Query psy10638
Match_columns 140
No_of_seqs 112 out of 1106
Neff 7.5
Searched_HMMs 46136
Date Fri Aug 16 23:35:36 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy10638.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/10638hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.7 1.8E-17 3.8E-22 132.8 7.4 68 31-98 168-235 (309)
2 KOG0842|consensus 99.7 1.6E-17 3.5E-22 131.9 6.4 70 31-100 149-218 (307)
3 KOG0489|consensus 99.7 1.3E-17 2.8E-22 130.9 4.2 68 33-100 157-224 (261)
4 KOG0484|consensus 99.7 2.6E-17 5.7E-22 111.4 4.1 70 31-100 13-82 (125)
5 KOG0843|consensus 99.7 5.1E-17 1.1E-21 119.6 5.5 65 33-97 100-164 (197)
6 KOG0487|consensus 99.7 8.1E-17 1.7E-21 128.0 6.5 68 31-98 231-298 (308)
7 KOG0850|consensus 99.7 2.1E-16 4.5E-21 120.2 7.6 67 31-97 118-184 (245)
8 KOG2251|consensus 99.7 1.2E-16 2.6E-21 120.9 5.4 68 30-97 32-99 (228)
9 KOG0485|consensus 99.7 1.5E-16 3.2E-21 120.3 5.8 68 31-98 100-167 (268)
10 KOG0848|consensus 99.6 1.8E-16 3.9E-21 122.9 5.7 63 36-98 200-262 (317)
11 PF00046 Homeobox: Homeobox do 99.6 2.8E-16 6E-21 96.1 5.1 57 36-92 1-57 (57)
12 KOG0494|consensus 99.6 1.4E-15 3.1E-20 117.6 7.0 63 34-96 140-202 (332)
13 KOG0492|consensus 99.6 6E-15 1.3E-19 110.9 7.1 73 26-98 134-207 (246)
14 KOG3802|consensus 99.6 2E-15 4.3E-20 122.7 3.9 62 34-95 293-354 (398)
15 KOG0483|consensus 99.5 1.4E-14 3.1E-19 109.2 6.2 79 36-114 51-129 (198)
16 TIGR01565 homeo_ZF_HD homeobox 99.5 1.3E-14 2.9E-19 89.3 4.9 53 35-87 1-57 (58)
17 KOG0493|consensus 99.5 3.9E-14 8.5E-19 109.8 5.9 59 36-94 247-305 (342)
18 cd00086 homeodomain Homeodomai 99.5 5E-14 1.1E-18 86.0 5.2 57 37-93 2-58 (59)
19 smart00389 HOX Homeodomain. DN 99.5 4.1E-14 8.8E-19 85.8 4.6 55 37-91 2-56 (56)
20 COG5576 Homeodomain-containing 99.4 2.2E-13 4.7E-18 99.5 5.8 68 31-98 47-114 (156)
21 KOG0491|consensus 99.4 1E-13 2.2E-18 101.0 1.1 65 34-98 99-163 (194)
22 KOG0486|consensus 99.4 7.7E-13 1.7E-17 104.8 6.0 66 33-98 110-175 (351)
23 KOG4577|consensus 99.4 6.8E-13 1.5E-17 104.2 4.6 66 33-98 165-230 (383)
24 KOG0844|consensus 99.3 7.4E-13 1.6E-17 104.7 4.1 65 32-96 178-242 (408)
25 KOG0847|consensus 99.3 5.5E-12 1.2E-16 95.8 5.4 64 31-94 163-226 (288)
26 KOG1168|consensus 99.1 3.6E-11 7.8E-16 94.7 2.1 64 32-95 306-369 (385)
27 KOG0490|consensus 99.1 5.9E-11 1.3E-15 90.4 2.9 64 32-95 57-120 (235)
28 KOG0849|consensus 98.9 1.4E-09 2.9E-14 89.0 6.0 66 31-96 172-237 (354)
29 KOG0775|consensus 98.9 1.8E-09 3.9E-14 84.4 4.0 52 42-93 183-234 (304)
30 KOG0774|consensus 98.5 1.2E-07 2.6E-12 74.0 4.0 65 35-99 188-255 (334)
31 KOG2252|consensus 98.4 3.2E-07 6.8E-12 77.8 5.3 60 31-90 416-475 (558)
32 PF05920 Homeobox_KN: Homeobox 98.3 2.3E-07 4.9E-12 53.0 1.5 34 56-89 7-40 (40)
33 KOG0490|consensus 98.0 6.4E-06 1.4E-10 62.6 4.2 66 30-95 148-213 (235)
34 KOG1146|consensus 97.4 0.00021 4.5E-09 66.2 5.2 63 33-95 901-963 (1406)
35 PF11569 Homez: Homeodomain le 97.1 0.0004 8.7E-09 42.3 2.1 42 46-87 9-50 (56)
36 KOG0773|consensus 96.2 0.004 8.7E-08 50.5 2.7 63 35-97 239-304 (342)
37 KOG3623|consensus 94.8 0.033 7.2E-07 49.6 3.8 48 47-94 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 93.7 0.15 3.2E-06 30.5 3.9 46 36-86 1-46 (53)
39 PF04545 Sigma70_r4: Sigma-70, 85.0 1.8 4E-05 24.8 3.6 43 41-88 4-46 (50)
40 PF04967 HTH_10: HTH DNA bindi 75.6 5.1 0.00011 24.0 3.3 40 42-81 1-42 (53)
41 KOG1146|consensus 74.4 5.5 0.00012 38.1 4.7 63 32-94 702-764 (1406)
42 PF09607 BrkDBD: Brinker DNA-b 73.8 7.9 0.00017 23.7 3.8 45 39-84 3-47 (58)
43 PF01527 HTH_Tnp_1: Transposas 70.3 2.9 6.4E-05 25.8 1.5 45 37-85 2-46 (76)
44 PF08281 Sigma70_r4_2: Sigma-7 67.4 9 0.00019 22.0 3.1 39 42-85 11-49 (54)
45 cd06171 Sigma70_r4 Sigma70, re 66.2 6.3 0.00014 21.7 2.2 40 42-86 11-50 (55)
46 cd00569 HTH_Hin_like Helix-tur 65.6 15 0.00032 17.9 4.0 37 42-83 6-42 (42)
47 PF10668 Phage_terminase: Phag 64.9 3.8 8.3E-05 25.2 1.2 20 64-83 24-43 (60)
48 PRK09646 RNA polymerase sigma 56.0 21 0.00046 26.1 4.1 47 42-93 143-189 (194)
49 TIGR03879 near_KaiC_dom probab 55.4 5 0.00011 25.7 0.5 34 52-85 22-55 (73)
50 PRK09642 RNA polymerase sigma 55.1 24 0.00053 24.6 4.1 31 64-94 124-154 (160)
51 COG3413 Predicted DNA binding 53.2 18 0.00038 27.3 3.3 39 41-79 155-195 (215)
52 PRK12514 RNA polymerase sigma 53.1 17 0.00036 26.1 3.0 30 64-93 147-176 (179)
53 PRK12526 RNA polymerase sigma 51.9 26 0.00056 26.0 4.0 32 63-94 170-201 (206)
54 PRK06759 RNA polymerase factor 51.5 24 0.00052 24.4 3.6 45 42-91 107-151 (154)
55 PRK09413 IS2 repressor TnpA; R 51.1 41 0.00089 23.0 4.6 43 39-85 10-52 (121)
56 PRK09652 RNA polymerase sigma 50.2 36 0.00077 23.9 4.4 47 42-93 129-175 (182)
57 PRK09639 RNA polymerase sigma 50.1 39 0.00085 23.6 4.6 47 42-94 113-159 (166)
58 KOG3623|consensus 49.5 11 0.00024 34.2 1.9 60 35-94 626-685 (1007)
59 PRK12512 RNA polymerase sigma 48.2 33 0.00071 24.6 4.0 47 42-93 132-178 (184)
60 PRK09648 RNA polymerase sigma 47.1 34 0.00074 24.7 3.9 46 42-92 140-185 (189)
61 PF13443 HTH_26: Cro/C1-type H 46.8 25 0.00054 20.7 2.7 27 64-90 12-38 (63)
62 PRK09644 RNA polymerase sigma 46.6 41 0.00089 23.7 4.2 31 64-94 126-156 (165)
63 cd04761 HTH_MerR-SF Helix-Turn 46.4 11 0.00024 20.9 1.0 23 65-87 3-25 (49)
64 PF13384 HTH_23: Homeodomain-l 46.4 11 0.00024 21.2 1.0 23 63-85 18-40 (50)
65 PRK11924 RNA polymerase sigma 46.3 34 0.00074 24.0 3.8 29 64-92 143-171 (179)
66 PRK12543 RNA polymerase sigma 46.2 57 0.0012 23.3 5.0 33 64-96 135-167 (179)
67 PF06056 Terminase_5: Putative 45.4 14 0.0003 22.4 1.3 27 64-92 15-41 (58)
68 TIGR02989 Sig-70_gvs1 RNA poly 45.3 34 0.00074 23.7 3.6 43 42-89 112-154 (159)
69 PRK12530 RNA polymerase sigma 45.1 47 0.001 24.2 4.4 47 42-93 135-181 (189)
70 TIGR02999 Sig-70_X6 RNA polyme 44.8 40 0.00086 24.1 4.0 29 64-92 152-180 (183)
71 PRK03975 tfx putative transcri 44.5 44 0.00095 24.0 4.0 50 39-94 4-53 (141)
72 TIGR02939 RpoE_Sigma70 RNA pol 43.8 29 0.00063 24.9 3.1 33 61-93 153-185 (190)
73 COG4367 Uncharacterized protei 43.5 37 0.0008 22.6 3.2 38 42-79 3-40 (97)
74 PF13518 HTH_28: Helix-turn-he 43.4 14 0.0003 20.8 1.1 22 64-85 14-35 (52)
75 PRK00118 putative DNA-binding 42.6 63 0.0014 21.9 4.4 48 42-94 18-65 (104)
76 PRK12515 RNA polymerase sigma 42.5 55 0.0012 23.6 4.5 31 64-94 149-179 (189)
77 TIGR02937 sigma70-ECF RNA poly 42.3 42 0.00091 22.3 3.6 28 64-91 128-155 (158)
78 PRK12519 RNA polymerase sigma 41.8 35 0.00075 24.7 3.3 32 62-93 157-188 (194)
79 PRK12537 RNA polymerase sigma 41.3 51 0.0011 23.7 4.1 28 64-91 151-178 (182)
80 PRK09047 RNA polymerase factor 41.2 61 0.0013 22.4 4.4 46 42-92 107-152 (161)
81 TIGR02959 SigZ RNA polymerase 41.1 61 0.0013 23.1 4.4 47 42-93 101-147 (170)
82 KOG3755|consensus 40.8 62 0.0013 29.0 5.0 47 49-95 517-575 (769)
83 PRK12541 RNA polymerase sigma 40.4 41 0.0009 23.5 3.4 29 64-92 130-158 (161)
84 PRK06986 fliA flagellar biosyn 40.2 36 0.00079 25.8 3.3 46 43-93 186-231 (236)
85 TIGR02948 SigW_bacill RNA poly 39.8 44 0.00096 23.8 3.5 30 63-92 153-182 (187)
86 PRK05602 RNA polymerase sigma 39.3 47 0.001 23.9 3.7 31 64-94 146-176 (186)
87 PRK09480 slmA division inhibit 39.2 36 0.00079 24.3 3.0 36 52-88 21-56 (194)
88 PF00196 GerE: Bacterial regul 38.9 43 0.00092 19.5 2.8 46 41-92 3-48 (58)
89 TIGR02985 Sig70_bacteroi1 RNA 38.6 57 0.0012 22.3 3.9 28 64-91 131-158 (161)
90 PRK06930 positive control sigm 38.3 68 0.0015 23.5 4.3 49 41-94 114-162 (170)
91 PRK12529 RNA polymerase sigma 37.6 60 0.0013 23.3 3.9 45 42-91 128-172 (178)
92 PF13411 MerR_1: MerR HTH fami 37.5 22 0.00047 21.3 1.4 20 66-85 4-23 (69)
93 PRK13919 putative RNA polymera 37.0 54 0.0012 23.5 3.6 30 63-92 152-181 (186)
