Query psy3429
Match_columns 192
No_of_seqs 200 out of 1230
Neff 7.1
Searched_HMMs 46136
Date Sat Aug 17 00:49:42 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3429.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3429hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0492|consensus 99.9 4.3E-22 9.3E-27 160.3 9.0 84 30-113 133-216 (246)
2 KOG0488|consensus 99.9 3.3E-22 7.2E-27 172.6 8.6 71 35-105 166-236 (309)
3 KOG0484|consensus 99.9 6.8E-22 1.5E-26 143.3 5.4 74 34-107 10-83 (125)
4 KOG0489|consensus 99.8 7.6E-22 1.6E-26 167.1 5.6 67 38-104 156-222 (261)
5 KOG0485|consensus 99.8 2.4E-20 5.2E-25 151.2 12.3 74 38-111 101-174 (268)
6 KOG0494|consensus 99.8 7.5E-21 1.6E-25 157.6 7.3 80 32-111 132-211 (332)
7 KOG0842|consensus 99.8 2.7E-20 5.9E-25 159.2 10.5 68 37-104 149-216 (307)
8 KOG0487|consensus 99.8 1.8E-20 4E-25 160.3 5.7 67 38-104 232-298 (308)
9 KOG0850|consensus 99.8 4E-20 8.6E-25 151.0 7.3 73 29-101 110-182 (245)
10 KOG0843|consensus 99.8 6.6E-20 1.4E-24 144.8 6.3 64 40-103 101-164 (197)
11 KOG2251|consensus 99.8 1.6E-19 3.4E-24 146.8 5.1 68 36-103 32-99 (228)
12 KOG0848|consensus 99.8 2.3E-19 5E-24 149.3 4.7 69 36-104 194-262 (317)
13 PF00046 Homeobox: Homeobox do 99.8 1.8E-18 3.9E-23 113.6 7.0 57 42-98 1-57 (57)
14 KOG0491|consensus 99.8 2.2E-19 4.7E-24 140.0 2.7 96 9-104 57-163 (194)
15 KOG0493|consensus 99.7 1.5E-17 3.3E-22 138.2 6.6 59 42-100 247-305 (342)
16 TIGR01565 homeo_ZF_HD homeobox 99.7 2.3E-17 4.9E-22 109.1 4.0 53 41-93 1-57 (58)
17 KOG0844|consensus 99.7 1.8E-17 3.9E-22 140.3 2.9 66 37-102 177-242 (408)
18 KOG0486|consensus 99.7 6.5E-17 1.4E-21 137.3 5.5 66 39-104 110-175 (351)
19 smart00389 HOX Homeodomain. DN 99.7 2.4E-16 5.3E-21 102.7 6.1 56 42-97 1-56 (56)
20 cd00086 homeodomain Homeodomai 99.7 4.1E-16 8.9E-21 102.3 7.1 57 42-98 1-57 (59)
21 KOG3802|consensus 99.6 3.3E-16 7.2E-21 137.0 1.9 71 31-101 284-354 (398)
22 KOG0483|consensus 99.6 1.3E-15 2.7E-20 123.8 4.8 61 41-101 50-110 (198)
23 KOG4577|consensus 99.5 2.5E-14 5.3E-19 120.6 9.9 68 36-103 162-229 (383)
24 COG5576 Homeodomain-containing 99.5 6.6E-15 1.4E-19 115.7 5.7 68 36-103 46-113 (156)
25 KOG0847|consensus 99.5 8.2E-15 1.8E-19 119.3 3.9 68 36-103 162-229 (288)
26 KOG0490|consensus 99.4 1.1E-13 2.4E-18 113.8 4.1 64 38-101 57-120 (235)
27 KOG0849|consensus 99.4 1.8E-12 3.9E-17 114.2 8.4 73 30-102 165-237 (354)
28 KOG1168|consensus 99.2 2.7E-12 5.9E-17 108.4 1.0 63 38-100 306-368 (385)
29 KOG0775|consensus 99.1 9.2E-11 2E-15 98.5 5.8 51 48-98 183-233 (304)
30 KOG0774|consensus 99.0 8.2E-10 1.8E-14 92.3 7.9 61 42-102 189-252 (334)
31 PF05920 Homeobox_KN: Homeobox 98.8 6.8E-09 1.5E-13 63.7 3.6 34 62-95 7-40 (40)
32 KOG2252|consensus 98.7 3.6E-08 7.8E-13 89.8 6.6 59 38-96 417-475 (558)
33 KOG0490|consensus 98.4 4.6E-07 1E-11 74.4 5.0 68 34-101 146-213 (235)
34 KOG1146|consensus 98.0 8.1E-06 1.8E-10 80.9 6.0 63 40-102 902-964 (1406)
35 PF11569 Homez: Homeodomain le 97.5 9.4E-05 2E-09 48.4 3.0 41 53-93 10-50 (56)
36 KOG0773|consensus 97.3 0.00017 3.8E-09 63.1 2.9 62 41-102 239-303 (342)
37 KOG3623|consensus 96.3 0.0068 1.5E-07 57.8 5.3 48 53-100 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 96.0 0.016 3.5E-07 37.3 4.7 47 42-93 1-47 (53)
39 KOG1924|consensus 95.9 0.09 1.9E-06 50.8 10.9 12 166-177 570-581 (1102)
40 PF04545 Sigma70_r4: Sigma-70, 92.7 0.42 9.1E-06 29.8 5.2 46 47-97 4-49 (50)
41 cd06171 Sigma70_r4 Sigma70, re 87.9 0.84 1.8E-05 27.5 3.4 44 47-95 10-53 (55)
42 PRK03975 tfx putative transcri 87.6 2.6 5.6E-05 32.7 6.6 51 45-101 4-54 (141)
43 KOG3755|consensus 87.3 1.2 2.5E-05 42.2 5.2 21 80-100 738-758 (769)
44 PF01527 HTH_Tnp_1: Transposas 86.3 0.95 2.1E-05 30.3 3.2 46 43-92 2-47 (76)
45 PF08281 Sigma70_r4_2: Sigma-7 85.3 3.2 6.9E-05 25.9 5.2 43 48-95 11-53 (54)
46 PF00196 GerE: Bacterial regul 83.7 3.3 7.2E-05 26.4 4.8 46 47-98 3-48 (58)
47 PRK04217 hypothetical protein; 81.8 6.1 0.00013 29.3 6.1 48 46-98 41-88 (110)
48 cd00569 HTH_Hin_like Helix-tur 81.0 4.8 0.0001 21.4 4.3 38 47-89 5-42 (42)
49 KOG1146|consensus 80.0 3.8 8.3E-05 42.0 5.7 60 41-100 705-764 (1406)
50 PF10668 Phage_terminase: Phag 79.6 1.6 3.4E-05 29.0 2.0 21 70-90 24-44 (60)
51 PF09607 BrkDBD: Brinker DNA-b 79.0 6.3 0.00014 25.9 4.7 45 45-90 3-47 (58)
52 PF04967 HTH_10: HTH DNA bindi 78.8 6.7 0.00015 25.2 4.8 42 48-89 1-44 (53)
53 PRK09646 RNA polymerase sigma 78.7 4.9 0.00011 31.8 5.1 49 47-100 142-190 (194)
54 smart00421 HTH_LUXR helix_turn 78.0 9.4 0.0002 23.1 5.4 43 47-95 3-45 (58)
55 PRK12526 RNA polymerase sigma 77.7 6.9 0.00015 31.4 5.8 32 69-100 170-201 (206)
56 PRK09642 RNA polymerase sigma 76.2 10 0.00022 28.8 6.1 31 70-100 124-154 (160)
57 COG4367 Uncharacterized protei 76.2 4.6 9.9E-05 28.9 3.7 41 47-87 2-42 (97)
58 PRK11924 RNA polymerase sigma 76.1 5.9 0.00013 30.2 4.8 33 69-101 142-174 (179)
59 PRK06759 RNA polymerase factor 76.1 9.4 0.0002 28.6 5.9 46 48-98 107-152 (154)
60 PRK12519 RNA polymerase sigma 75.5 4.9 0.00011 31.6 4.3 34 67-100 156-189 (194)
61 KOG3671|consensus 75.4 9.3 0.0002 35.5 6.4 27 165-191 410-436 (569)
62 PRK09639 RNA polymerase sigma 74.8 10 0.00022 28.8 5.8 48 48-101 113-160 (166)
63 TIGR00721 tfx DNA-binding prot 74.7 20 0.00044 27.6 7.3 48 45-98 4-51 (137)
64 PRK12514 RNA polymerase sigma 74.6 5.3 0.00012 31.0 4.2 31 69-99 146-176 (179)
65 TIGR03879 near_KaiC_dom probab 74.6 1.7 3.8E-05 29.9 1.2 35 57-91 21-55 (73)
66 PRK09652 RNA polymerase sigma 73.7 8 0.00017 29.6 5.0 49 47-100 128-176 (182)
67 PRK09644 RNA polymerase sigma 73.4 12 0.00026 28.6 5.9 33 69-101 125-157 (165)
68 TIGR02937 sigma70-ECF RNA poly 73.0 10 0.00022 27.5 5.2 46 48-98 111-156 (158)
69 PRK12530 RNA polymerase sigma 72.9 15 0.00032 29.0 6.4 49 48-101 135-183 (189)
70 PRK00118 putative DNA-binding 72.8 11 0.00025 27.6 5.3 48 48-100 18-65 (104)
71 PRK12543 RNA polymerase sigma 72.4 21 0.00045 27.8 7.1 38 69-106 134-171 (179)
72 PRK09413 IS2 repressor TnpA; R 71.9 9.5 0.00021 28.3 4.8 43 45-91 10-52 (121)
73 PRK12515 RNA polymerase sigma 71.3 16 0.00034 28.6 6.3 50 47-101 131-180 (189)
74 TIGR02959 SigZ RNA polymerase 71.2 16 0.00035 28.2 6.2 49 47-100 100-148 (170)
75 PF13936 HTH_38: Helix-turn-he 71.1 7 0.00015 23.8 3.3 40 46-90 3-42 (44)
76 TIGR02948 SigW_bacill RNA poly 69.7 14 0.00031 28.5 5.7 47 48-99 137-183 (187)
77 PRK12512 RNA polymerase sigma 69.6 13 0.00027 29.0 5.3 48 48-100 132-179 (184)
78 PF08280 HTH_Mga: M protein tr 69.4 11 0.00024 24.3 4.1 36 51-90 6-41 (59)
79 PRK05602 RNA polymerase sigma 69.2 15 0.00033 28.6 5.8 32 69-100 145-176 (186)
80 PRK12538 RNA polymerase sigma 68.9 17 0.00038 30.0 6.3 33 69-101 188-220 (233)
81 PRK09648 RNA polymerase sigma 68.6 13 0.00027 29.2 5.2 48 47-99 139-186 (189)
82 TIGR02985 Sig70_bacteroi1 RNA 68.5 17 0.00038 27.0 5.8 30 69-98 130-159 (161)
83 TIGR02939 RpoE_Sigma70 RNA pol 68.4 13 0.00028 28.9 5.2 36 65-100 151-186 (190)
84 cd04761 HTH_MerR-SF Helix-Turn 68.3 5.4 0.00012 24.0 2.4 21 71-91 3-23 (49)
85 cd06170 LuxR_C_like C-terminal 68.1 16 0.00035 22.1 4.7 38 49-92 2-39 (57)
86 PF13443 HTH_26: Cro/C1-type H 68.0 9.5 0.0002 24.4 3.6 28 70-97 12-39 (63)
87 PRK06930 positive control sigm 67.8 20 0.00043 28.4 6.1 50 47-101 114-163 (170)
88 PRK12545 RNA polymerase sigma 67.3 20 0.00043 28.6 6.1 33 69-101 156-188 (201)
89 TIGR02999 Sig-70_X6 RNA polyme 66.9 18 0.0004 27.9 5.7 46 48-98 135-180 (183)
90 TIGR02989 Sig-70_gvs1 RNA poly 66.8 16 0.00035 27.4 5.3 45 48-97 112-156 (159)
91 PRK12532 RNA polymerase sigma 66.3 22 0.00048 27.9 6.2 33 70-102 154-186 (195)
92 PRK06986 fliA flagellar biosyn 66.2 16 0.00035 29.9 5.6 48 48-100 185-232 (236)
93 PRK05657 RNA polymerase sigma 66.0 17 0.00036 31.8 5.8 53 47-100 262-314 (325)
94 PRK09047 RNA polymerase factor 65.6 29 0.00063 26.0 6.5 48 48-100 107-154 (161)
95 PRK09647 RNA polymerase sigma 65.5 23 0.0005 28.5 6.2 33 69-101 155-187 (203)
96 TIGR02943 Sig70_famx1 RNA poly 64.7 28 0.00061 27.4 6.5 50 48-102 132-181 (188)
97 TIGR02983 SigE-fam_strep RNA p 64.4 15 0.00033 27.8 4.7 46 49-99 112-157 (162)
98 PRK12541 RNA polymerase sigma 64.1 17 0.00037 27.5 5.0 31 69-99 129-159 (161)
99 PRK10403 transcriptional regul 63.9 12 0.00026 28.6 4.2 52 46-103 152-203 (215)
100 TIGR03001 Sig-70_gmx1 RNA poly 63.5 28 0.00061 29.0 6.5 35 69-103 178-212 (244)
101 PRK09637 RNA polymerase sigma 63.4 26 0.00056 27.4 6.1 31 68-98 122-152 (181)
102 PRK12524 RNA polymerase sigma 63.4 26 0.00056 27.7 6.1 32 69-100 153-184 (196)
103 smart00027 EH Eps15 homology d 63.3 22 0.00048 24.9 5.1 44 47-90 3-51 (96)
104 PRK10072 putative transcriptio 63.1 11 0.00024 27.2 3.5 40 48-94 33-72 (96)
105 PRK08301 sporulation sigma fac 62.7 21 0.00045 29.1 5.5 52 47-99 178-229 (234)
106 PRK12537 RNA polymerase sigma 62.7 23 0.0005 27.5 5.6 30 69-98 150-179 (182)
107 PF13518 HTH_28: Helix-turn-he 62.4 11 0.00023 23.0 3.0 24 70-93 14-37 (52)
108 PRK12518 RNA polymerase sigma 62.3 12 0.00026 28.7 3.9 36 65-100 133-168 (175)
109 KOG0773|consensus 62.1 12 0.00027 32.5 4.3 41 58-98 114-154 (342)
110 PRK12546 RNA polymerase sigma 61.7 23 0.0005 28.0 5.5 32 69-100 130-161 (188)
111 PRK08295 RNA polymerase factor 61.7 30 0.00066 27.2 6.2 33 67-99 169-201 (208)
112 PRK12533 RNA polymerase sigma 61.6 18 0.00039 29.5 5.0 32 69-100 151-182 (216)
113 PRK12516 RNA polymerase sigma 61.4 30 0.00065 27.3 6.1 32 70-101 134-165 (187)
114 TIGR02479 FliA_WhiG RNA polyme 60.9 24 0.00052 28.6 5.6 47 47-98 175-221 (224)
115 TIGR02954 Sig70_famx3 RNA poly 60.6 21 0.00046 27.3 5.0 47 48-99 120-166 (169)
116 TIGR02952 Sig70_famx2 RNA poly 60.5 22 0.00048 26.9 5.0 30 69-98 139-168 (170)
117 PRK15369 two component system 60.4 21 0.00045 26.9 4.9 46 46-97 148-193 (211)
118 PRK12547 RNA polymerase sigma 60.3 31 0.00067 26.3 5.9 47 48-99 113-159 (164)
119 PRK12520 RNA polymerase sigma 60.2 38 0.00083 26.5 6.5 51 48-103 132-182 (191)
120 PRK13919 putative RNA polymera 60.1 17 0.00036 28.3 4.4 46 48-98 136-181 (186)
121 PRK09645 RNA polymerase sigma 59.9 30 0.00065 26.4 5.8 47 48-99 119-165 (173)
122 PRK06811 RNA polymerase factor 59.9 21 0.00045 28.0 4.9 47 47-98 131-177 (189)
123 PRK07037 extracytoplasmic-func 59.8 34 0.00074 25.8 6.0 31 69-99 126-156 (163)
124 PRK11923 algU RNA polymerase s 59.8 18 0.00038 28.4 4.5 36 66-101 152-187 (193)
125 TIGR02393 RpoD_Cterm RNA polym 59.7 28 0.00062 28.6 5.9 53 47-100 176-228 (238)
126 PRK12544 RNA polymerase sigma 59.4 39 0.00085 27.2 6.6 49 48-101 149-197 (206)
127 TIGR02941 Sigma_B RNA polymera 59.1 24 0.00053 29.2 5.4 47 47-98 205-251 (255)
128 COG3413 Predicted DNA binding 59.1 20 0.00044 29.1 4.8 43 47-89 155-199 (215)
129 TIGR03020 EpsA transcriptional 59.0 22 0.00048 30.0 5.1 52 45-102 188-239 (247)
130 PRK10360 DNA-binding transcrip 58.8 18 0.00039 27.5 4.3 45 47-97 137-181 (196)
131 TIGR02859 spore_sigH RNA polym 58.6 31 0.00067 26.9 5.7 34 65-98 162-195 (198)
132 PRK12513 RNA polymerase sigma 58.3 17 0.00038 28.5 4.2 36 65-100 152-187 (194)
133 PRK08583 RNA polymerase sigma 58.2 20 0.00043 29.8 4.7 48 47-99 205-252 (257)
134 PRK12531 RNA polymerase sigma 58.2 33 0.00072 27.0 5.9 32 69-100 158-189 (194)
135 PRK07408 RNA polymerase sigma 57.7 19 0.00041 30.1 4.5 49 47-100 203-251 (256)
136 PRK07670 RNA polymerase sigma 57.5 21 0.00046 29.6 4.8 47 48-99 202-248 (251)
137 TIGR02947 SigH_actino RNA poly 57.0 21 0.00046 28.0 4.5 37 65-101 144-180 (193)
138 TIGR03541 reg_near_HchA LuxR f 56.7 27 0.00058 28.8 5.2 53 45-103 169-221 (232)
139 PRK07500 rpoH2 RNA polymerase 56.6 25 0.00053 30.1 5.1 51 47-100 227-277 (289)
140 PF13551 HTH_29: Winged helix- 56.6 65 0.0014 22.4 6.8 48 43-90 53-109 (112)
141 PRK10100 DNA-binding transcrip 56.5 30 0.00065 28.3 5.4 51 47-103 155-205 (216)
142 TIGR02950 SigM_subfam RNA poly 56.5 17 0.00036 27.2 3.7 34 65-98 118-151 (154)
143 PRK12523 RNA polymerase sigma 56.3 37 0.0008 26.1 5.7 31 69-99 136-166 (172)
144 PRK12539 RNA polymerase sigma 56.3 37 0.0008 26.4 5.8 47 48-99 132-178 (184)
145 PRK10651 transcriptional regul 56.1 27 0.00059 26.7 5.0 50 47-102 155-204 (216)
146 PRK12536 RNA polymerase sigma 56.1 37 0.0008 26.4 5.7 34 66-99 143-176 (181)
147 cd04762 HTH_MerR-trunc Helix-T 55.7 13 0.00028 21.8 2.4 23 71-93 3-25 (49)
148 PF12824 MRP-L20: Mitochondria 55.5 79 0.0017 25.0 7.5 47 45-93 83-129 (164)
149 PF13384 HTH_23: Homeodomain-l 55.1 12 0.00025 22.8 2.2 23 69-91 18-40 (50)
150 PRK09935 transcriptional regul 54.8 22 0.00047 27.2 4.2 47 46-98 148-194 (210)
151 TIGR02394 rpoS_proteo RNA poly 54.6 47 0.001 28.1 6.5 54 47-101 222-275 (285)
152 PRK09641 RNA polymerase sigma 54.3 26 0.00057 27.0 4.6 33 67-99 151-183 (187)
153 PRK05803 sporulation sigma fac 54.3 39 0.00085 27.6 5.8 52 47-99 175-226 (233)
154 PRK12511 RNA polymerase sigma 53.9 46 0.001 26.1 6.0 48 48-100 112-159 (182)
155 PRK06288 RNA polymerase sigma 53.8 30 0.00065 29.0 5.1 49 47-100 212-260 (268)
156 PRK12529 RNA polymerase sigma 53.7 42 0.00092 26.0 5.7 47 47-98 127-173 (178)
157 cd00131 PAX Paired Box domain 53.7 89 0.0019 23.4 7.3 46 47-92 75-127 (128)
158 cd01392 HTH_LacI Helix-turn-he 53.0 20 0.00044 21.8 3.1 21 73-93 2-22 (52)
159 PF13411 MerR_1: MerR HTH fami 52.6 14 0.0003 24.0 2.4 20 71-90 3-22 (69)
160 TIGR02392 rpoH_proteo alternat 52.3 31 0.00068 29.0 5.0 50 47-99 218-267 (270)
161 PRK09649 RNA polymerase sigma 52.3 38 0.00083 26.5 5.3 30 69-98 147-176 (185)
162 PRK09640 RNA polymerase sigma 51.9 25 0.00054 27.5 4.1 35 66-100 148-182 (188)
163 PRK07122 RNA polymerase sigma 51.7 28 0.00061 29.3 4.7 48 47-99 215-262 (264)
164 PF06056 Terminase_5: Putative 51.3 13 0.00028 24.2 2.0 27 70-98 15-41 (58)
165 PRK12535 RNA polymerase sigma 51.2 45 0.00097 26.5 5.6 31 70-100 151-181 (196)
166 PRK12522 RNA polymerase sigma 50.8 29 0.00064 26.6 4.3 32 69-100 136-167 (173)
167 PRK12542 RNA polymerase sigma 49.9 54 0.0012 25.4 5.8 32 69-100 139-170 (185)
168 TIGR02980 SigBFG RNA polymeras 49.8 34 0.00075 27.6 4.8 47 47-98 178-224 (227)
169 cd04763 HTH_MlrA-like Helix-Tu 49.7 17 0.00037 23.7 2.4 21 71-91 3-23 (68)
170 PRK12534 RNA polymerase sigma 49.6 27 0.00059 27.1 4.0 32 67-98 152-183 (187)
171 PRK12540 RNA polymerase sigma 49.2 60 0.0013 25.4 6.0 32 69-100 128-159 (182)
172 PRK05911 RNA polymerase sigma 49.2 37 0.00081 28.4 5.0 49 47-100 205-253 (257)
173 PF00424 REV: REV protein (ant 49.2 25 0.00055 25.2 3.3 35 54-102 15-49 (91)
174 PRK09643 RNA polymerase sigma 48.9 64 0.0014 25.4 6.1 30 69-98 151-180 (192)
175 PRK09390 fixJ response regulat 48.7 50 0.0011 24.6 5.3 33 71-103 159-191 (202)
176 PF00376 MerR: MerR family reg 48.7 18 0.00039 21.4 2.2 19 71-89 2-20 (38)
177 PRK11922 RNA polymerase sigma 48.0 30 0.00065 28.2 4.2 37 65-101 162-198 (231)
178 PRK12517 RNA polymerase sigma 48.0 90 0.002 24.5 6.8 35 69-103 145-179 (188)
179 PF12200 DUF3597: Domain of un 47.9 30 0.00064 26.4 3.7 29 66-94 83-116 (127)
