Query psy10107
Match_columns 140
No_of_seqs 213 out of 1162
Neff 6.3
Searched_HMMs 46136
Date Fri Aug 16 18:02:52 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10107.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10107hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 PF05920 Homeobox_KN: Homeobox 99.8 1E-19 2.3E-24 108.8 4.6 40 22-61 1-40 (40)
2 KOG0774|consensus 99.7 7.3E-19 1.6E-23 141.7 3.4 62 6-67 190-251 (334)
3 KOG0775|consensus 99.7 7E-17 1.5E-21 130.7 7.5 55 9-66 181-235 (304)
4 cd00086 homeodomain Homeodomai 99.7 4.4E-16 9.5E-21 97.8 7.1 57 6-65 2-58 (59)
5 PF00046 Homeobox: Homeobox do 99.6 3.2E-16 7E-21 98.7 6.1 56 6-64 2-57 (57)
6 smart00389 HOX Homeodomain. DN 99.6 5E-16 1.1E-20 97.0 6.7 55 6-63 2-56 (56)
7 KOG0773|consensus 99.5 1.7E-15 3.7E-20 125.8 2.4 61 7-67 242-302 (342)
8 KOG0489|consensus 99.4 2.3E-13 5.1E-18 110.2 5.1 60 6-68 161-220 (261)
9 KOG0843|consensus 99.4 5.6E-13 1.2E-17 102.6 5.9 59 7-68 105-163 (197)
10 KOG0487|consensus 99.4 2.6E-13 5.7E-18 112.1 2.6 59 6-67 237-295 (308)
11 KOG0850|consensus 99.3 3.8E-12 8.3E-17 101.1 5.6 59 6-67 124-182 (245)
12 KOG0493|consensus 99.3 4.3E-12 9.4E-17 102.8 4.9 59 5-66 247-305 (342)
13 KOG0488|consensus 99.2 7.8E-12 1.7E-16 103.7 5.1 59 6-67 174-232 (309)
14 KOG0842|consensus 99.2 1.1E-11 2.4E-16 102.4 5.6 58 6-66 155-212 (307)
15 TIGR01565 homeo_ZF_HD homeobox 99.2 2.2E-11 4.8E-16 78.2 4.2 51 6-59 3-57 (58)
16 KOG0485|consensus 99.2 1.3E-11 2.8E-16 97.8 3.5 59 6-67 106-164 (268)
17 KOG0492|consensus 99.1 3.7E-11 8.1E-16 94.5 4.4 59 4-65 144-202 (246)
18 KOG0848|consensus 99.1 1.6E-11 3.4E-16 99.7 2.2 58 8-68 203-260 (317)
19 COG5576 Homeodomain-containing 99.1 1.4E-10 2.9E-15 87.9 5.8 59 6-67 53-111 (156)
20 KOG0847|consensus 99.1 1.1E-10 2.3E-15 92.8 4.8 101 7-110 170-271 (288)
21 KOG0483|consensus 99.0 3.3E-10 7.1E-15 88.8 4.5 57 7-66 53-109 (198)
22 KOG0484|consensus 99.0 4.9E-10 1.1E-14 79.8 4.4 56 8-66 21-76 (125)
23 KOG2251|consensus 99.0 4.3E-10 9.2E-15 89.0 4.2 58 7-67 40-97 (228)
24 KOG0491|consensus 99.0 3.2E-10 6.9E-15 86.5 2.7 62 6-70 102-163 (194)
25 KOG0494|consensus 98.9 1.3E-09 2.8E-14 88.5 4.7 57 8-67 145-201 (332)
26 KOG0844|consensus 98.9 7E-10 1.5E-14 91.7 2.0 62 8-72 185-247 (408)
27 KOG3802|consensus 98.8 1.3E-09 2.9E-14 92.4 2.5 59 6-67 296-354 (398)
28 KOG2252|consensus 98.8 3.4E-08 7.4E-13 86.7 9.9 57 4-63 420-476 (558)
29 KOG0486|consensus 98.7 1.1E-08 2.3E-13 84.8 2.8 56 7-65 115-170 (351)
30 KOG4577|consensus 98.6 3.9E-08 8.4E-13 81.0 4.5 59 6-67 169-227 (383)
31 KOG0773|consensus 98.5 6.3E-08 1.4E-12 80.6 4.0 74 3-77 94-167 (342)
32 KOG0849|consensus 98.4 3.2E-07 6.9E-12 77.5 4.8 57 7-66 179-235 (354)
33 KOG0490|consensus 98.3 3.4E-07 7.5E-12 71.1 2.4 57 7-66 63-119 (235)
34 PF11569 Homez: Homeodomain le 97.7 2.3E-05 4.9E-10 49.9 2.5 43 16-61 10-52 (56)
35 KOG1168|consensus 97.7 1.2E-05 2.7E-10 66.5 0.9 54 9-65 314-367 (385)
36 KOG0490|consensus 97.1 0.00056 1.2E-08 53.0 3.9 57 7-66 156-212 (235)
37 KOG1146|consensus 95.1 0.023 4.9E-07 55.1 3.8 58 7-67 906-963 (1406)
38 KOG3623|consensus 94.6 0.13 2.8E-06 47.8 7.0 52 16-70 568-619 (1007)
39 PF04218 CENP-B_N: CENP-B N-te 92.5 0.45 9.8E-06 29.5 5.0 47 6-60 2-48 (53)
40 cd06171 Sigma70_r4 Sigma70, re 88.1 1 2.3E-05 25.8 3.7 46 10-63 10-55 (55)
41 PF08281 Sigma70_r4_2: Sigma-7 86.3 2.2 4.9E-05 25.6 4.6 45 10-62 10-54 (54)
42 PRK04217 hypothetical protein; 85.9 3.3 7.1E-05 29.6 5.9 56 4-67 36-91 (110)
43 PF04545 Sigma70_r4: Sigma-70, 85.7 2.2 4.7E-05 25.4 4.3 47 10-64 4-50 (50)
44 cd00569 HTH_Hin_like Helix-tur 85.6 2.8 6E-05 21.4 4.3 40 8-55 3-42 (42)
45 PRK06759 RNA polymerase factor 85.2 1.9 4E-05 30.9 4.5 48 10-65 106-153 (154)
46 PRK09642 RNA polymerase sigma 82.4 2.8 6.1E-05 30.3 4.5 30 38-67 126-155 (160)
47 PRK09646 RNA polymerase sigma 82.1 2.9 6.3E-05 31.5 4.6 49 11-67 143-191 (194)
48 PRK09413 IS2 repressor TnpA; R 82.0 4.9 0.00011 28.6 5.5 51 3-60 5-55 (121)
49 PRK09644 RNA polymerase sigma 81.9 3 6.5E-05 30.5 4.5 50 10-67 108-157 (165)
50 PRK11924 RNA polymerase sigma 81.9 2 4.4E-05 31.1 3.6 32 37-68 144-175 (179)
51 TIGR02939 RpoE_Sigma70 RNA pol 81.5 2.1 4.5E-05 31.7 3.6 32 36-67 156-187 (190)
52 TIGR02985 Sig70_bacteroi1 RNA 81.1 3.9 8.5E-05 29.0 4.8 47 11-65 114-160 (161)
53 PF01527 HTH_Tnp_1: Transposas 79.9 2.4 5.3E-05 27.0 3.1 46 6-59 2-48 (76)
54 TIGR02937 sigma70-ECF RNA poly 79.9 5.2 0.00011 27.5 5.0 47 11-65 111-157 (158)
55 PRK03975 tfx putative transcri 79.5 4.3 9.2E-05 30.3 4.6 49 9-66 5-53 (141)
56 PRK12520 RNA polymerase sigma 79.5 2.5 5.4E-05 31.7 3.5 33 38-70 151-183 (191)
57 PRK00118 putative DNA-binding 79.2 4.9 0.00011 28.5 4.6 49 10-66 17-65 (104)
58 PRK12514 RNA polymerase sigma 78.8 4.4 9.5E-05 29.9 4.6 48 11-66 130-177 (179)
59 PRK09652 RNA polymerase sigma 78.6 4.4 9.6E-05 29.4 4.5 48 11-66 129-176 (182)
60 TIGR02948 SigW_bacill RNA poly 78.5 4.7 0.0001 29.7 4.7 31 37-67 155-185 (187)
61 PF13518 HTH_28: Helix-turn-he 78.5 3 6.5E-05 24.5 3.0 26 36-61 14-39 (52)
62 PRK12526 RNA polymerase sigma 78.1 4.2 9.1E-05 31.1 4.4 31 37-67 172-202 (206)
63 PRK09047 RNA polymerase factor 78.1 4.7 0.0001 29.0 4.5 32 37-68 125-156 (161)
64 PRK12547 RNA polymerase sigma 77.8 4.9 0.00011 29.4 4.5 48 11-66 113-160 (164)
65 TIGR02983 SigE-fam_strep RNA p 77.8 5.4 0.00012 28.8 4.7 49 11-67 111-159 (162)
66 PRK06811 RNA polymerase factor 77.6 5 0.00011 30.1 4.6 49 10-66 131-179 (189)
67 PF00196 GerE: Bacterial regul 77.6 5.7 0.00012 24.3 4.2 48 10-66 3-50 (58)
68 TIGR02989 Sig-70_gvs1 RNA poly 77.6 5 0.00011 28.7 4.5 46 11-64 112-157 (159)
69 PRK08583 RNA polymerase sigma 77.3 6.3 0.00014 31.2 5.3 49 11-67 206-254 (257)
70 PRK12541 RNA polymerase sigma 77.2 4.6 0.0001 29.2 4.2 47 11-65 113-159 (161)
71 PRK13919 putative RNA polymera 76.8 5.8 0.00013 29.4 4.7 31 37-67 154-184 (186)
72 TIGR02999 Sig-70_X6 RNA polyme 76.6 5.5 0.00012 29.4 4.6 47 11-65 135-181 (183)
73 PF04967 HTH_10: HTH DNA bindi 76.2 12 0.00025 23.4 5.2 48 11-59 1-48 (53)
74 PRK12512 RNA polymerase sigma 76.1 5.6 0.00012 29.5 4.5 49 11-67 132-180 (184)
75 smart00421 HTH_LUXR helix_turn 76.0 13 0.00027 21.5 5.3 47 10-65 3-49 (58)
76 PRK05602 RNA polymerase sigma 75.8 5.2 0.00011 29.8 4.2 31 37-67 147-177 (186)
77 PRK12516 RNA polymerase sigma 75.3 5.2 0.00011 30.2 4.2 31 38-68 136-166 (187)
78 PF13443 HTH_26: Cro/C1-type H 75.1 2.7 5.8E-05 25.9 2.1 24 36-59 12-35 (63)
79 PRK12532 RNA polymerase sigma 74.9 4.2 9.2E-05 30.5 3.6 32 37-68 155-186 (195)
80 PRK12530 RNA polymerase sigma 74.8 4.3 9.3E-05 30.6 3.6 31 37-67 153-183 (189)
81 PRK12536 RNA polymerase sigma 74.8 6.4 0.00014 29.2 4.5 31 37-67 148-178 (181)
82 TIGR02954 Sig70_famx3 RNA poly 73.6 7 0.00015 28.5 4.4 48 11-66 120-167 (169)
83 PRK09648 RNA polymerase sigma 73.5 7.4 0.00016 29.0 4.6 49 10-66 139-187 (189)
84 PRK12544 RNA polymerase sigma 73.3 5.4 0.00012 30.7 3.9 33 38-70 168-200 (206)
85 PRK12546 RNA polymerase sigma 72.9 6.6 0.00014 29.8 4.2 49 11-67 114-162 (188)
86 PRK12523 RNA polymerase sigma 72.5 8.1 0.00018 28.4 4.5 48 11-66 120-167 (172)
87 PRK12533 RNA polymerase sigma 72.1 6.9 0.00015 30.6 4.3 49 10-66 134-182 (216)
88 PRK12531 RNA polymerase sigma 71.9 8.4 0.00018 29.0 4.6 30 38-67 161-190 (194)
89 PRK09649 RNA polymerase sigma 71.9 7.6 0.00017 29.1 4.3 30 37-66 149-178 (185)
90 TIGR02941 Sigma_B RNA polymera 71.7 8.5 0.00018 30.4 4.8 48 11-66 206-253 (255)
91 PRK12519 RNA polymerase sigma 71.2 6.4 0.00014 29.4 3.8 30 37-66 160-189 (194)
92 PRK15369 two component system 70.9 11 0.00023 26.9 4.8 47 10-65 149-195 (211)
93 TIGR02959 SigZ RNA polymerase 70.9 9.4 0.0002 28.1 4.6 50 10-67 100-149 (170)
94 PF10668 Phage_terminase: Phag 70.3 4.2 9.2E-05 26.1 2.2 19 36-54 24-42 (60)
95 PRK12537 RNA polymerase sigma 70.1 9.5 0.00021 28.3 4.5 29 37-65 152-180 (182)
96 PRK09645 RNA polymerase sigma 69.6 11 0.00023 27.6 4.6 49 11-67 119-167 (173)
97 TIGR02943 Sig70_famx1 RNA poly 69.5 7.2 0.00016 29.3 3.8 32 37-68 150-181 (188)
98 PRK09639 RNA polymerase sigma 68.6 6.7 0.00014 28.4 3.3 31 37-67 130-160 (166)
99 PRK12524 RNA polymerase sigma 68.1 11 0.00024 28.4 4.5 30 37-66 155-184 (196)
100 TIGR02479 FliA_WhiG RNA polyme 67.7 13 0.00029 28.6 5.0 47 11-65 176-222 (224)
101 PRK06986 fliA flagellar biosyn 67.6 9.6 0.00021 29.7 4.2 31 36-66 202-232 (236)
102 PF13384 HTH_23: Homeodomain-l 67.4 5.7 0.00012 23.3 2.3 25 35-59 18-42 (50)
103 PRK12515 RNA polymerase sigma 67.1 12 0.00027 27.8 4.6 50 10-67 131-180 (189)
104 PRK12542 RNA polymerase sigma 66.7 12 0.00027 27.7 4.5 29 38-66 142-170 (185)
105 PRK12543 RNA polymerase sigma 66.6 13 0.00028 27.5 4.6 48 11-66 118-165 (179)
106 PRK12545 RNA polymerase sigma 66.3 12 0.00027 28.4 4.5 30 38-67 159-188 (201)
107 PRK07670 RNA polymerase sigma 65.6 19 0.00042 28.4 5.7 48 11-66 202-249 (251)
108 PRK12535 RNA polymerase sigma 65.6 12 0.00027 28.4 4.4 31 37-67 152-182 (196)
109 PRK09647 RNA polymerase sigma 65.5 12 0.00025 28.8 4.2 30 38-67 158-187 (203)
110 PRK08295 RNA polymerase factor 65.1 19 0.00041 27.0 5.3 30 37-66 173-202 (208)
111 PRK12534 RNA polymerase sigma 64.9 14 0.0003 27.4 4.5 30 37-66 156-185 (187)
112 TIGR03001 Sig-70_gmx1 RNA poly 64.9 13 0.00029 29.6 4.6 31 37-67 180-210 (244)
113 cd00131 PAX Paired Box domain 64.9 28 0.00061 25.1 5.9 46 10-58 75-127 (128)
114 PRK12538 RNA polymerase sigma 64.6 11 0.00024 29.7 4.0 31 37-67 190-220 (233)
115 PRK12511 RNA polymerase sigma 64.5 14 0.0003 27.7 4.5 50 10-67 111-160 (182)
116 TIGR02859 spore_sigH RNA polym 64.4 20 0.00043 26.6 5.3 30 36-65 167-196 (198)
117 PRK07037 extracytoplasmic-func 64.4 16 0.00034 26.3 4.6 30 37-66 128-157 (163)
118 cd06170 LuxR_C_like C-terminal 64.3 19 0.00042 20.8 4.3 44 12-64 2-45 (57)
119 TIGR02952 Sig70_famx2 RNA poly 64.2 16 0.00034 26.3 4.6 47 11-65 123-169 (170)
120 PRK09415 RNA polymerase factor 63.9 13 0.00028 27.6 4.1 48 11-66 128-175 (179)
121 PRK12528 RNA polymerase sigma 63.9 16 0.00035 26.3 4.6 46 11-64 114-159 (161)
122 PRK12539 RNA polymerase sigma 63.2 15 0.00032 27.3 4.4 49 10-66 131-179 (184)
123 PRK12540 RNA polymerase sigma 63.2 20 0.00043 26.9 5.1 31 37-67 130-160 (182)
124 PRK08301 sporulation sigma fac 62.6 15 0.00033 28.5 4.4 31 36-66 200-230 (234)
125 PRK11511 DNA-binding transcrip 62.4 21 0.00046 25.3 4.9 44 11-58 6-49 (127)
126 TIGR02980 SigBFG RNA polymeras 62.1 16 0.00034 28.2 4.5 48 10-65 178-225 (227)
127 TIGR02950 SigM_subfam RNA poly 61.9 11 0.00024 26.7 3.4 31 35-65 122-152 (154)
128 PRK12522 RNA polymerase sigma 60.1 19 0.00041 26.3 4.4 31 37-67 138-168 (173)
129 PRK12527 RNA polymerase sigma 59.9 22 0.00047 25.6 4.7 49 11-67 106-154 (159)
130 TIGR02960 SigX5 RNA polymerase 59.7 19 0.0004 29.2 4.7 30 38-67 162-191 (324)
131 PF01381 HTH_3: Helix-turn-hel 59.7 6.6 0.00014 23.3 1.6 21 37-57 12-32 (55)
132 PRK06288 RNA polymerase sigma 59.4 19 0.00041 28.8 4.6 49 10-66 212-260 (268)
133 PRK12517 RNA polymerase sigma 59.4 21 0.00046 26.8 4.7 49 11-67 129-177 (188)
134 COG3413 Predicted DNA binding 59.1 34 0.00074 26.5 5.9 54 7-61 152-205 (215)
135 PRK07408 RNA polymerase sigma 58.5 18 0.00038 28.9 4.2 49 11-67 204-252 (256)
136 PRK06930 positive control sigm 58.3 22 0.00047 27.0 4.5 30 38-67 134-163 (170)
137 PRK12529 RNA polymerase sigma 58.2 24 0.00052 26.1 4.8 48 11-66 128-175 (178)
138 PRK12518 RNA polymerase sigma 58.2 13 0.00029 27.0 3.3 32 36-67 138-169 (175)
139 cd01392 HTH_LacI Helix-turn-he 57.7 7.5 0.00016 22.8 1.6 20 39-58 2-21 (52)
140 PRK09641 RNA polymerase sigma 56.9 14 0.0003 27.2 3.2 31 37-67 155-185 (187)
141 PRK12513 RNA polymerase sigma 56.5 15 0.00032 27.5 3.3 31 37-67 158-188 (194)
142 PRK10072 putative transcriptio 56.3 7.7 0.00017 27.0 1.6 23 37-59 49-71 (96)
143 TIGR00721 tfx DNA-binding prot 55.7 25 0.00055 26.0 4.4 47 9-64 5-51 (137)
144 PRK06704 RNA polymerase factor 55.4 21 0.00045 28.4 4.2 32 37-68 135-166 (228)
145 PRK09651 RNA polymerase sigma 55.3 19 0.0004 26.5 3.7 28 37-64 138-165 (172)
146 TIGR02947 SigH_actino RNA poly 55.1 16 0.00034 27.3 3.3 31 37-67 150-180 (193)
147 TIGR02885 spore_sigF RNA polym 54.4 30 0.00064 26.8 4.8 48 10-65 183-230 (231)
148 PRK07122 RNA polymerase sigma 54.3 27 0.00058 28.1 4.7 48 10-65 215-262 (264)
149 PRK09637 RNA polymerase sigma 54.2 20 0.00044 26.7 3.8 31 37-67 125-155 (181)
150 PRK05803 sporulation sigma fac 54.1 30 0.00066 26.9 4.9 53 10-66 175-227 (233)
151 TIGR02846 spore_sigmaK RNA pol 53.9 30 0.00066 26.8 4.8 52 10-65 174-225 (227)
152 PRK12525 RNA polymerase sigma 53.9 31 0.00067 25.1 4.7 47 11-65 119-165 (168)
153 PF13551 HTH_29: Winged helix- 53.8 52 0.0011 21.9 5.5 48 9-56 56-109 (112)
154 TIGR03826 YvyF flagellar opero 53.8 18 0.00039 26.9 3.3 44 17-64 33-76 (137)
155 TIGR03070 couple_hipB transcri 53.3 9.3 0.0002 22.4 1.5 22 37-58 18-39 (58)
156 PRK11922 RNA polymerase sigma 52.6 11 0.00024 29.4 2.1 34 35-68 166-199 (231)
157 cd00093 HTH_XRE Helix-turn-hel 52.6 16 0.00034 20.2 2.4 22 37-58 15-36 (58)
158 PRK08241 RNA polymerase factor 52.4 22 0.00049 29.1 4.0 29 37-65 172-200 (339)
159 TIGR03541 reg_near_HchA LuxR f 51.4 28 0.0006 27.3 4.3 49 9-66 170-218 (232)
160 cd04761 HTH_MerR-SF Helix-Turn 51.3 16 0.00035 20.9 2.3 18 38-55 4-21 (49)
161 PRK11923 algU RNA polymerase s 51.0 17 0.00037 27.1 2.9 31 37-67 157-187 (193)
162 PRK09643 RNA polymerase sigma 50.9 33 0.00072 25.7 4.5 31 37-67 153-183 (192)
163 PRK11552 putative DNA-binding 50.9 31 0.00066 26.7 4.4 44 16-61 16-59 (225)
164 PRK09636 RNA polymerase sigma 50.9 34 0.00073 27.6 4.8 30 38-67 135-164 (293)
165 PF13411 MerR_1: MerR HTH fami 50.2 16 0.00035 22.7 2.3 17 38-54 4-20 (69)
166 PRK08215 sporulation sigma fac 50.1 30 0.00064 27.4 4.3 49 10-66 209-257 (258)
167 TIGR02393 RpoD_Cterm RNA polym 50.0 38 0.00082 26.5 4.9 53 10-66 176-228 (238)
168 PRK05657 RNA polymerase sigma 49.9 39 0.00084 28.1 5.1 53 11-67 263-315 (325)
169 TIGR03020 EpsA transcriptional 49.6 29 0.00062 28.0 4.2 50 8-66 188-237 (247)
170 PRK10188 DNA-binding transcrip 49.6 33 0.00072 27.2 4.5 29 38-66 198-226 (240)
171 TIGR02392 rpoH_proteo alternat 49.5 44 0.00095 26.8 5.2 51 10-66 218-268 (270)
172 TIGR02394 rpoS_proteo RNA poly 49.2 41 0.0009 27.1 5.1 53 11-67 223-275 (285)
173 PHA01976 helix-turn-helix prot 48.2 14 0.00031 22.8 1.8 22 37-58 18-39 (67)
174 smart00530 HTH_XRE Helix-turn- 48.1 14 0.00031 20.2 1.6 22 37-58 13-34 (56)
175 PF06056 Terminase_5: Putative 48.0 18 0.00039 22.8 2.2 19 37-55 16-34 (58)
176 PRK13870 transcriptional regul 47.7 42 0.00091 26.5 4.8 29 38-66 192-220 (234)
177 PF03672 UPF0154: Uncharacteri 47.3 55 0.0012 21.3 4.4 36 15-53 18-55 (64)
178 PRK05572 sporulation sigma fac 46.7 37 0.0008 26.8 4.4 49 10-66 202-250 (252)
179 PRK09638 RNA polymerase sigma 46.7 26 0.00057 25.5 3.3 31 36-66 144-174 (176)
180 PRK09640 RNA polymerase sigma 46.1 27 0.00059 25.9 3.4 31 36-66 152-182 (188)
181 PRK12461 UDP-N-acetylglucosami 46.0 42 0.00092 27.0 4.6 52 5-56 194-247 (255)
182 PRK10651 transcriptional regul 45.9 38 0.00083 24.3 4.1 47 10-65 155-201 (216)
183 TIGR02984 Sig-70_plancto1 RNA 45.4 67 0.0015 23.4 5.4 29 37-65 159-187 (189)
184 PF09607 BrkDBD: Brinker DNA-b 45.1 72 0.0016 20.4 4.6 45 8-56 3-47 (58)
185 TIGR02835 spore_sigmaE RNA pol 44.9 26 0.00057 27.3 3.2 31 37-67 201-231 (234)
186 PF13936 HTH_38: Helix-turn-he 44.8 50 0.0011 19.2 3.7 40 9-56 3-42 (44)
187 TIGR02607 antidote_HigA addict 44.5 17 0.00038 23.0 1.8 23 37-59 21-43 (78)
188 cd04762 HTH_MerR-trunc Helix-T 44.4 26 0.00055 19.5 2.4 22 37-58 3-24 (49)
189 PF07638 Sigma70_ECF: ECF sigm 44.0 30 0.00065 26.1 3.3 31 36-66 153-183 (185)
190 TIGR02957 SigX4 RNA polymerase 43.9 46 0.00099 26.8 4.5 29 38-66 128-156 (281)
191 COG2963 Transposase and inacti 43.5 82 0.0018 21.7 5.3 48 8-62 5-53 (116)
192 PF14229 DUF4332: Domain of un 43.3 28 0.00062 24.9 2.9 29 31-59 26-54 (122)
193 PF13730 HTH_36: Helix-turn-he 43.3 69 0.0015 18.9 5.2 46 10-59 2-50 (55)
194 PF12323 HTH_OrfB_IS605: Helix 42.8 34 0.00074 20.0 2.8 35 30-65 9-43 (46)
195 PRK07500 rpoH2 RNA polymerase 42.3 55 0.0012 26.7 4.8 52 10-67 227-278 (289)
196 PRK09480 slmA division inhibit 42.1 56 0.0012 23.8 4.5 44 16-60 13-56 (194)
197 PF13551 HTH_29: Winged helix- 42.1 31 0.00067 23.0 2.9 27 36-62 14-40 (112)
198 KOG1146|consensus 41.8 35 0.00077 34.1 4.0 59 5-66 706-764 (1406)
199 PRK05911 RNA polymerase sigma 41.5 53 0.0011 26.2 4.5 48 11-66 206-253 (257)
200 PF03457 HA: Helicase associat 40.1 70 0.0015 19.9 4.1 40 16-64 12-51 (68)
201 smart00351 PAX Paired Box doma 40.0 1E+02 0.0022 22.0 5.4 43 11-61 18-60 (125)
202 PF12844 HTH_19: Helix-turn-he 38.8 20 0.00044 21.9 1.4 24 36-59 14-37 (64)
203 PRK06596 RNA polymerase factor 38.6 69 0.0015 26.0 4.8 52 10-67 230-281 (284)
204 TIGR01557 myb_SHAQKYF myb-like 38.5 99 0.0021 19.3 5.6 55 7-61 2-56 (57)
205 PRK10403 transcriptional regul 38.1 68 0.0015 22.9 4.3 48 10-66 153-200 (215)
206 PF04297 UPF0122: Putative hel 37.4 1.3E+02 0.0028 21.2 5.5 46 10-63 17-62 (101)
207 PF05269 Phage_CII: Bacterioph 37.1 44 0.00095 23.2 3.0 28 35-62 24-51 (91)
208 cd01104 HTH_MlrA-CarA Helix-Tu 37.0 36 0.00079 20.9 2.4 20 37-56 3-22 (68)
209 PF08671 SinI: Anti-repressor 36.9 50 0.0011 18.2 2.6 20 37-56 8-27 (30)
210 PF00376 MerR: MerR family reg 36.3 34 0.00074 19.5 2.0 17 38-54 3-19 (38)
211 PRK10360 DNA-binding transcrip 36.3 1.1E+02 0.0024 21.8 5.3 45 10-63 137-181 (196)
212 PRK12427 flagellar biosynthesi 36.1 1.2E+02 0.0025 23.8 5.7 46 11-64 184-229 (231)
213 PF00325 Crp: Bacterial regula 36.1 68 0.0015 17.9 3.1 25 36-60 4-28 (32)
214 PF06163 DUF977: Bacterial pro 35.7 81 0.0017 23.3 4.3 47 9-58 3-50 (127)
215 PF01726 LexA_DNA_bind: LexA D 35.7 1.1E+02 0.0023 19.5 4.5 43 10-57 3-49 (65)
216 TIGR01764 excise DNA binding d 35.3 43 0.00093 18.7 2.4 21 37-57 4-24 (49)
217 TIGR03879 near_KaiC_dom probab 35.2 38 0.00083 22.5 2.3 22 36-57 34-55 (73)
218 TIGR02997 Sig70-cyanoRpoD RNA 34.9 82 0.0018 25.6 4.8 49 11-63 250-298 (298)
219 cd04764 HTH_MlrA-like_sg1 Heli 34.9 38 0.00082 21.0 2.2 19 38-56 4-22 (67)
220 smart00351 PAX Paired Box doma 34.9 1.5E+02 0.0033 21.0 5.7 44 9-55 74-124 (125)
221 PF13873 Myb_DNA-bind_5: Myb/S 34.5 1.2E+02 0.0027 19.2 7.0 60 7-66 1-76 (78)
222 PRK10219 DNA-binding transcrip 34.5 93 0.002 20.9 4.3 40 14-57 5-44 (107)
223 PF14549 P22_Cro: DNA-binding 34.2 42 0.00091 21.3 2.3 18 37-54 12-29 (60)
224 KOG4040|consensus 34.2 38 0.00083 26.1 2.5 34 17-50 27-61 (186)
225 PRK15411 rcsA colanic acid cap 33.6 75 0.0016 24.3 4.1 47 10-65 137-183 (207)
226 PRK09635 sigI RNA polymerase s 33.6 77 0.0017 25.9 4.4 29 38-66 138-166 (290)
227 PRK10100 DNA-binding transcrip 33.2 80 0.0017 24.6 4.3 46 11-65 156-201 (216)
228 PRK09935 transcriptional regul 33.2 1E+02 0.0022 22.1 4.6 45 10-63 149-193 (210)
229 PRK05988 formate dehydrogenase 33.0 89 0.0019 23.4 4.3 27 27-53 34-60 (156)
230 smart00422 HTH_MERR helix_turn 32.9 42 0.00091 20.6 2.2 18 38-55 4-21 (70)
231 PRK13890 conjugal transfer pro 32.6 30 0.00064 24.7 1.6 23 37-59 21-43 (120)
232 PF05821 NDUF_B8: NADH-ubiquin 32.2 33 0.00073 26.5 1.9 34 21-54 26-60 (179)
233 PRK09706 transcriptional repre 32.1 30 0.00066 24.7 1.6 23 37-59 21-43 (135)
234 KOG4067|consensus 31.8 36 0.00077 26.8 2.0 48 12-66 133-187 (195)
235 cd04763 HTH_MlrA-like Helix-Tu 31.7 50 0.0011 20.5 2.4 19 38-56 4-22 (68)
236 TIGR03629 arch_S13P archaeal r 31.3 47 0.001 24.8 2.5 24 9-33 50-73 (144)
237 PF04703 FaeA: FaeA-like prote 30.9 52 0.0011 21.0 2.4 24 36-59 17-40 (62)
238 PF04936 DUF658: Protein of un 30.7 31 0.00067 26.7 1.5 33 35-67 15-47 (186)
239 PRK09958 DNA-binding transcrip 30.7 2E+02 0.0044 20.5 5.9 46 10-64 143-188 (204)
240 PF09636 XkdW: XkdW protein; 30.6 35 0.00077 24.5 1.7 33 11-43 40-73 (108)
241 PRK09726 antitoxin HipB; Provi 30.1 34 0.00074 22.7 1.5 22 37-58 28-49 (88)