94 PRK10072 putative transcriptio 36.7 20 0.00044 23.9 1.2 25 65-89 49-73 (96)
95 PRK12524 RNA polymerase sigma 35.7 64 0.0014 23.5 3.9 30 64-93 154-183 (196)
96 PRK12547 RNA polymerase sigma 35.4 69 0.0015 22.5 3.9 28 64-91 130-157 (164)
97 PRK12546 RNA polymerase sigma 35.0 59 0.0013 23.8 3.6 31 64-94 131-161 (188)
98 PRK04217 hypothetical protein; 34.9 83 0.0018 21.6 4.0 47 40-91 41-87 (110)
99 PF13936 HTH_38: Helix-turn-he 34.7 30 0.00064 19.4 1.5 40 40-84 3-42 (44)
100 PRK12538 RNA polymerase sigma 34.7 72 0.0016 24.3 4.1 32 63-94 188-219 (233)
101 TIGR02952 Sig70_famx2 RNA poly 34.6 69 0.0015 22.3 3.8 26 63-88 139-164 (170)
102 PRK07037 extracytoplasmic-func 34.4 76 0.0016 22.1 4.0 28 64-91 127-154 (163)
103 TIGR02983 SigE-fam_strep RNA p 34.0 70 0.0015 22.3 3.7 29 64-92 128-156 (162)
104 PF00376 MerR: MerR family reg 33.9 26 0.00056 19.2 1.1 18 66-83 3-20 (38)
105 PRK12532 RNA polymerase sigma 33.7 81 0.0018 22.8 4.2 31 64-94 154-184 (195)
106 TIGR02954 Sig70_famx3 RNA poly 33.6 74 0.0016 22.4 3.9 29 64-92 137-165 (169)
107 PRK09645 RNA polymerase sigma 33.5 79 0.0017 22.3 4.0 46 42-92 119-164 (173)
108 PRK12523 RNA polymerase sigma 33.4 78 0.0017 22.4 4.0 29 64-92 137-165 (172)
109 PRK12539 RNA polymerase sigma 33.3 75 0.0016 22.8 3.9 46 42-92 132-177 (184)
110 cd04762 HTH_MerR-trunc Helix-T 33.1 24 0.00051 19.1 0.9 24 65-88 3-26 (49)
111 TIGR02943 Sig70_famx1 RNA poly 33.1 1E+02 0.0022 22.4 4.6 31 64-94 149-179 (188)
112 TIGR03001 Sig-70_gmx1 RNA poly 33.0 1.1E+02 0.0024 23.6 5.0 34 64-97 179-212 (244)
113 TIGR02479 FliA_WhiG RNA polyme 32.3 58 0.0013 24.4 3.3 45 42-91 176-220 (224)
114 smart00421 HTH_LUXR helix_turn 32.3 69 0.0015 17.6 2.9 39 41-85 3-41 (58)
115 PRK08583 RNA polymerase sigma 32.2 57 0.0012 25.0 3.3 45 42-91 206-250 (257)
116 PRK08301 sporulation sigma fac 31.8 78 0.0017 23.8 3.9 50 42-92 179-228 (234)
117 PRK12520 RNA polymerase sigma 31.8 1.1E+02 0.0023 22.1 4.5 48 42-94 132-179 (191)
118 PRK09637 RNA polymerase sigma 31.5 82 0.0018 22.8 3.9 30 63-92 123-152 (181)
119 cd01392 HTH_LacI Helix-turn-he 31.4 57 0.0012 18.2 2.4 21 67-87 2-22 (52)
120 PRK05657 RNA polymerase sigma 31.0 73 0.0016 25.7 3.8 53 41-94 262-314 (325)
121 PRK12516 RNA polymerase sigma 30.8 1E+02 0.0022 22.4 4.3 31 64-94 134-164 (187)
122 PRK12533 RNA polymerase sigma 30.7 73 0.0016 24.0 3.6 31 64-94 152-182 (216)
123 cd04764 HTH_MlrA-like_sg1 Heli 30.6 30 0.00066 20.7 1.2 20 66-85 4-23 (67)
124 PRK12545 RNA polymerase sigma 30.4 1.1E+02 0.0024 22.4 4.5 31 64-94 157-187 (201)
125 PRK12531 RNA polymerase sigma 30.2 98 0.0021 22.5 4.1 29 64-92 159-187 (194)
126 PRK12536 RNA polymerase sigma 30.2 93 0.002 22.3 3.9 30 63-92 146-175 (181)
127 PRK09649 RNA polymerase sigma 30.0 79 0.0017 22.9 3.5 28 64-91 148-175 (185)
128 TIGR02941 Sigma_B RNA polymera 29.7 69 0.0015 24.5 3.3 46 42-92 206-251 (255)
129 PRK09651 RNA polymerase sigma 29.3 84 0.0018 22.3 3.6 30 63-92 136-165 (172)
130 COG2963 Transposase and inacti 29.2 1.2E+02 0.0025 20.3 4.0 42 39-84 5-47 (116)
131 PRK07670 RNA polymerase sigma 29.2 69 0.0015 24.5 3.2 46 42-92 202-247 (251)
132 PRK12518 RNA polymerase sigma 29.2 44 0.00096 23.6 2.0 34 61-94 135-168 (175)
133 PF08280 HTH_Mga: M protein tr 29.0 81 0.0018 18.6 2.9 35 45-83 6-40 (59)
134 PRK09641 RNA polymerase sigma 29.0 91 0.002 22.1 3.7 31 62-92 152-182 (187)
135 PRK06811 RNA polymerase factor 28.8 90 0.002 22.6 3.7 47 42-93 132-178 (189)
136 PRK11923 algU RNA polymerase s 28.6 1.1E+02 0.0023 22.1 4.0 32 63-94 155-186 (193)
137 PRK12542 RNA polymerase sigma 28.2 1E+02 0.0022 22.1 3.8 30 64-93 140-169 (185)
138 PHA02955 hypothetical protein; 28.0 86 0.0019 24.2 3.5 42 45-86 61-103 (213)
139 cd01104 HTH_MlrA-CarA Helix-Tu 27.7 36 0.00077 20.3 1.2 20 65-84 3-22 (68)
140 PRK12511 RNA polymerase sigma 27.5 1.1E+02 0.0023 22.2 3.9 29 64-92 129-157 (182)
141 PRK11552 putative DNA-binding 27.4 71 0.0015 24.0 3.0 42 49-92 21-62 (225)
142 PF13551 HTH_29: Winged helix- 27.1 1.5E+02 0.0033 18.9 4.3 48 37-84 53-109 (112)
143 PRK09647 RNA polymerase sigma 26.9 1.4E+02 0.003 22.2 4.4 30 64-93 156-185 (203)
144 cd04763 HTH_MlrA-like Helix-Tu 26.9 38 0.00083 20.4 1.2 21 65-85 3-23 (68)
145 PF15063 TC1: Thyroid cancer p 26.8 1.2E+02 0.0026 19.6 3.5 36 41-76 33-68 (79)
146 PRK12535 RNA polymerase sigma 26.6 1.1E+02 0.0023 22.5 3.8 29 64-92 151-179 (196)
147 PRK12522 RNA polymerase sigma 26.5 1.4E+02 0.0029 21.1 4.2 30 64-93 137-166 (173)
148 PRK12525 RNA polymerase sigma 25.9 1.1E+02 0.0025 21.5 3.7 44 42-90 119-162 (168)
149 COG1905 NuoE NADH:ubiquinone o 25.9 1.1E+02 0.0024 22.5 3.6 37 43-79 24-60 (160)
150 PRK12517 RNA polymerase sigma 25.8 2E+02 0.0042 20.9 5.0 31 64-94 146-176 (188)
151 PRK07122 RNA polymerase sigma 25.2 88 0.0019 24.4 3.2 46 42-92 216-261 (264)
152 TIGR02980 SigBFG RNA polymeras 25.1 1.2E+02 0.0026 22.6 3.9 45 41-90 178-222 (227)
153 PRK12544 RNA polymerase sigma 25.1 1.5E+02 0.0033 22.0 4.4 30 64-93 166-195 (206)
154 cd06170 LuxR_C_like C-terminal 24.8 99 0.0022 17.0 2.7 21 64-84 17-37 (57)
155 TIGR02859 spore_sigH RNA polym 24.7 1.2E+02 0.0027 21.7 3.8 31 60-90 163-193 (198)
156 PRK08295 RNA polymerase factor 24.6 1.3E+02 0.0028 21.8 3.9 30 63-92 171-200 (208)
157 PRK12528 RNA polymerase sigma 24.5 1.2E+02 0.0027 21.0 3.7 22 64-85 131-152 (161)
158 PRK06288 RNA polymerase sigma 24.4 1.1E+02 0.0025 23.6 3.7 47 42-93 213-259 (268)
159 TIGR01764 excise DNA binding d 24.3 43 0.00094 18.1 1.0 23 65-87 4-26 (49)
160 PRK07408 RNA polymerase sigma 23.8 87 0.0019 24.2 2.9 46 42-92 204-249 (256)
161 PRK12534 RNA polymerase sigma 23.6 1.1E+02 0.0023 21.9 3.2 26 63-88 154-179 (187)
162 PRK12540 RNA polymerase sigma 23.0 1.4E+02 0.0031 21.5 3.8 30 64-93 129-158 (182)
163 TIGR02950 SigM_subfam RNA poly 23.0 56 0.0012 22.5 1.6 31 61-91 120-150 (154)
164 PRK12513 RNA polymerase sigma 22.8 59 0.0013 23.5 1.7 34 60-93 153-186 (194)
165 PF01710 HTH_Tnp_IS630: Transp 22.6 1.2E+02 0.0027 20.5 3.2 37 43-84 4-40 (119)
166 KOG0773|consensus 22.5 65 0.0014 26.0 2.1 38 55-92 117-154 (342)
167 PF02796 HTH_7: Helix-turn-hel 22.3 1.2E+02 0.0026 16.8 2.6 37 42-83 6-42 (45)
168 cd00093 HTH_XRE Helix-turn-hel 21.9 55 0.0012 17.3 1.1 23 65-87 15-37 (58)
169 TIGR02947 SigH_actino RNA poly 21.8 64 0.0014 23.4 1.8 34 61-94 146-179 (193)
170 PRK10403 transcriptional regul 21.8 1.3E+02 0.0028 21.0 3.4 49 41-95 153-201 (215)
171 smart00027 EH Eps15 homology d 21.6 1.9E+02 0.004 18.5 3.8 44 41-84 3-51 (96)
172 TIGR02392 rpoH_proteo alternat 21.4 1.3E+02 0.0027 23.4 3.4 49 41-92 218-266 (270)
173 PRK06424 transcription factor; 21.4 1.9E+02 0.0042 20.7 4.1 25 65-89 100-124 (144)
174 TIGR02984 Sig-70_plancto1 RNA 21.2 1.2E+02 0.0027 21.4 3.2 44 42-90 141-184 (189)
175 PF04936 DUF658: Protein of un 21.1 46 0.00099 24.8 0.8 34 64-97 16-49 (186)
176 PF00424 REV: REV protein (ant 20.9 1.9E+02 0.0042 19.2 3.7 38 47-98 14-51 (91)
177 TIGR03070 couple_hipB transcri 20.7 58 0.0013 18.2 1.1 23 65-87 18-40 (58)
178 smart00422 HTH_MERR helix_turn 20.6 60 0.0013 19.3 1.2 20 66-85 4-23 (70)
179 PRK09640 RNA polymerase sigma 20.3 88 0.0019 22.6 2.2 32 62-93 150-181 (188)
180 PRK05911 RNA polymerase sigma 20.1 1.2E+02 0.0027 23.3 3.1 46 42-92 206-251 (257)
181 TIGR02957 SigX4 RNA polymerase 20.0 1.6E+02 0.0034 23.0 3.7 30 64-93 126-155 (281)
No 1
>KOG0488|consensus
Probab=99.71 E-value=1.8e-17 Score=132.76 Aligned_cols=68 Identities=47% Similarity=0.768 Sum_probs=63.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
.++|+|+.||.||..|+..||+.|++.+|++..+|+.||..|||+..+|++||||||+||||....+.
