Query psy1901
Match_columns 205
No_of_seqs 194 out of 1165
Neff 7.2
Searched_HMMs 46136
Date Fri Aug 16 19:10:22 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy1901.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/1901hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0487|consensus 99.8 5.6E-21 1.2E-25 164.9 6.6 70 31-100 231-300 (308)
2 KOG0842|consensus 99.8 4E-20 8.6E-25 159.6 11.5 74 31-104 149-222 (307)
3 KOG0489|consensus 99.8 1.2E-20 2.5E-25 161.4 5.3 67 33-99 157-223 (261)
4 KOG0485|consensus 99.8 6.6E-19 1.4E-23 143.9 10.6 70 32-101 101-170 (268)
5 KOG0488|consensus 99.8 1.6E-18 3.6E-23 151.1 11.9 66 32-97 169-234 (309)
6 KOG0484|consensus 99.7 8.2E-19 1.8E-23 128.1 4.0 68 31-98 13-80 (125)
7 KOG0850|consensus 99.7 5.8E-18 1.3E-22 139.4 7.5 66 31-96 118-183 (245)
8 KOG3802|consensus 99.7 8.4E-19 1.8E-23 154.5 2.1 64 32-95 291-354 (398)
9 KOG0844|consensus 99.7 6.6E-18 1.4E-22 144.0 7.4 64 34-97 180-243 (408)
10 PF00046 Homeobox: Homeobox do 99.7 1E-17 2.3E-22 110.9 6.0 57 36-92 1-57 (57)
11 KOG0843|consensus 99.7 8.9E-18 1.9E-22 133.7 6.0 64 34-97 101-164 (197)
12 KOG2251|consensus 99.7 6.7E-18 1.4E-22 138.4 5.3 68 30-97 32-99 (228)
13 KOG0494|consensus 99.7 5.6E-17 1.2E-21 135.6 7.6 65 34-98 140-204 (332)
14 KOG0848|consensus 99.7 3.1E-17 6.8E-22 137.7 5.6 65 33-97 197-261 (317)
15 KOG0492|consensus 99.7 5.7E-17 1.2E-21 131.7 6.1 68 33-100 142-209 (246)
16 KOG0493|consensus 99.7 8.6E-17 1.9E-21 134.7 6.7 58 36-93 247-304 (342)
17 TIGR01565 homeo_ZF_HD homeobox 99.6 4E-16 8.7E-21 103.8 4.6 53 35-87 1-57 (58)
18 cd00086 homeodomain Homeodomai 99.6 1.2E-15 2.7E-20 101.0 6.3 58 36-93 1-58 (59)
19 smart00389 HOX Homeodomain. DN 99.6 1.2E-15 2.7E-20 100.3 5.6 56 36-91 1-56 (56)
20 KOG0491|consensus 99.6 4.8E-16 1E-20 122.2 3.4 65 34-98 99-163 (194)
21 COG5576 Homeodomain-containing 99.6 5.4E-15 1.2E-19 117.2 6.0 65 33-97 49-113 (156)
22 KOG0483|consensus 99.5 6.6E-15 1.4E-19 120.6 4.9 64 35-98 50-113 (198)
23 KOG0486|consensus 99.5 2.4E-14 5.2E-19 122.7 6.3 65 34-98 111-175 (351)
24 KOG4577|consensus 99.4 3.1E-13 6.6E-18 114.9 4.7 65 34-98 166-230 (383)
25 KOG0847|consensus 99.3 5.5E-13 1.2E-17 109.5 3.7 69 32-100 164-232 (288)
26 KOG1168|consensus 99.3 7.2E-13 1.6E-17 112.7 2.5 63 32-94 306-368 (385)
27 KOG0849|consensus 99.3 3.5E-11 7.7E-16 107.1 10.9 78 19-96 160-237 (354)
28 KOG0490|consensus 99.2 5.8E-12 1.2E-16 104.8 4.5 64 32-95 57-120 (235)
29 KOG0774|consensus 99.2 1.9E-11 4E-16 102.8 7.1 62 36-97 189-253 (334)
30 KOG0775|consensus 99.2 6.6E-11 1.4E-15 100.1 8.0 61 33-93 165-234 (304)
31 PF05920 Homeobox_KN: Homeobox 98.7 7.8E-09 1.7E-13 63.8 3.1 35 55-89 6-40 (40)
32 KOG2252|consensus 98.6 9.9E-08 2.1E-12 87.8 7.0 63 31-93 416-478 (558)
33 KOG0490|consensus 98.2 1.4E-06 3E-11 72.4 4.8 65 31-95 149-213 (235)
34 KOG1146|consensus 97.8 3.7E-05 7.9E-10 77.1 5.6 63 33-95 901-963 (1406)
35 PF11569 Homez: Homeodomain le 97.4 0.00011 2.3E-09 48.4 2.5 41 47-87 10-50 (56)
36 KOG0773|consensus 97.4 0.0002 4.3E-09 63.5 5.0 64 35-98 239-305 (342)
37 KOG3623|consensus 96.1 0.0078 1.7E-07 57.8 4.7 48 47-94 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.4 0.035 7.6E-07 36.0 4.3 47 36-87 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 90.6 0.84 1.8E-05 28.6 4.9 46 41-91 4-49 (50)
40 cd06171 Sigma70_r4 Sigma70, re 87.3 0.86 1.9E-05 27.7 3.2 44 41-89 10-53 (55)
41 PF01527 HTH_Tnp_1: Transposas 86.0 0.67 1.4E-05 31.4 2.3 44 37-84 2-45 (76)
42 PRK03975 tfx putative transcri 83.9 4 8.6E-05 31.9 6.1 52 39-96 4-55 (141)
43 KOG1146|consensus 83.8 1.9 4.2E-05 44.5 5.3 63 32-94 702-764 (1406)
44 PF08281 Sigma70_r4_2: Sigma-7 83.6 3.5 7.5E-05 26.0 4.8 41 42-87 11-51 (54)
45 cd00569 HTH_Hin_like Helix-tur 81.8 5 0.00011 21.6 4.6 37 42-83 6-42 (42)
46 PF00196 GerE: Bacterial regul 80.5 4.3 9.4E-05 26.1 4.4 47 41-93 3-49 (58)
47 PLN03162 golden-2 like transcr 80.3 23 0.00049 32.2 10.1 67 33-99 231-299 (526)
48 PF10668 Phage_terminase: Phag 76.8 1.9 4E-05 28.8 1.8 21 64-84 24-44 (60)
49 PRK04217 hypothetical protein; 75.6 8.6 0.00019 28.8 5.3 49 40-93 41-89 (110)
50 PF09607 BrkDBD: Brinker DNA-b 75.1 7.3 0.00016 25.8 4.2 45 39-84 3-47 (58)
51 PF04967 HTH_10: HTH DNA bindi 74.3 9.3 0.0002 24.7 4.6 41 42-82 1-43 (53)
52 PRK09646 RNA polymerase sigma 74.2 8 0.00017 30.9 5.3 48 41-93 142-189 (194)
53 PRK06759 RNA polymerase factor 73.8 7.6 0.00017 29.5 4.9 47 41-92 106-152 (154)
54 PRK09642 RNA polymerase sigma 72.5 10 0.00023 29.0 5.4 48 42-94 107-154 (160)
55 smart00421 HTH_LUXR helix_turn 72.4 12 0.00027 22.8 4.9 43 41-89 3-45 (58)
56 PRK09652 RNA polymerase sigma 72.1 9.3 0.0002 29.5 5.1 48 41-93 128-175 (182)
57 PF13936 HTH_38: Helix-turn-he 71.1 5.5 0.00012 24.5 2.8 40 40-84 3-42 (44)
58 PRK09413 IS2 repressor TnpA; R 70.9 9.4 0.0002 28.6 4.7 43 39-85 10-52 (121)
59 PRK12526 RNA polymerase sigma 70.7 11 0.00024 30.6 5.4 47 42-93 154-200 (206)
60 PRK11924 RNA polymerase sigma 70.7 13 0.00028 28.6 5.6 47 42-93 126-172 (179)
61 COG4367 Uncharacterized protei 70.5 6.4 0.00014 28.4 3.3 41 41-81 2-42 (97)
62 TIGR02937 sigma70-ECF RNA poly 69.8 11 0.00023 27.7 4.8 47 41-92 110-156 (158)
63 PRK10072 putative transcriptio 68.8 9 0.00019 27.9 4.0 41 41-88 32-72 (96)
64 PRK09644 RNA polymerase sigma 68.0 15 0.00032 28.4 5.4 48 42-94 109-156 (165)
65 PRK00118 putative DNA-binding 66.5 22 0.00048 26.3 5.7 47 42-93 18-64 (104)
66 cd04761 HTH_MerR-SF Helix-Turn 66.3 5.2 0.00011 24.3 2.1 23 65-87 3-25 (49)
67 TIGR02989 Sig-70_gvs1 RNA poly 65.8 15 0.00032 28.0 4.9 45 41-90 111-155 (159)
68 PRK12512 RNA polymerase sigma 65.7 14 0.00031 29.0 5.0 49 41-94 131-179 (184)
69 TIGR00721 tfx DNA-binding prot 64.9 36 0.00077 26.5 6.9 48 39-92 4-51 (137)
70 PRK12515 RNA polymerase sigma 64.8 20 0.00042 28.4 5.6 49 41-94 131-179 (189)
71 PRK12519 RNA polymerase sigma 64.7 13 0.00028 29.5 4.6 47 42-93 142-188 (194)
72 TIGR02959 SigZ RNA polymerase 64.4 17 0.00037 28.4 5.2 48 41-93 100-147 (170)
73 PRK12514 RNA polymerase sigma 64.3 18 0.00038 28.3 5.2 47 42-93 130-176 (179)
74 PRK09648 RNA polymerase sigma 64.2 18 0.00038 28.7 5.3 47 41-92 139-185 (189)
75 TIGR02999 Sig-70_X6 RNA polyme 63.8 18 0.0004 28.2 5.3 46 42-92 135-180 (183)
76 PRK05602 RNA polymerase sigma 63.5 18 0.0004 28.5 5.3 47 42-93 129-175 (186)
77 TIGR02948 SigW_bacill RNA poly 63.4 16 0.00036 28.5 4.9 48 41-93 136-183 (187)
78 TIGR02985 Sig70_bacteroi1 RNA 63.3 19 0.00042 27.0 5.2 46 42-92 114-159 (161)
79 TIGR02939 RpoE_Sigma70 RNA pol 63.1 15 0.00033 28.7 4.7 31 63-93 155-185 (190)
80 PRK12538 RNA polymerase sigma 62.1 20 0.00043 29.9 5.4 32 64-95 189-220 (233)
81 PF13443 HTH_26: Cro/C1-type H 61.9 12 0.00027 24.0 3.3 28 64-91 12-39 (63)
82 PRK12543 RNA polymerase sigma 61.9 32 0.00069 27.0 6.3 51 42-97 118-168 (179)
83 PRK09480 slmA division inhibit 61.6 9.1 0.0002 30.0 3.1 41 47-88 16-56 (194)
84 PRK09639 RNA polymerase sigma 61.3 27 0.00059 26.7 5.7 48 41-94 112-159 (166)
85 PRK12541 RNA polymerase sigma 60.9 18 0.0004 27.7 4.7 46 42-92 113-158 (161)
86 PRK09047 RNA polymerase factor 60.3 27 0.00059 26.5 5.6 48 41-93 106-153 (161)
87 COG3413 Predicted DNA binding 60.3 17 0.00037 29.9 4.6 41 41-81 155-197 (215)
88 TIGR03879 near_KaiC_dom probab 59.7 4.1 8.9E-05 28.3 0.7 34 53-86 23-56 (73)
89 PRK12530 RNA polymerase sigma 59.5 28 0.00061 27.7 5.7 48 41-93 134-181 (189)
90 PF02724 CDC45: CDC45-like pro 59.1 12 0.00026 36.2 4.0 32 42-73 197-231 (622)
91 PRK06930 positive control sigm 58.7 30 0.00066 27.6 5.7 50 41-95 114-163 (170)
92 PRK12546 RNA polymerase sigma 58.6 22 0.00048 28.5 4.9 48 42-94 114-161 (188)
93 PRK07037 extracytoplasmic-func 58.4 28 0.0006 26.6 5.3 47 41-92 109-155 (163)
94 TIGR02952 Sig70_famx2 RNA poly 57.9 27 0.00058 26.7 5.2 46 41-91 122-167 (170)
95 PRK06811 RNA polymerase factor 57.8 23 0.00051 28.1 4.9 48 41-93 131-178 (189)
96 PF13551 HTH_29: Winged helix- 57.7 42 0.00091 23.7 5.9 48 37-84 53-109 (112)
97 TIGR02983 SigE-fam_strep RNA p 57.6 25 0.00054 26.9 4.9 47 42-93 111-157 (162)
98 PRK12537 RNA polymerase sigma 57.5 26 0.00057 27.5 5.2 46 42-92 134-179 (182)
99 PRK12532 RNA polymerase sigma 57.5 31 0.00067 27.4 5.6 48 42-94 137-184 (195)
100 PF06056 Terminase_5: Putative 57.3 8.8 0.00019 25.2 1.9 22 63-84 14-35 (58)
101 PF00376 MerR: MerR family reg 56.7 10 0.00022 22.7 2.0 20 65-84 2-21 (38)
102 TIGR02954 Sig70_famx3 RNA poly 56.7 27 0.00058 27.0 5.0 46 42-92 120-165 (169)
103 PF13518 HTH_28: Helix-turn-he 55.6 10 0.00022 23.3 2.0 23 64-86 14-36 (52)
104 PF08280 HTH_Mga: M protein tr 55.6 17 0.00036 23.6 3.1 36 45-84 6-41 (59)
105 PRK12516 RNA polymerase sigma 55.5 35 0.00075 27.2 5.6 48 42-94 117-164 (187)
106 PRK09637 RNA polymerase sigma 55.4 28 0.0006 27.6 5.0 46 42-92 107-152 (181)
107 PRK09647 RNA polymerase sigma 55.4 35 0.00076 27.7 5.7 48 42-94 139-186 (203)
108 PRK06986 fliA flagellar biosyn 55.3 29 0.00062 28.7 5.2 47 42-93 185-231 (236)
109 PF13384 HTH_23: Homeodomain-l 55.0 11 0.00024 23.2 2.1 23 63-85 18-40 (50)
110 TIGR02943 Sig70_famx1 RNA poly 55.0 41 0.00088 26.7 5.9 50 41-95 131-180 (188)
111 PRK13919 putative RNA polymera 54.8 32 0.0007 26.9 5.3 47 42-93 136-182 (186)
112 PRK12547 RNA polymerase sigma 54.8 33 0.00071 26.5 5.2 47 41-92 112-158 (164)
113 cd06170 LuxR_C_like C-terminal 54.8 41 0.00089 20.4 4.8 36 43-84 2-37 (57)
114 PRK12536 RNA polymerase sigma 54.7 32 0.0007 27.0 5.2 30 64-93 147-176 (181)
115 PRK12545 RNA polymerase sigma 54.3 41 0.00088 27.0 5.9 48 42-94 140-187 (201)
116 PF12824 MRP-L20: Mitochondria 54.1 70 0.0015 25.6 7.0 54 38-93 82-135 (164)
117 TIGR03001 Sig-70_gmx1 RNA poly 53.8 45 0.00098 28.1 6.2 53 42-99 162-214 (244)
118 PRK10403 transcriptional regul 53.8 16 0.00035 28.2 3.4 49 41-95 153-201 (215)
119 PRK09645 RNA polymerase sigma 53.3 36 0.00078 26.3 5.3 47 42-93 119-165 (173)
120 TIGR02479 FliA_WhiG RNA polyme 53.3 33 0.00071 28.1 5.2 47 41-92 175-221 (224)
121 PF13411 MerR_1: MerR HTH fami 52.6 12 0.00026 24.5 2.1 20 65-84 3-22 (69)
122 PRK11923 algU RNA polymerase s 52.3 37 0.0008 26.8 5.3 32 63-94 155-186 (193)
123 PRK12539 RNA polymerase sigma 52.2 36 0.00078 26.8 5.2 48 41-93 131-178 (184)
124 PRK10360 DNA-binding transcrip 51.9 24 0.00052 27.2 4.0 45 41-91 137-181 (196)
125 PRK12520 RNA polymerase sigma 51.6 47 0.001 26.3 5.8 50 42-96 132-181 (191)
126 smart00027 EH Eps15 homology d 51.5 41 0.00088 23.7 4.9 44 41-84 3-51 (96)
127 PRK12529 RNA polymerase sigma 51.4 39 0.00083 26.5 5.2 48 41-93 127-174 (178)
128 PRK12524 RNA polymerase sigma 51.3 38 0.00083 27.0 5.2 47 42-93 137-183 (196)
129 PRK12544 RNA polymerase sigma 51.1 47 0.001 27.0 5.8 49 41-94 148-196 (206)
130 PRK12533 RNA polymerase sigma 51.0 33 0.00072 28.2 4.9 47 42-93 135-181 (216)
131 cd04762 HTH_MerR-trunc Helix-T 50.8 14 0.00031 21.8 2.1 24 65-88 3-26 (49)
132 PRK12531 RNA polymerase sigma 50.4 43 0.00093 26.6 5.4 47 42-93 142-188 (194)
133 PRK08295 RNA polymerase factor 50.2 49 0.0011 26.3 5.7 46 42-93 156-201 (208)
134 cd00131 PAX Paired Box domain 50.2 66 0.0014 24.4 6.1 46 41-86 75-127 (128)
135 PRK12535 RNA polymerase sigma 50.1 42 0.0009 27.0 5.3 49 42-95 134-182 (196)
136 KOG0773|consensus 50.0 30 0.00064 30.5 4.7 41 53-93 115-155 (342)
137 COG2963 Transposase and inacti 49.9 34 0.00074 25.0 4.4 42 39-84 5-47 (116)
138 PRK05657 RNA polymerase sigma 49.8 42 0.00091 29.6 5.6 53 41-94 262-314 (325)
139 TIGR02859 spore_sigH RNA polym 49.7 43 0.00093 26.4 5.3 32 61-92 164-195 (198)
140 PRK09649 RNA polymerase sigma 49.6 37 0.0008 26.9 4.8 46 42-92 131-176 (185)
141 KOG3755|consensus 49.6 5.7 0.00012 38.1 0.1 46 49-94 706-758 (769)
142 PRK08301 sporulation sigma fac 49.4 40 0.00087 27.7 5.2 52 41-93 178-229 (234)
143 TIGR02941 Sigma_B RNA polymera 49.1 39 0.00085 28.3 5.2 48 41-93 205-252 (255)
144 PRK12523 RNA polymerase sigma 49.0 47 0.001 25.8 5.3 47 42-93 120-166 (172)
145 cd04763 HTH_MlrA-like Helix-Tu 48.7 15 0.00032 24.3 2.0 20 65-84 3-22 (68)
146 cd04764 HTH_MlrA-like_sg1 Heli 48.6 15 0.00032 24.2 2.0 21 65-85 3-23 (67)
147 PRK12513 RNA polymerase sigma 48.0 23 0.00051 28.0 3.5 34 60-93 153-186 (194)
148 PRK10100 DNA-binding transcrip 47.9 33 0.00072 28.3 4.5 49 41-95 155-203 (216)
149 PRK08583 RNA polymerase sigma 47.2 46 0.00099 27.9 5.3 48 41-93 205-252 (257)
150 PRK15369 two component system 47.0 39 0.00084 25.7 4.5 45 41-91 149-193 (211)
151 TIGR02980 SigBFG RNA polymeras 47.0 48 0.001 27.1 5.3 47 41-92 178-224 (227)
152 cd01392 HTH_LacI Helix-turn-he 46.4 12 0.00026 23.0 1.3 21 67-87 2-22 (52)
153 PRK12518 RNA polymerase sigma 46.0 23 0.00049 27.5 3.0 34 61-94 135-168 (175)
154 PF13730 HTH_36: Helix-turn-he 45.9 49 0.0011 20.6 4.1 43 41-84 2-47 (55)
155 TIGR02393 RpoD_Cterm RNA polym 45.8 62 0.0013 26.8 5.8 53 41-94 176-228 (238)
156 PRK09641 RNA polymerase sigma 45.6 49 0.0011 25.7 5.0 31 63-93 153-183 (187)
157 PF13412 HTH_24: Winged helix- 45.5 42 0.00091 20.3 3.7 37 43-83 2-38 (48)
158 PF01381 HTH_3: Helix-turn-hel 45.2 16 0.00036 22.7 1.8 23 65-87 12-34 (55)
159 PF02796 HTH_7: Helix-turn-hel 45.1 34 0.00074 20.8 3.2 37 42-83 6-42 (45)
160 PRK12522 RNA polymerase sigma 45.1 62 0.0013 25.0 5.4 30 64-93 137-166 (173)
161 TIGR03020 EpsA transcriptional 44.9 44 0.00096 28.4 4.8 52 39-96 188-239 (247)
162 PRK12542 RNA polymerase sigma 44.4 56 0.0012 25.6 5.1 47 42-93 123-169 (185)
163 TIGR02947 SigH_actino RNA poly 44.4 27 0.00057 27.7 3.3 34 61-94 146-179 (193)
164 PRK12511 RNA polymerase sigma 44.3 53 0.0012 26.0 5.0 48 41-93 111-158 (182)
165 PRK10651 transcriptional regul 44.3 48 0.001 25.6 4.7 47 41-93 155-201 (216)
166 PRK06288 RNA polymerase sigma 44.2 68 0.0015 27.1 5.9 49 41-94 212-260 (268)
167 PRK07408 RNA polymerase sigma 44.0 38 0.00082 28.6 4.3 48 41-93 203-250 (256)
168 PHA03379 EBNA-3A; Provisional 43.5 1.1E+02 0.0023 30.2 7.4 37 47-84 101-137 (935)
169 PRK12528 RNA polymerase sigma 43.2 59 0.0013 24.8 5.0 40 42-86 114-153 (161)
170 TIGR01764 excise DNA binding d 43.0 20 0.00043 21.3 1.8 23 65-87 4-26 (49)
171 COG2944 Predicted transcriptio 43.0 36 0.00079 25.2 3.5 41 41-88 43-83 (104)
172 PF00424 REV: REV protein (ant 42.7 35 0.00076 24.7 3.3 38 47-98 14-51 (91)
173 PRK09651 RNA polymerase sigma 42.6 52 0.0011 25.6 4.7 46 41-91 119-164 (172)
174 PRK07670 RNA polymerase sigma 42.4 57 0.0012 27.3 5.1 46 42-92 202-247 (251)
175 TIGR02957 SigX4 RNA polymerase 42.2 54 0.0012 28.0 5.0 47 42-93 109-155 (281)
176 TIGR02392 rpoH_proteo alternat 41.9 52 0.0011 27.9 4.9 50 41-93 218-267 (270)
177 TIGR01557 myb_SHAQKYF myb-like 41.6 67 0.0014 21.0 4.3 51 37-87 1-54 (57)
178 cd01104 HTH_MlrA-CarA Helix-Tu 41.5 22 0.00048 23.1 2.0 20 65-84 3-22 (68)
179 PRK12540 RNA polymerase sigma 41.3 67 0.0014 25.4 5.1 47 42-93 112-158 (182)
180 PRK09975 DNA-binding transcrip 40.8 19 0.00041 28.8 1.9 43 46-89 16-58 (213)
181 COG1905 NuoE NADH:ubiquinone o 40.6 43 0.00093 26.8 3.8 38 43-80 24-61 (160)
182 TIGR02835 spore_sigmaE RNA pol 40.5 65 0.0014 26.6 5.2 52 41-93 178-229 (234)
183 PRK09935 transcriptional regul 40.0 43 0.00094 25.8 3.8 47 40-92 148-194 (210)
184 KOG3623|consensus 39.9 19 0.00041 35.6 1.9 59 35-93 626-684 (1007)
185 PRK09636 RNA polymerase sigma 39.7 60 0.0013 27.8 5.0 47 42-93 116-162 (293)
186 PRK09415 RNA polymerase factor 39.6 64 0.0014 25.2 4.8 47 41-92 127-173 (179)
187 PRK09643 RNA polymerase sigma 39.5 83 0.0018 25.0 5.5 38 42-84 135-172 (192)
188 TIGR03541 reg_near_HchA LuxR f 39.5 53 0.0012 27.2 4.5 51 40-96 170-220 (232)
189 PF12200 DUF3597: Domain of un 39.2 37 0.00079 26.1 3.1 31 59-89 82-117 (127)
190 PF08279 HTH_11: HTH domain; 39.2 46 0.001 20.7 3.2 35 46-83 2-36 (55)
191 TIGR02885 spore_sigF RNA polym 39.2 59 0.0013 26.7 4.7 44 41-89 183-226 (231)
192 PRK11922 RNA polymerase sigma 38.9 47 0.001 27.4 4.0 36 59-94 162-197 (231)
193 PRK12534 RNA polymerase sigma 38.7 80 0.0017 24.7 5.2 46 42-92 138-183 (187)
194 PRK12527 RNA polymerase sigma 38.6 91 0.002 23.6 5.4 47 42-93 106-152 (159)
195 cd00093 HTH_XRE Helix-turn-hel 38.6 25 0.00054 20.6 1.8 23 65-87 15-37 (58)
196 PRK08215 sporulation sigma fac 38.5 60 0.0013 27.2 4.7 47 41-92 209-255 (258)
197 TIGR02950 SigM_subfam RNA poly 38.5 33 0.00072 25.8 2.9 33 60-92 119-151 (154)