242 PRK09483 response regulator; P 28.9 1.2E+02 0.0027 21.9 4.5 46 9-63 147-192 (217)
243 PF07037 DUF1323: Putative tra 28.8 47 0.001 24.3 2.1 19 37-55 3-21 (122)
244 PF06971 Put_DNA-bind_N: Putat 28.7 49 0.0011 20.3 1.9 17 37-53 31-47 (50)
245 COG1595 RpoE DNA-directed RNA 28.5 71 0.0015 23.6 3.2 30 38-67 147-176 (182)
246 PF08765 Mor: Mor transcriptio 28.2 70 0.0015 22.2 2.9 30 36-65 74-103 (108)
247 PRK07598 RNA polymerase sigma 28.1 1.3E+02 0.0028 26.3 5.1 52 10-65 350-401 (415)
248 TIGR01958 nuoE_fam NADH-quinon 27.7 1.2E+02 0.0026 22.2 4.2 34 27-60 27-63 (148)
249 PRK07405 RNA polymerase sigma 27.5 1.5E+02 0.0033 24.5 5.2 51 11-65 257-307 (317)
250 PF13560 HTH_31: Helix-turn-he 27.5 44 0.00095 20.5 1.6 25 36-60 16-40 (64)
251 cd07377 WHTH_GntR Winged helix 27.4 1.4E+02 0.003 17.6 4.6 47 15-61 6-52 (66)
252 PRK09390 fixJ response regulat 27.2 1.8E+02 0.0039 20.3 5.0 29 38-66 160-188 (202)
253 PRK13916 plasmid segregation p 27.2 49 0.0011 22.9 1.8 36 2-37 23-59 (97)
254 PRK04053 rps13p 30S ribosomal 27.2 61 0.0013 24.4 2.5 25 8-32 53-77 (149)
255 COG2938 Uncharacterized conser 27.1 1.3E+02 0.0029 20.9 4.0 41 18-60 32-72 (94)
256 PF07022 Phage_CI_repr: Bacter 26.6 34 0.00074 21.6 1.0 21 36-56 14-35 (66)
257 PRK07539 NADH dehydrogenase su 26.5 1.3E+02 0.0028 22.2 4.2 34 27-60 33-69 (154)
258 PF13412 HTH_24: Winged helix- 26.5 1.3E+02 0.0029 17.1 3.7 36 13-55 3-38 (48)
259 smart00354 HTH_LACI helix_turn 26.3 45 0.00098 21.1 1.5 22 37-58 3-24 (70)
260 PRK09191 two-component respons 26.2 1.5E+02 0.0033 22.5 4.7 49 11-67 89-137 (261)
261 PF04539 Sigma70_r3: Sigma-70 26.2 1.7E+02 0.0036 18.4 4.3 21 37-57 23-43 (78)
262 PF04814 HNF-1_N: Hepatocyte n 26.0 1.3E+02 0.0027 23.5 4.1 34 15-55 119-152 (180)
263 PRK09685 DNA-binding transcrip 25.7 2.1E+02 0.0045 22.6 5.6 40 14-56 197-236 (302)
264 PF12728 HTH_17: Helix-turn-he 25.3 77 0.0017 18.4 2.3 19 38-56 5-23 (51)
265 PF13613 HTH_Tnp_4: Helix-turn 25.2 57 0.0012 19.6 1.7 23 37-59 22-44 (53)
266 PF13542 HTH_Tnp_ISL3: Helix-t 25.1 79 0.0017 18.4 2.3 36 17-56 14-49 (52)
267 TIGR02850 spore_sigG RNA polym 24.9 1.2E+02 0.0027 23.8 4.1 48 10-65 206-253 (254)
268 KOG3755|consensus 24.7 45 0.00098 30.9 1.7 121 4-135 354-481 (769)
269 PRK07571 bidirectional hydroge 24.4 1.5E+02 0.0033 22.6 4.3 26 28-53 48-73 (169)
270 PRK10840 transcriptional regul 24.1 1.5E+02 0.0032 22.1 4.2 45 10-63 150-194 (216)
271 PHA02955 hypothetical protein; 24.1 1.4E+02 0.003 23.9 4.1 47 16-64 63-109 (213)
272 PRK10430 DNA-binding transcrip 24.0 2.1E+02 0.0046 21.7 5.2 47 10-60 158-204 (239)
273 PHA00542 putative Cro-like pro 23.8 62 0.0013 21.4 1.9 24 36-59 33-56 (82)
274 smart00595 MADF subfamily of S 23.8 1.2E+02 0.0025 19.6 3.2 30 38-67 31-60 (89)
275 PF02796 HTH_7: Helix-turn-hel 23.7 92 0.002 18.0 2.4 40 8-55 3-42 (45)
276 PRK05949 RNA polymerase sigma 23.6 1.8E+02 0.0038 24.3 4.9 51 11-65 267-317 (327)
277 PF07042 TrfA: TrfA protein; 23.4 1.6E+02 0.0035 24.4 4.6 49 8-59 208-256 (282)
278 PF13720 Acetyltransf_11: Udp 23.2 79 0.0017 21.1 2.3 42 5-46 22-63 (83)
279 PF01710 HTH_Tnp_IS630: Transp 22.6 72 0.0016 22.4 2.1 21 36-56 20-40 (119)
280 PF12949 HeH: HeH/LEM domain; 21.9 59 0.0013 18.5 1.2 28 15-43 5-32 (35)
281 cd01105 HTH_GlnR-like Helix-Tu 21.7 83 0.0018 20.9 2.2 17 38-54 5-21 (88)
282 PRK10026 arsenate reductase; P 21.7 1.5E+02 0.0033 21.9 3.8 34 17-51 16-58 (141)
283 PF01257 2Fe-2S_thioredx: Thio 21.5 87 0.0019 22.9 2.4 25 29-53 26-50 (145)
284 PF12200 DUF3597: Domain of un 21.4 2E+02 0.0043 21.2 4.2 34 32-65 83-121 (127)
285 PF09179 TilS: TilS substrate 21.1 1.6E+02 0.0035 18.0 3.3 31 13-44 12-42 (69)
286 PF06918 DUF1280: Protein of u 21.0 1.8E+02 0.004 23.1 4.3 38 8-45 62-100 (224)
287 PRK07406 RNA polymerase sigma 21.0 2.1E+02 0.0046 24.5 5.0 53 10-66 311-363 (373)
288 PF14053 DUF4248: Domain of un 21.0 1.7E+02 0.0037 19.0 3.5 35 11-53 20-61 (69)
289 PRK01844 hypothetical protein; 20.6 2.4E+02 0.0051 18.8 4.1 36 15-53 25-62 (72)
290 PF05589 DUF768: Protein of un 20.3 2.5E+02 0.0054 18.1 4.1 17 12-28 2-18 (64)
No 1
>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=99.79 E-value=1e-19 Score=108.79 Aligned_cols=40 Identities=58% Similarity=0.927 Sum_probs=36.4
Q ss_pred HHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 22 WLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 22 w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
||.+|..||||+.++|.+||.+|||+.+||++||.|+|+|
T Consensus 1 Wl~~h~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 1 WLLEHLHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp HHHHTTTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CHHHHCCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 8999999999999999999999999999999999999997
No 2
>KOG0774|consensus
Probab=99.74 E-value=7.3e-19 Score=141.71 Aligned_cols=62 Identities=32% Similarity=0.450 Sum_probs=59.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
..|.+|++.+++||.+||+.|+.||||++++|++||++++++..||+|||.|.|.|.|+.+.
T Consensus 190 RKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~ 251 (334)
T KOG0774|consen 190 RKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMG 251 (334)
T ss_pred HhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhh
Confidence 37899999999999999999999999999999999999999999999999999999998875
No 3
>KOG0775|consensus
Probab=99.68 E-value=7e-17 Score=130.70 Aligned_cols=55 Identities=42% Similarity=0.672 Sum_probs=52.2
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+||....+.+|++|| ..||||++++|++||++|||++.||.|||+|+|+|.|...
T Consensus 181 yCFKekSR~~LrewY---~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~~ 235 (304)
T KOG0775|consen 181 YCFKEKSRSLLREWY---LQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAAA 235 (304)
T ss_pred eehhHhhHHHHHHHH---hcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhcc
Confidence 689999999999999 8999999999999999999999999999999999999443
No 4
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.65 E-value=4.4e-16 Score=97.83 Aligned_cols=57 Identities=33% Similarity=0.416 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
..|..|+++++.+|++|| ..+|||+.+++..||.++||+..||.+||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEF---EKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 467899999999999999 779999999999999999999999999999999997753
No 5
>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=99.65 E-value=3.2e-16 Score=98.69 Aligned_cols=56 Identities=36% Similarity=0.477 Sum_probs=53.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
.+|..|+.+++.+|+.+| ..+|||+.+++..||..+||+..||.+||+|+|.+.|+
T Consensus 2 r~r~~~t~~q~~~L~~~f---~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 2 RKRTRFTKEQLKVLEEYF---QENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSHHHHHHHHHHH---HHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred cCCCCCCHHHHHHHHHHH---HHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 378999999999999999 77999999999999999999999999999999999875
No 6
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=5e-16 Score=97.03 Aligned_cols=55 Identities=31% Similarity=0.402 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.+|..|+.+++.+|+.|| ..++||+.+++..||..+||+..||.+||+|+|.|.+
T Consensus 2 k~r~~~~~~~~~~L~~~f---~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEF---QKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHH---HhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 467889999999999999 8999999999999999999999999999999999854
No 7
>KOG0773|consensus
Probab=99.54 E-value=1.7e-15 Score=125.83 Aligned_cols=61 Identities=44% Similarity=0.615 Sum_probs=57.6
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++..|++.++.+|+.|+++|..+|||+..+|..||++|||+..||+|||+|+|+|.++.+.
T Consensus 242 ~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 242 PQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 4569999999999999999999999999999999999999999999999999999887763
No 8
>KOG0489|consensus
Probab=99.41 E-value=2.3e-13 Score=110.22 Aligned_cols=60 Identities=30% Similarity=0.344 Sum_probs=57.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
..|+.||..|+-.|+.-| ..|.|-+...|.+||..++|++.||++||||||+|.||..+.
T Consensus 161 R~RtayT~~QllELEkEF---hfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 161 RRRTAFTRYQLLELEKEF---HFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCcccchhhhhhhhhhh---ccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 478999999999999999 999999999999999999999999999999999999998765
No 9
>KOG0843|consensus
Probab=99.39 E-value=5.6e-13 Score=102.61 Aligned_cols=59 Identities=25% Similarity=0.259 Sum_probs=55.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
.|+.|+.+|...|+..| ..+.|-.-.||..||+.++|++.||++||||+|.|.|+....
T Consensus 105 ~RT~ft~~Ql~~LE~~F---~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 105 IRTAFTPEQLLKLEHAF---EGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred cccccCHHHHHHHHHHH---hcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 68999999999999999 999999999999999999999999999999999999987543
No 10
>KOG0487|consensus
Probab=99.36 E-value=2.6e-13 Score=112.06 Aligned_cols=59 Identities=29% Similarity=0.291 Sum_probs=55.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++|.-+||.|+..|+.-| +.|-|.|++.|.+|++.++||+.||++||||||+|+||.++
T Consensus 237 KKRcPYTK~QtlELEkEF---lfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 237 KKRCPYTKHQTLELEKEF---LFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccCCchHHHHHHHHHHH---HHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 478889999999999999 99999999999999999999999999999999999999874
No 11
>KOG0850|consensus
Probab=99.29 E-value=3.8e-12 Score=101.14 Aligned_cols=59 Identities=29% Similarity=0.411 Sum_probs=57.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+||++++.-|...|+.-| .+..|.---||.+||..+|||.+||++||||+|-|.||.++
T Consensus 124 KPRTIYSS~QLqaL~rRF---QkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 124 KPRTIYSSLQLQALNRRF---QQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCcccccHHHHHHHHHHH---hhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 589999999999999999 99999999999999999999999999999999999999986
No 12
>KOG0493|consensus
Probab=99.27 E-value=4.3e-12 Score=102.79 Aligned_cols=59 Identities=29% Similarity=0.348 Sum_probs=55.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 5 MVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 5 ~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.||+.|+.+|.+.|+.-| ..|-|.++..|++||.+++|.+.||++||||+|.++||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF---~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEF---QENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHH---hhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 3589999999999999999 8899999999999999999999999999999999999874
No 13
>KOG0488|consensus
Probab=99.24 E-value=7.8e-12 Score=103.70 Aligned_cols=59 Identities=25% Similarity=0.347 Sum_probs=55.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++|+.||..|+..|+.-| .+--|.+..+|.+||..+|||-.||++||||||+|+|+...
T Consensus 174 ksRTaFT~~Ql~~LEkrF---~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 174 KSRTAFSDHQLFELEKRF---EKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cchhhhhHHHHHHHHHHH---HHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 478999999999999999 88899999999999999999999999999999999998864
No 14
>KOG0842|consensus
Probab=99.23 E-value=1.1e-11 Score=102.42 Aligned_cols=58 Identities=24% Similarity=0.337 Sum_probs=54.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
++|-.|++.|+-.|++-| ...-|-|..||+.||..++||.+||++||||+|-|-|+.-
T Consensus 155 KrRVLFSqAQV~ELERRF---rqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~ 212 (307)
T KOG0842|consen 155 KRRVLFSQAQVYELERRF---RQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQ 212 (307)
T ss_pred ccccccchhHHHHHHHHH---HhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhh
Confidence 467789999999999999 8889999999999999999999999999999999988764
No 15
>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=99.19 E-value=2.2e-11 Score=78.21 Aligned_cols=51 Identities=14% Similarity=0.117 Sum_probs=48.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCC----CCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPY----PTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPY----Ps~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
.+|+.|+.+|+..|+..| ..++| |+..++.+||..+||+..+|.+||+|-+
T Consensus 3 R~RT~Ft~~Q~~~Le~~f---e~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 3 RRRTKFTAEQKEKMRDFA---EKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCHHHHHHHHHHH---HHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 479999999999999999 99999 9999999999999999999999999953
No 16
>KOG0485|consensus
Probab=99.19 E-value=1.3e-11 Score=97.78 Aligned_cols=59 Identities=25% Similarity=0.315 Sum_probs=55.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++|++|++.|+..|+.-| ...-|-+.+||..||..+.||++||++||||+|.|.|++..
T Consensus 106 ktRTvFSraQV~qLEs~F---e~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 106 KTRTVFSRAQVFQLESTF---ELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred cchhhhhHHHHHHHHHHH---HHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 478999999999999999 88889999999999999999999999999999999999864
No 17
>KOG0492|consensus
Probab=99.14 E-value=3.7e-11 Score=94.52 Aligned_cols=59 Identities=25% Similarity=0.312 Sum_probs=55.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 4 NMVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 4 ~~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+.+||+-|+..|...|++-| ....|-+.+|+.+++.-+.||++||++||||+|.|.|+.
T Consensus 144 nRkPRtPFTtqQLlaLErkf---rekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRl 202 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKF---REKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRL 202 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHH---hHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHH
Confidence 45799999999999999999 888899999999999999999999999999999998875
No 18
>KOG0848|consensus
Probab=99.14 E-value=1.6e-11 Score=99.66 Aligned_cols=58 Identities=29% Similarity=0.351 Sum_probs=54.6
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
|-+++..|+-.|+.-| -.++|.|...|.+||..+||++.||++||||||.|.+|.+|+
T Consensus 203 RvVYTDhQRLELEKEf---h~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEF---HTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKK 260 (317)
T ss_pred eEEecchhhhhhhhhh---ccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHH
Confidence 5678999999999999 999999999999999999999999999999999999998876
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.11 E-value=1.4e-10 Score=87.95 Aligned_cols=59 Identities=27% Similarity=0.421 Sum_probs=55.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
..|...+..++.+|+..| ..+|||+..+|..|+..++|+++-|+.||||+|.+.|+...
T Consensus 53 ~~r~R~t~~Q~~vL~~~F---~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 53 SKRRRTTDEQLMVLEREF---EINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred ccceechHHHHHHHHHHh---ccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 467889999999999999 99999999999999999999999999999999999998763
No 20
>KOG0847|consensus
Probab=99.09 E-value=1.1e-10 Score=92.78 Aligned_cols=101 Identities=18% Similarity=0.211 Sum_probs=71.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccCCCCCCCCCCCCcccccc-
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKTDDDDDAIIS- 85 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~~p~~~~~~~~~~~~~- 85 (140)
.|..|+-.++..|+.-| ....|+--+++.+||...|+++.||.+||||+|.+.++..........+.++.+-....
T Consensus 170 srPTf~g~qi~~le~~f---eqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmasakkkqds~ae~~~g 246 (288)
T KOG0847|consen 170 SRPTFTGHQIYQLERKF---EQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMASAKKKQDSGAERGAG 246 (288)
T ss_pred cCCCccchhhhhhhhhh---hhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhhccccCCCccccccc
Confidence 46779999999999999 77889999999999999999999999999999999998765433322222222111111
Q ss_pred cCCccccCcccCchHHHhhhHHHHh
Q psy10107 86 DCDEKDKDDLMMDEEKMKQHHRMVK 110 (140)
Q Consensus 86 d~~~~~~~~l~~~~~~~~~~~~~~~ 110 (140)
-..++++||.|+.+-....++++|.
T Consensus 247 g~~~eeeDDeYNkPLDPnSDDEKIt 271 (288)
T KOG0847|consen 247 GAPSEEEDDEYNKPLDPNSDDEKIT 271 (288)
T ss_pred CCCccccccccCCCCCCCcchHHHH
Confidence 1234445667776655555555553
No 21
>KOG0483|consensus
Probab=99.01 E-value=3.3e-10 Score=88.81 Aligned_cols=57 Identities=23% Similarity=0.177 Sum_probs=52.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
....|+.+|+..|+.-| ..+-|-.+++|..||+++||.+.||.+||||+|.|.|...
T Consensus 53 kk~Rlt~eQ~~~LE~~F---~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kq 109 (198)
T KOG0483|consen 53 KKRRLTSEQVKFLEKSF---ESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQ 109 (198)
T ss_pred ccccccHHHHHHhHHhh---ccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchh
Confidence 56789999999999999 7777889999999999999999999999999999988653
No 22
>KOG0484|consensus
Probab=98.99 E-value=4.9e-10 Score=79.83 Aligned_cols=56 Identities=21% Similarity=0.345 Sum_probs=52.6
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
|+.|+..|...|+.-| ....||..-.|++||.+..|++..|++||||+|.+.+++-
T Consensus 21 RTTFTS~QLkELErvF---~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 21 RTTFTSAQLKELERVF---AETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhHHHHHHHHHHH---HhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 6889999999999999 7788999999999999999999999999999999998764
No 23
>KOG2251|consensus
Probab=98.98 E-value=4.3e-10 Score=89.02 Aligned_cols=58 Identities=22% Similarity=0.336 Sum_probs=54.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.|+.|+..|.++|++.| .+.-||+...+++||.+++|.+.+|.+||+|+|.+.|++.+
T Consensus 40 ERTtFtr~QlevLe~LF---~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 40 ERTTFTRKQLEVLEALF---AKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred ccceecHHHHHHHHHHH---HhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 57899999999999999 88999999999999999999999999999999999887644
No 24
>KOG0491|consensus
Probab=98.96 E-value=3.2e-10 Score=86.51 Aligned_cols=62 Identities=26% Similarity=0.320 Sum_probs=56.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccCCC
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 70 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~ 70 (140)
+-|++|+..+...|++-| ..--|-+-.++.+||..++|+++||+.||||+|++.|+..+..|
T Consensus 102 K~Rtvfs~~ql~~l~~rF---e~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 102 KARTVFSDPQLSGLEKRF---ERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhcccccCccccccHHHH---hhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 467889999999999999 77789999999999999999999999999999999998865443
No 25
>KOG0494|consensus
Probab=98.91 E-value=1.3e-09 Score=88.48 Aligned_cols=57 Identities=26% Similarity=0.376 Sum_probs=53.8
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
|++||..|.+.|+.-| +.-.||....|+.||..|+|.+.+|.+||||+|.|.++.-+
T Consensus 145 RTiFT~~Qle~LEkaF---keaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAF---KEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred cchhhHHHHHHHHHHH---hhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 6899999999999999 88899999999999999999999999999999999888754
No 26
>KOG0844|consensus
Probab=98.88 E-value=7e-10 Score=91.73 Aligned_cols=62 Identities=23% Similarity=0.332 Sum_probs=55.1
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc-ccCCCCC
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE-NKMTWEP 72 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~-~~~~~~p 72 (140)
|+.|+++|+..|+.-| .+--|-+...|.+||.+++|.+..|++||||+|+|.|++ ..+.|-.