T Consensus 168 ~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~g~ 235 (309)
T KOG0488|consen 168 TPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAEGG 235 (309)
T ss_pred CCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHhhh
Confidence 34778889999999999999999999999999999999999999999999999999999999987643
No 2
>KOG0842|consensus
Probab=99.71 E-value=1.6e-17 Score=131.91 Aligned_cols=70 Identities=40% Similarity=0.667 Sum_probs=64.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~ 100 (140)
...++||.|..|+..|+.+||+.|...+|++..+|+.||..|+||+.+|+|||||||-|+||..+.....
T Consensus 149 ~~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 149 GKRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred ccccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 3556777788999999999999999999999999999999999999999999999999999998766544
No 3
>KOG0489|consensus
Probab=99.69 E-value=1.3e-17 Score=130.88 Aligned_cols=68 Identities=51% Similarity=0.811 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100 (140)
Q Consensus 33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~ 100 (140)
++.||.||.||..|+..||+.|..|+|++...|.+||..|.|++++|+|||||||+||||..+.....
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~~~ 224 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKSSQ 224 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccccc
Confidence 45788999999999999999999999999999999999999999999999999999999988666544
No 4
>KOG0484|consensus
Probab=99.68 E-value=2.6e-17 Score=111.38 Aligned_cols=70 Identities=43% Similarity=0.601 Sum_probs=64.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQ 100 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~ 100 (140)
..++.||.||.|+..|+..|++.|.+.+||++-.+++||..+.|++..|+|||||||+|+||..+.....
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~a~~~ 82 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERAAIAK 82 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHHHHHH
Confidence 4567889999999999999999999999999999999999999999999999999999999988655433
No 5
>KOG0843|consensus
Probab=99.68 E-value=5.1e-17 Score=119.56 Aligned_cols=65 Identities=57% Similarity=0.865 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
.+.+|.||.|+.+|+..||..|+.+.|....+|+.||..|+|++.+|+|||||||.|.||...+.
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37889999999999999999999999999999999999999999999999999999999988665
No 6
>KOG0487|consensus
Probab=99.67 E-value=8.1e-17 Score=128.00 Aligned_cols=68 Identities=44% Similarity=0.624 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
..++.|++|..+|+.|+..||+.|..|.|++.+.|.+|++.|+|+++||+|||||||.|+||..++.-
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 34667888999999999999999999999999999999999999999999999999999999986543
No 7
>KOG0850|consensus
Probab=99.66 E-value=2.1e-16 Score=120.20 Aligned_cols=67 Identities=43% Similarity=0.695 Sum_probs=62.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
..+|.|+.||.++.-||..|.+.|+++.|+-..+|++||+.|||+..+|+|||||||.|.||..+.+
T Consensus 118 k~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k~g 184 (245)
T KOG0850|consen 118 KGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKKQG 184 (245)
T ss_pred CcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHhcC
Confidence 3566778899999999999999999999999999999999999999999999999999999988743
No 8
>KOG2251|consensus
Probab=99.65 E-value=1.2e-16 Score=120.88 Aligned_cols=68 Identities=49% Similarity=0.617 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
.++++.||+||.|+-.|+.+||..|.+..||+...+++||..|+|.+.+|+|||+|||+|+|+.+...
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 56788999999999999999999999999999999999999999999999999999999999988543
No 9
>KOG0485|consensus
Probab=99.65 E-value=1.5e-16 Score=120.30 Aligned_cols=68 Identities=44% Similarity=0.729 Sum_probs=62.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
+..++|+.||+|+..|+..||..|+..+|++..+|..||+.|.|++.+|+|||||||.||||+-.-..
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aad~ 167 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAADL 167 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhhhh
Confidence 44578899999999999999999999999999999999999999999999999999999999874443
No 10
>KOG0848|consensus
Probab=99.65 E-value=1.8e-16 Score=122.89 Aligned_cols=63 Identities=41% Similarity=0.604 Sum_probs=58.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
-+=|.+++.-|+..||+.|..++|+++..+.+||..|||++++|+|||||||+|+||..++..
T Consensus 200 DKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 200 DKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred cceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 344778999999999999999999999999999999999999999999999999999887665
No 11
>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=99.64 E-value=2.8e-16 Score=96.10 Aligned_cols=57 Identities=56% Similarity=0.684 Sum_probs=54.9
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
|+.|+.|+..++.+|+.+|..+++|+..+++.||..|||+..+|.+||+|+|.++||
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 577899999999999999999999999999999999999999999999999999986
No 12
>KOG0494|consensus
Probab=99.61 E-value=1.4e-15 Score=117.62 Aligned_cols=63 Identities=46% Similarity=0.708 Sum_probs=58.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96 (140)
Q Consensus 34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~ 96 (140)
++|+.||.|+.-|+..||+.|.+.+||+...|+.||..+.|.+.+|+|||||||+||||..+.
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 344459999999999999999999999999999999999999999999999999999997754
No 13
>KOG0492|consensus
Probab=99.57 E-value=6e-15 Score=110.90 Aligned_cols=73 Identities=38% Similarity=0.603 Sum_probs=63.5
Q ss_pred CCCCCCC-CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 26 SSCSSSS-SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 26 ~~~~~~~-~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
..|.... +..|++|+.|+..|+..||+.|....|.++.++.+++..|.|++.+|+|||||||+|.||-+..+.
T Consensus 134 ~~C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 134 TTCTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred ccchhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 3344333 445678999999999999999999999999999999999999999999999999999999775544
No 14
>KOG3802|consensus
Probab=99.56 E-value=2e-15 Score=122.68 Aligned_cols=62 Identities=27% Similarity=0.378 Sum_probs=60.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
|+||+||.|....+..||.+|.+|+.|+..++..||.+|+|...+|+|||||||.|+||...
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 78888999999999999999999999999999999999999999999999999999999885
No 15
>KOG0483|consensus
Probab=99.53 E-value=1.4e-14 Score=109.21 Aligned_cols=79 Identities=33% Similarity=0.501 Sum_probs=70.1
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHHHHHHHHHhhhhhHHH
Q psy10638 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQQRLAAIKQSQLNQQQ 114 (140)
Q Consensus 36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~~~~~~~~~~~~~~~~ 114 (140)
.+.+.+|+.+|+..|+..|+...+.....+..||..|||.+++|.|||||||+|||.++.+..+..++...........
T Consensus 51 ~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 51 KGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred ccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 3445679999999999999999999999999999999999999999999999999999999998888877665544443
No 16
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.53 E-value=1.3e-14 Score=89.30 Aligned_cols=53 Identities=30% Similarity=0.423 Sum_probs=50.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHhhHHHhcCCCcchhhhcccchh
Q psy10638 35 SKRVRTIFTPEQLERLEAEFERQQY----MVGPERLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 35 ~rr~Rt~~s~~q~~~Le~~F~~~~~----p~~~~~~~La~~lgl~~~qV~vWFqNrR 87 (140)
++|.||.|+++|+..|+..|+.++| |+..+++.||..+||++++|+|||+|.+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999975
No 17
>KOG0493|consensus
Probab=99.49 E-value=3.9e-14 Score=109.80 Aligned_cols=59 Identities=51% Similarity=0.828 Sum_probs=56.7
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
||+||.|+.+|+..|+..|..++|++...|..||.+|+|.+.+|+|||||+|+|-||-.
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 57899999999999999999999999999999999999999999999999999999855
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=99.49 E-value=5e-14 Score=86.04 Aligned_cols=57 Identities=60% Similarity=0.860 Sum_probs=53.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+.++.++..++.+|+.+|..++||+..++..||..+||+..+|.+||+|+|.+.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 457789999999999999999999999999999999999999999999999998764
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.49 E-value=4.1e-14 Score=85.82 Aligned_cols=55 Identities=62% Similarity=0.944 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
+.|+.|+..++.+|+..|..++||+..++..||..+||+..+|.+||.|+|.+.+
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 5567899999999999999999999999999999999999999999999998753
No 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.43 E-value=2.2e-13 Score=99.51 Aligned_cols=68 Identities=38% Similarity=0.462 Sum_probs=60.7
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
+.+..++.|.+.+..|+.+|+..|..+++|+...+..|+..|+|+++.|++||||+|++.|+......
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~~ 114 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGKV 114 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccch
Confidence 34456666777899999999999999999999999999999999999999999999999999875543
No 21
>KOG0491|consensus
Probab=99.38 E-value=1e-13 Score=100.96 Aligned_cols=65 Identities=51% Similarity=0.825 Sum_probs=60.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 34 KSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 34 ~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
++++-|++|+..++..|++.|+..+|.+..++.+||..|+|++.+|+.||||||+|.||..+...
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 34567999999999999999999999999999999999999999999999999999999886554
No 22
>KOG0486|consensus
Probab=99.37 E-value=7.7e-13 Score=104.78 Aligned_cols=66 Identities=52% Similarity=0.746 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
.|.||.|+.|+..|+..||..|.++.||+...+++||.-.+|++..|+|||.|||+||||+++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 367889999999999999999999999999999999999999999999999999999999987665
No 23
>KOG4577|consensus
Probab=99.36 E-value=6.8e-13 Score=104.21 Aligned_cols=66 Identities=32% Similarity=0.413 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
...||+||.+++.|++.|+.+|+..+.|....|+.|+.++||..++|+|||||||+|+||-++..-
T Consensus 165 ~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T KOG4577|consen 165 ASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAG 230 (383)
T ss_pred cccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcc
Confidence 346789999999999999999999999999999999999999999999999999999999776554
No 24
>KOG0844|consensus
Probab=99.34 E-value=7.4e-13 Score=104.69 Aligned_cols=65 Identities=51% Similarity=0.803 Sum_probs=60.1
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638 32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96 (140)
Q Consensus 32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~ 96 (140)
...-||-||.|+.+|+..||+.|-+..|.+...|.+||+.|+|.+..|+|||||||.|+||+..-
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 34557889999999999999999999999999999999999999999999999999999998743
No 25
>KOG0847|consensus
Probab=99.27 E-value=5.5e-12 Score=95.82 Aligned_cols=64 Identities=52% Similarity=0.896 Sum_probs=59.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
..++++-.|..|+..++..|+..|+...|+-..++.+||..+|+++.+|+|||||||.||||+.