198 PF07638 Sigma70_ECF: ECF sigm 38.4 79 0.0017 25.1 5.2 30 64-93 153-182 (185)
199 TIGR02960 SigX5 RNA polymerase 37.9 61 0.0013 27.9 4.7 48 41-93 142-189 (324)
200 PRK07500 rpoH2 RNA polymerase 37.7 67 0.0015 27.7 4.9 50 41-93 227-276 (289)
201 PRK12517 RNA polymerase sigma 37.6 1.3E+02 0.0028 23.8 6.4 49 42-95 129-177 (188)
202 TIGR03070 couple_hipB transcri 37.3 26 0.00056 21.6 1.8 23 65-87 18-40 (58)
203 TIGR02846 spore_sigmaK RNA pol 37.1 73 0.0016 26.2 4.9 52 40-92 173-224 (227)
204 PRK07122 RNA polymerase sigma 37.1 75 0.0016 27.0 5.1 47 41-92 215-261 (264)
205 PF01323 DSBA: DSBA-like thior 36.2 1.6E+02 0.0035 22.8 6.6 54 48-101 108-162 (193)
206 PRK05572 sporulation sigma fac 36.1 70 0.0015 26.7 4.7 47 41-92 202-248 (252)
207 PF12728 HTH_17: Helix-turn-he 35.8 32 0.0007 21.1 2.0 24 65-88 4-27 (51)
208 PF12114 Period_C: Period prot 35.6 58 0.0013 26.9 3.9 33 45-85 124-156 (195)
209 PRK12525 RNA polymerase sigma 35.5 1E+02 0.0022 23.8 5.2 46 41-91 118-163 (168)
210 PRK05803 sporulation sigma fac 35.4 1.1E+02 0.0024 25.1 5.8 51 41-92 175-225 (233)
211 TIGR02394 rpoS_proteo RNA poly 35.3 1.2E+02 0.0026 25.9 6.1 53 41-94 222-274 (285)
212 KOG2475|consensus 35.0 10 0.00023 35.8 -0.6 41 33-73 182-225 (587)
213 smart00595 MADF subfamily of S 34.9 67 0.0015 22.0 3.8 34 66-99 31-64 (89)
214 PRK05911 RNA polymerase sigma 34.8 1.1E+02 0.0023 25.9 5.6 48 41-93 205-252 (257)
215 TIGR02984 Sig-70_plancto1 RNA 34.8 71 0.0015 24.8 4.3 47 41-92 140-186 (189)
216 PRK09390 fixJ response regulat 34.8 67 0.0014 24.2 4.1 48 42-95 142-189 (202)
217 PRK09640 RNA polymerase sigma 34.4 50 0.0011 26.1 3.4 31 63-93 151-181 (188)
218 cd03025 DsbA_FrnE_like DsbA fa 34.2 1.8E+02 0.004 22.5 6.7 41 53-93 115-156 (193)
219 PRK09958 DNA-binding transcrip 34.0 77 0.0017 24.4 4.4 45 41-91 143-187 (204)
220 TIGR02607 antidote_HigA addict 33.8 31 0.00068 23.0 1.8 23 65-87 21-43 (78)
221 PRK15411 rcsA colanic acid cap 33.8 81 0.0018 25.6 4.6 45 41-91 137-181 (207)
222 PRK05988 formate dehydrogenase 33.5 72 0.0016 25.2 4.1 36 45-80 24-59 (156)
223 smart00422 HTH_MERR helix_turn 33.2 34 0.00074 22.2 1.9 20 65-84 3-22 (70)
224 PHA01976 helix-turn-helix prot 33.1 33 0.00072 22.2 1.8 23 65-87 18-40 (67)
225 PRK06704 RNA polymerase factor 32.7 99 0.0021 25.9 5.0 30 64-93 134-163 (228)
226 PRK06596 RNA polymerase factor 32.5 99 0.0022 26.5 5.2 50 41-93 230-279 (284)
227 PRK15008 HTH-type transcriptio 32.4 47 0.001 26.8 3.0 44 47-91 24-67 (212)
228 PRK09638 RNA polymerase sigma 32.2 49 0.0011 25.6 2.9 33 61-93 141-173 (176)
229 PRK11552 putative DNA-binding 31.8 65 0.0014 26.4 3.8 43 46-90 18-60 (225)
230 KOG3755|consensus 31.6 35 0.00077 32.9 2.3 58 35-92 647-708 (769)
231 PRK10840 transcriptional regul 31.5 1E+02 0.0022 24.6 4.8 43 41-89 150-192 (216)
232 cd03023 DsbA_Com1_like DsbA fa 31.0 2.1E+02 0.0046 20.9 7.0 41 48-88 71-111 (154)
233 cd01106 HTH_TipAL-Mta Helix-Tu 30.7 40 0.00087 24.2 2.1 23 65-87 3-25 (103)
234 cd03022 DsbA_HCCA_Iso DsbA fam 30.4 2.4E+02 0.0052 21.8 6.7 41 54-94 114-155 (192)
235 KOG1924|consensus 30.3 5.4E+02 0.012 26.2 10.0 133 43-190 472-609 (1102)
236 PF07022 Phage_CI_repr: Bacter 30.3 44 0.00096 22.1 2.1 22 65-86 15-37 (66)
237 smart00530 HTH_XRE Helix-turn- 30.0 41 0.00089 19.4 1.8 23 65-87 13-35 (56)
238 PRK11511 DNA-binding transcrip 30.0 71 0.0015 23.8 3.4 26 61-86 24-49 (127)
239 PRK08241 RNA polymerase factor 29.9 81 0.0017 27.4 4.2 29 64-92 171-199 (339)
240 PRK06424 transcription factor; 29.5 1.5E+02 0.0032 23.2 5.1 24 65-88 100-123 (144)
241 PTZ00183 centrin; Provisional 29.3 2E+02 0.0043 21.3 5.9 41 34-74 3-48 (158)
242 cd01105 HTH_GlnR-like Helix-Tu 29.1 42 0.00092 23.5 1.9 19 65-83 4-22 (88)
243 PF04539 Sigma70_r3: Sigma-70 29.0 90 0.0019 20.8 3.5 21 64-84 22-42 (78)
244 PF00249 Myb_DNA-binding: Myb- 28.7 1.2E+02 0.0025 18.4 3.7 44 39-85 1-46 (48)
245 PF05263 DUF722: Protein of un 28.6 90 0.0019 24.0 3.7 42 42-86 82-123 (130)
246 PHA02955 hypothetical protein; 28.4 77 0.0017 26.5 3.5 49 43-91 59-108 (213)
247 PRK09483 response regulator; P 27.9 1.3E+02 0.0027 23.4 4.7 45 40-90 147-191 (217)
248 PRK07539 NADH dehydrogenase su 27.9 99 0.0021 24.1 4.0 36 45-80 23-58 (154)
249 cd04774 HTH_YfmP Helix-Turn-He 27.5 49 0.0011 23.7 2.0 23 65-87 3-25 (96)
250 PF12802 MarR_2: MarR family; 27.4 86 0.0019 19.7 3.1 38 42-81 3-40 (62)
251 PF14229 DUF4332: Domain of un 27.3 60 0.0013 24.4 2.5 26 59-84 26-51 (122)
252 PF05703 Auxin_canalis: Auxin 27.2 94 0.002 26.5 3.9 24 75-98 99-122 (242)
253 cd04766 HTH_HspR Helix-Turn-He 26.9 49 0.0011 23.2 1.9 23 65-87 4-26 (91)
254 PRK10668 DNA-binding transcrip 26.9 35 0.00075 27.3 1.3 44 45-89 15-58 (215)
255 PRK11475 DNA-binding transcrip 26.8 1.4E+02 0.003 24.4 4.8 40 41-86 134-173 (207)
256 PRK10188 DNA-binding transcrip 26.7 1.7E+02 0.0037 24.4 5.5 50 40-95 178-227 (240)
257 COG3416 Uncharacterized protei 26.7 1.5E+02 0.0033 24.9 4.9 17 42-58 1-17 (233)
258 cd04780 HTH_MerR-like_sg5 Heli 26.6 50 0.0011 23.7 1.9 20 65-84 3-22 (95)
259 PRK07571 bidirectional hydroge 26.5 1.1E+02 0.0024 24.5 4.1 36 45-80 37-72 (169)
260 PF04936 DUF658: Protein of un 26.4 30 0.00065 27.8 0.8 34 61-94 13-46 (186)
261 TIGR01958 nuoE_fam NADH-quinon 26.4 1.1E+02 0.0024 23.7 4.0 36 45-80 17-52 (148)
262 PRK13890 conjugal transfer pro 26.2 45 0.00098 25.0 1.7 35 49-87 9-43 (120)
263 PF10078 DUF2316: Uncharacteri 26.2 45 0.00098 24.0 1.6 39 41-83 2-44 (89)
264 PF14549 P22_Cro: DNA-binding 26.1 1E+02 0.0022 20.4 3.2 27 65-93 12-38 (60)
265 PF12844 HTH_19: Helix-turn-he 25.8 98 0.0021 19.7 3.1 24 64-87 14-37 (64)
266 PF08667 BetR: BetR domain; I 25.8 1.1E+02 0.0025 24.0 3.9 38 46-83 6-43 (147)
267 PF13542 HTH_Tnp_ISL3: Helix-t 25.6 1.6E+02 0.0035 17.8 4.2 21 64-84 29-49 (52)
268 cd04779 HTH_MerR-like_sg4 Heli 25.3 53 0.0012 25.2 2.0 25 65-89 3-27 (134)
269 TIGR03830 CxxCG_CxxCG_HTH puta 25.3 84 0.0018 23.0 3.1 43 38-87 61-103 (127)
270 cd04768 HTH_BmrR-like Helix-Tu 25.3 57 0.0012 23.2 2.0 24 65-88 3-26 (96)
271 PF13565 HTH_32: Homeodomain-l 25.3 2.1E+02 0.0045 18.8 5.8 39 43-81 32-75 (77)
272 PF01257 2Fe-2S_thioredx: Thio 24.6 88 0.0019 24.1 3.1 35 46-80 15-49 (145)
273 TIGR03613 RutR pyrimidine util 24.3 43 0.00093 26.5 1.3 43 47-90 14-56 (202)
274 PRK14996 TetR family transcrip 24.1 95 0.0021 24.3 3.4 42 47-89 14-55 (192)
275 PF13743 Thioredoxin_5: Thiore 23.8 3E+02 0.0065 21.7 6.2 47 44-90 83-131 (176)
276 PRK07405 RNA polymerase sigma 23.8 1.6E+02 0.0034 25.8 4.9 52 41-93 256-307 (317)
277 PRK09635 sigI RNA polymerase s 23.7 1.5E+02 0.0032 25.6 4.7 29 65-93 137-165 (290)
278 PF06971 Put_DNA-bind_N: Putat 23.7 59 0.0013 20.7 1.6 17 65-81 31-47 (50)
279 PF14851 FAM176: FAM176 family 23.7 3.4E+02 0.0073 21.5 6.2 7 66-72 119-125 (153)
280 COG1595 RpoE DNA-directed RNA 23.5 95 0.0021 24.3 3.2 30 65-94 146-175 (182)
281 PF03672 UPF0154: Uncharacteri 23.1 1.9E+02 0.004 19.6 4.0 32 47-78 19-50 (64)
282 PF00440 TetR_N: Bacterial reg 23.0 75 0.0016 19.2 2.0 23 65-87 19-41 (47)
283 PRK10430 DNA-binding transcrip 23.0 1.2E+02 0.0026 24.7 3.8 45 41-86 158-202 (239)
284 PF13560 HTH_31: Helix-turn-he 22.5 65 0.0014 20.8 1.8 25 64-88 16-40 (64)
285 cd04782 HTH_BltR Helix-Turn-He 22.5 69 0.0015 22.8 2.0 22 65-86 3-24 (97)
286 PF01047 MarR: MarR family; I 22.4 1.2E+02 0.0026 18.9 3.0 38 42-83 1-38 (59)
287 cd04773 HTH_TioE_rpt2 Second H 22.4 70 0.0015 23.3 2.1 23 65-87 3-25 (108)
288 PRK11202 DNA-binding transcrip 21.9 38 0.00083 27.2 0.6 39 50-89 21-59 (203)
289 PRK09706 transcriptional repre 21.8 64 0.0014 24.3 1.8 24 65-88 21-44 (135)
290 PRK05949 RNA polymerase sigma 21.8 2.3E+02 0.0049 25.0 5.5 51 41-92 266-316 (327)
291 cd00592 HTH_MerR-like Helix-Tu 21.7 75 0.0016 22.4 2.1 22 65-86 3-24 (100)
292 cd04775 HTH_Cfa-like Helix-Tur 21.6 70 0.0015 23.0 1.9 22 64-85 3-24 (102)
293 PF04297 UPF0122: Putative hel 21.5 2.9E+02 0.0063 20.3 5.2 43 41-88 17-59 (101)
294 TIGR02054 MerD mercuric resist 21.1 73 0.0016 24.0 2.0 22 64-85 5-26 (120)
295 PRK09726 antitoxin HipB; Provi 21.0 69 0.0015 22.3 1.7 23 65-87 28-50 (88)
296 PF02954 HTH_8: Bacterial regu 21.0 1.8E+02 0.0039 17.2 3.4 31 46-80 6-36 (42)
297 PF07037 DUF1323: Putative tra 20.9 71 0.0015 24.3 1.8 21 65-85 3-23 (122)
298 cd03024 DsbA_FrnE DsbA family, 20.9 3.3E+02 0.0072 21.2 5.9 30 60-89 129-158 (201)
299 PF08671 SinI: Anti-repressor 20.9 1.1E+02 0.0023 17.5 2.1 19 66-84 9-27 (30)
300 cd04767 HTH_HspR-like_MBC Heli 20.9 77 0.0017 24.0 2.1 24 64-87 3-26 (120)
301 cd04788 HTH_NolA-AlbR Helix-Tu 20.8 75 0.0016 22.6 1.9 22 65-86 3-24 (96)
302 TIGR02997 Sig70-cyanoRpoD RNA 20.5 1.6E+02 0.0034 25.4 4.2 43 41-84 249-291 (298)
303 TIGR01636 phage_rinA phage tra 20.5 1.6E+02 0.0036 22.3 3.9 38 42-82 83-120 (134)
304 PRK07598 RNA polymerase sigma 20.3 2.5E+02 0.0054 25.9 5.6 52 41-93 350-401 (415)
305 cd01279 HTH_HspR-like Helix-Tu 20.3 82 0.0018 22.5 2.0 23 64-86 3-25 (98)
306 cd04789 HTH_Cfa Helix-Turn-Hel 20.0 80 0.0017 22.8 1.9 24 64-87 3-26 (102)
307 PRK13870 transcriptional regul 20.0 2.4E+02 0.0053 23.4 5.1 28 66-93 192-219 (234)
No 1
>KOG0487|consensus
Probab=99.83 E-value=5.6e-21 Score=164.89 Aligned_cols=70 Identities=34% Similarity=0.530 Sum_probs=64.7
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN 100 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~ 100 (205)
.-++.||||..+|+.|+.+||+.|..|.|++++.|.+|++.|+|+++||+|||||||+|+||..++....
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r~~ 300 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENRLK 300 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhhcc
Confidence 3478899999999999999999999999999999999999999999999999999999999998655443
No 2
>KOG0842|consensus
Probab=99.83 E-value=4e-20 Score=159.56 Aligned_cols=74 Identities=38% Similarity=0.620 Sum_probs=67.4
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhhhcc
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNS 104 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~~~s 104 (205)
.+++|||.|..|+..|+-+||+.|.+++|++..+|++||..|+||+.||||||||||-|.||+.++.......-
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~~~ 222 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEALLL 222 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcccC
Confidence 36778888999999999999999999999999999999999999999999999999999999988876655443
No 3
>KOG0489|consensus
Probab=99.81 E-value=1.2e-20 Score=161.43 Aligned_cols=67 Identities=37% Similarity=0.603 Sum_probs=62.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL 99 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~ 99 (205)
.+.||.|+.||.+|+.+||+.|+.|+|.++..|.|||..|+|+|+||+|||||||||+||..+....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~ 223 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSS 223 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhccccc
Confidence 4578999999999999999999999999999999999999999999999999999999998766543
No 4
>KOG0485|consensus
Probab=99.79 E-value=6.6e-19 Score=143.86 Aligned_cols=70 Identities=31% Similarity=0.578 Sum_probs=64.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhh
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNA 101 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~ 101 (205)
..+|||.||+|+..|+..||..|+...|.+..+|..||++|.|++.||+|||||||.||||+-......+
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ea~ 170 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADLEAA 170 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhhhhh
Confidence 4678889999999999999999999999999999999999999999999999999999999976654443
No 5
>KOG0488|consensus
Probab=99.78 E-value=1.6e-18 Score=151.11 Aligned_cols=66 Identities=42% Similarity=0.706 Sum_probs=62.9
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
.||+||.||.||..|+..||+.|++..|.+..+|.+||+.|||+..||++||||||+||||.....
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g 234 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEG 234 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhh
Confidence 488899999999999999999999999999999999999999999999999999999999987663
No 6
>KOG0484|consensus
Probab=99.75 E-value=8.2e-19 Score=128.09 Aligned_cols=68 Identities=68% Similarity=0.981 Sum_probs=63.7
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
.++|.||-|+.|+..|+..||+.|...+||++..|++||.++.|++..|+|||||||+|.||+++...
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~ 80 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAI 80 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHH
Confidence 46788999999999999999999999999999999999999999999999999999999999876543
No 7
>KOG0850|consensus
Probab=99.73 E-value=5.8e-18 Score=139.44 Aligned_cols=66 Identities=39% Similarity=0.658 Sum_probs=62.3
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
..||.||.||.++.-||..|.+.|++++|+-..+|.+||..|||+..||+|||||||.|.||..+.
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~ 183 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQ 183 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhc
Confidence 357778899999999999999999999999999999999999999999999999999999999773
No 8
>KOG3802|consensus
Probab=99.73 E-value=8.4e-19 Score=154.49 Aligned_cols=64 Identities=25% Similarity=0.468 Sum_probs=60.7
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
..|||||||+|+..++..||++|.+|++|+.+++.+||++|+|++.+|+|||||||+|.||...
T Consensus 291 ~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 291 QSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 3488999999999999999999999999999999999999999999999999999999999743
No 9
>KOG0844|consensus
Probab=99.73 E-value=6.6e-18 Score=143.99 Aligned_cols=64 Identities=39% Similarity=0.611 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
.-||-||.|+++|+.+||+.|.+..|-++..|.|||..|+|.+..|+|||||||+|+||++..+
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 4478899999999999999999999999999999999999999999999999999999987654
No 10
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.72 E-value=1e-17 Score=110.94 Aligned_cols=57 Identities=49% Similarity=0.768 Sum_probs=55.3
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
||+|+.|+.+|+.+|+++|..++||+..+++.||..|||+..+|++||+|+|.+.||
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 11
>KOG0843|consensus
Probab=99.71 E-value=8.9e-18 Score=133.74 Aligned_cols=64 Identities=41% Similarity=0.658 Sum_probs=61.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
|.||.||.|+.+|+..||..|..|+|..-.+|+.||..|+|++.||+|||||||.|.||+..+.
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 7789999999999999999999999999999999999999999999999999999999987664
No 12
>KOG2251|consensus
Probab=99.71 E-value=6.7e-18 Score=138.42 Aligned_cols=68 Identities=63% Similarity=0.900 Sum_probs=64.6
Q ss_pred CccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 30 PLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 30 ~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
...+|.||.||+|+.+|+.+||.+|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|++++.+
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 34689999999999999999999999999999999999999999999999999999999999987765
No 13
>KOG0494|consensus
Probab=99.69 E-value=5.6e-17 Score=135.64 Aligned_cols=65 Identities=58% Similarity=0.886 Sum_probs=59.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
|+|+-||.|+..|+..||+.|....||+...|+.||.+++|.+++|+|||||||+||||.++...
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 33444899999999999999999999999999999999999999999999999999999877643
No 14
>KOG0848|consensus
Probab=99.68 E-value=3.1e-17 Score=137.65 Aligned_cols=65 Identities=35% Similarity=0.626 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
|.+-|-|.+++..|+.+||+.|.-++|+++..+.|||..|||+||||+|||||||+|+||..++.
T Consensus 197 RTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 197 RTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 33445688999999999999999999999999999999999999999999999999999987665
No 15
>KOG0492|consensus
Probab=99.67 E-value=5.7e-17 Score=131.74 Aligned_cols=68 Identities=37% Similarity=0.658 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN 100 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~ 100 (205)
+-.|+.|+.|+.+|+..||+.|.+.+|.++.+|.+++..|.|++.||+|||||||+|.||.+..+.+.
T Consensus 142 k~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 142 KPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred CCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 44577899999999999999999999999999999999999999999999999999999986655443
No 16
>KOG0493|consensus
Probab=99.67 E-value=8.6e-17 Score=134.66 Aligned_cols=58 Identities=41% Similarity=0.795 Sum_probs=56.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
||.||.|+.+|+.+|...|+.|.|.+++.|.+||.+|+|.+.||+|||||+|+|.||.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKs 304 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKS 304 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhc
Confidence 6789999999999999999999999999999999999999999999999999999986
No 17
>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=99.62 E-value=4e-16 Score=103.84 Aligned_cols=53 Identities=23% Similarity=0.431 Sum_probs=51.0
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcCCC----CCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 35 QRRSRTTFTGDQLEELERAFQRTQY----PDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 35 ~rr~R~~~s~~q~~~Le~~F~~~~~----ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+||.||.|+.+|+..|+++|..++| |+..+|.+||..|||++++|+|||||.+
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 9999999999999999999999999975
No 18
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.61 E-value=1.2e-15 Score=101.03 Aligned_cols=58 Identities=53% Similarity=0.925 Sum_probs=54.7
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++.|..++.+|+.+|+++|..++||+..++..||.++||++.+|++||+|+|.+.++.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3567889999999999999999999999999999999999999999999999998864
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.61 E-value=1.2e-15 Score=100.27 Aligned_cols=56 Identities=57% Similarity=0.926 Sum_probs=52.5
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
++.|+.|+.+|+.+|+.+|..|+||+..++.+||..+||+..+|++||+|+|.+.|
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 35678899999999999999999999999999999999999999999999998754
No 20
>KOG0491|consensus
Probab=99.60 E-value=4.8e-16 Score=122.24 Aligned_cols=65 Identities=40% Similarity=0.714 Sum_probs=60.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
+++|-|++|+..|+..||+.|+.+.|.+..+|.|||..|+|+++||+.||||||+|.||..+..+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~~ 163 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNNQ 163 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhccC
Confidence 45678999999999999999999999999999999999999999999999999999999876644
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.55 E-value=5.4e-15 Score=117.21 Aligned_cols=65 Identities=32% Similarity=0.541 Sum_probs=59.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
...+++|++.+.+|+.+|++.|..|+||+...|..|+..|+|+++-|+|||||||++.|+.....
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 45577788899999999999999999999999999999999999999999999999999986543
No 22
>KOG0483|consensus
Probab=99.53 E-value=6.6e-15 Score=120.61 Aligned_cols=64 Identities=27% Similarity=0.488 Sum_probs=57.5
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
.++++.+|+.+|+..||+.|..+.+....++..||+.|||..+||.|||||||+|||.++....
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d 113 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD 113 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence 3444556999999999999999999999999999999999999999999999999998765544
No 23
>KOG0486|consensus
Probab=99.50 E-value=2.4e-14 Score=122.74 Aligned_cols=65 Identities=65% Similarity=0.946 Sum_probs=62.5
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
|+||.|+-|+.+|+..||.+|.+|.||+...|++||--++|++.+|+|||.|||+||||+++.++
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67888999999999999999999999999999999999999999999999999999999988776
No 24
>KOG4577|consensus
Probab=99.39 E-value=3.1e-13 Score=114.89 Aligned_cols=65 Identities=38% Similarity=0.593 Sum_probs=60.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
..||.||+|+..|++.|...|+..++|-+..|++|+.++||.-++|||||||||+|+||-+++..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 45889999999999999999999999999999999999999999999999999999999876643
No 25
>KOG0847|consensus
Probab=99.34 E-value=5.5e-13 Score=109.49 Aligned_cols=69 Identities=41% Similarity=0.702 Sum_probs=62.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhh
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLN 100 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~ 100 (205)
..++|-.|.+|+-.|+..||+.|.+.+|+--.+|.+||..+||++.||+|||||||.||||+...+...
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAaEmas 232 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAAEMAS 232 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhccchhh
Confidence 356666788999999999999999999999999999999999999999999999999999997665443
No 26
>KOG1168|consensus
Probab=99.31 E-value=7.2e-13 Score=112.72 Aligned_cols=63 Identities=25% Similarity=0.429 Sum_probs=59.2
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
..-+|||||.+-.-++..||.+|..++.|+-+.+..||++|.|.+.+|+|||||+|+|.||++
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 456688999999999999999999999999999999999999999999999999999999964
No 27
>KOG0849|consensus
Probab=99.26 E-value=3.5e-11 Score=107.11 Aligned_cols=78 Identities=54% Similarity=0.850 Sum_probs=69.4
Q ss_pred CCCCCCCCCCCCccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 19 DESDTESEPGIPLKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 19 ~~~~~~~~~~~~~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
.+.+....++...+++.+|+|++|+..|+..||+.|..++||+...|++||.+++|++..|++||+|||++++|....
T Consensus 160 ~~~~~~~~p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 160 LSADDEEPPGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccCCccccccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 334444555666788889999999999999999999999999999999999999999999999999999999998744
No 28
>KOG0490|consensus
Probab=99.24 E-value=5.8e-12 Score=104.79 Aligned_cols=64 Identities=48% Similarity=0.614 Sum_probs=61.3
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
+.++|+.|+.|+..|+.+||+.|...+||+...|+.||..++|++..|+|||||||+|+++.++
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 5788899999999999999999999999999999999999999999999999999999999865
No 29
>KOG0774|consensus
Probab=99.23 E-value=1.9e-11 Score=102.80 Aligned_cols=62 Identities=34% Similarity=0.629 Sum_probs=57.1
Q ss_pred CCCCCCCCHHHHHHHHHHhh---cCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 36 RRSRTTFTGDQLEELERAFQ---RTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~---~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
||||..|++....+|.++|. .|+||+.+.+++||+++|++..||..||.|+|.+.||.....
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~ 253 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKN 253 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhh
Confidence 67888999999999999994 689999999999999999999999999999999999975443
No 30
>KOG0775|consensus
Probab=99.18 E-value=6.6e-11 Score=100.09 Aligned_cols=61 Identities=36% Similarity=0.547 Sum_probs=52.3
Q ss_pred CCCCCCCCCCCHHH---------HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 33 RKQRRSRTTFTGDQ---------LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 33 ~k~rr~R~~~s~~q---------~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
||.--.||.+..|| +.+|.++|.+|+||+..++.+||+++||+..||-+||.|||+|+|-.
T Consensus 165 rKfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 165 RKFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred ccCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 33334577655554 77999999999999999999999999999999999999999999944
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=98.74 E-value=7.8e-09 Score=63.85 Aligned_cols=35 Identities=37% Similarity=0.675 Sum_probs=29.7
Q ss_pred hcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 55 QRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 55 ~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
..++||+.+++.+||.++||+.+||..||-|.|.|
T Consensus 6 ~~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 6 LHNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TTSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 35799999999999999999999999999999975
No 32
>KOG2252|consensus
Probab=98.59 E-value=9.9e-08 Score=87.77 Aligned_cols=63 Identities=24% Similarity=0.323 Sum_probs=57.1
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..-+.||.|.+|+..|+..|..+|..+++|+.++.+.|+.+|+|....|.+||-|-|.|.+-+
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl~~ 478 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSLDK 478 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcccc
Confidence 345567789999999999999999999999999999999999999999999999999886444
No 33
>KOG0490|consensus
Probab=98.23 E-value=1.4e-06 Score=72.36 Aligned_cols=65 Identities=54% Similarity=0.799 Sum_probs=60.8
Q ss_pred ccCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 31 LKRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 31 ~~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
...+.++.|+.+...|+..|+..|..+.+|+...++.|+..+|+....|++||+|+|.+.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 35677889999999999999999999999999999999999999999999999999999998754
No 34
>KOG1146|consensus
Probab=97.76 E-value=3.7e-05 Score=77.12 Aligned_cols=63 Identities=27% Similarity=0.381 Sum_probs=58.8
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
-.+|++|+.++..|+++|..+|....||..++.+.|-+.+++.+++|++||||-|.|.|+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345778999999999999999999999999999999999999999999999999999998755
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.43 E-value=0.00011 Score=48.43 Aligned_cols=41 Identities=22% Similarity=0.463 Sum_probs=31.1
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+..|+++|...+++.......|..+.+|+..||+.||-.|+
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 45699999999999999999999999999999999996554
No 36
>KOG0773|consensus
Probab=97.42 E-value=0.0002 Score=63.47 Aligned_cols=64 Identities=25% Similarity=0.386 Sum_probs=53.7
Q ss_pred CCCCCCCCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 35 QRRSRTTFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 35 ~rr~R~~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
++|.+..+......+|+.+... .+||+..++..||+++||+..||.+||.|.|-|..+-.....
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHH
Confidence 4455668999999999988543 589999999999999999999999999999998887655443
No 37
>KOG3623|consensus
Probab=96.09 E-value=0.0078 Score=57.83 Aligned_cols=48 Identities=21% Similarity=0.250 Sum_probs=44.9
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+.+|..+|..|..|+.++...||.++||..+.|+.||++++.......
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 778999999999999999999999999999999999999998877754
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.37 E-value=0.035 Score=36.03 Aligned_cols=47 Identities=15% Similarity=0.360 Sum_probs=36.4
Q ss_pred CCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 36 RRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 36 rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
||+|..++-++...+-+.++... ...+||..+|+...+|..|..|+.
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 57888999999888888887776 578999999999999999998753
No 39
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=90.60 E-value=0.84 Score=28.61 Aligned_cols=46 Identities=17% Similarity=0.260 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..+|...|..+ ..-.++|+.+|++...|+.+...-..|.|
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 47889999999998332 34678999999999999988765555544
No 40
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=87.28 E-value=0.86 Score=27.71 Aligned_cols=44 Identities=14% Similarity=0.177 Sum_probs=33.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
.++..+..+++..|... ....++|+.+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46778888888887433 346788999999999999998654443
No 41
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=85.99 E-value=0.67 Score=31.40 Aligned_cols=44 Identities=14% Similarity=0.268 Sum_probs=30.5
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 37 RSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 37 r~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
++|..|+.++...+-..+.... ....+||.++||....|..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC----CceEeeecccccccccccHHHH
Confidence 4667899999888777763332 5688999999999999999985
No 42
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=83.93 E-value=4 Score=31.94 Aligned_cols=52 Identities=21% Similarity=0.188 Sum_probs=40.0
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
...+++.|+.+|...+ .. ....+||+.||++...|..|..+.+.+.|+....
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 3568999999997743 22 2356899999999999999999777777665443
No 43
>KOG1146|consensus
Probab=83.82 E-value=1.9 Score=44.49 Aligned_cols=63 Identities=24% Similarity=0.321 Sum_probs=57.5
Q ss_pred cCCCCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 32 KRKQRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 32 ~~k~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.-+-++-|..+-.++..+|-.+|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++..
T Consensus 702 ~~~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 702 SPRDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 345567778888999999999999999999999999999999999999999999999998875
No 44
>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=83.60 E-value=3.5 Score=25.98 Aligned_cols=41 Identities=17% Similarity=0.193 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+++.+..++.-.|..+ ....++|+.+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5677777777765443 3578899999999999999997443
No 45
>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=81.76 E-value=5 Score=21.62 Aligned_cols=37 Identities=19% Similarity=0.338 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
++.++...+...|.. .+ ...++|+.+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~-~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAA-GE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHc-CC----CHHHHHHHHCCCHHHHHHhC
Confidence 566666666666653 22 46688999999999988874
No 46
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=80.46 E-value=4.3 Score=26.11 Aligned_cols=47 Identities=21% Similarity=0.224 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.||+.++.+|.-+..-.. ..++|..++++++.|..+..+=+.|..-.
T Consensus 3 ~LT~~E~~vl~~l~~G~~------~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGMS------NKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhcCC------cchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 578889999887764433 78899999999999999887766665443
No 47
>PLN03162 golden-2 like transcription factor; Provisional
Probab=80.25 E-value=23 Score=32.22 Aligned_cols=67 Identities=13% Similarity=0.068 Sum_probs=44.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHH-hhcC-CCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901 33 RKQRRSRTTFTGDQLEELERA-FQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL 99 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~-F~~~-~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~ 99 (205)
..+||.|-++|.+.-..+-+. .+.. ..-+...+.+|-..-||+...|+.-.|--|...|+...++..
T Consensus 231 ~g~KKpRLrWTpELH~rFVeAV~qLG~dKATPK~ILelMnV~GLTRenVKSHLQKYRl~rk~l~~rEaE 299 (526)
T PLN03162 231 PGKKKAKVDWTPELHRRFVHAVEQLGVEKAFPSRILELMGVQCLTRHNIASHLQKYRSHRRHLAAREAE 299 (526)
T ss_pred CCCCCCcccCCHHHHHHHHHHHHHhCcCccchHHHHHHcCCCCcCHHHHHHHHHHHHHhcccccchhhh
Confidence 445677888888854444333 3333 234556666666677999999999999888877765544443
No 48
>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=76.83 E-value=1.9 Score=28.85 Aligned_cols=21 Identities=24% Similarity=0.529 Sum_probs=18.1
Q ss_pred HHHHHHHhhCCchhhhhhhhh
Q psy1901 64 TREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFq 84 (205)
.-.+||++||+++.+|+.|=.
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHhh
Confidence 356789999999999999964
No 49
>PRK04217 hypothetical protein; Provisional
Probab=75.58 E-value=8.6 Score=28.76 Aligned_cols=49 Identities=16% Similarity=0.177 Sum_probs=38.2
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..++.+|+.++...|...- ...+||+.+|++...|+..+..-+.+.|..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre~ 89 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQM 89 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3578899888877764443 577899999999999999987666666554
No 50
>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=75.05 E-value=7.3 Score=25.85 Aligned_cols=45 Identities=16% Similarity=0.230 Sum_probs=24.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
|..|+.......-++|....---..+|. .|.+.|+.+++|+-|-+
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 4456666655555555444332223344 49999999999999985
No 51
>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=74.27 E-value=9.3 Score=24.75 Aligned_cols=41 Identities=29% Similarity=0.324 Sum_probs=33.1
Q ss_pred CCHHHHHHHHHHhhcCC--CCCHHHHHHHHHhhCCchhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQ--YPDVYTREELAQKTKLTEARVQVW 82 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~--~ps~~~r~~LA~~l~l~~~qV~~W 82 (205)
+|..|+.+|...|...= +|-.....+||+.||+++.-|..=
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~ 43 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEH 43 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHH
Confidence 57889999999987654 366677899999999999876553
No 52
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=74.16 E-value=8 Score=30.95 Aligned_cols=48 Identities=23% Similarity=0.266 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..++.+|...|..+ ....+||+.||++...|+.++..-|.+.|+.
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 36666777776554333 3467899999999999999997666666654
No 53
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=73.78 E-value=7.6 Score=29.47 Aligned_cols=47 Identities=17% Similarity=0.159 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.++.++...|..+ ....+||+.+|++...|+.|...-+.+.|+
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 46666777776655433 347899999999999999998755555543
No 54
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=72.55 E-value=10 Score=29.01 Aligned_cols=48 Identities=13% Similarity=0.196 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.+..++.-.|... ....+||+.+|++...|+..+..-|.+.|+..
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555443222 23568999999999999999986666666653
No 55
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=72.43 E-value=12 Score=22.78 Aligned_cols=43 Identities=23% Similarity=0.278 Sum_probs=30.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
.++..+..++..++ . . ....+||+.+|++...|..|...-+.|
T Consensus 3 ~l~~~e~~i~~~~~-~-g----~s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLA-E-G----LTNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36777888776543 2 2 246889999999999999988744333
No 56
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=72.08 E-value=9.3 Score=29.52 Aligned_cols=48 Identities=15% Similarity=0.108 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.+|.-.|..+ ....+||+.+|++...|+.|...-+.+.|+.
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777777665322 2467899999999999999998655555554
No 57
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=71.09 E-value=5.5 Score=24.48 Aligned_cols=40 Identities=13% Similarity=0.219 Sum_probs=21.4
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
..|+.+|+..++.++... .-..+||+.||.....|..+..
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 457888899998887544 3466799999999999988764
No 58
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=70.91 E-value=9.4 Score=28.59 Aligned_cols=43 Identities=12% Similarity=0.141 Sum_probs=30.9
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhc
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqN 85 (205)
|..++.++....-.....+. ....++|..+|++...|..|.+-
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 45578887665544444444 24677899999999999999753
No 59
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=70.69 E-value=11 Score=30.57 Aligned_cols=47 Identities=19% Similarity=0.250 Sum_probs=32.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++..+..+|...|..+ ....+||+.+|++...|+.++..-+.+.++.
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 200 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQ 200 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5556666665443222 3467899999999999999887666666554
No 60
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=70.65 E-value=13 Score=28.65 Aligned_cols=47 Identities=17% Similarity=0.134 Sum_probs=33.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|...|.. .....+||+.+|++...|+.|...-|.+.|+.
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~~ 172 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLREC 172 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 555555565555432 23457999999999999999998666666654
No 61
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=70.48 E-value=6.4 Score=28.38 Aligned_cols=41 Identities=17% Similarity=0.196 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQV 81 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~ 81 (205)
+++++|+.+-.+.|+.|--.+.-..+++|..||.++.-|+-
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 57888888888887777777778899999999988866543
No 62
>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=69.84 E-value=11 Score=27.73 Aligned_cols=47 Identities=17% Similarity=0.227 Sum_probs=32.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.+..+|...|.. .....+||+.+|+++..|+.+...-+.|.|+
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 3566666666555432 2346689999999999999998766555554
No 63
>PRK10072 putative transcriptional regulator; Provisional
Probab=68.78 E-value=9 Score=27.91 Aligned_cols=41 Identities=22% Similarity=0.269 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
..+...+..|.+.-.. ...+||+.+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 3466666666554322 2678999999999999999988764
No 64
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=67.98 E-value=15 Score=28.43 Aligned_cols=48 Identities=19% Similarity=0.076 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.+..+|.-.|.. .....+||..+|++...|+.|.+.-|.+.|+..
T Consensus 109 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 109 LPVIEAQAILLCDVH-----ELTYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CCHHHHHHHHhHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 455555555443222 234678999999999999999986666666653
No 65
>PRK00118 putative DNA-binding protein; Validated
Probab=66.51 E-value=22 Score=26.26 Aligned_cols=47 Identities=17% Similarity=0.179 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++..|..++...|..+ ....+||+.+|++...|..|...-|.+.|+.
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~ 64 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDY 64 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5667777776665443 3467899999999999999998766666654
No 66
>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=66.34 E-value=5.2 Score=24.33 Aligned_cols=23 Identities=17% Similarity=0.111 Sum_probs=19.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..++|+.+|++.+.|+.|.++..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46889999999999999976543
No 67
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=65.75 E-value=15 Score=27.96 Aligned_cols=45 Identities=29% Similarity=0.220 Sum_probs=31.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~ 90 (205)
.+++.+..++...|.. .....+||+.+||+...|+++...-|.+.
T Consensus 111 ~L~~~~r~v~~l~~~~-----g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 111 KLPERQRELLQLRYQR-----GVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HCCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 4666677777664432 23468899999999999998876444443
No 68
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=65.72 E-value=14 Score=28.96 Aligned_cols=49 Identities=20% Similarity=0.177 Sum_probs=35.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.+++.++.+|.-.|... ..-.+||..+|++...|+.++..-|.+.|+..
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 35666666666654332 34678999999999999999987777766653
No 69
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=64.94 E-value=36 Score=26.45 Aligned_cols=48 Identities=25% Similarity=0.251 Sum_probs=37.7
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+.++..|+.+|+-.+ .. ....+||+.||++...|..+-..-+.+.++
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 4568999999998742 22 256789999999999999998877777665
No 70
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=64.76 E-value=20 Score=28.42 Aligned_cols=49 Identities=16% Similarity=0.245 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.+++.+..+|+-.|... ....+||+.+|++...|++-+..-|.+.|+..
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45666666665554322 24678999999999999998876666666653
No 71
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=64.75 E-value=13 Score=29.52 Aligned_cols=47 Identities=19% Similarity=0.241 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.| .......+||+.+|++...|+.|+..-|.+.|+.
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4444555554443 2234567899999999999999997666665554
No 72
>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=64.42 E-value=17 Score=28.37 Aligned_cols=48 Identities=15% Similarity=0.214 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.+|.-.|..+ ....+||+.+|++...|+.+...-|.+.++.
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46677777776655333 2467899999999999999887555555554
No 73
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=64.26 E-value=18 Score=28.32 Aligned_cols=47 Identities=19% Similarity=0.413 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|... ...++||+.+|+++..|++++..-|.+.|+.
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 5555665555554322 2367899999999999999987555555543
No 74
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=64.15 E-value=18 Score=28.65 Aligned_cols=47 Identities=30% Similarity=0.170 Sum_probs=33.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.|+.++.-.|... ....+||..+|++...|+.+...-|.+.|+
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 46666666666654332 347899999999999999988655555544
No 75
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=63.75 E-value=18 Score=28.23 Aligned_cols=46 Identities=26% Similarity=0.179 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+++.++.++.-.|... ....+||+.||+++..|++.+..-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665554333 236789999999999999988766665554
No 76
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=63.54 E-value=18 Score=28.45 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=31.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|...|.. .....+||+.+|++...|+.+...-|.+.|+.
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 175 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRAQ 175 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 455555555444322 22357899999999999999987666666654
No 77
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=63.43 E-value=16 Score=28.50 Aligned_cols=48 Identities=17% Similarity=0.192 Sum_probs=33.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|...|. ......++|+.+|++...|+.+++.-|.+.|..
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456666666655433 234467899999999999999997666665553
No 78
>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=63.30 E-value=19 Score=27.03 Aligned_cols=46 Identities=15% Similarity=0.088 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
++..+..+|.-.|.. .....+||+.+|+++..|+.+...-|.+.|+
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 455566666554432 2246779999999999999988755555443
No 79
>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=63.12 E-value=15 Score=28.75 Aligned_cols=31 Identities=13% Similarity=0.146 Sum_probs=24.3
Q ss_pred HHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 63 YTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..-.+||+.+|++...|+++...-|.+.|+.
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467899999999999999987555555544
No 80
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=62.07 E-value=20 Score=29.91 Aligned_cols=32 Identities=28% Similarity=0.350 Sum_probs=26.1
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
...+||+.||++...|+.....-|.+.|+...
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 46789999999999999999877777766543
No 81
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=61.91 E-value=12 Score=24.03 Aligned_cols=28 Identities=18% Similarity=0.337 Sum_probs=17.9
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
...+||+.+|++...|..|+.++..+..
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 4678899999999999999987744433
No 82
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=61.87 E-value=32 Score=26.96 Aligned_cols=51 Identities=16% Similarity=0.213 Sum_probs=35.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQ 97 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~ 97 (205)
+++.++.++.-.|..+ ....+||+.+|++...|+.....-|.+.|+.....
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4555555554433222 24678999999999999999988888877765443
No 83
>PRK09480 slmA division inhibitor protein; Provisional
Probab=61.61 E-value=9.1 Score=30.04 Aligned_cols=41 Identities=20% Similarity=0.302 Sum_probs=32.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
+....+.|..++. ..-...+||++.|+++..+-.+|.||-.
T Consensus 16 l~aa~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 16 LQALAQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHHHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 3344445656656 7788999999999999999999999874
No 84
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=61.28 E-value=27 Score=26.71 Aligned_cols=48 Identities=21% Similarity=0.308 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.++..+..+|.-.| .. ....+||..+|++...|+.+...-|.+.|+..
T Consensus 112 ~L~~~~r~il~l~~--~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 112 KMTERDRTVLLLRF--SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred cCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 36666677776666 22 24678999999999999999976666666543
No 85
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=60.93 E-value=18 Score=27.68 Aligned_cols=46 Identities=17% Similarity=0.171 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
++..|..+|.-.|..+ ....+||..+|++...|+.+...-|.+.|+
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 5566666665544222 236789999999999999988755555554
No 86
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=60.29 E-value=27 Score=26.51 Aligned_cols=48 Identities=19% Similarity=0.134 Sum_probs=33.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.++.-.|.... ...+||..||++...|++....-|.+.|+.
T Consensus 106 ~Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 106 KLPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred hCCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 466666666666543322 367899999999999999887555555543
No 87
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=60.29 E-value=17 Score=29.86 Aligned_cols=41 Identities=24% Similarity=0.411 Sum_probs=34.3
Q ss_pred CCCHHHHHHHHHHhhcC--CCCCHHHHHHHHHhhCCchhhhhh
Q psy1901 41 TFTGDQLEELERAFQRT--QYPDVYTREELAQKTKLTEARVQV 81 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~--~~ps~~~r~~LA~~l~l~~~qV~~ 81 (205)
.+|..|+.+|...|... -||-.-...+||++||+++.-+..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~e 197 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSE 197 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHH
Confidence 69999999999999765 357777789999999999976543
No 88
>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=59.73 E-value=4.1 Score=28.28 Aligned_cols=34 Identities=21% Similarity=0.106 Sum_probs=25.1
Q ss_pred HhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 53 AFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 53 ~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
.|....|-......+||+.+|+++..|+.|+.+.
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 3443344444567899999999999999999753
No 89
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=59.51 E-value=28 Score=27.67 Aligned_cols=48 Identities=13% Similarity=0.180 Sum_probs=33.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..++.+|.-.|... ....+||+.+|+++..|+.+...-|.+.|+.
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 35666666666655332 2367899999999999999987656555554
No 90
>PF02724 CDC45: CDC45-like protein; InterPro: IPR003874 CDC45 is an essential gene required for initiation of DNA replication in Saccharomyces cerevisiae (cell division control protein 45), forming a complex with MCM5/CDC46. Homologs of CDC45 have been identified in human [], mouse and the smut fungus, Melampsora spp., (tsd2 protein) among others.; GO: 0006270 DNA-dependent DNA replication initiation
Probab=59.15 E-value=12 Score=36.16 Aligned_cols=32 Identities=19% Similarity=0.147 Sum_probs=22.7
Q ss_pred CCHHHHHHHHHHhhcCC---CCCHHHHHHHHHhhC
Q psy1901 42 FTGDQLEELERAFQRTQ---YPDVYTREELAQKTK 73 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~---~ps~~~r~~LA~~l~ 73 (205)
...+....++.+|.+.- .|+.-..-.||.+|+
T Consensus 197 ~~~~~~~~i~~yY~~gs~~g~ssa~~~y~La~~l~ 231 (622)
T PF02724_consen 197 EREEYREEIEKYYSQGSYYGKSSAVLMYELASSLG 231 (622)
T ss_pred HHHHHHHHHHHHHhcCceecccHHHHHHHHHHHhC
Confidence 34555667888886665 477788888888876
No 91
>PRK06930 positive control sigma-like factor; Validated
Probab=58.66 E-value=30 Score=27.62 Aligned_cols=50 Identities=16% Similarity=0.177 Sum_probs=36.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
.+++.++.+|.-.|..+ ..-.+||..+|++...|+.++..-+.+.++...
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 46777777776654332 236789999999999999999877777666533
No 92
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=58.64 E-value=22 Score=28.48 Aligned_cols=48 Identities=25% Similarity=0.225 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.+..+|.-.|. ......++|..||++...|++++..-|.+.|+..
T Consensus 114 Lp~~~r~v~~L~~~-----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 114 LPDEQREALILVGA-----SGFSYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 55555555555432 2233678999999999999999987777766653
No 93
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=58.38 E-value=28 Score=26.62 Aligned_cols=47 Identities=13% Similarity=0.116 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.+..+|.-.|... ....+||+.+|++...|+.....-+.+.|+
T Consensus 109 ~L~~~~r~v~~l~~~~~-----~s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 109 ELPARTRYAFEMYRLHG-----ETQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666665554332 236789999999999999987655555444
No 94
>TIGR02952 Sig70_famx2 RNA polymerase sigma-70 factor, TIGR02952 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in a limited number of Gram-positive bacterial lineages.
Probab=57.90 E-value=27 Score=26.75 Aligned_cols=46 Identities=20% Similarity=0.159 Sum_probs=30.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..+|.-.|... ....+||+.||++...|+....--|.+.|
T Consensus 122 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l~ra~~~Lr 167 (170)
T TIGR02952 122 ILTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQFRAIKKLA 167 (170)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35566666665544322 34678999999999999987754444443
No 95
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=57.82 E-value=23 Score=28.05 Aligned_cols=48 Identities=25% Similarity=0.260 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|.-.|... ....+||+.+|++...|+...+.-|.+.|+.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 46677777776554322 3467899999999999998776555555444
No 96
>PF13551 HTH_29: Winged helix-turn helix
Probab=57.66 E-value=42 Score=23.73 Aligned_cols=48 Identities=13% Similarity=0.194 Sum_probs=31.6
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCC-----CCHHHHHH-H-HHh--hCCchhhhhhhhh
Q psy1901 37 RSRTTFTGDQLEELERAFQRTQY-----PDVYTREE-L-AQK--TKLTEARVQVWFS 84 (205)
Q Consensus 37 r~R~~~s~~q~~~Le~~F~~~~~-----ps~~~r~~-L-A~~--l~l~~~qV~~WFq 84 (205)
+.+..++.++...|.+++..++. .+.....+ | .+. +.++...|..|++
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 33344999999999999988762 34444433 3 222 2577888887774
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=57.63 E-value=25 Score=26.87 Aligned_cols=47 Identities=17% Similarity=0.198 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++..+..+|.-.|.. ...-.+||..+|++...|+.+...-|.+.|+.
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 157 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLREL 157 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 445555555554422 23467899999999999999987666666654
No 98
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=57.53 E-value=26 Score=27.52 Aligned_cols=46 Identities=17% Similarity=0.286 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+++.+..++.-.|..+ ....+||+.+|++...|+.+...-+.+.|+
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 4555555555444222 246789999999999999988755555544
No 99
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=57.46 E-value=31 Score=27.41 Aligned_cols=48 Identities=13% Similarity=0.191 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.++.+|.-.|... ..-.+||+.+|++...|+.....-|.+.|+..
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555443222 23578999999999999999886666666654
No 100
>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=57.29 E-value=8.8 Score=25.24 Aligned_cols=22 Identities=18% Similarity=0.440 Sum_probs=19.3
Q ss_pred HHHHHHHHhhCCchhhhhhhhh
Q psy1901 63 YTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFq 84 (205)
....+||+.||+..+.|..|-+
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH
Confidence 3467899999999999999985
No 101
>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=56.74 E-value=10 Score=22.69 Aligned_cols=20 Identities=10% Similarity=0.099 Sum_probs=16.4
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
+.++|+.+|++.+.|+.|=.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 46889999999999999953
No 102
>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=56.73 E-value=27 Score=26.96 Aligned_cols=46 Identities=15% Similarity=0.246 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
++..+..++...|... ....++|+.||++...|+.+...-|.+.|+
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665554333 346789999999999999988655555544
No 103
>PF13518 HTH_28: Helix-turn-helix domain
Probab=55.57 E-value=10 Score=23.30 Aligned_cols=23 Identities=17% Similarity=0.395 Sum_probs=19.3
Q ss_pred HHHHHHHhhCCchhhhhhhhhch
Q psy1901 64 TREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
...++|.++||+..+|..|.+.-
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHH
Confidence 45679999999999999999643
No 104
>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=55.57 E-value=17 Score=23.64 Aligned_cols=36 Identities=25% Similarity=0.336 Sum_probs=27.2
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
.|+..|+-.+. +...+.. +||..+|++++.|+.-..
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 47788888888 6666554 899999999999887553
No 105
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=55.52 E-value=35 Score=27.20 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
++..++.+|.-.|... ..-.+||+.||++...|+.....-|.+.|+..
T Consensus 117 Lp~~~r~i~~L~~~~g-----~s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 117 LPDDQREAIILVGASG-----FAYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555543222 23578999999999999999876666666653
No 106
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=55.42 E-value=28 Score=27.58 Aligned_cols=46 Identities=17% Similarity=0.213 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+++.++.+|.-.|.. .....+||..+|++...|+..+..-|.+.|+
T Consensus 107 L~~~~r~i~~l~~~~-----g~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 107 LPEKYAEALRLTELE-----GLSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 455555555544322 2346789999999999999988755555544
No 107
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=55.36 E-value=35 Score=27.69 Aligned_cols=48 Identities=17% Similarity=0.134 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.+..++.-.|... ....+||+.||++...|+.+...-|.+.|+..
T Consensus 139 L~~~~r~v~~L~~~~g-----~s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~l 186 (203)
T PRK09647 139 LPPEFRAAVVLCDIEG-----LSYEEIAATLGVKLGTVRSRIHRGRQQLRAAL 186 (203)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555444443222 23578999999999999999976666655543
No 108
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=55.29 E-value=29 Score=28.72 Aligned_cols=47 Identities=21% Similarity=0.238 Sum_probs=34.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.++.+|...|... ....+||+.+|++...|+.+...-+.+.|+.
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5566666666655332 2468999999999999999998777777664
No 109
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=55.04 E-value=11 Score=23.18 Aligned_cols=23 Identities=17% Similarity=0.495 Sum_probs=17.6
Q ss_pred HHHHHHHHhhCCchhhhhhhhhc
Q psy1901 63 YTREELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFqN 85 (205)
....++|+.||++...|..|.+.
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 45778999999999999999853
No 110
>TIGR02943 Sig70_famx1 RNA polymerase sigma-70 factor, TIGR02943 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family.
Probab=55.02 E-value=41 Score=26.73 Aligned_cols=50 Identities=14% Similarity=0.201 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
.+++.++.+|.-.|..+ ....+||+.+|++...|+.....-|.+.|+...
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 131 HLPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred hCCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35556666665554332 346889999999999999988766666655543
No 111
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=54.83 E-value=32 Score=26.92 Aligned_cols=47 Identities=19% Similarity=0.230 Sum_probs=31.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++..+..+|.-.|.. ...-.+||+.+|++...|+.+...-|.+.|+.
T Consensus 136 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~~ 182 (186)
T PRK13919 136 LSPEERRVIEVLYYQ-----GYTHREAAQLLGLPLGTLKTRARRALSRLKEV 182 (186)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555666666544322 23457899999999999999887555555443
No 112
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=54.83 E-value=33 Score=26.46 Aligned_cols=47 Identities=19% Similarity=0.198 Sum_probs=32.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.++.+|.-.|... ....+||+.+|++...|+.+...-|.+.|.
T Consensus 112 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 112 LLSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35666666666554322 346789999999999999988755555544
No 113
>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=54.81 E-value=41 Score=20.41 Aligned_cols=36 Identities=22% Similarity=0.184 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 43 s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
+..+..++...+ .. ....++|+.++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455666665543 22 2567889999999999999886
No 114
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=54.71 E-value=32 Score=26.98 Aligned_cols=30 Identities=30% Similarity=0.241 Sum_probs=24.6
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
...+||+.+|++...|++....-|.+.|+.
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999997666666653
No 115
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=54.34 E-value=41 Score=27.05 Aligned_cols=48 Identities=17% Similarity=0.173 Sum_probs=32.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+++.++.+|.-.|... ....+||+.+|++...|++....-|.+.|+.-
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555443222 23678999999999999998876666666543
No 116
>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=54.14 E-value=70 Score=25.56 Aligned_cols=54 Identities=19% Similarity=0.321 Sum_probs=41.4
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+...++++++..+.++-..+ |....+..||++.|++..-|.+-..-...+.+..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~e~~~~~ 135 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPKEKKKEM 135 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCHHHHHHH
Confidence 44689999999998885544 5778899999999999988888775555444433
No 117
>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=53.81 E-value=45 Score=28.06 Aligned_cols=53 Identities=13% Similarity=0.256 Sum_probs=36.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL 99 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~ 99 (205)
+...++.++.-.|..+ ....+||..+|++...|+.+...-|.+.|+....+..
T Consensus 162 Lp~~~R~v~~L~~~eg-----~S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~ 214 (244)
T TIGR03001 162 LSERERHLLRLHFVDG-----LSMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLA 214 (244)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444443222 2367899999999999999998888877776555443
No 118
>PRK10403 transcriptional regulator NarP; Provisional
Probab=53.78 E-value=16 Score=28.19 Aligned_cols=49 Identities=20% Similarity=0.276 Sum_probs=37.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
.++..+..+|+..... ..+++||+.++++++.|+...+|=+.|.....+
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~~ 201 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRSR 201 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCCH
Confidence 5889999998866532 346788999999999999999877777655433
No 119
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=53.33 E-value=36 Score=26.32 Aligned_cols=47 Identities=17% Similarity=0.276 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|... ....+||+.||+++..|+.....-|.+.|+.
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 5666666666654332 2367899999999999999886555555543
No 120
>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=53.29 E-value=33 Score=28.10 Aligned_cols=47 Identities=21% Similarity=0.229 Sum_probs=35.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.++..+..+|...|.... ...+||..+|++...|+.+...-+.+.|+
T Consensus 175 ~L~~~~r~il~l~y~~~~-----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 175 SLSEREQLVLSLYYYEEL-----NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred hCCHHHHHHHHHHHhCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 467777888877764332 46899999999999999988765555554
No 121
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=52.64 E-value=12 Score=24.55 Aligned_cols=20 Identities=10% Similarity=0.160 Sum_probs=17.9
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
+.++|+.+|++...|+.|-.
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 56899999999999999964
No 122
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=52.28 E-value=37 Score=26.80 Aligned_cols=32 Identities=19% Similarity=0.225 Sum_probs=25.3
Q ss_pred HHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 63 YTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
..-.+||+.+|+++..|+.....-|.+.|+..
T Consensus 155 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 155 LSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34678999999999999998876666666543
No 123
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=52.17 E-value=36 Score=26.79 Aligned_cols=48 Identities=13% Similarity=0.072 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|+-.|.. .....+||+.||++...|+.+...-|.+.|+.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 131 RLPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3666666666654432 23467899999999999999887655555553
No 124
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=51.85 E-value=24 Score=27.18 Aligned_cols=45 Identities=22% Similarity=0.209 Sum_probs=35.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..+|+-+... ..+++||+.++++++.|+...++=|.|..
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 5888888888776643 25788999999999999998877666654
No 125
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=51.64 E-value=47 Score=26.25 Aligned_cols=50 Identities=20% Similarity=0.161 Sum_probs=35.0
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
+++.++.++.-.|... ....+||..+|++...|++....-|.+.|+....
T Consensus 132 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 181 (191)
T PRK12520 132 LPPRTGRVFMMREWLE-----LETEEICQELQITATNAWVLLYRARMRLRECLDL 181 (191)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 5666666666554332 2367899999999999999987666666665433
No 126
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=51.54 E-value=41 Score=23.70 Aligned_cols=44 Identities=9% Similarity=0.132 Sum_probs=35.6
Q ss_pred CCCHHHHHHHHHHhhc-----CCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 41 TFTGDQLEELERAFQR-----TQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~-----~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
-++.+|+..|.+.|.. ..+.+..+..++-..+|+++..|..+|.
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 4688899999999854 3578888888887888999888888774
No 127
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=51.44 E-value=39 Score=26.54 Aligned_cols=48 Identities=10% Similarity=0.065 Sum_probs=34.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.|+.++.-.|..+ ...++||+.||+++..|+..+..-+.+.+..
T Consensus 127 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~~~ 174 (178)
T PRK12529 127 TLRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCLSL 174 (178)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 46677777776654332 2367899999999999999887666665443
No 128
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=51.27 E-value=38 Score=26.97 Aligned_cols=47 Identities=11% Similarity=0.072 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|.. ...-.+||+.+|++...|+.++.--|.+.|+.
T Consensus 137 L~~~~r~i~~L~~~~-----g~s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 137 LPERQRQAVVLRHIE-----GLSNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 444455444443322 22357899999999999999997666665554
No 129
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=51.13 E-value=47 Score=26.98 Aligned_cols=49 Identities=16% Similarity=0.171 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.+++.++.++.-.|... ....+||+.+|++...|+.....-|.+.|+..
T Consensus 148 ~L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 148 GLPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35666666666555332 23578999999999999999886666666654
No 130
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=51.02 E-value=33 Score=28.23 Aligned_cols=47 Identities=17% Similarity=0.102 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
++..++.+|.-.|..+ ....+||+.||+++..|+.+...-|.+.++.
T Consensus 135 Lp~~~R~v~~L~y~eg-----~s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~ 181 (216)
T PRK12533 135 LPVEYREVLVLRELED-----MSYREIAAIADVPVGTVMSRLARARRRLAAL 181 (216)
T ss_pred CCHHHHhHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5555566665544322 2367899999999999999887555555554
No 131
>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=50.83 E-value=14 Score=21.81 Aligned_cols=24 Identities=13% Similarity=0.332 Sum_probs=20.3
Q ss_pred HHHHHHhhCCchhhhhhhhhchHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
..++|+.||++...|..|.++...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 468899999999999999876554
No 132
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=50.41 E-value=43 Score=26.63 Aligned_cols=47 Identities=13% Similarity=0.208 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|... ..-.+||+.||++...|+.-+..-|.+.|+.
T Consensus 142 Lp~~~r~v~~l~~~eg-----~s~~EIA~~lgis~~tVk~rl~ra~~~Lr~~ 188 (194)
T PRK12531 142 LPKAQRDVLQAVYLEE-----LPHQQVAEMFDIPLGTVKSRLRLAVEKLRHS 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 5556666665543322 2367899999999999988776555555543
No 133
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=50.20 E-value=49 Score=26.35 Aligned_cols=46 Identities=17% Similarity=0.158 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|..+| ....-.+||..+|++...|++-+..-|.+.|+.
T Consensus 156 L~~~~r~vl~l~~------e~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 156 LSELEKEVLELYL------DGKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred CCHHHHHHHHHHH------ccCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555554422 224467899999999999998776555555553
No 134
>cd00131 PAX Paired Box domain
Probab=50.15 E-value=66 Score=24.37 Aligned_cols=46 Identities=9% Similarity=0.044 Sum_probs=31.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCC-------chhhhhhhhhch
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKL-------TEARVQVWFSNR 86 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l-------~~~qV~~WFqNr 86 (205)
..+..+...++.+...++..+..+..++...-|+ +...|-.||+++
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 3456666667777788888887777655333355 778887777654
No 135
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=50.10 E-value=42 Score=26.99 Aligned_cols=49 Identities=20% Similarity=0.171 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
+++.+..++.-.|..+ ....+||+.+|++...|+.+...-|.+.|+...
T Consensus 134 Lp~~~r~v~~l~~~~g-----~s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 134 LPPERREALILTQVLG-----YTYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 5555555554443222 236789999999999999998766666665533
No 136
>KOG0773|consensus
Probab=49.97 E-value=30 Score=30.50 Aligned_cols=41 Identities=39% Similarity=0.607 Sum_probs=36.4
Q ss_pred HhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 53 AFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 53 ~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.-..++|++..+...|+...+|+..+|.+||-|-|.+.+..
T Consensus 115 ~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 115 EHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 34568999999999999999999999999999999887775
No 137
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=49.89 E-value=34 Score=24.99 Aligned_cols=42 Identities=17% Similarity=0.232 Sum_probs=35.4
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCC-chhhhhhhhh
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKL-TEARVQVWFS 84 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l-~~~qV~~WFq 84 (205)
|.+|+.+.+..+-+.+....+ ...+||.++|+ ...++..|-.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 678999999888888877765 68899999996 9999888875
No 138
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=49.77 E-value=42 Score=29.57 Aligned_cols=53 Identities=30% Similarity=0.303 Sum_probs=40.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.++..++.+|...|.... ......++||..+|++...|+.+...-+.+.|+..
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 578888888888774332 23345689999999999999999987777776653
No 139
>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=49.72 E-value=43 Score=26.39 Aligned_cols=32 Identities=16% Similarity=0.140 Sum_probs=23.8
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
......+||+.+|++...|++.+.--|.+.|+
T Consensus 164 ~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 164 DGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34457899999999999999877654444443
No 140
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=49.63 E-value=37 Score=26.88 Aligned_cols=46 Identities=17% Similarity=0.071 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+++.|+.++.-.|... ..-.+||+.+|++...|+.+...-|.+.|+
T Consensus 131 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 131 LTTDQREALLLTQLLG-----LSYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CCHHHhHHhhhHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 4444555544433222 235789999999999999988644444443
No 141
>KOG3755|consensus
Probab=49.63 E-value=5.7 Score=38.06 Aligned_cols=46 Identities=17% Similarity=0.193 Sum_probs=32.7
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHhhC-------CchhhhhhhhhchHHHHHHHH
Q psy1901 49 ELERAFQRTQYPDVYTREELAQKTK-------LTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 49 ~Le~~F~~~~~ps~~~r~~LA~~l~-------l~~~qV~~WFqNrR~k~kr~~ 94 (205)
+-+.+|..+..++.-...+--+.+. ...+.|+.||.|||.++|+-+
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 3355677777777766555444443 467889999999999998864
No 142
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=49.43 E-value=40 Score=27.72 Aligned_cols=52 Identities=15% Similarity=0.172 Sum_probs=35.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.++.-.|... +-......+||+.+|++...|+.+...-|.+.|+.
T Consensus 178 ~Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~ 229 (234)
T PRK08301 178 KLSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKKE 229 (234)
T ss_pred hCCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777777766211 12223478899999999999999887666666554
No 143
>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=49.06 E-value=39 Score=28.25 Aligned_cols=48 Identities=8% Similarity=0.215 Sum_probs=35.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.+|.-.|.... ...+||+.+|++...|+.+...-+.+.|+.
T Consensus 205 ~L~~~~r~ii~l~~~~g~-----s~~eIA~~lgis~~~V~~~~~ra~~~Lr~~ 252 (255)
T TIGR02941 205 ILSEREKSIIHCTFEENL-----SQKETGERLGISQMHVSRLQRQAISKLKEA 252 (255)
T ss_pred cCCHHHHHHHHHHHcCCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467777777777764332 357999999999999999887666665553
No 144
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=48.96 E-value=47 Score=25.75 Aligned_cols=47 Identities=9% Similarity=0.099 Sum_probs=32.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|... ..-.+||+.+|++...|+.+...-+.+.+..
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~~~ 166 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCYIA 166 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555555543222 2367899999999999999987666666544
No 145
>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=48.73 E-value=15 Score=24.29 Aligned_cols=20 Identities=20% Similarity=0.258 Sum_probs=18.1
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
..++|+.+|++...|+.|.+
T Consensus 3 i~e~A~~~gVs~~tlr~ye~ 22 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 56899999999999999975
No 146
>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=48.60 E-value=15 Score=24.15 Aligned_cols=21 Identities=5% Similarity=0.113 Sum_probs=18.5
Q ss_pred HHHHHHhhCCchhhhhhhhhc
Q psy1901 65 REELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqN 85 (205)
..++|+.+|++.+.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 568999999999999999864
No 147
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=48.00 E-value=23 Score=28.05 Aligned_cols=34 Identities=24% Similarity=0.229 Sum_probs=26.4
Q ss_pred CCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 60 PDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 60 ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..-....+||+.+|++...|+.+...-|.+.|+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3334568999999999999999887666666654
No 148
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=47.90 E-value=33 Score=28.27 Aligned_cols=49 Identities=16% Similarity=0.139 Sum_probs=38.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
.+++.++.+|+-... . ....+||++|+++++.|+.+..+-..|..-+.+
T Consensus 155 ~Lt~rE~~Vl~l~~~--G----~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~nr 203 (216)
T PRK10100 155 LLTHREKEILNKLRI--G----ASNNEIARSLFISENTVKTHLYNLFKKIAVKNR 203 (216)
T ss_pred CCCHHHHHHHHHHHc--C----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 489999999988875 2 225789999999999999999877776655433
No 149
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=47.17 E-value=46 Score=27.88 Aligned_cols=48 Identities=10% Similarity=0.224 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.++.+|.-.|... ....+||+.+|++...|+.|...-+.+.|+.
T Consensus 205 ~L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr~~ 252 (257)
T PRK08583 205 VLSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLREA 252 (257)
T ss_pred hCCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 46777777777765332 2358899999999999999987666665544
No 150
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=47.02 E-value=39 Score=25.73 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..+|+- +..+ + ...++|+.++++++.|+.+.+|=+.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3333 2 2678999999999999999987666654
No 151
>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=47.01 E-value=48 Score=27.09 Aligned_cols=47 Identities=17% Similarity=0.237 Sum_probs=34.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.+..+|...|... ....+||+.+|++...|+.|...-+.+.|+
T Consensus 178 ~L~~~~r~vl~l~y~~~-----~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 178 ALPERERRILLLRFFED-----KTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred cCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57777777777776432 347789999999999999988655554443
No 152
>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=46.36 E-value=12 Score=23.02 Aligned_cols=21 Identities=14% Similarity=0.259 Sum_probs=19.3
Q ss_pred HHHHhhCCchhhhhhhhhchH
Q psy1901 67 ELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 67 ~LA~~l~l~~~qV~~WFqNrR 87 (205)
+||+.+|++...|..|+.|+.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 689999999999999999884
No 153
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=45.98 E-value=23 Score=27.46 Aligned_cols=34 Identities=24% Similarity=0.298 Sum_probs=27.0
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
....-++||+.+|++...|+..+..-|.+.|+..
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3344689999999999999999987777766653
No 154
>PF13730 HTH_36: Helix-turn-helix domain
Probab=45.86 E-value=49 Score=20.58 Aligned_cols=43 Identities=12% Similarity=-0.059 Sum_probs=29.3
Q ss_pred CCCHHHHHHHHHHhhc---CCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 41 TFTGDQLEELERAFQR---TQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~---~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
.+++.++.++-.++.. +.. ...-...||+.+|++.+.|+.++.
T Consensus 2 ~Ls~~~~~v~~~l~~~~~~~~~-~~pS~~~la~~~g~s~~Tv~~~i~ 47 (55)
T PF13730_consen 2 NLSPTAKLVYLYLASYANKNGG-CFPSQETLAKDLGVSRRTVQRAIK 47 (55)
T ss_pred CCCHHHHHHHHHHHHhcCCCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 3566666666555432 333 333578899999999999988775
No 155
>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=45.77 E-value=62 Score=26.82 Aligned_cols=53 Identities=21% Similarity=0.173 Sum_probs=40.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.+++.+..+|...|....+ ......+||..+|++...|+.....-+.|.|...
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 5788888888888743322 2234788999999999999999887777776653
No 156
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=45.61 E-value=49 Score=25.75 Aligned_cols=31 Identities=26% Similarity=0.339 Sum_probs=24.3
Q ss_pred HHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 63 YTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..-.++|+.+|++...|+.....-|.+.|+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4467899999999999998887666665553
No 157
>PF13412 HTH_24: Winged helix-turn-helix DNA-binding; PDB: 1I1G_B 2IA0_B 3I4P_A 2GQQ_A 2L4A_A 2CFX_B 2DBB_B 2EFO_A 2EFQ_A 2PN6_A ....
Probab=45.47 E-value=42 Score=20.34 Aligned_cols=37 Identities=22% Similarity=0.253 Sum_probs=24.7
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 43 s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
+..+..+|...+. ++. -.+.+||+.+|++...|..-+
T Consensus 2 ~~~~~~Il~~l~~-~~~---~t~~ela~~~~is~~tv~~~l 38 (48)
T PF13412_consen 2 DETQRKILNYLRE-NPR---ITQKELAEKLGISRSTVNRYL 38 (48)
T ss_dssp -HHHHHHHHHHHH-CTT---S-HHHHHHHHTS-HHHHHHHH
T ss_pred CHHHHHHHHHHHH-cCC---CCHHHHHHHhCCCHHHHHHHH
Confidence 4567788877766 333 446789999999998886544
No 158
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=45.15 E-value=16 Score=22.66 Aligned_cols=23 Identities=22% Similarity=0.365 Sum_probs=19.5
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||+.+|++...|..|..+++
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 47899999999999999998855
No 159
>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=45.14 E-value=34 Score=20.82 Aligned_cols=37 Identities=16% Similarity=0.389 Sum_probs=25.9
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
++.++...+.+++... ..+.+||+.+|++...|.-++
T Consensus 6 ~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 5665666666676554 347889999999999887765
No 160
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=45.14 E-value=62 Score=25.03 Aligned_cols=30 Identities=10% Similarity=0.277 Sum_probs=23.2
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.-.++|+.+|++...|+.....-|.+.|+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999887555555543
No 161
>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=44.89 E-value=44 Score=28.41 Aligned_cols=52 Identities=17% Similarity=0.104 Sum_probs=39.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
...+++.++.+|+-.. .. ....+||+.|++++..|+...+|=+.|.+-..+.
T Consensus 188 ~~~LT~RE~evl~l~a--~G----~s~~eIA~~L~IS~~TVk~hl~~i~~KL~v~nr~ 239 (247)
T TIGR03020 188 AGLITAREAEILAWVR--DG----KTNEEIAAILGISSLTVKNHLQHIFKKLDVRNRA 239 (247)
T ss_pred ccCCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHhCCCCHH
Confidence 3468999999998653 33 3467899999999999999998877776655443
No 162
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=44.39 E-value=56 Score=25.64 Aligned_cols=47 Identities=19% Similarity=0.253 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.++.++.-.|... ....+||+.+|++...|+.....-|.+.|+.
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 5556666665543222 3467899999999999999887666655554
No 163
>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=44.36 E-value=27 Score=27.75 Aligned_cols=34 Identities=26% Similarity=0.324 Sum_probs=26.6
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.-....+||+.||++...|+.+...-|.+.|+..
T Consensus 146 ~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 179 (193)
T TIGR02947 146 EGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQL 179 (193)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345689999999999999999986666666553
No 164
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=44.34 E-value=53 Score=26.02 Aligned_cols=48 Identities=17% Similarity=0.112 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..+..+|.-.|... ....+||+.+|++...|+.+...-|.+.|+.
T Consensus 111 ~Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 158 (182)
T PRK12511 111 DLPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIGRARAALRAF 158 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHHH
Confidence 35666666666544322 2367899999999999999886555555443
No 165
>PRK10651 transcriptional regulator NarL; Provisional
Probab=44.30 E-value=48 Score=25.55 Aligned_cols=47 Identities=17% Similarity=0.242 Sum_probs=36.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|+-.... ....+||++++++++.|++..+|=|.|..-+
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~ 201 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLK 201 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 3899999999765422 1356789999999999999998877776544
No 166
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=44.18 E-value=68 Score=27.11 Aligned_cols=49 Identities=20% Similarity=0.256 Sum_probs=36.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.+++.+..+|...|... ....+||..+|++...|+.....-+.+.|+..
T Consensus 212 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 212 TLPEREKKVLILYYYED-----LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 46777777777766432 34688999999999999988876666666653
No 167
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=44.01 E-value=38 Score=28.60 Aligned_cols=48 Identities=21% Similarity=0.216 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..+..+|...|.. .....+||..+|++...|+.+..--+.|.|+.
T Consensus 203 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~ 250 (256)
T PRK07408 203 QLEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKKL 250 (256)
T ss_pred cCCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3566667777666643 23568899999999999999987555555554
No 168
>PHA03379 EBNA-3A; Provisional
Probab=43.52 E-value=1.1e+02 Score=30.17 Aligned_cols=37 Identities=11% Similarity=0.099 Sum_probs=24.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
..+|...|..--+|+......|=-.-+|+-.+ -|||+
T Consensus 101 rqL~hAayaA~lqPdtRaL~~LFgdqnlnTeq-fI~ya 137 (935)
T PHA03379 101 RKLLQAIGAAATHPDTRAIDQFFGSQISNTQR-YLMYA 137 (935)
T ss_pred HHHHHHHHHHhhCcchHHHHHHHhhccCCHHH-HHHHH
Confidence 45666677777778877776665555565544 57875
No 169
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=43.22 E-value=59 Score=24.78 Aligned_cols=40 Identities=13% Similarity=0.043 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
+++.|..++.-.|... ..-.+||+.+|++...|+.+...-
T Consensus 114 L~~~~r~v~~L~~~~g-----~s~~EIA~~l~is~~tV~~~l~ra 153 (161)
T PRK12528 114 LPPLVKRAFLLAQVDG-----LGYGEIATELGISLATVKRYLNKA 153 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 5566666665554332 235789999999999999887643
No 170
>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=42.99 E-value=20 Score=21.32 Aligned_cols=23 Identities=17% Similarity=0.114 Sum_probs=19.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..++|+.||++...|..|.++.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 56789999999999999986554
No 171
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=42.95 E-value=36 Score=25.23 Aligned_cols=41 Identities=12% Similarity=0.306 Sum_probs=34.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
.++..++..+++.+... ...+|..||++..-|+.|=|+|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 48888899998887544 367899999999999999998863
No 172
>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=42.69 E-value=35 Score=24.70 Aligned_cols=38 Identities=24% Similarity=0.351 Sum_probs=20.6
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
+.+..-.|+.|+||..+-... | =.|||.+|+++..+..
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~ 51 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIR 51 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHH
Confidence 344555689999998542221 1 1488999988866543
No 173
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=42.61 E-value=52 Score=25.56 Aligned_cols=46 Identities=17% Similarity=0.175 Sum_probs=29.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..++.-.| .......+||+.+|++...|+++...-+.+.+
T Consensus 119 ~L~~~~r~i~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 119 GLNGKTREAFLLSQ-----LDGLTYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred hCCHHHhHHhhhhh-----ccCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 35555555554433 22234789999999999999998854444433
No 174
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=42.44 E-value=57 Score=27.25 Aligned_cols=46 Identities=17% Similarity=0.246 Sum_probs=33.0
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+++.++.+|.-.|. ....-.+||..+|++...|+.++..-|.+.|+
T Consensus 202 L~~~~r~vl~l~~~-----~~~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 202 LSEKEQLVISLFYK-----EELTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56666777766553 22346899999999999999988765555554
No 175
>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=42.18 E-value=54 Score=27.99 Aligned_cols=47 Identities=19% Similarity=0.117 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.|+.+|.-.|... ..-.+||+.||+++..|+..++.-|.+.|..
T Consensus 109 L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 109 LSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4555555554433222 2257899999999999999998777666654
No 176
>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=41.91 E-value=52 Score=27.92 Aligned_cols=50 Identities=18% Similarity=0.233 Sum_probs=38.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..+..+|...|... ....-.+||+.+|++...|+....+-..|.|+.
T Consensus 218 ~L~~rer~vl~l~y~~~---~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~~ 267 (270)
T TIGR02392 218 SLDARSRRIIEARWLDD---DKLTLQELAAEYGVSAERIRQIEKNAMKKLKAA 267 (270)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 57888888888888431 123457999999999999999887777776654
No 177
>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=41.59 E-value=67 Score=20.96 Aligned_cols=51 Identities=25% Similarity=0.262 Sum_probs=31.8
Q ss_pred CCCCCCCHHHHHHHHHHhhcCCCCCH---HHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 37 RSRTTFTGDQLEELERAFQRTQYPDV---YTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 37 r~R~~~s~~q~~~Le~~F~~~~~ps~---~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
++|..++.+.-..+.+........+. ..+.++-...+|+..||+.=.|.-|
T Consensus 1 k~r~~WT~eeh~~Fl~ai~~~G~g~~a~pk~I~~~~~~~~lT~~qV~SH~QKy~ 54 (57)
T TIGR01557 1 KPRVVWTEDLHDRFLQAVQKLGGPDWATPKRILELMVVDGLTRDQVASHLQKYR 54 (57)
T ss_pred CCCCCCCHHHHHHHHHHHHHhCCCcccchHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 35667788777666666666666455 5444444445678888877665443
No 178
>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=41.47 E-value=22 Score=23.15 Aligned_cols=20 Identities=15% Similarity=0.295 Sum_probs=18.0
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
..++|+.+|++...|+.|.+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46899999999999999985
No 179
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=41.28 E-value=67 Score=25.42 Aligned_cols=47 Identities=17% Similarity=0.138 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+.+.++.++.-.|.. .....+||+.||++...|+.....-|.+.|+.
T Consensus 112 Lp~~~R~v~~L~~~~-----g~s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 112 LPQDQREALILVGAS-----GFSYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 555566665554422 23467899999999999999887555555544
No 180
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=40.79 E-value=19 Score=28.81 Aligned_cols=43 Identities=14% Similarity=0.197 Sum_probs=33.4
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
-+....+.|....|-..- ..+||+..|+++.-+-.+|.||-.=
T Consensus 16 Il~aa~~lf~~~G~~~~t-i~~Ia~~agvsk~t~Y~~F~sKe~L 58 (213)
T PRK09975 16 LIETAIAQFALRGVSNTT-LNDIADAANVTRGAIYWHFENKTQL 58 (213)
T ss_pred HHHHHHHHHHHcCcccCC-HHHHHHHcCCCHHHHHHHcCCHHHH
Confidence 344555667777776554 6788999999999999999998763
No 181
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=40.56 E-value=43 Score=26.76 Aligned_cols=38 Identities=21% Similarity=0.142 Sum_probs=33.2
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 43 s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
...-+.+|...+.+..|.+...+..+|..|||+...|.
T Consensus 24 rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v~ 61 (160)
T COG1905 24 RSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARVY 61 (160)
T ss_pred hhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHhe
Confidence 35567889999999999999999999999999988773
No 182
>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=40.54 E-value=65 Score=26.59 Aligned_cols=52 Identities=15% Similarity=0.163 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..++.-.|.... -......+||+.+|++...|+.+...-+.+.|+.
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 467777777776652110 1123467899999999999998886555555553
No 183
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=40.03 E-value=43 Score=25.81 Aligned_cols=47 Identities=19% Similarity=0.212 Sum_probs=36.0
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
..+++.+..+|+-+... ..+++||++|+++.+.|+.+.++=|.|..-
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 35788888888754433 457899999999999999998877666543
No 184
>KOG3623|consensus
Probab=39.88 E-value=19 Score=35.57 Aligned_cols=59 Identities=15% Similarity=0.243 Sum_probs=46.6
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 35 QRRSRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 35 ~rr~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+-|.|+.+..++-.-|..+|..+--++..+-..++.+|...+.+|.+||++|+...+..
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~ 684 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPM 684 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCC
Confidence 34455667777777788888888777777777777788889999999999999887764
No 185
>PRK09636 RNA polymerase sigma factor SigJ; Provisional
Probab=39.66 E-value=60 Score=27.76 Aligned_cols=47 Identities=13% Similarity=-0.006 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.|+.++.-.|... ....+||+.+|+++..|+..++.-|.+.|+.
T Consensus 116 L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVk~~l~RAr~~Lr~~ 162 (293)
T PRK09636 116 LSPLERAAFLLHDVFG-----VPFDEIASTLGRSPAACRQLASRARKHVRAA 162 (293)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 4455555544433222 2357899999999999999998666666654
No 186
>PRK09415 RNA polymerase factor sigma C; Reviewed
Probab=39.60 E-value=64 Score=25.24 Aligned_cols=47 Identities=17% Similarity=0.205 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.++..++.+|.-.|... ....++|+.+|++...|+.+..--|.+.|+
T Consensus 127 ~L~~~~r~v~~l~~~~g-----~s~~EIA~~l~is~~tv~~~l~Ra~~~Lr~ 173 (179)
T PRK09415 127 SLPIKYREVIYLFYYEE-----LSIKEIAEVTGVNENTVKTRLKKAKELLKK 173 (179)
T ss_pred hCCHHHhhHhHhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35556656655443222 235789999999999999988755555544
No 187
>PRK09643 RNA polymerase sigma factor SigM; Reviewed
Probab=39.52 E-value=83 Score=24.98 Aligned_cols=38 Identities=16% Similarity=0.145 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
++..++.+|+-.|... ....+||..+|++...|+.=..
T Consensus 135 Lp~~~r~i~~l~~~~g-----~s~~EIA~~lg~s~~tV~~rl~ 172 (192)
T PRK09643 135 LPVEQRAALVAVDMQG-----YSVADAARMLGVAEGTVKSRCA 172 (192)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHH
Confidence 4555555555443322 3467899999999999976443
No 188
>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=39.48 E-value=53 Score=27.23 Aligned_cols=51 Identities=14% Similarity=0.153 Sum_probs=37.5
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhH
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNS 96 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~ 96 (205)
..+++.++.+|.-.. .. ..-.+||..||++++.|+.+..|-+.|.+...+.
T Consensus 170 ~~Lt~re~evl~~~a--~G----~t~~eIa~~l~is~~Tv~~~l~~~~~kl~~~~~~ 220 (232)
T TIGR03541 170 GVLSEREREVLAWTA--LG----RRQADIAAILGISERTVENHLRSARRKLGVATTA 220 (232)
T ss_pred ccCCHHHHHHHHHHH--CC----CCHHHHHHHHCcCHHHHHHHHHHHHHHHCCCCHH
Confidence 357777777776643 22 3457889999999999999998887777655443
No 189
>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=39.24 E-value=37 Score=26.11 Aligned_cols=31 Identities=23% Similarity=0.441 Sum_probs=20.7
Q ss_pred CCCHHHHHHHHHhhCCch-----hhhhhhhhchHHH
Q psy1901 59 YPDVYTREELAQKTKLTE-----ARVQVWFSNRRAR 89 (205)
Q Consensus 59 ~ps~~~r~~LA~~l~l~~-----~qV~~WFqNrR~k 89 (205)
-.+...|++||.+||++. .+..+|....-++
T Consensus 82 DSSl~aRkeLA~eL~~~~~~~dsA~~NiwLhk~Vm~ 117 (127)
T PF12200_consen 82 DSSLAARKELAKELGYTGDYNDSASMNIWLHKQVMQ 117 (127)
T ss_dssp --SHHHHHHHHHHHT---SS-HHHHHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHhCCCCCCCccHHHHHHHHHHHHH
Confidence 467899999999999887 5678888744443
No 190
>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=39.24 E-value=46 Score=20.69 Aligned_cols=35 Identities=17% Similarity=0.172 Sum_probs=22.9
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
|..+|.-.+....+ -...+||+.|+++.+.|+.-.
T Consensus 2 ~~~il~~L~~~~~~---it~~eLa~~l~vS~rTi~~~i 36 (55)
T PF08279_consen 2 QKQILKLLLESKEP---ITAKELAEELGVSRRTIRRDI 36 (55)
T ss_dssp HHHHHHHHHHTTTS---BEHHHHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHcCCC---cCHHHHHHHhCCCHHHHHHHH
Confidence 34556555555554 345689999999999887644
No 191
>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=39.22 E-value=59 Score=26.66 Aligned_cols=44 Identities=9% Similarity=0.099 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
.++..+..+|...|..+ ....+||+.+|++...|+.+-..-..|
T Consensus 183 ~L~~~e~~i~~~~~~~~-----~t~~eIA~~lgis~~~V~~~~~~al~~ 226 (231)
T TIGR02885 183 KLDERERQIIMLRYFKD-----KTQTEVANMLGISQVQVSRLEKKVLKK 226 (231)
T ss_pred cCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 56777777777776432 357899999999999998766433333
No 192
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=38.94 E-value=47 Score=27.37 Aligned_cols=36 Identities=31% Similarity=0.315 Sum_probs=27.6
Q ss_pred CCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 59 YPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 59 ~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
|.......+||+.+|++...|++....-|.+.|+..
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l 197 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESL 197 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 344455789999999999999998876666666654
No 193
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=38.70 E-value=80 Score=24.70 Aligned_cols=46 Identities=28% Similarity=0.377 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
+.+.+..++...|. ....-++||..||++...|+.-...-|.+.|.
T Consensus 138 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 138 LEPPRSELIRTAFF-----EGITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 45555555555442 22346789999999999998866544444433
No 194
>PRK12527 RNA polymerase sigma factor; Reviewed
Probab=38.62 E-value=91 Score=23.64 Aligned_cols=47 Identities=9% Similarity=0.079 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+++.+..+|.-.|... ....+||..+|++...|+.....-+.+.++.
T Consensus 106 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~ra~~~Lr~~ 152 (159)
T PRK12527 106 LPPACRDSFLLRKLEG-----LSHQQIAEHLGISRSLVEKHIVNAMKHCRVR 152 (159)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 4445555554443222 2357899999999999998776544444443
No 195
>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=38.58 E-value=25 Score=20.56 Aligned_cols=23 Identities=26% Similarity=0.385 Sum_probs=19.9
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
...+|+.+|++...|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 45889999999999999998764
No 196
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=38.48 E-value=60 Score=27.24 Aligned_cols=47 Identities=19% Similarity=0.194 Sum_probs=34.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.++..+..+|+..|..+ ....+||+.+|++...|+..-.+-+.|.|+
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 57888888888887433 346789999999999998876554444443
No 197
>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=38.46 E-value=33 Score=25.78 Aligned_cols=33 Identities=24% Similarity=0.308 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 60 PDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 60 ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.......+||+.+|+++..|+++..--|.+.|+
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344557899999999999999988755555443
No 198
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=38.37 E-value=79 Score=25.14 Aligned_cols=30 Identities=30% Similarity=0.472 Sum_probs=23.7
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
..++||+.||++++.|+..++.-|.+.++.
T Consensus 153 s~~EIA~~lgiS~~tV~r~l~~aR~~l~~~ 182 (185)
T PF07638_consen 153 SVEEIAERLGISERTVRRRLRRARAWLRRE 182 (185)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 457899999999999998887666555443
No 199
>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=37.90 E-value=61 Score=27.90 Aligned_cols=48 Identities=19% Similarity=0.039 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.|+.+|.-.|... ..-.+||+.||++...|+..+..-|.+.|+.
T Consensus 142 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 189 (324)
T TIGR02960 142 YLPPRQRAVLLLRDVLG-----WRAAETAELLGTSTASVNSALQRARATLDEV 189 (324)
T ss_pred hCCHHHhhHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHh
Confidence 34555555555443222 2357899999999999999887656555554
No 200
>PRK07500 rpoH2 RNA polymerase factor sigma-32; Reviewed
Probab=37.70 E-value=67 Score=27.70 Aligned_cols=50 Identities=20% Similarity=0.213 Sum_probs=38.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..+..+|...|. +-....-.+||+.+|++...|+.+...-+.|.|..
T Consensus 227 ~L~~rer~vl~lr~~---~~~~~t~~EIa~~lgvs~~~V~q~~~~Al~kLr~~ 276 (289)
T PRK07500 227 TLNERELRIIRERRL---REDGATLEALGEELGISKERVRQIEARALEKLRRA 276 (289)
T ss_pred cCCHHHHHHHHHHhc---CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 578888888888874 11234578999999999999999887666666654
No 201
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=37.62 E-value=1.3e+02 Score=23.79 Aligned_cols=49 Identities=20% Similarity=0.241 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
+...+..++.-.|.. .....+||..||++...|+++..--|.+.++...
T Consensus 129 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 129 LDPEYREPLLLQVIG-----GFSGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CCHHHHHHHHHHHHh-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 455555555444322 2346789999999999999988755655555543
No 202
>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=37.25 E-value=26 Score=21.58 Aligned_cols=23 Identities=9% Similarity=0.021 Sum_probs=20.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||..+|++...|.-|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 57899999999999999997764
No 203
>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=37.06 E-value=73 Score=26.16 Aligned_cols=52 Identities=17% Similarity=0.153 Sum_probs=34.3
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
..+++.++.+|.-.|....+ .....++||+.+|++...|+.+...-+.+.|+
T Consensus 173 ~~L~~~~r~il~l~y~~~~~-e~~S~~EIAe~lgis~~tV~~~~~rAl~~Lr~ 224 (227)
T TIGR02846 173 SVLDGREREVIEMRYGLGDG-RRKTQREIAKILGISRSYVSRIEKRALMKLYK 224 (227)
T ss_pred HhCCHHHHHHHHHHHcCCCC-CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35777788888777632110 12346789999999999998776544444444
No 204
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=37.05 E-value=75 Score=27.00 Aligned_cols=47 Identities=19% Similarity=0.290 Sum_probs=35.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.++..++.+|...|.. .....+||+.+|++...|+.+...-+.+.|+
T Consensus 215 ~L~~rer~vl~l~y~~-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 215 ALPERERTVLVLRFFE-----SMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred cCCHHHHHHHHHHhcC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4677777778777643 2346899999999999999988766655554
No 205
>PF01323 DSBA: DSBA-like thioredoxin domain; InterPro: IPR001853 DSBA is a sub-family of the Thioredoxin family []. The efficient and correct folding of bacterial disulphide bonded proteins in vivo is dependent upon a class of periplasmic oxidoreductase proteins called DsbA, after the Escherichia coli enzyme. The bacterial protein-folding factor DsbA is the most oxidizing of the thioredoxin family. DsbA catalyses disulphide-bond formation during the folding of secreted proteins. The extremely oxidizing nature of DsbA has been proposed to result from either domain motion or stabilising active-site interactions in the reduced form. DsbA's highly oxidizing nature is a result of hydrogen bond, electrostatic and helix-dipole interactions that favour the thiolate over the disulphide at the active site []. In the pathogenic bacterium Vibrio cholerae, the DsbA homologue (TcpG) is responsible for the folding, maturation and secretion of virulence factors. While the overall architecture of TcpG and DsbA is similar and the surface features are retained in TcpG, there are significant differences. For example, the kinked active site helix results from a three-residue loop in DsbA, but is caused by a proline in TcpG (making TcpG more similar to thioredoxin in this respect). Furthermore, the proposed peptide binding groove of TcpG is substantially shortened compared with that of DsbA due to a six-residue deletion. Also, the hydrophobic pocket of TcpG is more shallow and the acidic patch is much less extensive than that of E. coli DsbA [].; GO: 0015035 protein disulfide oxidoreductase activity; PDB: 3GL5_A 3DKS_D 3RPP_C 3RPN_B 1YZX_A 3L9V_C 2IMD_A 2IME_A 2IMF_A 2B3S_B ....
Probab=36.21 E-value=1.6e+02 Score=22.75 Aligned_cols=54 Identities=7% Similarity=0.046 Sum_probs=34.0
Q ss_pred HHHHHHhhcCCCCCHH-HHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhh
Q psy1901 48 EELERAFQRTQYPDVY-TREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNA 101 (205)
Q Consensus 48 ~~Le~~F~~~~~ps~~-~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~ 101 (205)
.+.+.+|.....++.. ...++++++||...++.-.+..-..+..-+........
T Consensus 108 al~~a~~~~~~~i~~~~vl~~~~~~~Gld~~~~~~~~~~~~~~~~~~~~~~~a~~ 162 (193)
T PF01323_consen 108 ALFRAYFVEGRDISDPDVLAEIAEEAGLDPDEFDAALDSPEVKAALEEDTAEARQ 162 (193)
T ss_dssp HHHHHHHTSST-TSSHHHHHHHHHHTT--HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHhcccCCCCHHHHHHHHHHcCCcHHHHHHHhcchHHHHHHHHHHHHHHH
Confidence 3455567767766665 48999999999999999988775554444443333333
No 206
>PRK05572 sporulation sigma factor SigF; Validated
Probab=36.08 E-value=70 Score=26.72 Aligned_cols=47 Identities=9% Similarity=0.121 Sum_probs=35.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.++..+..+|...|..+ ....+||+.+|++...|..+-..-..|.|+
T Consensus 202 ~L~~~~~~v~~l~~~~~-----~s~~eIA~~lgis~~~V~~~~~ral~kLr~ 248 (252)
T PRK05572 202 ELDERERLIVYLRYFKD-----KTQSEVAKRLGISQVQVSRLEKKILKQMKE 248 (252)
T ss_pred cCCHHHHHHHHHHHhCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 57888888888877433 446889999999999998877655555544
No 207
>PF12728 HTH_17: Helix-turn-helix domain
Probab=35.82 E-value=32 Score=21.13 Aligned_cols=24 Identities=17% Similarity=0.322 Sum_probs=19.6
Q ss_pred HHHHHHhhCCchhhhhhhhhchHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
..++|+.||++...|..|.++...
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999965543
No 208
>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=35.60 E-value=58 Score=26.87 Aligned_cols=33 Identities=24% Similarity=0.381 Sum_probs=25.2
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhc
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqN 85 (205)
+.+..|+.+=..+|..+..||++|+ +|-.|.|.
T Consensus 124 eD~ekLk~mq~~QP~fs~~Qk~EL~--------qvh~wiq~ 156 (195)
T PF12114_consen 124 EDREKLKSMQKQQPRFSNEQKEELA--------QVHPWIQS 156 (195)
T ss_pred HHHHHHHHHHhhCCcchHHHHHHHH--------HhhHHHHc
Confidence 3456666666678899999999988 67888863
No 209
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=35.53 E-value=1e+02 Score=23.79 Aligned_cols=46 Identities=9% Similarity=0.100 Sum_probs=31.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..++.-.|..+ ..-.+||+.||++...|+.+..+-+.+.+
T Consensus 118 ~L~~~~r~v~~L~~~eg-----~s~~EIA~~l~is~~tV~~~l~ra~~~~~ 163 (168)
T PRK12525 118 GLSGKARAAFLMSQLEG-----LTYVEIGERLGVSLSRIHQYMVEAFKCCY 163 (168)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666665554332 23678999999999999988765554444
No 210
>PRK05803 sporulation sigma factor SigK; Reviewed
Probab=35.43 E-value=1.1e+02 Score=25.14 Aligned_cols=51 Identities=16% Similarity=0.118 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.++.++.-.|.... ......++||+.+|++...|+.+-..-+.+.|+
T Consensus 175 ~Lp~~~R~i~~l~y~~~~-~e~~S~~EIA~~lgis~~tV~~~~~rA~~kLr~ 225 (233)
T PRK05803 175 ILDEREKEVIEMRYGLGN-GKEKTQREIAKALGISRSYVSRIEKRALKKLFK 225 (233)
T ss_pred hCCHHHHHHHHHHhCCCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777777662111 222457889999999999998875444444444
No 211
>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=35.26 E-value=1.2e+02 Score=25.90 Aligned_cols=53 Identities=30% Similarity=0.277 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
.++..++.+|.-.|.... .....-.+||..||++...|+.+...-+.+.|+..
T Consensus 222 ~Lp~~~R~Vl~l~ygL~~-~e~~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 222 ELNERQREVLARRFGLLG-YEPATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred cCCHHHHHHHHHHhCCCC-CCCccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 577888888887762111 12234678999999999999998876666666543
No 212
>KOG2475|consensus
Probab=34.99 E-value=10 Score=35.77 Aligned_cols=41 Identities=20% Similarity=0.176 Sum_probs=30.9
Q ss_pred CCCCCCCCCCCHHHHHHHHHHhhcCC---CCCHHHHHHHHHhhC
Q psy1901 33 RKQRRSRTTFTGDQLEELERAFQRTQ---YPDVYTREELAQKTK 73 (205)
Q Consensus 33 ~k~rr~R~~~s~~q~~~Le~~F~~~~---~ps~~~r~~LA~~l~ 73 (205)
.-+||+|.....+-..+|.++|+... .++....-+||..||
T Consensus 182 ~~krr~rr~~e~e~~~Il~eYy~~gt~~g~ss~~~lfela~ml~ 225 (587)
T KOG2475|consen 182 ASKRRERRKWEKERRTILFEYYESGTWHGSSSAVTLFELASMLG 225 (587)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcceeecCchHHHHHHHHHHhc
Confidence 33455666677888899999998843 477788888888886
No 213
>smart00595 MADF subfamily of SANT domain.
Probab=34.90 E-value=67 Score=22.03 Aligned_cols=34 Identities=29% Similarity=0.406 Sum_probs=28.9
Q ss_pred HHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHh
Q psy1901 66 EELAQKTKLTEARVQVWFSNRRARLRKQLNSQQL 99 (205)
Q Consensus 66 ~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~ 99 (205)
.+||.++|.+...|+.-+.|-|.+.++..+....
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~ 64 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQN 64 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999999999888666543
No 214
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=34.85 E-value=1.1e+02 Score=25.90 Aligned_cols=48 Identities=15% Similarity=0.190 Sum_probs=34.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+.+.+..+|...|.. .....+||..+|++...|+.+...-+.+.|+.
T Consensus 205 ~L~~~er~vi~l~y~e-----~~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 205 ALEEKERKVMALYYYE-----ELVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4677777777777643 23468999999999999999876555555544
No 215
>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=34.80 E-value=71 Score=24.82 Aligned_cols=47 Identities=21% Similarity=0.239 Sum_probs=31.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.++.++...|. ......+||..||++...|+.=...-|.+.|+
T Consensus 140 ~L~~~~r~vi~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Ra~~~Lr~ 186 (189)
T TIGR02984 140 KLPEDYREVILLRHL-----EGLSFAEVAERMDRSEGAVSMLWVRGLARLRQ 186 (189)
T ss_pred cCCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 366667777666542 23346789999999999998866544444443
No 216
>PRK09390 fixJ response regulator FixJ; Provisional
Probab=34.78 E-value=67 Score=24.22 Aligned_cols=48 Identities=8% Similarity=0.174 Sum_probs=32.1
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
+++.+..+|+..+... .-.++|+.+++++..|+++.++-|.|.+....
T Consensus 142 l~~~e~~vl~~~~~~~------~~~~ia~~l~~s~~tv~~~~~~~~~kl~~~~~ 189 (202)
T PRK09390 142 LSERERQVMDGLVAGL------SNKVIARDLDISPRTVEVYRANVMTKMQAGSL 189 (202)
T ss_pred hhhhHHHHHHHHHccC------chHHHHHHcCCCHHHHHHHHHHHHHHHccccH
Confidence 4555556665433221 24668999999999999988877777655433
No 217
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=34.36 E-value=50 Score=26.05 Aligned_cols=31 Identities=13% Similarity=0.253 Sum_probs=25.2
Q ss_pred HHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 63 YTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 63 ~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
...++||..+|++...|+++...-|.+.|+.
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3468999999999999999997666666654
No 218
>cd03025 DsbA_FrnE_like DsbA family, FrnE-like subfamily; composed of uncharacterized proteins containing a CXXC motif with similarity to DsbA and FrnE. FrnE is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=34.17 E-value=1.8e+02 Score=22.53 Aligned_cols=41 Identities=17% Similarity=0.029 Sum_probs=28.3
Q ss_pred HhhcCCCCCH-HHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 53 AFQRTQYPDV-YTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 53 ~F~~~~~ps~-~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
+|....-++. ....+||.++||....+...+.....+..-+
T Consensus 115 ~~~~~~~i~~~~~l~~ia~~~Gld~~~~~~~~~s~~~~~~l~ 156 (193)
T cd03025 115 HYVEGRDLADTEVLRELAIELGLDVEEFLEDFQSDEAKQAIQ 156 (193)
T ss_pred HHHcCCCCCCHHHHHHHHHHcCCCHHHHHHHHcChHHHHHHH
Confidence 3444554554 4788899999999998888777665543333
No 219
>PRK09958 DNA-binding transcriptional activator EvgA; Provisional
Probab=34.00 E-value=77 Score=24.39 Aligned_cols=45 Identities=11% Similarity=0.261 Sum_probs=36.1
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+++.+..+|+-++.-. .+++||..++++++.|+.--++=|.|..
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 48999999998887543 3788999999999999997776666653
No 220
>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=33.81 E-value=31 Score=23.03 Aligned_cols=23 Identities=17% Similarity=0.244 Sum_probs=20.2
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||+.+|++...|..|+.+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46899999999999999997664
No 221
>PRK15411 rcsA colanic acid capsular biosynthesis activation protein A; Provisional
Probab=33.75 E-value=81 Score=25.59 Aligned_cols=45 Identities=7% Similarity=0.128 Sum_probs=32.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
.+|+.++++|.-+- +.+. -++||++|+++++.|+.-..|=..|..
T Consensus 137 ~LT~RE~eVL~lla--~G~s----nkeIA~~L~iS~~TVk~h~~~I~~KL~ 181 (207)
T PRK15411 137 SLSRTESSMLRMWM--AGQG----TIQISDQMNIKAKTVSSHKGNIKRKIK 181 (207)
T ss_pred cCCHHHHHHHHHHH--cCCC----HHHHHHHcCCCHHHHHHHHHHHHHHhC
Confidence 48999999987664 3322 478999999999999987755444443
No 222
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=33.54 E-value=72 Score=25.16 Aligned_cols=36 Identities=19% Similarity=0.127 Sum_probs=30.3
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
..+.+|...=....|.+.+....||+.|||+..+|.
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 456677777677789999999999999999998873
No 223
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=33.25 E-value=34 Score=22.24 Aligned_cols=20 Identities=10% Similarity=0.107 Sum_probs=17.5
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
..++|+.+|++.+.|+.|..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~ 22 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYER 22 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 46789999999999999964
No 224
>PHA01976 helix-turn-helix protein
Probab=33.11 E-value=33 Score=22.21 Aligned_cols=23 Identities=13% Similarity=0.307 Sum_probs=20.1
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||+.+|++...|..|..+++
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56899999999999999997654
No 225
>PRK06704 RNA polymerase factor sigma-70; Validated
Probab=32.72 E-value=99 Score=25.86 Aligned_cols=30 Identities=20% Similarity=0.319 Sum_probs=23.9
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
...+||+.+|+++..|+.+...-|.+.|+.
T Consensus 134 S~~EIAe~LgiS~~tVksrL~Rark~Lr~~ 163 (228)
T PRK06704 134 SIADIAKVCSVSEGAVKASLFRSRNRLKTV 163 (228)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357899999999999999887666665544
No 226
>PRK06596 RNA polymerase factor sigma-32; Reviewed
Probab=32.54 E-value=99 Score=26.54 Aligned_cols=50 Identities=20% Similarity=0.212 Sum_probs=35.9
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.++..+..+|...|... ....-.+||+.+|++...|+-+-..-..|.|+.
T Consensus 230 ~L~~rEr~VL~lry~~~---~~~Tl~EIA~~lgvS~~rVrqi~~~Al~kLR~~ 279 (284)
T PRK06596 230 GLDERSRDIIEARWLDD---DKSTLQELAAEYGVSAERVRQIEKNAMKKLKAA 279 (284)
T ss_pred cCCHHHHHHHHHHhcCC---CCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 47778888888887432 234467999999999999998765555555443
No 227
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=32.41 E-value=47 Score=26.78 Aligned_cols=44 Identities=14% Similarity=0.255 Sum_probs=33.4
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
+..-.+.|....|-... ..+||+..|++..-|...|.||..=..
T Consensus 24 L~AA~~lf~e~Gy~~~s-~~dIA~~aGvs~gtiY~hF~sKe~L~~ 67 (212)
T PRK15008 24 LSAALDTFSQFGFHGTR-LEQIAELAGVSKTNLLYYFPSKEALYI 67 (212)
T ss_pred HHHHHHHHHHhCcccCC-HHHHHHHhCcCHHHHHHHCCCHHHHHH
Confidence 33444557778876554 677899999999999999999886443
No 228
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=32.16 E-value=49 Score=25.57 Aligned_cols=33 Identities=30% Similarity=0.364 Sum_probs=25.8
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.....++||+.+|++...|+.+...-|.+.++.
T Consensus 141 ~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~~ 173 (176)
T PRK09638 141 YGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRKE 173 (176)
T ss_pred cCCCHHHHHHHHCCChhHHHHHHHHHHHHHHHH
Confidence 345568999999999999999887666666553
No 229
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=31.85 E-value=65 Score=26.44 Aligned_cols=43 Identities=12% Similarity=0.165 Sum_probs=35.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHH
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~ 90 (205)
-+..-.+.|..+.|- ....+||+..|+++.-|..+|.||..=.
T Consensus 18 Il~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~ 60 (225)
T PRK11552 18 LIAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLY 60 (225)
T ss_pred HHHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 344555668899987 4688999999999999999999988643
No 230
>KOG3755|consensus
Probab=31.63 E-value=35 Score=32.93 Aligned_cols=58 Identities=24% Similarity=0.438 Sum_probs=49.5
Q ss_pred CCCCCCCCCHHHHHHHHHHhhcC-CCCCHHH---HHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 35 QRRSRTTFTGDQLEELERAFQRT-QYPDVYT---REELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 35 ~rr~R~~~s~~q~~~Le~~F~~~-~~ps~~~---r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
++++|+.+..+-+.+|..+-..- -||+.+. +.-|..++.+.++-+.-.|||.|.-.|+
T Consensus 647 ~p~~~~~isge~~~~~qs~i~~~gl~pd~~a~~~~~~LSa~~~~pk~~~~k~f~~~~~ev~~ 708 (769)
T KOG3755|consen 647 KPRKRTKISGEALGILQSFITDVGLYPDKEAPYFIKTLSAQLDLPKKTIIKFFQNQRYEVKH 708 (769)
T ss_pred CccccceecccchHHHHHHHHHhccCchhhcccccchhhhhhcccHHHHHHhhhcceeecch
Confidence 46788999999999998876544 4899988 9999999999999999999999876654
No 231
>PRK10840 transcriptional regulator RcsB; Provisional
Probab=31.46 E-value=1e+02 Score=24.57 Aligned_cols=43 Identities=12% Similarity=0.020 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
.+++.++.+|.-...-. .-.+||++|+++++.|+.-.+|=..|
T Consensus 150 ~Lt~rE~evl~~~~~G~------s~~eIA~~l~iS~~TV~~h~~~i~~K 192 (216)
T PRK10840 150 RLSPKESEVLRLFAEGF------LVTEIAKKLNRSIKTISSQKKSAMMK 192 (216)
T ss_pred cCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 48999999998876332 36789999999999999865443333
No 232
>cd03023 DsbA_Com1_like DsbA family, Com1-like subfamily; composed of proteins similar to Com1, a 27-kDa outer membrane-associated immunoreactive protein originally found in both acute and chronic disease strains of the pathogenic bacteria Coxiella burnetti. It contains a CXXC motif, assumed to be imbedded in a DsbA-like structure. Its homology to DsbA suggests that the protein is a protein disulfide oxidoreductase. The role of such a protein in pathogenesis is unknown.
Probab=30.97 E-value=2.1e+02 Score=20.86 Aligned_cols=41 Identities=15% Similarity=0.074 Sum_probs=30.1
Q ss_pred HHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 48 EELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 48 ~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
...+.+|......+......+|..+||....+...+.....
T Consensus 71 ~~~~~lf~~~~~~~~~~l~~~a~~~gl~~~~~~~~~~~~~~ 111 (154)
T cd03023 71 EFHNALMATRGRLNEESLLRIAKKAGLDEAKLKKDMDDPEI 111 (154)
T ss_pred HHHHHHHhcCCCCCHHHHHHHHHHcCCCHHHHHHHhhChHH
Confidence 34555566555567788889999999999988887765443
No 233
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=30.69 E-value=40 Score=24.23 Aligned_cols=23 Identities=13% Similarity=0.033 Sum_probs=19.5
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+.++|+.+|++...|+.|..+..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 56899999999999999986544
No 234
>cd03022 DsbA_HCCA_Iso DsbA family, 2-hydroxychromene-2-carboxylate (HCCA) isomerase subfamily; HCCA isomerase is a glutathione (GSH) dependent enzyme involved in the naphthalene catabolic pathway. It converts HCCA, a hemiketal formed spontaneously after ring cleavage of 1,2-dihydroxynapthalene by a dioxygenase, into cis-o-hydroxybenzylidenepyruvate (cHBPA). This is the fourth reaction in a six-step pathway that converts napthalene into salicylate. HCCA isomerase is unique to bacteria that degrade polycyclic aromatic compounds. It is closely related to the eukaryotic protein, GSH transferase kappa (GSTK).
Probab=30.38 E-value=2.4e+02 Score=21.77 Aligned_cols=41 Identities=7% Similarity=-0.035 Sum_probs=28.9
Q ss_pred hhcCCCC-CHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 54 FQRTQYP-DVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 54 F~~~~~p-s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
|....-+ +......+|..+||....+..++.....+.+-++
T Consensus 114 ~~~~~~i~~~~~l~~~a~~~Gld~~~~~~~~~~~~~~~~l~~ 155 (192)
T cd03022 114 WGEGLDIADPAVLAAVAAAAGLDADELLAAADDPAVKAALRA 155 (192)
T ss_pred hCCCCCCCCHHHHHHHHHHcCCCHHHHHHHcCCHHHHHHHHH
Confidence 3344433 4566788999999999999999977665544433
No 235
>KOG1924|consensus
Probab=30.35 E-value=5.4e+02 Score=26.18 Aligned_cols=133 Identities=14% Similarity=0.037 Sum_probs=0.0
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHhHHHhhhhcccccCCCCCCCcCCCCCCC
Q psy1901 43 TGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLNSQQLNAFNSMSLHHQYADSAANFSHQS 122 (205)
Q Consensus 43 s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~~~~~~~~~s~~~~~~~~~~~~~~s~~~ 122 (205)
+.+.-..|++.|.+.- ..+.+.+.++ |.+-.|.+-.....+.-.....-.+.....+......+.
T Consensus 472 seqkA~e~~kk~~ke~----ta~qe~qael-----------~k~e~Ki~~l~ae~~al~s~~~~~~~~~~iP~PP~~pp~ 536 (1102)
T KOG1924|consen 472 SEQKAAELEKKFDKEL----TARQEAQAEL-----------QKHEEKIKLLEAEKQALSSPSQLLPIDGGIPPPPPLPPT 536 (1102)
T ss_pred HHHHHHHHHHHHHHHH----hHHHHHHHHH-----------HHhhhhcccCchhhhhccCcccCCCCCCCCCCCCCCCCC
Q ss_pred CCCChhhhh-hhhcccccccccCCCCCCCCCCCCCCCCCCCCCCCCCCCCC----CCCccccCCCcCCCCCCc
Q psy1901 123 HPTSWAQQA-ASYATAGAALTAGYNSHAYSSATPEFPVSGPGYHQTNQHCA----DSTAAWSRHHSSSTKSPV 190 (205)
Q Consensus 123 ~~~s~~~~a-~~~aaa~aa~~a~~~~~~~~~~~P~~p~~~p~~~~~~~~~~----~~~~~~~~~~~~~~~~~~ 190 (205)
......+.. .+--..++...+..++.+.-...|++|...||+-.++.++. .|-+|.-.+..-.-++||
T Consensus 537 gG~g~pppPppPPlpggag~PPPPpplPg~aG~PPpPppppg~~gppPPPpp~g~~Gg~ppPP~~gm~pmaPv 609 (1102)
T KOG1924|consen 537 GGTGPPPPPPPPPLPGGAGPPPPPPPLPGIAGGPPPPPPPPGGGGPPPPPPPGGFLGGPPPPPPPGMFPMAPV 609 (1102)
T ss_pred CCCCCCCCCCCCCCCCCCCCCccCCCCCcccCCCCccCCCCCCCCCCCcCCCCCCCCCCCCCCCCCccccccc
No 236
>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=30.29 E-value=44 Score=22.09 Aligned_cols=22 Identities=18% Similarity=0.447 Sum_probs=16.6
Q ss_pred HHHHHHhhCCchhhhh-hhhhch
Q psy1901 65 REELAQKTKLTEARVQ-VWFSNR 86 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~-~WFqNr 86 (205)
..+||+.||++...|. .|....
T Consensus 15 ~~~lA~~lgis~st~s~~~~~r~ 37 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKKRG 37 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHHSS
T ss_pred HHHHHHHhCcCHHHhhHHHHhCC
Confidence 5689999999999999 888543
No 237
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=29.99 E-value=41 Score=19.35 Aligned_cols=23 Identities=26% Similarity=0.367 Sum_probs=19.7
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||+.+|++...|..|..+++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~~ 35 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGKR 35 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 55889999999999999987664
No 238
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=29.99 E-value=71 Score=23.85 Aligned_cols=26 Identities=12% Similarity=0.258 Sum_probs=21.7
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
......+||+.+||+.+.+..+|+.-
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 34567899999999999999999754
No 239
>PRK08241 RNA polymerase factor sigma-70; Validated
Probab=29.90 E-value=81 Score=27.44 Aligned_cols=29 Identities=24% Similarity=0.237 Sum_probs=23.8
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
...+||+.||++...|+.....-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 199 (339)
T PRK08241 171 SAAEVAELLDTSVAAVNSALQRARATLAE 199 (339)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHhh
Confidence 46789999999999999988766666665
No 240
>PRK06424 transcription factor; Provisional
Probab=29.48 E-value=1.5e+02 Score=23.20 Aligned_cols=24 Identities=13% Similarity=-0.021 Sum_probs=21.2
Q ss_pred HHHHHHhhCCchhhhhhhhhchHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
..+||+.+|++...|.-|..+++.
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~ 123 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLL 123 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCC
Confidence 568999999999999999988764
No 241
>PTZ00183 centrin; Provisional
Probab=29.28 E-value=2e+02 Score=21.27 Aligned_cols=41 Identities=24% Similarity=0.259 Sum_probs=32.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHhhc-----CCCCCHHHHHHHHHhhCC
Q psy1901 34 KQRRSRTTFTGDQLEELERAFQR-----TQYPDVYTREELAQKTKL 74 (205)
Q Consensus 34 k~rr~R~~~s~~q~~~Le~~F~~-----~~~ps~~~r~~LA~~l~l 74 (205)
|++-.+..++..++..|+..|.. +.+.+..+-..+...+|+
T Consensus 3 ~~~~~~~~~~~~~~~~~~~~F~~~D~~~~G~i~~~e~~~~l~~~g~ 48 (158)
T PTZ00183 3 KRRSERPGLTEDQKKEIREAFDLFDTDGSGTIDPKELKVAMRSLGF 48 (158)
T ss_pred ccccccCCCCHHHHHHHHHHHHHhCCCCCCcccHHHHHHHHHHhCC
Confidence 44556778999999999999853 467888888888777764
No 242
>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=29.11 E-value=42 Score=23.53 Aligned_cols=19 Identities=16% Similarity=0.357 Sum_probs=17.1
Q ss_pred HHHHHHhhCCchhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWF 83 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WF 83 (205)
+.++|+.+|++...++.|-
T Consensus 4 i~evA~~~gvs~~tLR~ye 22 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWE 22 (88)
T ss_pred HHHHHHHHCcCHHHHHHHH
Confidence 5689999999999999994
No 243
>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=28.95 E-value=90 Score=20.82 Aligned_cols=21 Identities=24% Similarity=0.357 Sum_probs=16.1
Q ss_pred HHHHHHHhhCCchhhhhhhhh
Q psy1901 64 TREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFq 84 (205)
...+||+.|||+...|+..++
T Consensus 22 t~eEiA~~lgis~~~v~~~l~ 42 (78)
T PF04539_consen 22 TDEEIAEELGISVEEVRELLQ 42 (78)
T ss_dssp BHHHHHHHHTS-HHHHHHHHH
T ss_pred CHHHHHHHHcccHHHHHHHHH
Confidence 456899999999999887663
No 244
>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=28.66 E-value=1.2e+02 Score=18.42 Aligned_cols=44 Identities=18% Similarity=0.277 Sum_probs=27.6
Q ss_pred CCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhC--Cchhhhhhhhhc
Q psy1901 39 RTTFTGDQLEELERAFQRTQYPDVYTREELAQKTK--LTEARVQVWFSN 85 (205)
Q Consensus 39 R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~--l~~~qV~~WFqN 85 (205)
|..+|.++...|.+.+...+.-.. ..||..++ -+..||+.=|+|
T Consensus 1 r~~Wt~eE~~~l~~~v~~~g~~~W---~~Ia~~~~~~Rt~~qc~~~~~~ 46 (48)
T PF00249_consen 1 RGPWTEEEDEKLLEAVKKYGKDNW---KKIAKRMPGGRTAKQCRSRYQN 46 (48)
T ss_dssp S-SS-HHHHHHHHHHHHHSTTTHH---HHHHHHHSSSSTHHHHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHHhCCcHH---HHHHHHcCCCCCHHHHHHHHHh
Confidence 456899999999999877764433 34455555 666666655543
No 245
>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=28.56 E-value=90 Score=24.03 Aligned_cols=42 Identities=14% Similarity=0.262 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
+..+.+.+++-.|..-...+. ..+|.++++++++++-|++.-
T Consensus 82 l~de~k~Ii~lry~~r~~~TW---~~IA~~l~i~erta~r~~~~f 123 (130)
T PF05263_consen 82 LIDEEKRIIKLRYDRRSRRTW---YQIAQKLHISERTARRWRDRF 123 (130)
T ss_pred hCHHHHHHHHHHHcccccchH---HHHHHHhCccHHHHHHHHHHH
Confidence 344444455444544433333 467889999999999887643
No 246
>PHA02955 hypothetical protein; Provisional
Probab=28.36 E-value=77 Score=26.53 Aligned_cols=49 Identities=10% Similarity=-0.032 Sum_probs=36.9
Q ss_pred CHHHHHHHHHHhhcC-CCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHH
Q psy1901 43 TGDQLEELERAFQRT-QYPDVYTREELAQKTKLTEARVQVWFSNRRARLR 91 (205)
Q Consensus 43 s~~q~~~Le~~F~~~-~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~k 91 (205)
...++..|-+.|... .-.+.++|.+++++||+....|..||.+.-.+..
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~~~q~C 108 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTDLQLHC 108 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccchhhhhc
Confidence 345566666666554 5677889999999999999888999987665544
No 247
>PRK09483 response regulator; Provisional
Probab=27.92 E-value=1.3e+02 Score=23.41 Aligned_cols=45 Identities=11% Similarity=0.151 Sum_probs=32.0
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHH
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~ 90 (205)
..+++.++.+|+-+. ..+. -.+||..|+++++.|+.-.+|=+.|.
T Consensus 147 ~~Lt~rE~~vl~~~~--~G~~----~~~Ia~~l~is~~TV~~~~~~i~~Kl 191 (217)
T PRK09483 147 ASLSERELQIMLMIT--KGQK----VNEISEQLNLSPKTVNSYRYRMFSKL 191 (217)
T ss_pred cccCHHHHHHHHHHH--CCCC----HHHHHHHhCCCHHHHHHHHHHHHHHc
Confidence 358999999996542 2222 34899999999999988666555443
No 248
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=27.86 E-value=99 Score=24.12 Aligned_cols=36 Identities=11% Similarity=0.077 Sum_probs=29.3
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
.-+.+|...=....|.+.+....+|+.+||+..+|.
T Consensus 23 ~ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v~ 58 (154)
T PRK07539 23 AVIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDVE 58 (154)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 455666666666789999999999999999988873
No 249
>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=27.54 E-value=49 Score=23.70 Aligned_cols=23 Identities=17% Similarity=0.202 Sum_probs=19.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+.++|+.+|++...|+.|.....
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~Gl 25 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIGL 25 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 56899999999999999976433
No 250
>PF12802 MarR_2: MarR family; PDB: 3ECO_B 2QWW_B 3KP6_B 3KP4_B 3KP2_A 3KP5_A 3KP3_B 3KP7_A 3NQO_B 3K0L_B ....
Probab=27.42 E-value=86 Score=19.66 Aligned_cols=38 Identities=21% Similarity=0.224 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQV 81 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~ 81 (205)
++..|..+|...+..... .....+||+.+++++..|..
T Consensus 3 lt~~q~~vL~~l~~~~~~--~~t~~~la~~l~~~~~~vs~ 40 (62)
T PF12802_consen 3 LTPSQFRVLMALARHPGE--ELTQSELAERLGISKSTVSR 40 (62)
T ss_dssp STHHHHHHHHHHHHSTTS--GEEHHHHHHHHTS-HHHHHH
T ss_pred cCHHHHHHHHHHHHCCCC--CcCHHHHHHHHCcCHHHHHH
Confidence 678888899888765553 23577899999999877654
No 251
>PF14229 DUF4332: Domain of unknown function (DUF4332)
Probab=27.30 E-value=60 Score=24.42 Aligned_cols=26 Identities=23% Similarity=0.364 Sum_probs=22.9
Q ss_pred CCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 59 YPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 59 ~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
-.+...|.+||.++|++.+.|.-|-.
T Consensus 26 ~~~~~~r~~La~~~~i~~~~l~~w~~ 51 (122)
T PF14229_consen 26 GDTPLGRKALAKKLGISERNLLKWVN 51 (122)
T ss_pred CCCHHHHHHHHHhcCCCHHHHHHHHh
Confidence 46778899999999999999999964
No 252
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=27.22 E-value=94 Score=26.55 Aligned_cols=24 Identities=8% Similarity=0.443 Sum_probs=16.8
Q ss_pred chhhhhhhhhchHHHHHHHHhHHH
Q psy1901 75 TEARVQVWFSNRRARLRKQLNSQQ 98 (205)
Q Consensus 75 ~~~qV~~WFqNrR~k~kr~~~~~~ 98 (205)
.-+.|..||+.++.|.|.+.+.+.
T Consensus 99 ~~~~i~~w~~~~~~kkkee~R~~~ 122 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKKEEARAHN 122 (242)
T ss_pred ccchHHHHHHHHHHHHHHHHHHHH
Confidence 467899999998886555444443
No 253
>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=26.92 E-value=49 Score=23.22 Aligned_cols=23 Identities=4% Similarity=-0.032 Sum_probs=19.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+.++|+.+|++.+.|+.|.....
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 57899999999999999975433
No 254
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=26.88 E-value=35 Score=27.33 Aligned_cols=44 Identities=16% Similarity=0.224 Sum_probs=34.7
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
+-+..-.+.|.+..|-... ..+||+..|+++.-+-.+|.||-.=
T Consensus 15 ~Il~AA~~lf~e~G~~~~t-~~~Ia~~agvs~~tlY~~F~sKe~L 58 (215)
T PRK10668 15 HILDAALRLFSQQGVSATS-LADIAKAAGVTRGAIYWHFKNKSDL 58 (215)
T ss_pred HHHHHHHHHHHHcCcccCC-HHHHHHHhCCChHHHHHHCCCHHHH
Confidence 3455566678888876554 6788999999999999999988764
No 255
>PRK11475 DNA-binding transcriptional activator BglJ; Provisional
Probab=26.77 E-value=1.4e+02 Score=24.43 Aligned_cols=40 Identities=10% Similarity=0.018 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
.+|+.++++|+-.-.-. .-++||.+|+++++.|+.--.|=
T Consensus 134 ~LT~RE~eVL~ll~~G~------snkeIA~~L~iS~~TV~~h~~~I 173 (207)
T PRK11475 134 MLSPTEREILRFMSRGY------SMPQIAEQLERNIKTIRAHKFNV 173 (207)
T ss_pred CCCHHHHHHHHHHHCCC------CHHHHHHHHCCCHHHHHHHHHHH
Confidence 58899999998776432 25789999999999998755433
No 256
>PRK10188 DNA-binding transcriptional activator SdiA; Provisional
Probab=26.69 E-value=1.7e+02 Score=24.40 Aligned_cols=50 Identities=18% Similarity=0.180 Sum_probs=34.2
Q ss_pred CCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHHh
Q psy1901 40 TTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQLN 95 (205)
Q Consensus 40 ~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~~ 95 (205)
..+|+.++++|.=.- .. ..-.+||..|+++++.|+.-.+|=+.|..-..+
T Consensus 178 ~~LT~rE~evl~~~a--~G----~t~~eIa~~l~is~~TV~~h~~~~~~KL~~~nr 227 (240)
T PRK10188 178 MNFSKREKEILKWTA--EG----KTSAEIAMILSISENTVNFHQKNMQKKFNAPNK 227 (240)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHhCCCHHHHHHHHHHHHHHhCCCCH
Confidence 356777776665442 22 234689999999999999988877766554433
No 257
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.67 E-value=1.5e+02 Score=24.86 Aligned_cols=17 Identities=29% Similarity=0.462 Sum_probs=13.5
Q ss_pred CCHHHHHHHHHHhhcCC
Q psy1901 42 FTGDQLEELERAFQRTQ 58 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~ 58 (205)
++++++..||.+|.+-.
T Consensus 1 MtpeE~qlle~lf~rlk 17 (233)
T COG3416 1 MTPEEKQLLENLFHRLK 17 (233)
T ss_pred CCHHHHHHHHHHHHHHh
Confidence 47888999999997654
No 258
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.55 E-value=50 Score=23.65 Aligned_cols=20 Identities=15% Similarity=0.414 Sum_probs=17.8
Q ss_pred HHHHHHhhCCchhhhhhhhh
Q psy1901 65 REELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFq 84 (205)
+.++|+.+|++.+.|+.|-.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 57899999999999999975
No 259
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=26.52 E-value=1.1e+02 Score=24.53 Aligned_cols=36 Identities=25% Similarity=0.170 Sum_probs=28.0
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
..+.+|...=....|.+.+..+.+|+.|||+..+|.
T Consensus 37 ~li~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V~ 72 (169)
T PRK07571 37 ALIEVLHKAQELFGYLERDLLLYVARQLKLPLSRVY 72 (169)
T ss_pred HHHHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHHH
Confidence 345555555566689999999999999999887763
No 260
>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=26.41 E-value=30 Score=27.85 Aligned_cols=34 Identities=26% Similarity=0.371 Sum_probs=28.9
Q ss_pred CHHHHHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 61 DVYTREELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 61 s~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
....+.+|+..++++..+|-+|..|-+...+...
T Consensus 13 ~tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~ 46 (186)
T PF04936_consen 13 ATGTIDELADYFDVSRTSVSVWIKNGKDPKRAKP 46 (186)
T ss_pred ccccHHHHHHHHccCHHHHHHHHHcCCCcccccc
Confidence 3456889999999999999999999998877653
No 261
>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=26.37 E-value=1.1e+02 Score=23.65 Aligned_cols=36 Identities=11% Similarity=0.026 Sum_probs=28.6
Q ss_pred HHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 45 DQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 45 ~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
.-+.+|...=....|.+.+....+|+.|||+..+|.
T Consensus 17 ~li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v~ 52 (148)
T TIGR01958 17 AIMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWVY 52 (148)
T ss_pred HHHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHHH
Confidence 455566666566689999999999999999887763
No 262
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=26.19 E-value=45 Score=24.99 Aligned_cols=35 Identities=11% Similarity=0.250 Sum_probs=26.3
Q ss_pred HHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 49 ELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 49 ~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
.|.+...... -.+.+||+.+|++...|..|.++++
T Consensus 9 ~l~~ll~~~G----lsq~eLA~~~Gis~~~is~iE~g~~ 43 (120)
T PRK13890 9 NVLRLLDERH----MTKKELSERSGVSISFLSDLTTGKA 43 (120)
T ss_pred HHHHHHHHcC----CCHHHHHHHHCcCHHHHHHHHcCCC
Confidence 3444444444 2367899999999999999999886
No 263
>PF10078 DUF2316: Uncharacterized protein conserved in bacteria (DUF2316); InterPro: IPR018757 Members of this family of hypothetical bacterial proteins have no known function.
Probab=26.16 E-value=45 Score=24.02 Aligned_cols=39 Identities=15% Similarity=0.265 Sum_probs=26.4
Q ss_pred CCCHHHHH----HHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 41 TFTGDQLE----ELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 41 ~~s~~q~~----~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
+++++|+. .|.+.|.... -..+.+|..|+++...|..=+
T Consensus 2 SLn~~Q~~~T~~ELq~nf~~~~----ls~~~ia~dL~~s~~~le~vL 44 (89)
T PF10078_consen 2 SLNPEQRRATRQELQANFELSG----LSLEQIAADLGTSPEHLEQVL 44 (89)
T ss_pred CCCHHHHHHHHHHHHHHHHHcC----CCHHHHHHHhCCCHHHHHHHH
Confidence 35566644 5777777666 446778999998888775433
No 264
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=26.07 E-value=1e+02 Score=20.38 Aligned_cols=27 Identities=19% Similarity=0.394 Sum_probs=18.6
Q ss_pred HHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
...||+.||++..-|..| +.+.-.++.
T Consensus 12 ~~~lAkalGVs~~aVs~W--~~~IP~~ra 38 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW--GERIPAERA 38 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH--HTS--HHHH
T ss_pred HHHHHHHHCCCHHHHHHh--cCccCHHHH
Confidence 458999999999999999 444444443
No 265
>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=25.82 E-value=98 Score=19.67 Aligned_cols=24 Identities=21% Similarity=0.376 Sum_probs=16.9
Q ss_pred HHHHHHHhhCCchhhhhhhhhchH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
...++|+.+|++...|..|-.+++
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 356778888888888888887766
No 266
>PF08667 BetR: BetR domain; InterPro: IPR013975 CheY-like phosphoacceptor (or receiver [REC]) domain is a common module in a variety of response regulators of the bacterial signal transduction systems. BetR is one of the many response regulators and is encoded mainly in Burkholderia spp. It is a N-terminal helix-turn-helix domain (HTH) and has been shown to be related to the XRE-type HTH domain (IPR001387 from INTERPRO), it has been suggested that BetR would have dimerization, protein-protein interaction, and activation/relief-of-inhibition properties [].
Probab=25.77 E-value=1.1e+02 Score=24.00 Aligned_cols=38 Identities=16% Similarity=0.137 Sum_probs=31.1
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
-...+.+.+..+..+..+...+||+.|||+...+..+.
T Consensus 6 ~~erV~~Ll~~~Gi~kr~~~s~LA~iL~Is~ssa~RKL 43 (147)
T PF08667_consen 6 IAERVRELLDRKGIPKRKHASELADILGISYSSAYRKL 43 (147)
T ss_pred HHHHHHHHHHHcCCcchhhHHHHHHHHCCCHHHHHHHh
Confidence 45667788888899999999999999999999874443
No 267
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=25.62 E-value=1.6e+02 Score=17.80 Aligned_cols=21 Identities=14% Similarity=0.243 Sum_probs=18.3
Q ss_pred HHHHHHHhhCCchhhhhhhhh
Q psy1901 64 TREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFq 84 (205)
....+|+.+|++...|+.+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 367899999999999998884
No 268
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.33 E-value=53 Score=25.22 Aligned_cols=25 Identities=8% Similarity=0.073 Sum_probs=20.8
Q ss_pred HHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
+.++|+.+|++.+.|+.|.+....+
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~GLl~ 27 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLGLLT 27 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCCC
Confidence 5689999999999999999754443
No 269
>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=25.30 E-value=84 Score=23.00 Aligned_cols=43 Identities=7% Similarity=0.020 Sum_probs=29.3
Q ss_pred CCCCCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchH
Q psy1901 38 SRTTFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 38 ~R~~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
....++..++..+.+.... ...+||+.+|++...|.-|-..+.
T Consensus 61 ~~~~~~~~~i~~~r~~~gl-------tq~~lA~~lg~~~~tis~~e~g~~ 103 (127)
T TIGR03830 61 VDGLLTPPEIRRIRKKLGL-------SQREAAELLGGGVNAFSRYERGEV 103 (127)
T ss_pred ccCCcCHHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHCCCC
Confidence 3445666666666555422 235789999999999999987665
No 270
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.29 E-value=57 Score=23.24 Aligned_cols=24 Identities=8% Similarity=-0.045 Sum_probs=20.2
Q ss_pred HHHHHHhhCCchhhhhhhhhchHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
+.++|+.+|++...++.|.+...-
T Consensus 3 i~eva~~~gvs~~tLRyye~~Gll 26 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDIGLF 26 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 578999999999999999875433
No 271
>PF13565 HTH_32: Homeodomain-like domain
Probab=25.26 E-value=2.1e+02 Score=18.83 Aligned_cols=39 Identities=13% Similarity=0.054 Sum_probs=25.9
Q ss_pred CHHHHHHHHHHhhcCCCCCHHHHHH-HHHhhCC----chhhhhh
Q psy1901 43 TGDQLEELERAFQRTQYPDVYTREE-LAQKTKL----TEARVQV 81 (205)
Q Consensus 43 s~~q~~~Le~~F~~~~~ps~~~r~~-LA~~l~l----~~~qV~~ 81 (205)
+.++...|.+.+..++..+..++.+ |..+.|+ +...|.-
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~~~~~S~~tv~R 75 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGISVRVSRSTVYR 75 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCCCCCccHhHHHH
Confidence 6777799999998888666665544 4555553 4444443
No 272
>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=24.57 E-value=88 Score=24.13 Aligned_cols=35 Identities=23% Similarity=0.166 Sum_probs=25.7
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
-+.+|...=....|.+.+....+|+.|||+..+|.
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 45566666566689999999999999999988873
No 273
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=24.33 E-value=43 Score=26.45 Aligned_cols=43 Identities=16% Similarity=0.298 Sum_probs=31.9
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARL 90 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~ 90 (205)
+..-.+.|....|-... ..+||+..|+++.-|-..|.||-.=.
T Consensus 14 l~aA~~lf~e~G~~~~s-~~~IA~~agvs~~~lY~hF~sKe~L~ 56 (202)
T TIGR03613 14 LSAALDTFSRFGFHGTS-LEQIAELAGVSKTNLLYYFPSKDALY 56 (202)
T ss_pred HHHHHHHHHHhCcccCC-HHHHHHHhCCCHHHHHHHcCCHHHHH
Confidence 33444557777765444 67889999999999999999886533
No 274
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=24.10 E-value=95 Score=24.31 Aligned_cols=42 Identities=17% Similarity=0.247 Sum_probs=33.2
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
+..-.+.|..+.|-.. ....||+..|+++.-|-.+|.||..=
T Consensus 14 l~aA~~lf~e~G~~~t-Si~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 14 LQAAMRVALAEGFAAM-TVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHHhcChhhc-cHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 4445566888888543 47889999999999999999988763
No 275
>PF13743 Thioredoxin_5: Thioredoxin; PDB: 3KZQ_C.
Probab=23.81 E-value=3e+02 Score=21.74 Aligned_cols=47 Identities=19% Similarity=0.163 Sum_probs=30.9
Q ss_pred HHHHHHHHHHh-hcCC-CCCHHHHHHHHHhhCCchhhhhhhhhchHHHH
Q psy1901 44 GDQLEELERAF-QRTQ-YPDVYTREELAQKTKLTEARVQVWFSNRRARL 90 (205)
Q Consensus 44 ~~q~~~Le~~F-~~~~-~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~ 90 (205)
..-+..|.+.+ .... |-+.+...+||+++||........|+..-.+.
T Consensus 83 ~~fL~~lQ~a~~~~~~~~s~~~~l~~iA~~~gLD~~~F~~d~~S~~~~~ 131 (176)
T PF13743_consen 83 RRFLRALQEALFLEGKNYSDEELLLEIAEELGLDVEMFKEDLHSDEAKQ 131 (176)
T ss_dssp HHHHHHHHHHHHTS---TTSHHHHHHHHHHTT--HHHHHHHHTSHHHHH
T ss_pred HHHHHHHHHHHHhcCCCCCHHHHHHHHHHHhCCCHHHHHHHHhChHHHH
Confidence 34566666665 4444 45559999999999999999888886555443
No 276
>PRK07405 RNA polymerase sigma factor SigD; Validated
Probab=23.77 E-value=1.6e+02 Score=25.85 Aligned_cols=52 Identities=19% Similarity=0.237 Sum_probs=38.4
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|.-.|..... .....++||+.+||+...|+..-..-+.|.|+.
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 4778888888888854322 224578999999999999999887666666653
No 277
>PRK09635 sigI RNA polymerase sigma factor SigI; Provisional
Probab=23.71 E-value=1.5e+02 Score=25.63 Aligned_cols=29 Identities=7% Similarity=0.138 Sum_probs=23.8
Q ss_pred HHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
-.+||+.||+++..|+..++.-|.+.|..
T Consensus 137 ~~EIA~~Lgis~~tVr~~l~RAr~~Lr~~ 165 (290)
T PRK09635 137 YQQIATTIGSQASTCRQLAHRARRKINES 165 (290)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHhh
Confidence 46899999999999999998666666553
No 278
>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=23.69 E-value=59 Score=20.74 Aligned_cols=17 Identities=35% Similarity=0.438 Sum_probs=13.4
Q ss_pred HHHHHHhhCCchhhhhh
Q psy1901 65 REELAQKTKLTEARVQV 81 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~ 81 (205)
-.+||+.+|++..||+-
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 46899999999999873
No 279
>PF14851 FAM176: FAM176 family
Probab=23.69 E-value=3.4e+02 Score=21.52 Aligned_cols=7 Identities=43% Similarity=0.245 Sum_probs=3.1
Q ss_pred HHHHHhh
Q psy1901 66 EELAQKT 72 (205)
Q Consensus 66 ~~LA~~l 72 (205)
.++|+.|
T Consensus 119 ~e~A~rl 125 (153)
T PF14851_consen 119 LERAQRL 125 (153)
T ss_pred HHHHHHH
Confidence 3345444
No 280
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=23.49 E-value=95 Score=24.30 Aligned_cols=30 Identities=30% Similarity=0.422 Sum_probs=24.9
Q ss_pred HHHHHHhhCCchhhhhhhhhchHHHHHHHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRARLRKQL 94 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~k~kr~~ 94 (205)
-.++|+.+|++...|+.+..--|.+.++..
T Consensus 146 ~~EIA~~l~i~~~tVks~l~ra~~~l~~~l 175 (182)
T COG1595 146 YEEIAEILGISVGTVKSRLHRARKKLREQL 175 (182)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 468999999999999999987777766653
No 281
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=23.07 E-value=1.9e+02 Score=19.55 Aligned_cols=32 Identities=3% Similarity=-0.007 Sum_probs=26.0
Q ss_pred HHHHHHHhhcCCCCCHHHHHHHHHhhCCchhh
Q psy1901 47 LEELERAFQRTQYPDVYTREELAQKTKLTEAR 78 (205)
Q Consensus 47 ~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~q 78 (205)
+..+++.+.+|+-.+++....+..+.|-...+
T Consensus 19 r~~~~k~l~~NPpine~mir~M~~QMG~kpSe 50 (64)
T PF03672_consen 19 RKYMEKQLKENPPINEKMIRAMMMQMGRKPSE 50 (64)
T ss_pred HHHHHHHHHHCCCCCHHHHHHHHHHhCCCccH
Confidence 45678888899999999999999999855544
No 282
>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=23.01 E-value=75 Score=19.24 Aligned_cols=23 Identities=9% Similarity=0.372 Sum_probs=20.5
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
...||+++|+++..+-..|.||-
T Consensus 19 ~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 19 IRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHHHHHccchhhHHHHcCCHH
Confidence 67889999999999999998864
No 283
>PRK10430 DNA-binding transcriptional activator DcuR; Provisional
Probab=22.98 E-value=1.2e+02 Score=24.71 Aligned_cols=45 Identities=13% Similarity=0.172 Sum_probs=32.0
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhch
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
.+++.++.+|..+...+ +-....-++||+++++++..|+.-+.+-
T Consensus 158 ~Lt~re~~~l~~~i~~~-~~~g~s~~eIA~~l~iS~~Tv~~~~~~~ 202 (239)
T PRK10430 158 GLTPQTLRTLCQWIDAH-QDYEFSTDELANAVNISRVSCRKYLIWL 202 (239)
T ss_pred CCCHHHHHHHHHHHHhC-CCCCcCHHHHHHHhCchHHHHHHHHHHH
Confidence 47777777776655433 3333456889999999999999877643
No 284
>PF13560 HTH_31: Helix-turn-helix domain; PDB: 3F51_C 3F52_A 3PXP_A 2OFY_A.
Probab=22.54 E-value=65 Score=20.78 Aligned_cols=25 Identities=20% Similarity=0.322 Sum_probs=20.7
Q ss_pred HHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
...++|..+|++...|..|..+++.
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 4678999999999999999988885
No 285
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=22.52 E-value=69 Score=22.83 Aligned_cols=22 Identities=9% Similarity=0.048 Sum_probs=18.9
Q ss_pred HHHHHHhhCCchhhhhhhhhch
Q psy1901 65 REELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNr 86 (205)
+.++|+.+|++.+.++.|.+..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKIG 24 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 5689999999999999997643
No 286
>PF01047 MarR: MarR family; InterPro: IPR000835 The MarR-type HTH domain is a DNA-binding, winged helix-turn-helix (wHTH) domain of about 135 amino acids present in transcription regulators of the MarR/SlyA family, involved in the development of antibiotic resistance. This family of transcription regulators is named after Escherichia coli MarR, a repressor of genes which activate the multiple antibiotic resistance and oxidative stress regulons, and after slyA from Salmonella typhimurium and E. coli, a transcription regulator that is required for virulence and survival in the macrophage environment. Regulators with the MarR-type HTH domain are present in bacteria and archaea and control a variety of biological functions, including resistance to multiple antibiotics, household disinfectants, organic solvents, oxidative stress agents and regulation of the virulence factor synthesis in pathogens of humans and plants. Many of the MarR-like regulators respond to aromatic compounds [, , ]. The crystal structures of MarR, MexR and SlyA have been determined and show a winged HTH DNA-binding core flanked by helices involved in dimerisation. The DNA-binding domains are ascribed to the superfamily of winged helix proteins, containing a three (four)-helix (H) bundle and a three-stranded antiparallel beta-sheet (B) in the topology: H1-(H1')-H2-B1-H3-H4-B2-B3-H5-H6. Helices 3 and 4 comprise the helix-turn-helix motif and the beta-sheet is called the wing. Helix 4 is termed the recognition helix, like in other HTHs where it binds the DNA major groove. The helices 1, 5 and 6 are involved in dimerisation, as most MarR-like transcription regulators form dimers [, ]. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 1JGS_A 2NYX_D 2PEX_B 2PFB_A 3BPX_A 3BPV_A 2BV6_A 3BJA_A 3E6M_B 2ETH_A ....
Probab=22.41 E-value=1.2e+02 Score=18.86 Aligned_cols=38 Identities=24% Similarity=0.298 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWF 83 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WF 83 (205)
++..|..+|...+...+ ....+||+.++++...|..+.
T Consensus 1 lt~~q~~iL~~l~~~~~----~~~~~la~~~~~~~~~~t~~i 38 (59)
T PF01047_consen 1 LTPSQFRILRILYENGG----ITQSELAEKLGISRSTVTRII 38 (59)
T ss_dssp STHHHHHHHHHHHHHSS----EEHHHHHHHHTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHcCC----CCHHHHHHHHCCChhHHHHHH
Confidence 46788889988887665 334589999999988777655
No 287
>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=22.39 E-value=70 Score=23.34 Aligned_cols=23 Identities=17% Similarity=0.222 Sum_probs=19.5
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
+.++|+.+|++.+.|+.|.+...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (108)
T cd04773 3 IGELAHLLGVPPSTLRHWEKEGL 25 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 56899999999999999976543
No 288
>PRK11202 DNA-binding transcriptional repressor FabR; Provisional
Probab=21.92 E-value=38 Score=27.17 Aligned_cols=39 Identities=8% Similarity=0.153 Sum_probs=30.5
Q ss_pred HHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 50 LERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 50 Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
++..|....|-... ..+||++.|+++.-+-.-|.||-.=
T Consensus 21 ~~~l~~~~G~~~~s-i~~IA~~Agvs~~t~Y~hF~sKe~L 59 (203)
T PRK11202 21 FSQLSAERSFSSLS-LREVAREAGIAPTSFYRHFRDMDEL 59 (203)
T ss_pred HHHHHhcCCcccCC-HHHHHHHhCCCcchHHHHCCCHHHH
Confidence 34466777776554 6788999999999999999987654
No 289
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=21.84 E-value=64 Score=24.32 Aligned_cols=24 Identities=17% Similarity=0.428 Sum_probs=21.2
Q ss_pred HHHHHHhhCCchhhhhhhhhchHH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
..+||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 468999999999999999988763
No 290
>PRK05949 RNA polymerase sigma factor; Validated
Probab=21.77 E-value=2.3e+02 Score=25.02 Aligned_cols=51 Identities=22% Similarity=0.227 Sum_probs=37.7
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRK 92 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr 92 (205)
.+++.+..+|.-.|..... .....++||+.+|++...|+.....-+.|.|+
T Consensus 266 ~L~~rer~Vi~lr~gl~~~-e~~Tl~EIa~~lgiS~erVrq~~~rAl~kLr~ 316 (327)
T PRK05949 266 ELTPQQREVLTLRFGLEDG-KELSLAKVGERLNLSRERVRQLEHQALAHLRR 316 (327)
T ss_pred hCCHHHHHHHHHHhccCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4778888888888754321 12357889999999999999988766666665
No 291
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=21.74 E-value=75 Score=22.42 Aligned_cols=22 Identities=9% Similarity=0.072 Sum_probs=18.6
Q ss_pred HHHHHHhhCCchhhhhhhhhch
Q psy1901 65 REELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNr 86 (205)
..++|+.+|++...|+.|-+..
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~G 24 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKG 24 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4688999999999999996543
No 292
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=21.62 E-value=70 Score=23.02 Aligned_cols=22 Identities=14% Similarity=0.147 Sum_probs=19.0
Q ss_pred HHHHHHHhhCCchhhhhhhhhc
Q psy1901 64 TREELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqN 85 (205)
.+.++|+.+|++.+.++.|-+.
T Consensus 3 ~i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 3 TIGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHC
Confidence 3678999999999999999853
No 293
>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=21.53 E-value=2.9e+02 Score=20.26 Aligned_cols=43 Identities=19% Similarity=0.186 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRA 88 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~ 88 (205)
.+|..|..+|+-+|..+ .--.+||..+|++..-|.-|.+.-+.
T Consensus 17 LLT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ikr~~~ 59 (101)
T PF04297_consen 17 LLTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIKRAEK 59 (101)
T ss_dssp GS-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred HCCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 36888999998776443 35678999999999999999864433
No 294
>TIGR02054 MerD mercuric resistence transcriptional repressor protein MerD. This model represents a transcriptional repressor protein of the MerR family (pfam00376) whose expression is regulated by the mercury-sensitive transcriptional activator, MerR. MerD has been shown to repress the transcription of the mer operon.
Probab=21.15 E-value=73 Score=24.02 Aligned_cols=22 Identities=18% Similarity=0.209 Sum_probs=19.3
Q ss_pred HHHHHHHhhCCchhhhhhhhhc
Q psy1901 64 TREELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqN 85 (205)
.+.+||+.+||+.+.|+.|-+.
T Consensus 5 tI~elA~~~gvs~~tlR~Ye~~ 26 (120)
T TIGR02054 5 TISRLAEDAGVSVHVVRDYLLR 26 (120)
T ss_pred cHHHHHHHHCcCHHHHHHHHHC
Confidence 4789999999999999999753
No 295
>PRK09726 antitoxin HipB; Provisional
Probab=21.01 E-value=69 Score=22.30 Aligned_cols=23 Identities=26% Similarity=0.375 Sum_probs=20.4
Q ss_pred HHHHHHhhCCchhhhhhhhhchH
Q psy1901 65 REELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
..+||+.+|++...|..|..+++
T Consensus 28 q~elA~~~gvs~~tis~~e~g~~ 50 (88)
T PRK09726 28 QSELAKKIGIKQATISNFENNPD 50 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHCCCC
Confidence 67899999999999999998654
No 296
>PF02954 HTH_8: Bacterial regulatory protein, Fis family; InterPro: IPR002197 The Factor for Inversion Stimulation (FIS) protein is a regulator of bacterial functions, and binds specifically to weakly related DNA sequences [,]. It activates ribosomal RNA transcription, and is involved in upstream activation of rRNA promoters. The protein has been shown to play a role in the regulation of virulence factors in both Salmonella typhimurium and Escherichia coli []. Some of its functions include inhibition of the initiation of DNA replication from the OriC site, and promotion of Hin-mediated DNA inversion. In its C-terminal extremity, FIS encodes a helix-turn-helix (HTH) DNA- binding motif, which shares a high degree of similarity with other HTH motifs of more primitive bacterial transcriptional regulators, such as the nitrogen assimilation regulatory proteins (NtrC) from species like Azobacter, Rhodobacter and Rhizobium. This has led to speculation that both evolved from a single common ancestor []. The 3-dimensional structure of the E. coli FIS DNA-binding protein has been determined by means of X-ray diffraction to 2.0A resolution [,]. FIS is composed of four alpha-helices tightly intertwined to form a globular dimer with two protruding HTH motifs. The 24 N-terminal amino acids are poorly defined, indicating that they might act as `feelers' suitable for DNA or protein (invertase) recognition []. Other proteins belonging to this subfamily include: E. coli: atoC, hydG, ntrC, fhlA, tyrR, Rhizobium spp.: ntrC, nifA, dctD ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NTC_A 3JRH_A 3JRB_A 3IV5_A 3JRI_A 1ETQ_A 1ETW_B 1ETY_A 3JRF_A 3JRA_A ....
Probab=21.00 E-value=1.8e+02 Score=17.22 Aligned_cols=31 Identities=10% Similarity=0.116 Sum_probs=20.7
Q ss_pred HHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhh
Q psy1901 46 QLEELERAFQRTQYPDVYTREELAQKTKLTEARVQ 80 (205)
Q Consensus 46 q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~ 80 (205)
+...|+.....+. ..+.+.|+.|||+.+.+.
T Consensus 6 E~~~i~~aL~~~~----gn~~~aA~~Lgisr~tL~ 36 (42)
T PF02954_consen 6 EKQLIRQALERCG----GNVSKAARLLGISRRTLY 36 (42)
T ss_dssp HHHHHHHHHHHTT----T-HHHHHHHHTS-HHHHH
T ss_pred HHHHHHHHHHHhC----CCHHHHHHHHCCCHHHHH
Confidence 4556666666665 346788999999987754
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=20.93 E-value=71 Score=24.35 Aligned_cols=21 Identities=29% Similarity=0.507 Sum_probs=18.7
Q ss_pred HHHHHHhhCCchhhhhhhhhc
Q psy1901 65 REELAQKTKLTEARVQVWFSN 85 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqN 85 (205)
-++||..+|+....|.-|...
T Consensus 3 ~eELA~~tG~srQTINrWvRk 23 (122)
T PF07037_consen 3 PEELAELTGYSRQTINRWVRK 23 (122)
T ss_pred HHHHHHHhCccHHHHHHHHHh
Confidence 478999999999999999853
No 298
>cd03024 DsbA_FrnE DsbA family, FrnE subfamily; FrnE is a DsbA-like protein containing a CXXC motif. It is presumed to be a thiol oxidoreductase involved in polyketide biosynthesis, specifically in the production of the aromatic antibiotics frenolicin and nanaomycins.
Probab=20.89 E-value=3.3e+02 Score=21.23 Aligned_cols=30 Identities=17% Similarity=0.145 Sum_probs=24.2
Q ss_pred CCHHHHHHHHHhhCCchhhhhhhhhchHHH
Q psy1901 60 PDVYTREELAQKTKLTEARVQVWFSNRRAR 89 (205)
Q Consensus 60 ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k 89 (205)
-+.....+||..+||....+...+.....+
T Consensus 129 ~~~~~l~~~a~~~Gld~~~~~~~~~~~~~~ 158 (201)
T cd03024 129 GDRDVLVDLAEEAGLDAAEARAVLASDEYA 158 (201)
T ss_pred CCHHHHHHHHHHcCCCHHHHHHHhcCcccc
Confidence 456788999999999999998888765444
No 299
>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=20.88 E-value=1.1e+02 Score=17.50 Aligned_cols=19 Identities=11% Similarity=0.296 Sum_probs=13.7
Q ss_pred HHHHHhhCCchhhhhhhhh
Q psy1901 66 EELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 66 ~~LA~~l~l~~~qV~~WFq 84 (205)
..-|...||+..+|+..+.
T Consensus 9 i~eA~~~Gls~eeir~FL~ 27 (30)
T PF08671_consen 9 IKEAKESGLSKEEIREFLE 27 (30)
T ss_dssp HHHHHHTT--HHHHHHHHH
T ss_pred HHHHHHcCCCHHHHHHHHH
Confidence 3448999999999998774
No 300
>cd04767 HTH_HspR-like_MBC Helix-Turn-Helix DNA binding domain of putative HspR-like transcription regulators. Putative helix-turn-helix (HTH) transcription regulator HspR-like proteins. Unlike the characterized HspR, these proteins have a C-terminal domain with putative metal binding cysteines (MBC). Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind spe
Probab=20.86 E-value=77 Score=23.99 Aligned_cols=24 Identities=8% Similarity=0.205 Sum_probs=19.8
Q ss_pred HHHHHHHhhCCchhhhhhhhhchH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
.+.++|+.+|++.+.++.|.+...
T Consensus 3 sI~eVA~~~GVs~~TLR~wE~~GL 26 (120)
T cd04767 3 PIGVVAELLNIHPETLRIWERHGL 26 (120)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCC
Confidence 357899999999999999976433
No 301
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.81 E-value=75 Score=22.58 Aligned_cols=22 Identities=23% Similarity=0.181 Sum_probs=19.0
Q ss_pred HHHHHHhhCCchhhhhhhhhch
Q psy1901 65 REELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 65 r~~LA~~l~l~~~qV~~WFqNr 86 (205)
+.++|+.+|++.+.|+.|-+..
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 5689999999999999998643
No 302
>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=20.47 E-value=1.6e+02 Score=25.40 Aligned_cols=43 Identities=19% Similarity=0.183 Sum_probs=31.8
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhh
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFS 84 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFq 84 (205)
.+++.+..+|...|....+ ....-.+||+.+|++...|+....
T Consensus 249 ~L~~rer~Vi~lr~gl~~~-~~~Tl~EIa~~lgiS~erVrq~~~ 291 (298)
T TIGR02997 249 ELTPRERQVLRLRFGLDGG-EPLTLAEIGRRLNLSRERVRQIEA 291 (298)
T ss_pred cCCHHHHHHHHHHhccCCC-CCcCHHHHHHHHCcCHHHHHHHHH
Confidence 4788888888888753222 224578999999999999988664
No 303
>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=20.45 E-value=1.6e+02 Score=22.25 Aligned_cols=38 Identities=11% Similarity=0.052 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhh
Q psy1901 42 FTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVW 82 (205)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~W 82 (205)
++.++..+++..|..+.. ..-.+||..+|+++..|..+
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 677777788777754332 24677899999999887543
No 304
>PRK07598 RNA polymerase sigma factor SigC; Validated
Probab=20.27 E-value=2.5e+02 Score=25.90 Aligned_cols=52 Identities=19% Similarity=0.276 Sum_probs=37.5
Q ss_pred CCCHHHHHHHHHHhhcCCCCCHHHHHHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 41 TFTGDQLEELERAFQRTQYPDVYTREELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~ps~~~r~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+++.+..+|.-.|..... ......+||+.+|++...|+.+...-+.|.|..
T Consensus 350 ~L~~reR~VI~LRygl~d~-~~~Tl~EIA~~LGvS~erVRqie~rAl~KLR~~ 401 (415)
T PRK07598 350 DLTSRERDVIRMRFGLADG-HTYSLAEIGRALDLSRERVRQIESKALQKLRQP 401 (415)
T ss_pred hCCHHHHHHHHHHHhcCCC-CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHhch
Confidence 4788888888888753221 112468899999999999999987666666643
No 305
>cd01279 HTH_HspR-like Helix-Turn-Helix DNA binding domain of HspR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator HspR and related proteins, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=20.26 E-value=82 Score=22.54 Aligned_cols=23 Identities=9% Similarity=-0.025 Sum_probs=19.2
Q ss_pred HHHHHHHhhCCchhhhhhhhhch
Q psy1901 64 TREELAQKTKLTEARVQVWFSNR 86 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNr 86 (205)
.+.++|+.+|++.+.++.|.+..
T Consensus 3 ~i~eva~~~gVs~~tLR~ye~~G 25 (98)
T cd01279 3 PISVAAELLGIHPQTLRVYDRLG 25 (98)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCC
Confidence 35789999999999999997543
No 306
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.04 E-value=80 Score=22.75 Aligned_cols=24 Identities=21% Similarity=0.189 Sum_probs=19.8
Q ss_pred HHHHHHHhhCCchhhhhhhhhchH
Q psy1901 64 TREELAQKTKLTEARVQVWFSNRR 87 (205)
Q Consensus 64 ~r~~LA~~l~l~~~qV~~WFqNrR 87 (205)
.+.++|+.+|++.+.|+.|-+...
T Consensus 3 ~i~eva~~~gvs~~tlR~ye~~Gl 26 (102)
T cd04789 3 TISELAEKAGISRSTLLYYEKLGL 26 (102)
T ss_pred CHHHHHHHHCcCHHHHHHHHHCCC
Confidence 357899999999999999986443
No 307
>PRK13870 transcriptional regulator TraR; Provisional
Probab=20.04 E-value=2.4e+02 Score=23.43 Aligned_cols=28 Identities=21% Similarity=0.241 Sum_probs=23.3
Q ss_pred HHHHHhhCCchhhhhhhhhchHHHHHHH
Q psy1901 66 EELAQKTKLTEARVQVWFSNRRARLRKQ 93 (205)
Q Consensus 66 ~~LA~~l~l~~~qV~~WFqNrR~k~kr~ 93 (205)
.+||..||++++-|+.-++|=+.|.--.
T Consensus 192 ~EIa~ILgISe~TV~~Hl~na~~KLga~ 219 (234)
T PRK13870 192 EEIADVEGVKYNSVRVKLREAMKRFDVR 219 (234)
T ss_pred HHHHHHHCCCHHHHHHHHHHHHHHcCCC
Confidence 5899999999999999988877775444
Done!