180 cd01104 HTH_MlrA-CarA Helix-Tu 47.6 19 0.00042 23.2 2.4 20 71-90 3-22 (68)
181 TIGR02835 spore_sigmaE RNA pol 47.3 59 0.0013 26.6 5.8 52 47-99 178-229 (234)
182 TIGR02885 spore_sigF RNA polym 46.9 45 0.00097 27.1 5.1 46 47-97 183-228 (231)
183 PRK09480 slmA division inhibit 46.8 23 0.0005 27.3 3.2 41 53-94 13-56 (194)
184 PRK08215 sporulation sigma fac 46.1 45 0.00098 27.7 5.0 47 47-98 209-255 (258)
185 cd04764 HTH_MlrA-like_sg1 Heli 46.0 21 0.00046 23.1 2.5 21 71-91 3-23 (67)
186 PF15063 TC1: Thyroid cancer p 45.9 43 0.00092 23.3 3.9 38 45-82 31-68 (79)
187 PRK09651 RNA polymerase sigma 45.8 62 0.0013 24.9 5.5 31 68-98 135-165 (172)
188 PLN03162 golden-2 like transcr 45.5 2.4E+02 0.0052 25.7 12.2 65 40-104 232-298 (526)
189 PF07638 Sigma70_ECF: ECF sigm 45.4 62 0.0014 25.5 5.5 30 69-98 152-181 (185)
190 PTZ00183 centrin; Provisional 45.1 1.1E+02 0.0024 22.5 6.7 42 39-80 2-48 (158)
191 COG2963 Transposase and inacti 45.1 74 0.0016 22.9 5.5 44 45-92 5-49 (116)
192 PF01381 HTH_3: Helix-turn-hel 44.9 14 0.00031 22.7 1.4 23 71-93 12-34 (55)
193 TIGR02957 SigX4 RNA polymerase 44.7 56 0.0012 27.6 5.5 29 71-99 127-155 (281)
194 PRK12527 RNA polymerase sigma 44.3 92 0.002 23.4 6.2 31 69-99 122-152 (159)
195 PRK09636 RNA polymerase sigma 44.3 59 0.0013 27.5 5.5 30 70-99 133-162 (293)
196 COG2944 Predicted transcriptio 44.1 29 0.00063 25.5 3.1 40 48-94 44-83 (104)
197 PF13412 HTH_24: Winged helix- 44.1 53 0.0011 19.7 3.9 38 49-90 2-39 (48)
198 PRK12528 RNA polymerase sigma 43.6 70 0.0015 24.1 5.4 26 70-95 131-156 (161)
199 COG1595 RpoE DNA-directed RNA 43.5 38 0.00082 26.3 4.0 33 69-101 144-176 (182)
200 TIGR02984 Sig-70_plancto1 RNA 43.2 50 0.0011 25.4 4.6 47 47-98 140-186 (189)
201 TIGR02846 spore_sigmaK RNA pol 43.1 73 0.0016 25.9 5.8 51 47-98 174-224 (227)
202 PRK09638 RNA polymerase sigma 42.7 35 0.00075 26.1 3.6 34 65-98 139-172 (176)
203 smart00595 MADF subfamily of S 42.5 66 0.0014 21.8 4.7 32 72-103 31-62 (89)
204 PRK12525 RNA polymerase sigma 42.2 75 0.0016 24.2 5.4 45 48-97 119-163 (168)
205 PRK06424 transcription factor; 42.1 21 0.00045 27.7 2.2 24 71-94 100-123 (144)
206 PRK06596 RNA polymerase factor 42.1 63 0.0014 27.5 5.4 49 47-98 230-278 (284)
207 PF08279 HTH_11: HTH domain; 42.1 50 0.0011 20.3 3.7 35 52-89 2-36 (55)
208 PRK05572 sporulation sigma fac 41.5 60 0.0013 26.9 5.1 48 46-98 201-248 (252)
209 TIGR03070 couple_hipB transcri 41.5 17 0.00037 22.2 1.4 23 71-93 18-40 (58)
210 cd00093 HTH_XRE Helix-turn-hel 41.3 20 0.00043 20.8 1.7 23 71-93 15-37 (58)
211 PRK11511 DNA-binding transcrip 40.9 46 0.00099 24.7 3.9 28 65-92 22-49 (127)
212 PF10078 DUF2316: Uncharacteri 40.1 23 0.0005 25.3 2.0 38 48-89 3-44 (89)
213 TIGR01764 excise DNA binding d 39.8 33 0.00072 20.1 2.5 22 71-92 4-25 (49)
214 TIGR02960 SigX5 RNA polymerase 39.6 70 0.0015 27.2 5.3 31 70-100 160-190 (324)
215 COG1905 NuoE NADH:ubiquinone o 39.6 53 0.0012 26.0 4.2 37 50-86 25-61 (160)
216 PRK10188 DNA-binding transcrip 39.0 85 0.0018 26.0 5.6 53 45-103 177-229 (240)
217 TIGR01557 myb_SHAQKYF myb-like 38.3 1.1E+02 0.0024 19.8 5.5 51 44-94 2-55 (57)
218 PF13565 HTH_32: Homeodomain-l 38.2 1.1E+02 0.0025 19.9 6.1 40 49-88 32-76 (77)
219 PRK09958 DNA-binding transcrip 38.1 69 0.0015 24.4 4.7 45 47-97 143-187 (204)
220 PF02796 HTH_7: Helix-turn-hel 37.9 67 0.0014 19.3 3.6 38 47-89 5-42 (45)
221 PRK09415 RNA polymerase factor 37.2 49 0.0011 25.6 3.7 30 70-99 145-174 (179)
222 KOG1923|consensus 36.9 51 0.0011 32.4 4.3 19 71-89 205-223 (830)
223 PRK10430 DNA-binding transcrip 36.5 57 0.0012 26.3 4.1 44 47-91 158-201 (239)
224 PF13730 HTH_36: Helix-turn-he 36.3 48 0.001 20.4 2.9 43 48-91 3-48 (55)
225 PF07022 Phage_CI_repr: Bacter 36.2 38 0.00081 22.2 2.5 21 71-91 15-36 (66)
226 PRK15411 rcsA colanic acid cap 35.9 93 0.002 25.0 5.2 45 47-97 137-181 (207)
227 PHA01976 helix-turn-helix prot 35.6 28 0.0006 22.4 1.7 23 71-93 18-40 (67)
228 TIGR02607 antidote_HigA addict 35.3 28 0.0006 23.1 1.7 23 71-93 21-43 (78)
229 PF03672 UPF0154: Uncharacteri 35.3 1.1E+02 0.0023 20.6 4.4 35 53-87 19-55 (64)
230 PHA02955 hypothetical protein; 35.0 45 0.00097 27.7 3.2 46 50-95 60-106 (213)
231 PRK06704 RNA polymerase factor 34.8 60 0.0013 26.9 4.0 31 70-100 134-164 (228)
232 PF04297 UPF0122: Putative hel 34.8 1.7E+02 0.0036 21.4 5.8 47 47-98 17-63 (101)
233 PF12728 HTH_17: Helix-turn-he 34.8 42 0.00091 20.4 2.4 22 71-92 4-25 (51)
234 PRK10840 transcriptional regul 34.7 96 0.0021 24.4 5.1 44 47-96 150-193 (216)
235 PRK07405 RNA polymerase sigma 34.4 1.1E+02 0.0024 26.5 5.7 52 47-99 256-307 (317)
236 PF05703 Auxin_canalis: Auxin 34.4 1.1E+02 0.0023 26.0 5.4 18 81-98 99-116 (242)
237 PRK05988 formate dehydrogenase 34.2 81 0.0017 24.6 4.4 36 51-86 24-59 (156)
238 PRK09483 response regulator; P 33.5 1.1E+02 0.0023 23.5 5.1 45 46-96 147-191 (217)
239 smart00422 HTH_MERR helix_turn 32.8 40 0.00086 21.7 2.2 20 71-90 3-22 (70)
240 PF01726 LexA_DNA_bind: LexA D 32.7 1E+02 0.0022 20.4 4.1 41 47-89 3-47 (65)
241 PF06971 Put_DNA-bind_N: Putat 32.6 34 0.00074 21.7 1.7 17 71-87 31-47 (50)
242 PRK11552 putative DNA-binding 32.6 59 0.0013 26.4 3.6 39 57-97 23-61 (225)
243 PRK13870 transcriptional regul 32.4 1.2E+02 0.0026 25.1 5.4 33 71-103 191-223 (234)
244 PF03457 HA: Helicase associat 32.3 1E+02 0.0022 20.0 4.1 43 52-100 11-53 (68)
245 TIGR01958 nuoE_fam NADH-quinon 32.1 90 0.002 23.9 4.4 36 51-86 17-52 (148)
246 PRK07539 NADH dehydrogenase su 32.0 90 0.0019 24.1 4.4 35 52-86 24-58 (154)
247 PF01257 2Fe-2S_thioredx: Thio 31.8 80 0.0017 24.1 4.0 35 52-86 15-49 (145)
248 PRK11475 DNA-binding transcrip 31.2 1.8E+02 0.0039 23.5 6.2 46 46-97 133-178 (207)
249 PF08765 Mor: Mor transcriptio 31.0 55 0.0012 23.7 2.8 26 70-95 74-99 (108)
250 smart00530 HTH_XRE Helix-turn- 31.0 35 0.00076 19.5 1.5 23 71-93 13-35 (56)
251 PRK09975 DNA-binding transcrip 29.7 59 0.0013 25.6 3.1 41 54-95 18-58 (213)
252 PRK08241 RNA polymerase factor 29.5 1E+02 0.0022 26.5 4.8 30 69-98 170-199 (339)
253 PRK05949 RNA polymerase sigma 29.4 1.6E+02 0.0036 25.6 6.0 51 47-98 266-316 (327)
254 PF06163 DUF977: Bacterial pro 29.3 83 0.0018 24.0 3.6 42 47-91 4-49 (127)
255 cd08315 Death_TRAILR_DR4_DR5 D 29.0 84 0.0018 22.5 3.5 35 53-87 3-38 (96)
256 TIGR03826 YvyF flagellar opero 29.0 27 0.00059 26.9 0.9 47 48-94 20-72 (137)
257 PF04936 DUF658: Protein of un 28.8 26 0.00057 27.9 0.8 31 69-99 15-45 (186)
258 PRK07571 bidirectional hydroge 28.7 1.1E+02 0.0024 24.3 4.4 35 52-86 38-72 (169)
259 PRK15008 HTH-type transcriptio 28.7 2E+02 0.0043 22.8 6.0 47 52-99 20-69 (212)
260 TIGR02850 spore_sigG RNA polym 28.6 1.1E+02 0.0024 25.3 4.6 47 46-97 205-251 (254)
261 PRK13890 conjugal transfer pro 28.4 36 0.00078 25.3 1.5 23 71-93 21-43 (120)
262 cd01106 HTH_TipAL-Mta Helix-Tu 28.4 54 0.0012 23.3 2.4 21 71-91 3-23 (103)
263 PRK09726 antitoxin HipB; Provi 28.3 1.2E+02 0.0026 20.8 4.1 23 71-93 28-50 (88)
264 PF14229 DUF4332: Domain of un 27.3 72 0.0016 23.7 3.0 25 65-89 26-50 (122)
265 PF04703 FaeA: FaeA-like prote 27.2 62 0.0013 21.4 2.3 21 70-90 17-37 (62)
266 PF01710 HTH_Tnp_IS630: Transp 27.0 52 0.0011 24.2 2.1 35 51-90 6-40 (119)
267 PF13542 HTH_Tnp_ISL3: Helix-t 26.8 67 0.0015 19.5 2.3 20 71-90 30-49 (52)
268 PHA03308 transcriptional regul 26.4 86 0.0019 31.0 3.9 17 39-55 1292-1308(1463)
269 PF13551 HTH_29: Winged helix- 26.3 72 0.0016 22.2 2.7 24 70-93 14-37 (112)
270 TIGR02997 Sig70-cyanoRpoD RNA 26.2 1.1E+02 0.0025 26.0 4.4 48 47-95 249-296 (298)
271 PF08671 SinI: Anti-repressor 26.0 59 0.0013 18.4 1.7 17 74-90 11-27 (30)
272 cd01105 HTH_GlnR-like Helix-Tu 26.0 59 0.0013 22.6 2.2 19 71-89 4-22 (88)
273 PRK07598 RNA polymerase sigma 25.9 2.1E+02 0.0045 26.1 6.2 52 47-99 350-401 (415)
274 cd04774 HTH_YfmP Helix-Turn-He 25.9 64 0.0014 22.9 2.4 21 71-91 3-23 (96)
275 PF04539 Sigma70_r3: Sigma-70 25.0 66 0.0014 21.3 2.2 20 70-89 22-41 (78)
276 KOG2066|consensus 24.7 79 0.0017 31.2 3.3 47 55-101 511-557 (846)
277 cd04766 HTH_HspR Helix-Turn-He 24.5 72 0.0016 22.1 2.4 21 71-91 4-24 (91)
278 PF08880 QLQ: QLQ; InterPro: 24.5 70 0.0015 18.9 2.0 14 47-60 2-15 (37)
279 PF03444 HrcA_DNA-bdg: Winged 24.3 1.9E+02 0.0042 20.1 4.4 38 48-87 2-42 (78)
280 COG5484 Uncharacterized conser 24.1 41 0.00089 28.8 1.2 34 62-97 13-46 (279)
281 PF13404 HTH_AsnC-type: AsnC-t 24.0 61 0.0013 19.5 1.7 19 69-87 18-36 (42)
282 PF12114 Period_C: Period prot 24.0 1.4E+02 0.0031 24.4 4.3 30 53-90 126-155 (195)
283 TIGR00270 conserved hypothetic 24.0 58 0.0013 25.4 2.0 25 71-95 85-109 (154)
284 PRK09706 transcriptional repre 24.0 52 0.0011 24.6 1.7 24 71-94 21-44 (135)
285 PF13560 HTH_31: Helix-turn-he 23.9 50 0.0011 21.1 1.4 25 70-94 16-40 (64)
286 PF13022 HTH_Tnp_1_2: Helix-tu 23.9 2.9E+02 0.0063 21.5 5.7 26 67-92 33-59 (142)
287 KOG0048|consensus 23.5 3.1E+02 0.0067 22.7 6.4 46 44-94 61-107 (238)
288 PF12844 HTH_19: Helix-turn-he 23.5 1.1E+02 0.0024 19.3 3.0 24 70-93 14-37 (64)
289 PF12244 DUF3606: Protein of u 23.2 91 0.002 20.1 2.5 19 69-87 21-39 (57)
290 cd04779 HTH_MerR-like_sg4 Heli 23.2 74 0.0016 24.2 2.4 21 71-91 3-23 (134)
291 PRK14996 TetR family transcrip 23.1 1.2E+02 0.0027 23.4 3.8 41 54-95 15-55 (192)
292 PF05263 DUF722: Protein of un 22.9 1.4E+02 0.003 22.8 3.8 23 69-91 100-122 (130)
293 cd04780 HTH_MerR-like_sg5 Heli 22.8 73 0.0016 22.6 2.2 20 71-90 3-22 (95)
294 PRK12427 flagellar biosynthesi 22.6 2.9E+02 0.0063 22.5 6.1 44 47-95 183-226 (231)
295 PF02787 CPSase_L_D3: Carbamoy 22.6 3E+02 0.0065 20.5 5.6 45 53-97 46-90 (123)
296 PRK07921 RNA polymerase sigma 22.6 2.8E+02 0.006 24.2 6.2 51 47-98 262-312 (324)
297 PF07037 DUF1323: Putative tra 22.5 76 0.0016 24.0 2.2 20 71-90 3-22 (122)
298 TIGR03629 arch_S13P archaeal r 22.4 70 0.0015 24.8 2.1 17 46-62 50-66 (144)
299 PRK15451 tRNA cmo(5)U34 methyl 22.1 2.1E+02 0.0046 23.4 5.2 45 47-93 189-234 (247)
300 PRK00215 LexA repressor; Valid 22.0 1.3E+02 0.0028 23.9 3.7 43 48-92 2-48 (205)
301 PF00249 Myb_DNA-binding: Myb- 21.5 2E+02 0.0042 17.2 5.5 44 45-91 1-46 (48)
302 TIGR03147 cyt_nit_nrfF cytochr 21.3 62 0.0013 24.6 1.6 26 67-92 59-86 (126)
303 cd04768 HTH_BmrR-like Helix-Tu 21.3 91 0.002 21.9 2.4 21 71-91 3-23 (96)
304 KOG3623|consensus 21.2 41 0.00088 33.1 0.7 58 43-100 628-685 (1007)
305 cd04773 HTH_TioE_rpt2 Second H 21.2 89 0.0019 22.5 2.4 21 71-91 3-23 (108)
306 TIGR03830 CxxCG_CxxCG_HTH puta 21.0 1.2E+02 0.0026 21.9 3.2 23 71-93 81-103 (127)
307 PF00440 TetR_N: Bacterial reg 20.8 93 0.002 18.6 2.1 36 57-93 6-41 (47)
308 KOG2675|consensus 20.7 1.3E+02 0.0028 27.8 3.7 12 87-98 168-179 (480)
309 TIGR01636 phage_rinA phage tra 20.7 1.6E+02 0.0035 22.1 3.8 38 48-88 83-120 (134)
310 PF05269 Phage_CII: Bacterioph 20.5 1E+02 0.0022 22.0 2.5 28 71-98 26-53 (91)
311 PF14549 P22_Cro: DNA-binding 20.3 1.2E+02 0.0027 19.8 2.7 18 71-88 12-29 (60)
No 1
>KOG0492|consensus
Probab=99.87 E-value=4.3e-22 Score=160.29 Aligned_cols=84 Identities=85% Similarity=1.163 Sum_probs=79.4
Q ss_pred CCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHHHHh
Q psy3429 30 KLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKM 109 (192)
Q Consensus 30 ~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~~~~ 109 (192)
...|.++|++.+|+.||-||.+||..||+.|++.+|.++.||.|++..|.|+++||||||||||+|.||.++.+.++.++
T Consensus 133 p~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek~km 212 (246)
T KOG0492|consen 133 PTTCTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEKLKM 212 (246)
T ss_pred cccchhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHHhhh
Confidence 34588899999999999999999999999999999999999999999999999999999999999999999999999998
Q ss_pred hhhh
Q psy3429 110 SAIA 113 (192)
Q Consensus 110 ~~~~ 113 (192)
+...
T Consensus 213 aa~~ 216 (246)
T KOG0492|consen 213 AAKS 216 (246)
T ss_pred hhcc
Confidence 7654
No 2
>KOG0488|consensus
Probab=99.87 E-value=3.3e-22 Score=172.57 Aligned_cols=71 Identities=49% Similarity=0.742 Sum_probs=65.4
Q ss_pred ccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHH
Q psy3429 35 LRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIE 105 (192)
Q Consensus 35 ~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~ 105 (192)
....||+||.||+||..||.+||+.|++++|++..+|.+||..|||++.||++||||||+||||+..+..+
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~~ 236 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGGE 236 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhhc
Confidence 34458889999999999999999999999999999999999999999999999999999999998876443
No 3
>KOG0484|consensus
Probab=99.85 E-value=6.8e-22 Score=143.31 Aligned_cols=74 Identities=42% Similarity=0.695 Sum_probs=67.0
Q ss_pred cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHHH
Q psy3429 34 NLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKI 107 (192)
Q Consensus 34 ~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~~ 107 (192)
++..++|+||.||+||..||.+||+.|...+||++..|+|||.++.|++.+|+|||||||+|.||+++....++
T Consensus 10 ~l~ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~~ 83 (125)
T KOG0484|consen 10 GLTEKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAKM 83 (125)
T ss_pred ChhHHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHHh
Confidence 34567788999999999999999999999999999999999999999999999999999999999876654443
No 4
>KOG0489|consensus
Probab=99.85 E-value=7.6e-22 Score=167.05 Aligned_cols=67 Identities=46% Similarity=0.697 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
..+.||.||.||..|+.+||+.|+.|+|+++..|.|||..|+|+|+||||||||||+||||..+...
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3457899999999999999999999999999999999999999999999999999999999876554
No 5
>KOG0485|consensus
Probab=99.84 E-value=2.4e-20 Score=151.19 Aligned_cols=74 Identities=50% Similarity=0.711 Sum_probs=68.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHHHHhhh
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSA 111 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~~~~~~ 111 (192)
+.+|||.||+|+..|+..||..|+..+|++..||..||.+|.|+|+||||||||||.||||+...+.+.+.+..
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~sl~~ 174 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAASLHY 174 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhhhcch
Confidence 34778899999999999999999999999999999999999999999999999999999999888877766654
No 6
>KOG0494|consensus
Probab=99.83 E-value=7.5e-21 Score=157.59 Aligned_cols=80 Identities=35% Similarity=0.502 Sum_probs=69.4
Q ss_pred cccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHHHHhhh
Q psy3429 32 NVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEKIKMSA 111 (192)
Q Consensus 32 ~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~~~~~~ 111 (192)
..+.++++++|+.||.||..|+++||+.|++.+||+...|+-||.+++|.|++|+|||||||+||||.+++......++.