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 3456666788999999999999999999999999999999999999999999999999999976
No 26
>KOG1168|consensus
Probab=99.09 E-value=3.6e-11 Score=94.66 Aligned_cols=64 Identities=31% Similarity=0.424 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
...+||+||.+.+.....||.+|...+.|+.+.+..||..|+|...+|+|||||.|.|.||...
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~~ 369 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMKR 369 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhhh
Confidence 4567788999999999999999999999999999999999999999999999999999998653
No 27
>KOG0490|consensus
Probab=99.08 E-value=5.9e-11 Score=90.45 Aligned_cols=64 Identities=39% Similarity=0.442 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
..+.++.|+.|+..++..|++.|+..+||+...++.||..+++++..|++||+|+|+++++...
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 4567888999999999999999999999999999999999999999999999999999999874
No 28
>KOG0849|consensus
Probab=98.95 E-value=1.4e-09 Score=88.96 Aligned_cols=66 Identities=47% Similarity=0.713 Sum_probs=61.2
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~ 96 (140)
..++.+|.|+.|+..|+..|++.|+.++||+...++.||.+.++++..|.+||+|+|++++|....
T Consensus 172 ~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~~ 237 (354)
T KOG0849|consen 172 LQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHRD 237 (354)
T ss_pred ccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcccc
Confidence 355677789999999999999999999999999999999999999999999999999999998743
No 29
>KOG0775|consensus
Probab=98.87 E-value=1.8e-09 Score=84.43 Aligned_cols=52 Identities=31% Similarity=0.399 Sum_probs=48.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
|...-+.+|..+|..++||+..++.+||..+||+..+|-+||+|||.|+|-.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 5566788999999999999999999999999999999999999999999943
No 30
>KOG0774|consensus
Probab=98.49 E-value=1.2e-07 Score=74.02 Aligned_cols=65 Identities=31% Similarity=0.454 Sum_probs=57.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHHH
Q psy10638 35 SKRVRTIFTPEQLERLEAEFE---RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQQ 99 (140)
Q Consensus 35 ~rr~Rt~~s~~q~~~Le~~F~---~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~~ 99 (140)
.+|+|..|+.....+|..+|- .++||+...++.||.++|++..+|..||.|+|-+.+|..-..++
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~e 255 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQE 255 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhh
Confidence 356778899999999999996 56799999999999999999999999999999999997655543
No 31
>KOG2252|consensus
Probab=98.43 E-value=3.2e-07 Score=77.78 Aligned_cols=60 Identities=25% Similarity=0.280 Sum_probs=55.4
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 31 SSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 31 ~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
.....|++|.+|+..|+..|..+|..+++|+.++...|+..|||....|.+||.|-|.|.
T Consensus 416 ~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 416 KMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 344567789999999999999999999999999999999999999999999999988775
No 32
>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=98.33 E-value=2.3e-07 Score=53.01 Aligned_cols=34 Identities=29% Similarity=0.467 Sum_probs=28.5
Q ss_pred hcCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638 56 RQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89 (140)
Q Consensus 56 ~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k 89 (140)
.++||+..++..|+..+||+..+|..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 4689999999999999999999999999998864
No 33
>KOG0490|consensus
Probab=98.02 E-value=6.4e-06 Score=62.63 Aligned_cols=66 Identities=42% Similarity=0.571 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 30 SSSSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 30 ~~~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
....+.++.|+.+...++..|...|....+|+...+..|+..+|++...|.+||+|+|.+.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 345667788999999999999999999999999999999999999999999999999999998764
No 34
>KOG1146|consensus
Probab=97.43 E-value=0.00021 Score=66.16 Aligned_cols=63 Identities=30% Similarity=0.364 Sum_probs=58.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 33 SKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 33 ~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
-.+++.|+.++..++..|...|....++...+.+.|...+++..+.|.+||+|.|.+.++...
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 345677899999999999999999999999999999999999999999999999999998764
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.08 E-value=0.0004 Score=42.29 Aligned_cols=42 Identities=19% Similarity=0.353 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchh
Q psy10638 46 QLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 46 q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR 87 (140)
....|+.+|...+++...+...|....+|+..+|+.||-.+.
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 345699999999999999999999999999999999997654
No 36
>KOG0773|consensus
Probab=96.15 E-value=0.004 Score=50.52 Aligned_cols=63 Identities=29% Similarity=0.361 Sum_probs=50.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHHh---cCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 35 SKRVRTIFTPEQLERLEAEFER---QQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 35 ~rr~Rt~~s~~q~~~Le~~F~~---~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
..|.+..+......+|+.++.. .+||+..++..|+..+||+..+|.+||-|.|-+..+-....
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 4455667899999999977332 46899999999999999999999999999988876655433
No 37
>KOG3623|consensus
Probab=94.79 E-value=0.033 Score=49.57 Aligned_cols=48 Identities=21% Similarity=0.227 Sum_probs=44.9
Q ss_pred HHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 47 LERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 47 ~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
..+|+.+|..|..|+..+...|+...||..+.|+.||.++++......
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 778999999999999999999999999999999999999998887755
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=93.66 E-value=0.15 Score=30.47 Aligned_cols=46 Identities=20% Similarity=0.302 Sum_probs=34.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638 36 KRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR 86 (140)
Q Consensus 36 rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNr 86 (140)
++.|..+|.++...+-..++... ....||..+|+....|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 46778899988888888887776 47788999999999999999874
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=84.97 E-value=1.8 Score=24.84 Aligned_cols=43 Identities=14% Similarity=0.233 Sum_probs=31.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhh
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~ 88 (140)
.+++.+..+|...| ........+|..+|++...|+.+...-..
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 46788899999998 22334677899999999999887654333
No 40
>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=75.61 E-value=5.1 Score=23.96 Aligned_cols=40 Identities=25% Similarity=0.218 Sum_probs=32.5
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHhhHHHhcCCCcchhhh
Q psy10638 42 FTPEQLERLEAEFERQQY--MVGPERLYLAHTLNLTEAQVKV 81 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~--p~~~~~~~La~~lgl~~~qV~v 81 (140)
+|+.|+.+|..+|+..-| |-......||..||++..-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578899999999998875 5566778899999999876544
No 41
>KOG1146|consensus
Probab=74.40 E-value=5.5 Score=38.15 Aligned_cols=63 Identities=21% Similarity=0.241 Sum_probs=56.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 32 SSKSKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 32 ~~~~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
+.+.++.+..+-.+..-.|-++|-.+..|+......|....+.+.+.+.+||+|-+.|.++..
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 345667788888899999999999999999999999999999999999999999999988755
No 42
>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=73.75 E-value=7.9 Score=23.69 Aligned_cols=45 Identities=22% Similarity=0.308 Sum_probs=23.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhccc
Q psy10638 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFq 84 (140)
|..|+.......-.+|.....--.. -...|..+|++++.|+-|.+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~nc~~~-~RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNNCKGN-QRAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TTTTT--HHHHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccchhhh-HHHHHHHhCccHHHHHHHHH
Confidence 4456666555444555444332222 23359999999999999953
No 43
>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=70.32 E-value=2.9 Score=25.82 Aligned_cols=45 Identities=18% Similarity=0.297 Sum_probs=28.6
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccc
Q psy10638 37 RVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 37 r~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqN 85 (140)
+.|..|++++...+-..+... ......+|..+||++..+..|-.-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHH
Confidence 345678998888776665222 245677899999999999999643
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=67.39 E-value=9 Score=22.05 Aligned_cols=39 Identities=21% Similarity=0.247 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccc
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqN 85 (140)
+++.+..++...|-. ......+|..+|+++..|+.|...
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHH
Confidence 455666666555433 335678899999999999999864
No 45
>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=66.19 E-value=6.3 Score=21.68 Aligned_cols=40 Identities=13% Similarity=0.165 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNR 86 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNr 86 (140)
++..+..++...|... .....+|..+|++...|..|....
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~ 50 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRA 50 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHH
Confidence 5666777777766422 245667999999999999987543
No 46
>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=65.56 E-value=15 Score=17.89 Aligned_cols=37 Identities=19% Similarity=0.286 Sum_probs=24.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcc
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWF 83 (140)
++......+...|... . ....++..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 5566666666666532 2 45567889999988888774
No 47
>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=64.93 E-value=3.8 Score=25.21 Aligned_cols=20 Identities=20% Similarity=0.454 Sum_probs=17.0
Q ss_pred HHhhHHHhcCCCcchhhhcc
Q psy10638 64 ERLYLAHTLNLTEAQVKVWF 83 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWF 83 (140)
....||..||+++..|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 34567999999999999994
No 48
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=55.98 E-value=21 Score=26.07 Aligned_cols=47 Identities=21% Similarity=0.203 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..+|...|- .......||..||++...|+.++..-|.+.++.
T Consensus 143 L~~~~r~vl~l~~~-----~~~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 143 LTDTQRESVTLAYY-----GGLTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 44555555544432 223567789999999999999986555555443
No 49
>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=55.37 E-value=5 Score=25.68 Aligned_cols=34 Identities=21% Similarity=0.156 Sum_probs=25.2
Q ss_pred HHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccc
Q psy10638 52 AEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 52 ~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqN 85 (140)
..|....+........||..+|+++..|+.|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3444444444456778999999999999999875
No 50
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=55.07 E-value=24 Score=24.65 Aligned_cols=31 Identities=13% Similarity=0.025 Sum_probs=23.8
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..+|+++..|++.+..-|.+.|+..
T Consensus 124 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 124 SYQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999876555555544
No 51
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=53.21 E-value=18 Score=27.30 Aligned_cols=39 Identities=23% Similarity=0.234 Sum_probs=33.5
Q ss_pred CCCHHHHHHHHHHHHhcC--CCCHHHHhhHHHhcCCCcchh
Q psy10638 41 IFTPEQLERLEAEFERQQ--YMVGPERLYLAHTLNLTEAQV 79 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~--~p~~~~~~~La~~lgl~~~qV 79 (140)
.+|+.|+.+|..+|...- +|-......||..||+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 699999999999999888 466777788999999988654
No 52
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=53.15 E-value=17 Score=26.10 Aligned_cols=30 Identities=17% Similarity=0.313 Sum_probs=23.2
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..+|+++..|++++..-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 467889999999999999887555555443
No 53
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=51.94 E-value=26 Score=25.98 Aligned_cols=32 Identities=25% Similarity=0.166 Sum_probs=24.0
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.....||..+|++...|+.++..-+.+.++..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34677899999999999998865555555443
No 54
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=51.48 E-value=24 Score=24.40 Aligned_cols=45 Identities=18% Similarity=0.084 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
+++.+..++...|-. ......||..+|++...|+.|...-+.+-|
T Consensus 107 L~~~~r~ii~l~~~~-----~~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFV-----GKTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 444555555444322 234678899999999999999764444433
No 55
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=51.13 E-value=41 Score=22.99 Aligned_cols=43 Identities=12% Similarity=0.103 Sum_probs=29.1
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccc
Q psy10638 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqN 85 (140)
|..|+.+.....-..+..+.. ....+|..+|+++..|..|...