T Consensus 185 RTAFTReQIaRLEKEF---yrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlamaWPh 247 (408)
T KOG0844|consen 185 RTAFTREQIARLEKEF---YRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAMAWPH 247 (408)
T ss_pred HhhhhHHHHHHHHHHH---HHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhccCCC
Confidence 5789999999998888 677799999999999999999999999999999998887 4566653
No 27
>KOG3802|consensus
Probab=98.84 E-value=1.3e-09 Score=92.36 Aligned_cols=59 Identities=24% Similarity=0.290 Sum_probs=55.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++|+.+...++..|+..| .+||-|+.+|.-+||..++|...-|.+||||||.|.|+...
T Consensus 296 KKRTSie~~vr~aLE~~F---~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 296 KKRTSIEVNVRGALEKHF---LKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccccceeHHHHHHHHHHH---HhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 477889999999999999 99999999999999999999999999999999999998864
No 28
>KOG2252|consensus
Probab=98.80 E-value=3.4e-08 Score=86.67 Aligned_cols=57 Identities=33% Similarity=0.429 Sum_probs=54.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 4 NMVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 4 ~~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
..+||.+|+..|++.|...| ..++||+.++.+.|+.+++|.+..|.|||.|+|+|.+
T Consensus 420 ~KKPRlVfTd~QkrTL~aiF---ke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIF---KENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCCceeeecHHHHHHHHHHH---hcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 45699999999999999999 9999999999999999999999999999999999963
No 29
>KOG0486|consensus
Probab=98.67 E-value=1.1e-08 Score=84.80 Aligned_cols=56 Identities=27% Similarity=0.402 Sum_probs=52.3
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-|+-|+-.+.+.|+.|| ..|-||+.+.|++||.=++||+..|.+||+|+|.+.++.
T Consensus 115 QrthFtSqqlqele~tF---~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkr 170 (351)
T KOG0486|consen 115 QRTHFTSQQLQELEATF---QRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKR 170 (351)
T ss_pred hhhhhHHHHHHHHHHHH---hhccCCccchhhHHHhhccccchhhhhhcccchhhhhhh
Confidence 35779999999999999 999999999999999999999999999999999997764
No 30
>KOG4577|consensus
Probab=98.62 E-value=3.9e-08 Score=81.00 Aligned_cols=59 Identities=27% Similarity=0.345 Sum_probs=55.0
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.||+..+..+.+.|+..| ...|-|-.--|++|+.+|||...-|++||||+|.+.|+-.|
T Consensus 169 RPRTTItAKqLETLK~AY---n~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T KOG4577|consen 169 RPRTTITAKQLETLKQAY---NTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKK 227 (383)
T ss_pred CCcceeeHHHHHHHHHHh---cCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhh
Confidence 489999999999999999 99999999999999999999999999999999999876543
No 31
>KOG0773|consensus
Probab=98.55 E-value=6.3e-08 Score=80.58 Aligned_cols=74 Identities=64% Similarity=0.866 Sum_probs=67.2
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccCCCCCCCCCC
Q psy10107 3 MNMVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTWEPKNKTD 77 (140)
Q Consensus 3 ~~~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~~p~~~~~ 77 (140)
..+.+|.+.+.+. .+|+.|+.+|..++||++.++..|+..++++..||.+||.|+|+|.++.+++.|.+.....
T Consensus 94 ~~~~~~~n~~~~s-~~~~~~~~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~~~~~~~~~~~~~ 167 (342)
T KOG0773|consen 94 DKGARRGNATRES-ATLKAWLEEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKELKMTWGPTPLAL 167 (342)
T ss_pred ccccccccccccc-cccccchhhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhccCCCCCCccccc
Confidence 3455778888888 9999999999999999999999999999999999999999999999999999998865543
No 32
>KOG0849|consensus
Probab=98.40 E-value=3.2e-07 Score=77.51 Aligned_cols=57 Identities=21% Similarity=0.360 Sum_probs=53.9
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|+.|+..+...|+++| ..++||....++.||.++++++..|..||+|+|.|.++..
T Consensus 179 ~rtsft~~Q~~~le~~f---~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 179 NRTSFSPSQLEALEECF---QRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccchHHHHHHHh---cCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 35689999999999999 9999999999999999999999999999999999988876
No 33
>KOG0490|consensus
Probab=98.30 E-value=3.4e-07 Score=71.13 Aligned_cols=57 Identities=23% Similarity=0.215 Sum_probs=53.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|..|+..+.+.|+.-| ...+||....++.||..+++++..|.+||+|+|.+.+++.
T Consensus 63 ~rt~~~~~ql~~ler~f---~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 63 ARCKFTISQLDELERAF---EKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cCCCCCcCHHHHHHHhh---cCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 56889999999999999 8889999999999999999999999999999999988764
No 34
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.73 E-value=2.3e-05 Score=49.95 Aligned_cols=43 Identities=21% Similarity=0.298 Sum_probs=30.9
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
.+.|+++| ..+.+..+.+...|+.+++|+..||..||.-++.+
T Consensus 10 ~~pL~~Yy---~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~e 52 (56)
T PF11569_consen 10 IQPLEDYY---LKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQE 52 (56)
T ss_dssp -HHHHHHH---HHT----TTHHHHHHHHTT--HHHHHHHHHHHS--
T ss_pred hHHHHHHH---HHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhccc
Confidence 35599999 67788999999999999999999999999877544
No 35
>KOG1168|consensus
Probab=97.69 E-value=1.2e-05 Score=66.47 Aligned_cols=54 Identities=22% Similarity=0.335 Sum_probs=47.4
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+..-.--++-|++|| ..-|-|+.+....||+++.|...-|.+||+|+|++.|+.
T Consensus 314 TSIAAPEKRsLEayF---avQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 314 TSIAAPEKRSLEAYF---AVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred ccccCcccccHHHHh---ccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 333344467899999 999999999999999999999999999999999998874
No 36
>KOG0490|consensus
Probab=97.11 E-value=0.00056 Score=53.02 Aligned_cols=57 Identities=26% Similarity=0.413 Sum_probs=52.4
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+|..+...+...|..-| ...+||....+..|+..+|++...|.+||+|.|.+.++..
T Consensus 156 ~~~~~~~~~~~~~~~~~---~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 156 PRTTFTENQLEVLETVF---RATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred CccccccchhHhhhhcc---cCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 56788888999998888 9999999999999999999999999999999999988764
No 37
>KOG1146|consensus
Probab=95.08 E-value=0.023 Score=55.09 Aligned_cols=58 Identities=22% Similarity=0.261 Sum_probs=52.5
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.|+.++..++.+|+..| ..--||..++-+.|....+|...-|..||+|+|.+.++..-
T Consensus 906 ~~~~~~d~qlk~i~~~~---~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 906 YRTQESDLQLKIIKACY---EAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hccchhHHHHHHHHHHH---hhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 35678889999999999 88889999999999999999999999999999999888753
No 38
>KOG3623|consensus
Probab=94.56 E-value=0.13 Score=47.77 Aligned_cols=52 Identities=19% Similarity=0.297 Sum_probs=46.0
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccCCC
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENKMTW 70 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~ 70 (140)
+.+|+++| ..|++|+.++...+|.+.||...-|+.||.+.+..........-
T Consensus 568 ~sllkayy---aln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~rsps 619 (1007)
T KOG3623|consen 568 TSLLKAYY---ALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVERSPS 619 (1007)
T ss_pred HHHHHHHH---HhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhccCcc
Confidence 78899999 99999999999999999999999999999999988765544333
No 39
>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=92.48 E-value=0.45 Score=29.46 Aligned_cols=47 Identities=19% Similarity=0.020 Sum_probs=31.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 6 VPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 6 ~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
.+|..||-+..-.+-..+ ...+ ....||+.+|++..+|.+|..|+..
T Consensus 2 rkR~~LTl~eK~~iI~~~---e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~~ 48 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRL---EEGE-----SKRDIAREFGVSRSTVSTILKNKDK 48 (53)
T ss_dssp SSSSS--HHHHHHHHHHH---HCTT------HHHHHHHHT--CCHHHHHHHCHHH
T ss_pred CCCccCCHHHHHHHHHHH---HcCC-----CHHHHHHHhCCCHHHHHHHHHhHHH
Confidence 367788877754444444 5554 5889999999999999999999643
No 40
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=88.08 E-value=1 Score=25.76 Aligned_cols=46 Identities=15% Similarity=0.073 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.++...+.++...+.+ ...-.++|..+|++..+|..|....+.+.|
T Consensus 10 ~l~~~~~~~~~~~~~~--------~~~~~~ia~~~~~s~~~i~~~~~~~~~~l~ 55 (55)
T cd06171 10 KLPEREREVILLRFGE--------GLSYEEIAEILGISRSTVRQRLHRALKKLR 55 (55)
T ss_pred hCCHHHHHHHHHHHhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 3567777777776521 124577899999999999999988887754
No 41
>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=86.27 E-value=2.2 Score=25.57 Aligned_cols=45 Identities=16% Similarity=0.051 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRL 62 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~ 62 (140)
.+|+.++.++...| -..-.-.++|..+|++...|.+|+..+|++.
T Consensus 10 ~L~~~~r~i~~l~~--------~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~L 54 (54)
T PF08281_consen 10 QLPERQREIFLLRY--------FQGMSYAEIAEILGISESTVKRRLRRARKKL 54 (54)
T ss_dssp CS-HHHHHHHHHHH--------TS---HHHHHHHCTS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH--------HHCcCHHHHHHHHCcCHHHHHHHHHHHHhhC
Confidence 35677777776654 1223457899999999999999999988763
No 42
>PRK04217 hypothetical protein; Provisional
Probab=85.88 E-value=3.3 Score=29.65 Aligned_cols=56 Identities=13% Similarity=-0.084 Sum_probs=45.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 4 NMVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 4 ~~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.+.|-..++.++++++..++.+.. .-.+||+.+|++...|.+.+..++.+++....
T Consensus 36 ~~~p~~~Lt~eereai~l~~~eGl--------S~~EIAk~LGIS~sTV~r~L~RArkkLre~L~ 91 (110)
T PRK04217 36 PPKPPIFMTYEEFEALRLVDYEGL--------TQEEAGKRMGVSRGTVWRALTSARKKVAQMLV 91 (110)
T ss_pred CCCCcccCCHHHHHHHHHHHHcCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 345667889999988877763332 45779999999999999999999999988764
No 43
>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=85.71 E-value=2.2 Score=25.42 Aligned_cols=47 Identities=11% Similarity=0.046 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
.++++.+.+|...| | -.-.-.++|..+|++...|..+...+..++|+
T Consensus 4 ~L~~~er~vi~~~y-------~-~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR~ 50 (50)
T PF04545_consen 4 QLPPREREVIRLRY-------F-EGLTLEEIAERLGISRSTVRRILKRALKKLRK 50 (50)
T ss_dssp TS-HHHHHHHHHHH-------T-ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-------c-CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhcC
Confidence 57888899998887 1 12345789999999999999999999888764
No 44
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=85.62 E-value=2.8 Score=21.37 Aligned_cols=40 Identities=8% Similarity=-0.107 Sum_probs=27.8
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhh
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF 55 (140)
+..++.+....+...+ . +.+ ...++|+.+|++...|.+|+
T Consensus 3 ~~~~~~~~~~~i~~~~---~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLL---A-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHH---H-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 4456666666665555 2 333 45688899999999999984
No 45
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=85.20 E-value=1.9 Score=30.95 Aligned_cols=48 Identities=21% Similarity=0.086 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.+++.++.++...|.+. -.-.++|..+|++...|.++...+|.++++.
T Consensus 106 ~L~~~~r~ii~l~~~~~--------~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~~ 153 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG--------KTMGEIALETEMTYYQVRWIYRQALEKMRNS 153 (154)
T ss_pred hCCHHHHHHHHHHHhcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHhhc
Confidence 45666777765444221 2256899999999999999999999988753
No 46
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=82.41 E-value=2.8 Score=30.30 Aligned_cols=30 Identities=27% Similarity=0.297 Sum_probs=26.9
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|.+.+.-+|.++|+..+
T Consensus 126 ~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (160)
T PRK09642 126 QEIALQEKIEVKTVEMKLYRARKWIKKHWK 155 (160)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 578999999999999999999999988753
No 47
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=82.09 E-value=2.9 Score=31.52 Aligned_cols=49 Identities=14% Similarity=-0.028 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
|+..++.+|...+.+. -.-.++|..+|++...|.+++..+|+++++...
T Consensus 143 L~~~~r~vl~l~~~~~--------~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l~ 191 (194)
T PRK09646 143 LTDTQRESVTLAYYGG--------LTYREVAERLAVPLGTVKTRMRDGLIRLRDCLG 191 (194)
T ss_pred CCHHHHHHHHHHHHcC--------CCHHHHHHHhCCChHhHHHHHHHHHHHHHHHhc
Confidence 5566666665443222 234678999999999999999999999988754
No 48
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=81.99 E-value=4.9 Score=28.58 Aligned_cols=51 Identities=10% Similarity=-0.013 Sum_probs=37.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 3 MNMVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 3 ~~~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
|-+.+|+.|+.+.+...-... ..+.+ ...++|..+|++..+|.+|..-.+.
T Consensus 5 ~~~~~rr~ys~EfK~~aV~~~---~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~ 55 (121)
T PRK09413 5 LGPEKRRRRTTQEKIAIVQQS---FEPGM----TVSLVARQHGVAASQLFLWRKQYQE 55 (121)
T ss_pred CCCCCCCCCCHHHHHHHHHHH---HcCCC----CHHHHHHHHCcCHHHHHHHHHHHhh
Confidence 456678899999866554444 33443 3567899999999999999666554
No 49
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=81.89 E-value=3 Score=30.45 Aligned_cols=50 Identities=16% Similarity=0.034 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++..+++++.-.+.++. .-.++|..+|++...|.++..-.|+++++...
T Consensus 108 ~L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 108 TLPVIEAQAILLCDVHEL--------TYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred hCCHHHHHHHHhHHHhcC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356666666665542222 23688999999999999999999999988753
No 50
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=81.85 E-value=2 Score=31.12 Aligned_cols=32 Identities=19% Similarity=0.147 Sum_probs=28.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.++|..+|++...|.+|+.-+|.++++....
T Consensus 144 ~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~~ 175 (179)
T PRK11924 144 YREIAEILGVPVGTVKSRLRRARQLLRECLEA 175 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46899999999999999999999999987654
No 51
>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=81.45 E-value=2.1 Score=31.73 Aligned_cols=32 Identities=16% Similarity=0.090 Sum_probs=28.0
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.-.++|..+|++...|.++...+|+++|+..+
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l~ 187 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIAIRLR 187 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 34688999999999999999999999987653
No 52
>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=81.14 E-value=3.9 Score=28.97 Aligned_cols=47 Identities=15% Similarity=0.028 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
++...++++...+ . ..+ .-.++|..+|++...|.++....|+++++.
T Consensus 114 L~~~~r~il~l~~---~-~~~----~~~eIA~~lgis~~tv~~~~~ra~~~Lr~~ 160 (161)
T TIGR02985 114 LPEQCRKIFILSR---F-EGK----SYKEIAEELGISVKTVEYHISKALKELRKE 160 (161)
T ss_pred CCHHHHHHHHHHH---H-cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4455555555433 1 222 235689999999999999999999998864
No 53
>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=79.94 E-value=2.4 Score=27.01 Aligned_cols=46 Identities=11% Similarity=0.091 Sum_probs=30.1
Q ss_pred CCCCCCCHHHHHHH-HHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 6 VPEYVGTEIYKATL-KAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 6 ~~R~~~~~~~~~~L-~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
..|+.|+.+.+..+ ...+ -......++|.+.|++..+|.+|-.-.+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~--------~~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL--------ESGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHH--------HHHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH--------HCCCceEeeecccccccccccHHHHHHh
Confidence 35678888886554 4443 2336788999999999999999977776
No 54
>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=79.86 E-value=5.2 Score=27.50 Aligned_cols=47 Identities=17% Similarity=0.127 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+++.++.++...+ ...+ .-.++|..+|+++..|.++....+.+.++.
T Consensus 111 L~~~~~~ii~~~~----~~g~----s~~eIA~~l~~s~~~v~~~~~~~~~kl~~~ 157 (158)
T TIGR02937 111 LPEREREVLVLRY----LEGL----SYKEIAEILGISVGTVKRRLKRARKKLREL 157 (158)
T ss_pred CCHHHHHHHhhHH----hcCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4556666654432 1233 345899999999999999999999988764
No 55
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=79.52 E-value=4.3 Score=30.32 Aligned_cols=49 Identities=20% Similarity=0.045 Sum_probs=38.9
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
..|++.++++|...+ .. -...++|..+|++...|.+|...++.++++..
T Consensus 5 ~~Lt~rqreVL~lr~-----~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 5 SFLTERQIEVLRLRE-----RG----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred cCCCHHHHHHHHHHH-----cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 568899999997632 22 23468999999999999999999999887653
No 56
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=79.45 E-value=2.5 Score=31.69 Aligned_cols=33 Identities=21% Similarity=0.270 Sum_probs=29.8
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcccCCC
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENKMTW 70 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~ 70 (140)
.++|..+|++..-|.+.+..+|+++++.....|
T Consensus 151 ~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~~ 183 (191)
T PRK12520 151 EEICQELQITATNAWVLLYRARMRLRECLDLHW 183 (191)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999998876655
No 57
>PRK00118 putative DNA-binding protein; Validated
Probab=79.25 E-value=4.9 Score=28.49 Aligned_cols=49 Identities=10% Similarity=-0.010 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++..++.++..++.+ .-.-.++|..+|++...|.+|+..+|.+.++..
T Consensus 17 ~L~ekqRevl~L~y~e--------g~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 17 LLTEKQRNYMELYYLD--------DYSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred cCCHHHHHHHHHHHHc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4677888888776632 223467999999999999999999999988754
No 58
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=78.77 E-value=4.4 Score=29.90 Aligned_cols=48 Identities=17% Similarity=0.113 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++.++.++...|.+. + .-.++|..+|+++..|.+++..+|.++|+..
T Consensus 130 L~~~~r~i~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 177 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG----L----SYKELAERHDVPLNTMRTWLRRSLLKLRECL 177 (179)
T ss_pred CCHHHHHHHHHHHHcC----C----CHHHHHHHHCCChHHHHHHHHHHHHHHHHHh
Confidence 4556666655554211 1 2468899999999999999999999988753
No 59
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=78.55 E-value=4.4 Score=29.38 Aligned_cols=48 Identities=15% Similarity=0.035 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++.++.++...+. ... .-.++|..+|++...|.+|...+++++++..
T Consensus 129 L~~~~r~vl~l~~~--~~~------s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 129 LPEELRTAITLREI--EGL------SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CCHHHHHHHHHHHH--cCC------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 55666666654331 111 2357899999999999999999999988765
No 60
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=78.52 E-value=4.7 Score=29.71 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=27.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+++..+|++++...+
T Consensus 155 ~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T TIGR02948 155 LKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 4678999999999999999999999987653
No 61
>PF13518 HTH_28: Helix-turn-helix domain
Probab=78.48 E-value=3 Score=24.50 Aligned_cols=26 Identities=15% Similarity=0.162 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
...++|.++|++..+|..|.+..+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~~~ 39 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYREG 39 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHHhc
Confidence 34669999999999999998887763
No 62
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=78.14 E-value=4.2 Score=31.10 Aligned_cols=31 Identities=23% Similarity=0.137 Sum_probs=27.3
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+++..+++++++...
T Consensus 172 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 202 (206)
T PRK12526 172 QEQLAQQLNVPLGTVKSRLRLALAKLKVQMG 202 (206)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 3678999999999999999999999887753
No 63
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=78.10 E-value=4.7 Score=28.96 Aligned_cols=32 Identities=19% Similarity=0.029 Sum_probs=28.0
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.++|..+|++...|.+...-+|+++++....
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 156 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKALEA 156 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 36789999999999999999999999887643
No 64
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=77.84 E-value=4.9 Score=29.39 Aligned_cols=48 Identities=13% Similarity=-0.021 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++.+++++.-.+.+.. .-.++|..+|++...|.++..-+|++++...
T Consensus 113 L~~~~r~v~~l~~~~g~--------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 160 (164)
T PRK12547 113 LSADQREAIILIGASGF--------SYEDAAAICGCAVGTIKSRVSRARNRLQELL 160 (164)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 45555555554432221 2357899999999999999999999998765
No 65
>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=77.84 E-value=5.4 Score=28.81 Aligned_cols=49 Identities=14% Similarity=0.058 Sum_probs=35.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++..++.++...|.+ . -.-.++|..+|++...|.++...+|.++++...
T Consensus 111 L~~~~r~i~~l~~~~----g----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 159 (162)
T TIGR02983 111 LPARQRAVVVLRYYE----D----LSEAQVAEALGISVGTVKSRLSRALARLRELLE 159 (162)
T ss_pred CCHHHHHHhhhHHHh----c----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 455666666544322 1 223678999999999999999999999987653
No 66
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=77.64 E-value=5 Score=30.10 Aligned_cols=49 Identities=10% Similarity=0.071 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++++++.++.-.|.+ ..+ -.++|+.+|++...|.+...-+|.++++..
T Consensus 131 ~L~~~~r~i~~l~~~~--g~s------~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~~ 179 (189)
T PRK06811 131 DLEKLDREIFIRRYLL--GEK------IEEIAKKLGLTRSAIDNRLSRGRKKLQKNK 179 (189)
T ss_pred hCCHHHHHHHHHHHHc--cCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHcc
Confidence 4677777777654422 222 368999999999999999999999988764
No 67
>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=77.60 E-value=5.7 Score=24.28 Aligned_cols=48 Identities=15% Similarity=-0.005 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.||+...++|.-+. . . ..-.++|...|+++..|.....+.++|..-.+
T Consensus 3 ~LT~~E~~vl~~l~---~--G----~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~~ 50 (58)
T PF00196_consen 3 SLTERELEVLRLLA---Q--G----MSNKEIAEELGISEKTVKSHRRRIMKKLGVKN 50 (58)
T ss_dssp SS-HHHHHHHHHHH---T--T----S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-SS
T ss_pred ccCHHHHHHHHHHH---h--c----CCcchhHHhcCcchhhHHHHHHHHHHHhCCCC
Confidence 57788888887765 2 2 24578999999999999999999999976543
No 68
>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=77.57 E-value=5 Score=28.75 Aligned_cols=46 Identities=20% Similarity=0.087 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
+++.++.++...+. . . -.-.++|..+|++...|.++..-.|++++.
T Consensus 112 L~~~~r~v~~l~~~--~--g----~~~~eIA~~l~is~~tv~~~l~Rar~~Lr~ 157 (159)
T TIGR02989 112 LPERQRELLQLRYQ--R--G----VSLTALAEQLGRTVNAVYKALSRLRVRLRD 157 (159)
T ss_pred CCHHHHHHHHHHHh--c--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHh
Confidence 56666666655331 1 2 123678999999999999999999988775
No 69
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=77.32 E-value=6.3 Score=31.17 Aligned_cols=49 Identities=12% Similarity=0.042 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+++.++.+|...|++.. .-.++|..+|++...|..|...++.++|+...
T Consensus 206 L~~~~r~vl~l~~~~g~--------s~~eIA~~l~is~~tV~~~~~ra~~kLr~~l~ 254 (257)
T PRK08583 206 LSDREKSIIQCTFIENL--------SQKETGERLGISQMHVSRLQRQAIKKLREAAF 254 (257)
T ss_pred CCHHHHHHHHHHHhCCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 56666666655542211 23788999999999999999999999987754
No 70
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=77.21 E-value=4.6 Score=29.24 Aligned_cols=47 Identities=15% Similarity=-0.023 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
|+..++.++.-.+.+ ..+ -.++|..+|++...|..+....|.++++.
T Consensus 113 L~~~~r~v~~l~~~~--~~s------~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 113 LPLERRNVLLLRDYY--GFS------YKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHhhhHHhc--CCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 556666665543311 112 36789999999999999999999998754
No 71
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=76.80 E-value=5.8 Score=29.38 Aligned_cols=31 Identities=23% Similarity=0.140 Sum_probs=27.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.++...+|.+++...+
T Consensus 154 ~~eIA~~lgis~~~V~~~l~ra~~~Lr~~l~ 184 (186)
T PRK13919 154 HREAAQLLGLPLGTLKTRARRALSRLKEVLR 184 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhc
Confidence 3678999999999999999999999987654
No 72
>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=76.60 E-value=5.5 Score=29.36 Aligned_cols=47 Identities=13% Similarity=-0.010 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+++.++.++.-.+.+. . .-.++|..+|+++..|.+.+..+|.++++.