T Consensus 132 ~~~~kkk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~mae 211 (332)
T KOG0494|consen 132 PDNAKKKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAE 211 (332)
T ss_pred CcccccccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhh
Confidence 33455556666679999999999999999999999999999999999999999999999999999999887665555543
No 7
>KOG0842|consensus
Probab=99.83 E-value=2.7e-20 Score=159.18 Aligned_cols=68 Identities=50% Similarity=0.781 Sum_probs=63.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 37 KHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 37 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
..++|||.|..|++.|+.+||+.|++++|++..|||+||..|+||++||||||||||-|.||+++...
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~ 216 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKA 216 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhh
Confidence 35677888999999999999999999999999999999999999999999999999999999876543
No 8
>KOG0487|consensus
Probab=99.81 E-value=1.8e-20 Score=160.30 Aligned_cols=67 Identities=46% Similarity=0.730 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
-+..||||--+|+.|+.+||+.|-.|.|++++.|.||++.|+|+|+||||||||||+|+||+.+++.
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 3666888999999999999999999999999999999999999999999999999999999886543
No 9
>KOG0850|consensus
Probab=99.81 E-value=4e-20 Score=151.01 Aligned_cols=73 Identities=51% Similarity=0.783 Sum_probs=67.6
Q ss_pred CCCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 29 PKLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 29 ~~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.....-..+.||.||.||.|+.-||..|+++|++++|+-..||.|||..|||+-+||||||||||.|.||+.+
T Consensus 110 ~~e~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 110 PSERRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cceeccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3444556888999999999999999999999999999999999999999999999999999999999999876
No 10
>KOG0843|consensus
Probab=99.80 E-value=6.6e-20 Score=144.78 Aligned_cols=64 Identities=52% Similarity=0.811 Sum_probs=60.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 40 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
+-||.||.|+.+|+..||.+|+.|+|....||++||..|+|++.||||||||||.|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5578899999999999999999999999999999999999999999999999999999987554
No 11
>KOG2251|consensus
Probab=99.78 E-value=1.6e-19 Score=146.79 Aligned_cols=68 Identities=40% Similarity=0.665 Sum_probs=64.5
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 36 RKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 36 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
...+|+||.||+|+.+|+++||+.|.+.+||++..||+||.+|+|.+-+|+|||+|||+|+|++++.+
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 55788899999999999999999999999999999999999999999999999999999999987654
No 12
>KOG0848|consensus
Probab=99.77 E-value=2.3e-19 Score=149.31 Aligned_cols=69 Identities=41% Similarity=0.677 Sum_probs=63.8
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 36 RKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 36 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
.+-|.|-|.|.++|..|+.+||+.|..++|++++.+.|||..|+|+|+||||||||||+|+||+.++..
T Consensus 194 ~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 194 VKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 355666788999999999999999999999999999999999999999999999999999999887664
No 13
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.76 E-value=1.8e-18 Score=113.61 Aligned_cols=57 Identities=53% Similarity=0.765 Sum_probs=55.3
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
||+|+.|+.+|+.+||++|..++||+..++++||..+||+..+|++||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999986
No 14
>KOG0491|consensus
Probab=99.76 E-value=2.2e-19 Score=140.02 Aligned_cols=96 Identities=47% Similarity=0.655 Sum_probs=81.0
Q ss_pred cccccccCCCCCCC-----CCCCCCCCCcccccCCC------CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHh
Q psy3429 9 LNEILILSSPLLSD-----SNKGDPPKLNVNLRKHK------PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSS 77 (192)
Q Consensus 9 ~~~~~~~~s~~~~~-----s~~~~~~~~~~~~~~~~------~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~ 77 (192)
..++++..+++++. +..|..+++-.++...+ ++||-||+|+..|+..||+.|+.++|.+..+|.|||..
T Consensus 57 s~lll~a~sp~~~hk~~~~~~kgv~p~lalglgn~~~~~~~~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~ 136 (194)
T KOG0491|consen 57 SMLLLIADSPDSSHKLLLASPKGVQPTLALGLGNKKTARLHCRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANA 136 (194)
T ss_pred ccceeeccCCcccccccccCCCccchhHhhhcccchhhhHHHHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHH
Confidence 34577889999888 56666665555444433 35788999999999999999999999999999999999
Q ss_pred cCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 78 LHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 78 l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
|+|+++||+.||||||+|.||+++...
T Consensus 137 L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 137 LSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 999999999999999999999876653
No 15
>KOG0493|consensus
Probab=99.71 E-value=1.5e-17 Score=138.17 Aligned_cols=59 Identities=47% Similarity=0.841 Sum_probs=56.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
||.||.||.+||..|+..|+.|+|++...|++||.+|+|+|.||+|||||+|+|.||..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 68899999999999999999999999999999999999999999999999999999843
No 16
>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=99.68 E-value=2.3e-17 Score=109.06 Aligned_cols=53 Identities=23% Similarity=0.407 Sum_probs=50.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 41 NRKPRTPFTTQQLLSLEKKFREKQY----LSIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 41 ~rr~Rt~ft~~Ql~~Le~~F~~~~y----ps~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
+||.||.||.+|+..||+.|+.++| ++..++++||..|||++.+|+|||||.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 4789999999999999999999999 9999999999999999999999999964
No 17
>KOG0844|consensus
Probab=99.67 E-value=1.8e-17 Score=140.29 Aligned_cols=66 Identities=44% Similarity=0.708 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 37 KHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 37 ~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
-..+-||.||.||.|||..||+.|.+..|-++..|.|||..|||.|..|||||||||+|+||+...
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 444558999999999999999999999999999999999999999999999999999999997643
No 18
>KOG0486|consensus
Probab=99.66 E-value=6.5e-17 Score=137.32 Aligned_cols=66 Identities=38% Similarity=0.660 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 39 KPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 39 ~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
+|+||.||.|+.+|+.+||..|++|.||+...|||||.-++|+|.+|+|||.|||+||||.++.+.
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 378999999999999999999999999999999999999999999999999999999999876654
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.65 E-value=2.4e-16 Score=102.70 Aligned_cols=56 Identities=55% Similarity=0.832 Sum_probs=52.6
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
++.|+.|+.+|+.+|+++|..++||+..++++||..+||+..+|++||+|+|.+.+
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 45688899999999999999999999999999999999999999999999998753
No 20
>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=4.1e-16 Score=102.34 Aligned_cols=57 Identities=60% Similarity=0.851 Sum_probs=54.2
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
++.|+.|+.+|+.+||++|..++||+..++++||..+||++.+|++||+|+|.+.++
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 356889999999999999999999999999999999999999999999999999876
No 21
>KOG3802|consensus
Probab=99.59 E-value=3.3e-16 Score=136.98 Aligned_cols=71 Identities=30% Similarity=0.419 Sum_probs=63.5
Q ss_pred CcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 31 LNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 31 ~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..+......+|||+||.|....+..||++|.+|+.|+..|+.+||++|+|...+|+|||+|||.|+||...
T Consensus 284 ~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 284 SIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred CHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 34444444588899999999999999999999999999999999999999999999999999999999643
No 22
>KOG0483|consensus
Probab=99.58 E-value=1.3e-15 Score=123.78 Aligned_cols=61 Identities=33% Similarity=0.506 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 41 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..+++.+|+.+|+..||+.|+.+.|....++..||+.|||.++||.|||||||+|||.++.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kql 110 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQL 110 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhh
Confidence 3445567999999999999999999999999999999999999999999999999998653
No 23
>KOG4577|consensus
Probab=99.55 E-value=2.5e-14 Score=120.60 Aligned_cols=68 Identities=35% Similarity=0.557 Sum_probs=62.6
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 36 RKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 36 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
......||.||++|..||+.|+.+|+..+.|.+..||+|+.++||.-++|+|||||||+|+||.++..
T Consensus 162 ~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T KOG4577|consen 162 EGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDA 229 (383)
T ss_pred ccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhc
Confidence 34455689999999999999999999999999999999999999999999999999999999987643
No 24
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=6.6e-15 Score=115.70 Aligned_cols=68 Identities=34% Similarity=0.555 Sum_probs=61.3
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 36 RKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 36 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
......+++|++.+.+|+.+|++.|+.++||+..+|.+|+..|+|+++-|++||||+|++.|+.....
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 34455577888899999999999999999999999999999999999999999999999999976543
No 25
>KOG0847|consensus
Probab=99.51 E-value=8.2e-15 Score=119.31 Aligned_cols=68 Identities=41% Similarity=0.730 Sum_probs=63.6
Q ss_pred cCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 36 RKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 36 ~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
.++++++..|.+|+-.|+..||+.|+..+|+-..+|.+||..+|+++.||+|||||||.||||+...+
T Consensus 162 ~kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaE 229 (288)
T KOG0847|consen 162 NLNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAE 229 (288)
T ss_pred CcCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccc
Confidence 47788889999999999999999999999999999999999999999999999999999999976544
No 26
>KOG0490|consensus
Probab=99.42 E-value=1.1e-13 Score=113.80 Aligned_cols=64 Identities=34% Similarity=0.472 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..++||.|+.|+..|+++||++|++.+||+...|+.||..+++++..|++||||||+||++.+.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 6778999999999999999999999999999999999999999999999999999999998764
No 27
>KOG0849|consensus
Probab=99.36 E-value=1.8e-12 Score=114.19 Aligned_cols=73 Identities=33% Similarity=0.535 Sum_probs=65.8
Q ss_pred CCcccccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 30 KLNVNLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 30 ~~~~~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
........+++.||+||+|+.+|++.||+.|+.++||++..|++||.++++++.+|++||+|||+|++|....
T Consensus 165 ~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 165 EEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred cccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 3444556677788889999999999999999999999999999999999999999999999999999997643
No 28
>KOG1168|consensus
Probab=99.21 E-value=2.7e-12 Score=108.42 Aligned_cols=63 Identities=29% Similarity=0.433 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
...|||+||.+-....+.||++|..++.|+.+.+..||++|+|...+|+|||+|.|.|.||+.
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 445678899999999999999999999999999999999999999999999999999999843
No 29
>KOG0775|consensus
Probab=99.12 E-value=9.2e-11 Score=98.45 Aligned_cols=51 Identities=31% Similarity=0.491 Sum_probs=47.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
|...-+..|.++|.+++||+..++.|||+++||+..||-+||+|||.|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 445558899999999999999999999999999999999999999999983
No 30
>KOG0774|consensus
Probab=99.03 E-value=8.2e-10 Score=92.31 Aligned_cols=61 Identities=28% Similarity=0.439 Sum_probs=56.2
Q ss_pred CCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFR---EKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
||+|..|++.-.++|+++|. .|+||+..++++||+++|++..||.+||.|+|-+.||....
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k 252 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGK 252 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhh
Confidence 67899999999999999996 67899999999999999999999999999999999986533
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.78 E-value=6.8e-09 Score=63.65 Aligned_cols=34 Identities=29% Similarity=0.546 Sum_probs=29.1
Q ss_pred hcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 62 EKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 62 ~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++||+..++++||.++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 5789999999999999999999999999999975
No 32
>KOG2252|consensus
Probab=98.68 E-value=3.6e-08 Score=89.83 Aligned_cols=59 Identities=29% Similarity=0.363 Sum_probs=54.8
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHH
Q psy3429 38 HKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKA 96 (192)
Q Consensus 38 ~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~ 96 (192)
.-..||.|.+||..|++.|.++|+.+++|+.++.+.|+..|||....|.+||-|.|.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 33457789999999999999999999999999999999999999999999999999775
No 33
>KOG0490|consensus
Probab=98.38 E-value=4.6e-07 Score=74.37 Aligned_cols=68 Identities=35% Similarity=0.580 Sum_probs=61.8
Q ss_pred cccCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 34 NLRKHKPNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 34 ~~~~~~~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
......+.++.|+.|...|+..|+..|..+.+|+...+++|+..+|+++..|++||+|+|.+.++...
T Consensus 146 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 146 KGPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cCCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 33445667888999999999999999999999999999999999999999999999999999998654
No 34
>KOG1146|consensus
Probab=98.02 E-value=8.1e-06 Score=80.90 Aligned_cols=63 Identities=24% Similarity=0.378 Sum_probs=58.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 40 PNRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 40 ~~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
.+|++|+.++..||+++...|....|+..++.|.|-..+++..+.|.+||||.|.|.|+....
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~n 964 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKLN 964 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhhc
Confidence 357889999999999999999999999999999999999999999999999999999987653
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.51 E-value=9.4e-05 Score=48.37 Aligned_cols=41 Identities=22% Similarity=0.408 Sum_probs=31.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 53 LLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 53 l~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
+..|+++|...+++...+..+|..+.+|+..||+.||-.++
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 45699999999999999999999999999999999997654
No 36
>KOG0773|consensus
Probab=97.28 E-value=0.00017 Score=63.12 Aligned_cols=62 Identities=21% Similarity=0.286 Sum_probs=52.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 41 NRKPRTPFTTQQLLSLEKKFRE---KQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 41 ~rr~Rt~ft~~Ql~~Le~~F~~---~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
++|.+..|..+.+.+|+.+... .+||+..++..||.++||+..||.+||.|.|.|..+-...
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 4555678999999999988433 4699999999999999999999999999999887765443
No 37
>KOG3623|consensus
Probab=96.28 E-value=0.0068 Score=57.76 Aligned_cols=48 Identities=19% Similarity=0.272 Sum_probs=45.4
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 53 LLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 53 l~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
+..|.++|..|..|+..+-..+|.+.||..+.|+.||+++++++.+.+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999988755
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=96.05 E-value=0.016 Score=37.32 Aligned_cols=47 Identities=15% Similarity=0.391 Sum_probs=35.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 42 RKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 42 rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
||+|..+|-++...+-..++... ...+||.++|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 57789999999888877777766 578899999999999999999854
No 39
>KOG1924|consensus
Probab=95.92 E-value=0.09 Score=50.81 Aligned_cols=12 Identities=50% Similarity=1.137 Sum_probs=4.5
Q ss_pred CCCCCCCCCCCC
Q psy3429 166 PMPQNSPPGGSD 177 (192)
Q Consensus 166 P~p~~~~~~~s~ 177 (192)
|||++.++++..
T Consensus 570 PPpPppppg~~g 581 (1102)
T KOG1924|consen 570 PPPPPPPPGGGG 581 (1102)
T ss_pred CCccCCCCCCCC
Confidence 333333333333
No 40
>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=92.66 E-value=0.42 Score=29.76 Aligned_cols=46 Identities=11% Similarity=0.163 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
.++..+..+|...|.. ...-.++|..+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 4678899999999822 234678899999999999998876665554
No 41
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=87.85 E-value=0.84 Score=27.47 Aligned_cols=44 Identities=14% Similarity=0.183 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++..+..+++..|... ....++|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45677778887776422 346778999999999999998765443
No 42
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=87.57 E-value=2.6 Score=32.71 Aligned_cols=51 Identities=16% Similarity=0.179 Sum_probs=39.8
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
...++..|+.+|+..+ .. ....++|..+|++...|+.|.++.+.+.++...
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~ 54 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARE 54 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4678999999998843 22 336689999999999999999988777776543
No 43
>KOG3755|consensus
Probab=87.30 E-value=1.2 Score=42.21 Aligned_cols=21 Identities=38% Similarity=0.846 Sum_probs=16.2
Q ss_pred CChhHHHHhhHhHHHHHHHHH
Q psy3429 80 LTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 80 Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
...+.|+.||.|||.++++.+
T Consensus 738 ~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 738 FESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred hhhcchHHHHHHHHHHHhhhh
Confidence 345568899999999988754
No 44
>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=86.34 E-value=0.95 Score=30.31 Aligned_cols=46 Identities=11% Similarity=0.239 Sum_probs=29.2
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhH
Q psy3429 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNR 92 (192)
Q Consensus 43 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNr 92 (192)
++|..|+.++...+-..+... .....++|.++|++...|..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHH
Confidence 457889998876665555222 2567789999999999999997543
No 45
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=85.33 E-value=3.2 Score=25.90 Aligned_cols=43 Identities=21% Similarity=0.246 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
++..+..++...| .....-.++|..+|+++..|+.|.+.-|.+
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~~ 53 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRARKK 53 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHHhh
Confidence 4555555655543 344567889999999999999999865543
No 46
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=83.71 E-value=3.3 Score=26.43 Aligned_cols=46 Identities=20% Similarity=0.141 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.||..++.+|+....-. ...++|..+|+++..|+.+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888888887776443 37889999999999999999887766543
No 47
>PRK04217 hypothetical protein; Provisional
Probab=81.84 E-value=6.1 Score=29.30 Aligned_cols=48 Identities=15% Similarity=0.062 Sum_probs=36.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..++.+|+.++...|...- ...+||+.+|++...|+..+...+.+.+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4577888888877764333 56789999999999999998876666554
No 48
>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=80.98 E-value=4.8 Score=21.43 Aligned_cols=38 Identities=13% Similarity=0.205 Sum_probs=27.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
.++.++...+...|.. .+ ...++|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 3566766666666653 22 46678999999999998884
No 49
>KOG1146|consensus
Probab=79.98 E-value=3.8 Score=42.04 Aligned_cols=60 Identities=15% Similarity=0.300 Sum_probs=55.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 41 NRKPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 41 ~rr~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++-|..+-.+++.+|-++|..+.-|+.+.+.-|..+...+.+++.+||+|-|.|.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 466788888899999999999999999999999999999999999999999999988754
No 50
>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=79.57 E-value=1.6 Score=28.99 Aligned_cols=21 Identities=14% Similarity=0.469 Sum_probs=17.7
Q ss_pred HHHHHHHhcCCChhHHHHhhH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFq 90 (192)
.-.+||.+||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 356789999999999999953
No 51
>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=79.02 E-value=6.3 Score=25.94 Aligned_cols=45 Identities=18% Similarity=0.294 Sum_probs=22.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
|..|+.......-.+|.....--...|. -|.++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4566665544333444333322223333 49999999999999975
No 52
>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=78.85 E-value=6.7 Score=25.23 Aligned_cols=42 Identities=14% Similarity=0.127 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcC--CCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 48 FTTQQLLSLEKKFREKQ--YLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~--yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
+|..|+++|..+|+..= +|-...-.+||++||++..-|..-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 57899999999987654 3556667889999999998776544
No 53
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=78.68 E-value=4.9 Score=31.84 Aligned_cols=49 Identities=14% Similarity=0.095 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|...| .....-.++|+.||++...|+++...-|.+.|+..
T Consensus 142 ~L~~~~r~vl~l~~-----~~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~l 190 (194)
T PRK09646 142 ALTDTQRESVTLAY-----YGGLTYREVAERLAVPLGTVKTRMRDGLIRLRDCL 190 (194)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHHh
Confidence 35555555555443 22245678999999999999999987777766643
No 54
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=77.99 E-value=9.4 Score=23.10 Aligned_cols=43 Identities=21% Similarity=0.189 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++..+..++...+. . ....++|..+|++...|..|.+.-+.|
T Consensus 3 ~l~~~e~~i~~~~~~--g----~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLAE--G----LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 467778887766432 2 246788999999999999998754433
No 55
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=77.75 E-value=6.9 Score=31.41 Aligned_cols=32 Identities=19% Similarity=0.135 Sum_probs=26.4
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
....++|..+|+++..|+++..+-+.+.++..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999987777776654
No 56
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=76.24 E-value=10 Score=28.77 Aligned_cols=31 Identities=13% Similarity=0.063 Sum_probs=26.1
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.-.++|..+|+++..|++++..-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3568899999999999999988887777654
No 57
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=76.15 E-value=4.6 Score=28.92 Aligned_cols=41 Identities=15% Similarity=0.218 Sum_probs=34.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKI 87 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~ 87 (192)
.++++|+.+-...|+.|--.+....+++|.+||.++.-|.-
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~lek 42 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLEK 42 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHHH
Confidence 46788988888888888888888899999999999876553
No 58
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=76.12 E-value=5.9 Score=30.23 Aligned_cols=33 Identities=18% Similarity=0.137 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..-.++|..+|++...|+.|...-|.+.|+...
T Consensus 142 ~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 142 LSYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 446789999999999999999887777776543
No 59
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=76.11 E-value=9.4 Score=28.64 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
++..+..++...|- ......|+|..+|+++..|+.|...-+.+.|+
T Consensus 107 L~~~~r~ii~l~~~-----~~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 107 LDEKEKYIIFERFF-----VGKTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 44555555544432 23447889999999999999999876666554
No 60
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=75.51 E-value=4.9 Score=31.61 Aligned_cols=34 Identities=18% Similarity=0.117 Sum_probs=27.4
Q ss_pred CHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 67 SIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 67 s~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
......++|..+|+++..|+.|+..-|.+.|+..
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345778999999999999999987777777643
No 61
>KOG3671|consensus
Probab=75.36 E-value=9.3 Score=35.54 Aligned_cols=27 Identities=37% Similarity=0.727 Sum_probs=14.5
Q ss_pred CCCCCCCCCCCCCCCCCCCCCCCCCCC
Q psy3429 165 APMPQNSPPGGSDMKASPPRPSPSPTM 191 (192)
Q Consensus 165 ~P~p~~~~~~~s~~~~~pp~p~~~~~~ 191 (192)
.|++++.+..+|....++|++|++|+|
T Consensus 410 ~PpPPPPs~~g~~Pp~apPppPPPPPm 436 (569)
T KOG3671|consen 410 PPPPPPPSLPGSAPPSAPPPPPPPPPM 436 (569)
T ss_pred CCCCCCCcccCCCCCCCCCCCCcCCCC
Confidence 344455555556655555555555554
No 62
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=74.78 E-value=10 Score=28.85 Aligned_cols=48 Identities=19% Similarity=0.230 Sum_probs=34.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
++..+..+|...| . ...-.++|..+|++...|+.+...-|.+.|+...
T Consensus 113 L~~~~r~il~l~~--~----g~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 113 MTERDRTVLLLRF--S----GYSYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4555555555554 2 2346788999999999999999877777776543
No 63
>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=74.70 E-value=20 Score=27.55 Aligned_cols=48 Identities=21% Similarity=0.212 Sum_probs=38.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.+.++..|+.+|+..+ .. ....++|..+|++...|+.|-.+-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999998842 22 246789999999999999999887777775
No 64
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=74.63 E-value=5.3 Score=30.99 Aligned_cols=31 Identities=10% Similarity=0.252 Sum_probs=25.6
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
...+++|..+|+++..|++++..-|.+.|+.
T Consensus 146 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 146 LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 3478899999999999999998777776654
No 65
>TIGR03879 near_KaiC_dom probable regulatory domain. This model describes a common domain shared by two different families of proteins, each of which occurs regularly next to its corresponding partner family, a probable regulatory with homology to KaiC. By implication, this protein family likely is also involved in sensory transduction and/or regulation.
Probab=74.57 E-value=1.7 Score=29.91 Aligned_cols=35 Identities=17% Similarity=0.081 Sum_probs=27.3
Q ss_pred HHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHh
Q psy3429 57 EKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 57 e~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
+..|....|.......+||..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455555555566889999999999999999975
No 66
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=73.75 E-value=8 Score=29.56 Aligned_cols=49 Identities=6% Similarity=-0.048 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|...|- ......++|..+|+++..|+.|...-+.+.++..
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456666666665542 2234668899999999999999987776666543
No 67
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=73.39 E-value=12 Score=28.59 Aligned_cols=33 Identities=24% Similarity=0.173 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
...+++|..+|+++..|++|.+.-|.+.|+..+
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 157 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLK 157 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 446889999999999999999887777776543
No 68
>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=72.99 E-value=10 Score=27.52 Aligned_cols=46 Identities=15% Similarity=0.151 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
++..+..++...|- ......++|..+|+++..|+.|...-+.|.|+
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 44555555544332 23356789999999999999998876666554
No 69
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=72.92 E-value=15 Score=29.03 Aligned_cols=49 Identities=6% Similarity=0.055 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
++..+..++...|-. ...-.++|..+|+++..|+++...-|.+.|+...
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 183 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQACLS 183 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344455555444322 2346789999999999999999877777776543
No 70
>PRK00118 putative DNA-binding protein; Validated
Probab=72.76 E-value=11 Score=27.59 Aligned_cols=48 Identities=10% Similarity=0.104 Sum_probs=35.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
++..|..++...|... ....++|..+|++...|..|....|.+.+...
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4566666766555442 34567999999999999999988887777654
No 71
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=72.41 E-value=21 Score=27.75 Aligned_cols=38 Identities=16% Similarity=0.100 Sum_probs=31.2
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEIEK 106 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~~~ 106 (192)
..-.++|..+|+++..|++....-|.+.|+........
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~~~~ 171 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIEEIF 171 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999999998888876655443
No 72
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=71.86 E-value=9.5 Score=28.29 Aligned_cols=43 Identities=16% Similarity=0.203 Sum_probs=29.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHh
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
|..|+.++....-.....+. ....++|.++|++...|..|.+.
T Consensus 10 rr~ys~EfK~~aV~~~~~~g----~sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPG----MTVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCC----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 55678877554333333333 23567899999999999999754
No 73
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=71.30 E-value=16 Score=28.63 Aligned_cols=50 Identities=14% Similarity=0.131 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.++..+..+|+..|- ....-.++|..+|++...|++.+..-|.+.++..+
T Consensus 131 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (189)
T PRK12515 131 KLSPAHREIIDLVYY-----HEKSVEEVGEIVGIPESTVKTRMFYARKKLAELLK 180 (189)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 345555555544332 22346788999999999999999887777776543
No 74
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=71.17 E-value=16 Score=28.21 Aligned_cols=49 Identities=20% Similarity=0.146 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|...| ......+++|..+|+++..|+++...-|.+.++..
T Consensus 100 ~L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 148 (170)
T TIGR02959 100 ELPDEYREAIRLTE-----LEGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKELL 148 (170)
T ss_pred hCCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 45555555555543 22234678999999999999999887776666643
No 75
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.12 E-value=7 Score=23.77 Aligned_cols=40 Identities=13% Similarity=0.128 Sum_probs=21.0
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
..||.+|...++..++.. ....+||+.+|.+..-|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 467888888888776533 4466799999999999988874
No 76
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=69.72 E-value=14 Score=28.55 Aligned_cols=47 Identities=17% Similarity=0.199 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
++..+..+++..| .....-+++|..+|++...|+++++.-|.+.+..
T Consensus 137 L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 137 LPPKYRMVIVLKY-----MEDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHhHHhhhHH-----hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4444444444432 2345577899999999999999998777776653
No 77
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=69.56 E-value=13 Score=28.97 Aligned_cols=48 Identities=15% Similarity=0.048 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
++..+..++...|- ....-+++|..+|++...|+.++..-|.+.|+..
T Consensus 132 L~~~~r~v~~l~~~-----~g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 132 LPPRQRDVVQSISV-----EGASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 44455555544432 2344678999999999999999988887777643
No 78
>PF08280 HTH_Mga: M protein trans-acting positive regulator (MGA) HTH domain; InterPro: IPR013199 Mga is a DNA-binding protein that activates the expression of several important virulence genes in group A streptococcus in response to changing environmental conditions [].; PDB: 2WTE_A 3SQN_A.
Probab=69.36 E-value=11 Score=24.32 Aligned_cols=36 Identities=22% Similarity=0.418 Sum_probs=28.4
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 51 QQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 51 ~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
.|+..|+-.+. +...+.. +||..+|++++.|+.-..
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 57888888888 7777655 899999999999987654
No 79
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=69.20 E-value=15 Score=28.58 Aligned_cols=32 Identities=6% Similarity=0.100 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-.++|..+|++...|+.+...-|.+.|+..
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 145 LSNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999987777766643
No 80
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=68.93 E-value=17 Score=29.95 Aligned_cols=33 Identities=15% Similarity=0.234 Sum_probs=27.4
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..-.++|..+|+++..|+++...-|.+.|+...
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 446789999999999999999888887776544
No 81
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=68.58 E-value=13 Score=29.17 Aligned_cols=48 Identities=13% Similarity=-0.003 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.+...|..+++..|-. ...-+++|..+|++...|+.+...-|.+.|+.
T Consensus 139 ~L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 186 (189)
T PRK09648 139 TLPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRAE 186 (189)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3455555555554322 24478899999999999999987766666553
No 82
>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=68.49 E-value=17 Score=26.96 Aligned_cols=30 Identities=10% Similarity=0.181 Sum_probs=23.7
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
....++|..+|+++..|+.+...-|.|.|+
T Consensus 130 ~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 130 KSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 346778999999999999988766666554
No 83
>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=68.37 E-value=13 Score=28.88 Aligned_cols=36 Identities=8% Similarity=-0.057 Sum_probs=27.5
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
|.....-.++|..+|+++..|+++...-|.+.|+..
T Consensus 151 ~~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 151 ELEGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 334445688999999999999999977776666543
No 84
>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=68.29 E-value=5.4 Score=24.03 Aligned_cols=21 Identities=5% Similarity=0.115 Sum_probs=18.1
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|.++
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~ 23 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERI 23 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999754
No 85
>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=68.08 E-value=16 Score=22.11 Aligned_cols=38 Identities=21% Similarity=0.198 Sum_probs=26.8
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhH
Q psy3429 49 TTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNR 92 (192)
Q Consensus 49 t~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNr 92 (192)
+..+..++...+ .. ....++|+.++++...|+.|...-
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~~~ 39 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLRNI 39 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 455666665543 22 256788999999999999998643
No 86
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=68.02 E-value=9.5 Score=24.37 Aligned_cols=28 Identities=0% Similarity=0.182 Sum_probs=18.5
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
...+||+.+|++...|..|+.++..+..
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~ 39 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPS 39 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----
T ss_pred CHHHHHHHHCcCHHHHHHHHhccccccc
Confidence 4678999999999999999998744433
No 87
>PRK06930 positive control sigma-like factor; Validated
Probab=67.82 E-value=20 Score=28.40 Aligned_cols=50 Identities=12% Similarity=0.071 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.++..+..++...|... ..-.++|..+|++...|+.+..+-+.|.++...
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l~ 163 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQIN 163 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46666666666543222 235778999999999999999988887776544
No 88
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=67.32 E-value=20 Score=28.62 Aligned_cols=33 Identities=15% Similarity=0.253 Sum_probs=27.2
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..-.++|..+|+++..|++....-|.+.|+...
T Consensus 156 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l~ 188 (201)
T PRK12545 156 FEIDDICTELTLTANHCSVLLYRARTRLRTCLS 188 (201)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999999999888877777554
No 89
>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=66.92 E-value=18 Score=27.92 Aligned_cols=46 Identities=17% Similarity=0.068 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
+...+..++...|-. ...-.++|..+|+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFA-----GLTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 445555555444322 2346788999999999999999877776665
No 90
>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=66.80 E-value=16 Score=27.41 Aligned_cols=45 Identities=16% Similarity=0.115 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
++..+..++... |.......++|..+|++...|+++...-|.+.+
T Consensus 112 L~~~~r~v~~l~-----~~~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 112 LPERQRELLQLR-----YQRGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHHHH-----HhcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 445555555443 233445788999999999999998876665544
No 91
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=66.33 E-value=22 Score=27.95 Aligned_cols=33 Identities=6% Similarity=0.123 Sum_probs=27.5
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
.-.++|..+|++...|+++...-|.+.|+....
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~~ 186 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCLQI 186 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999998888877776543
No 92
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=66.22 E-value=16 Score=29.88 Aligned_cols=48 Identities=13% Similarity=0.136 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
+...+..++...| .....-.++|..+|++...|+.+...-+.+.|+..
T Consensus 185 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~l 232 (236)
T PRK06986 185 LPEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRARL 232 (236)
T ss_pred CCHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3444455554444 23335678999999999999999998888777643
No 93
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=66.00 E-value=17 Score=31.77 Aligned_cols=53 Identities=13% Similarity=0.156 Sum_probs=40.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..|..+|+..|.... ......++||..+|++...|+.+...-+.|.|+..
T Consensus 262 ~L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 262 ELNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred cCCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 567777888877763322 33455788999999999999999988888877654
No 94
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=65.58 E-value=29 Score=26.04 Aligned_cols=48 Identities=13% Similarity=0.107 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
++..|..++.-.|- ....-.++|..+|++...|++....-|.+.|+..
T Consensus 107 Lp~~~r~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 154 (161)
T PRK09047 107 LPARQREAFLLRYW-----EDMDVAETAAAMGCSEGSVKTHCSRATHALAKAL 154 (161)
T ss_pred CCHHHHHHHHHHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44455555544332 2233678999999999999999877666666543
No 95
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=65.54 E-value=23 Score=28.46 Aligned_cols=33 Identities=12% Similarity=0.148 Sum_probs=26.3
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..-.++|..+|+++..|+++...-|.+.++..+
T Consensus 155 ~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l~ 187 (203)
T PRK09647 155 LSYEEIAATLGVKLGTVRSRIHRGRQQLRAALA 187 (203)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 346788999999999999999877777666443
No 96
>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=64.73 E-value=28 Score=27.38 Aligned_cols=50 Identities=10% Similarity=0.092 Sum_probs=34.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
+...+..++...| .......++|..+|++...|+++...-|.+.|+....
T Consensus 132 L~~~~r~v~~l~~-----~~g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~~ 181 (188)
T TIGR02943 132 LPEQTARVFMMRE-----VLGFESDEICQELEISTSNCHVLLYRARLSLRACLSI 181 (188)
T ss_pred CCHHHHHHHHHHH-----HhCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444433 2234478899999999999999988777777765543
No 97
>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=64.41 E-value=15 Score=27.79 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=31.5
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 49 TTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 49 t~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
+..+..+++..| .....-.++|..+|++...|+++...-|.+.++.
T Consensus 112 ~~~~r~i~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 112 PARQRAVVVLRY-----YEDLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CHHHHHHhhhHH-----HhcCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 344444444443 2234467889999999999999988777776654
No 98
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=64.14 E-value=17 Score=27.53 Aligned_cols=31 Identities=23% Similarity=0.249 Sum_probs=24.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
..-.++|..+|++...|+.+...-|.+.++.
T Consensus 129 ~s~~eIA~~lgis~~tv~~~l~Rar~~L~~~ 159 (161)
T PRK12541 129 FSYKEIAEMTGLSLAKVKIELHRGRKETKSI 159 (161)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 3467889999999999999988777666643
No 99
>PRK10403 transcriptional regulator NarP; Provisional
Probab=63.94 E-value=12 Score=28.58 Aligned_cols=52 Identities=19% Similarity=0.224 Sum_probs=39.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
..+|..+..+|+...+. ..+.++|+.++++++.|++..+|=+.|.....+.+
T Consensus 152 ~~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~~~ 203 (215)
T PRK10403 152 SVLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSRVA 203 (215)
T ss_pred ccCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 35888888888766533 34678899999999999999998887765444333
No 100
>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=63.53 E-value=28 Score=29.01 Aligned_cols=35 Identities=9% Similarity=0.201 Sum_probs=28.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
..-+|+|..+|+++..|+++...-|.+.|+..+.+
T Consensus 178 ~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 178 LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999998888877765443
No 101
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=63.42 E-value=26 Score=27.45 Aligned_cols=31 Identities=26% Similarity=0.215 Sum_probs=24.8
Q ss_pred HHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 68 IAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 68 ~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
...-+++|..+|++...|+..+..-|.+.++
T Consensus 122 g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 122 GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3446789999999999999999866666555
No 102
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=63.38 E-value=26 Score=27.69 Aligned_cols=32 Identities=9% Similarity=0.087 Sum_probs=26.1
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|++...|++++..-|.+.|+..
T Consensus 153 ~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 153 LSNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34678899999999999999987777766643
No 103
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=63.33 E-value=22 Score=24.86 Aligned_cols=44 Identities=14% Similarity=0.139 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 47 PFTTQQLLSLEKKFRE-----KQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~-----~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
-++.+|+..|...|.. +.+.+..+..++-..+|+++..|..+|.
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 4688999999999864 3578888888877778999988888875
No 104
>PRK10072 putative transcriptional regulator; Provisional
Probab=63.12 E-value=11 Score=27.18 Aligned_cols=40 Identities=20% Similarity=0.230 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
.+...+..|...... ...+||+.+|++...|..|.+.+|.
T Consensus 33 ~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 33 TSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred CChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 355556666443222 2678999999999999999988764
No 105
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=62.74 E-value=21 Score=29.14 Aligned_cols=52 Identities=10% Similarity=0.072 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..++...|.. .+.....-.++|..+|++...|+.+...-|.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l-~~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGL-NGGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhcc-CCCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3555556666555421 112334477899999999999999988777776654
No 106
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=62.73 E-value=23 Score=27.54 Aligned_cols=30 Identities=20% Similarity=0.318 Sum_probs=24.5
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-.++|..+|++...|++|...-|.+.|+
T Consensus 150 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 150 CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 346788999999999999998877766554
No 107
>PF13518 HTH_28: Helix-turn-helix domain
Probab=62.40 E-value=11 Score=22.98 Aligned_cols=24 Identities=17% Similarity=0.403 Sum_probs=19.7
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
...++|..+|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 355689999999999999986543
No 108
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=62.32 E-value=12 Score=28.75 Aligned_cols=36 Identities=17% Similarity=0.159 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
|.....-+++|..+|+++..|++.+..-|.+.++..
T Consensus 133 ~~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 133 DLEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred HhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344455788999999999999999988777777654
No 109
>KOG0773|consensus
Probab=62.10 E-value=12 Score=32.55 Aligned_cols=41 Identities=34% Similarity=0.481 Sum_probs=35.9
Q ss_pred HHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 58 KKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 58 ~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-+.+.|++..+...|+...+|+-.+|.+||-|.|.+.+.
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 33456889999999999999999999999999999888776
No 110
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=61.74 E-value=23 Score=28.04 Aligned_cols=32 Identities=19% Similarity=0.066 Sum_probs=26.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
....++|..+|++...|++++..-|.+.|+..
T Consensus 130 ~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 130 FSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999988887777654
No 111
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=61.74 E-value=30 Score=27.25 Aligned_cols=33 Identities=12% Similarity=0.095 Sum_probs=25.9
Q ss_pred CHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 67 SIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 67 s~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
....-.++|..+|++...|++.+...|.+.|+.
T Consensus 169 e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 169 DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 345577899999999999998887766666654
No 112
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=61.63 E-value=18 Score=29.52 Aligned_cols=32 Identities=13% Similarity=0.078 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|+++..|+++...-|.+.++..
T Consensus 151 ~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 151 MSYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999887776666644
No 113
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=61.44 E-value=30 Score=27.28 Aligned_cols=32 Identities=9% Similarity=0.069 Sum_probs=26.0
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.-.++|..||+++..|+++...-|.+.++...
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45788999999999999999877777666543
No 114
>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=60.95 E-value=24 Score=28.58 Aligned_cols=47 Identities=21% Similarity=0.250 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..+|...|-.. ....++|..+|++...|+.+...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45667777777665322 246889999999999999998776666554
No 115
>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=60.60 E-value=21 Score=27.28 Aligned_cols=47 Identities=13% Similarity=0.162 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
++..+..++...|-. .....++|..+|+++..|+++...-|.+.++.
T Consensus 120 L~~~~r~i~~l~~~~-----g~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~~ 166 (169)
T TIGR02954 120 LNDKYQTAIILRYYH-----DLTIKEIAEVMNKPEGTVKTYLHRALKKLKKR 166 (169)
T ss_pred CCHHHhHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444445555444322 23467889999999999999887766666653
No 116
>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=60.51 E-value=22 Score=26.94 Aligned_cols=30 Identities=33% Similarity=0.161 Sum_probs=23.3
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-.++|..+|+++..|++....-|.+.|+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 446788999999999999888665555554
No 117
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=60.42 E-value=21 Score=26.92 Aligned_cols=46 Identities=17% Similarity=0.185 Sum_probs=35.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
..++..+..+|+. +..+ + ...++|+.+++++..|+.|.+|-+.|..
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 3488888888876 3333 2 3678899999999999999998776654
No 118
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=60.32 E-value=31 Score=26.34 Aligned_cols=47 Identities=11% Similarity=-0.027 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
++..+..++...| .....-.++|..+|+++..|+++...-|.+.|..
T Consensus 113 L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 159 (164)
T PRK12547 113 LSADQREAIILIG-----ASGFSYEDAAAICGCAVGTIKSRVSRARNRLQEL 159 (164)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4444444444432 2233467899999999999999998777666653
No 119
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=60.19 E-value=38 Score=26.45 Aligned_cols=51 Identities=12% Similarity=0.092 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
++..|..++...|-. ...-.++|..+|+++..|++....-|.+.|+.....
T Consensus 132 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 182 (191)
T PRK12520 132 LPPRTGRVFMMREWL-----ELETEEICQELQITATNAWVLLYRARMRLRECLDLH 182 (191)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555444322 234678999999999999999988777777655443
No 120
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=60.14 E-value=17 Score=28.29 Aligned_cols=46 Identities=13% Similarity=0.087 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
++..+..+|...| .....-.++|..+|++...|+++...-|.+.|+
T Consensus 136 L~~~~r~vl~l~~-----~~~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 136 LSPEERRVIEVLY-----YQGYTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444444444332 223346788999999999999998766666554
No 121
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=59.93 E-value=30 Score=26.45 Aligned_cols=47 Identities=13% Similarity=0.128 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
++..+..+|...|-. ...-+++|..+|+++..|+.....-|.+.|+.
T Consensus 119 L~~~~r~vl~L~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-----GWSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 445555555544322 23367899999999999999987666666654
No 122
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=59.88 E-value=21 Score=28.04 Aligned_cols=47 Identities=13% Similarity=0.155 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..++...|- .....+++|+.+|++...|++..+.-|.+.|+
T Consensus 131 ~L~~~~r~i~~l~~~-----~g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 131 DLEKLDREIFIRRYL-----LGEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred hCCHHHHHHHHHHHH-----ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345555555554332 22446789999999999999888766655554
No 123
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=59.85 E-value=34 Score=25.79 Aligned_cols=31 Identities=10% Similarity=0.252 Sum_probs=24.3
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
....++|+.+|++...|+......+.+.++.
T Consensus 126 ~s~~EIA~~lgis~~tV~~~l~ra~~~lr~~ 156 (163)
T PRK07037 126 ETQKDIARELGVSPTLVNFMIRDALVHCRKC 156 (163)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3477899999999999999877666665543
No 124
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=59.83 E-value=18 Score=28.38 Aligned_cols=36 Identities=8% Similarity=0.069 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 66 LSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 66 ps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.....-.++|..+|+++..|++....-|.+.|+..+
T Consensus 152 ~~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 152 FDGLSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 344456889999999999999999877777776543
No 125
>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=59.74 E-value=28 Score=28.56 Aligned_cols=53 Identities=9% Similarity=0.071 Sum_probs=39.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|..+|....+ ....-.++|..+|++...|+.+..+-+.|.|...
T Consensus 176 ~L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~~ 228 (238)
T TIGR02393 176 TLTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHPS 228 (238)
T ss_pred hCCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhhH
Confidence 4667777777777743222 2234778999999999999999988888877653
No 126
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=59.42 E-value=39 Score=27.17 Aligned_cols=49 Identities=10% Similarity=0.111 Sum_probs=33.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
++..|..++...|-. .....++|..+|++...|+++...-|.+.|+...
T Consensus 149 L~~~~r~v~~L~~~~-----g~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l~ 197 (206)
T PRK12544 149 LPAKYARVFMMREFI-----ELETNEICHAVDLSVSNLNVLLYRARLRLRECLE 197 (206)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 444454444444322 2235789999999999999999888877777554
No 127
>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=59.10 E-value=24 Score=29.19 Aligned_cols=47 Identities=15% Similarity=0.180 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..++...|... ..-.++|..+|++...|+.+...-+.+.|+
T Consensus 205 ~L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 205 ILSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred cCCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666677776665332 235789999999999999998877766665
No 128
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=59.07 E-value=20 Score=29.12 Aligned_cols=43 Identities=14% Similarity=0.253 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhc--CCCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 47 PFTTQQLLSLEKKFREK--QYLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~--~yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
.+|..|+++|..+|+.. -||-...-.+||+++|++..-+..-.