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 345788776544443333332 3566799999999999999643
No 56
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=50.24 E-value=36 Score=23.94 Aligned_cols=47 Identities=13% Similarity=0.032 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..+|...|- .......||..+|++...|+.|...-+.+.++.
T Consensus 129 L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 175 (182)
T PRK09652 129 LPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIFRAREALRAK 175 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 55555555555432 222456789999999999999987545444443
No 57
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=50.07 E-value=39 Score=23.62 Aligned_cols=47 Identities=21% Similarity=0.198 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
+++.+..+|...| .. .....||..+|++...|+.+...-+.+.|+..
T Consensus 113 L~~~~r~il~l~~--~g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l 159 (166)
T PRK09639 113 MTERDRTVLLLRF--SG----YSYKEIAEALGIKESSVGTTLARAKKKFRKIY 159 (166)
T ss_pred CCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4555555555555 22 24567899999999999999865555555543
No 58
>KOG3623|consensus
Probab=49.48 E-value=11 Score=34.24 Aligned_cols=60 Identities=22% Similarity=0.230 Sum_probs=48.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 35 SKRVRTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 35 ~rr~Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
..+.++....++-..|..+|+....++..+...++..|-..+..|.+||++|+...+...
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 445567777788888889998888888777777788888888999999999988776644
No 59
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=48.23 E-value=33 Score=24.64 Aligned_cols=47 Identities=17% Similarity=0.194 Sum_probs=31.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..+|...|-. ......||..||++...|+.++..-+.+.|..
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAAK 178 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 444455555444332 23467789999999999999987666655544
No 60
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=47.14 E-value=34 Score=24.70 Aligned_cols=46 Identities=20% Similarity=0.086 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..++...|-. ......||..+|++...|+.+...-+.+.|+
T Consensus 140 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVV-----GLSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 455555555554333 2346788999999999999987544444443
No 61
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=46.83 E-value=25 Score=20.66 Aligned_cols=27 Identities=7% Similarity=0.070 Sum_probs=15.7
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
....||..+|++...|..|+.++....
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~ 38 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNP 38 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT----
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccc
Confidence 345678888888888888887664333
No 62
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=46.56 E-value=41 Score=23.68 Aligned_cols=31 Identities=16% Similarity=0.037 Sum_probs=23.7
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
..+.||..+|++...|++|...-|.+.++.-
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 156 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKALL 156 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999999875555555443
No 63
>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=46.40 E-value=11 Score=20.94 Aligned_cols=23 Identities=9% Similarity=-0.022 Sum_probs=18.5
Q ss_pred HhhHHHhcCCCcchhhhcccchh
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR 87 (140)
...+|..+|+++..|+.|..+..
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35678999999999999976543
No 64
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=46.39 E-value=11 Score=21.24 Aligned_cols=23 Identities=17% Similarity=0.277 Sum_probs=16.9
Q ss_pred HHHhhHHHhcCCCcchhhhcccc
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqN 85 (140)
.....+|..||++...|..|...
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 34677899999999999999753
No 65
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=46.33 E-value=34 Score=23.97 Aligned_cols=29 Identities=21% Similarity=0.192 Sum_probs=22.5
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..+|++...|+.|...-+.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45788999999999999998655555444
No 66
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=46.17 E-value=57 Score=23.35 Aligned_cols=33 Identities=18% Similarity=0.144 Sum_probs=25.8
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHhHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLE 96 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~ 96 (140)
....||..||++...|++....-+.+.|+.-..
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~ 167 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQI 167 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999887777766665533
No 67
>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=45.44 E-value=14 Score=22.38 Aligned_cols=27 Identities=26% Similarity=0.503 Sum_probs=20.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..||++...|..|-. |.+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 356789999999999999964 444433
No 68
>TIGR02989 Sig-70_gvs1 RNA polymerase sigma-70 factor, Rhodopirellula/Verrucomicrobium family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are abundantly found in the species Rhodopirellula baltica (11), and Verrucomicrobium spinosum (16) and to a lesser extent in Gemmata obscuriglobus (2).
Probab=45.32 E-value=34 Score=23.72 Aligned_cols=43 Identities=23% Similarity=0.204 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIK 89 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k 89 (140)
+++.+..++...| ........||..+|++...|+++...-|.+
T Consensus 112 L~~~~r~v~~l~~-----~~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 112 LPERQRELLQLRY-----QRGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4444444444433 233356778999999999999886544433
No 69
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=45.07 E-value=47 Score=24.17 Aligned_cols=47 Identities=6% Similarity=0.077 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..++...|-. ......||..||+++..|+.+...-|.+.|+.
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 344444444444322 22467789999999999999986555555443
No 70
>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=44.79 E-value=40 Score=24.07 Aligned_cols=29 Identities=14% Similarity=0.006 Sum_probs=22.1
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....+|..||+++..|++.+..-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999988655554443
No 71
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=44.50 E-value=44 Score=24.00 Aligned_cols=50 Identities=24% Similarity=0.243 Sum_probs=36.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
...+++.+..+|... .. . .....+|..||++...|..|....+.+.++..
T Consensus 4 ~~~Lt~rqreVL~lr-~~-G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~ 53 (141)
T PRK03975 4 ESFLTERQIEVLRLR-ER-G----LTQQEIADILGTSRANVSSIEKRARENIEKAR 53 (141)
T ss_pred ccCCCHHHHHHHHHH-Hc-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 356889999999773 22 2 23567899999999999999876555554443
No 72
>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=43.79 E-value=29 Score=24.86 Aligned_cols=33 Identities=12% Similarity=0.031 Sum_probs=24.1
Q ss_pred CHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 61 VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 61 ~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
.......||..+|++...|+++...-|.+-|+.
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~ 185 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIR 185 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 334567889999999999999886555544443
No 73
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.55 E-value=37 Score=22.63 Aligned_cols=38 Identities=26% Similarity=0.334 Sum_probs=26.8
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchh
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQV 79 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV 79 (140)
++++|...-...|..+--.+....+.+|..||+++..|
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 45666666666666666666667888999999887544
No 74
>PF13518 HTH_28: Helix-turn-helix domain
Probab=43.43 E-value=14 Score=20.83 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=18.2
Q ss_pred HHhhHHHhcCCCcchhhhcccc
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqN 85 (140)
....+|..+|++...|..|...
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3556899999999999999753
No 75
>PRK00118 putative DNA-binding protein; Validated
Probab=42.56 E-value=63 Score=21.93 Aligned_cols=48 Identities=13% Similarity=0.048 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
++..+..++...|.... ....||..+|++...|..|+...+.+.+...
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~ 65 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLEDYE 65 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 45566666655544432 4566899999999999999876665555543
No 76
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=42.53 E-value=55 Score=23.61 Aligned_cols=31 Identities=16% Similarity=0.097 Sum_probs=23.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..+|++...|++.+..-|.+.++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998765555555543
No 77
>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=42.30 E-value=42 Score=22.33 Aligned_cols=28 Identities=25% Similarity=0.262 Sum_probs=21.2
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....||..+|+++..|..|...-+.+.+
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4567899999999999998765444443
No 78
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=41.81 E-value=35 Score=24.74 Aligned_cols=32 Identities=22% Similarity=0.244 Sum_probs=24.0
Q ss_pred HHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 62 GPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 62 ~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
......||..+|++...|+.|+..-+.+.++.
T Consensus 157 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 188 (194)
T PRK12519 157 GLSQSEIAKRLGIPLGTVKARARQGLLKLREL 188 (194)
T ss_pred CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 34567789999999999999986555555443
No 79
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=41.31 E-value=51 Score=23.68 Aligned_cols=28 Identities=21% Similarity=0.322 Sum_probs=21.3
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....||..+|++...|+.|...-+.+-|
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 4677899999999999998764444433
No 80
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=41.18 E-value=61 Score=22.44 Aligned_cols=46 Identities=15% Similarity=0.095 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..++...|-. ......||..||++...|++....-+.+.|.
T Consensus 107 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 152 (161)
T PRK09047 107 LPARQREAFLLRYWE-----DMDVAETAAAMGCSEGSVKTHCSRATHALAK 152 (161)
T ss_pred CCHHHHHHHHHHHHh-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444444555443322 2235778999999999999887644444443
No 81
>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=41.13 E-value=61 Score=23.08 Aligned_cols=47 Identities=21% Similarity=0.160 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..+|...|- .......||..+|+++..|+.+...-|.+.++.
T Consensus 101 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 147 (170)
T TIGR02959 101 LPDEYREAIRLTEL-----EGLSQQEIAEKLGLSLSGAKSRVQRGRKKLKEL 147 (170)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 44444444444332 223467789999999999999876544444443
No 82
>KOG3755|consensus
Probab=40.81 E-value=62 Score=28.98 Aligned_cols=47 Identities=11% Similarity=-0.016 Sum_probs=30.3
Q ss_pred HHHHHHHhcCCCCHHHHhhH------------HHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 49 RLEAEFERQQYMVGPERLYL------------AHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 49 ~Le~~F~~~~~p~~~~~~~L------------a~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
.+.++|..+..+...+..+. -..+++..+-++.||.+|++.+++...
T Consensus 517 ~~~k~~a~~~~g~~~el~r~~e~~~~~n~~~~EN~~~~~rh~~~l~q~er~a~~~~~~N 575 (769)
T KOG3755|consen 517 LFAKVAAEKSQGWLCELLRWKECPSPENRTLWENYLHIIRHFLKLPQKERDAIYERESN 575 (769)
T ss_pred HHHHHHhhCCCchHHHHHHhhhCCChhhhhhhhcchhHHHhhhccchhhhhHHHhhhcc
Confidence 55566666665443333332 222456667799999999999998765
No 83
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=40.35 E-value=41 Score=23.51 Aligned_cols=29 Identities=21% Similarity=0.178 Sum_probs=21.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....+|..+|++...|+.+...-|.+-++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45778999999999999987654444443
No 84
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=40.18 E-value=36 Score=25.76 Aligned_cols=46 Identities=11% Similarity=0.065 Sum_probs=31.0
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 43 s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
++.+..++...| ........||..+|++...|+.+...-+.+.|+.
T Consensus 186 ~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 186 PEREQLVLSLYY-----QEELNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CHHHHHHHHhHh-----ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 444444444444 2233567889999999999999987666666554
No 85
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=39.76 E-value=44 Score=23.81 Aligned_cols=30 Identities=23% Similarity=0.211 Sum_probs=22.8
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....+|..+|++...|+.++..-|.+.+.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 153 LSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456778999999999999998655555444
No 86
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=39.32 E-value=47 Score=23.87 Aligned_cols=31 Identities=13% Similarity=0.181 Sum_probs=23.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..+|++...|+.+...-|.+.++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQL 176 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998865555555543
No 87
>PRK09480 slmA division inhibitor protein; Provisional
Probab=39.16 E-value=36 Score=24.28 Aligned_cols=36 Identities=17% Similarity=0.101 Sum_probs=29.4
Q ss_pred HHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhh
Q psy10638 52 AEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRI 88 (140)
Q Consensus 52 ~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~ 88 (140)
..|...+. .......||...|++...+-.+|.|+-.
T Consensus 21 ~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~ 56 (194)
T PRK09480 21 QMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKAR 56 (194)
T ss_pred HHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHH
Confidence 34555555 7788899999999999999999999753
No 88
>PF00196 GerE: Bacterial regulatory proteins, luxR family; InterPro: IPR000792 This domain is a DNA-binding, helix-turn-helix (HTH) domain of about 65 amino acids, present in transcription regulators of the LuxR/FixJ family of response regulators. The domain is named after Vibrio fischeri luxR, a transcriptional activator for quorum-sensing control of luminescence. LuxR-type HTH domain proteins occur in a variety of organisms. The DNA-binding HTH domain is usually located in the C-terminal region; the N-terminal region often containing an autoinducer-binding domain or a response regulatory domain. Most luxR-type regulators act as transcription activators, but some can be repressors or have a dual role for different sites. LuxR-type HTH regulators control a wide variety of activities in various biological processes. The luxR-type, DNA-binding HTH domain forms a four-helical bundle structure. The HTH motif comprises the second and third helices, known as the scaffold and recognition helix, respectively. The HTH binds DNA in the major groove, where the N-terminal part of the recognition helix makes most of the DNA contacts. The fourth helix is involved in dimerisation of gerE and traR. Signalling events by one of the four activation mechanisms described below lead to multimerisation of the regulator. The regulators bind DNA as multimers [, , ]. LuxR-type HTH proteins can be activated by one of four different mechanisms: 1) Regulators which belong to a two-component sensory transduction system where the protein is activated by its phosphorylation, generally on an aspartate residue, by a transmembrane kinase [, ]. Some proteins that belong to this category are: Rhizobiaceae fixJ (global regulator inducing expression of nitrogen-fixation genes in microaerobiosis) Escherichia coli and Salmonella typhimurium uhpA (activates hexose phosphate transport gene uhpT) E. coli narL and narP (activate nitrate reductase operon) Enterobacteria rcsB (regulation of exopolysaccharide biosynthesis in enteric and plant pathogenesis) Bordetella pertussis bvgA (virulence factor) Bacillus subtilis coma (involved in expression of late-expressing competence genes) 2) Regulators which are activated, or in very rare cases repressed, when bound to N-acyl homoserine lactones, which are used as quorum sensing molecules in a variety of Gram-negative bacteria []: V. fischeri luxR (activates bioluminescence operon) Agrobacterium tumefaciens traR (regulation of Ti plasmid transfer) Erwinia carotovora carR (control of carbapenem antibiotics biosynthesis) E. carotovora expR (virulence factor for soft rot disease; activates plant tissue macerating enzyme genes) Pseudomonas aeruginosa lasR (activates elastase gene lasB) Erwinia chrysanthemi echR and Erwinia stewartii esaR Pseudomonas chlororaphis phzR (positive regulator of phenazine antibiotic production) Pseudomonas aeruginosa rhlR (activates rhlAB operon and lasB gene) 3) Autonomous effector domain regulators, without a regulatory domain, represented by gerE []. B. subtilis gerE (transcription activator and repressor for the regulation of spore formation) 4) Multiple ligand-binding regulators, exemplified by malT []. E. coli malT (activates maltose operon; MalT binds ATP and maltotriose); GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3SZT_A 3CLO_A 1H0M_A 1L3L_A 3C57_B 1ZLK_B 1ZLJ_H 3C3W_B 1RNL_A 1ZG1_A ....
Probab=38.92 E-value=43 Score=19.54 Aligned_cols=46 Identities=24% Similarity=0.176 Sum_probs=30.6
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.||..+..+|..... ......+|..+|+++..|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~------G~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQ------GMSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHT------TS-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHh------cCCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 467777777755432 2346778999999999999987665555443
No 89
>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=38.60 E-value=57 Score=22.30 Aligned_cols=28 Identities=14% Similarity=0.127 Sum_probs=20.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....||..+|+++..|+.+...-+.+.+
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566899999999999988764444433
No 90
>PRK06930 positive control sigma-like factor; Validated
Probab=38.26 E-value=68 Score=23.49 Aligned_cols=49 Identities=16% Similarity=0.100 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.+++.+..++...|-.. .....+|..+|++...|+.++..-+.+.++.-
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~~l 162 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIARQI 162 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 35666666665544222 23567899999999999999876666555543
No 91
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=37.57 E-value=60 Score=23.31 Aligned_cols=45 Identities=11% Similarity=0.139 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
+++.+..++...|-.. .....||..||+++..|+..+..-+.+.+
T Consensus 128 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~~ 172 (178)
T PRK12529 128 LRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTCL 172 (178)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555543322 24577899999999999998875555544
No 92
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=37.46 E-value=22 Score=21.33 Aligned_cols=20 Identities=10% Similarity=0.218 Sum_probs=16.8
Q ss_pred hhHHHhcCCCcchhhhcccc
Q psy10638 66 LYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 66 ~~La~~lgl~~~qV~vWFqN 85 (140)
..+|..+|++...|+.|-..
T Consensus 4 ~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46799999999999999544
No 93
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=37.01 E-value=54 Score=23.49 Aligned_cols=30 Identities=13% Similarity=0.047 Sum_probs=21.7
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....||..+|++...|+.+...-|.+.+.
T Consensus 152 ~s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 152 YTHREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345778999999999999887644444433
No 94
>PRK10072 putative transcriptional regulator; Provisional
Probab=36.67 E-value=20 Score=23.93 Aligned_cols=25 Identities=28% Similarity=0.248 Sum_probs=21.2
Q ss_pred HhhHHHhcCCCcchhhhcccchhhH
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRRIK 89 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR~k 89 (140)
...||..+|++...|..|...++.-
T Consensus 49 Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 49 IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 5678999999999999999877643
No 95
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=35.65 E-value=64 Score=23.49 Aligned_cols=30 Identities=7% Similarity=0.011 Sum_probs=22.9
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..||++...|+.++.--|.+.|+.
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~ 183 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAAL 183 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999986555555443
No 96
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=35.37 E-value=69 Score=22.54 Aligned_cols=28 Identities=11% Similarity=-0.018 Sum_probs=21.3
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....||..+|+++..|+.+...-|.+-|
T Consensus 130 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 130 SYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4677899999999999998764444433
No 97
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=35.01 E-value=59 Score=23.79 Aligned_cols=31 Identities=13% Similarity=-0.009 Sum_probs=24.5
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....+|..||++...|++++..-|.+.|+..
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l 161 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELL 161 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999999876666665544
No 98
>PRK04217 hypothetical protein; Provisional
Probab=34.94 E-value=83 Score=21.57 Aligned_cols=47 Identities=15% Similarity=0.044 Sum_probs=33.4
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 40 t~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
..++..+..++...|...- ....||..+|++...|...+..-+.+.+
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4578888887776654433 4667899999999999887764444433
No 99
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.74 E-value=30 Score=19.39 Aligned_cols=40 Identities=23% Similarity=0.248 Sum_probs=19.6
Q ss_pred CCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhccc
Q psy10638 40 TIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 40 t~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFq 84 (140)
..++..++..++..+... .....||..||++...|..|..
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 356777888887776533 3456689999999988887753
No 100
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=34.68 E-value=72 Score=24.34 Aligned_cols=32 Identities=19% Similarity=0.149 Sum_probs=24.4
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.....||..||++...|+++...-|.+.|+..
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l 219 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLL 219 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34577899999999999998876565555543
No 101
>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=34.64 E-value=69 Score=22.33 Aligned_cols=26 Identities=23% Similarity=0.038 Sum_probs=19.3
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhh
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRI 88 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~ 88 (140)
.....||..||++...|+....--|.
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~ 164 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIK 164 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 34577899999999999887643333
No 102
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=34.41 E-value=76 Score=22.08 Aligned_cols=28 Identities=14% Similarity=0.252 Sum_probs=20.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....+|..+|++...|+....--+.+.+
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4677899999999999987654444433
No 103
>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=34.04 E-value=70 Score=22.26 Aligned_cols=29 Identities=17% Similarity=0.243 Sum_probs=22.1
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....+|..+|++...|+.+...-+.+-++
T Consensus 128 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 128 SEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999987655555444
No 104
>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=33.85 E-value=26 Score=19.19 Aligned_cols=18 Identities=11% Similarity=0.124 Sum_probs=14.2
Q ss_pred hhHHHhcCCCcchhhhcc
Q psy10638 66 LYLAHTLNLTEAQVKVWF 83 (140)
Q Consensus 66 ~~La~~lgl~~~qV~vWF 83 (140)
..+|..+|++...|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 457889999999999983
No 105
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=33.73 E-value=81 Score=22.83 Aligned_cols=31 Identities=6% Similarity=0.055 Sum_probs=23.5
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..||++...|+.+...-|.+.|+..
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999998865555555543
No 106
>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=33.62 E-value=74 Score=22.38 Aligned_cols=29 Identities=24% Similarity=0.285 Sum_probs=21.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....+|..||++...|+++..--|.+-++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999887544444443
No 107
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=33.50 E-value=79 Score=22.28 Aligned_cols=46 Identities=24% Similarity=0.270 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..+|...|-. ......||..||+++..|+.....-+.+.|+
T Consensus 119 L~~~~r~vl~L~~~~-----g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 164 (173)
T PRK09645 119 LSPEHRAVLVRSYYR-----GWSTAQIAADLGIPEGTVKSRLHYALRALRL 164 (173)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 444444454443322 2245778999999999999987644444444
No 108
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=33.45 E-value=78 Score=22.41 Aligned_cols=29 Identities=10% Similarity=0.139 Sum_probs=22.7
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..+|++...|+.+...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998765555544
No 109
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=33.27 E-value=75 Score=22.84 Aligned_cols=46 Identities=15% Similarity=0.006 Sum_probs=29.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..++...|- .......||..||++...|+.+...-+.+.++
T Consensus 132 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12539 132 LPEKMRLAIQAVKL-----EGLSVAEAATRSGMSESAVKVSVHRGLKALAA 177 (184)
T ss_pred CCHHHHHHHHHHHH-----cCCcHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444444443322 23356778999999999999987654444443
No 110
>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=33.09 E-value=24 Score=19.06 Aligned_cols=24 Identities=13% Similarity=0.380 Sum_probs=19.1
Q ss_pred HhhHHHhcCCCcchhhhcccchhh
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRRI 88 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR~ 88 (140)
...+|..||++...|..|..+..-
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 356788999999999999766543
No 111
>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=33.07 E-value=1e+02 Score=22.35 Aligned_cols=31 Identities=16% Similarity=0.240 Sum_probs=22.9
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..+|++...|+.....-|.+.++..
T Consensus 149 s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l 179 (188)
T TIGR02943 149 ESDEICQELEISTSNCHVLLYRARLSLRACL 179 (188)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999888765555544443
No 112
>TIGR03001 Sig-70_gmx1 RNA polymerase sigma-70 factor, Myxococcales family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in multiple copies in the order Myxococcales. This model supercedes TIGR02233, which has now been retired.
Probab=32.98 E-value=1.1e+02 Score=23.57 Aligned_cols=34 Identities=9% Similarity=0.132 Sum_probs=26.5
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
....||..+|++...|+.+...-|.+-++.....
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~ 212 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRR 212 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHH
Confidence 4677899999999999999987766666655433
No 113
>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=32.33 E-value=58 Score=24.35 Aligned_cols=45 Identities=18% Similarity=0.126 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
+++.+..+|...|-. ......||..+|++...|+.+...-+.+.|
T Consensus 176 L~~~~r~il~l~y~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYE-----ELNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 455666666665532 224578899999999999988765444444
No 114
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=32.30 E-value=69 Score=17.57 Aligned_cols=39 Identities=26% Similarity=0.271 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccc
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqN 85 (140)
.++..+..++...+ . . .....+|..+|++...|..|...
T Consensus 3 ~l~~~e~~i~~~~~-~-g----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLA-E-G----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 35677777665532 1 1 24577899999999999998763
No 115
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=32.23 E-value=57 Score=25.00 Aligned_cols=45 Identities=11% Similarity=0.135 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
+++.+..+|...|-. ......||..||++...|+.|...-+.+.|
T Consensus 206 L~~~~r~vl~l~~~~-----g~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIE-----NLSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhC-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 555566666655432 224577899999999999998765444444
No 116
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=31.85 E-value=78 Score=23.78 Aligned_cols=50 Identities=10% Similarity=0.078 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..++...|... +........+|..+|++...|+.+...-+.+-|+
T Consensus 179 Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 179 LSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555554210 0233346778999999999999987655544444
No 117
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=31.78 E-value=1.1e+02 Score=22.15 Aligned_cols=48 Identities=15% Similarity=0.100 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
+++.+..++...|-. ......||..+|++...|++....-|.+.++..
T Consensus 132 Lp~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (191)
T PRK12520 132 LPPRTGRVFMMREWL-----ELETEEICQELQITATNAWVLLYRARMRLRECL 179 (191)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 444454554444322 234577899999999999998775555555543
No 118
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=31.51 E-value=82 Score=22.75 Aligned_cols=30 Identities=23% Similarity=0.274 Sum_probs=22.2
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....||..+|++...|+..+..-|.+.++
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKE 152 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346778999999999999888644444443
No 119
>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=31.38 E-value=57 Score=18.20 Aligned_cols=21 Identities=14% Similarity=0.167 Sum_probs=16.4
Q ss_pred hHHHhcCCCcchhhhcccchh
Q psy10638 67 YLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 67 ~La~~lgl~~~qV~vWFqNrR 87 (140)
.||..+|++...|..|+.++.
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 467888888888888887763
No 120
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=30.96 E-value=73 Score=25.75 Aligned_cols=53 Identities=17% Similarity=0.085 Sum_probs=37.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.+++.++.+|...|.-.. ........||..+|++...|+.+...-+.+.|+..
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 467777777777663322 23345678899999999999999876666655543
No 121
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=30.81 E-value=1e+02 Score=22.42 Aligned_cols=31 Identities=10% Similarity=-0.017 Sum_probs=23.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..||+++..|+.+...-|.+.++..
T Consensus 134 s~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l 164 (187)
T PRK12516 134 AYEEAAEICGCAVGTIKSRVNRARQRLQEIL 164 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999998875555555543
No 122
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=30.69 E-value=73 Score=24.02 Aligned_cols=31 Identities=10% Similarity=-0.003 Sum_probs=23.3
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..||+++..|+.+...-|.+.++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999998765555555543
No 123
>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=30.57 E-value=30 Score=20.73 Aligned_cols=20 Identities=0% Similarity=0.130 Sum_probs=17.0
Q ss_pred hhHHHhcCCCcchhhhcccc
Q psy10638 66 LYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 66 ~~La~~lgl~~~qV~vWFqN 85 (140)
..+|..+|++...++.|-.+
T Consensus 4 ~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 4 KEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHCcCHHHHHHHHHh
Confidence 46789999999999999754
No 124
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=30.43 E-value=1.1e+02 Score=22.42 Aligned_cols=31 Identities=23% Similarity=0.202 Sum_probs=23.3
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....||..+|+++..|++....-|.+-|+.-
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999998765555555544
No 125
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=30.18 E-value=98 Score=22.47 Aligned_cols=29 Identities=17% Similarity=0.147 Sum_probs=21.1
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..||++...|++.+..-+.+.|+
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45678999999999998876544444443
No 126
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=30.18 E-value=93 Score=22.26 Aligned_cols=30 Identities=20% Similarity=0.038 Sum_probs=23.0
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....+|..||++...|++.+..-|.+.|+
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346778999999999999988655555544
No 127
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=29.99 E-value=79 Score=22.87 Aligned_cols=28 Identities=7% Similarity=-0.101 Sum_probs=21.0
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
....||..+|+++..|+.+...-|.+.|
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 175 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALL 175 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4577899999999999998754444333
No 128
>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=29.68 E-value=69 Score=24.53 Aligned_cols=46 Identities=11% Similarity=0.169 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..+|...|-.. .....||..+|++...|+.+...-+.+-|+
T Consensus 206 L~~~~r~ii~l~~~~g-----~s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 206 LSEREKSIIHCTFEEN-----LSQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CCHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 5566666666665322 245788999999999999987654444443
No 129
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=29.33 E-value=84 Score=22.33 Aligned_cols=30 Identities=17% Similarity=0.123 Sum_probs=22.3
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....||..+|++...|+++...-+.+.+.
T Consensus 136 ~s~~EIA~~lgis~~tV~~~l~Ra~~~~~~ 165 (172)
T PRK09651 136 LTYSEIAHKLGVSVSSVKKYVAKATEHCLL 165 (172)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346788999999999999987654444443
No 130
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.25 E-value=1.2e+02 Score=20.27 Aligned_cols=42 Identities=19% Similarity=0.216 Sum_probs=32.3
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCC-Ccchhhhccc
Q psy10638 39 RTIFTPEQLERLEAEFERQQYMVGPERLYLAHTLNL-TEAQVKVWFQ 84 (140)
Q Consensus 39 Rt~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl-~~~qV~vWFq 84 (140)
+..|+.+....+-..+..... ....+|..+|+ ....+..|-.
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 667899888777666665554 46778999996 8888888865
No 131
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=29.19 E-value=69 Score=24.54 Aligned_cols=46 Identities=11% Similarity=0.148 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..++...|- .......||..+|++...|+.++..-+.+-|+
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 44555555555442 23346778999999999999988655554443
No 132
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=29.16 E-value=44 Score=23.62 Aligned_cols=34 Identities=24% Similarity=0.142 Sum_probs=25.8
Q ss_pred CHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 61 VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 61 ~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.......+|..+|++...|+..+..-|.+.++..
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 3345678999999999999999876666665544
No 133
>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=28.99 E-value=81 Score=18.64 Aligned_cols=35 Identities=29% Similarity=0.345 Sum_probs=24.3
Q ss_pred HHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcc
Q psy10638 45 EQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83 (140)
Q Consensus 45 ~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWF 83 (140)
.++..|+-.|. +...+.. .||..+|++++.|+...
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 35666777777 6655444 78999999998887654
No 134
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=28.98 E-value=91 Score=22.14 Aligned_cols=31 Identities=23% Similarity=0.205 Sum_probs=22.9
Q ss_pred HHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 62 GPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 62 ~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
......+|..||++...|++....-|.+.++
T Consensus 152 ~~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T PRK09641 152 DLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3456778999999999998887655555544
No 135
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.79 E-value=90 Score=22.55 Aligned_cols=47 Identities=19% Similarity=0.193 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..++...|-. ......||..+|++...|+.....-|.+-++.
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 455555555443322 23457789999999999998766444444443
No 136
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=28.60 E-value=1.1e+02 Score=22.08 Aligned_cols=32 Identities=13% Similarity=-0.014 Sum_probs=24.0
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.....+|..+|+++..|+.....-|.+-|+.-
T Consensus 155 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l 186 (193)
T PRK11923 155 LSYEDIASVMQCPVGTVRSRIFRAREAIDKAL 186 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34677899999999999998765555555544
No 137
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=28.24 E-value=1e+02 Score=22.13 Aligned_cols=30 Identities=20% Similarity=0.299 Sum_probs=22.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..+|++...|+.....-|.+.++.
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~ 169 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNM 169 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 457789999999999999876555555443
No 138
>PHA02955 hypothetical protein; Provisional
Probab=27.97 E-value=86 Score=24.18 Aligned_cols=42 Identities=10% Similarity=0.072 Sum_probs=32.6
Q ss_pred HHHHHHHHHHHhc-CCCCHHHHhhHHHhcCCCcchhhhcccch
Q psy10638 45 EQLERLEAEFERQ-QYMVGPERLYLAHTLNLTEAQVKVWFQNR 86 (140)
Q Consensus 45 ~q~~~Le~~F~~~-~~p~~~~~~~La~~lgl~~~qV~vWFqNr 86 (140)
.++..|.+.|.+. ...+..++..++++||+....|..||.+.
T Consensus 61 ~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t~ 103 (213)
T PHA02955 61 KNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKTD 103 (213)
T ss_pred HHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccch
Confidence 4556666666655 57888999999999999987788888753
No 139
>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=27.73 E-value=36 Score=20.27 Aligned_cols=20 Identities=10% Similarity=0.210 Sum_probs=17.1
Q ss_pred HhhHHHhcCCCcchhhhccc
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFq 84 (140)
...+|..+|++...++.|..
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35679999999999999986
No 140
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=27.53 E-value=1.1e+02 Score=22.22 Aligned_cols=29 Identities=14% Similarity=0.051 Sum_probs=21.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..||++...|+++..--|.+-++
T Consensus 129 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 157 (182)
T PRK12511 129 SYQEAAAVLGIPIGTLMSRIGRARAALRA 157 (182)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 46778999999999999987544444443
No 141
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=27.36 E-value=71 Score=24.03 Aligned_cols=42 Identities=12% Similarity=0.089 Sum_probs=33.3
Q ss_pred HHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 49 RLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 49 ~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.-...|....|- .....||...|++..-|..+|.++..-..-
T Consensus 21 aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~a 62 (225)
T PRK11552 21 AALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYLA 62 (225)
T ss_pred HHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHHH
Confidence 334458888877 568889999999999999999998765433
No 142
>PF13551 HTH_29: Winged helix-turn helix
Probab=27.15 E-value=1.5e+02 Score=18.94 Aligned_cols=48 Identities=15% Similarity=0.155 Sum_probs=30.1
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCC-----CCHHHHhh-H-HHhc--CCCcchhhhccc
Q psy10638 37 RVRTIFTPEQLERLEAEFERQQY-----MVGPERLY-L-AHTL--NLTEAQVKVWFQ 84 (140)
Q Consensus 37 r~Rt~~s~~q~~~Le~~F~~~~~-----p~~~~~~~-L-a~~l--gl~~~qV~vWFq 84 (140)
+.+..+++++...|...+...+. ++...... | .... .++...|..|+.
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 33334899999999999998773 34444433 3 3333 355667777763
No 143
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=26.94 E-value=1.4e+02 Score=22.15 Aligned_cols=30 Identities=20% Similarity=0.185 Sum_probs=22.6
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..||+++..|+.+...-|.+.++.
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999986555554443
No 144
>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=26.90 E-value=38 Score=20.39 Aligned_cols=21 Identities=10% Similarity=0.129 Sum_probs=17.6
Q ss_pred HhhHHHhcCCCcchhhhcccc
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqN 85 (140)
...+|..+|++...++.|...
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 356799999999999999764
No 145
>PF15063 TC1: Thyroid cancer protein 1
Probab=26.79 E-value=1.2e+02 Score=19.57 Aligned_cols=36 Identities=19% Similarity=0.247 Sum_probs=28.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCc
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTE 76 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~ 76 (140)
-|....+..|.+.|+...-...++|..|.-.++-..
T Consensus 33 IFe~vn~~qlqrLF~~sGD~kAEeRA~iI~~~~~d~ 68 (79)
T PF15063_consen 33 IFENVNLDQLQRLFQKSGDKKAEERARIIWECAQDP 68 (79)
T ss_pred hhhccCHHHHHHHHHHccchhHHHHHHHHHhhCCCH
Confidence 477888889999999999999999988765555433
No 146
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=26.63 E-value=1.1e+02 Score=22.54 Aligned_cols=29 Identities=7% Similarity=-0.012 Sum_probs=22.0
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
....||..||++...|+++...-|.+.|+
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~ 179 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIA 179 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999987654444443
No 147
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=26.53 E-value=1.4e+02 Score=21.12 Aligned_cols=30 Identities=17% Similarity=0.209 Sum_probs=22.1
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
.-..+|..+|++...|+.....-+.+-++.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 166 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREH 166 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999876544444443
No 148
>PRK12525 RNA polymerase sigma factor; Provisional
Probab=25.94 E-value=1.1e+02 Score=21.50 Aligned_cols=44 Identities=5% Similarity=0.032 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
+++.+..++...|-. .....++|..||++...|+.+..+-+...
T Consensus 119 L~~~~r~v~~L~~~e-----g~s~~EIA~~l~is~~tV~~~l~ra~~~~ 162 (168)
T PRK12525 119 LSGKARAAFLMSQLE-----GLTYVEIGERLGVSLSRIHQYMVEAFKCC 162 (168)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 444444444443322 22457789999999999998875444333
No 149
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=25.89 E-value=1.1e+02 Score=22.52 Aligned_cols=37 Identities=16% Similarity=0.149 Sum_probs=31.7
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchh
Q psy10638 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQV 79 (140)
Q Consensus 43 s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV 79 (140)
...-+..|...++...+.+......+|..||++...|
T Consensus 24 rsAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 24 RSALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hhHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 3456778889999999999999999999999997655
No 150
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=25.80 E-value=2e+02 Score=20.87 Aligned_cols=31 Identities=16% Similarity=0.156 Sum_probs=22.7
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
....+|..||+++..|+++..--|.+.++..
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 176 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEAL 176 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4577899999999999998764444444443
No 151
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=25.18 E-value=88 Score=24.38 Aligned_cols=46 Identities=11% Similarity=0.146 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..+|...|- .......||..+|++...|+.+...-+.+.|+
T Consensus 216 L~~rer~vl~l~y~-----~~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 216 LPERERTVLVLRFF-----ESMTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHHHhc-----CCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45555556666553 23345788999999999999987655444443
No 152
>TIGR02980 SigBFG RNA polymerase sigma-70 factor, sigma-B/F/G subfamily. This group of similar sigma-70 factors includes clades found in Bacilli (including the sporulation factors SigF:TIGR02885 and SigG:TIGR02850 as well as SigB:TIGR02941), and the high GC gram positive bacteria (Actinobacteria) where a variable number of them are found depending on the lineage.
Probab=25.11 E-value=1.2e+02 Score=22.57 Aligned_cols=45 Identities=13% Similarity=0.129 Sum_probs=30.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
.+++.+..+|...|-. ......||..+|++...|..|...-+.+.
T Consensus 178 ~L~~~~r~vl~l~y~~-----~~s~~eIA~~lgis~~~v~~~~~ra~~~L 222 (227)
T TIGR02980 178 ALPERERRILLLRFFE-----DKTQSEIAERLGISQMHVSRLLRRALKKL 222 (227)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4666666666665532 23467789999999999999875444333
No 153
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=25.07 E-value=1.5e+02 Score=21.96 Aligned_cols=30 Identities=20% Similarity=0.393 Sum_probs=22.5
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..+|++...|+.+...-|.+-|+.
T Consensus 166 s~~EIAe~lgis~~tV~~~l~RAr~~Lr~~ 195 (206)
T PRK12544 166 ETNEICHAVDLSVSNLNVLLYRARLRLREC 195 (206)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 357789999999999999876555554443
No 154
>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=24.77 E-value=99 Score=17.01 Aligned_cols=21 Identities=24% Similarity=0.344 Sum_probs=17.7
Q ss_pred HHhhHHHhcCCCcchhhhccc
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFq 84 (140)
....+|..++++...|..|..
T Consensus 17 s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 456788999999999999875
No 155
>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=24.66 E-value=1.2e+02 Score=21.70 Aligned_cols=31 Identities=19% Similarity=0.117 Sum_probs=22.2
Q ss_pred CCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 60 MVGPERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 60 p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
........||..+|++...|++++.--|.+-
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L 193 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSIDNALQRVKRKL 193 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3444567889999999999998775444433
No 156
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=24.59 E-value=1.3e+02 Score=21.84 Aligned_cols=30 Identities=20% Similarity=0.107 Sum_probs=21.9
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.....||..+|++...|++.+..-|.+.++
T Consensus 171 ~s~~EIA~~lgis~~tV~~~l~rar~~Lr~ 200 (208)
T PRK08295 171 KSYQEIAEELNRHVKSIDNALQRVKRKLEK 200 (208)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 456778999999999998876654444444
No 157
>PRK12528 RNA polymerase sigma factor; Provisional
Probab=24.53 E-value=1.2e+02 Score=20.98 Aligned_cols=22 Identities=23% Similarity=0.238 Sum_probs=17.9
Q ss_pred HHhhHHHhcCCCcchhhhcccc
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqN 85 (140)
....||..+|++...|+++...
T Consensus 131 s~~EIA~~l~is~~tV~~~l~r 152 (161)
T PRK12528 131 GYGEIATELGISLATVKRYLNK 152 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4567899999999999988653
No 158
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=24.43 E-value=1.1e+02 Score=23.59 Aligned_cols=47 Identities=11% Similarity=0.137 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
+++.+..+|...|-. ......||..+|++...|+.....-+.+-|+.
T Consensus 213 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~ 259 (268)
T PRK06288 213 LPEREKKVLILYYYE-----DLTLKEIGKVLGVTESRISQLHTKAVLQLRAK 259 (268)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 555555566555532 23467789999999999988776555555544
No 159
>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=24.33 E-value=43 Score=18.08 Aligned_cols=23 Identities=13% Similarity=0.030 Sum_probs=17.9
Q ss_pred HhhHHHhcCCCcchhhhcccchh
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR 87 (140)
...+|..||++...|..|..+.+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 35678889999999999876553
No 160
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=23.81 E-value=87 Score=24.19 Aligned_cols=46 Identities=17% Similarity=0.115 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..+|...|-. ......||..+|++...|+.+..--+.+.|+
T Consensus 204 L~~~~r~vl~l~y~~-----~~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~ 249 (256)
T PRK07408 204 LEERTREVLEFVFLH-----DLTQKEAAERLGISPVTVSRRVKKGLDQLKK 249 (256)
T ss_pred CCHHHHHHHHHHHHC-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 455555555555532 3356778999999999999987654444444
No 161
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=23.56 E-value=1.1e+02 Score=21.94 Aligned_cols=26 Identities=19% Similarity=0.150 Sum_probs=19.1
Q ss_pred HHHhhHHHhcCCCcchhhhcccchhh
Q psy10638 63 PERLYLAHTLNLTEAQVKVWFQNRRI 88 (140)
Q Consensus 63 ~~~~~La~~lgl~~~qV~vWFqNrR~ 88 (140)
.....||..||++...|+.....-|.
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~ 179 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLA 179 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHH
Confidence 35677899999999998876543333
No 162
>PRK12540 RNA polymerase sigma factor; Provisional
Probab=22.99 E-value=1.4e+02 Score=21.51 Aligned_cols=30 Identities=13% Similarity=-0.035 Sum_probs=22.2
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
....||..||++...|+.....-|.+-++.
T Consensus 129 s~~EIA~~Lgis~~tV~~~l~RAr~~Lr~~ 158 (182)
T PRK12540 129 SYEDAAAICGCAVGTIKSRVNRARSKLSAL 158 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 467789999999999999876444444443
No 163
>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=22.98 E-value=56 Score=22.46 Aligned_cols=31 Identities=26% Similarity=0.141 Sum_probs=22.7
Q ss_pred CHHHHhhHHHhcCCCcchhhhcccchhhHHH
Q psy10638 61 VGPERLYLAHTLNLTEAQVKVWFQNRRIKWR 91 (140)
Q Consensus 61 ~~~~~~~La~~lgl~~~qV~vWFqNrR~k~k 91 (140)
.......||..+|+++..|+++..--|.+.+
T Consensus 120 ~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 120 KEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred ccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3445678999999999999998764444433
No 164
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=22.79 E-value=59 Score=23.54 Aligned_cols=34 Identities=21% Similarity=0.063 Sum_probs=24.9
Q ss_pred CCHHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 60 MVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 60 p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
........||..+|++...|+.+...-|.+.|+.
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 186 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLREL 186 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3344567889999999999998876555555543
No 165
>PF01710 HTH_Tnp_IS630: Transposase; InterPro: IPR002622 Transposase proteins are necessary for efficient DNA transposition. This entry includes insertion sequences from Synechocystis sp. (strain PCC 6803) three of which are characterised as homologous to bacterial IS5- and IS4- and to several members of the IS630-Tc1-mariner superfamily []. More information about these proteins can be found at Protein of the Month: Transposase [].
Probab=22.56 E-value=1.2e+02 Score=20.54 Aligned_cols=37 Identities=16% Similarity=0.257 Sum_probs=25.7
Q ss_pred CHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhccc
Q psy10638 43 TPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 43 s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFq 84 (140)
+-..+...-.+|+... ....+|..++++...|..||.
T Consensus 4 S~DlR~rVl~~~~~g~-----s~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 4 SLDLRQRVLAYIEKGK-----SIREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred CHHHHHHHHHHHHccc-----hHHHHHHHhCcHHHHHHHHHH
Confidence 3444444455666543 345578899999999999998
No 166
>KOG0773|consensus
Probab=22.48 E-value=65 Score=25.96 Aligned_cols=38 Identities=34% Similarity=0.501 Sum_probs=32.9
Q ss_pred HhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 55 ERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 55 ~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
..+.|++..+...++....++..+|.+||-|.+.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 45778999999999999999999999999998877666
No 167
>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=22.31 E-value=1.2e+02 Score=16.82 Aligned_cols=37 Identities=14% Similarity=0.286 Sum_probs=22.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcc
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWF 83 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWF 83 (140)
++.++...+...+... .....||..+|++...|.-++
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 4554445554545444 246778999999998877665
No 168
>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=21.93 E-value=55 Score=17.33 Aligned_cols=23 Identities=17% