHHhc
Confidence 346899999999988877664 56889999999999987777644
No 212
>TIGR02392 rpoH_proteo alternative sigma factor RpoH. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoH and further restricted to the Proteobacteria. This protein may be called sigma-32, sigma factor H, heat shock sigma factor, and alternative sigma factor RpoH. Note that in some species the single locus rpoH may be replaced by two or more differentially regulated stress response sigma factors.
Probab=31.14 E-value=1.5e+02 Score=23.27 Aligned_cols=49 Identities=18% Similarity=0.154 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
.++..+..+|...|.. + ....-.++|..+|++...|.-.-.+-..|-++
T Consensus 218 ~L~~rer~vl~l~y~~--~-~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--D-DKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3566677777777742 1 13456789999999999999777555444443
No 213
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=31.02 E-value=2e+02 Score=20.78 Aligned_cols=30 Identities=20% Similarity=0.414 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-.++|..+|++...|+.....-|.+-+.
T Consensus 139 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 168 (185)
T PRK12542 139 LTYQEISSVMGITEANVRKQFERARKRVQN 168 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455788999999999999977655555444
No 214
>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=30.98 E-value=51 Score=21.72 Aligned_cols=21 Identities=24% Similarity=0.281 Sum_probs=17.8
Q ss_pred HHHHHHHcCCChhHHHHHHHh
Q psy8536 35 KAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqn 55 (186)
..++|+.+|++...|+.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999853
No 215
>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=30.97 E-value=2.1e+02 Score=20.85 Aligned_cols=33 Identities=15% Similarity=0.136 Sum_probs=24.0
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
....-.+||..+|++...|+.....-|.+-++.
T Consensus 146 ~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~ 178 (188)
T TIGR02943 146 LGFESDEICQELEISTSNCHVLLYRARLSLRAC 178 (188)
T ss_pred hCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 345567899999999999998776555554443
No 216
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=30.89 E-value=1.7e+02 Score=20.69 Aligned_cols=44 Identities=20% Similarity=0.256 Sum_probs=33.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
..+|..+.++|.- +..+ + ...++|+.++++++.|..+.++=+.|
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~k 191 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRK 191 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 3488888888876 3322 2 35788999999999999998775555
No 217
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=30.85 E-value=1.7e+02 Score=23.29 Aligned_cols=49 Identities=14% Similarity=0.107 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
.++..+..+|...|. +-......++|+.+|++...|+..-..-..+-+.
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~ 275 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRR 275 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456677777777763 1234567899999999999999877655555443
No 218
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=30.76 E-value=1.8e+02 Score=22.06 Aligned_cols=34 Identities=15% Similarity=0.021 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
....-.++|..+|+++..|+..-..-|.+-+...
T Consensus 149 eg~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 149 EDMSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345678899999999999988865555555443
No 219
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=30.47 E-value=1.1e+02 Score=22.39 Aligned_cols=35 Identities=14% Similarity=0.066 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 30 ITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 30 p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
.....-.++|+.+|+++..|......-|.+-++..
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33444578899999999999988866555555443
No 220
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=30.32 E-value=1e+02 Score=22.72 Aligned_cols=34 Identities=21% Similarity=0.252 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
|.....-.++|..+|++...|+.-...-|.+-++
T Consensus 167 ~~e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 167 YLDGKSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred HHccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445666788999999999998877655555444
No 221
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=30.30 E-value=73 Score=17.74 Aligned_cols=21 Identities=29% Similarity=0.373 Sum_probs=18.4
Q ss_pred HHHHHHHHcCCChhHHHHHHH
Q psy8536 34 RKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFq 54 (186)
....+|..+|++...|...|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 567789999999999998884
No 222
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=30.29 E-value=1.1e+02 Score=21.78 Aligned_cols=32 Identities=16% Similarity=0.176 Sum_probs=22.7
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
....-+++|+.+|++...|......-+.+-++
T Consensus 134 ~~~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 165 (173)
T PRK12522 134 EQYSYKEMSEILNIPIGTVKYRLNYAKKQMRE 165 (173)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 33445678999999999999887654444443
No 223
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=30.13 E-value=1.3e+02 Score=21.63 Aligned_cols=43 Identities=26% Similarity=0.166 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|.....+|....+. ...++||.+++++.+.|+.+-.+=|.|
T Consensus 149 ~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~k 191 (210)
T PRK09935 149 VLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGK 191 (210)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4677777777643332 678889999999999999988766655
No 224
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=30.08 E-value=59 Score=17.35 Aligned_cols=22 Identities=27% Similarity=0.398 Sum_probs=18.8
Q ss_pred HHHHHHHcCCChhHHHHHHHhh
Q psy8536 35 KAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnr 56 (186)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4578999999999999998765
No 225
>KOG0773|consensus
Probab=30.04 E-value=80 Score=25.76 Aligned_cols=38 Identities=32% Similarity=0.398 Sum_probs=33.2
Q ss_pred hhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 25 HYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 25 ~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..++|++.....-|+...+|+..+|..||-|-+.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 35889999999999999999999999999888777544
No 226
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=29.98 E-value=2.2e+02 Score=20.72 Aligned_cols=31 Identities=23% Similarity=0.123 Sum_probs=23.0
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..-.++|..+|++...|+.+...-|.+-++.
T Consensus 128 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 128 LSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 4567889999999999998876555554443
No 227
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=29.75 E-value=88 Score=22.34 Aligned_cols=24 Identities=33% Similarity=0.562 Sum_probs=18.1
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
...+..+||.++|+++..+--|-+
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~ 56 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQ 56 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHH
T ss_pred ccchHHHHHHHhCCCHHHHHHHHh
Confidence 456788899999999999999974
No 228
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=29.58 E-value=2.3e+02 Score=20.73 Aligned_cols=30 Identities=17% Similarity=0.088 Sum_probs=21.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
...-.++|+.+|++...|+.-...-+.+-+
T Consensus 157 g~s~~EIA~~lgis~~tVk~rl~ra~~~Lr 186 (194)
T PRK12531 157 ELPHQQVAEMFDIPLGTVKSRLRLAVEKLR 186 (194)
T ss_pred CCCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 345578899999999999877654444433
No 229
>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=29.03 E-value=87 Score=17.98 Aligned_cols=37 Identities=24% Similarity=0.149 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~ 50 (186)
+|..|..+|......... .....+||+.++++...|.
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs 39 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVS 39 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHH
Confidence 677888888777765543 2467789999999987765
No 230
>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=28.93 E-value=22 Score=16.58 Aligned_cols=11 Identities=27% Similarity=0.761 Sum_probs=8.8
Q ss_pred ceeeeeeeehh
Q psy8536 92 FQVKIWFQNRR 102 (186)
Q Consensus 92 ~riq~WFqNrR 102 (186)
.+|-.||.|++
T Consensus 3 ikCiNWFE~~g 13 (22)
T PF08452_consen 3 IKCINWFESRG 13 (22)
T ss_pred cEEeehhhhCC
Confidence 56778999876
No 231
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=28.85 E-value=1.2e+02 Score=22.02 Aligned_cols=34 Identities=15% Similarity=0.253 Sum_probs=25.5
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
|.....-+++|..+|++...|+.+...-+.+-+.
T Consensus 147 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 180 (188)
T PRK09640 147 FVAELEFQEIADIMHMGLSATKMRYKRALDKLRE 180 (188)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3344566889999999999999998655555444
No 232
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=28.50 E-value=2.9e+02 Score=21.78 Aligned_cols=52 Identities=23% Similarity=0.245 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
++..+..+|.-.|... |.....-.++|..+|++...|+.+...-+.+-++..
T Consensus 223 Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 223 LNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred CCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555566665555211 123355778899999999999998866555555443
No 233
>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=28.50 E-value=35 Score=20.59 Aligned_cols=23 Identities=30% Similarity=0.551 Sum_probs=17.1
Q ss_pred HHHHHHHHcCCChhHHH-HHHHhh
Q psy8536 34 RKAELANSLGLSERQVK-IWFQNR 56 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~-~WFqnr 56 (186)
...+||+.+|++...|. .|....
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~r~ 37 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKKRG 37 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHHSS
T ss_pred CHHHHHHHhCcCHHHhhHHHHhCC
Confidence 34589999999999999 898543
No 234
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=28.41 E-value=99 Score=20.86 Aligned_cols=41 Identities=22% Similarity=0.357 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
++...+..+++.+.. .....|.-||++...|+.|=|+|+.-
T Consensus 44 ls~~eIk~iRe~~~l-------SQ~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 44 LSPTEIKAIREKLGL-------SQPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCHHHHHHHHHHhCC-------CHHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 666667777766653 34567889999999999999887643
No 235
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=28.33 E-value=2.5e+02 Score=20.88 Aligned_cols=30 Identities=23% Similarity=0.289 Sum_probs=22.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
..-.++|..+|+++..|+.+...-|.+-++
T Consensus 155 ~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~ 184 (203)
T PRK09647 155 LSYEEIAATLGVKLGTVRSRIHRGRQQLRA 184 (203)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 445678999999999999888655544443
No 236
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=28.31 E-value=1.5e+02 Score=23.23 Aligned_cols=45 Identities=20% Similarity=0.321 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
++..+..+|...|. ....-.++|..+|++...|..+...-+.+.+
T Consensus 216 L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr 260 (264)
T PRK07122 216 LPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLR 260 (264)
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 45555666666653 2345688999999999999988765444443
No 237
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=28.21 E-value=2.2e+02 Score=20.22 Aligned_cols=29 Identities=24% Similarity=0.318 Sum_probs=22.4
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
..-.++|+.+|++...|+.+...-+.+.+
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 136 MGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45578899999999999998865555444
No 238
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.17 E-value=52 Score=21.16 Aligned_cols=20 Identities=10% Similarity=0.238 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|..+|++...|..|-+
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999964
No 239
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.03 E-value=1.8e+02 Score=20.82 Aligned_cols=33 Identities=27% Similarity=0.231 Sum_probs=23.8
Q ss_pred CCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 30 ITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 30 p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
.....-.++|..+|++...|......-|.+-++
T Consensus 150 ~~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 150 IEDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred hhCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344556788999999999998877655555443
No 240
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.39 E-value=2.3e+02 Score=20.18 Aligned_cols=29 Identities=24% Similarity=0.283 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
|.....-.++|+.+|++...|+.+...-+
T Consensus 132 ~~~g~s~~EIA~~lgis~~tV~~~l~Ra~ 160 (172)
T PRK09651 132 QLDGLTYSEIAHKLGVSVSSVKKYVAKAT 160 (172)
T ss_pred hccCCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 33445567899999999999998874333
No 241
>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=27.26 E-value=1.3e+02 Score=19.71 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=23.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..-..+|+.+|+++.+|-.|..+-+.+....
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~a~l 54 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKMAML 54 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHHHHH
Confidence 3456689999999999999987655554443
No 242
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=27.01 E-value=1.1e+02 Score=22.44 Aligned_cols=30 Identities=37% Similarity=0.397 Sum_probs=22.7
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
...-+++|..+|++++.|......=|...+
T Consensus 151 Gls~~EIA~~lgiS~~tV~r~l~~aR~~l~ 180 (185)
T PF07638_consen 151 GLSVEEIAERLGISERTVRRRLRRARAWLR 180 (185)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 346678999999999999987765554433
No 243
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=26.92 E-value=85 Score=18.49 Aligned_cols=19 Identities=21% Similarity=0.289 Sum_probs=14.9
Q ss_pred HHHHHHHHHHcCCChhHHH
Q psy8536 32 IRRKAELANSLGLSERQVK 50 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~ 50 (186)
..+...+|.++|+++.+++
T Consensus 20 ~~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 20 PYEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHHCcCHHHHH
Confidence 4567778889998888866
No 244
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=26.83 E-value=2.3e+02 Score=19.85 Aligned_cols=23 Identities=30% Similarity=0.417 Sum_probs=18.1
Q ss_pred HHHHHHHHHcCCChhHHHHHHHh
Q psy8536 33 RRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqn 55 (186)
..-.++|..+|++...|+.+...
T Consensus 130 ~s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 130 LGYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHH
Confidence 34567899999999999987643
No 245
>TIGR03826 YvyF flagellar operon protein TIGR03826. This gene is found in flagellar operons of Bacillus-related organisms. Its function has not been determined and an official gene symbol has not been assigned, although the gene is designated yvyF in B. subtilus. A tentative assignment as a regulator is suggested in the NCBI record GI:16080597.
Probab=26.65 E-value=1.1e+02 Score=21.64 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=22.9
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.....++++.+|+++.+|..|-...|..
T Consensus 46 ~ati~eV~e~tgVs~~~I~~~IreGRL~ 73 (137)
T TIGR03826 46 QATVSEIVEETGVSEKLILKFIREGRLQ 73 (137)
T ss_pred CCCHHHHHHHHCcCHHHHHHHHHcCCee
Confidence 3566788999999999999999765544
No 246
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.35 E-value=2.7e+02 Score=20.54 Aligned_cols=31 Identities=13% Similarity=0.014 Sum_probs=22.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
..-.++|+.+|++...|+.+...-|.+-++.
T Consensus 150 ~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~ 180 (196)
T PRK12535 150 YTYEEAAKIADVRVGTIRSRVARARADLIAA 180 (196)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999998876555554443
No 247
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=26.34 E-value=2.3e+02 Score=22.53 Aligned_cols=41 Identities=20% Similarity=0.189 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
.++..+..+|...|..+ ....-.++|..+|++..+|.-.=.
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~ 270 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEK 270 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHH
Confidence 35666777777777432 245577999999999999986553
No 248
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=26.17 E-value=2.5e+02 Score=20.16 Aligned_cols=29 Identities=21% Similarity=0.281 Sum_probs=21.6
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
..-.++|..+|++...|+.+...-|.+-+
T Consensus 144 ~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr 172 (179)
T PRK09415 144 LSIKEIAEVTGVNENTVKTRLKKAKELLK 172 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 44578899999999999988764444443
No 249
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.16 E-value=59 Score=21.26 Aligned_cols=20 Identities=25% Similarity=0.471 Sum_probs=17.0
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++.+.|+.|=.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999863
No 250
>TIGR03629 arch_S13P archaeal ribosomal protein S13P. This model describes exclusively the archaeal ribosomal protein S13P. It excludes the homologous eukaryotic 40S ribosomal protein S18 and bacterial 30S ribosomal protein S13.
Probab=26.00 E-value=65 Score=23.05 Aligned_cols=16 Identities=19% Similarity=0.239 Sum_probs=9.5
Q ss_pred CCCHHHHHHHHHHHhh
Q psy8536 11 VYSDQQRLELEKEFHY 26 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~ 26 (186)
-+|.+|+..|....+.
T Consensus 51 ~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 51 YLDDEEIEKLEEAVEN 66 (144)
T ss_pred cCCHHHHHHHHHHHHh
Confidence 4566666666655543
No 251
>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=25.97 E-value=71 Score=23.34 Aligned_cols=31 Identities=19% Similarity=0.241 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
|.....-.++|..+|++...|...+..-|.+
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~ 192 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRK 192 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4455667789999999999999877544443
No 252
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.91 E-value=82 Score=16.54 Aligned_cols=22 Identities=27% Similarity=0.379 Sum_probs=18.4
Q ss_pred HHHHHHHcCCChhHHHHHHHhh
Q psy8536 35 KAELANSLGLSERQVKIWFQNR 56 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnr 56 (186)
...||..+|++...|..|-.+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 5578999999999999887654
No 253
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=25.76 E-value=2.1e+02 Score=22.31 Aligned_cols=46 Identities=20% Similarity=0.183 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
+++.+..+|...|. ....-.++|..+|++...|..+-..-+.+-++
T Consensus 206 L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 206 LEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44555555655553 33456889999999999999877544444443
No 254
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=25.57 E-value=94 Score=23.60 Aligned_cols=37 Identities=11% Similarity=0.167 Sum_probs=31.8
Q ss_pred HHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 22 KEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 22 ~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
..|....|- ....+||+..|++...|-.+|.++..-.
T Consensus 24 ~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 24 AQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 348888877 7888999999999999999999987653
No 255
>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=25.55 E-value=83 Score=20.58 Aligned_cols=20 Identities=35% Similarity=0.577 Sum_probs=17.3
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|..
T Consensus 3 I~e~a~~~gvs~~tLR~ye~ 22 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEE 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999963
No 256
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.47 E-value=67 Score=22.61 Aligned_cols=21 Identities=24% Similarity=0.373 Sum_probs=18.1
Q ss_pred HHHHHHHcCCChhHHHHHHHh
Q psy8536 35 KAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqn 55 (186)
..++|+.+|++.+.|+.|.+.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 357899999999999999953
No 257
>smart00595 MADF subfamily of SANT domain.
Probab=25.15 E-value=1.8e+02 Score=18.16 Aligned_cols=35 Identities=34% Similarity=0.510 Sum_probs=28.4
Q ss_pred HHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhhhh
Q psy8536 35 KAELANSLGLSERQVKIWFQNRRAKERKQLKKREE 69 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~~~ 69 (186)
=.+||.++|.+...|+.-+.|=|....+.......
T Consensus 30 W~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 30 WEEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34589999999999999999999988877665543
No 258
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=25.07 E-value=1.8e+02 Score=20.95 Aligned_cols=25 Identities=24% Similarity=0.218 Sum_probs=18.1
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
....-.++|..+|++...|..--..
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~R 176 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRR 176 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHH
Confidence 3345677899999999888865543
No 259
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=24.99 E-value=68 Score=19.19 Aligned_cols=18 Identities=39% Similarity=0.802 Sum_probs=15.3
Q ss_pred HHHHHHHcCCChhHHHHH
Q psy8536 35 KAELANSLGLSERQVKIW 52 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~W 52 (186)
...||+.||++..-|--|
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 260
>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=24.93 E-value=1.2e+02 Score=23.14 Aligned_cols=31 Identities=19% Similarity=0.256 Sum_probs=22.4
Q ss_pred HHHHHHHHHHcCCChhHHHHHHHhhHHHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKIWFQNRRAKERK 62 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~ 62 (186)
...-.++|+.+|++...|..+...-+.+-++
T Consensus 198 g~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~ 228 (234)
T TIGR02835 198 EKTQKEVADMLGISQSYISRLEKRILKRLKK 228 (234)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3466778999999999998887554444443
No 261
>PF00165 HTH_AraC: Bacterial regulatory helix-turn-helix proteins, AraC family; PDB: 1WPK_A 1ZGW_A 1U8B_A.
Probab=24.90 E-value=1.1e+02 Score=16.23 Aligned_cols=26 Identities=15% Similarity=0.172 Sum_probs=15.9
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
+-......+||..+|++......=|+
T Consensus 5 ~~~~~~l~~iA~~~g~S~~~f~r~Fk 30 (42)
T PF00165_consen 5 LQQKLTLEDIAEQAGFSPSYFSRLFK 30 (42)
T ss_dssp T-SS--HHHHHHHHTS-HHHHHHHHH
T ss_pred ccCCCCHHHHHHHHCCCHHHHHHHHH
Confidence 34445677889999988777766664
No 262
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.87 E-value=1.5e+02 Score=21.51 Aligned_cols=33 Identities=36% Similarity=0.412 Sum_probs=25.8
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
..-.++|..+|++...|+.+...-|.+.+....
T Consensus 144 ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 144 LSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 445678999999999999999777766665443
No 263
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=24.75 E-value=3e+02 Score=20.53 Aligned_cols=32 Identities=19% Similarity=0.312 Sum_probs=24.1
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQL 64 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~ 64 (186)
..-.++|..+|++...|+.....-|.+-++..
T Consensus 165 ~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 165 LETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34578999999999999988865555555443
No 264
>PF06569 DUF1128: Protein of unknown function (DUF1128); InterPro: IPR009507 This family consists of several short, hypothetical bacterial proteins of unknown function.
Probab=24.30 E-value=1.8e+02 Score=18.17 Aligned_cols=34 Identities=15% Similarity=0.260 Sum_probs=26.4
Q ss_pred CCCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcC
Q psy8536 10 VVYSDQQRLELEKEFH---YSRYITIRRKAELANSLG 43 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~ 43 (186)
..|+..+-+.|...|. .....++.+...+|.+||
T Consensus 31 ~~f~~~~yedl~diy~~V~~K~~fS~sEm~aI~~ELG 67 (71)
T PF06569_consen 31 EDFSEEKYEDLKDIYEMVMSKDSFSPSEMQAIAEELG 67 (71)
T ss_pred HhCChhhHHHHHHHHHHHHhccCCCHHHHHHHHHHHH
Confidence 3567777777777775 556788999999999998
No 265
>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=24.21 E-value=96 Score=16.40 Aligned_cols=20 Identities=15% Similarity=0.134 Sum_probs=13.8
Q ss_pred HHHHHHHHHcCCChhHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIW 52 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~W 52 (186)
+....||.+.|++..++..|
T Consensus 7 Dtl~~IA~~~~~~~~~l~~~ 26 (44)
T PF01476_consen 7 DTLWSIAKRYGISVDELMEL 26 (44)
T ss_dssp --HHHHHHHTTS-HHHHHHH
T ss_pred CcHHHHHhhhhhhHhHHHHh
Confidence 45677899999998887765
No 266
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=24.14 E-value=70 Score=21.94 Aligned_cols=24 Identities=21% Similarity=0.178 Sum_probs=20.9
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
.+.+||..+|++...|..|.+++.
T Consensus 20 sq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 20 TKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 477899999999999999998764
No 267
>PRK10651 transcriptional regulator NarL; Provisional
Probab=24.11 E-value=1.9e+02 Score=20.65 Aligned_cols=44 Identities=18% Similarity=0.129 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
.+|..+.++|+-.... ..-.++|++++++.+.|....++=+.|-
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl 198 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKM 198 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHc
Confidence 3888888888765422 2456779999999999999887766663
No 268
>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=24.02 E-value=79 Score=20.57 Aligned_cols=20 Identities=25% Similarity=0.323 Sum_probs=17.7
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|..+|++...|+.|-+
T Consensus 3 i~eva~~~gvs~~tLRyye~ 22 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDD 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999985
No 269
>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=23.98 E-value=1.9e+02 Score=22.60 Aligned_cols=46 Identities=22% Similarity=0.102 Sum_probs=35.5
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHHH
Q psy8536 9 RVVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAKE 60 (186)
Q Consensus 9 r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~ 60 (186)
...+|..+.++|.-... ...-.++|..||+++..|+....|=+.|-
T Consensus 188 ~~~LT~RE~evl~l~a~------G~s~~eIA~~L~IS~~TVk~hl~~i~~KL 233 (247)
T TIGR03020 188 AGLITAREAEILAWVRD------GKTNEEIAAILGISSLTVKNHLQHIFKKL 233 (247)
T ss_pred ccCCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHh
Confidence 34689999999986432 24567889999999999999987766553
No 270
>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=23.96 E-value=68 Score=21.17 Aligned_cols=20 Identities=10% Similarity=0.278 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++.+.|..|-+
T Consensus 4 i~eva~~~gvs~~tLR~ye~ 23 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYES 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 271
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=23.93 E-value=1.8e+02 Score=20.29 Aligned_cols=38 Identities=18% Similarity=0.139 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIW 52 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~W 52 (186)
++..+..+++..|..+.. ..-..+|..+|+++..|..+
T Consensus 83 Ld~~er~II~~rY~~~~~---~t~~~Ia~~l~iS~~t~~r~ 120 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRP---LTLVGLAQQLFISKSTAYRL 120 (134)
T ss_pred CCHHHHHHHHHHHccCCC---CCHHHHHHHhCCCHHHHHHH
Confidence 567777788887754332 35678899999999988654
No 272
>PRK05572 sporulation sigma factor SigF; Validated
Probab=23.92 E-value=2.4e+02 Score=21.71 Aligned_cols=44 Identities=20% Similarity=0.274 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.++..+..++...|. ......++|..+|++...|..+-..-..+
T Consensus 202 ~L~~~~~~v~~l~~~-----~~~s~~eIA~~lgis~~~V~~~~~ral~k 245 (252)
T PRK05572 202 ELDERERLIVYLRYF-----KDKTQSEVAKRLGISQVQVSRLEKKILKQ 245 (252)
T ss_pred cCCHHHHHHHHHHHh-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 355666667766663 23566889999999999998766443333
No 273
>PRK15183 Vi polysaccharide biosynthesis protein TviA; Provisional
Probab=23.87 E-value=68 Score=21.71 Aligned_cols=36 Identities=31% Similarity=0.367 Sum_probs=25.8
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCh
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSE 46 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~ 46 (186)
.+++.-.++|+..|-..+.--...|.+||-++|+.+
T Consensus 95 flsesgmeelqdrfmns~st~yrwrke~a~kfgvr~ 130 (143)
T PRK15183 95 FLSESGMEELQDRFMNSSSTMYRWRKELAVKFGVRE 130 (143)
T ss_pred hhhhccHHHHHHHHccChHHHHHHHHHHHHHhcCCC
Confidence 345556677888887766666678888888888654
No 274
>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=23.78 E-value=70 Score=20.84 Aligned_cols=20 Identities=35% Similarity=0.398 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++.+.|+.|-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDH 22 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999984
No 275
>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=23.77 E-value=2.5e+02 Score=20.10 Aligned_cols=29 Identities=24% Similarity=0.180 Sum_probs=20.2
Q ss_pred CHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 31 TIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 31 ~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
....-.++|..+|++...|..=...-|.+
T Consensus 155 ~g~s~~eIA~~lgis~~~v~~~l~Ra~~~ 183 (189)
T TIGR02984 155 EGLSFAEVAERMDRSEGAVSMLWVRGLAR 183 (189)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 44566788999999999988654433333
No 276
>PF07471 Phage_Nu1: Phage DNA packaging protein Nu1; InterPro: IPR010906 This entry is represented by the Bacteriophage lambda, Nu1, terminase small subunit. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. Terminase, the DNA packaging enzyme of bacteriophage lambda, is a heteromultimer composed of subunits Nu1 and A. The smaller Nu1 terminase subunit has a low-affinity ATPase stimulated by non-specific DNA [].; PDB: 1J9I_A.
Probab=23.72 E-value=74 Score=23.31 Aligned_cols=21 Identities=43% Similarity=0.764 Sum_probs=16.2
Q ss_pred HHHHHHHcCCChhHHHHHHHh
Q psy8536 35 KAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqn 55 (186)
+.+||..+|+++..|.-|-.+
T Consensus 5 k~~lA~i~gvS~~ti~~W~~~ 25 (164)
T PF07471_consen 5 KKELAEIFGVSERTIDKWQRQ 25 (164)
T ss_dssp HHHHHHHTT--HHHHHHHTTT
T ss_pred HHHHHHHHCCCHHHHHHHHHC
Confidence 678999999999999999643
No 277
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=23.65 E-value=2.2e+02 Score=22.07 Aligned_cols=40 Identities=25% Similarity=0.360 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
.++..+..+|...|.. .....++|..+|++...|...-.+
T Consensus 209 ~L~~~er~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~ 248 (258)
T PRK08215 209 KLNDREKLILNLRFFQ-----GKTQMEVAEEIGISQAQVSRLEKA 248 (258)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHH
Confidence 4566677777777632 245678999999999999876543
No 278
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=23.63 E-value=64 Score=22.38 Aligned_cols=23 Identities=17% Similarity=0.410 Sum_probs=20.1
Q ss_pred HHHHHHHcCCChhHHHHHHHhhH
Q psy8536 35 KAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFqnrr 57 (186)
..+||..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997664
No 279
>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=23.60 E-value=78 Score=19.39 Aligned_cols=18 Identities=44% Similarity=0.704 Sum_probs=11.6
Q ss_pred HHHHcCCChhHHHHHHHh
Q psy8536 38 LANSLGLSERQVKIWFQN 55 (186)
Q Consensus 38 la~~~~l~~~~v~~WFqn 55 (186)
||..+|++.+.+...|..
T Consensus 1 lA~~~~~s~~~l~~~f~~ 18 (81)
T PF12833_consen 1 LADELGMSERYLSRIFKK 18 (81)
T ss_dssp HHHHCTS-HHHHHHHHHH
T ss_pred ChHHhCcCHHHHHHHHHH
Confidence 577777777777776644
No 280
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.58 E-value=1.7e+02 Score=20.52 Aligned_cols=45 Identities=22% Similarity=0.279 Sum_probs=31.1
Q ss_pred CCCCHHHHHHHHHHH-hhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 10 VVYSDQQRLELEKEF-HYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f-~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
..||.+|.+.|...- +...--...+..+|+..+|++...|+.-|.
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GRiTi~ql~~~TGasR~Tvk~~lr 48 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGRITIKQLVAKTGASRNTVKRYLR 48 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCCccHHHHHHHHCCCHHHHHHHHH
Confidence 368999998887652 111112235667788899999999988774
No 281
>PRK13558 bacterio-opsin activator; Provisional
Probab=23.43 E-value=1.1e+02 Score=27.31 Aligned_cols=41 Identities=24% Similarity=0.287 Sum_probs=34.5
Q ss_pred CCCCHHHHHHHHHHHhhcC--CCCHHHHHHHHHHcCCChhHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSR--YITIRRKAELANSLGLSERQVK 50 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~--~p~~~~r~~la~~~~l~~~~v~ 50 (186)
..+|..|.++|+.+|...= .|-...-.+||..||++...+.
T Consensus 606 ~~lt~~q~e~l~~a~~~gyf~~pr~~~~~e~a~~l~is~~t~~ 648 (665)
T PRK13558 606 NDLTDRQLTALQKAYVSGYFEWPRRVEGEELAESMGISRSTFH 648 (665)
T ss_pred hhCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHH
Confidence 3699999999999997544 3777889999999999987765
No 282
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=23.39 E-value=1.8e+02 Score=19.06 Aligned_cols=34 Identities=15% Similarity=0.226 Sum_probs=17.7
Q ss_pred HHHHHHhhcCCCCHH-HHHHHHHHcCCChhHHHHHHHhhHHHHHHHHHhh
Q psy8536 19 ELEKEFHYSRYITIR-RKAELANSLGLSERQVKIWFQNRRAKERKQLKKR 67 (186)
Q Consensus 19 ~L~~~f~~~~~p~~~-~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~~~ 67 (186)
+.+-.|+.|+||... ++.. -.|||.+|++.+...
T Consensus 16 iIk~LyqsnPyP~~~GTr~a---------------RRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 16 IIKILYQSNPYPSPEGTRQA---------------RRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHTS-S--S-S-HHH---------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHccccCCCCCCcccc---------------ccchhhhHHHHHHHH
Confidence 334458899999743 2221 257888888766543
No 283
>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=23.36 E-value=71 Score=21.09 Aligned_cols=20 Identities=25% Similarity=0.356 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++.+.|+.|-+
T Consensus 4 i~eva~~~gvs~~tlR~ye~ 23 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEK 23 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999974
No 284
>PF04936 DUF658: Protein of unknown function (DUF658); InterPro: IPR007020 This entry is represented by Bacteriophage r1t, Orf18. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches. These are proteins of unknown function found in Lactococcus lactis and in their associated bacteriophage.
Probab=23.29 E-value=70 Score=23.44 Aligned_cols=31 Identities=26% Similarity=0.518 Sum_probs=26.2
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAKERKQ 63 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~ 63 (186)
....+|+..++++..+|-.|-.|.+...+..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999998765544
No 285
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=23.27 E-value=1.9e+02 Score=17.67 Aligned_cols=33 Identities=24% Similarity=0.286 Sum_probs=25.6
Q ss_pred HHHHHHHhhcCCCCHHHHHHHHHHcCC--ChhHHH
Q psy8536 18 LELEKEFHYSRYITIRRKAELANSLGL--SERQVK 50 (186)
Q Consensus 18 ~~L~~~f~~~~~p~~~~r~~la~~~~l--~~~~v~ 50 (186)
..+++.+.+||=.+......+..+.|- ++.+|+
T Consensus 20 ~~~~k~l~~NPpine~mir~M~~QMG~kpSekqi~ 54 (64)
T PF03672_consen 20 KYMEKQLKENPPINEKMIRAMMMQMGRKPSEKQIK 54 (64)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHhCCCccHHHHH
Confidence 456777888998899999999999985 455544
No 286
>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=23.12 E-value=93 Score=19.02 Aligned_cols=21 Identities=29% Similarity=0.474 Sum_probs=16.0
Q ss_pred HHHHHHHHHcCCChhHHHHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WF 53 (186)
..-++||..+|++...|....
T Consensus 21 Pt~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 21 PTDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp -BHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHcccHHHHHHHH
Confidence 456789999999999988655
No 287
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.03 E-value=85 Score=20.47 Aligned_cols=20 Identities=20% Similarity=0.293 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDK 22 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 288
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=22.67 E-value=68 Score=18.89 Aligned_cols=26 Identities=35% Similarity=0.446 Sum_probs=20.4
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRA 58 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~ 58 (186)
....++|..+|++...|..|-.+++.
T Consensus 15 ls~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 15 LSQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp S-HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CCHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 46778999999999999999877763
No 289
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.61 E-value=1.8e+02 Score=21.94 Aligned_cols=43 Identities=16% Similarity=0.039 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
.+|..++.+|......+ +-....-.++|..+|+++..|+.-+.
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~ 200 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLI 200 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHH
Confidence 36666666655544322 33344567789999999999997764
No 290
>PF01325 Fe_dep_repress: Iron dependent repressor, N-terminal DNA binding domain; InterPro: IPR022687 The DtxR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 65 residues present in metalloregulators of the DtxR/MntR family. The family is named after Corynebacterium diphtheriae DtxR, an iron-specific diphtheria toxin repressor, and Bacillus subtilis MntR, a manganese transport regulator. Iron-responsive metalloregulators such as DtxR and IdeR occur in Gram-positive bacteria of the high GC branch, while manganese-responsive metalloregulators like MntR are described in diverse genera of Gram-positive and Gram-negative bacteria and also in Archaea [].The metalloregulators like DtxR/MntR contain the DNA-binding DtxR-type HTH domain usually in the N-terminal part. The C-terminal part contains a dimerisation domain with two metal-binding sites, although the primary metal-binding site is less conserved in the Mn(II)-regulators. Fe(II)-regulated proteins contain an SH3-like domain as a C-terminal extension, which is absent in Mn(II)-regulated MntR [, ]. Metal-ion dependent regulators orchestrate the virulence of several important human pathogens. The DtxR protein regulates the expression of diphtheria toxinin response to environmental iron concentrations. Furthermore, DtxR and IdeR control iron uptake []. Homeostasis of manganese, which is an essential nutrient, is regulated by MntR. A typical DtxR-type metalloregulator binds two divalent metal effectors per monomer, upon which allosteric changes occur that moderate binding to the cognate DNA operators. Iron-bound DtxR homodimers bind to an interrupted palindrome of 19 bp, protecting a sequence of ~30 bp. The crystal structures of iron-regulated and manganese-regulated repressors show that the DNA binding domain contains three alpha-helices and a pair of antiparallel beta-strands. Helices 2 and 3 comprise the helix-turn-helix motif and the beta-strands are called the wing []. This wHTH topology is similar to the lysR-type HTH (see PDOC00043 from PROSITEDOC). Most DtxR-type metalloregulators bind as dimers to the DNA major groove. Several proteins are known to contain a DtxR-type HTH domain. These include- Corynebacterium diphtheriae DtxR, a diphtheria toxin repressor [], which regulates the expression of the high-affinity iron uptake system, other iron-sensitive genes, and the bacteriophage tox gene. Metal-bound DtxR represses transcription by binding the tox operator; if iron is limiting, conformational changes of the wHTH disrupt DNA-binding and the diphtheria toxin is produced. Mycobacterium tuberculosis IdeR, an iron-dependent regulator that is essential for this pathogen. The regulator represses genes for iron acquisition and activates iron storage genes, and is a positive regulator of oxidative stress responses []. Bacillus subtilis MntR, a manganese transport regulator, binds Mn2+ as an effector and is a transcriptional repressor of transporters for the import of manganese. Treponema pallidum troR, a metal-dependent transcriptional repressor. Archaeoglobus fulgidus MDR1 (troR), a metal-dependent transcriptional repressor, which negatively regulates its own transcription. This entry covers the entire DtxR-type HTH domain.; GO: 0005506 iron ion binding; PDB: 3HRT_B 3HRS_A 3HRU_B 2X4H_D 1ON1_B 2HYF_C 2F5E_A 3R60_B 1ON2_B 2F5F_A ....
Probab=22.54 E-value=56 Score=19.41 Aligned_cols=41 Identities=20% Similarity=0.206 Sum_probs=27.6
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHH
Q psy8536 13 SDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWF 53 (186)
Q Consensus 13 t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WF 53 (186)
|...-..|+..|....--.......||+.+|++...|..=.
T Consensus 3 t~~~e~YL~~Iy~l~~~~~~v~~~~iA~~L~vs~~tvt~ml 43 (60)
T PF01325_consen 3 TESEEDYLKAIYELSEEGGPVRTKDIAERLGVSPPTVTEML 43 (60)
T ss_dssp SCHHHHHHHHHHHHHHCTSSBBHHHHHHHHTS-HHHHHHHH
T ss_pred CcHHHHHHHHHHHHHcCCCCccHHHHHHHHCCChHHHHHHH
Confidence 34445667777776554455667789999999988876433
No 291
>TIGR01557 myb_SHAQKYF myb-like DNA-binding domain, SHAQKYF class. This model describes a DNA-binding domain restricted to (but common in) plant proteins, many of which also contain a response regulator domain. The domain appears related to the Myb-like DNA-binding domain described by Pfam model pfam00249. It is distinguished in part by a well-conserved motif SH[AL]QKY[RF] at the C-terminal end of the motif.
Probab=22.49 E-value=1.8e+02 Score=17.13 Aligned_cols=52 Identities=19% Similarity=0.144 Sum_probs=32.1
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH---cCCChhHHHHHHHhhHH
Q psy8536 7 KYRVVYSDQQRLELEKEFHYSRYITIRRKAELANS---LGLSERQVKIWFQNRRA 58 (186)
Q Consensus 7 r~r~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~---~~l~~~~v~~WFqnrr~ 58 (186)
++|...|++.-..+.........++...-..|++. .+|+..||..=.|..|.
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 35677888777666666666666555333444444 46678888876665443
No 292
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=22.46 E-value=67 Score=24.14 Aligned_cols=39 Identities=10% Similarity=0.090 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHh
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQN 55 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqn 55 (186)
.+|+.++++|.-.-+ ...-.++|+++|++++.|+.-..|
T Consensus 137 ~LT~RE~eVL~lla~------G~snkeIA~~L~iS~~TVk~h~~~ 175 (207)
T PRK15411 137 SLSRTESSMLRMWMA------GQGTIQISDQMNIKAKTVSSHKGN 175 (207)
T ss_pred cCCHHHHHHHHHHHc------CCCHHHHHHHcCCCHHHHHHHHHH
Confidence 388888888855433 234478999999999999976643
No 293
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=22.38 E-value=1.1e+02 Score=22.13 Aligned_cols=39 Identities=10% Similarity=0.050 Sum_probs=31.4
Q ss_pred HHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 20 LEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 20 L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
-...|....| .......||...|++...|-.+|.++..-
T Consensus 17 A~~lf~e~G~-~~tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 17 AMRVALAEGF-AAMTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHhcCh-hhccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 3444777777 46677889999999999999999988663
No 294
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=22.32 E-value=2.9e+02 Score=19.54 Aligned_cols=27 Identities=15% Similarity=0.202 Sum_probs=20.5
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
..-+++|..+|++...|+.+-.+-+..
T Consensus 135 ~s~~EIA~~l~is~~tV~~~l~ra~~~ 161 (168)
T PRK12525 135 LTYVEIGERLGVSLSRIHQYMVEAFKC 161 (168)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 455788999999999999877544443
No 295
>PTZ00183 centrin; Provisional
Probab=22.12 E-value=2.7e+02 Score=19.08 Aligned_cols=42 Identities=24% Similarity=0.292 Sum_probs=32.2
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHh-----hcCCCCHHHHHHHHHHcCC
Q psy8536 3 RTKDKYRVVYSDQQRLELEKEFH-----YSRYITIRRKAELANSLGL 44 (186)
Q Consensus 3 ~~~rr~r~~~t~~q~~~L~~~f~-----~~~~p~~~~r~~la~~~~l 44 (186)
|+.+-.+..++..++..|+..|. .+.+.+..+-..+...+|+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 2 RKRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 45556678999999999999986 3556777777777777775
No 296
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.02 E-value=86 Score=20.31 Aligned_cols=20 Identities=30% Similarity=0.468 Sum_probs=17.1
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|..|-+
T Consensus 3 ~~eva~~~gi~~~tlr~~~~ 22 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEE 22 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999963
No 297
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=21.96 E-value=1.8e+02 Score=22.08 Aligned_cols=37 Identities=30% Similarity=0.333 Sum_probs=27.7
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKERKQLK 65 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~~~~~ 65 (186)
|.....-.++|+.+|++...|+.....-|.+-++...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4556677889999999999999877655555555443
No 298
>TIGR02846 spore_sigmaK RNA polymerase sigma-K factor. The sporulation-specific transcription factor sigma-K (also called sigma-27) is expressed in the mother cell compartment of endospore-forming bacteria such as Bacillus subtilis. Like its close homolog sigma-E (sigma-29) (see TIGR02835), also specific to the mother cell compartment, it must be activated by a proteolytic cleavage. Note that in Bacillus subtilis (and apparently also Clostridium tetani), but not in other endospore forming species such as Bacillus anthracis, the sigK gene is generated by a non-germline (mother cell only) chromosomal rearrangement that recombines coding regions for the N-terminal and C-terminal regions of sigma-K.
Probab=21.79 E-value=3.2e+02 Score=20.65 Aligned_cols=26 Identities=23% Similarity=0.245 Sum_probs=19.7
Q ss_pred HHHHHHHHHcCCChhHHHHHHHhhHH
Q psy8536 33 RRKAELANSLGLSERQVKIWFQNRRA 58 (186)
Q Consensus 33 ~~r~~la~~~~l~~~~v~~WFqnrr~ 58 (186)
..-+++|+.+|++...|..+...-+.
T Consensus 195 ~S~~EIAe~lgis~~tV~~~~~rAl~ 220 (227)
T TIGR02846 195 KTQREIAKILGISRSYVSRIEKRALM 220 (227)
T ss_pred cCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46778999999999999776543333
No 299
>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=21.76 E-value=97 Score=20.40 Aligned_cols=19 Identities=32% Similarity=0.616 Sum_probs=17.0
Q ss_pred HHHHHHcCCChhHHHHHHH
Q psy8536 36 AELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 36 ~~la~~~~l~~~~v~~WFq 54 (186)
.++|+.+|++...++.|-+
T Consensus 4 ~EvA~~~gVs~~tLR~ye~ 22 (99)
T cd04765 4 GEVAEILGLPPHVLRYWET 22 (99)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999975
No 300
>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=21.75 E-value=86 Score=21.32 Aligned_cols=38 Identities=24% Similarity=0.348 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
|+-+-+...-..+.... ...++|..++++...|..|++
T Consensus 3 YS~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 3 YSLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CCHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 44444554445555432 455679999999999999997
No 301
>PRK00215 LexA repressor; Validated
Probab=21.64 E-value=1.5e+02 Score=22.12 Aligned_cols=41 Identities=24% Similarity=0.295 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCC-ChhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFH---YSRYITIRRKAELANSLGL-SERQVKIWFQ 54 (186)
Q Consensus 12 ~t~~q~~~L~~~f~---~~~~p~~~~r~~la~~~~l-~~~~v~~WFq 54 (186)
+|..|..+|+.... ...++ ....+||..+|+ +...|..+.+
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~ 46 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLK 46 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHH
Confidence 57889998887763 33333 356789999999 8888887764
No 302
>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=21.53 E-value=1.2e+02 Score=19.26 Aligned_cols=20 Identities=35% Similarity=0.536 Sum_probs=15.3
Q ss_pred HHHHHHHHHHcCCChhHHHH
Q psy8536 32 IRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 32 ~~~r~~la~~~~l~~~~v~~ 51 (186)
...=.++|+.+||++..|..
T Consensus 11 ~~~wk~~~R~LGlse~~Id~ 30 (80)
T cd08313 11 PRRWKEFVRRLGLSDNEIER 30 (80)
T ss_pred HHHHHHHHHHcCCCHHHHHH
Confidence 34445689999999988873
No 303
>PF08784 RPA_C: Replication protein A C terminal; InterPro: IPR014892 This protein corresponds to the C-terminal of the single stranded DNA binding protein RPA (replication protein A). RPA is involved in many DNA metabolic pathways including DNA replication, DNA repair, recombination, cell cycle and DNA damage checkpoints. ; PDB: 1QUQ_C 2PQA_C 3KDF_B 2Z6K_B 2PI2_B 1L1O_E 1DPU_A 1Z1D_A.
Probab=21.48 E-value=1e+02 Score=20.10 Aligned_cols=40 Identities=25% Similarity=0.139 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
++..|..+|+-.=..+.........+|+++|++++.+|+.
T Consensus 45 ~~~~~~~Vl~~i~~~~~~~~Gv~v~~I~~~l~~~~~~v~~ 84 (102)
T PF08784_consen 45 LSPLQDKVLNFIKQQPNSEEGVHVDEIAQQLGMSENEVRK 84 (102)
T ss_dssp S-HHHHHHHHHHHC----TTTEEHHHHHHHSTS-HHHHHH
T ss_pred CCHHHHHHHHHHHhcCCCCCcccHHHHHHHhCcCHHHHHH
Confidence 4555666665444446667778889999999999988863
No 304
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.46 E-value=1.9e+02 Score=21.88 Aligned_cols=43 Identities=28% Similarity=0.199 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|..++++|+-..+- ..-.++|+.+++++..|+.+..+-..|
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~K 197 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKK 197 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4788888888776652 335678999999999999988766555
No 305
>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=21.33 E-value=89 Score=20.86 Aligned_cols=20 Identities=30% Similarity=0.562 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|-+
T Consensus 3 i~eva~~~gvs~~tlR~ye~ 22 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEK 22 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 306
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=21.30 E-value=2.4e+02 Score=19.80 Aligned_cols=40 Identities=20% Similarity=0.351 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHH
Q psy8536 12 YSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 12 ~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFq 54 (186)
++++...+++..|..-. ...=..+|.+++++++++.-|+.
T Consensus 82 l~de~k~Ii~lry~~r~---~~TW~~IA~~l~i~erta~r~~~ 121 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRS---RRTWYQIAQKLHISERTARRWRD 121 (130)
T ss_pred hCHHHHHHHHHHHcccc---cchHHHHHHHhCccHHHHHHHHH
Confidence 45556666666665443 23445679999999999998874
No 307
>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=21.27 E-value=83 Score=21.07 Aligned_cols=20 Identities=25% Similarity=0.295 Sum_probs=17.5
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|..+|++...|+.|-.
T Consensus 3 Ige~A~~~gvs~~tlR~ye~ 22 (107)
T cd01111 3 ISQLALDAGVSVHIVRDYLL 22 (107)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
No 308
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=21.17 E-value=2.8e+02 Score=19.77 Aligned_cols=43 Identities=14% Similarity=0.122 Sum_probs=33.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHHHHHhhHHH
Q psy8536 11 VYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKIWFQNRRAK 59 (186)
Q Consensus 11 ~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~ 59 (186)
.+|..+.++|...+... ..++||..++++++.|..--.+=|.|
T Consensus 143 ~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~K 185 (204)
T PRK09958 143 SLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEK 185 (204)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 58888888888877643 47889999999999999776655555
No 309
>PF10945 DUF2629: Protein of unknown function (DUF2629); InterPro: IPR024487 Some members in this family of proteins are annotated as YhjR however currently no function is known.
Probab=21.10 E-value=1.3e+02 Score=16.89 Aligned_cols=29 Identities=28% Similarity=0.496 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHhhcC--CCCHHHHHHHHHHc
Q psy8536 14 DQQRLELEKEFHYSR--YITIRRKAELANSL 42 (186)
Q Consensus 14 ~~q~~~L~~~f~~~~--~p~~~~r~~la~~~ 42 (186)
.+-+..|..+|.... |-|+...+.|...+
T Consensus 3 ~dDi~~L~~~fslp~~~Y~DIsr~e~l~~~~ 33 (44)
T PF10945_consen 3 QDDIAALSQAFSLPDINYIDISREERLNQAL 33 (44)
T ss_pred hhHHHHHHHHhCCCCccHHHHHHHHHHHHHH
Confidence 356889999998655 88898888887655
No 310
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=20.97 E-value=95 Score=17.69 Aligned_cols=21 Identities=29% Similarity=0.420 Sum_probs=17.6
Q ss_pred HHHHHHHHcCCChhHHHHHHH
Q psy8536 34 RKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFq 54 (186)
.-+.||...|+++..|..||.
T Consensus 21 ~~~~La~~FgIs~stvsri~~ 41 (53)
T PF13613_consen 21 TFQDLAYRFGISQSTVSRIFH 41 (53)
T ss_pred cHhHHhhheeecHHHHHHHHH
Confidence 346789999999999999885
No 311
>PF11212 DUF2999: Protein of unknown function (DUF2999); InterPro: IPR021376 This family of proteins with unknown function appears to be restricted to Gammaproteobacteria.
Probab=20.91 E-value=2.3e+02 Score=17.76 Aligned_cols=38 Identities=18% Similarity=0.173 Sum_probs=28.7
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCChhHHHH
Q psy8536 10 VVYSDQQRLELEKEFHYSRYITIRRKAELANSLGLSERQVKI 51 (186)
Q Consensus 10 ~~~t~~q~~~L~~~f~~~~~p~~~~r~~la~~~~l~~~~v~~ 51 (186)
..++++|+..|-..+-.|+ ..-+.+..++|++....+-
T Consensus 11 hnvsd~qi~elFq~lT~NP----l~AMa~i~qLGip~eKLQ~ 48 (82)
T PF11212_consen 11 HNVSDEQINELFQALTQNP----LAAMATIQQLGIPQEKLQQ 48 (82)
T ss_pred cCCCHHHHHHHHHHHhhCH----HHHHHHHHHcCCCHHHHHH
Confidence 4678899999988888877 4556667788988776654
No 312
>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=20.79 E-value=78 Score=18.44 Aligned_cols=24 Identities=25% Similarity=0.428 Sum_probs=19.3
Q ss_pred HHHHHHHHcCCChhHHHHHHHhhH
Q psy8536 34 RKAELANSLGLSERQVKIWFQNRR 57 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFqnrr 57 (186)
....+|..+|++...|..|-.+++
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~ 37 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR 37 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc
Confidence 467789999999999999987766
No 313
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=20.56 E-value=1.8e+02 Score=20.64 Aligned_cols=33 Identities=21% Similarity=0.106 Sum_probs=24.5
Q ss_pred CCCHHHHHHHHHHcCCChhHHHHHHHhhHHHHH
Q psy8536 29 YITIRRKAELANSLGLSERQVKIWFQNRRAKER 61 (186)
Q Consensus 29 ~p~~~~r~~la~~~~l~~~~v~~WFqnrr~~~~ 61 (186)
|.....-+++|+.+|++...|..+...-+.+.+
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~ 171 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLR 171 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHH
Confidence 445566788999999999999887754444443
No 314
>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=20.56 E-value=1e+02 Score=21.23 Aligned_cols=21 Identities=24% Similarity=0.325 Sum_probs=18.3
Q ss_pred HHHHHHHHcCCChhHHHHHHH
Q psy8536 34 RKAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 34 ~r~~la~~~~l~~~~v~~WFq 54 (186)
...+||..+|++.+.|+.|=+
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~ 25 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLL 25 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHH
Confidence 456899999999999999964
No 315
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.55 E-value=86 Score=21.01 Aligned_cols=19 Identities=26% Similarity=0.378 Sum_probs=16.8
Q ss_pred HHHHHHHcCCChhHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWF 53 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WF 53 (186)
..++|+.+|++.+.|..|=
T Consensus 3 i~e~a~~~gvs~~tlr~ye 21 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYE 21 (113)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 3578999999999999996
No 316
>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=20.35 E-value=82 Score=20.19 Aligned_cols=20 Identities=35% Similarity=0.403 Sum_probs=15.7
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
=..||+.||+++.+|..=-.
T Consensus 16 Wk~laR~LGlse~~Id~i~~ 35 (86)
T cd08306 16 WRKLARKLGLSETKIESIEE 35 (86)
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34589999999999985443
No 317
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.18 E-value=89 Score=20.82 Aligned_cols=20 Identities=20% Similarity=0.240 Sum_probs=17.4
Q ss_pred HHHHHHHcCCChhHHHHHHH
Q psy8536 35 KAELANSLGLSERQVKIWFQ 54 (186)
Q Consensus 35 r~~la~~~~l~~~~v~~WFq 54 (186)
..++|+.+|++...|+.|-.
T Consensus 3 i~eva~~~gis~~tlR~ye~ 22 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDK 22 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999974
Done!