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~ehL 199 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEHL 199 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHHH
Confidence 69999999999999754 35667778899999999986655333
No 129
>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=59.02 E-value=22 Score=29.98 Aligned_cols=52 Identities=17% Similarity=0.048 Sum_probs=39.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
...+|..+.++|+-..+ . ....++|..||+++..|+.+.+|-+.|.+...+.
T Consensus 188 ~~~LT~RE~evl~l~a~--G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~ 239 (247)
T TIGR03020 188 AGLITAREAEILAWVRD--G----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRA 239 (247)
T ss_pred ccCCCHHHHHHHHHHHC--C----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHH
Confidence 34689999999986542 2 3467889999999999999999887776654433
No 130
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=58.77 E-value=18 Score=27.54 Aligned_cols=45 Identities=22% Similarity=0.208 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
.+|..+..+|+..++. ..++++|..++++++.|++..++=|.|-.
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5888888888776543 25888999999999999999888776644
No 131
>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=58.62 E-value=31 Score=26.93 Aligned_cols=34 Identities=18% Similarity=0.210 Sum_probs=26.3
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
|.....-.++|..+|+++..|++++..-|.+.|+
T Consensus 162 ~~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 162 YLDGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HHcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445567889999999999999988766666554
No 132
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=58.29 E-value=17 Score=28.48 Aligned_cols=36 Identities=19% Similarity=0.081 Sum_probs=28.3
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
|.....-+++|..+|++...|+++...-|.+.|+..
T Consensus 152 ~~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 152 EHGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred hccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 344455788999999999999999887777766644
No 133
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=58.17 E-value=20 Score=29.79 Aligned_cols=48 Identities=13% Similarity=0.125 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..+|...|-. ...-.++|..+|++...|+.|...-+.|.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3566666666665532 22357899999999999999988777766653
No 134
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=58.16 E-value=33 Score=26.97 Aligned_cols=32 Identities=9% Similarity=0.056 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|++...|++.+..-|.+.|+..
T Consensus 158 ~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~l 189 (194)
T PRK12531 158 LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHSM 189 (194)
T ss_pred CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHh
Confidence 34678999999999999988877776666543
No 135
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=57.69 E-value=19 Score=30.12 Aligned_cols=49 Identities=16% Similarity=0.116 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.+...+..+|...|.. ...-.++|..+|++...|+.+...-+.|.|+..
T Consensus 203 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 203 QLEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred cCCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3555556666655532 345678999999999999999987777766543
No 136
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=57.47 E-value=21 Score=29.56 Aligned_cols=47 Identities=15% Similarity=0.236 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
+...+..++...|- ....-.++|..+|++...|+.++..-|.+.|+.
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 248 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKKL 248 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 45556666655542 233467899999999999999998777766653
No 137
>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=57.05 E-value=21 Score=28.01 Aligned_cols=37 Identities=8% Similarity=-0.027 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
|.....-.++|..+|+++..|+++...-|.+.|+...
T Consensus 144 ~~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 144 DVEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hhcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4444557889999999999999999887777776543
No 138
>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=56.74 E-value=27 Score=28.76 Aligned_cols=53 Identities=15% Similarity=0.112 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
...++..++++|.-..+ ...-.++|..+|++++.|+.+..|-+.|.+...+.+
T Consensus 169 ~~~Lt~re~evl~~~a~------G~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~~ 221 (232)
T TIGR03541 169 AGVLSEREREVLAWTAL------GRRQADIAAILGISERTVENHLRSARRKLGVATTAQ 221 (232)
T ss_pred hccCCHHHHHHHHHHHC------CCCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHHH
Confidence 34678888888876531 144678899999999999999999888776554443
No 139
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=56.63 E-value=25 Score=30.10 Aligned_cols=51 Identities=12% Similarity=0.091 Sum_probs=38.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|..+|- |-....-.++|..+|++...|+.+-..-+.|.|...
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~l 277 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRAL 277 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577778888887763 123345788999999999999999887777776544
No 140
>PF13551 HTH_29: Winged helix-turn helix
Probab=56.59 E-value=65 Score=22.45 Aligned_cols=48 Identities=19% Similarity=0.380 Sum_probs=32.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcC-----CCCHHHHHH-H-HHh--cCCChhHHHHhhH
Q psy3429 43 KPRTPFTTQQLLSLEKKFREKQ-----YLSIAERAE-F-SSS--LHLTETQVKIWFQ 90 (192)
Q Consensus 43 r~Rt~ft~~Ql~~Le~~F~~~~-----yps~~~r~~-L-A~~--l~Ls~~qV~~WFq 90 (192)
+.+..++.++...|.+.+..+. ..+..+..+ | .+. +.++...|..|++
T Consensus 53 ~~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 53 RPRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3344499999999999998876 344444443 4 222 3578888888875
No 141
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=56.54 E-value=30 Score=28.26 Aligned_cols=51 Identities=24% Similarity=0.168 Sum_probs=39.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
.+|..++++|+...+- ....++|+.|++++..|+.+..|-..|..-....+
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr~e 205 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAVKNRTQ 205 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 4889999999888652 23578899999999999999998877766544433
No 142
>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=56.49 E-value=17 Score=27.19 Aligned_cols=34 Identities=21% Similarity=0.166 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
|.....-+++|..+|+++..|+++...-|.+.++
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455668899999999999999998876666554
No 143
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=56.32 E-value=37 Score=26.05 Aligned_cols=31 Identities=13% Similarity=0.190 Sum_probs=25.0
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
..-.++|..+|+++..|+++..+-+.+.+..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 136 MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999999998777666543
No 144
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=56.28 E-value=37 Score=26.41 Aligned_cols=47 Identities=17% Similarity=0.135 Sum_probs=32.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
++..+..+++..| .....-.++|..+|++...|+.+...-|.+.|+.
T Consensus 132 L~~~~r~v~~l~~-----~~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 132 LPEKMRLAIQAVK-----LEGLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CCHHHHHHHHHHH-----HcCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4455555554432 2334577899999999999999997777666654
No 145
>PRK10651 transcriptional regulator NarL; Provisional
Probab=56.11 E-value=27 Score=26.67 Aligned_cols=50 Identities=18% Similarity=0.143 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
.++..+.++|+...+. ....++|++++++++.|++..+|-|.|..-....
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~~~ 204 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLKSRV 204 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCHH
Confidence 4899999988776422 2356789999999999999999888776544433
No 146
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=56.08 E-value=37 Score=26.35 Aligned_cols=34 Identities=21% Similarity=0.074 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 66 LSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 66 ps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
......+++|..+|++...|++....-|.+.|+.
T Consensus 143 ~~g~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 143 LEGLSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3334577899999999999999998777776663
No 147
>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=55.73 E-value=13 Score=21.79 Aligned_cols=23 Identities=13% Similarity=0.397 Sum_probs=19.3
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..++|+.+|++...|..|.++.+
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~ 25 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGK 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCC
Confidence 46889999999999999986543
No 148
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=55.49 E-value=79 Score=25.03 Aligned_cols=47 Identities=9% Similarity=0.105 Sum_probs=36.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
...++.+++.++.+.-..+ |..-.+..||+++|++..-|.+-..--.
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 4689999999998885554 5667789999999999887776554333
No 149
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=55.10 E-value=12 Score=22.82 Aligned_cols=23 Identities=17% Similarity=0.333 Sum_probs=17.5
Q ss_pred HHHHHHHHhcCCChhHHHHhhHh
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
....++|+.+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 45778999999999999999864
No 150
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=54.78 E-value=22 Score=27.24 Aligned_cols=47 Identities=17% Similarity=0.126 Sum_probs=36.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..++..+..+|+...+. ..++++|.+++++.+.|+++..+-|.|..-
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~~ 194 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLGL 194 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcCC
Confidence 35788888888654433 558899999999999999999888777543
No 151
>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=54.57 E-value=47 Score=28.11 Aligned_cols=54 Identities=20% Similarity=0.183 Sum_probs=38.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.++..+..+|...|... |.....-.++|..||++...|+.+...-+.+.|+...
T Consensus 222 ~Lp~~~R~Vl~l~ygL~-~~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l~ 275 (285)
T TIGR02394 222 ELNERQREVLARRFGLL-GYEPATLEEVAAEVGLTRERVRQIQVEALKKLRRILE 275 (285)
T ss_pred cCCHHHHHHHHHHhCCC-CCCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 46666677776665211 1223457788999999999999999888877777543
No 152
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=54.27 E-value=26 Score=27.01 Aligned_cols=33 Identities=21% Similarity=0.167 Sum_probs=26.2
Q ss_pred CHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 67 SIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 67 s~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
....-+++|..+|++...|+++...-|.+.|+.
T Consensus 151 ~~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 151 EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344567899999999999999988777776653
No 153
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=54.26 E-value=39 Score=27.58 Aligned_cols=52 Identities=10% Similarity=0.036 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..++...|-... .....-+++|..+|++...|+++-...+.+.|+.
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~~ 226 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFKE 226 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 355556666655541111 2334578899999999999998866556555554
No 154
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=53.86 E-value=46 Score=26.10 Aligned_cols=48 Identities=13% Similarity=0.036 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
++..+..+++..|- ....-.++|..+|++...|+++...-|.+.++..
T Consensus 112 Lp~~~R~v~~L~~~-----eg~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~~ 159 (182)
T PRK12511 112 LPEEQRAALHLVAI-----EGLSYQEAAAVLGIPIGTLMSRIGRARAALRAFE 159 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 44555555544332 2234678999999999999999876666666543
No 155
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=53.77 E-value=30 Score=29.00 Aligned_cols=49 Identities=12% Similarity=0.072 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.++..+..+|...|.. ...-.++|..+|++...|+....+-+.+.|+..
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 4556666666665532 234678999999999999998887777777654
No 156
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=53.69 E-value=42 Score=26.02 Aligned_cols=47 Identities=6% Similarity=0.080 Sum_probs=32.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..|..++.-.|-. ...-+|+|..+|+++..|+....+.+.+.+.
T Consensus 127 ~Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 127 TLRPRVKQAFLMATLD-----GMKQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3555666655554322 2346789999999999999998876666543
No 157
>cd00131 PAX Paired Box domain
Probab=53.69 E-value=89 Score=23.40 Aligned_cols=46 Identities=11% Similarity=-0.002 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCC-------ChhHHHHhhHhH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHL-------TETQVKIWFQNR 92 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~L-------s~~qV~~WFqNr 92 (192)
..+.++...+++....++..+..|..++...-|+ +...|..||+++
T Consensus 75 ~~~~~~~~~i~~~v~~~p~~Tl~El~~~L~~~gv~~~~~~~s~stI~R~L~~~ 127 (128)
T cd00131 75 VATPEVVKKIEIYKQENPGMFAWEIRDRLLQEGVCDKSNVPSVSSINRILRNK 127 (128)
T ss_pred cCCHHHHHHHHHHHHHCCCCCHHHHHHHHHHcCCcccCCCCCHHHHHHHHHhc
Confidence 4466777777777788888777766554223355 888888888753
No 158
>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=52.96 E-value=20 Score=21.75 Aligned_cols=21 Identities=5% Similarity=0.137 Sum_probs=18.9
Q ss_pred HHHHhcCCChhHHHHhhHhHH
Q psy3429 73 EFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 73 ~LA~~l~Ls~~qV~~WFqNrR 93 (192)
+||+.+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999873
No 159
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=52.63 E-value=14 Score=23.96 Aligned_cols=20 Identities=10% Similarity=0.208 Sum_probs=17.4
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
..++|+.+|++...|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999954
No 160
>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=52.34 E-value=31 Score=28.99 Aligned_cols=50 Identities=10% Similarity=0.127 Sum_probs=37.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..+|..+|-. + ....-.++|..+|++...|+.+..+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~--~-~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLD--D-DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcC--C-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5777788888887732 1 123457899999999999999888877777653
No 161
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=52.31 E-value=38 Score=26.48 Aligned_cols=30 Identities=7% Similarity=-0.042 Sum_probs=23.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-+|+|..+|+++..|+++...-|.+.|+
T Consensus 147 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 147 LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 346789999999999999998766655554
No 162
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=51.88 E-value=25 Score=27.52 Aligned_cols=35 Identities=14% Similarity=0.201 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 66 LSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 66 ps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.....-+++|..+|++...|+++...-|.+.|+..
T Consensus 148 ~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 148 VAELEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 33445788999999999999999987777766643
No 163
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=51.68 E-value=28 Score=29.31 Aligned_cols=48 Identities=10% Similarity=0.187 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..+|+.+|.. ...-.++|..+|++...|+.+...-+.+.|+.
T Consensus 215 ~L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 262 (264)
T PRK07122 215 ALPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRDQ 262 (264)
T ss_pred cCCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4566666677666632 23468899999999999999988777766653
No 164
>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=51.31 E-value=13 Score=24.20 Aligned_cols=27 Identities=22% Similarity=0.300 Sum_probs=21.1
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
...++|..||++...|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 456899999999999999985 444443
No 165
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=51.16 E-value=45 Score=26.51 Aligned_cols=31 Identities=10% Similarity=0.014 Sum_probs=25.5
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.-.++|..+|++...|+++...-|.+.|+..
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l 181 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAAT 181 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 4678999999999999999987777766644
No 166
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=50.78 E-value=29 Score=26.61 Aligned_cols=32 Identities=16% Similarity=0.144 Sum_probs=25.9
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|+++..|+++...-|.+.++..
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 136 YSYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999987777766644
No 167
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=49.91 E-value=54 Score=25.44 Aligned_cols=32 Identities=25% Similarity=0.374 Sum_probs=25.8
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|+++..|++....-|.+.++..
T Consensus 139 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 139 LTYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999999887777766643
No 168
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=49.78 E-value=34 Score=27.63 Aligned_cols=47 Identities=15% Similarity=0.199 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..++...|.. ...-.++|..+|++...|+.|...-+.+.|+
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5666677777666532 2357789999999999999998766666554
No 169
>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=49.75 E-value=17 Score=23.74 Aligned_cols=21 Identities=10% Similarity=0.208 Sum_probs=18.2
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 467899999999999999753
No 170
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=49.64 E-value=27 Score=27.12 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=24.5
Q ss_pred CHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 67 SIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 67 s~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
....-+++|..+|+++..|++....-|.+.|.
T Consensus 152 ~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 152 EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 33456788999999999999887766666554
No 171
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=49.25 E-value=60 Score=25.43 Aligned_cols=32 Identities=13% Similarity=0.036 Sum_probs=25.4
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
..-+++|..+|+++..|+.....-|.+.|+..
T Consensus 128 ~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~l 159 (182)
T PRK12540 128 FSYEDAAAICGCAVGTIKSRVNRARSKLSALL 159 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999877666666543
No 172
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=49.24 E-value=37 Score=28.37 Aligned_cols=49 Identities=10% Similarity=0.053 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.+...+..+|...|. ....-.++|..+|++...|+.+...-+.+.|+..
T Consensus 205 ~L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~l 253 (257)
T PRK05911 205 ALEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRATL 253 (257)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 355566666666653 2334678999999999999999877776666543
No 173
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=49.17 E-value=25 Score=25.22 Aligned_cols=35 Identities=17% Similarity=0.214 Sum_probs=18.4
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHH
Q psy3429 54 LSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEA 102 (192)
Q Consensus 54 ~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~ 102 (192)
.+..-.|+.|+||...-... | =.|||.+|++.+.+
T Consensus 15 RiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 34444588899997432111 1 15888898887654
No 174
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=48.94 E-value=64 Score=25.35 Aligned_cols=30 Identities=23% Similarity=0.179 Sum_probs=21.6
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-.++|..+|++...|++=...-|.+.|+
T Consensus 151 ~s~~EIA~~lg~s~~tV~~rl~rar~~Lr~ 180 (192)
T PRK09643 151 YSVADAARMLGVAEGTVKSRCARGRARLAE 180 (192)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346788999999999998765544544444
No 175
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=48.73 E-value=50 Score=24.62 Aligned_cols=33 Identities=15% Similarity=0.190 Sum_probs=25.9
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
-.++|..+|+++..|+++-.+-|.|.+.....+
T Consensus 159 ~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~~~ 191 (202)
T PRK09390 159 NKVIARDLDISPRTVEVYRANVMTKMQAGSLSE 191 (202)
T ss_pred hHHHHHHcCCCHHHHHHHHHHHHHHHccccHHH
Confidence 456788999999999999988887766655444
No 176
>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=48.69 E-value=18 Score=21.40 Aligned_cols=19 Identities=11% Similarity=0.179 Sum_probs=15.4
Q ss_pred HHHHHHhcCCChhHHHHhh
Q psy3429 71 RAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WF 89 (192)
.-++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999995
No 177
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=48.00 E-value=30 Score=28.23 Aligned_cols=37 Identities=19% Similarity=0.153 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
|......+++|..+|++...|++....-|.+.|+...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 4455667899999999999999998877777776543
No 178
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=47.97 E-value=90 Score=24.49 Aligned_cols=35 Identities=20% Similarity=0.180 Sum_probs=27.9
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
..-+++|..+|+++..|+++...-|.+.++.....
T Consensus 145 ~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~~ 179 (188)
T PRK12517 145 FSGEEIAEILDLNKNTVMTRLFRARNQLKEALEKP 179 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 44678999999999999999987777777665433
No 179
>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=47.86 E-value=30 Score=26.39 Aligned_cols=29 Identities=28% Similarity=0.519 Sum_probs=20.1
Q ss_pred CCHHHHHHHHHhcCCCh-----hHHHHhhHhHHH
Q psy3429 66 LSIAERAEFSSSLHLTE-----TQVKIWFQNRRA 94 (192)
Q Consensus 66 ps~~~r~~LA~~l~Ls~-----~qV~~WFqNrR~ 94 (192)
.+...|.+||.+||++. .+..+|....-+
T Consensus 83 SSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm 116 (127)
T PF12200_consen 83 SSLAARKELAKELGYTGDYNDSASMNIWLHKQVM 116 (127)
T ss_dssp -SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHH
Confidence 56788999999999875 578889975433
No 180
>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=47.57 E-value=19 Score=23.20 Aligned_cols=20 Identities=5% Similarity=0.212 Sum_probs=17.8
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
..++|+.+|++...|+.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999985
No 181
>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=47.26 E-value=59 Score=26.57 Aligned_cols=52 Identities=10% Similarity=0.076 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..++...|-... .....-.++|..+|++...|+++...-+.+.|+.
T Consensus 178 ~Lp~~~R~ii~L~~~l~~-~eg~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 178 KLNDREKKIMELRFGLVG-GTEKTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHHccCC-CCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 455556566655542100 1223467889999999999999987766666653
No 182
>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=46.87 E-value=45 Score=27.06 Aligned_cols=46 Identities=13% Similarity=0.123 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
.++..+..++...|.. .....++|..+|++...|..+-..-..|.|
T Consensus 183 ~L~~~e~~i~~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 183 KLDERERQIIMLRYFK-----DKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred cCCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 5666666666666532 245788999999999999887665444443
No 183
>PRK09480 slmA division inhibitor protein; Provisional
Probab=46.79 E-value=23 Score=27.33 Aligned_cols=41 Identities=10% Similarity=0.104 Sum_probs=32.2
Q ss_pred HHHHHHH---HHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 53 LLSLEKK---FREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 53 l~~Le~~---F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
..+|++. |..+.. ......+||++.|++...+-.+|.|+..
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 3444443 555556 8888999999999999999999999764
No 184
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=46.08 E-value=45 Score=27.69 Aligned_cols=47 Identities=13% Similarity=0.222 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..+|+..|... ....++|..+|++...|+.+-.+-..|.|+
T Consensus 209 ~L~~~er~vi~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQG-----KTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57777888888877432 346789999999999998887665555544
No 185
>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=46.00 E-value=21 Score=23.12 Aligned_cols=21 Identities=10% Similarity=0.167 Sum_probs=18.2
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999764
No 186
>PF15063 TC1: Thyroid cancer protein 1
Probab=45.93 E-value=43 Score=23.30 Aligned_cols=38 Identities=18% Similarity=0.146 Sum_probs=29.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCCh
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTE 82 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~ 82 (192)
--.|....+..|.+.|+...=...+||.++.-.+.-..
T Consensus 31 aNIFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~ 68 (79)
T PF15063_consen 31 ANIFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDP 68 (79)
T ss_pred hhhhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCH
Confidence 34688888889999999999888888888765555433
No 187
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=45.85 E-value=62 Score=24.87 Aligned_cols=31 Identities=13% Similarity=0.111 Sum_probs=23.9
Q ss_pred HHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 68 IAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 68 ~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
...-.++|..+|++...|+++...-+.+.+.
T Consensus 135 g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 135 GLTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3447889999999999999998655555443
No 188
>PLN03162 golden-2 like transcription factor; Provisional
Probab=45.50 E-value=2.4e+02 Score=25.68 Aligned_cols=65 Identities=14% Similarity=0.095 Sum_probs=43.6
Q ss_pred CCCCCCCCCCHHH-HHHHHHHHHhc-CCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHHH
Q psy3429 40 PNRKPRTPFTTQQ-LLSLEKKFREK-QYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAEI 104 (192)
Q Consensus 40 ~~rr~Rt~ft~~Q-l~~Le~~F~~~-~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~~ 104 (192)
.+||.|-+.|.+- .+.+++..+.. ..-....+.+|-..-||+..+|+.-.|--|...|+...++.
T Consensus 232 g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEa 298 (526)
T PLN03162 232 GKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREA 298 (526)
T ss_pred CCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhh
Confidence 3556777888754 34445554444 23445556677777799999999999998888776544433
No 189
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=45.36 E-value=62 Score=25.47 Aligned_cols=30 Identities=23% Similarity=0.314 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
...+|+|..+|++++.|+..++.-|.+.++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356789999999999999988877755444
No 190
>PTZ00183 centrin; Provisional
Probab=45.08 E-value=1.1e+02 Score=22.50 Aligned_cols=42 Identities=19% Similarity=0.171 Sum_probs=32.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHhcCC
Q psy3429 39 KPNRKPRTPFTTQQLLSLEKKFRE-----KQYLSIAERAEFSSSLHL 80 (192)
Q Consensus 39 ~~~rr~Rt~ft~~Ql~~Le~~F~~-----~~yps~~~r~~LA~~l~L 80 (192)
++++-.+..|+..++..|+.+|.. +.+.+..+-..+...+|+
T Consensus 2 ~~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 2 RKRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred CccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 345556788999999999999863 567888888777777664
No 191
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=45.06 E-value=74 Score=22.93 Aligned_cols=44 Identities=14% Similarity=0.184 Sum_probs=33.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCC-ChhHHHHhhHhH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHL-TETQVKIWFQNR 92 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~L-s~~qV~~WFqNr 92 (192)
|..|+.+....+=+.+....+ ...++|+++|+ +..++..|-+.-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHH
Confidence 778999987666666555554 57789999996 999999886543
No 192
>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=44.90 E-value=14 Score=22.74 Aligned_cols=23 Identities=13% Similarity=0.299 Sum_probs=19.3
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||+.+|++...|..|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998844
No 193
>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=44.75 E-value=56 Score=27.58 Aligned_cols=29 Identities=14% Similarity=0.121 Sum_probs=25.2
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
-.|+|..+|+++..|+.+++.-|.+.+..