T Consensus 135 Lp~~~r~v~~l~~~~g--~------s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 181 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG--L------TVEEIAELLGVSVRTVERDWRFARAWLADE 181 (183)
T ss_pred CCHHHHHHHHHHHHcC--C------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5556666655443211 1 236789999999999999999999998865
No 73
>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=76.19 E-value=12 Score=23.35 Aligned_cols=48 Identities=23% Similarity=0.060 Sum_probs=37.0
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
||+.|+++|...+ +.-..-+|-...-.+||..+|++..-|..=+.++-
T Consensus 1 LT~~Q~e~L~~A~-~~GYfd~PR~~tl~elA~~lgis~st~~~~LRrae 48 (53)
T PF04967_consen 1 LTDRQREILKAAY-ELGYFDVPRRITLEELAEELGISKSTVSEHLRRAE 48 (53)
T ss_pred CCHHHHHHHHHHH-HcCCCCCCCcCCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5788999998876 33344568889999999999999999887554443
No 74
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=76.09 E-value=5.6 Score=29.48 Aligned_cols=49 Identities=10% Similarity=-0.067 Sum_probs=36.4
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+++..++++...+.+ .-.-.+||..+|++...|.+++..+|.+++....
T Consensus 132 L~~~~r~v~~l~~~~--------g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l~ 180 (184)
T PRK12512 132 LPPRQRDVVQSISVE--------GASIKETAAKLSMSEGAVRVALHRGLAALAAKFR 180 (184)
T ss_pred CCHHHHHHHHHHHHc--------CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhh
Confidence 555666666554322 1234678999999999999999999999998763
No 75
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=76.04 E-value=13 Score=21.47 Aligned_cols=47 Identities=17% Similarity=0.053 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.++....+++..++ . . ....++|..+|++...|..|....+.+..-.
T Consensus 3 ~l~~~e~~i~~~~~---~--g----~s~~eia~~l~is~~tv~~~~~~~~~kl~~~ 49 (58)
T smart00421 3 SLTPREREVLRLLA---E--G----LTNKEIAERLGISEKTVKTHLSNIMRKLGVR 49 (58)
T ss_pred CCCHHHHHHHHHHH---c--C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHCCC
Confidence 36777777775543 1 1 2457899999999999999999887776533
No 76
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=75.82 E-value=5.2 Score=29.76 Aligned_cols=31 Identities=19% Similarity=0.358 Sum_probs=27.7
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|+.+|++...|.++...+|.++++...
T Consensus 147 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (186)
T PRK05602 147 NIEAAAVMDISVDALESLLARGRRALRAQLA 177 (186)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999999998764
No 77
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=75.30 E-value=5.2 Score=30.20 Aligned_cols=31 Identities=19% Similarity=0.197 Sum_probs=28.0
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
.++|..+|+++..|.+....+|+++++....
T Consensus 136 ~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~~ 166 (187)
T PRK12516 136 EEAAEICGCAVGTIKSRVNRARQRLQEILQI 166 (187)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 5789999999999999999999999988754
No 78
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=75.10 E-value=2.7 Score=25.90 Aligned_cols=24 Identities=17% Similarity=0.081 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
....||+.+|++..+|..|+.+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 457899999999999999999774
No 79
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=74.90 E-value=4.2 Score=30.53 Aligned_cols=32 Identities=13% Similarity=0.156 Sum_probs=28.3
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.++|..+|++...|.+.+..+|+++|+....
T Consensus 155 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 155 SDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 36789999999999999999999999987653
No 80
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=74.80 E-value=4.3 Score=30.56 Aligned_cols=31 Identities=10% Similarity=0.073 Sum_probs=27.5
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|+++..|.++..-+|+++|+...
T Consensus 153 ~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 153 SEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999987654
No 81
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=74.77 E-value=6.4 Score=29.24 Aligned_cols=31 Identities=13% Similarity=0.071 Sum_probs=27.5
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|+++..|.+.+..+|+++|+...
T Consensus 148 ~~EIA~~l~is~~tV~~~l~rar~~Lr~~l~ 178 (181)
T PRK12536 148 VAETAQLTGLSESAVKVGIHRGLKALAAKIR 178 (181)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3678999999999999999999999998653
No 82
>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=73.62 E-value=7 Score=28.52 Aligned_cols=48 Identities=17% Similarity=0.137 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
++..+++++..-|++. -.-.++|..+|+++..|.+...-+|.++++..
T Consensus 120 L~~~~r~i~~l~~~~g--------~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~l 167 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD--------LTIKEIAEVMNKPEGTVKTYLHRALKKLKKRL 167 (169)
T ss_pred CCHHHhHHHHHHHHcC--------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 5566666665443221 12367899999999999999999999988754
No 83
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=73.49 E-value=7.4 Score=28.99 Aligned_cols=49 Identities=18% Similarity=-0.093 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|++.+++++..-|.+ .-.-.++|..+|++...|..+...+|.++|+..
T Consensus 139 ~L~~~~r~i~~l~~~~--------g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 187 (189)
T PRK09648 139 TLPEKQREILILRVVV--------GLSAEETAEAVGSTPGAVRVAQHRALARLRAEI 187 (189)
T ss_pred hCCHHHHHHHHHHHHc--------CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 3566666666554322 123578999999999999999999999988753
No 84
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=73.29 E-value=5.4 Score=30.75 Aligned_cols=33 Identities=15% Similarity=0.317 Sum_probs=29.3
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcccCCC
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENKMTW 70 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~~~ 70 (140)
.++|..+|++...|.+...-+|+++|+..+.+|
T Consensus 168 ~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~~~~ 200 (206)
T PRK12544 168 NEICHAVDLSVSNLNVLLYRARLRLRECLENKW 200 (206)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHh
Confidence 678999999999999999999999998876544
No 85
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=72.85 E-value=6.6 Score=29.78 Aligned_cols=49 Identities=14% Similarity=0.022 Sum_probs=35.3
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+++.+++++.-.+. . .+ .-.++|..+|++...|.+++.-+|+++|+...
T Consensus 114 Lp~~~r~v~~L~~~--~--g~----s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 114 LPDEQREALILVGA--S--GF----SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CCHHHhHHhhhHHh--c--CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 45555666554431 1 11 23578999999999999999999999998753
No 86
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=72.47 E-value=8.1 Score=28.37 Aligned_cols=48 Identities=10% Similarity=-0.033 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
|+.+++.++.-.+. ...+ -.++|..+|++...|.++...++++.+...
T Consensus 120 Lp~~~r~v~~L~~~--~g~s------~~EIA~~lgis~~tV~~~l~ra~~~~~~~l 167 (172)
T PRK12523 120 LSSKARAAFLYNRL--DGMG------HAEIAERLGVSVSRVRQYLAQGLRQCYIAL 167 (172)
T ss_pred CCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 45566666554432 2222 367899999999999999999999987654
No 87
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=72.08 E-value=6.9 Score=30.56 Aligned_cols=49 Identities=24% Similarity=0.155 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|+..++.++...|+++. + -.++|..+|+++..|.+.....|+++++..
T Consensus 134 ~Lp~~~R~v~~L~y~eg~--s------~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 134 KLPVEYREVLVLRELEDM--S------YREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred cCCHHHHhHhhhHHhcCC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 355566666655442222 2 367899999999999999999999999875
No 88
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=71.93 E-value=8.4 Score=28.98 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=26.6
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|.+-+..+|+++++...
T Consensus 161 ~EIA~~lgis~~tVk~rl~ra~~~Lr~~l~ 190 (194)
T PRK12531 161 QQVAEMFDIPLGTVKSRLRLAVEKLRHSMD 190 (194)
T ss_pred HHHHHHhCcCHHHHHHHHHHHHHHHHHHhh
Confidence 578999999999999999999999887653
No 89
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=71.88 E-value=7.6 Score=29.08 Aligned_cols=30 Identities=17% Similarity=0.131 Sum_probs=26.5
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.+||..+|+++..|.+...-+|+++++..
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~~ 178 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARDALLADA 178 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 367899999999999999999999998743
No 90
>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=71.67 E-value=8.5 Score=30.39 Aligned_cols=48 Identities=17% Similarity=0.075 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
++..++.++...|.+.. .-.++|..+|++...|..+...++.++|+.+
T Consensus 206 L~~~~r~ii~l~~~~g~--------s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~~ 253 (255)
T TIGR02941 206 LSEREKSIIHCTFEENL--------SQKETGERLGISQMHVSRLQRQAISKLKEAA 253 (255)
T ss_pred CCHHHHHHHHHHHcCCC--------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 55666666655542221 2368999999999999999999999988653
No 91
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=71.22 E-value=6.4 Score=29.40 Aligned_cols=30 Identities=13% Similarity=0.032 Sum_probs=26.6
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.++|..+|++...|.+++..+|.++++..
T Consensus 160 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 160 QSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999988754
No 92
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=70.93 E-value=11 Score=26.95 Aligned_cols=47 Identities=23% Similarity=0.169 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.+++..+++|.-+- ++ | ...++|+.++++...|.++..+.+++..-.
T Consensus 149 ~lt~~e~~vl~l~~-~g----~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~~ 195 (211)
T PRK15369 149 LLTPRERQILKLIT-EG----Y----TNRDIAEQLSISIKTVETHRLNMMRKLDVH 195 (211)
T ss_pred CCCHHHHHHHHHHH-CC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 37888888887643 22 2 147889999999999999999999997643
No 93
>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=70.88 E-value=9.4 Score=28.12 Aligned_cols=50 Identities=14% Similarity=0.145 Sum_probs=36.7
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.|++.++.++...+.+. | .-.++|..+|++...|.++..-.|++++....
T Consensus 100 ~L~~~~r~v~~l~~~~g----~----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG----L----SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred hCCHHHHHHHHHHHHcC----C----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45666666665543221 1 23678999999999999999999999988764
No 94
>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=70.27 E-value=4.2 Score=26.13 Aligned_cols=19 Identities=11% Similarity=0.195 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChhhHhHh
Q psy10107 36 EKIMLAIITKMTLTQVSTW 54 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nW 54 (140)
.-.+||.++|++..||..|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 4578999999999999999
No 95
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=70.11 E-value=9.5 Score=28.32 Aligned_cols=29 Identities=17% Similarity=0.274 Sum_probs=25.8
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-.++|..+|++...|.++...+|++++..
T Consensus 152 ~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 180 (182)
T PRK12537 152 HAEIAQRLGAPLGTVKAWIKRSLKALREC 180 (182)
T ss_pred HHHHHHHHCCChhhHHHHHHHHHHHHHHH
Confidence 36789999999999999999999998764
No 96
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=69.59 E-value=11 Score=27.60 Aligned_cols=49 Identities=14% Similarity=-0.027 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+++.++.+|.--+.+ ..+ -.++|..+|+++..|.....-+|.++++...
T Consensus 119 L~~~~r~vl~L~~~~--g~s------~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 167 (173)
T PRK09645 119 LSPEHRAVLVRSYYR--GWS------TAQIAADLGIPEGTVKSRLHYALRALRLALQ 167 (173)
T ss_pred CCHHHHHHHHHHHHc--CCC------HHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 455566665443322 112 3678999999999999999999999998764
No 97
>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=69.53 E-value=7.2 Score=29.34 Aligned_cols=32 Identities=9% Similarity=0.050 Sum_probs=28.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.+||..+|++..-|.+...-.|+++++....
T Consensus 150 ~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 150 SDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999999987653
No 98
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=68.62 E-value=6.7 Score=28.36 Aligned_cols=31 Identities=19% Similarity=0.191 Sum_probs=27.7
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.+||..+|++...|.++...+|.++|+...
T Consensus 130 ~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 130 YKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999988764
No 99
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=68.07 E-value=11 Score=28.37 Aligned_cols=30 Identities=17% Similarity=0.168 Sum_probs=27.0
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.++|..+|++...|.+++.-+|+++++..
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999999998865
No 100
>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=67.74 E-value=13 Score=28.64 Aligned_cols=47 Identities=17% Similarity=0.152 Sum_probs=35.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
++...+.+|...|.+. -.-.++|..+|++...|..+...+++++|+.
T Consensus 176 L~~~~r~il~l~y~~~--------~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 222 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE--------LNLKEIGEVLGLTESRVSQIHSQALKKLRAK 222 (224)
T ss_pred CCHHHHHHHHHHHhCC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 5666666666554221 1347899999999999999999999998864
No 101
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=67.61 E-value=9.6 Score=29.74 Aligned_cols=31 Identities=16% Similarity=0.193 Sum_probs=27.7
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.-.++|..+|++...|.++...+++++++..
T Consensus 202 s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 202 NLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3578899999999999999999999998765
No 102
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=67.39 E-value=5.7 Score=23.33 Aligned_cols=25 Identities=16% Similarity=0.126 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 35 GEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 35 ~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
....++|+.+|++...|.+|....+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr~~ 42 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKRYR 42 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT---
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHcc
Confidence 3467899999999999999976654
No 103
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=67.05 E-value=12 Score=27.79 Aligned_cols=50 Identities=14% Similarity=0.064 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.|+++++.+|.--+. ... .-.++|..+|++...|.+-+..+|+++++..+
T Consensus 131 ~L~~~~r~vl~l~~~--~~~------s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYY--HEK------SVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHH--cCC------CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 355556666544331 212 23678999999999999999999999988754
No 104
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=66.74 E-value=12 Score=27.73 Aligned_cols=29 Identities=21% Similarity=0.287 Sum_probs=26.3
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|..+|++...|.+....+|.++++..
T Consensus 142 ~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 142 QEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 67899999999999999999999988765
No 105
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=66.63 E-value=13 Score=27.47 Aligned_cols=48 Identities=8% Similarity=0.098 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+|+.++.++.--+.++. .-.++|..+|++...|.+.....|.+.|+..
T Consensus 118 Lp~~~r~i~~l~~~e~~--------s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 165 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY--------SQEEIAQLLQIPIGTVKSRIHAALKKLRQKE 165 (179)
T ss_pred CCHHHHHHHHHHHHccC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45555555544332221 2367899999999999999999999998765
No 106
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=66.31 E-value=12 Score=28.37 Aligned_cols=30 Identities=20% Similarity=0.134 Sum_probs=27.1
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|.+.+..+|+++++...
T Consensus 159 ~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 159 DDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999999988763
No 107
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=65.65 E-value=19 Score=28.37 Aligned_cols=48 Identities=13% Similarity=0.098 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++..+.++...|. ..-.-.++|..+|++...|.+.+..+|+++|...
T Consensus 202 L~~~~r~vl~l~~~--------~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 249 (251)
T PRK07670 202 LSEKEQLVISLFYK--------EELTLTEIGQVLNLSTSRISQIHSKALFKLKKLL 249 (251)
T ss_pred CCHHHHHHHHHHHh--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 45555566554431 1123478899999999999999999999988654
No 108
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=65.55 E-value=12 Score=28.40 Aligned_cols=31 Identities=19% Similarity=0.141 Sum_probs=27.5
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|+++..|.++...+|+++++...
T Consensus 152 ~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 152 YEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 3678999999999999999999999998754
No 109
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=65.53 E-value=12 Score=28.83 Aligned_cols=30 Identities=17% Similarity=0.180 Sum_probs=27.4
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|.+++.-+|+++++..+
T Consensus 158 ~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 158 EEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 578999999999999999999999998764
No 110
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=65.14 E-value=19 Score=27.03 Aligned_cols=30 Identities=13% Similarity=0.101 Sum_probs=26.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.++|..+|++...|.+-+..+|+++++..
T Consensus 173 ~~EIA~~lgis~~tV~~~l~rar~~Lr~~l 202 (208)
T PRK08295 173 YQEIAEELNRHVKSIDNALQRVKRKLEKYL 202 (208)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999888754
No 111
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=64.93 E-value=14 Score=27.38 Aligned_cols=30 Identities=23% Similarity=0.243 Sum_probs=26.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.++|..+|++...|.+-...+|+++|...
T Consensus 156 ~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l 185 (187)
T PRK12534 156 YEELAARTDTPIGTVKSWIRRGLAKLKACL 185 (187)
T ss_pred HHHHHHHhCCChhHHHHHHHHHHHHHHHHH
Confidence 367899999999999999999999988653
No 112
>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=64.92 E-value=13 Score=29.58 Aligned_cols=31 Identities=26% Similarity=0.431 Sum_probs=27.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+++..+|.++++...
T Consensus 180 ~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~ 210 (244)
T TIGR03001 180 MDRIGAMYQVHRSTVSRWVAQARERLLERTR 210 (244)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999999887754
No 113
>cd00131 PAX Paired Box domain
Probab=64.89 E-value=28 Score=25.11 Aligned_cols=46 Identities=13% Similarity=0.091 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-------ChhhHhHhhhhH
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKM-------TLTQVSTWFANA 58 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL-------t~~QV~nWF~N~ 58 (140)
..+......+..+. ..||.-|..|-.++-...|+ +..+|..||.++
T Consensus 75 ~~~~~~~~~i~~~v---~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYK---QENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 34555556566666 78898888776665335566 999999998764
No 114
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=64.60 E-value=11 Score=29.70 Aligned_cols=31 Identities=16% Similarity=0.244 Sum_probs=27.6
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+.+..+|+++|+...
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999999998764
No 115
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=64.46 E-value=14 Score=27.75 Aligned_cols=50 Identities=16% Similarity=0.060 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++..++.++.-.+++ .+ .-.++|..+|++...|.++..-+|.++++...
T Consensus 111 ~Lp~~~R~v~~L~~~e----g~----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~~ 160 (182)
T PRK12511 111 DLPEEQRAALHLVAIE----GL----SYQEAAAVLGIPIGTLMSRIGRARAALRAFEE 160 (182)
T ss_pred hCCHHHHHHHHHHHHc----CC----CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3566666666554322 22 23678999999999999999999999887654
No 116
>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=64.36 E-value=20 Score=26.61 Aligned_cols=30 Identities=13% Similarity=0.142 Sum_probs=26.0
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.-.++|..+|++...|.+.+.-.|+++|+.
T Consensus 167 s~~eIA~~l~~s~~tV~~~l~r~r~~L~~~ 196 (198)
T TIGR02859 167 SYQEIACDLNRHVKSIDNALQRVKRKLEKY 196 (198)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 346789999999999999999999988764
No 117
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=64.36 E-value=16 Score=26.34 Aligned_cols=30 Identities=17% Similarity=-0.034 Sum_probs=26.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
-.++|+.+|++...|.....-+|++.++..
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ra~~~lr~~l 157 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIRDALVHCRKCL 157 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999999999888764
No 118
>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=64.30 E-value=19 Score=20.77 Aligned_cols=44 Identities=20% Similarity=0.145 Sum_probs=30.3
Q ss_pred CHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 12 TEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 12 ~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
+..+..++..++ .. ..-.++|+.++++...|..|....+.+...
T Consensus 2 ~~~e~~i~~~~~-----~~----~s~~eia~~l~~s~~tv~~~~~~~~~~l~~ 45 (57)
T cd06170 2 TPREREVLRLLA-----EG----KTNKEIADILGISEKTVKTHLRNIMRKLGV 45 (57)
T ss_pred CHHHHHHHHHHH-----cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHhCC
Confidence 455566664433 12 245789999999999999998866665443
No 119
>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=64.19 E-value=16 Score=26.33 Aligned_cols=47 Identities=15% Similarity=0.005 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+++.++.++.-.|. .. -.-.++|..+|++...|.+...-.|.++|+.
T Consensus 123 L~~~~r~vl~l~~~--~g------~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~~ 169 (170)
T TIGR02952 123 LTPKQQHVIALRFG--QN------LPIAEVARILGKTEGAVKILQFRAIKKLARQ 169 (170)
T ss_pred CCHHHHHHHHHHHh--cC------CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 45555566555331 11 2236789999999999999998888888764
No 120
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=63.95 E-value=13 Score=27.57 Aligned_cols=48 Identities=21% Similarity=0.159 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++.++.++...+.+ ..+ -.++|..+|++...|.++..-+|.+++...
T Consensus 128 L~~~~r~v~~l~~~~--g~s------~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~l 175 (179)
T PRK09415 128 LPIKYREVIYLFYYE--ELS------IKEIAEVTGVNENTVKTRLKKAKELLKKGL 175 (179)
T ss_pred CCHHHhhHhHhHHhc--CCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 556666665443321 222 367899999999999999999999988764
No 121
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=63.87 E-value=16 Score=26.29 Aligned_cols=46 Identities=13% Similarity=-0.044 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
+++.++.++.-.+. ...+ -.++|..+|++...|.++...++++...
T Consensus 114 L~~~~r~v~~L~~~--~g~s------~~EIA~~l~is~~tV~~~l~ra~~~~~~ 159 (161)
T PRK12528 114 LPPLVKRAFLLAQV--DGLG------YGEIATELGISLATVKRYLNKAAMRCYF 159 (161)
T ss_pred CCHHHHHHHHHHHH--cCCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45556665544331 2222 3578999999999999999998887653
No 122
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=63.21 E-value=15 Score=27.31 Aligned_cols=49 Identities=14% Similarity=-0.061 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|++.++.++...+.+ . -.-.++|..+|++...|.++....|+++++..
T Consensus 131 ~L~~~~r~v~~l~~~~--g------~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE--G------LSVAEAATRSGMSESAVKVSVHRGLKALAALI 179 (184)
T ss_pred hCCHHHHHHHHHHHHc--C------CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3566666666654322 1 23467899999999999999999999988764
No 123
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=63.19 E-value=20 Score=26.87 Aligned_cols=31 Identities=16% Similarity=0.045 Sum_probs=27.8
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|...+.-+|+++++...
T Consensus 130 ~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l~ 160 (182)
T PRK12540 130 YEDAAAICGCAVGTIKSRVNRARSKLSALLY 160 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999999999998865
No 124
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=62.60 E-value=15 Score=28.49 Aligned_cols=31 Identities=23% Similarity=0.172 Sum_probs=27.5
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.-.++|..+|++...|.++...+|+++|+..
T Consensus 200 s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 200 TQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999999999998764
No 125
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=62.45 E-value=21 Score=25.35 Aligned_cols=44 Identities=9% Similarity=0.197 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhH
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~ 58 (140)
-....+..+.+|+.+|...+ ++ -.+||..+|+++.++..+|+..
T Consensus 6 ~~~~~i~~~~~~I~~~~~~~-~s---l~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 6 TDAITIHSILDWIEDNLESP-LS---LEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred ccHHHHHHHHHHHHHhcCCC-CC---HHHHHHHHCcCHHHHHHHHHHH
Confidence 34455667788998887766 44 4678899999999999988765
No 126
>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=62.11 E-value=16 Score=28.16 Aligned_cols=48 Identities=17% Similarity=0.118 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.|++.++.++...|.+ .-.-.++|..+|++...|..|...+++++++.
T Consensus 178 ~L~~~~r~vl~l~y~~--------~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~~ 225 (227)
T TIGR02980 178 ALPERERRILLLRFFE--------DKTQSEIAERLGISQMHVSRLLRRALKKLREQ 225 (227)
T ss_pred cCCHHHHHHHHHHHhc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4666666666665421 12457899999999999999999999998864
No 127
>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=61.90 E-value=11 Score=26.75 Aligned_cols=31 Identities=26% Similarity=0.251 Sum_probs=26.8
Q ss_pred HHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 35 GEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 35 ~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-.-.++|..+|+++..|.++..-+|.++++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~~ 152 (154)
T TIGR02950 122 FSYKEIAELLNLSLAKVKSNLFRARKELKKL 152 (154)
T ss_pred CcHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3557789999999999999999999998763
No 128
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=60.14 E-value=19 Score=26.33 Aligned_cols=31 Identities=10% Similarity=0.192 Sum_probs=27.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|...+..+|+++++..+
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l~ 168 (173)
T PRK12522 138 YKEMSEILNIPIGTVKYRLNYAKKQMREHLE 168 (173)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3678999999999999999999999987653
No 129
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=59.90 E-value=22 Score=25.57 Aligned_cols=49 Identities=10% Similarity=-0.000 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++++.++++...+.+.. .-.++|..+|++..-|.+....+|+++++...
T Consensus 106 L~~~~r~v~~l~~~~~~--------s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~l~ 154 (159)
T PRK12527 106 LPPACRDSFLLRKLEGL--------SHQQIAEHLGISRSLVEKHIVNAMKHCRVRMR 154 (159)
T ss_pred CCHHHHHHHHHHHHcCC--------CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45555555544432221 23678999999999999999999999888754
No 130
>TIGR02960 SigX5 RNA polymerase sigma-70 factor, TIGR02960 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=59.73 E-value=19 Score=29.20 Aligned_cols=30 Identities=17% Similarity=0.120 Sum_probs=27.3
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|+++..|.+.+.-+|+++|+..+
T Consensus 162 ~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 191 (324)
T TIGR02960 162 AETAELLGTSTASVNSALQRARATLDEVGP 191 (324)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHhcc
Confidence 678999999999999999999999998765
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=59.73 E-value=6.6 Score=23.31 Aligned_cols=21 Identities=14% Similarity=-0.007 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhhHhHhhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFAN 57 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N 57 (140)
..+||+.+|++...|..|..+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g 32 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENG 32 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTT
T ss_pred HHHHHHHhCCCcchhHHHhcC
Confidence 478999999999999999888
No 132
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=59.41 E-value=19 Score=28.79 Aligned_cols=49 Identities=16% Similarity=0.071 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.+++..+.+|...|.+ .-.-.++|..+|++...|......+++++++..
T Consensus 212 ~L~~~~r~vl~l~~~~--------~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYE--------DLTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3566666666555422 223578999999999999999999999988764
No 133
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=59.39 E-value=21 Score=26.79 Aligned_cols=49 Identities=20% Similarity=0.102 Sum_probs=35.5
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
|+..++.++...+.++. .-.++|..+|++..-|.++..-+|.++++..+
T Consensus 129 Lp~~~r~v~~l~~~~g~--------s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 129 LDPEYREPLLLQVIGGF--------SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CCHHHHHHHHHHHHhCC--------CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 55555565544432222 23688999999999999999999999887754
No 134
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=59.06 E-value=34 Score=26.48 Aligned_cols=54 Identities=17% Similarity=0.063 Sum_probs=41.8
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
....||..|+++|+.-| ..-..-||-...-.+||+++|++..-+..=+.++-+|
T Consensus 152 ~~~~LTdrQ~~vL~~A~-~~GYFd~PR~~~l~dLA~~lGISkst~~ehLRrAe~K 205 (215)
T COG3413 152 GKNDLTDRQLEVLRLAY-KMGYFDYPRRVSLKDLAKELGISKSTLSEHLRRAERK 205 (215)
T ss_pred ccccCCHHHHHHHHHHH-HcCCCCCCccCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 34469999999998886 2234467899999999999999999887755555444
No 135
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=58.46 E-value=18 Score=28.88 Aligned_cols=49 Identities=16% Similarity=-0.025 Sum_probs=36.5
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++...+.+|...|.+ .-.-.++|..+|++...|..+..-++.++++..+
T Consensus 204 L~~~~r~vl~l~y~~--------~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l~ 252 (256)
T PRK07408 204 LEERTREVLEFVFLH--------DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLLQ 252 (256)
T ss_pred CCHHHHHHHHHHHHC--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHhh
Confidence 455555665555421 2345788999999999999999999999988764
No 136
>PRK06930 positive control sigma-like factor; Validated
Probab=58.29 E-value=22 Score=27.00 Aligned_cols=30 Identities=10% Similarity=0.189 Sum_probs=26.5
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|..++..++.++++...
T Consensus 134 ~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 134 SEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 678999999999999999999999887653
No 137
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=58.24 E-value=24 Score=26.10 Aligned_cols=48 Identities=10% Similarity=-0.074 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
||++++.++.-.+.+ ..+ -.++|..+|+++..|...+..++.+....+
T Consensus 128 Lp~~~R~v~~L~~~~--g~s------~~EIA~~lgis~~tVk~~l~rAl~~~~~~~ 175 (178)
T PRK12529 128 LRPRVKQAFLMATLD--GMK------QKDIAQALDIALPTVKKYIHQAYVTCLSLM 175 (178)
T ss_pred CCHHHHHHHHHHHHc--CCC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHhC
Confidence 566666666554322 222 367899999999999999999888876553
No 138
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=58.16 E-value=13 Score=27.03 Aligned_cols=32 Identities=25% Similarity=0.269 Sum_probs=28.1
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.-.++|..+|++...|.+.+...|++.++..+
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l~ 169 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRKFLQ 169 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678999999999999999999999988754
No 139
>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=57.69 E-value=7.5 Score=22.82 Aligned_cols=20 Identities=15% Similarity=0.144 Sum_probs=18.6
Q ss_pred HHHHHhCCChhhHhHhhhhH
Q psy10107 39 MLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 39 ~La~~tgLt~~QV~nWF~N~ 58 (140)
+||+.+|++...|..|+.+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~ 21 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGK 21 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCC
Confidence 68999999999999999887
No 140
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=56.86 E-value=14 Score=27.19 Aligned_cols=31 Identities=19% Similarity=0.249 Sum_probs=27.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+....+|+++++..+
T Consensus 155 ~~eIA~~lgis~~~v~~~l~Rar~~Lr~~l~ 185 (187)
T PRK09641 155 LKEISEILDLPVGTVKTRIHRGREALRKQLR 185 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999999999987653
No 141
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=56.48 E-value=15 Score=27.46 Aligned_cols=31 Identities=16% Similarity=0.090 Sum_probs=27.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.++...+|+++|....
T Consensus 158 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~ 188 (194)
T PRK12513 158 LEEIAELTGVPEETVKSRLRYALQKLRELLA 188 (194)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999988653
No 142
>PRK10072 putative transcriptional regulator; Provisional
Probab=56.30 E-value=7.7 Score=27.00 Aligned_cols=23 Identities=13% Similarity=0.159 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R 59 (140)
..+||+.+|++...|.+|...+|
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r 71 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRV 71 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 45679999999999999987664
No 143
>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=55.71 E-value=25 Score=26.05 Aligned_cols=47 Identities=21% Similarity=0.017 Sum_probs=37.9
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
..|+..++++|.-.. ..+ ...++|..+|++...|..+-..++.++++
T Consensus 5 ~~Lte~qr~VL~Lr~-----~Gl----Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE-----KGL----SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH-----cCC----CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 457888888886632 222 46789999999999999999999999886
No 144
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=55.40 E-value=21 Score=28.36 Aligned_cols=32 Identities=19% Similarity=0.169 Sum_probs=28.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.++|+.+|+++.-|.++..-.|.++++....
T Consensus 135 ~~EIAe~LgiS~~tVksrL~Rark~Lr~~l~~ 166 (228)
T PRK06704 135 IADIAKVCSVSEGAVKASLFRSRNRLKTVSEE 166 (228)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 36789999999999999999999999987643
No 145
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=55.34 E-value=19 Score=26.52 Aligned_cols=28 Identities=14% Similarity=0.094 Sum_probs=23.9
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
-.++|..+|++...|.++...++.+.+.
T Consensus 138 ~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 138 YSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4688999999999999999888877654
No 146
>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=55.07 E-value=16 Score=27.32 Aligned_cols=31 Identities=19% Similarity=0.212 Sum_probs=27.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+++.-+|+++++...
T Consensus 150 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 150 YKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4677999999999999999999999988753
No 147
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=54.45 E-value=30 Score=26.76 Aligned_cols=48 Identities=13% Similarity=0.055 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.|+...+.++...|. ....-.++|..+|++...|..+-..+..|+|..
T Consensus 183 ~L~~~e~~i~~~~~~--------~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr~~ 230 (231)
T TIGR02885 183 KLDERERQIIMLRYF--------KDKTQTEVANMLGISQVQVSRLEKKVLKKMKEK 230 (231)
T ss_pred cCCHHHHHHHHHHHH--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 456666666665542 123578899999999999999999988888754
No 148
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=54.35 E-value=27 Score=28.06 Aligned_cols=48 Identities=19% Similarity=0.138 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.++...+.+|...|.+ . -.-.++|..+|++...|..+...++.+++..
T Consensus 215 ~L~~rer~vl~l~y~~----~----~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE----S----MTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3556666666665521 2 2347899999999999999999999998864
No 149
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=54.18 E-value=20 Score=26.74 Aligned_cols=31 Identities=16% Similarity=0.155 Sum_probs=27.3
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+.+..+|+++++...
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 125 QKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999999999999999999888654
No 150
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=54.14 E-value=30 Score=26.87 Aligned_cols=53 Identities=17% Similarity=0.035 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.+++..+.++...+ ..+- -....-.++|..+|++...|.++...+++++++..
T Consensus 175 ~Lp~~~R~i~~l~y---~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~l 227 (233)
T PRK05803 175 ILDEREKEVIEMRY---GLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKEL 227 (233)
T ss_pred hCCHHHHHHHHHHh---CCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35566666665543 1000 11234578999999999999999888888887764
No 151
>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=53.89 E-value=30 Score=26.82 Aligned_cols=52 Identities=17% Similarity=0.029 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.|++.++.++...|+...... -.-.++|..+|+++..|..+...+++++++.
T Consensus 174 ~L~~~~r~il~l~y~~~~~e~----~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~~ 225 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDGRR----KTQREIAKILGISRSYVSRIEKRALMKLYKE 225 (227)
T ss_pred hCCHHHHHHHHHHHcCCCCCC----cCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 355666666655541000111 2357899999999999999988889888765
No 152
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=53.87 E-value=31 Score=25.14 Aligned_cols=47 Identities=9% Similarity=-0.000 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
|++.++.++.-.+.+. .+ -.++|..+|++...|.++...++...+..
T Consensus 119 L~~~~r~v~~L~~~eg--~s------~~EIA~~l~is~~tV~~~l~ra~~~~~~~ 165 (168)
T PRK12525 119 LSGKARAAFLMSQLEG--LT------YVEIGERLGVSLSRIHQYMVEAFKCCYQG 165 (168)
T ss_pred CCHHHHHHHHHHHHcC--CC------HHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 5556666654433222 12 36789999999999999998888876654
No 153
>PF13551 HTH_29: Winged helix-turn helix
Probab=53.82 E-value=52 Score=21.86 Aligned_cols=48 Identities=17% Similarity=-0.005 Sum_probs=30.5
Q ss_pred CCCCHHHHHHHHHHHHhhcCCC--CCCHHHHHH-H-HHHh--CCChhhHhHhhh
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNP--YPTKGEKIM-L-AIIT--KMTLTQVSTWFA 56 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nP--YPs~~~k~~-L-a~~t--gLt~~QV~nWF~ 56 (140)
..++.++.+.|.+++.++.... ..+...-.+ | .+.+ .++...|..|+.
T Consensus 56 ~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 56 KRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3389999999999995543322 344444443 4 3333 467788888764
No 154
>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=53.78 E-value=18 Score=26.88 Aligned_cols=44 Identities=14% Similarity=0.170 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 17 ~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
...++++ ..||-+. +.-.+++..||+++.+|..|..--|--...
T Consensus 33 ~kV~~yL---r~~p~~~-ati~eV~e~tgVs~~~I~~~IreGRL~~~~ 76 (137)
T TIGR03826 33 EKVYKFL---RKHENRQ-ATVSEIVEETGVSEKLILKFIREGRLQLKH 76 (137)
T ss_pred HHHHHHH---HHCCCCC-CCHHHHHHHHCcCHHHHHHHHHcCCeeccC
Confidence 3456666 5566422 567889999999999999997666555443
No 155
>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=53.26 E-value=9.3 Score=22.45 Aligned_cols=22 Identities=14% Similarity=0.009 Sum_probs=19.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..+||..+|++...|..|....
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~ 39 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGK 39 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4789999999999999998654
No 156
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=52.60 E-value=11 Score=29.37 Aligned_cols=34 Identities=21% Similarity=0.041 Sum_probs=29.5
Q ss_pred HHHHHHHHHhCCChhhHhHhhhhHHHhhhhcccC
Q psy10107 35 GEKIMLAIITKMTLTQVSTWFANARRRLKKENKM 68 (140)
Q Consensus 35 ~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~~ 68 (140)
-.-.++|..+|++...|.+...-+|.++|+....
T Consensus 166 ~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~~ 199 (231)
T PRK11922 166 LSVEETAQALGLPEETVKTRLHRARRLLRESLAR 199 (231)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 3457889999999999999999999999988653
No 157
>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=52.58 E-value=16 Score=20.18 Aligned_cols=22 Identities=14% Similarity=-0.035 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
...+|..+|++...|..|..+.
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~ 36 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGK 36 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCC
Confidence 4589999999999999997765
No 158
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=52.43 E-value=22 Score=29.07 Aligned_cols=29 Identities=17% Similarity=0.222 Sum_probs=25.9
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-.++|..+|++...|.+.+.-+|+++|+.
T Consensus 172 ~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 200 (339)
T PRK08241 172 AAEVAELLDTSVAAVNSALQRARATLAER 200 (339)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHhhc
Confidence 36789999999999999999999999874
No 159
>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=51.39 E-value=28 Score=27.30 Aligned_cols=49 Identities=24% Similarity=0.260 Sum_probs=37.0
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
..|++..+++| .|.. .. ..-.++|..+|+++..|..+..|.++|....+
T Consensus 170 ~~Lt~re~evl-~~~a----~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~ 218 (232)
T TIGR03541 170 GVLSEREREVL-AWTA----LG----RRQADIAAILGISERTVENHLRSARRKLGVAT 218 (232)
T ss_pred ccCCHHHHHHH-HHHH----CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCC
Confidence 45777778877 3442 11 33467899999999999999999999987554
No 160
>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=51.31 E-value=16 Score=20.91 Aligned_cols=18 Identities=17% Similarity=0.080 Sum_probs=16.3
Q ss_pred HHHHHHhCCChhhHhHhh
Q psy10107 38 IMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF 55 (140)
.++|+.+|++...|..|.
T Consensus 4 ~e~a~~~gv~~~tlr~~~ 21 (49)
T cd04761 4 GELAKLTGVSPSTLRYYE 21 (49)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999994
No 161
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=50.98 E-value=17 Score=27.06 Aligned_cols=31 Identities=16% Similarity=0.147 Sum_probs=27.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|++...|.+...-+|+++|+..+
T Consensus 157 ~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 157 YEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 3677999999999999999999999998764
No 162
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=50.90 E-value=33 Score=25.73 Aligned_cols=31 Identities=19% Similarity=0.048 Sum_probs=26.5
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.+||..+|++...|.+=+..+|+++++..+
T Consensus 153 ~~EIA~~lg~s~~tV~~rl~rar~~Lr~~l~ 183 (192)
T PRK09643 153 VADAARMLGVAEGTVKSRCARGRARLAELLG 183 (192)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3578999999999999999888999888754
No 163
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=50.90 E-value=31 Score=26.75 Aligned_cols=44 Identities=9% Similarity=0.116 Sum_probs=36.4
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
.++|..-+.....+.|- ..-..||+..|++..-|..+|.++..=
T Consensus 16 ~~Il~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L 59 (225)
T PRK11552 16 QQLIAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDL 59 (225)
T ss_pred HHHHHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHH
Confidence 45666666666888886 688999999999999999999998763
No 164
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=50.88 E-value=34 Score=27.60 Aligned_cols=30 Identities=10% Similarity=0.057 Sum_probs=26.7
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|+.+|+++.-|.+.+..+|+++++...
T Consensus 135 ~EIA~~lg~s~~tVk~~l~RAr~~Lr~~~~ 164 (293)
T PRK09636 135 DEIASTLGRSPAACRQLASRARKHVRAARP 164 (293)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHhhCC
Confidence 567999999999999999999999998653
No 165
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=50.23 E-value=16 Score=22.66 Aligned_cols=17 Identities=6% Similarity=0.090 Sum_probs=16.0
Q ss_pred HHHHHHhCCChhhHhHh
Q psy10107 38 IMLAIITKMTLTQVSTW 54 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nW 54 (140)
.++|+.+|++..+|..|
T Consensus 4 ~eva~~~gvs~~tlr~y 20 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYY 20 (69)
T ss_dssp HHHHHHTTTTHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 57999999999999999
No 166
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=50.13 E-value=30 Score=27.42 Aligned_cols=49 Identities=16% Similarity=0.035 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|+...+.++..-|++ . ..-.++|..+|++...|...-..+..++++.+
T Consensus 209 ~L~~~er~vi~~~~~~----~----~t~~eIA~~lgis~~~V~~~~~~al~kLr~~l 257 (258)
T PRK08215 209 KLNDREKLILNLRFFQ----G----KTQMEVAEEIGISQAQVSRLEKAALKHMRKYI 257 (258)
T ss_pred cCCHHHHHHHHHHHhc----C----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 4666666666665521 1 23578999999999999999999999988754
No 167
>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=49.98 E-value=38 Score=26.46 Aligned_cols=53 Identities=13% Similarity=-0.016 Sum_probs=38.6
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.+++..+.+|...| ...-+ ..-.-.++|..+|++...|......+.+++|...
T Consensus 176 ~L~~~er~vl~l~y---gl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRY---GLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHh---CCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 35666677776655 11111 2235788999999999999999999999998764
No 168
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=49.89 E-value=39 Score=28.15 Aligned_cols=53 Identities=15% Similarity=-0.017 Sum_probs=36.9
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++..++.+|..-|.-+ |-..-.-.+||..+|++...|..+...++.++|+...
T Consensus 263 L~~~~R~vl~lrygL~----~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l~ 315 (325)
T PRK05657 263 LNDKQREVLARRFGLL----GYEAATLEDVAREIGLTRERVRQIQVEALRRLREILQ 315 (325)
T ss_pred CCHHHHHHHHHHhccC----CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555554433111 1223345789999999999999999999999998764
No 169
>TIGR03020 EpsA transcriptional regulator EpsA. Proteins in this family include a C-terminal LuxR transcriptional regulator domain (pfam00196). These proteins are positioned proximal to either EpsH-containing exopolysaccharide biosynthesis operons of the Methylobacillus type, or the associated PEP-CTERM-containing genes.
Probab=49.63 E-value=29 Score=28.02 Aligned_cols=50 Identities=16% Similarity=0.171 Sum_probs=38.8
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
...||+..+++|. |+. ..| .-.++|..+|+++..|++...|.++|..-.+
T Consensus 188 ~~~LT~RE~evl~-l~a----~G~----s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~n 237 (247)
T TIGR03020 188 AGLITAREAEILA-WVR----DGK----TNEEIAAILGISSLTVKNHLQHIFKKLDVRN 237 (247)
T ss_pred ccCCCHHHHHHHH-HHH----CCC----CHHHHHHHHCcCHHHHHHHHHHHHHHhCCCC
Confidence 4568999999997 542 222 3467889999999999999999999976554
No 170
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=49.60 E-value=33 Score=27.16 Aligned_cols=29 Identities=17% Similarity=0.271 Sum_probs=25.4
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|..+++++..|..=..|.++|+.-.+
T Consensus 198 ~eIa~~l~is~~TV~~h~~~~~~KL~~~n 226 (240)
T PRK10188 198 AEIAMILSISENTVNFHQKNMQKKFNAPN 226 (240)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 46799999999999999999999977554
No 171
>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=49.48 E-value=44 Score=26.75 Aligned_cols=51 Identities=16% Similarity=-0.016 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++...+.+|...| .. +. .-.-.++|..+|++...|......+..|+|+..
T Consensus 218 ~L~~rer~vl~l~y---~~--~~-~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~l 268 (270)
T TIGR02392 218 SLDARSRRIIEARW---LD--DD-KLTLQELAAEYGVSAERIRQIEKNAMKKLKAAL 268 (270)
T ss_pred cCCHHHHHHHHHHh---cC--CC-CcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHh
Confidence 46667777776665 21 11 234579999999999999999999999988754
No 172
>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=49.23 E-value=41 Score=27.08 Aligned_cols=53 Identities=13% Similarity=-0.012 Sum_probs=37.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
++...+.+|...|.-+ |-..-.-.++|..+|++...|..+...++.++|+...
T Consensus 223 Lp~~~R~Vl~l~ygL~----~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 223 LNERQREVLARRFGLL----GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred CCHHHHHHHHHHhCCC----CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 5555566665443000 1122346789999999999999999999999998764
No 173
>PHA01976 helix-turn-helix protein
Probab=48.20 E-value=14 Score=22.77 Aligned_cols=22 Identities=9% Similarity=-0.008 Sum_probs=18.9
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..+||..+|++...|.+|....
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~ 39 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADK 39 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCC
Confidence 4689999999999999997554
No 174
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=48.15 E-value=14 Score=20.23 Aligned_cols=22 Identities=14% Similarity=-0.055 Sum_probs=18.6
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..+||+.+|++..+|..|..+.
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 4689999999999999996554
No 175
>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=48.03 E-value=18 Score=22.77 Aligned_cols=19 Identities=16% Similarity=0.109 Sum_probs=16.7
Q ss_pred HHHHHHHhCCChhhHhHhh
Q psy10107 37 KIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF 55 (140)
-.+||+.+|++...|.+|-
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~ 34 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWK 34 (58)
T ss_pred HHHHHHHHCCChHHHHHHH
Confidence 3679999999999999993
No 176
>PRK13870 transcriptional regulator TraR; Provisional
Probab=47.66 E-value=42 Score=26.52 Aligned_cols=29 Identities=14% Similarity=0.154 Sum_probs=25.2
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|..+|+++.-|+.=+.|+|+|+--.+
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KLga~n 220 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRFDVRS 220 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCCCC
Confidence 46799999999999999999999976554
No 177
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=47.28 E-value=55 Score=21.29 Aligned_cols=36 Identities=14% Similarity=0.100 Sum_probs=27.3
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC--ChhhHhH
Q psy10107 15 YKATLKAWLNEHKKNPYPTKGEKIMLAIITKM--TLTQVST 53 (140)
Q Consensus 15 ~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL--t~~QV~n 53 (140)
++..++..| .+||=.+++.-+.+..+-|- +++||+.
T Consensus 18 ar~~~~k~l---~~NPpine~mir~M~~QMG~kpSekqi~Q 55 (64)
T PF03672_consen 18 ARKYMEKQL---KENPPINEKMIRAMMMQMGRKPSEKQIKQ 55 (64)
T ss_pred HHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCccHHHHHH
Confidence 345566666 88998899999999999985 5556653
No 178
>PRK05572 sporulation sigma factor SigF; Validated
Probab=46.74 E-value=37 Score=26.76 Aligned_cols=49 Identities=12% Similarity=-0.037 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.|++..+.++...|. ....-.++|..+|++...|..+-..+..++++..
T Consensus 202 ~L~~~~~~v~~l~~~--------~~~s~~eIA~~lgis~~~V~~~~~ral~kLr~~l 250 (252)
T PRK05572 202 ELDERERLIVYLRYF--------KDKTQSEVAKRLGISQVQVSRLEKKILKQMKEKL 250 (252)
T ss_pred cCCHHHHHHHHHHHh--------CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 456666666665542 1234578999999999999999999999988754
No 179
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=46.68 E-value=26 Score=25.47 Aligned_cols=31 Identities=16% Similarity=0.142 Sum_probs=26.8
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.-.+||..+|++...|.++...+|.+.++..
T Consensus 144 s~~eIA~~l~is~~~V~~~l~ra~~~l~~~l 174 (176)
T PRK09638 144 TYEEIAKMLNIPEGTVKSRVHHGIKQLRKEW 174 (176)
T ss_pred CHHHHHHHHCCChhHHHHHHHHHHHHHHHHh
Confidence 3467899999999999999999999988753
No 180
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=46.06 E-value=27 Score=25.95 Aligned_cols=31 Identities=23% Similarity=0.236 Sum_probs=27.3
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.-.++|..+|++...|.++...+|.++++..
T Consensus 152 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 152 EFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999999999988764
No 181
>PRK12461 UDP-N-acetylglucosamine acyltransferase; Provisional
Probab=45.99 E-value=42 Score=26.99 Aligned_cols=52 Identities=6% Similarity=-0.111 Sum_probs=37.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCCh--hhHhHhhh
Q psy10107 5 MVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTL--TQVSTWFA 56 (140)
Q Consensus 5 ~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~--~QV~nWF~ 56 (140)
+++|..|++++...|++.|..-.+...+..+-.++|.++..-++ ..+-.||.
T Consensus 194 gl~r~g~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~f~~ 247 (255)
T PRK12461 194 GLRRRGFSSRAIRALKRAYKIIYRSGLSVQQAVAELELQQFESPEVEELIDFIK 247 (255)
T ss_pred hhhhcCCCHHHHHHHHHHHHHHHhcCCCHHHHHHHHHHhccCCHHHHHHHHHHH
Confidence 57899999999999999887766677667777777777665433 23555553
No 182
>PRK10651 transcriptional regulator NarL; Provisional
Probab=45.94 E-value=38 Score=24.34 Aligned_cols=47 Identities=17% Similarity=0.106 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.|++...++|+-+. .+ + .-.++|+.++++...|.+...+.|+|..-.
T Consensus 155 ~Lt~rE~~vl~~l~----~g-~----~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLIA----QG-L----PNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHHH----cC-C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 38888888886653 11 2 245678889999999999999999997544
No 183
>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=45.38 E-value=67 Score=23.39 Aligned_cols=29 Identities=17% Similarity=0.058 Sum_probs=25.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-.++|..+|++...|.+=...+|+++|+.
T Consensus 159 ~~eIA~~lgis~~~v~~~l~Ra~~~Lr~~ 187 (189)
T TIGR02984 159 FAEVAERMDRSEGAVSMLWVRGLARLRQI 187 (189)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999999888764
No 184
>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=45.13 E-value=72 Score=20.36 Aligned_cols=45 Identities=16% Similarity=0.178 Sum_probs=23.9
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhh
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~ 56 (140)
|..|+-.-.-..-+++.+|-.+- ..-..-|++.|++..+|.-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~----~~~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCK----GNQRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTT----T-HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchh----hhHHHHHHHhCccHHHHHHHHH
Confidence 44555554444445554333322 3446689999999999999965
No 185
>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=44.86 E-value=26 Score=27.30 Aligned_cols=31 Identities=23% Similarity=0.184 Sum_probs=27.2
Q ss_pred HHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 37 KIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
-.++|..+|+++..|.++..-+|.++|+..+
T Consensus 201 ~~EIA~~Lgis~~tV~~~l~ra~~~LR~~l~ 231 (234)
T TIGR02835 201 QKEVADMLGISQSYISRLEKRILKRLKKEIN 231 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHhh
Confidence 4678999999999999999999999988653
No 186
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=44.78 E-value=50 Score=19.22 Aligned_cols=40 Identities=15% Similarity=-0.051 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhh
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~ 56 (140)
+.|+.+.+..+..++ ... ....+||..+|.+..-|.++..
T Consensus 3 ~~Lt~~eR~~I~~l~---~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALL---EQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHH---CS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHH---HcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 457788888888886 322 3456799999999999999864
No 187
>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=44.54 E-value=17 Score=23.02 Aligned_cols=23 Identities=17% Similarity=0.069 Sum_probs=19.8
Q ss_pred HHHHHHHhCCChhhHhHhhhhHH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R 59 (140)
..+||+.+|++...|..|+.+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999987653
No 188
>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=44.44 E-value=26 Score=19.52 Aligned_cols=22 Identities=9% Similarity=0.212 Sum_probs=18.7
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..++|+.+|++...|..|..+-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g 24 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 3678999999999999997653
No 189
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=43.98 E-value=30 Score=26.06 Aligned_cols=31 Identities=19% Similarity=0.115 Sum_probs=26.6
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.-.++|..+|+++..|...+..+|.+.+.+.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~l 183 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRREL 183 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3467899999999999999999998887664
No 190
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=43.88 E-value=46 Score=26.78 Aligned_cols=29 Identities=21% Similarity=0.209 Sum_probs=26.0
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|..+|+++..|...+.-+|++++...
T Consensus 128 ~EIA~~lg~s~~tVr~~l~RAr~~Lr~~~ 156 (281)
T TIGR02957 128 EEIASIVGKSEANCRQLVSRARRHLDARR 156 (281)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHhhC
Confidence 56799999999999999999999998754
No 191
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=43.51 E-value=82 Score=21.67 Aligned_cols=48 Identities=13% Similarity=0.003 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-ChhhHhHhhhhHHHhh
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKM-TLTQVSTWFANARRRL 62 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL-t~~QV~nWF~N~R~R~ 62 (140)
|..|+.+-+.-+-+-+ ....+ ....+|++.|+ ...++..|-+..+...
T Consensus 5 ~r~~s~EfK~~iv~~~---~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~~~ 53 (116)
T COG2963 5 RKKYSPEFKLEAVALY---LRGGD----TVSEVAREFGIVSATQLYKWRIQLQKGG 53 (116)
T ss_pred cccCCHHHHHHHHHHH---HhcCc----cHHHHHHHhCCCChHHHHHHHHHHHHcc
Confidence 7788888876665554 33343 57899999996 9999999987777653
No 192
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=43.27 E-value=28 Score=24.89 Aligned_cols=29 Identities=17% Similarity=0.117 Sum_probs=24.4
Q ss_pred CCCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 31 YPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 31 YPs~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
-+++..|.+||..+|++...|..|-.-+.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~~Ad 54 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVNQAD 54 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHhHHH
Confidence 35889999999999999999999954443
No 193
>PF13730 HTH_36: Helix-turn-helix domain
Probab=43.26 E-value=69 Score=18.86 Aligned_cols=46 Identities=13% Similarity=0.000 Sum_probs=30.2
Q ss_pred CCCHHHHHHHHHHHHhh---cCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 10 VGTEIYKATLKAWLNEH---KKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h---~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
.++..++.++-. +..| ....||+ ...||..+|++...|..++..-.
T Consensus 2 ~Ls~~~~~v~~~-l~~~~~~~~~~~pS---~~~la~~~g~s~~Tv~~~i~~L~ 50 (55)
T PF13730_consen 2 NLSPTAKLVYLY-LASYANKNGGCFPS---QETLAKDLGVSRRTVQRAIKELE 50 (55)
T ss_pred CCCHHHHHHHHH-HHHhcCCCCCCCcC---HHHHHHHHCcCHHHHHHHHHHHH
Confidence 455555555532 2222 2337886 67789999999999998876543
No 194
>PF12323 HTH_OrfB_IS605: Helix-turn-helix domain; InterPro: IPR021027 This entry represents an N-terminal helix-turn-helix domain found in a variety of putative transposases [, , ]. It is usually associated with PF01385 from PFAM and PF07282 from PFAM.
Probab=42.78 E-value=34 Score=19.95 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=25.6
Q ss_pred CCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 30 PYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 30 PYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
=|||++++..|.+..|.. ..|-||....|...-+.
T Consensus 9 l~Pt~~Q~~~L~~~~~~~-R~vyN~~L~~~~~~y~~ 43 (46)
T PF12323_consen 9 LYPTKEQEEKLERWFGAC-RFVYNWALAERKEAYKQ 43 (46)
T ss_pred EecCHHHHHHHHHHHHHH-HHHHHHHHHHHHHHHHH
Confidence 488999999998877654 56778877777765443
No 195
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=42.29 E-value=55 Score=26.68 Aligned_cols=52 Identities=12% Similarity=-0.066 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++...+.+|...|. |=....-.+||..+|++...|......+++++|....
T Consensus 227 ~L~~rer~vl~lr~~------~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l~ 278 (289)
T PRK07500 227 TLNERELRIIRERRL------REDGATLEALGEELGISKERVRQIEARALEKLRRALL 278 (289)
T ss_pred cCCHHHHHHHHHHhc------CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 356666666666541 1122356889999999999999999999999987654
No 196
>PRK09480 slmA division inhibitor protein; Provisional
Probab=42.13 E-value=56 Score=23.80 Aligned_cols=44 Identities=16% Similarity=0.129 Sum_probs=34.5
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
.++|......-..+++ ....-..||++.|++...|-.+|.|+-.
T Consensus 13 ~~Il~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 13 EQILQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 4555554433356667 8899999999999999999999999773
No 197
>PF13551 HTH_29: Winged helix-turn helix
Probab=42.12 E-value=31 Score=23.02 Aligned_cols=27 Identities=15% Similarity=0.119 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhh
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRL 62 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~ 62 (140)
...++|+.+|++...|.+|....+..-
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~~~G 40 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYREGG 40 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHHccc
Confidence 467899999999999999998877654
No 198
>KOG1146|consensus
Probab=41.75 E-value=35 Score=34.09 Aligned_cols=59 Identities=17% Similarity=0.050 Sum_probs=50.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 5 MVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 5 ~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.+.|.+.-.++..+|-.|+ ..+--|+.....-|.-....+..++.+||.|-|-|.+++.
T Consensus 706 ~~~~~~~~~~aa~~l~~a~---~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 706 KLLRLTILPEAAMILGRAY---MQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccCcccccHHHHhhhhhcc---cCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3455666668889999998 7777889999999999999999999999999999998875
No 199
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=41.51 E-value=53 Score=26.16 Aligned_cols=48 Identities=13% Similarity=0.035 Sum_probs=34.9
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+++..+.++...|. ..-.-.++|..+|++...|..+..-++.++++..
T Consensus 206 L~~~er~vi~l~y~--------e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 206 LEEKERKVMALYYY--------EELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred CCHHHHHHHHHHHh--------cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45555555555441 1223578899999999999999999999988764
No 200
>PF03457 HA: Helicase associated domain; InterPro: IPR005114 This short domain is found in multiple copies in bacterial helicase proteins. The domain is predicted to contain 3 alpha helices. The function of this domain may be to bind nucleic acid.; PDB: 2KTA_A.
Probab=40.06 E-value=70 Score=19.94 Aligned_cols=40 Identities=28% Similarity=0.387 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
.+.|.+|..+|-..--|...... -..+..|+.++|++.++
T Consensus 12 ~~~l~~y~~~~G~~~vp~~~~~~---------~~~Lg~Wl~~qR~~~r~ 51 (68)
T PF03457_consen 12 YEALKAYKEEHGHLNVPRDYVTD---------GFPLGQWLNNQRRKYRK 51 (68)
T ss_dssp HHHHHHHHHHHS--S-SS--------------SSHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHCCCCCCcccCcC---------CCcHHHHHHHHHHHHHc
Confidence 46788888888643334332111 56789999999999886
No 201
>smart00351 PAX Paired Box domain.
Probab=39.97 E-value=1e+02 Score=21.96 Aligned_cols=43 Identities=5% Similarity=-0.123 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
++.+.+..+-..+ .. . ....++|+.+|++...|..|.+-.+..
T Consensus 18 ~s~~~R~riv~~~---~~-G----~s~~~iA~~~gvs~~tV~kwi~r~~~~ 60 (125)
T smart00351 18 LPDEERQRIVELA---QN-G----VRPCDISRQLCVSHGCVSKILGRYYET 60 (125)
T ss_pred CCHHHHHHHHHHH---Hc-C----CCHHHHHHHHCcCHHHHHHHHHHHHHc
Confidence 6677766655554 21 2 134689999999999999998877654
No 202
>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=38.83 E-value=20 Score=21.87 Aligned_cols=24 Identities=17% Similarity=0.043 Sum_probs=19.2
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
....+|..+|++..+|..|-.+.+
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 356889999999999999988854
No 203
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=38.57 E-value=69 Score=25.98 Aligned_cols=52 Identities=19% Similarity=0.041 Sum_probs=37.6
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++...+.+|...| .. + ..-.-.++|..+|++..+|...-..+..++|...+
T Consensus 230 ~L~~rEr~VL~lry---~~--~-~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~l~ 281 (284)
T PRK06596 230 GLDERSRDIIEARW---LD--D-DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAAIE 281 (284)
T ss_pred cCCHHHHHHHHHHh---cC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35566666666655 21 1 22346799999999999999999999999887653
No 204
>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=38.52 E-value=99 Score=19.29 Aligned_cols=55 Identities=18% Similarity=0.196 Sum_probs=35.1
Q ss_pred CCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 7 PEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
+|...|.+--......+...-.....++....++...++||..||..=.|..|.+
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~k 56 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRLK 56 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHcc
Confidence 5666776665554444433333234555666566666889999999887777654
No 205
>PRK10403 transcriptional regulator NarP; Provisional
Probab=38.05 E-value=68 Score=22.92 Aligned_cols=48 Identities=19% Similarity=0.160 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++....++|..+. + + | ...+||+.++++...|.+...+.|+|..-.+
T Consensus 153 ~Lt~~e~~vl~~~~-~---g-~----s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 153 VLTERELDVLHELA-Q---G-L----SNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred cCCHHHHHHHHHHH-C---C-C----CHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 47777788876443 1 1 2 3468899999999999999999999875443
No 206
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=37.43 E-value=1.3e+02 Score=21.17 Aligned_cols=46 Identities=15% Similarity=0.083 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.+|..|+++|.-+| -..---.++|..+|+|..-|..|..-.+.++.
T Consensus 17 LLT~kQ~~~l~lyy--------~eDlSlsEIAe~~~iSRqaV~d~ikr~~~~L~ 62 (101)
T PF04297_consen 17 LLTEKQREILELYY--------EEDLSLSEIAEELGISRQAVYDSIKRAEKKLE 62 (101)
T ss_dssp GS-HHHHHHHHHHC--------TS---HHHHHHHCTS-HHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHH--------ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 37888888887664 33345678999999999999999988887754
No 207
>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=37.10 E-value=44 Score=23.16 Aligned_cols=28 Identities=11% Similarity=0.148 Sum_probs=22.1
Q ss_pred HHHHHHHHHhCCChhhHhHhhhhHHHhh
Q psy10107 35 GEKIMLAIITKMTLTQVSTWFANARRRL 62 (140)
Q Consensus 35 ~~k~~La~~tgLt~~QV~nWF~N~R~R~ 62 (140)
-.-..+|+..|+++.||+.|..+.+.+.
T Consensus 24 ~gq~~vA~~~Gv~eStISR~k~~~~~~~ 51 (91)
T PF05269_consen 24 VGQKKVAEAMGVDESTISRWKNDFIEKM 51 (91)
T ss_dssp HHHHHHHHHHTSSTTTHHHHHHHHHHHH
T ss_pred HhhHHHHHHhCCCHHHHHHHHhhHHHHH
Confidence 3456789999999999999977655443
No 208
>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=36.97 E-value=36 Score=20.90 Aligned_cols=20 Identities=15% Similarity=0.192 Sum_probs=17.4
Q ss_pred HHHHHHHhCCChhhHhHhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~ 56 (140)
..++|+.+|++...|..|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999964
No 209
>PF08671 SinI: Anti-repressor SinI; InterPro: IPR010981 The SinR repressor is part of a group of Sin (sporulation inhibition) proteins in Bacillus subtilis that regulate the commitment to sporulation in response to extreme adversity []. SinR is a tetrameric repressor protein that binds to the promoters of genes essential for entry into sporulation and prevents their transcription. This repression is overcome through the activity of SinI, which disrupts the SinR tetramer through the formation of a SinI-SinR heterodimer, thereby allowing sporulation to proceed. The SinR structure consists of two domains: a dimerisation domain stabilised by a hydrophobic core, and a DNA-binding domain that is identical to domains of the bacteriophage 434 CI and Cro proteins that regulate prophage induction. The dimerisation domain is a four-helical bundle formed from two helices from the C-terminal residues of SinR and two helices from the central residues of SinI. These regions in SinR and SinI are similar in both structure and sequence. The interaction of SinR monomers to form tetramers is weaker than between SinR and SinI, since SinI can effectively disrupt SinR tetramers. This entry represents the dimerisation domain in both SinI and SinR proteins.; GO: 0005488 binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1B0N_A 2YAL_A.
Probab=36.94 E-value=50 Score=18.25 Aligned_cols=20 Identities=10% Similarity=0.134 Sum_probs=14.5
Q ss_pred HHHHHHHhCCChhhHhHhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~ 56 (140)
-..-|+..||+..+|...+.
T Consensus 8 Li~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 8 LIKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHHcCCCHHHHHHHHH
Confidence 34568999999999998875
No 210
>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=36.30 E-value=34 Score=19.53 Aligned_cols=17 Identities=6% Similarity=0.010 Sum_probs=14.5
Q ss_pred HHHHHHhCCChhhHhHh
Q psy10107 38 IMLAIITKMTLTQVSTW 54 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nW 54 (140)
.++|+.+|++...|..|
T Consensus 3 ~e~A~~~gvs~~tlR~y 19 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYY 19 (38)
T ss_dssp HHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHCCCHHHHHHH
Confidence 47899999999999999
No 211
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=36.26 E-value=1.1e+02 Score=21.76 Aligned_cols=45 Identities=13% Similarity=-0.021 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.+++...++|+-.. ++ | ...+||+..+++...|.+...+.|+|..
T Consensus 137 ~Lt~~E~~il~~l~-~g----~----~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLA-QG----M----AVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHH-CC----C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 46777777775543 22 3 5678899999999999999999988864
No 212
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=36.10 E-value=1.2e+02 Score=23.78 Aligned_cols=46 Identities=11% Similarity=0.130 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
++...+.++...|.+ ...-.++|..+|++..+|..--...+.++|.
T Consensus 184 L~~~er~vi~l~~~~--------~~t~~EIA~~lgis~~~V~q~~~~~~~kLr~ 229 (231)
T PRK12427 184 LDEREQLILHLYYQH--------EMSLKEIALVLDLTEARICQLNKKIAQKIKS 229 (231)
T ss_pred CCHHHHHHHHHHHHc--------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHh
Confidence 555666666665521 1235789999999999999988888887763
No 213
>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=36.08 E-value=68 Score=17.89 Aligned_cols=25 Identities=20% Similarity=0.121 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
.+.+||..+|++..-|+.=|..-++
T Consensus 4 tr~diA~~lG~t~ETVSR~l~~l~~ 28 (32)
T PF00325_consen 4 TRQDIADYLGLTRETVSRILKKLER 28 (32)
T ss_dssp -HHHHHHHHTS-HHHHHHHHHHHHH
T ss_pred CHHHHHHHhCCcHHHHHHHHHHHHH
Confidence 4789999999999999887765554
No 214
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=35.73 E-value=81 Score=23.27 Aligned_cols=47 Identities=19% Similarity=0.059 Sum_probs=35.7
Q ss_pred CCCCHHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhCCChhhHhHhhhhH
Q psy10107 9 YVGTEIYKATLKAWLNEH-KKNPYPTKGEKIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h-~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~ 58 (140)
+.||++++..|.....+. ..+.. ....+|+..||++..+|..-|...
T Consensus 3 ~~~T~eer~eLk~rIvElVRe~GR---iTi~ql~~~TGasR~Tvk~~lreL 50 (127)
T PF06163_consen 3 RVFTPEEREELKARIVELVREHGR---ITIKQLVAKTGASRNTVKRYLREL 50 (127)
T ss_pred CcCCHHHHHHHHHHHHHHHHHcCC---ccHHHHHHHHCCCHHHHHHHHHHH
Confidence 579999999999988776 44554 345677888999999988876543
No 215
>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=35.72 E-value=1.1e+02 Score=19.50 Aligned_cols=43 Identities=21% Similarity=0.255 Sum_probs=25.9
Q ss_pred CCCHHHHHHH---HHHHHhhcCCCCCCHHHHHHHHHHhCCC-hhhHhHhhhh
Q psy10107 10 VGTEIYKATL---KAWLNEHKKNPYPTKGEKIMLAIITKMT-LTQVSTWFAN 57 (140)
Q Consensus 10 ~~~~~~~~~L---~~w~~~h~~nPYPs~~~k~~La~~tgLt-~~QV~nWF~N 57 (140)
.+|+.|.++| .+++ ..+.||. .-.+||..+|+. ..-|..-+.-
T Consensus 3 ~LT~rQ~~vL~~I~~~~---~~~G~~P--t~rEIa~~~g~~S~~tv~~~L~~ 49 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYI---EENGYPP--TVREIAEALGLKSTSTVQRHLKA 49 (65)
T ss_dssp ---HHHHHHHHHHHHHH---HHHSS-----HHHHHHHHTSSSHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHH---HHcCCCC--CHHHHHHHhCCCChHHHHHHHHH
Confidence 4677777777 4444 5566663 677899999996 7777665443
No 216
>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=35.28 E-value=43 Score=18.70 Aligned_cols=21 Identities=10% Similarity=-0.129 Sum_probs=17.5
Q ss_pred HHHHHHHhCCChhhHhHhhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFAN 57 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N 57 (140)
..++|+.+|++...|..|...
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~ 24 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHE 24 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHc
Confidence 357888999999999999643
No 217
>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=35.21 E-value=38 Score=22.50 Aligned_cols=22 Identities=14% Similarity=-0.058 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCChhhHhHhhhh
Q psy10107 36 EKIMLAIITKMTLTQVSTWFAN 57 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N 57 (140)
.-.+||..+|++...|.+|+.+
T Consensus 34 S~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 34 TASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CHHHHHHHHCcCHHHHHHHHhc
Confidence 3578999999999999999763
No 218
>TIGR02997 Sig70-cyanoRpoD RNA polymerase sigma factor, cyanobacterial RpoD-like family. This family includes a number of closely related sigma-70 (TIGR02937) factors in the cyanobacteria. All appear most closely related to the essential sigma-70 factor RpoD, and some score above trusted to the RpoD C-terminal domain model (TIGR02393).
Probab=34.93 E-value=82 Score=25.61 Aligned_cols=49 Identities=16% Similarity=0.086 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
+++..+.+|...|.-+...+ ..-.++|..+|++...|......++.++|
T Consensus 250 L~~rer~Vi~lr~gl~~~~~----~Tl~EIa~~lgiS~erVrq~~~rAl~kLr 298 (298)
T TIGR02997 250 LTPRERQVLRLRFGLDGGEP----LTLAEIGRRLNLSRERVRQIEAKALRKLR 298 (298)
T ss_pred CCHHHHHHHHHHhccCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHcC
Confidence 66667777766551111223 35688999999999999999888887764
No 219
>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=34.93 E-value=38 Score=21.01 Aligned_cols=19 Identities=5% Similarity=-0.050 Sum_probs=16.8
Q ss_pred HHHHHHhCCChhhHhHhhh
Q psy10107 38 IMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~ 56 (140)
.++|+.+|++...|..|-.
T Consensus 4 ~evA~~~gvs~~tlR~~~~ 22 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEK 22 (67)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 220
>smart00351 PAX Paired Box domain.
Probab=34.93 E-value=1.5e+02 Score=20.99 Aligned_cols=44 Identities=11% Similarity=0.053 Sum_probs=27.2
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC-------ChhhHhHhh
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKM-------TLTQVSTWF 55 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL-------t~~QV~nWF 55 (140)
...+......+.... ..+|.-+..+....-...|+ +...|..||
T Consensus 74 ~~~~~~~~~~I~~~~---~~~p~~t~~el~~~L~~~gv~~~~~~Ps~sti~~~l 124 (125)
T smart00351 74 KVATPKVVKKIADYK---QENPGIFAWEIRDRLLSEGVCDKDNVPSVSSINRIL 124 (125)
T ss_pred CccCHHHHHHHHHHH---HHCCCCCHHHHHHHHHHcCCCcCCCCCChhhHHHhh
Confidence 334445555555555 78888888666443335555 667787776
No 221
>PF13873 Myb_DNA-bind_5: Myb/SANT-like DNA-binding domain
Probab=34.53 E-value=1.2e+02 Score=19.19 Aligned_cols=60 Identities=23% Similarity=0.194 Sum_probs=41.2
Q ss_pred CCCCCCHHHHHHHHHHHHhhc---CCCCCCH---HHHH----HHHHHh------CCChhhHhHhhhhHHHhhhhcc
Q psy10107 7 PEYVGTEIYKATLKAWLNEHK---KNPYPTK---GEKI----MLAIIT------KMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 7 ~R~~~~~~~~~~L~~w~~~h~---~nPYPs~---~~k~----~La~~t------gLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+..+|+.+...+|-..+.+|. .+.+.+. ..|. +|+..+ .-+..|+...+.|-+.+.|+..
T Consensus 1 R~~~fs~~E~~~Lv~~v~~~~~il~~k~~~~~~~~~k~~~W~~I~~~lN~~~~~~Rs~~~lkkkW~nlk~~~Kk~~ 76 (78)
T PF13873_consen 1 RKPNFSEEEKEILVELVEKHKDILENKFSDSVSNKEKRKAWEEIAEELNALGPGKRSWKQLKKKWKNLKSKAKKKL 76 (78)
T ss_pred CCCCCCHHHHHHHHHHHHHhHHHHhcccccHHHHHHHHHHHHHHHHHHHhcCCCCCCHHHHHHHHHHHHHHHHHHh
Confidence 357899999999999987773 3333322 2232 344444 4688899999999998888764
No 222
>PRK10219 DNA-binding transcriptional regulator SoxS; Provisional
Probab=34.50 E-value=93 Score=20.89 Aligned_cols=40 Identities=23% Similarity=0.278 Sum_probs=28.1
Q ss_pred HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhh
Q psy10107 14 IYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFAN 57 (140)
Q Consensus 14 ~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N 57 (140)
+....+..|+.+|...| ++ -.+||..+|++..++..=|+-
T Consensus 5 ~~~~~~~~~i~~~~~~~-~~---~~~lA~~~~~S~~~l~r~f~~ 44 (107)
T PRK10219 5 KIIQTLIAWIDEHIDQP-LN---IDVVAKKSGYSKWYLQRMFRT 44 (107)
T ss_pred HHHHHHHHHHHHhcCCC-CC---HHHHHHHHCCCHHHHHHHHHH
Confidence 45666788988887766 44 467788888888877655443
No 223
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=34.20 E-value=42 Score=21.31 Aligned_cols=18 Identities=28% Similarity=0.368 Sum_probs=15.7
Q ss_pred HHHHHHHhCCChhhHhHh
Q psy10107 37 KIMLAIITKMTLTQVSTW 54 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nW 54 (140)
...||+.+|++..-|..|
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 468999999999999999
No 224
>KOG4040|consensus
Probab=34.16 E-value=38 Score=26.15 Aligned_cols=34 Identities=29% Similarity=0.548 Sum_probs=26.7
Q ss_pred HHHHHHHHhhcCCCCCC-HHHHHHHHHHhCCChhh
Q psy10107 17 ATLKAWLNEHKKNPYPT-KGEKIMLAIITKMTLTQ 50 (140)
Q Consensus 17 ~~L~~w~~~h~~nPYPs-~~~k~~La~~tgLt~~Q 50 (140)
...-.|...|.-.|||+ ++||..-|++.||-+..
T Consensus 27 rt~~gw~kD~kPgpyP~teeER~AAAkKY~lrpEd 61 (186)
T KOG4040|consen 27 RTFDGWYKDHKPGPYPTTEEERRAAAKKYGLRPED 61 (186)
T ss_pred ccccccccccCCCCCCCCHHHHHHHHHHhCCCHhh
Confidence 44567888899999996 57888888888886654
No 225
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=33.63 E-value=75 Score=24.34 Aligned_cols=47 Identities=17% Similarity=0.269 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.||+..+++|.-+- ..+. -.++|++++++++.|++-..+..+|..-.
T Consensus 137 ~LT~RE~eVL~lla-----~G~s----nkeIA~~L~iS~~TVk~h~~~I~~KL~v~ 183 (207)
T PRK15411 137 SLSRTESSMLRMWM-----AGQG----TIQISDQMNIKAKTVSSHKGNIKRKIKTH 183 (207)
T ss_pred cCCHHHHHHHHHHH-----cCCC----HHHHHHHcCCCHHHHHHHHHHHHHHhCCC
Confidence 37888888886664 2332 36789999999999999888888776543
No 226
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=33.57 E-value=77 Score=25.85 Aligned_cols=29 Identities=14% Similarity=0.168 Sum_probs=25.8
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|..+|+++..|...+.-+|++++...
T Consensus 138 ~EIA~~Lgis~~tVr~~l~RAr~~Lr~~~ 166 (290)
T PRK09635 138 QQIATTIGSQASTCRQLAHRARRKINESR 166 (290)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHhhC
Confidence 56799999999999999999999988754
No 227
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=33.22 E-value=80 Score=24.55 Aligned_cols=46 Identities=15% Similarity=-0.015 Sum_probs=34.1
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
||+..+++|+-.. . .+ .-.++|+.+++++..|+++..+..+|..-.
T Consensus 156 Lt~rE~~Vl~l~~---~--G~----s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~ 201 (216)
T PRK10100 156 LTHREKEILNKLR---I--GA----SNNEIARSLFISENTVKTHLYNLFKKIAVK 201 (216)
T ss_pred CCHHHHHHHHHHH---c--CC----CHHHHHHHhCCCHHHHHHHHHHHHHHhCCC
Confidence 6777777775554 1 22 235789999999999999999998886544
No 228
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=33.22 E-value=1e+02 Score=22.10 Aligned_cols=45 Identities=16% Similarity=-0.012 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.+++....+|+-+. ++ -...+||..++++..-|.++..+.|+|..
T Consensus 149 ~lt~re~~vl~~l~-~g--------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 149 VLSNREVTILRYLV-SG--------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred cCCHHHHHHHHHHH-cC--------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 36666667775443 11 34678888999999999999999999865
No 229
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=33.04 E-value=89 Score=23.41 Aligned_cols=27 Identities=11% Similarity=0.118 Sum_probs=23.9
Q ss_pred cCCCCCCHHHHHHHHHHhCCChhhHhH
Q psy10107 27 KKNPYPTKGEKIMLAIITKMTLTQVST 53 (140)
Q Consensus 27 ~~nPYPs~~~k~~La~~tgLt~~QV~n 53 (140)
....|.+.+....+|+.+|+++.+|..
T Consensus 34 ~~~G~Ip~e~~~~iA~~l~v~~~~V~~ 60 (156)
T PRK05988 34 DEFGYVPEDAVPVIAEALNLSRAEVHG 60 (156)
T ss_pred HHcCCCCHHHHHHHHHHhCCCHHHHHH
Confidence 445799999999999999999999865
No 230
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=32.87 E-value=42 Score=20.64 Aligned_cols=18 Identities=6% Similarity=0.049 Sum_probs=16.3
Q ss_pred HHHHHHhCCChhhHhHhh
Q psy10107 38 IMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF 55 (140)
.++|+.+|++...|..|-
T Consensus 4 ~eva~~~gvs~~tlr~~~ 21 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYE 21 (70)
T ss_pred HHHHHHHCcCHHHHHHHH
Confidence 578999999999999994
No 231
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=32.61 E-value=30 Score=24.72 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R 59 (140)
+.+||..+|++...|..|.++.+
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 56799999999999999998764
No 232
>PF05821 NDUF_B8: NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI or NDUFB8); InterPro: IPR008699 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 []. This family consists of several eukaryotic NADH-ubiquinone oxidoreductase ASHI subunit (CI-ASHI) proteins. NADH:ubiquinone oxidoreductase (complex I) is an extremely complicated multiprotein complex located in the inner mitochondrial membrane. Its main function is the transport of electrons from NADH to ubiquinone, which is accompanied by translocation of protons from the mitochondrial matrix to the intermembrane space. Human complex I appears to consist of 41 subunits [].; GO: 0003954 NADH dehydrogenase activity, 0008137 NADH dehydrogenase (ubiquinone) activity, 0005739 mitochondrion
Probab=32.22 E-value=33 Score=26.55 Aligned_cols=34 Identities=24% Similarity=0.439 Sum_probs=26.1
Q ss_pred HHHHhhcCCCCC-CHHHHHHHHHHhCCChhhHhHh
Q psy10107 21 AWLNEHKKNPYP-TKGEKIMLAIITKMTLTQVSTW 54 (140)
Q Consensus 21 ~w~~~h~~nPYP-s~~~k~~La~~tgLt~~QV~nW 54 (140)
-|-..++=.||| |++||...|++.||....-.-+
T Consensus 26 ~~~kd~~PgpyP~t~eer~aaAkKY~l~pedY~P~ 60 (179)
T PF05821_consen 26 GWNKDWKPGPYPKTPEERAAAAKKYGLRPEDYEPY 60 (179)
T ss_pred cCCccCCCCCCCCCHHHHHHHHHHcCCCHHHcCCC
Confidence 343445667998 7899999999999988875544
No 233
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=32.11 E-value=30 Score=24.70 Aligned_cols=23 Identities=22% Similarity=0.332 Sum_probs=20.4
Q ss_pred HHHHHHHhCCChhhHhHhhhhHH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R 59 (140)
..+||..+|++...|..|..+.+
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~ 43 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDET 43 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999998864
No 234
>KOG4067|consensus
Probab=31.78 E-value=36 Score=26.81 Aligned_cols=48 Identities=17% Similarity=0.291 Sum_probs=32.9
Q ss_pred CHHHHHHHHHHHHhh-------cCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 12 TEIYKATLKAWLNEH-------KKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 12 ~~~~~~~L~~w~~~h-------~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
+.-+.++|.++|.-- ...|| + +-.++-++.+++.+|+.+.++|+++..
T Consensus 133 ~~~aqki~~nf~Nf~qsfa~~~~q~~~-n------~~s~~~VP~~v~~~W~~kFq~rl~~np 187 (195)
T KOG4067|consen 133 KSFAQKILTNFFNFMQSFAVSIAQIPP-N------LPSETFVPIRVFDDWYDKFQNRLANNP 187 (195)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhccCC-C------CcccccccHHHHHHHHHHHHHHHhcCC
Confidence 455666777665211 23332 2 455678999999999999999988764
No 235
>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=31.73 E-value=50 Score=20.54 Aligned_cols=19 Identities=16% Similarity=0.267 Sum_probs=16.8
Q ss_pred HHHHHHhCCChhhHhHhhh
Q psy10107 38 IMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~ 56 (140)
.++|+.+|++...|..|..
T Consensus 4 ~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 4 GEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 236
>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=31.34 E-value=47 Score=24.80 Aligned_cols=24 Identities=8% Similarity=-0.060 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCC
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPT 33 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs 33 (140)
.-++.++...|..++.+ ...++|.
T Consensus 50 ~~Lt~~qi~~l~~~i~~-~~~~iP~ 73 (144)
T TIGR03629 50 GYLDDEEIEKLEEAVEN-YEYGIPS 73 (144)
T ss_pred ccCCHHHHHHHHHHHHh-ccccCCH
Confidence 45777777777777744 3344333
No 237
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=30.95 E-value=52 Score=21.03 Aligned_cols=24 Identities=8% Similarity=0.101 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
...++|..+||+..|+..|+..--
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~~Le 40 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLEKLE 40 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHH
Confidence 345899999999999999986543
No 238
>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=30.70 E-value=31 Score=26.73 Aligned_cols=33 Identities=27% Similarity=0.328 Sum_probs=28.1
Q ss_pred HHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 35 GEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 35 ~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
....+|+.-.+++..+|..|..|=+--.+..++
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~ 47 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAKPK 47 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCcccccch
Confidence 467899999999999999999998877766654
No 239
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=30.68 E-value=2e+02 Score=20.51 Aligned_cols=46 Identities=13% Similarity=0.043 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
.+++...++|.-++ ... .+.+||...+++...|.+--.+-|+|..-
T Consensus 143 ~lt~~E~~vl~~l~---~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl~~ 188 (204)
T PRK09958 143 SLSKQEISVMRYIL---DGK------DNNDIAEKMFISNKTVSTYKSRLMEKLEC 188 (204)
T ss_pred cCCHHHHHHHHHHH---cCC------CHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 48888888888886 222 36789999999999999998888888643
No 240
>PF09636 XkdW: XkdW protein; InterPro: IPR019094 This entry includes the phage SPbeta protein YorD, the function of which is not known, It also contains the protein XkdW (P54342 from SWISSPROT) from the Phage-like element PBSX in Bacillus subtilis. XkdW is approximately 100 residues long and contains two alpha helices and two beta strands, and is probably monomeric. XkdW is expressed in bacteria but is probably viral in origin. Its function is unknown. PBSX, a defective prophage of B. subtilis, is a chromosomally based element which encodes a non-infectious phage-like particle with bactericidal activity. PBSX is induced by agents which elicit the SOS response [].; PDB: 2HG7_A.
Probab=30.60 E-value=35 Score=24.45 Aligned_cols=33 Identities=24% Similarity=0.296 Sum_probs=13.2
Q ss_pred CCHHHHHHHHHHHHhhcCCC-CCCHHHHHHHHHH
Q psy10107 11 GTEIYKATLKAWLNEHKKNP-YPTKGEKIMLAII 43 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nP-YPs~~~k~~La~~ 43 (140)
.+.-+..-|..|+.++..+| |+.+.+...|+.+
T Consensus 40 ~p~Pt~~El~~a~ee~~~~p~~~~P~qle~L~qe 73 (108)
T PF09636_consen 40 APQPTEAELQSAWEELQKNPDYEPPNQLELLGQE 73 (108)
T ss_dssp S----HHHHHHHHHHHHHS---------------
T ss_pred CCCCCHHHHHHHHHHHHhcCCCCCchhhhHHHHH
Confidence 45667788999999998888 7777777777654
No 241
>PRK09726 antitoxin HipB; Provisional
Probab=30.07 E-value=34 Score=22.73 Aligned_cols=22 Identities=18% Similarity=0.140 Sum_probs=19.6
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..+||+.+|++...|..|..+.
T Consensus 28 q~elA~~~gvs~~tis~~e~g~ 49 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNP 49 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCC
Confidence 5789999999999999998864
No 242
>PRK09483 response regulator; Provisional
Probab=28.88 E-value=1.2e+02 Score=21.94 Aligned_cols=46 Identities=7% Similarity=-0.087 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 9 YVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 9 ~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
..|++...++|.-+. ..+.+ .++|..++++...|++-..|.++|.-
T Consensus 147 ~~Lt~rE~~vl~~~~-----~G~~~----~~Ia~~l~is~~TV~~~~~~i~~Kl~ 192 (217)
T PRK09483 147 ASLSERELQIMLMIT-----KGQKV----NEISEQLNLSPKTVNSYRYRMFSKLN 192 (217)
T ss_pred cccCHHHHHHHHHHH-----CCCCH----HHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 347888888885442 23333 28899999999999998888887753
No 243
>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=28.77 E-value=47 Score=24.31 Aligned_cols=19 Identities=21% Similarity=0.349 Sum_probs=17.2
Q ss_pred HHHHHHHhCCChhhHhHhh
Q psy10107 37 KIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF 55 (140)
-++||..||++..-|+-|.
T Consensus 3 ~eELA~~tG~srQTINrWv 21 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWV 21 (122)
T ss_pred HHHHHHHhCccHHHHHHHH
Confidence 4689999999999999994
No 244
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=28.68 E-value=49 Score=20.27 Aligned_cols=17 Identities=29% Similarity=0.120 Sum_probs=13.1
Q ss_pred HHHHHHHhCCChhhHhH
Q psy10107 37 KIMLAIITKMTLTQVST 53 (140)
Q Consensus 37 k~~La~~tgLt~~QV~n 53 (140)
-.+||+.+|++..||.-
T Consensus 31 S~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 31 SQELAEALGITPAQVRK 47 (50)
T ss_dssp HHHHHHHHTS-HHHHHH
T ss_pred HHHHHHHHCCCHHHhcc
Confidence 35789999999999963
No 245
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=28.54 E-value=71 Score=23.56 Aligned_cols=30 Identities=20% Similarity=0.327 Sum_probs=26.7
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.++|..+|++...|..+..-+|.+.+....
T Consensus 147 ~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 147 EEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 567999999999999999999999887764
No 246
>PF08765 Mor: Mor transcription activator family; InterPro: IPR014875 Mor (Middle operon regulator) is a sequence specific DNA binding protein. It mediates transcription activation through its interactions with the C-terminal domains of the alpha and sigma subunits of bacterial RNA polymerase. The N-terminal region of Mor is the dimerisation region, and the C-terminal contains a helix-turn-helix motif which binds DNA []. ; PDB: 1RR7_A.
Probab=28.17 E-value=70 Score=22.18 Aligned_cols=30 Identities=20% Similarity=0.169 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
-..+||.+.|||..+|.+=..-.|.+..+.
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~~~~~ 103 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRRERRR 103 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH-----
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHh
Confidence 357999999999999988777666665544
No 247
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=28.12 E-value=1.3e+02 Score=26.27 Aligned_cols=52 Identities=10% Similarity=0.084 Sum_probs=38.9
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.+++.++.+|.-.|.-.-..++ .-.++|..+|++...|..+...+++++|.+
T Consensus 350 ~L~~reR~VI~LRygl~d~~~~----Tl~EIA~~LGvS~erVRqie~rAl~KLR~~ 401 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGHTY----SLAEIGRALDLSRERVRQIESKALQKLRQP 401 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCCCC----CHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 3677777887766621112333 457899999999999999999999998865
No 248
>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=27.74 E-value=1.2e+02 Score=22.19 Aligned_cols=34 Identities=9% Similarity=0.072 Sum_probs=26.7
Q ss_pred cCCCCCCHHHHHHHHHHhCCChhhHhH---hhhhHHH
Q psy10107 27 KKNPYPTKGEKIMLAIITKMTLTQVST---WFANARR 60 (140)
Q Consensus 27 ~~nPYPs~~~k~~La~~tgLt~~QV~n---WF~N~R~ 60 (140)
....|.+++....+|..+|++..+|.. ++...+.
T Consensus 27 ~~~G~i~~~~~~~iA~~l~~~~~~v~~v~tFY~~f~~ 63 (148)
T TIGR01958 27 EQKGWVTPEAIAAVAEMLGIPPVWVYEVATFYSMFDT 63 (148)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHHHHHHhHHhhcCc
Confidence 334799999999999999999998765 4544444
No 249
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=27.55 E-value=1.5e+02 Score=24.48 Aligned_cols=51 Identities=14% Similarity=0.051 Sum_probs=36.8
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
++...+.++..-|.-+-..+ ..-.++|..+|++...|......+++++|+.
T Consensus 257 L~~rer~Vi~lr~gl~~~~~----~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 257 LTPQQKEVIALRFGLEDGQP----LTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred CCHHHHHHHHHHhhcCCCCC----cCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56666666665551111222 3568899999999999999999999998874
No 250
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=27.47 E-value=44 Score=20.54 Aligned_cols=25 Identities=20% Similarity=0.048 Sum_probs=20.0
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
...++|..+|++...|..|-..++.
T Consensus 16 s~~~lA~~~g~s~s~v~~iE~G~~~ 40 (64)
T PF13560_consen 16 SQAQLADRLGVSQSTVSRIERGRRP 40 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSSS
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCCC
Confidence 4678999999999999999887764
No 251
>cd07377 WHTH_GntR Winged helix-turn-helix (WHTH) DNA-binding domain of the GntR family of transcriptional regulators. This CD represents the winged HTH DNA-binding domain of the GntR (named after the gluconate operon repressor in Bacillus subtilis) family of bacterial transcriptional regulators and their putative homologs found in eukaryota and archaea. The GntR family has over 6000 members distributed among almost all bacterial species, which is comprised of FadR, HutC, MocR, YtrA, AraR, PlmA, and other subfamilies for the regulation of the most varied biological process. The monomeric proteins of the GntR family are characterized by two function domains: a small highly conserved winged helix-turn-helix prokaryotic DNA binding domain in the N-terminus, and a very diverse regulatory ligand-binding domain in the C-terminus for effector-binding/oligomerization, which provides the basis for the subfamily classifications. Binding of the effector to GntR-like transcriptional regulators is
Probab=27.39 E-value=1.4e+02 Score=17.56 Aligned_cols=47 Identities=13% Similarity=-0.005 Sum_probs=27.4
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHh
Q psy10107 15 YKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRR 61 (140)
Q Consensus 15 ~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R 61 (140)
....+..-+..+...+-.......+||..++++...|...+..-...
T Consensus 6 ~~~~i~~~i~~~~~~~~~~~~~~~~la~~~~is~~~v~~~l~~L~~~ 52 (66)
T cd07377 6 IADQLREAILSGELKPGDRLPSERELAEELGVSRTTVREALRELEAE 52 (66)
T ss_pred HHHHHHHHHHcCCCCCCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHC
Confidence 34444444433322222211235679999999999998877655543
No 252
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=27.21 E-value=1.8e+02 Score=20.29 Aligned_cols=29 Identities=14% Similarity=0.172 Sum_probs=24.1
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++|+..|++..-|.++..+.|.|.+..+
T Consensus 160 ~~ia~~l~~s~~tv~~~~~~~~~kl~~~~ 188 (202)
T PRK09390 160 KVIARDLDISPRTVEVYRANVMTKMQAGS 188 (202)
T ss_pred HHHHHHcCCCHHHHHHHHHHHHHHHcccc
Confidence 55788889999999999999999876543
No 253
>PRK13916 plasmid segregation protein ParR; Provisional
Probab=27.21 E-value=49 Score=22.91 Aligned_cols=36 Identities=25% Similarity=0.474 Sum_probs=28.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhhcC-CCCCCHHHH
Q psy10107 2 FMNMVPEYVGTEIYKATLKAWLNEHKK-NPYPTKGEK 37 (140)
Q Consensus 2 ~~~~~~R~~~~~~~~~~L~~w~~~h~~-nPYPs~~~k 37 (140)
||.++||-..+...+++|+.+..+--. .|-|+.+-.
T Consensus 23 FL~~~P~GT~~~~iR~~L~rYI~~~G~~~PiP~~~~T 59 (97)
T PRK13916 23 FLENVPRGTKTAHIREALRRYIEEIGENPPIPSKEHT 59 (97)
T ss_pred HHHHCCCCCccHHHHHHHHHHHHhcCCCCCCCccccc
Confidence 678999999999999999999976644 455655444
No 254
>PRK04053 rps13p 30S ribosomal protein S13P; Reviewed
Probab=27.19 E-value=61 Score=24.37 Aligned_cols=25 Identities=8% Similarity=-0.019 Sum_probs=19.8
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCC
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYP 32 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYP 32 (140)
-..++.++...|..++.+....++|
T Consensus 53 ~~~Lt~~qi~~l~~~i~~~~~~~iP 77 (149)
T PRK04053 53 LGYLSDEEIEKIEEALEDPAEEGIP 77 (149)
T ss_pred cCcCCHHHHHHHHHHHHhhccccCc
Confidence 3568899999999998776667777
No 255
>COG2938 Uncharacterized conserved protein [Function unknown]
Probab=27.13 E-value=1.3e+02 Score=20.94 Aligned_cols=41 Identities=7% Similarity=0.099 Sum_probs=31.4
Q ss_pred HHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 18 TLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 18 ~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
+|..++..|... -+.+++.++-+.+...-.++-+||.|...
T Consensus 32 il~~Fae~~~~~--lsd~el~~f~~LLe~~D~dL~~Wi~g~~~ 72 (94)
T COG2938 32 ILGPFAEKEFDS--LSDEELDEFERLLECEDNDLFNWIMGHGE 72 (94)
T ss_pred HHHHHHHHHHhh--CCHHHHHHHHHHHcCCcHHHHHHHhCCCC
Confidence 344555444433 38899999999999999999999988654
No 256
>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=26.57 E-value=34 Score=21.57 Aligned_cols=21 Identities=19% Similarity=0.222 Sum_probs=15.6
Q ss_pred HHHHHHHHhCCChhhHh-Hhhh
Q psy10107 36 EKIMLAIITKMTLTQVS-TWFA 56 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~-nWF~ 56 (140)
...+||+.+|++...|. +|..
T Consensus 14 ~~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 14 SDKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp SCHHHHCCTT--HHHHH-HHHH
T ss_pred CHHHHHHHhCcCHHHhhHHHHh
Confidence 34689999999999999 8853
No 257
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=26.49 E-value=1.3e+02 Score=22.20 Aligned_cols=34 Identities=12% Similarity=0.106 Sum_probs=26.9
Q ss_pred cCCCCCCHHHHHHHHHHhCCChhhHhH---hhhhHHH
Q psy10107 27 KKNPYPTKGEKIMLAIITKMTLTQVST---WFANARR 60 (140)
Q Consensus 27 ~~nPYPs~~~k~~La~~tgLt~~QV~n---WF~N~R~ 60 (140)
....|.+++....+|+.+|++..+|.. ++...+.
T Consensus 33 ~~~g~ip~~~~~~iA~~l~v~~~~v~~v~tFY~~f~~ 69 (154)
T PRK07539 33 EQRGWVPDEAIEAVADYLGMPAIDVEEVATFYSMIFR 69 (154)
T ss_pred HHhCCCCHHHHHHHHHHhCcCHHHHHHHHHHHhhhCc
Confidence 335899999999999999999999765 4444443
No 258
>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=26.45 E-value=1.3e+02 Score=17.12 Aligned_cols=36 Identities=22% Similarity=0.342 Sum_probs=23.2
Q ss_pred HHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhh
Q psy10107 13 EIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 13 ~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF 55 (140)
....++|. .+ ..+|.. ...+||+.+|++...|..-+
T Consensus 3 ~~~~~Il~-~l---~~~~~~---t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 3 ETQRKILN-YL---RENPRI---TQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp HHHHHHHH-HH---HHCTTS----HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHH-HH---HHcCCC---CHHHHHHHhCCCHHHHHHHH
Confidence 34556664 34 446754 46789999999999887644
No 259
>smart00354 HTH_LACI helix_turn _helix lactose operon repressor.
Probab=26.31 E-value=45 Score=21.14 Aligned_cols=22 Identities=14% Similarity=0.049 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChhhHhHhhhhH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANA 58 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~ 58 (140)
..+||+.+|++...|+..+.+.
T Consensus 3 ~~~iA~~~gvS~~TVSr~ln~~ 24 (70)
T smart00354 3 IKDVARLAGVSKATVSRVLNGN 24 (70)
T ss_pred HHHHHHHHCCCHHHHHHHHCCC
Confidence 3589999999999999998764
No 260
>PRK09191 two-component response regulator; Provisional
Probab=26.20 E-value=1.5e+02 Score=22.49 Aligned_cols=49 Identities=12% Similarity=0.011 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
+++.+++++.--+.+.. . -.++|..+|+++.-|..-...+|++.+....
T Consensus 89 L~~~~r~v~~l~~~~~~--s------~~eIA~~l~~s~~tV~~~l~ra~~~l~~~~~ 137 (261)
T PRK09191 89 LTPLPRQAFLLTALEGF--S------VEEAAEILGVDPAEAEALLDDARAEIARQVA 137 (261)
T ss_pred CCHHHhHHHHHHHHhcC--C------HHHHHHHHCCCHHHHHHHHHHHHHHHhccCC
Confidence 56666666655432222 2 4678999999999999999988888876543
No 261
>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=26.19 E-value=1.7e+02 Score=18.39 Aligned_cols=21 Identities=10% Similarity=0.074 Sum_probs=16.4
Q ss_pred HHHHHHHhCCChhhHhHhhhh
Q psy10107 37 KIMLAIITKMTLTQVSTWFAN 57 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N 57 (140)
-.+||..+|++..+|...+.-
T Consensus 23 ~eEiA~~lgis~~~v~~~l~~ 43 (78)
T PF04539_consen 23 DEEIAEELGISVEEVRELLQA 43 (78)
T ss_dssp HHHHHHHHTS-HHHHHHHHHH
T ss_pred HHHHHHHHcccHHHHHHHHHh
Confidence 457899999999999987753
No 262
>PF04814 HNF-1_N: Hepatocyte nuclear factor 1 (HNF-1), N terminus; InterPro: IPR006899 This domain consists of the N terminus of homeobox-containing transcription factor HNF-1. This region contains a dimerisation sequence [] and an acidic region that may be involved in transcription activation. Mutations and the common Ala/Val 98 polymorphism in HNF-1 cause the type 3 form of maturity-onset diabetes of the young (MODY3) [].; GO: 0045893 positive regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 2GYP_B 1IC8_B 2H8R_B 1G2Y_D 1F93_H 1G39_D 1G2Z_B 1JB6_B.
Probab=26.00 E-value=1.3e+02 Score=23.53 Aligned_cols=34 Identities=21% Similarity=0.373 Sum_probs=22.0
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhh
Q psy10107 15 YKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 15 ~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF 55 (140)
+.+..+.|+.+|.-- -.+++..|||+...|+.|+
T Consensus 119 VkeeIK~fl~~h~Is-------Q~~V~q~TGisQS~lSq~L 152 (180)
T PF04814_consen 119 VKEEIKAFLQQHNIS-------QREVVQVTGISQSHLSQHL 152 (180)
T ss_dssp HHHHHHHHHHHCT---------CHHHHHHHT--HHHHHHHH
T ss_pred HHHHHHHHHHHcCCc-------HHHHHHHhhhhHHHHHHHH
Confidence 445566666444322 2578999999999999997
No 263
>PRK09685 DNA-binding transcriptional activator FeaR; Provisional
Probab=25.73 E-value=2.1e+02 Score=22.62 Aligned_cols=40 Identities=10% Similarity=0.027 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhh
Q psy10107 14 IYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 14 ~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~ 56 (140)
.....+.++..+|...|-.+. ..||...|++...+..-|+
T Consensus 197 ~~l~~~~~~I~~~l~~~~ls~---~~lA~~~giS~r~L~r~Fk 236 (302)
T PRK09685 197 RQFQKVVALIDQSIQEEILRP---EWIAGELGISVRSLYRLFA 236 (302)
T ss_pred HHHHHHHHHHHHhcCCCCCCH---HHHHHHHCCCHHHHHHHHH
Confidence 345567788989988885554 6789999999998877775
No 264
>PF12728 HTH_17: Helix-turn-helix domain
Probab=25.25 E-value=77 Score=18.42 Aligned_cols=19 Identities=16% Similarity=0.247 Sum_probs=16.5
Q ss_pred HHHHHHhCCChhhHhHhhh
Q psy10107 38 IMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~ 56 (140)
.++|+.+|++...|..|..
T Consensus 5 ~e~a~~l~is~~tv~~~~~ 23 (51)
T PF12728_consen 5 KEAAELLGISRSTVYRWIR 23 (51)
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5778889999999999974
No 265
>PF13613 HTH_Tnp_4: Helix-turn-helix of DDE superfamily endonuclease
Probab=25.15 E-value=57 Score=19.62 Aligned_cols=23 Identities=22% Similarity=0.008 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhHhHhhhhHH
Q psy10107 37 KIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 37 k~~La~~tgLt~~QV~nWF~N~R 59 (140)
-..||...|++...|..||..--
T Consensus 22 ~~~La~~FgIs~stvsri~~~~~ 44 (53)
T PF13613_consen 22 FQDLAYRFGISQSTVSRIFHEWI 44 (53)
T ss_pred HhHHhhheeecHHHHHHHHHHHH
Confidence 35789999999999999987543
No 266
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.10 E-value=79 Score=18.37 Aligned_cols=36 Identities=11% Similarity=0.097 Sum_probs=24.3
Q ss_pred HHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhh
Q psy10107 17 ATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 17 ~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~ 56 (140)
..|+.|..+-.... ++ ...+|+.+|++...|.+.|.
T Consensus 14 ~~~~~~i~~~~~~~-~s---~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 14 KRLEQYILKLLRES-RS---FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHHHHhhc-CC---HHHHHHHHCCCHHHHHHHHH
Confidence 44445544333333 23 56789999999999999885
No 267
>TIGR02850 spore_sigG RNA polymerase sigma-G factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigG. It is also desginated stage III sporulation protein G (SpoIIIG). This protein is rather closely related to sigma-F (SpoIIAC), another sporulation sigma factor.
Probab=24.85 E-value=1.2e+02 Score=23.84 Aligned_cols=48 Identities=19% Similarity=0.061 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
.|+...+.++...|. .+ ..-.++|..+|++...|...-..+..++++.
T Consensus 206 ~L~~rer~vi~~~~~----~~----~t~~eIA~~lgis~~~V~~~~~ral~kLr~~ 253 (254)
T TIGR02850 206 RLNEREKMILNMRFF----EG----KTQMEVAEEIGISQAQVSRLEKAALKHMRKY 253 (254)
T ss_pred cCCHHHHHHHHHHHc----CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 456666677666652 12 2357899999999999999888888777653
No 268
>KOG3755|consensus
Probab=24.70 E-value=45 Score=30.89 Aligned_cols=121 Identities=12% Similarity=-0.016 Sum_probs=0.0
Q ss_pred CCCCCCC-CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhh----HhHhhhhHHHhhhhcccCCCCCCCCCCC
Q psy10107 4 NMVPEYV-GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQ----VSTWFANARRRLKKENKMTWEPKNKTDD 78 (140)
Q Consensus 4 ~~~~R~~-~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~Q----V~nWF~N~R~R~k~~~~~~~~p~~~~~~ 78 (140)
.+.||.. .+..+...|..||.+ |.-.++..--.+.+.+... --|||+|.|.-.++.--..-.....-..
T Consensus 354 Pp~pRa~~~P~~ql~~lq~~fs~------~~~qQv~d~~~rl~~sqav~gr~~~N~~q~~~s~~~raE~~~~s~s~sll~ 427 (769)
T KOG3755|consen 354 PPYPRAQLKPGFQLNLLQSEFSE------PIYQQVRDELKRLDESQAVFGRVAFNRTQGLLSEILRAEEDPHSASQSLLV 427 (769)
T ss_pred CCCchhhcCccccchhhhhhhcc------HHHHHHHHHHHHhhhhhhhhhhhhhhhhhhhhccccchhcccccchHHHHH
Q ss_pred Ccccccc--cCCccccCcccCchHHHhhhHHHHhhhcCCCCCCCCCCcccccCCCCCCC
Q psy10107 79 DDDAIIS--DCDEKDKDDLMMDEEKMKQHHRMVKAVLGTSSILTFPCSIVKLTIPGNGS 135 (140)
Q Consensus 79 ~~~~~~~--d~~~~~~~~l~~~~~~~~~~~~~~~~~~~~S~~~~~p~s~~~~~~~~~g~ 135 (140)
..-++++ -..+.+.+.++.+.....-.. .++.|..+.||-+..+--++....
T Consensus 428 ~~~a~~N~~~~Pe~e~dsi~~~e~p~smnn-----ssm~~~~l~SP~slr~~d~~t~s~ 481 (769)
T KOG3755|consen 428 NLRAMQNFLILPEPERDSIYQDERPRSMNN-----SSMESLSLTSPKSLRGPDLKTFST 481 (769)
T ss_pred HHHHHHhhhcCCcccccccccccCcccccc-----cccccccccCCccCCccccccccc
No 269
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=24.44 E-value=1.5e+02 Score=22.57 Aligned_cols=26 Identities=19% Similarity=0.146 Sum_probs=23.3
Q ss_pred CCCCCCHHHHHHHHHHhCCChhhHhH
Q psy10107 28 KNPYPTKGEKIMLAIITKMTLTQVST 53 (140)
Q Consensus 28 ~nPYPs~~~k~~La~~tgLt~~QV~n 53 (140)
...|.+++..+.+|+.+|++..+|..
T Consensus 48 ~~GyIp~e~~~~iA~~l~v~~a~V~g 73 (169)
T PRK07571 48 LFGYLERDLLLYVARQLKLPLSRVYG 73 (169)
T ss_pred HcCCCCHHHHHHHHHHhCcCHHHHHH
Confidence 45799999999999999999999765
No 270
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=24.14 E-value=1.5e+02 Score=22.12 Aligned_cols=45 Identities=11% Similarity=0.034 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhh
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLK 63 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k 63 (140)
.|++..+++|+... ..| .-.++|+.++++...|.+-..|.-+|..
T Consensus 150 ~Lt~rE~evl~~~~-----~G~----s~~eIA~~l~iS~~TV~~h~~~i~~Kl~ 194 (216)
T PRK10840 150 RLSPKESEVLRLFA-----EGF----LVTEIAKKLNRSIKTISSQKKSAMMKLG 194 (216)
T ss_pred cCCHHHHHHHHHHH-----CCC----CHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 46666666665553 222 2356799999999999998777777754
No 271
>PHA02955 hypothetical protein; Provisional
Probab=24.12 E-value=1.4e+02 Score=23.94 Aligned_cols=47 Identities=13% Similarity=-0.071 Sum_probs=33.8
Q ss_pred HHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhh
Q psy10107 16 KATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKK 64 (140)
Q Consensus 16 ~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~ 64 (140)
...|-+-|.|-... -++++|.+++.++|+....|..||.+.=.|.-+
T Consensus 63 f~lli~a~~Et~~~--Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q~C~ 109 (213)
T PHA02955 63 FQLLIEALIETIEN--FPEKEQKEIAADIGINIDDYKAGKKTDLQLHCE 109 (213)
T ss_pred HHHHHHHHHHHHHh--CCHHHHHHHHHHhCCChhhccCcccchhhhhcc
Confidence 34444444444333 267999999999999998899999998877553
No 272
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=24.04 E-value=2.1e+02 Score=21.73 Aligned_cols=47 Identities=15% Similarity=0.147 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHH
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARR 60 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~ 60 (140)
.+++...++|..|..+|....+ .-.++|.+++++...|.+-+.+...
T Consensus 158 ~Lt~re~~~l~~~i~~~~~~g~----s~~eIA~~l~iS~~Tv~~~~~~~~~ 204 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAHQDYEF----STDELANAVNISRVSCRKYLIWLVN 204 (239)
T ss_pred CCCHHHHHHHHHHHHhCCCCCc----CHHHHHHHhCchHHHHHHHHHHHHh
Confidence 4677777777788766655554 4467999999999999998887743
No 273
>PHA00542 putative Cro-like protein
Probab=23.85 E-value=62 Score=21.36 Aligned_cols=24 Identities=8% Similarity=0.155 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 36 EKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
...+||+.+|++...|..|.....
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~ 56 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRH 56 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCC
Confidence 456799999999999999987663
No 274
>smart00595 MADF subfamily of SANT domain.
Probab=23.77 E-value=1.2e+02 Score=19.64 Aligned_cols=30 Identities=20% Similarity=0.258 Sum_probs=26.3
Q ss_pred HHHHHHhCCChhhHhHhhhhHHHhhhhccc
Q psy10107 38 IMLAIITKMTLTQVSTWFANARRRLKKENK 67 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nWF~N~R~R~k~~~~ 67 (140)
.+||.++|.+..+|..-+.|-|.+.+++.+
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~ 60 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELK 60 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 568999999999999999999999887754
No 275
>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=23.69 E-value=92 Score=18.01 Aligned_cols=40 Identities=8% Similarity=-0.077 Sum_probs=24.7
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhh
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWF 55 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF 55 (140)
+..+++++.+.+...+ .. . ....+||+.+|++...|-.++
T Consensus 3 p~~~~~~~~~~i~~l~---~~-G----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELY---AE-G----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSHCCHHHHHHHH---HT-T------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHH---HC-C----CCHHHHHHHHCcCHHHHHHHH
Confidence 3456665555554543 22 2 346889999999999998775
No 276
>PRK05949 RNA polymerase sigma factor; Validated
Probab=23.64 E-value=1.8e+02 Score=24.30 Aligned_cols=51 Identities=10% Similarity=-0.011 Sum_probs=36.6
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhc
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKE 65 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~ 65 (140)
+++..+.+|..-|.-+...+ ..-.++|..+|++...|......+++++|+.
T Consensus 267 L~~rer~Vi~lr~gl~~~e~----~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~~ 317 (327)
T PRK05949 267 LTPQQREVLTLRFGLEDGKE----LSLAKVGERLNLSRERVRQLEHQALAHLRRR 317 (327)
T ss_pred CCHHHHHHHHHHhccCCCCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 56666677665541111122 3567899999999999999999999998873
No 277
>PF07042 TrfA: TrfA protein; InterPro: IPR010751 This family consists of several bacterial TrfA proteins. The trfA operon of broad-host-range IncP plasmids is essential to activate the origin of vegetative replication in diverse species. The trfA operon encodes two ORFs. The first ORF is highly conserved and encodes a putative single-stranded DNA binding protein (Ssb). The second, trfA, contains two translational starts as in the IncP alpha plasmids, generating related polypeptides of 406 (TrfA1) and 282 (TrfA2) amino acids. TrfA2 is very similar to the IncP alpha product, whereas the N-terminal region of TrfA1 shows very little similarity to the equivalent region of IncP alpha TrfA1. This region has been implicated in the ability of IncP alpha plasmids to replicate efficiently in Pseudomonas aeruginosa [].
Probab=23.43 E-value=1.6e+02 Score=24.40 Aligned_cols=49 Identities=16% Similarity=0.239 Sum_probs=32.7
Q ss_pred CCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHH
Q psy10107 8 EYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANAR 59 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R 59 (140)
|..+......-|..+|..|. .|||-.-++-.. -+|-...++..|=++-+
T Consensus 208 R~~L~~~lA~wLh~yyaSH~-~P~P~kvetl~~--lcGS~~~~l~~FR~~Lk 256 (282)
T PF07042_consen 208 RRKLSPRLAKWLHGYYASHK-KPYPIKVETLRE--LCGSESSRLRKFRQQLK 256 (282)
T ss_pred HhhcCcHHHHHHHHHHhcCC-CCCCccHHHHHH--HcCCCccCHHHHHHHHH
Confidence 44455554566888888885 699987766544 46777778887755433
No 278
>PF13720 Acetyltransf_11: Udp N-acetylglucosamine O-acyltransferase; Domain 2; PDB: 3I3A_A 3I3X_A 3HSQ_B 2JF2_A 1LXA_A 2AQ9_A 2QIV_X 2QIA_A 2JF3_A 4EQY_F ....
Probab=23.25 E-value=79 Score=21.10 Aligned_cols=42 Identities=5% Similarity=-0.260 Sum_probs=29.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC
Q psy10107 5 MVPEYVGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKM 46 (140)
Q Consensus 5 ~~~R~~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL 46 (140)
+++|..|++++...|+..|..-...+.+-.+-..+|......
T Consensus 22 GLrR~Gfs~~~i~~l~~ayr~l~~~~~~~~~a~~~l~~~~~~ 63 (83)
T PF13720_consen 22 GLRRRGFSKEEISALRRAYRILFRSGLTLEEALEELEEEYPD 63 (83)
T ss_dssp HHHHTTS-HHHHHHHHHHHHHHHTSSS-HHHHHHHHHHHTTS
T ss_pred HHHHcCCCHHHHHHHHHHHHHHHhCCCCHHHHHHHHHHhccC
Confidence 457899999999999988866666676666666666654443
No 279
>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=22.64 E-value=72 Score=22.43 Aligned_cols=21 Identities=14% Similarity=0.091 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCChhhHhHhhh
Q psy10107 36 EKIMLAIITKMTLTQVSTWFA 56 (140)
Q Consensus 36 ~k~~La~~tgLt~~QV~nWF~ 56 (140)
...++|+..+++..-|.+||+
T Consensus 20 s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 20 SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred hHHHHHHHhCcHHHHHHHHHH
Confidence 467789999999999999999
No 280
>PF12949 HeH: HeH/LEM domain; PDB: 2OUT_A.
Probab=21.85 E-value=59 Score=18.53 Aligned_cols=28 Identities=32% Similarity=0.464 Sum_probs=17.3
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHH
Q psy10107 15 YKATLKAWLNEHKKNPYPTKGEKIMLAII 43 (140)
Q Consensus 15 ~~~~L~~w~~~h~~nPYPs~~~k~~La~~ 43 (140)
.+..|+.++.+|-- .||+.+.|.+|..-
T Consensus 5 tV~~Lk~iL~~~~I-~~ps~AkKaeLv~L 32 (35)
T PF12949_consen 5 TVAQLKRILDEHGI-EFPSNAKKAELVAL 32 (35)
T ss_dssp -SHHHHHHHHHHT----SSS--SHHHHHH
T ss_pred cHHHHHHHHHHcCC-CCCCCCCHHHHHHH
Confidence 35678888877754 89999999998754
No 281
>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=21.71 E-value=83 Score=20.91 Aligned_cols=17 Identities=18% Similarity=0.309 Sum_probs=15.8
Q ss_pred HHHHHHhCCChhhHhHh
Q psy10107 38 IMLAIITKMTLTQVSTW 54 (140)
Q Consensus 38 ~~La~~tgLt~~QV~nW 54 (140)
.++|+.+|++..+|..|
T Consensus 5 ~evA~~~gvs~~tLR~y 21 (88)
T cd01105 5 GEVSKLTGVSPRQLRYW 21 (88)
T ss_pred HHHHHHHCcCHHHHHHH
Confidence 57899999999999999
No 282
>PRK10026 arsenate reductase; Provisional
Probab=21.65 E-value=1.5e+02 Score=21.86 Aligned_cols=34 Identities=15% Similarity=0.263 Sum_probs=21.9
Q ss_pred HHHHHHHHhh---------cCCCCCCHHHHHHHHHHhCCChhhH
Q psy10107 17 ATLKAWLNEH---------KKNPYPTKGEKIMLAIITKMTLTQV 51 (140)
Q Consensus 17 ~~L~~w~~~h---------~~nPYPs~~~k~~La~~tgLt~~QV 51 (140)
+.-.+||.+| ...| ||.++-..+...+|+....+
T Consensus 16 RKA~~wL~~~gi~~~~~d~~~~p-pt~~eL~~~l~~~g~~~~~l 58 (141)
T PRK10026 16 RNTLEMIRNSGTEPTIIHYLETP-PTRDELVKLIADMGISVRAL 58 (141)
T ss_pred HHHHHHHHHCCCCcEEEeeeCCC-cCHHHHHHHHHhCCCCHHHH
Confidence 3345777666 2344 78888888888887654443
No 283
>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=21.50 E-value=87 Score=22.90 Aligned_cols=25 Identities=12% Similarity=-0.021 Sum_probs=20.0
Q ss_pred CCCCCHHHHHHHHHHhCCChhhHhH
Q psy10107 29 NPYPTKGEKIMLAIITKMTLTQVST 53 (140)
Q Consensus 29 nPYPs~~~k~~La~~tgLt~~QV~n 53 (140)
..|.+++.-..+|+.+|++..+|..
T Consensus 26 ~g~i~~~~~~~iA~~l~i~~~~v~~ 50 (145)
T PF01257_consen 26 YGYIPEEALEEIAEALGIPPAEVYG 50 (145)
T ss_dssp HSS--HHHHHHHHHHHTS-HHHHHH
T ss_pred cCCCCHHHHHHHHHHHCCCHHHHHH
Confidence 5799999999999999999999865
No 284
>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=21.36 E-value=2e+02 Score=21.23 Aligned_cols=34 Identities=15% Similarity=0.115 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHhCCCh-----hhHhHhhhhHHHhhhhc
Q psy10107 32 PTKGEKIMLAIITKMTL-----TQVSTWFANARRRLKKE 65 (140)
Q Consensus 32 Ps~~~k~~La~~tgLt~-----~QV~nWF~N~R~R~k~~ 65 (140)
.+.+.|.+||.++|.+- .+.++|+..+=++.-.+
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~kLA~ 121 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQKLAE 121 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHHHHGG
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHHHHHH
Confidence 47799999999999876 57888998877665444
No 285
>PF09179 TilS: TilS substrate binding domain; InterPro: IPR015262 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the substrate-binding domain of lysidine-tRNA(Ile) synthetase, which ligates lysine onto the cytidine present at position 34 of the AUA codon-specific tRNA(Ile) that contains the anticodon CAU, in an ATP-dependent manner. Cytidine is converted to lysidine, thus changing the amino acid specificity of the tRNA from methionine to isoleucine. The N-terminal region contains the highly conserved SGGXDS motif, predicted to be a PP-loop motif involved in ATP binding. The only examples in which the wobble position of a tRNA must discriminate between G and A of mRNA are AUA (Ile) versus AUG (Met) and UGA (stop) versus UGG (Trp). In all bacteria, the wobble position of the tRNA(Ile) recognizing AUA is lysidine, a lysine derivative of cytidine. This domain is found, apparently, in all bacteria in a single copy. Eukaryotic sequences appear to be organellar. The domain architecture of this protein is variable; some, including characterised proteins of Escherichia coli and Bacillus subtilis known to be tRNA(Ile)-lysidine synthetase, include a conserved 50-residue domain that many other members lack. This protein belongs to the ATP-binding PP-loop family. It appears in the literature and protein databases as TilS, YacA, and putative cell cycle protein MesJ (a misnomer). The PP-loop motif appears to be a modified version of the P-loop of nucleotide binding domain that is involved in phosphate binding []. Named PP-motif, since it appears to be a part of a previously uncharacterised ATP pyrophophatase domain. ATP sulfurylases, E. coli NtrL, and B. subtilis OutB consist of this domain alone. In other proteins, the pyrophosphatase domain is associated with amidotransferase domains (type I or type II), a putative citrulline-aspartate ligase domain or a nitrilase/amidase domain. The HUP domain class (after HIGH-signature proteins, UspA, and PP-ATPase) groups together PP-loop ATPases, the nucleotide-binding domains of class I aminoacyl-tRNA synthetases, UspA protein (USPA domains), photolyases, and electron transport flavoproteins (ETFP). The HUP domain is a distinct class of alpha/beta domain[]. More information about this protein can be found at Protein of the Month: ATP Synthases [].; GO: 0000166 nucleotide binding, 0005524 ATP binding, 0016879 ligase activity, forming carbon-nitrogen bonds, 0008033 tRNA processing, 0005737 cytoplasm; PDB: 1NI5_A 3A2K_A.
Probab=21.12 E-value=1.6e+02 Score=17.96 Aligned_cols=31 Identities=16% Similarity=0.282 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHh
Q psy10107 13 EIYKATLKAWLNEHKKNPYPTKGEKIMLAIIT 44 (140)
Q Consensus 13 ~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~t 44 (140)
..++.+|+.|+.++ ..+-|+...-+++...+
T Consensus 12 ~~q~~lLR~wL~~~-g~~~ps~~~l~~i~~~l 42 (69)
T PF09179_consen 12 ARQRRLLRRWLRQL-GLPMPSQAHLEQILRQL 42 (69)
T ss_dssp HHHHHHHHHHHHHT-T-T--HHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHC-CCCCCCHHHHHHHHHHH
Confidence 45688899999776 34667777777776655
No 286
>PF06918 DUF1280: Protein of unknown function (DUF1280); InterPro: IPR009689 This family represents a conserved region approximately 200 residues long within a number of proteins of unknown function that seem to be specific to Caenorhabditis elegans.
Probab=21.04 E-value=1.8e+02 Score=23.14 Aligned_cols=38 Identities=13% Similarity=0.202 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHHhh-cCCCCCCHHHHHHHHHHhC
Q psy10107 8 EYVGTEIYKATLKAWLNEH-KKNPYPTKGEKIMLAIITK 45 (140)
Q Consensus 8 R~~~~~~~~~~L~~w~~~h-~~nPYPs~~~k~~La~~tg 45 (140)
+.+|+..+...++.||.++ ...++|+......|.+..+
T Consensus 62 k~~LSd~~lk~~K~~~k~~lg~Dvf~Sr~~i~~l~k~~s 100 (224)
T PF06918_consen 62 KFNLSDGFLKKFKKFLKEFLGFDVFPSRKSIDELEKKVS 100 (224)
T ss_pred EecCCHHHHHHHHHHHHHhCCCCCCCCHHHHHHHHHhcC
Confidence 4578899999999999886 5699999999999877765
No 287
>PRK07406 RNA polymerase sigma factor RpoD; Validated
Probab=21.02 E-value=2.1e+02 Score=24.46 Aligned_cols=53 Identities=15% Similarity=0.072 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCCChhhHhHhhhhHHHhhhhcc
Q psy10107 10 VGTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITKMTLTQVSTWFANARRRLKKEN 66 (140)
Q Consensus 10 ~~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgLt~~QV~nWF~N~R~R~k~~~ 66 (140)
.++...+.+|...|..+...+ ..-.+||..+|++...|..=-..+.+|+|...
T Consensus 311 ~L~~rEr~IL~lrygl~~~~~----~Tl~EIA~~lgiS~eRVRQie~rAL~KLR~~~ 363 (373)
T PRK07406 311 TLSPRERDVLRLRYGLDDGRM----KTLEEIGQIFNVTRERIRQIEAKALRKLRHPN 363 (373)
T ss_pred cCCHHHHHHHHHHHhcCCCCC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHhchh
Confidence 477778888877662211222 34688999999999999999888888888653
No 288
>PF14053 DUF4248: Domain of unknown function (DUF4248)
Probab=20.97 E-value=1.7e+02 Score=18.99 Aligned_cols=35 Identities=26% Similarity=0.319 Sum_probs=23.9
Q ss_pred CCHHHHHHHHHHHHhhcCCCCCCHHHHHHHHHHhC-------CChhhHhH
Q psy10107 11 GTEIYKATLKAWLNEHKKNPYPTKGEKIMLAIITK-------MTLTQVST 53 (140)
Q Consensus 11 ~~~~~~~~L~~w~~~h~~nPYPs~~~k~~La~~tg-------Lt~~QV~n 53 (140)
-+..+++.|+.|. ..|| +-.++|.. +| +|+.||..
T Consensus 20 ~~~sA~r~L~rwI---~~~~----~L~~~L~~-~Gy~~~~r~~TP~QV~l 61 (69)
T PF14053_consen 20 TPSSAVRKLRRWI---RRNP----ELLEELEA-TGYHPRQRSFTPRQVRL 61 (69)
T ss_pred CHHHHHHHHHHHH---HHCH----HHHHHHHH-cCCCCCCEecCHHHHHH
Confidence 3466789999999 6666 66666643 33 67777765
No 289
>PRK01844 hypothetical protein; Provisional
Probab=20.63 E-value=2.4e+02 Score=18.80 Aligned_cols=36 Identities=14% Similarity=0.206 Sum_probs=27.8
Q ss_pred HHHHHHHHHHhhcCCCCCCHHHHHHHHHHhCC--ChhhHhH
Q psy10107 15 YKATLKAWLNEHKKNPYPTKGEKIMLAIITKM--TLTQVST 53 (140)
Q Consensus 15 ~~~~L~~w~~~h~~nPYPs~~~k~~La~~tgL--t~~QV~n 53 (140)
++..++.+| .+||=.+++.-+.+..+-|- +++||+.
T Consensus 25 ark~~~k~l---k~NPpine~mir~Mm~QMGqkPSekki~Q 62 (72)
T PRK01844 25 ARKYMMNYL---QKNPPINEQMLKMMMMQMGQKPSQKKINQ 62 (72)
T ss_pred HHHHHHHHH---HHCCCCCHHHHHHHHHHhCCCccHHHHHH
Confidence 356677777 99998999999999999986 4455543
No 290
>PF05589 DUF768: Protein of unknown function (DUF768); InterPro: IPR008486 This family consists of several uncharacterised hypothetical proteins from Rhizobium loti (Mesorhizobium loti).
Probab=20.31 E-value=2.5e+02 Score=18.13 Aligned_cols=17 Identities=18% Similarity=0.305 Sum_probs=13.4
Q ss_pred CHHHHHHHHHHHHhhcC
Q psy10107 12 TEIYKATLKAWLNEHKK 28 (140)
Q Consensus 12 ~~~~~~~L~~w~~~h~~ 28 (140)
+....+.|..|..+|..
T Consensus 2 S~r~~~Fl~~WI~e~V~ 18 (64)
T PF05589_consen 2 STRGIEFLDSWIAENVP 18 (64)
T ss_pred cchHHHHHHHHHHhcCC
Confidence 45567899999999863
Done!