T Consensus 127 ~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 127 YEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 56889999999999999999888887764
No 194
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=44.35 E-value=92 Score=23.36 Aligned_cols=31 Identities=10% Similarity=0.134 Sum_probs=24.0
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
....++|..+|+++..|++....-+.+.++.
T Consensus 122 ~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 122 LSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 3467889999999999998887666665554
No 195
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=44.30 E-value=59 Score=27.53 Aligned_cols=30 Identities=13% Similarity=0.122 Sum_probs=25.8
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.-+|+|+.+|+++..|+..++.-|.+.++.
T Consensus 133 s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 133 PFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 367889999999999999999888887764
No 196
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=44.13 E-value=29 Score=25.53 Aligned_cols=40 Identities=18% Similarity=0.408 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
++..++..+.+.+... ..++|..||++..-|+.|=|+|+.
T Consensus 44 ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 44 LSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 8888888888777654 467899999999999999998763
No 197
>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=44.07 E-value=53 Score=19.69 Aligned_cols=38 Identities=13% Similarity=0.165 Sum_probs=24.8
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 49 TTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 49 t~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
+..+..+|+..++ ++. ....+||+.+|++...|..-++
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l~ 39 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYLK 39 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHHH
Confidence 3456777766655 443 4477899999999988876553
No 198
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=43.63 E-value=70 Score=24.10 Aligned_cols=26 Identities=15% Similarity=0.291 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.-.++|..+|++...|+++...-+.+
T Consensus 131 s~~EIA~~l~is~~tV~~~l~ra~~~ 156 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNKAAMR 156 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36788999999999999988755444
No 199
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=43.47 E-value=38 Score=26.35 Aligned_cols=33 Identities=21% Similarity=0.215 Sum_probs=27.0
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
..-.|+|..+|++...|+.|....|.+.++...
T Consensus 144 ls~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 144 LSYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 345788999999999999999888888776543
No 200
>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=43.21 E-value=50 Score=25.39 Aligned_cols=47 Identities=13% Similarity=0.110 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..++...| .....-.++|..+|++...|++=...-|.+.|+
T Consensus 140 ~L~~~~r~vi~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRH-----LEGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34555555555533 233456788999999999999877666666554
No 201
>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=43.06 E-value=73 Score=25.87 Aligned_cols=51 Identities=10% Similarity=0.044 Sum_probs=33.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..++...|-.+.+ ....-+++|+.+|++...|+.+...-+.+.|+
T Consensus 174 ~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 174 VLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred hCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4566666666666521110 22346789999999999998887655555544
No 202
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=42.73 E-value=35 Score=26.14 Aligned_cols=34 Identities=15% Similarity=0.099 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
|......+++|..+|++...|+.+...-|.+.++
T Consensus 139 ~~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 139 HYYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hhcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 4455667889999999999999998777766665
No 203
>smart00595 MADF subfamily of SANT domain.
Probab=42.47 E-value=66 Score=21.83 Aligned_cols=32 Identities=22% Similarity=0.270 Sum_probs=26.6
Q ss_pred HHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 72 AEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 72 ~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
.+||.++|.+...|+.-+.|-|.+-++..+..
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~ 62 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRL 62 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 45789999999999999999999888865443
No 204
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=42.19 E-value=75 Score=24.23 Aligned_cols=45 Identities=7% Similarity=0.023 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
++..+..++...| .....-+|+|..+|++...|+.+..+.+.+.+
T Consensus 119 L~~~~r~v~~L~~-----~eg~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 119 LSGKARAAFLMSQ-----LEGLTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4455555544432 22234678999999999999998876665544
No 205
>PRK06424 transcription factor; Provisional
Probab=42.14 E-value=21 Score=27.73 Aligned_cols=24 Identities=4% Similarity=0.061 Sum_probs=21.1
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
.++||..+|++...|..|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999988764
No 206
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=42.09 E-value=63 Score=27.48 Aligned_cols=49 Identities=12% Similarity=0.147 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..+|..+|-.. ....-.++|..+|++..+|+.+-..-..|.|+
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~ 278 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKA 278 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46666777777776321 23345789999999999998877665555554
No 207
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=42.07 E-value=50 Score=20.34 Aligned_cols=35 Identities=14% Similarity=0.176 Sum_probs=23.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 52 Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
|..+|+..++...+.+ ..+||..++++.+.|+.-.
T Consensus 2 ~~~il~~L~~~~~~it---~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 2 QKQILKLLLESKEPIT---AKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHHTTTSBE---HHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCCcC---HHHHHHHhCCCHHHHHHHH
Confidence 3455555555555544 5689999999998887554
No 208
>PRK05572 sporulation sigma factor SigF; Validated
Probab=41.54 E-value=60 Score=26.86 Aligned_cols=48 Identities=13% Similarity=0.139 Sum_probs=35.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..++..+..++...|.. .....++|..+|++...|..+-..-..|.|+
T Consensus 201 ~~L~~~~~~v~~l~~~~-----~~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 201 RELDERERLIVYLRYFK-----DKTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred HcCCHHHHHHHHHHHhC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35777777777777632 2456889999999999998887766666554
No 209
>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=41.52 E-value=17 Score=22.20 Aligned_cols=23 Identities=4% Similarity=-0.012 Sum_probs=20.3
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999997764
No 210
>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=41.26 E-value=20 Score=20.77 Aligned_cols=23 Identities=13% Similarity=0.290 Sum_probs=19.7
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..++|..+|++...|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45789999999999999998763
No 211
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=40.91 E-value=46 Score=24.67 Aligned_cols=28 Identities=11% Similarity=0.045 Sum_probs=22.6
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhhHhH
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWFQNR 92 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WFqNr 92 (192)
+-.....++||+.+|++.+.+..+|+..
T Consensus 22 ~~~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 22 LESPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred cCCCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 3344567889999999999999999765
No 212
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=40.07 E-value=23 Score=25.33 Aligned_cols=38 Identities=11% Similarity=0.171 Sum_probs=26.5
Q ss_pred CCHHHH----HHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 48 FTTQQL----LSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 48 ft~~Ql----~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
++.+|. .+|.+.|+... ...+++|..||++...|..=+
T Consensus 3 Ln~~Q~~~T~~ELq~nf~~~~----ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 3 LNPEQRRATRQELQANFELSG----LSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred CCHHHHHHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHH
Confidence 455554 56667777666 446788999999988877433
No 213
>TIGR01764 excise DNA binding domain, excisionase family. An excisionase, or Xis protein, is a small protein that binds and promotes excisive recombination; it is not enzymatically active. This model represents a number of putative excisionases and related proteins from temperate phage, plasmids, and transposons, as well as DNA binding domains of other proteins, such as a DNA modification methylase. This model identifies mostly small proteins and N-terminal regions of large proteins, but some proteins appear to have two copies. This domain appears similar, in both sequence and predicted secondary structure (PSIPRED) to the MerR family of transcriptional regulators (pfam00376).
Probab=39.78 E-value=33 Score=20.07 Aligned_cols=22 Identities=14% Similarity=0.095 Sum_probs=18.5
Q ss_pred HHHHHHhcCCChhHHHHhhHhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNR 92 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNr 92 (192)
..++|+.+|++...|..|.++.
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g 25 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEG 25 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcC
Confidence 4678999999999999998654
No 214
>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=39.63 E-value=70 Score=27.19 Aligned_cols=31 Identities=23% Similarity=0.187 Sum_probs=25.9
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.-.|+|..||+++..|+.....-|.+.|+..
T Consensus 160 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 190 (324)
T TIGR02960 160 RAAETAELLGTSTASVNSALQRARATLDEVG 190 (324)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHhc
Confidence 3578899999999999999988777777654
No 215
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=39.55 E-value=53 Score=26.00 Aligned_cols=37 Identities=14% Similarity=0.117 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 50 TQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 50 ~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
..-+..|..+++...|......+.+|..||++...|.
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 4568889999999999999999999999999987765
No 216
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=38.96 E-value=85 Score=26.00 Aligned_cols=53 Identities=17% Similarity=0.184 Sum_probs=37.5
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
...+|..++++|.-..+- ..-.++|..|+++++.|+.-.+|-+.|..-..+.+
T Consensus 177 ~~~LT~rE~evl~~~a~G------~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr~q 229 (240)
T PRK10188 177 EMNFSKREKEILKWTAEG------KTSAEIAMILSISENTVNFHQKNMQKKFNAPNKTQ 229 (240)
T ss_pred CCCCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCHHH
Confidence 346777777777655322 23567899999999999999998887765444443
No 217
>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=38.35 E-value=1.1e+02 Score=19.75 Aligned_cols=51 Identities=20% Similarity=0.084 Sum_probs=30.2
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCH---HHHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 44 PRTPFTTQQLLSLEKKFREKQYLSI---AERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 44 ~Rt~ft~~Ql~~Le~~F~~~~yps~---~~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
.|...|.+.-..+..+.+.-...+- ....++-...+|+..||+.=.|.-|.
T Consensus 2 ~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~~ 55 (57)
T TIGR01557 2 PRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYRL 55 (57)
T ss_pred CCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHHc
Confidence 4566677554444444444444333 55545444567789999887776554
No 218
>PF13565 HTH_32: Homeodomain-like domain
Probab=38.25 E-value=1.1e+02 Score=19.93 Aligned_cols=40 Identities=15% Similarity=0.101 Sum_probs=27.8
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHHH-HHHhcCC----ChhHHHHh
Q psy3429 49 TTQQLLSLEKKFREKQYLSIAERAE-FSSSLHL----TETQVKIW 88 (192)
Q Consensus 49 t~~Ql~~Le~~F~~~~yps~~~r~~-LA~~l~L----s~~qV~~W 88 (192)
+.++...+.+.+..++..+..+..+ |+..+|+ +...|..|
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R~ 76 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYRI 76 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHHh
Confidence 6788789999998888777666655 5666553 55555444
No 219
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=38.09 E-value=69 Score=24.39 Aligned_cols=45 Identities=9% Similarity=0.228 Sum_probs=36.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
.+|..+.++|+..++-. .+++||..++++++.|++.-.+=|.|..
T Consensus 143 ~lt~~E~~vl~~l~~g~------~~~~I~~~l~~s~~tv~~~~~~l~~Kl~ 187 (204)
T PRK09958 143 SLSKQEISVMRYILDGK------DNNDIAEKMFISNKTVSTYKSRLMEKLE 187 (204)
T ss_pred cCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 58888888888887543 3788999999999999998887777654
No 220
>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=37.86 E-value=67 Score=19.32 Aligned_cols=38 Identities=13% Similarity=0.300 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
.++.+++..+.+.+... ....++|+.+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 35565555555555444 346789999999999888776
No 221
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=37.18 E-value=49 Score=25.64 Aligned_cols=30 Identities=17% Similarity=0.169 Sum_probs=24.4
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.-+++|..+|++...|+.+...-|.+.|+.
T Consensus 145 s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~~ 174 (179)
T PRK09415 145 SIKEIAEVTGVNENTVKTRLKKAKELLKKG 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999988766666653
No 222
>KOG1923|consensus
Probab=36.92 E-value=51 Score=32.37 Aligned_cols=19 Identities=11% Similarity=-0.101 Sum_probs=8.4
Q ss_pred HHHHHHhcCCChhHHHHhh
Q psy3429 71 RAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WF 89 (192)
|+.++..-+.-..++.+|=
T Consensus 205 r~~~~~~~~~~~dels~m~ 223 (830)
T KOG1923|consen 205 REPQSYQRKALLDELSCMQ 223 (830)
T ss_pred hhHHHHHHHHhcchhHHHH
Confidence 3333333333345566664
No 223
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=36.50 E-value=57 Score=26.32 Aligned_cols=44 Identities=11% Similarity=0.110 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHh
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
.++..++.+|..+...+ +-....-.++|..+++++..|+..+.+
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~ 201 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIW 201 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHH
Confidence 47787777776665433 444456788999999999999988864
No 224
>PF13730 HTH_36: Helix-turn-helix domain
Probab=36.33 E-value=48 Score=20.40 Aligned_cols=43 Identities=7% Similarity=0.056 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHH---hcCCCCHHHHHHHHHhcCCChhHHHHhhHh
Q psy3429 48 FTTQQLLSLEKKFR---EKQYLSIAERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 48 ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
++..++.++-..+. .+.. +-...+.||+.+|++.+.|+.+...
T Consensus 3 Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 3 LSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 45555555544432 2233 3335788999999999999988754
No 225
>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=36.18 E-value=38 Score=22.24 Aligned_cols=21 Identities=14% Similarity=0.436 Sum_probs=16.3
Q ss_pred HHHHHHhcCCChhHHH-HhhHh
Q psy3429 71 RAEFSSSLHLTETQVK-IWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~-~WFqN 91 (192)
..+||+.+|++...|. .|...
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r 36 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKR 36 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHS
T ss_pred HHHHHHHhCcCHHHhhHHHHhC
Confidence 5689999999999999 89854
No 226
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=35.86 E-value=93 Score=24.97 Aligned_cols=45 Identities=13% Similarity=0.119 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
.+|+.++++|...-+- ..-.++|++|+++++.|+.-..|=..|..
T Consensus 137 ~LT~RE~eVL~lla~G------~snkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWMAG------QGTIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 4888888888766332 22578999999999999988876555544
No 227
>PHA01976 helix-turn-helix protein
Probab=35.61 E-value=28 Score=22.41 Aligned_cols=23 Identities=13% Similarity=0.186 Sum_probs=20.0
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||..+|++...|..|..+++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999987654
No 228
>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=35.34 E-value=28 Score=23.07 Aligned_cols=23 Identities=13% Similarity=0.254 Sum_probs=20.2
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||+.+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997764
No 229
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=35.34 E-value=1.1e+02 Score=20.60 Aligned_cols=35 Identities=17% Similarity=0.162 Sum_probs=27.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhcCC--ChhHHHH
Q psy3429 53 LLSLEKKFREKQYLSIAERAEFSSSLHL--TETQVKI 87 (192)
Q Consensus 53 l~~Le~~F~~~~yps~~~r~~LA~~l~L--s~~qV~~ 87 (192)
+..+|+.+++|+-.+.+....+..+.|- ++++|+-
T Consensus 19 r~~~~k~l~~NPpine~mir~M~~QMG~kpSekqi~Q 55 (64)
T PF03672_consen 19 RKYMEKQLKENPPINEKMIRAMMMQMGRKPSEKQIKQ 55 (64)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHhCCCccHHHHHH
Confidence 4567888899998999999999888874 5555553
No 230
>PHA02955 hypothetical protein; Provisional
Probab=35.01 E-value=45 Score=27.67 Aligned_cols=46 Identities=11% Similarity=0.086 Sum_probs=36.0
Q ss_pred HHHHHHHHHHHHhc-CCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 50 TQQLLSLEKKFREK-QYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 50 ~~Ql~~Le~~F~~~-~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
..|+..|-+.|.+. .-...++|.+++.+||+.-..|..||.+.-.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q 106 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQL 106 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhh
Confidence 35677777777665 57788999999999999887789999875443
No 231
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=34.84 E-value=60 Score=26.89 Aligned_cols=31 Identities=19% Similarity=0.226 Sum_probs=25.3
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
.-.|+|+.+|+++..|+++...-|.+.|+..
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~l 164 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTVS 164 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4578899999999999999887777766544
No 232
>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=34.80 E-value=1.7e+02 Score=21.37 Aligned_cols=47 Identities=19% Similarity=0.169 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.+|..|...|+-+|..+ ..-.|+|..+|++..-|.-|.+.-+.+...
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~~L~~ 63 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEKKLEE 63 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 47888999998776544 456789999999999999999765554433
No 233
>PF12728 HTH_17: Helix-turn-helix domain
Probab=34.78 E-value=42 Score=20.40 Aligned_cols=22 Identities=18% Similarity=0.338 Sum_probs=18.5
Q ss_pred HHHHHHhcCCChhHHHHhhHhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNR 92 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNr 92 (192)
..++|+.||++...|..|.++.
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g 25 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQG 25 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcC
Confidence 4678999999999999998654
No 234
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=34.74 E-value=96 Score=24.40 Aligned_cols=44 Identities=9% Similarity=-0.040 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKA 96 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~ 96 (192)
.+|+.++++|+...+- ..-.++|++++++++.|+.-..|=..|.
T Consensus 150 ~Lt~rE~evl~~~~~G------~s~~eIA~~l~iS~~TV~~h~~~i~~Kl 193 (216)
T PRK10840 150 RLSPKESEVLRLFAEG------FLVTEIAKKLNRSIKTISSQKKSAMMKL 193 (216)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHHCCCHHHHHHHHHHHHHHc
Confidence 5899999999887533 3367899999999999998776655444
No 235
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=34.37 E-value=1.1e+02 Score=26.53 Aligned_cols=52 Identities=15% Similarity=0.149 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..+|...|....+ ....-+++|..+|++...|+..-..-+.|.|+.
T Consensus 256 ~L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVRqi~~rAl~kLr~~ 307 (317)
T PRK07405 256 DLTPQQKEVIALRFGLEDG-QPLTLAKIGERLNISRERVRQIEREALSKLRKR 307 (317)
T ss_pred cCCHHHHHHHHHHhhcCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4666667777777753322 224578899999999999999988877777763
No 236
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=34.37 E-value=1.1e+02 Score=26.00 Aligned_cols=18 Identities=22% Similarity=0.584 Sum_probs=13.8
Q ss_pred ChhHHHHhhHhHHHHHHH
Q psy3429 81 TETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 81 s~~qV~~WFqNrR~k~kr 98 (192)
.-..|..||+.++.|.|-
T Consensus 99 ~~~~i~~w~~~~~~kkke 116 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKE 116 (242)
T ss_pred ccchHHHHHHHHHHHHHH
Confidence 467899999998886443
No 237
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=34.24 E-value=81 Score=24.63 Aligned_cols=36 Identities=19% Similarity=0.193 Sum_probs=29.7
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 51 QQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 51 ~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
.-+.+|...=+...|.+....+++|+.||++..+|.
T Consensus 24 ~li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V~ 59 (156)
T PRK05988 24 ALLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEVH 59 (156)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHHH
Confidence 446666666667789999999999999999988765
No 238
>PRK09483 response regulator; Provisional
Probab=33.50 E-value=1.1e+02 Score=23.55 Aligned_cols=45 Identities=18% Similarity=0.146 Sum_probs=32.8
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKA 96 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~ 96 (192)
..||..++++|+... ..+ .-.++|..++++++.|+.--+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~----~~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQ----KVNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCC----CHHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 458898989986543 222 234899999999999998777666554
No 239
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=32.81 E-value=40 Score=21.69 Aligned_cols=20 Identities=5% Similarity=0.086 Sum_probs=17.0
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
..++|+.+|++...|+.|-.
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 240
>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=32.72 E-value=1e+02 Score=20.38 Aligned_cols=41 Identities=24% Similarity=0.255 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHH---HHhcCCCCHHHHHHHHHhcCCC-hhHHHHhh
Q psy3429 47 PFTTQQLLSLEKK---FREKQYLSIAERAEFSSSLHLT-ETQVKIWF 89 (192)
Q Consensus 47 ~ft~~Ql~~Le~~---F~~~~yps~~~r~~LA~~l~Ls-~~qV~~WF 89 (192)
.+|..|.++|+-. ...+.|+. ...|||+.+|+. ..-|..-.
T Consensus 3 ~LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 3 ELTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp ---HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 3677777776644 56777774 567889999997 66665433
No 241
>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=32.60 E-value=34 Score=21.65 Aligned_cols=17 Identities=29% Similarity=0.438 Sum_probs=13.7
Q ss_pred HHHHHHhcCCChhHHHH
Q psy3429 71 RAEFSSSLHLTETQVKI 87 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~ 87 (192)
-.+||+.+|++..||+-
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 56889999999999973
No 242
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=32.59 E-value=59 Score=26.40 Aligned_cols=39 Identities=10% Similarity=0.125 Sum_probs=32.5
Q ss_pred HHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 57 EKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 57 e~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
...|..+.|- ....+||+..|++..-|-.+|.||..=..
T Consensus 23 ~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~ 61 (225)
T PRK11552 23 LAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYL 61 (225)
T ss_pred HHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHH
Confidence 3448899987 56888999999999999999999876543
No 243
>PRK13870 transcriptional regulator TraR; Provisional
Probab=32.44 E-value=1.2e+02 Score=25.05 Aligned_cols=33 Identities=9% Similarity=0.078 Sum_probs=26.0
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHHHHHHHHHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRAKAKRLQEAE 103 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~~~ 103 (192)
-.|+|..||++++-|+.-.+|-|.|..-..+.+
T Consensus 191 ~~EIa~ILgISe~TV~~Hl~na~~KLga~nr~q 223 (234)
T PRK13870 191 MEEIADVEGVKYNSVRVKLREAMKRFDVRSKAH 223 (234)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHcCCCCHHH
Confidence 457889999999999999999887765444433
No 244
>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=32.26 E-value=1e+02 Score=20.01 Aligned_cols=43 Identities=16% Similarity=0.227 Sum_probs=23.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 52 Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
-+..|.++.............. .....+..|..|.|.+.++..
T Consensus 11 ~~~~l~~y~~~~G~~~vp~~~~------~~~~~Lg~Wl~~qR~~~r~g~ 53 (68)
T PF03457_consen 11 RYEALKAYKEEHGHLNVPRDYV------TDGFPLGQWLNNQRRKYRKGK 53 (68)
T ss_dssp HHHHHHHHHHHHS--S-SS-----------SSHHHHHHHHHHHHHHHT-
T ss_pred HHHHHHHHHHHHCCCCCCcccC------cCCCcHHHHHHHHHHHHHcCC
Confidence 3556666665555322221111 115678899999999988843
No 245
>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=32.14 E-value=90 Score=23.91 Aligned_cols=36 Identities=14% Similarity=0.087 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 51 QQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 51 ~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
.-+.+|...=+...|.+....+++|+.+|++..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345566666566689999999999999999987765
No 246
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=32.03 E-value=90 Score=24.12 Aligned_cols=35 Identities=9% Similarity=0.126 Sum_probs=28.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 52 Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
-+.+|...=+...|.+....+.+|+.+|++..+|.
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 45566666566789999999999999999988765
No 247
>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=31.85 E-value=80 Score=24.13 Aligned_cols=35 Identities=20% Similarity=0.213 Sum_probs=26.6
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 52 Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
-+.+|...=+...|.+....+++|+.+|++..+|.
T Consensus 15 ll~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v~ 49 (145)
T PF01257_consen 15 LLPILHEVQEEYGYIPEEALEEIAEALGIPPAEVY 49 (145)
T ss_dssp HHHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHHH
Confidence 46667666667789999999999999999988776
No 248
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=31.22 E-value=1.8e+02 Score=23.51 Aligned_cols=46 Identities=11% Similarity=-0.011 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
..+|..++++|+...+-. .-.++|.+|+++++.|+.--.|=-.|..
T Consensus 133 ~~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV~~h~~~I~~KLg 178 (207)
T PRK11475 133 RMLSPTEREILRFMSRGY------SMPQIAEQLERNIKTIRAHKFNVMSKLG 178 (207)
T ss_pred CCCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHHcC
Confidence 358888888888775432 3578899999999999987766554443
No 249
>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=30.99 E-value=55 Score=23.71 Aligned_cols=26 Identities=19% Similarity=0.252 Sum_probs=16.8
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
...+||.+.||++++|..=....+.+
T Consensus 74 n~~eLA~kyglS~r~I~~Ii~~~~~~ 99 (108)
T PF08765_consen 74 NVRELARKYGLSERQIYRIIKRVRRR 99 (108)
T ss_dssp -HHHHHHHHT--HHHHHHHHHHHHH-
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46789999999999987666544433
No 250
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=30.97 E-value=35 Score=19.47 Aligned_cols=23 Identities=13% Similarity=0.271 Sum_probs=19.4
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||+.+|++...|..|-.+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 45789999999999999987654
No 251
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.68 E-value=59 Score=25.57 Aligned_cols=41 Identities=10% Similarity=0.143 Sum_probs=30.9
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 54 LSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 54 ~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
....+.|....|-... ..+||++.|++..-+-.+|.|+..=
T Consensus 18 ~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 18 ETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 3334447777776644 6778999999999999999987653
No 252
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=29.52 E-value=1e+02 Score=26.47 Aligned_cols=30 Identities=23% Similarity=0.153 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
..-.|+|..+|+++..|+.....-|.+.|+
T Consensus 170 ~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 170 WSAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 346789999999999999998877777666
No 253
>PRK05949 RNA polymerase sigma factor; Validated
Probab=29.41 E-value=1.6e+02 Score=25.64 Aligned_cols=51 Identities=22% Similarity=0.171 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..+|...|.....- ...-+++|..+|++...|+......+.|.|+
T Consensus 266 ~L~~rer~Vi~lr~gl~~~e-~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 266 ELTPQQREVLTLRFGLEDGK-ELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred hCCHHHHHHHHHHhccCCCC-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 36667777777776533221 2346789999999999999998877777766
No 254
>PF06163 DUF977: Bacterial protein of unknown function (DUF977); InterPro: IPR010382 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=29.27 E-value=83 Score=23.98 Aligned_cols=42 Identities=17% Similarity=0.300 Sum_probs=29.1
Q ss_pred CCCHHHHHHHHHHH----HhcCCCCHHHHHHHHHhcCCChhHHHHhhHh
Q psy3429 47 PFTTQQLLSLEKKF----REKQYLSIAERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F----~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
.||++|..+|...- .++...+ ..+|+..+|++...|+..|.+
T Consensus 4 ~~T~eer~eLk~rIvElVRe~GRiT---i~ql~~~TGasR~Tvk~~lre 49 (127)
T PF06163_consen 4 VFTPEEREELKARIVELVREHGRIT---IKQLVAKTGASRNTVKRYLRE 49 (127)
T ss_pred cCCHHHHHHHHHHHHHHHHHcCCcc---HHHHHHHHCCCHHHHHHHHHH
Confidence 68899988887662 3444444 456777888888888877754
No 255
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=29.04 E-value=84 Score=22.46 Aligned_cols=35 Identities=14% Similarity=0.284 Sum_probs=24.1
Q ss_pred HHHHHHHHHhc-CCCCHHHHHHHHHhcCCChhHHHH
Q psy3429 53 LLSLEKKFREK-QYLSIAERAEFSSSLHLTETQVKI 87 (192)
Q Consensus 53 l~~Le~~F~~~-~yps~~~r~~LA~~l~Ls~~qV~~ 87 (192)
...|..+|..- ......+=.+||+.|||++..|..
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 35677777644 344455566799999999887764
No 256
>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=29.02 E-value=27 Score=26.89 Aligned_cols=47 Identities=13% Similarity=0.111 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHHHhcC-----CCC-HHHHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 48 FTTQQLLSLEKKFREKQ-----YLS-IAERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~-----yps-~~~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
+...-....|+.|++-. +|. .....+++..+|+++.+|..|...-|-
T Consensus 20 iCp~C~~~~e~~f~kV~~yLr~~p~~~ati~eV~e~tgVs~~~I~~~IreGRL 72 (137)
T TIGR03826 20 VCPSCYEEEEREFEKVYKFLRKHENRQATVSEIVEETGVSEKLILKFIREGRL 72 (137)
T ss_pred cCHHHhHHHHHHHHHHHHHHHHCCCCCCCHHHHHHHHCcCHHHHHHHHHcCCe
Confidence 45555666677765332 232 234678899999999999999976553
No 257
>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=28.80 E-value=26 Score=27.95 Aligned_cols=31 Identities=16% Similarity=0.424 Sum_probs=26.5
Q ss_pred HHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
....+|+.-++++..+|-+|..|-+...+..
T Consensus 15 gt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~ 45 (186)
T PF04936_consen 15 GTIDELADYFDVSRTSVSVWIKNGKDPKRAK 45 (186)
T ss_pred ccHHHHHHHHccCHHHHHHHHHcCCCccccc
Confidence 4578899999999999999999988776653
No 258
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=28.74 E-value=1.1e+02 Score=24.30 Aligned_cols=35 Identities=20% Similarity=0.070 Sum_probs=27.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHH
Q psy3429 52 QLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVK 86 (192)
Q Consensus 52 Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~ 86 (192)
-+.+|...=+...|.+....+.+|+.||++..+|.
T Consensus 38 li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 38 LIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 35555555566689999999999999999987665
No 259
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=28.73 E-value=2e+02 Score=22.79 Aligned_cols=47 Identities=11% Similarity=0.160 Sum_probs=34.8
Q ss_pred HHHHHHHH---HHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 52 QLLSLEKK---FREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 52 Ql~~Le~~---F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
...+|+++ |....|-... ..+||++.|++..-|-..|.|+..=....
T Consensus 20 r~~IL~AA~~lf~e~Gy~~~s-~~dIA~~aGvs~gtiY~hF~sKe~L~~a~ 69 (212)
T PRK15008 20 KKAILSAALDTFSQFGFHGTR-LEQIAELAGVSKTNLLYYFPSKEALYIAV 69 (212)
T ss_pred HHHHHHHHHHHHHHhCcccCC-HHHHHHHhCcCHHHHHHHCCCHHHHHHHH
Confidence 34444444 7788876544 66779999999999999999987655543
No 260
>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=28.59 E-value=1.1e+02 Score=25.32 Aligned_cols=47 Identities=13% Similarity=0.187 Sum_probs=32.3
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 46 TPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
..++..+..++...|.. .....++|..+|++...|+..-..-..|.|
T Consensus 205 ~~L~~rer~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~ral~kLr 251 (254)
T TIGR02850 205 KRLNEREKMILNMRFFE-----GKTQMEVAEEIGISQAQVSRLEKAALKHMR 251 (254)
T ss_pred HcCCHHHHHHHHHHHcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 35777777778777732 234778999999999998766554444433
No 261
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=28.44 E-value=36 Score=25.31 Aligned_cols=23 Identities=9% Similarity=0.057 Sum_probs=21.1
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
+++||..+|++...|..|.++++
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCC
Confidence 67899999999999999999875
No 262
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=28.43 E-value=54 Score=23.29 Aligned_cols=21 Identities=5% Similarity=0.002 Sum_probs=18.1
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|..+
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEI 23 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999754
No 263
>PRK09726 antitoxin HipB; Provisional
Probab=28.32 E-value=1.2e+02 Score=20.83 Aligned_cols=23 Identities=9% Similarity=0.284 Sum_probs=20.1
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||+.+|++...|..|..+++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 67899999999999999998653
No 264
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.31 E-value=72 Score=23.73 Aligned_cols=25 Identities=16% Similarity=0.260 Sum_probs=21.7
Q ss_pred CCCHHHHHHHHHhcCCChhHHHHhh
Q psy3429 65 YLSIAERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 65 yps~~~r~~LA~~l~Ls~~qV~~WF 89 (192)
-.+...|.+||..++++.+.|..|-
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~ 50 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWV 50 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHH
Confidence 3566778899999999999999995
No 265
>PF04703 FaeA: FaeA-like protein; PDB: 2JT1_A 2HTJ_A.
Probab=27.22 E-value=62 Score=21.40 Aligned_cols=21 Identities=19% Similarity=0.379 Sum_probs=17.2
Q ss_pred HHHHHHHhcCCChhHHHHhhH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFq 90 (192)
...++|..+|++..+|+.|..
T Consensus 17 ~T~eiA~~~gls~~~aR~yL~ 37 (62)
T PF04703_consen 17 KTREIADALGLSIYQARYYLE 37 (62)
T ss_dssp EHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 355899999999999999985
No 266
>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=26.95 E-value=52 Score=24.21 Aligned_cols=35 Identities=9% Similarity=0.152 Sum_probs=24.5
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 51 QQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 51 ~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
+-....-++++... ...++|..++++..-|..||+
T Consensus 6 DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 6 DLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 33333444555432 456789999999999999998
No 267
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=26.83 E-value=67 Score=19.46 Aligned_cols=20 Identities=15% Similarity=0.222 Sum_probs=17.8
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
...+|+.+|++...|+.+|.
T Consensus 30 ~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 30 FKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 56789999999999999985
No 268
>PHA03308 transcriptional regulator ICP4; Provisional
Probab=26.44 E-value=86 Score=31.04 Aligned_cols=17 Identities=12% Similarity=0.184 Sum_probs=12.9
Q ss_pred CCCCCCCCCCCHHHHHH
Q psy3429 39 KPNRKPRTPFTTQQLLS 55 (192)
Q Consensus 39 ~~~rr~Rt~ft~~Ql~~ 55 (192)
..|||-|..+..+|..+
T Consensus 1292 ~~KKRGRK~LPpe~Ka~ 1308 (1463)
T PHA03308 1292 GGKRRGRQRLPIRDRVY 1308 (1463)
T ss_pred CccccCCCCCChHHhhh
Confidence 34677788899988766
No 269
>PF13551 HTH_29: Winged helix-turn helix
Probab=26.26 E-value=72 Score=22.23 Aligned_cols=24 Identities=25% Similarity=0.447 Sum_probs=20.3
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
...++|+.+|++...|..|.++-+
T Consensus 14 ~~~~ia~~lg~s~~Tv~r~~~~~~ 37 (112)
T PF13551_consen 14 TIAEIARRLGISRRTVYRWLKRYR 37 (112)
T ss_pred cHHHHHHHHCcCHHHHHHHHHHHH
Confidence 467899999999999999986543
No 270
>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=26.18 E-value=1.1e+02 Score=26.01 Aligned_cols=48 Identities=19% Similarity=0.132 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++..+..+|...|....+ ....-+++|..+|++...|+..-..-+.|
T Consensus 249 ~L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~~~rAl~k 296 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQIEAKALRK 296 (298)
T ss_pred cCCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3667777777777743222 22457889999999999999877644433
No 271
>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=26.04 E-value=59 Score=18.42 Aligned_cols=17 Identities=6% Similarity=0.251 Sum_probs=13.0
Q ss_pred HHHhcCCChhHHHHhhH
Q psy3429 74 FSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 74 LA~~l~Ls~~qV~~WFq 90 (192)
-|...||+..+|+..+.
T Consensus 11 eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 11 EAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHTT--HHHHHHHHH
T ss_pred HHHHcCCCHHHHHHHHH
Confidence 38899999999999875
No 272
>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=25.98 E-value=59 Score=22.58 Aligned_cols=19 Identities=21% Similarity=0.329 Sum_probs=16.7
Q ss_pred HHHHHHhcCCChhHHHHhh
Q psy3429 71 RAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WF 89 (192)
..++|+.+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 4578999999999999993
No 273
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=25.87 E-value=2.1e+02 Score=26.12 Aligned_cols=52 Identities=15% Similarity=0.125 Sum_probs=36.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRL 99 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~ 99 (192)
.++..+..+|...|.....- ...-.++|..+|++...|+.+....+.|.|..
T Consensus 350 ~L~~reR~VI~LRygl~d~~-~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~ 401 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADGH-TYSLAEIGRALDLSRERVRQIESKALQKLRQP 401 (415)
T ss_pred hCCHHHHHHHHHHHhcCCCC-CCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 46677777777777532211 12367899999999999999987777776643
No 274
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=25.86 E-value=64 Score=22.86 Aligned_cols=21 Identities=24% Similarity=0.254 Sum_probs=17.9
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|.+.
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~ 23 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999753
No 275
>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=25.02 E-value=66 Score=21.27 Aligned_cols=20 Identities=15% Similarity=0.285 Sum_probs=15.6
Q ss_pred HHHHHHHhcCCChhHHHHhh
Q psy3429 70 ERAEFSSSLHLTETQVKIWF 89 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WF 89 (192)
..++||..+|++...|+..+
T Consensus 22 t~eEiA~~lgis~~~v~~~l 41 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELL 41 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHH
Confidence 36789999999998888665
No 276
>KOG2066|consensus
Probab=24.73 E-value=79 Score=31.25 Aligned_cols=47 Identities=6% Similarity=-0.149 Sum_probs=40.5
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHHH
Q psy3429 55 SLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQE 101 (192)
Q Consensus 55 ~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~~ 101 (192)
.++.+|.+++|++...+.-.++.+.+-.-..+.||-+++++......
T Consensus 511 La~LYl~d~~Y~~Al~~ylklk~~~vf~lI~k~nL~d~i~~~Iv~Lm 557 (846)
T KOG2066|consen 511 LAHLYLYDNKYEKALPIYLKLQDKDVFDLIKKHNLFDQIKDQIVLLM 557 (846)
T ss_pred HHHHHHHccChHHHHHHHHhccChHHHHHHHHHhhHHHHHHHHHHHH
Confidence 56778999999999999999999988889999999999988766543
No 277
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=24.52 E-value=72 Score=22.12 Aligned_cols=21 Identities=0% Similarity=-0.026 Sum_probs=18.0
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|-+.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~ 24 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERL 24 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999743
No 278
>PF08880 QLQ: QLQ; InterPro: IPR014978 QLQ is named after the conserved Gln, Leu, Gln motif. QLQ is found at the N terminus of SWI2/SNF2 protein, which has been shown to be involved in protein-protein interactions. QLQ has been postulated to be involved in mediating protein interactions []. ; GO: 0005524 ATP binding, 0016818 hydrolase activity, acting on acid anhydrides, in phosphorus-containing anhydrides, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=24.46 E-value=70 Score=18.93 Aligned_cols=14 Identities=43% Similarity=0.686 Sum_probs=11.8
Q ss_pred CCCHHHHHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKF 60 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F 60 (192)
.||.+|+..||.-.
T Consensus 2 ~FT~~Ql~~L~~Qi 15 (37)
T PF08880_consen 2 PFTPAQLQELRAQI 15 (37)
T ss_pred CCCHHHHHHHHHHH
Confidence 69999999998763
No 279
>PF03444 HrcA_DNA-bdg: Winged helix-turn-helix transcription repressor, HrcA DNA-binding; InterPro: IPR005104 Prokaryotic cells have a defence mechanism against a sudden heat-shock stress. Commonly, they induce a set of proteins that protect cellular proteins from being denatured by heat. Among such proteins are the GroE and DnaK chaperones whose transcription is regulated by a heat-shock repressor protein HrcA. HrcA is a winged helix-turn-helix repressor that negatively regulates the transcription of dnaK and groE operons by binding the upstream CIRCE (controlling inverted repeat of chaperone expression) element. In Bacillus subtilis this element is a perfect 9 base pair inverted repeat separated by a 9 base pair spacer. The crystal structure of a heat-inducible transcriptional repressor, HrcA, from Thermotoga maritima has been reported at 2.2A resolution. HrcA is composed of three domains: an N-terminal winged helix-turn-helix domain (WHTH), a GAF-like domain, and an inserted dimerizing domain (IDD). The IDD shows a unique structural fold with an anti-parallel beta-sheet composed of three beta-strands sided by four alpha-helices. HrcA crystallises as a dimer, which is formed through hydrophobic contact between the IDDs and a limited contact that involves conserved residues between the GAF-like domains []. The structural studies suggest that the inactive form of HrcA is the dimer and this is converted to its DNA-binding form by interaction with GroEL, which binds to a conserved C-terminal sequence region [, ]. Comparison of the HrcA-CIRCE complexes from B. subtilis and Bacillus thermoglucosidasius (Geobacillus thermoglucosidasius), which grow at vastly different ranges of temperature shows that the thermostability profiles were consistent with the difference in the growth temperatures suggesting that HrcA can function as a thermosensor to detect temperature changes in cells []. Any increase in temperature causes the dissociation of the HrcA from the CIRCE complex with the concomitant activation of transcription of the groE and dnaK operons. This domain represents the winged helix-turn-helix DNA-binding domain which is located close to the N terminus of HrcA. This domain is also found at the N terminus of a set of uncharacterised proteins that have two C-terminal CBS domains. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent
Probab=24.26 E-value=1.9e+02 Score=20.08 Aligned_cols=38 Identities=13% Similarity=0.057 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHH---HHhcCCCCHHHHHHHHHhcCCChhHHHH
Q psy3429 48 FTTQQLLSLEKK---FREKQYLSIAERAEFSSSLHLTETQVKI 87 (192)
Q Consensus 48 ft~~Ql~~Le~~---F~~~~yps~~~r~~LA~~l~Ls~~qV~~ 87 (192)
+|..|..+|... |.+..-|-. -.+||+.++++..-|++
T Consensus 2 Lt~rq~~IL~alV~~Y~~~~~PVg--Sk~ia~~l~~s~aTIRN 42 (78)
T PF03444_consen 2 LTERQREILKALVELYIETGEPVG--SKTIAEELGRSPATIRN 42 (78)
T ss_pred CCHHHHHHHHHHHHHHHhcCCCcC--HHHHHHHHCCChHHHHH
Confidence 567777777766 555554443 34567889988877654
No 280
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=24.11 E-value=41 Score=28.78 Aligned_cols=34 Identities=21% Similarity=0.377 Sum_probs=25.9
Q ss_pred hcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 62 EKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 62 ~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
++.|.....-.+||..||++..+|+.|-+ |-.|.
T Consensus 13 kk~yl~gmk~~dIAeklGvspntiksWKr--r~gWs 46 (279)
T COG5484 13 KKDYLKGMKLKDIAEKLGVSPNTIKSWKR--RDGWS 46 (279)
T ss_pred HHHHHhhccHHHHHHHhCCChHHHHHHHH--hcCCC
Confidence 34455556677899999999999999975 55554
No 281
>PF13404 HTH_AsnC-type: AsnC-type helix-turn-helix domain; PDB: 2ZNY_E 2ZNZ_G 1RI7_A 2CYY_A 2E1C_A 2VC1_B 2QZ8_A 2W29_C 2IVM_B 2VBX_B ....
Probab=24.04 E-value=61 Score=19.46 Aligned_cols=19 Identities=32% Similarity=0.426 Sum_probs=13.8
Q ss_pred HHHHHHHHhcCCChhHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKI 87 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~ 87 (192)
.--.+||+.+||++..|..
T Consensus 18 ~s~~~la~~lglS~~~v~~ 36 (42)
T PF13404_consen 18 RSYAELAEELGLSESTVRR 36 (42)
T ss_dssp S-HHHHHHHHTS-HHHHHH
T ss_pred ccHHHHHHHHCcCHHHHHH
Confidence 3456799999999998863
No 282
>PF12114 Period_C: Period protein 2/3C-terminal region; InterPro: IPR022728 This domain is found in eukaryotes and is typically between 164 to 200 amino acids in length. Sequences represented by this entry are found C-terminal to PF08447 from PFAM.
Probab=24.02 E-value=1.4e+02 Score=24.38 Aligned_cols=30 Identities=23% Similarity=0.388 Sum_probs=16.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhH
Q psy3429 53 LLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 53 l~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFq 90 (192)
++.|+..=+.++..+..+|+||+ +|..|.|
T Consensus 126 ~ekLk~mq~~QP~fs~~Qk~EL~--------qvh~wiq 155 (195)
T PF12114_consen 126 REKLKSMQKQQPRFSNEQKEELA--------QVHPWIQ 155 (195)
T ss_pred HHHHHHHHhhCCcchHHHHHHHH--------HhhHHHH
Confidence 44444444445566666666665 4556664
No 283
>TIGR00270 conserved hypothetical protein TIGR00270.
Probab=24.01 E-value=58 Score=25.44 Aligned_cols=25 Identities=8% Similarity=0.104 Sum_probs=21.3
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++||..+|++...|..|-.+.+.-
T Consensus 85 qeeLA~~lgvs~s~IsriE~G~~~P 109 (154)
T TIGR00270 85 QEQLAKKIQEKESLIKKIENAEIEP 109 (154)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 6789999999999999999876433
No 284
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=23.97 E-value=52 Score=24.57 Aligned_cols=24 Identities=4% Similarity=0.379 Sum_probs=21.0
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999988753
No 285
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=23.94 E-value=50 Score=21.12 Aligned_cols=25 Identities=20% Similarity=0.339 Sum_probs=20.7
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRRA 94 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR~ 94 (192)
...++|..+|++...|..|-.+++.
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 4678999999999999999998874
No 286
>PF13022 HTH_Tnp_1_2: Helix-turn-helix of insertion element transposase; PDB: 2AO9_I.
Probab=23.88 E-value=2.9e+02 Score=21.46 Aligned_cols=26 Identities=19% Similarity=0.401 Sum_probs=18.2
Q ss_pred CHHHHHHHHHhcCCChhHHHHhh-HhH
Q psy3429 67 SIAERAEFSSSLHLTETQVKIWF-QNR 92 (192)
Q Consensus 67 s~~~r~~LA~~l~Ls~~qV~~WF-qNr 92 (192)
......++|.++|++...+-.|= +|+
T Consensus 33 ~r~T~~eiAee~Gis~~tLYrWr~~~~ 59 (142)
T PF13022_consen 33 ERRTQAEIAEEVGISRSTLYRWRQQNK 59 (142)
T ss_dssp --S-HHHHHHHHTS-HHHHHHHHHH-H
T ss_pred ccchHHHHHHHhCCCHHHHHHHHhcCH
Confidence 44567889999999999999996 454
No 287
>KOG0048|consensus
Probab=23.49 E-value=3.1e+02 Score=22.65 Aligned_cols=46 Identities=17% Similarity=0.120 Sum_probs=30.4
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhc-CCChhHHHHhhHhHHH
Q psy3429 44 PRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSL-HLTETQVKIWFQNRRA 94 (192)
Q Consensus 44 ~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l-~Ls~~qV~~WFqNrR~ 94 (192)
+|..||.+.-.++-+....-. ..-..||..| |-|+..||++. |-+.
T Consensus 61 krg~fT~eEe~~Ii~lH~~~G----NrWs~IA~~LPGRTDNeIKN~W-nt~l 107 (238)
T KOG0048|consen 61 KRGNFSDEEEDLIIKLHALLG----NRWSLIAGRLPGRTDNEVKNHW-NTHL 107 (238)
T ss_pred cCCCCCHHHHHHHHHHHHHHC----cHHHHHHhhCCCcCHHHHHHHH-HHHH
Confidence 377899977666655544332 1255567777 88999999975 4444
No 288
>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=23.49 E-value=1.1e+02 Score=19.25 Aligned_cols=24 Identities=8% Similarity=0.277 Sum_probs=17.9
Q ss_pred HHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 70 ERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 70 ~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
...++|..+|++..+|..|-.+++
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 356778888888888888888765
No 289
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=23.20 E-value=91 Score=20.09 Aligned_cols=19 Identities=21% Similarity=0.240 Sum_probs=13.6
Q ss_pred HHHHHHHHhcCCChhHHHH
Q psy3429 69 AERAEFSSSLHLTETQVKI 87 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~ 87 (192)
.+...+|++||+++.+++.
T Consensus 21 ~ev~ywa~~~gvt~~~L~~ 39 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLRE 39 (57)
T ss_pred HHHHHHHHHHCcCHHHHHH
Confidence 4566678888888877663
No 290
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=23.16 E-value=74 Score=24.20 Aligned_cols=21 Identities=0% Similarity=0.078 Sum_probs=18.4
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++.+.|+.|.+.
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~ 23 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNL 23 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999864
No 291
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=23.05 E-value=1.2e+02 Score=23.39 Aligned_cols=41 Identities=10% Similarity=0.075 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 54 LSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 54 ~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
..-.+.|.++.|-. ....+||+..|++..-|-.+|.||..=
T Consensus 15 ~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 15 QAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 33444588888844 457788999999999999999997663
No 292
>PF05263 DUF722: Protein of unknown function (DUF722); InterPro: IPR007927 This entry is represented by Bacteriophage bIL285, Orf38. The characteristics of the protein distribution suggest prophage matches in addition to the phage matches.
Probab=22.94 E-value=1.4e+02 Score=22.79 Aligned_cols=23 Identities=17% Similarity=0.435 Sum_probs=17.3
Q ss_pred HHHHHHHHhcCCChhHHHHhhHh
Q psy3429 69 AERAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 69 ~~r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..=..+|..+++++++++.|++.
T Consensus 100 ~TW~~IA~~l~i~erta~r~~~~ 122 (130)
T PF05263_consen 100 RTWYQIAQKLHISERTARRWRDR 122 (130)
T ss_pred chHHHHHHHhCccHHHHHHHHHH
Confidence 33456788889999998888653
No 293
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.77 E-value=73 Score=22.57 Aligned_cols=20 Identities=15% Similarity=0.315 Sum_probs=17.0
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
..++|+.+|++...|+.|=+
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999998854
No 294
>PRK12427 flagellar biosynthesis sigma factor; Provisional
Probab=22.57 E-value=2.9e+02 Score=22.55 Aligned_cols=44 Identities=18% Similarity=0.206 Sum_probs=28.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAK 95 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k 95 (192)
.++..+..+|...|... ..-.++|..+|++..+|...-+.-+.|
T Consensus 183 ~L~~~er~vi~l~~~~~-----~t~~EIA~~lgis~~~V~q~~~~~~~k 226 (231)
T PRK12427 183 QLDEREQLILHLYYQHE-----MSLKEIALVLDLTEARICQLNKKIAQK 226 (231)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 45566666666666322 236788999999998776555444333
No 295
>PF02787 CPSase_L_D3: Carbamoyl-phosphate synthetase large chain, oligomerisation domain; InterPro: IPR005480 Carbamoyl phosphate synthase (CPSase) is a heterodimeric enzyme composed of a small and a large subunit (with the exception of CPSase III, see below). CPSase catalyses the synthesis of carbamoyl phosphate from biocarbonate, ATP and glutamine (6.3.5.5 from EC) or ammonia (6.3.4.16 from EC), and represents the first committed step in pyrimidine and arginine biosynthesis in prokaryotes and eukaryotes, and in the urea cycle in most terrestrial vertebrates [, ]. CPSase has three active sites, one in the small subunit and two in the large subunit. The small subunit contains the glutamine binding site and catalyses the hydrolysis of glutamine to glutamate and ammonia. The large subunit has two homologous carboxy phosphate domains, both of which have ATP-binding sites; however, the N-terminal carboxy phosphate domain catalyses the phosphorylation of biocarbonate, while the C-terminal domain catalyses the phosphorylation of the carbamate intermediate []. The carboxy phosphate domain found duplicated in the large subunit of CPSase is also present as a single copy in the biotin-dependent enzymes acetyl-CoA carboxylase (6.4.1.2 from EC) (ACC), propionyl-CoA carboxylase (6.4.1.3 from EC) (PCCase), pyruvate carboxylase (6.4.1.1 from EC) (PC) and urea carboxylase (6.3.4.6 from EC). Most prokaryotes carry one form of CPSase that participates in both arginine and pyrimidine biosynthesis, however certain bacteria can have separate forms. The large subunit in bacterial CPSase has four structural domains: the carboxy phosphate domain 1, the oligomerisation domain, the carbamoyl phosphate domain 2 and the allosteric domain []. CPSase heterodimers from Escherichia coli contain two molecular tunnels: an ammonia tunnel and a carbamate tunnel. These inter-domain tunnels connect the three distinct active sites, and function as conduits for the transport of unstable reaction intermediates (ammonia and carbamate) between successive active sites []. The catalytic mechanism of CPSase involves the diffusion of carbamate through the interior of the enzyme from the site of synthesis within the N-terminal domain of the large subunit to the site of phosphorylation within the C-terminal domain. Eukaryotes have two distinct forms of CPSase: a mitochondrial enzyme (CPSase I) that participates in both arginine biosynthesis and the urea cycle; and a cytosolic enzyme (CPSase II) involved in pyrimidine biosynthesis. CPSase II occurs as part of a multi-enzyme complex along with aspartate transcarbamoylase and dihydroorotase; this complex is referred to as the CAD protein []. The hepatic expression of CPSase is transcriptionally regulated by glucocorticoids and/or cAMP []. There is a third form of the enzyme, CPSase III, found in fish, which uses glutamine as a nitrogen source instead of ammonia []. CPSase III is closely related to CPSase I, and is composed of a single polypeptide that may have arisen from gene fusion of the glutaminase and synthetase domains []. This entry represents the oligomerisation domain found in the large subunit of carbamoyl phosphate synthases as well as in certain other carboxy phsophate domain-containing enzymes.; GO: 0006807 nitrogen compound metabolic process; PDB: 1M6V_C 1CS0_C 1C30_E 1C3O_G 1BXR_A 1T36_E 1A9X_A 1KEE_G 1CE8_A 1JDB_H ....
Probab=22.56 E-value=3e+02 Score=20.49 Aligned_cols=45 Identities=13% Similarity=0.183 Sum_probs=23.4
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHH
Q psy3429 53 LLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAK 97 (192)
Q Consensus 53 l~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~k 97 (192)
+..+|+.+......-..+...-|+++|.+.++|..+..---...+
T Consensus 46 Iv~~e~~L~~~~~~~~~~~L~~aK~~GFsD~~IA~l~~~~e~~vr 90 (123)
T PF02787_consen 46 IVDMEKELKEYLNELDPELLRKAKRLGFSDRQIARLWGVSEEEVR 90 (123)
T ss_dssp HHHHHHHHHHHGGG--HHHHHHHHHTT--HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHhhccchHHHHHHHHHcCCCHHHHHhccCCCHHHHH
Confidence 344444444422233344555599999999999887655433333
No 296
>PRK07921 RNA polymerase sigma factor SigB; Reviewed
Probab=22.55 E-value=2.8e+02 Score=24.21 Aligned_cols=51 Identities=8% Similarity=0.070 Sum_probs=34.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
.++..+..+|..+|.....- ...-.+||..+|++..+|+.--..--.|.|+
T Consensus 262 ~L~eREr~Vl~~rygl~~~~-~~Tl~eIa~~lgvS~eRVrQIe~~Al~KLr~ 312 (324)
T PRK07921 262 TLDEREQQVIRLRFGLDDGQ-PRTLDQIGKLFGLSRERVRQIEREVMSKLRN 312 (324)
T ss_pred hCCHHHHHHHHHHHhcCCCC-CcCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 46777777887777643321 1346788999999998888766555555444
No 297
>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=22.45 E-value=76 Score=24.00 Aligned_cols=20 Identities=10% Similarity=0.341 Sum_probs=18.2
Q ss_pred HHHHHHhcCCChhHHHHhhH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQ 90 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFq 90 (192)
-+|||..+|++..-|.-|..
T Consensus 3 ~eELA~~tG~srQTINrWvR 22 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVR 22 (122)
T ss_pred HHHHHHHhCccHHHHHHHHH
Confidence 47999999999999999985
No 298
>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=22.43 E-value=70 Score=24.81 Aligned_cols=17 Identities=12% Similarity=0.219 Sum_probs=11.6
Q ss_pred CCCCHHHHHHHHHHHHh
Q psy3429 46 TPFTTQQLLSLEKKFRE 62 (192)
Q Consensus 46 t~ft~~Ql~~Le~~F~~ 62 (192)
.-++.+|+..|+.+.+.
T Consensus 50 ~~Lt~~qi~~l~~~i~~ 66 (144)
T TIGR03629 50 GYLDDEEIEKLEEAVEN 66 (144)
T ss_pred ccCCHHHHHHHHHHHHh
Confidence 35777777777777654
No 299
>PRK15451 tRNA cmo(5)U34 methyltransferase; Provisional
Probab=22.06 E-value=2.1e+02 Score=23.45 Aligned_cols=45 Identities=9% Similarity=0.186 Sum_probs=24.1
Q ss_pred CCCHHHHHHHHHHHHhcCCC-CHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 47 PFTTQQLLSLEKKFREKQYL-SIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 47 ~ft~~Ql~~Le~~F~~~~yp-s~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
-++.+++......++..-++ +..+-.+|.++.|.. .|.+|||+-.
T Consensus 189 g~s~~ei~~~~~~~~~~~~~~~~~~~~~~L~~aGF~--~v~~~~~~~~ 234 (247)
T PRK15451 189 GYSELEISQKRSMLENVMLTDSVETHKARLHKAGFE--HSELWFQCFN 234 (247)
T ss_pred CCCHHHHHHHHHHHHhhcccCCHHHHHHHHHHcCch--hHHHHHHHHh
Confidence 34444444433444433333 555556666666644 5778887643
No 300
>PRK00215 LexA repressor; Validated
Probab=22.00 E-value=1.3e+02 Score=23.94 Aligned_cols=43 Identities=23% Similarity=0.241 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHH---hcCCCCHHHHHHHHHhcCC-ChhHHHHhhHhH
Q psy3429 48 FTTQQLLSLEKKFR---EKQYLSIAERAEFSSSLHL-TETQVKIWFQNR 92 (192)
Q Consensus 48 ft~~Ql~~Le~~F~---~~~yps~~~r~~LA~~l~L-s~~qV~~WFqNr 92 (192)
+|..|..+|+...+ .+.++ ....+||..+|+ +...|..+.+.-
T Consensus 2 lt~~q~~il~~i~~~~~~~~~~--~s~~ela~~~~~~~~~tv~~~l~~L 48 (205)
T PRK00215 2 LTKRQQEILDFIRDHIEETGYP--PSRREIADALGLRSPSAVHEHLKAL 48 (205)
T ss_pred CCHHHHHHHHHHHHHHHHhCCC--CCHHHHHHHhCCCChHHHHHHHHHH
Confidence 57888888877753 23332 236689999999 888888877543
No 301
>PF00249 Myb_DNA-binding: Myb-like DNA-binding domain; InterPro: IPR014778 The retroviral oncogene v-myb, and its cellular counterpart c-myb, encode nuclear DNA-binding proteins. These belong to the SANT domain family that specifically recognise the sequence YAAC(G/T)G [, ]. In myb, one of the most conserved regions consisting of three tandem repeats has been shown to be involved in DNA-binding [].; PDB: 1X41_A 2XAF_B 2XAG_B 2XAH_B 2UXN_B 2Y48_B 2XAQ_B 2X0L_B 2IW5_B 2XAJ_B ....
Probab=21.51 E-value=2e+02 Score=17.22 Aligned_cols=44 Identities=18% Similarity=0.218 Sum_probs=28.7
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcC--CChhHHHHhhHh
Q psy3429 45 RTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLH--LTETQVKIWFQN 91 (192)
Q Consensus 45 Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~--Ls~~qV~~WFqN 91 (192)
|..+|.++...|.+.+.+...- .=..||..++ -+..||+.-|+|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~---~W~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKD---NWKKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTT---HHHHHHHHHSSSSTHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCc---HHHHHHHHcCCCCCHHHHHHHHHh
Confidence 4578899999998888766643 2233555555 677888876665
No 302
>TIGR03147 cyt_nit_nrfF cytochrome c nitrite reductase, accessory protein NrfF.
Probab=21.27 E-value=62 Score=24.63 Aligned_cols=26 Identities=19% Similarity=0.181 Sum_probs=17.6
Q ss_pred CHHHHHHHHHhc--CCChhHHHHhhHhH
Q psy3429 67 SIAERAEFSSSL--HLTETQVKIWFQNR 92 (192)
Q Consensus 67 s~~~r~~LA~~l--~Ls~~qV~~WFqNr 92 (192)
....|.++.+.+ |.++.+|.-||.+|
T Consensus 59 A~dmR~~Vr~~i~~G~Sd~eI~~~~v~R 86 (126)
T TIGR03147 59 AYDLRHEVYSMVNEGKSNQQIIDFMTAR 86 (126)
T ss_pred HHHHHHHHHHHHHcCCCHHHHHHHHHHh
Confidence 345566665555 77888888888654
No 303
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.26 E-value=91 Score=21.94 Aligned_cols=21 Identities=10% Similarity=0.091 Sum_probs=18.4
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...++.|.+.
T Consensus 3 i~eva~~~gvs~~tLRyye~~ 23 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDI 23 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 457899999999999999865
No 304
>KOG3623|consensus
Probab=21.19 E-value=41 Score=33.08 Aligned_cols=58 Identities=17% Similarity=0.288 Sum_probs=43.4
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHHHHHHHHH
Q psy3429 43 KPRTPFTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRRAKAKRLQ 100 (192)
Q Consensus 43 r~Rt~ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR~k~kr~~ 100 (192)
|-|+.+..++-..|..+++.+--++-.+-..++.+|...+.+|.+||++|+...+...
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 3456677777777888888777776666666666677788899999999998776643
No 305
>cd04773 HTH_TioE_rpt2 Second Helix-Turn-Helix DNA binding domain of the regulatory protein TioE. Putative helix-turn-helix (HTH) regulatory protein, TioE, and related proteins. TioE is part of the thiocoraline gene cluster, which is involved in the biosynthesis of the antitumor thiocoraline from the marine actinomycete, Micromonospora. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. Proteins in this family are unique within the MerR superfamily in that they are composed of just two adjacent MerR-like N-terminal domains; this CD mainly contains the C-terminal or second repeat (rpt2) of these tandem MerR-like domain proteins.
Probab=21.17 E-value=89 Score=22.54 Aligned_cols=21 Identities=14% Similarity=0.366 Sum_probs=18.1
Q ss_pred HHHHHHhcCCChhHHHHhhHh
Q psy3429 71 RAEFSSSLHLTETQVKIWFQN 91 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqN 91 (192)
..++|+.+|++...|+.|.++
T Consensus 3 i~eva~~~gvs~~tlR~ye~~ 23 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKE 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 467899999999999999754
No 306
>TIGR03830 CxxCG_CxxCG_HTH putative zinc finger/helix-turn-helix protein, YgiT family. This model describes a family of predicted regulatory proteins with a conserved zinc finger/HTH architecture. The amino-terminal region contains a novel domain, featuring two CXXC motifs and occuring in a number of small bacterial proteins as well as in the present family. The carboxyl-terminal region consists of a helix-turn-helix domain, modeled by pfam01381. The predicted function is DNA binding and transcriptional regulation.
Probab=21.03 E-value=1.2e+02 Score=21.89 Aligned_cols=23 Identities=9% Similarity=-0.067 Sum_probs=18.4
Q ss_pred HHHHHHhcCCChhHHHHhhHhHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
..+||..+|++...|.-|-..+.
T Consensus 81 q~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 81 QREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 35788889999999999987654
No 307
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=20.82 E-value=93 Score=18.63 Aligned_cols=36 Identities=14% Similarity=0.289 Sum_probs=25.8
Q ss_pred HHHHHhcCCCCHHHHHHHHHhcCCChhHHHHhhHhHH
Q psy3429 57 EKKFREKQYLSIAERAEFSSSLHLTETQVKIWFQNRR 93 (192)
Q Consensus 57 e~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~WFqNrR 93 (192)
.+.|....|-... ..+||+++|++..-+-..|.|+-
T Consensus 6 ~~l~~~~G~~~~s-~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 6 LELFAEKGYEAVS-IRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHTTTSS-HHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHhCHHhCC-HHHHHHHHccchhhHHHHcCCHH
Confidence 3445555544433 56789999999999999998854
No 308
>KOG2675|consensus
Probab=20.74 E-value=1.3e+02 Score=27.84 Aligned_cols=12 Identities=25% Similarity=0.443 Sum_probs=6.4
Q ss_pred HhhHhHHHHHHH
Q psy3429 87 IWFQNRRAKAKR 98 (192)
Q Consensus 87 ~WFqNrR~k~kr 98 (192)
.++-||-.|+.|
T Consensus 168 ~FY~NrvLkEyk 179 (480)
T KOG2675|consen 168 QFYTNRVLKEYK 179 (480)
T ss_pred HHHHHHHHHHhc
Confidence 344555555554
No 309
>TIGR01636 phage_rinA phage transcriptional activator, RinA family. This model represents a family of phage proteins, including RinA, a transcriptional activator in staphylococcal phage phi 11. This family shows similarity to ArpU, a phage-related putative autolysin regulator, and to some sporulation-specific sigma factors.
Probab=20.65 E-value=1.6e+02 Score=22.07 Aligned_cols=38 Identities=8% Similarity=0.116 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHhcCCChhHHHHh
Q psy3429 48 FTTQQLLSLEKKFREKQYLSIAERAEFSSSLHLTETQVKIW 88 (192)
Q Consensus 48 ft~~Ql~~Le~~F~~~~yps~~~r~~LA~~l~Ls~~qV~~W 88 (192)
++.++..+++..|-.... ..-.++|..+|+++..|..|
T Consensus 83 Ld~~er~II~~rY~~~~~---~t~~~Ia~~l~iS~~t~~r~ 120 (134)
T TIGR01636 83 ADEQTRVIIQELYMKKRP---LTLVGLAQQLFISKSTAYRL 120 (134)
T ss_pred CCHHHHHHHHHHHccCCC---CCHHHHHHHhCCCHHHHHHH
Confidence 556666666666533222 24677888999998887644
No 310
>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=20.54 E-value=1e+02 Score=22.05 Aligned_cols=28 Identities=11% Similarity=0.270 Sum_probs=22.2
Q ss_pred HHHHHHhcCCChhHHHHhhHhHHHHHHH
Q psy3429 71 RAEFSSSLHLTETQVKIWFQNRRAKAKR 98 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~WFqNrR~k~kr 98 (192)
-..+|+.+|+++.+|..|..+-+.++-.
T Consensus 26 q~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 26 QKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 4568999999999999998776655554
No 311
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=20.32 E-value=1.2e+02 Score=19.75 Aligned_cols=18 Identities=17% Similarity=0.540 Sum_probs=15.4
Q ss_pred HHHHHHhcCCChhHHHHh
Q psy3429 71 RAEFSSSLHLTETQVKIW 88 (192)
Q Consensus 71 r~~LA~~l~Ls~~qV~~W 88 (192)
...||+.||++..-|-.|
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 357899999999999999
Done!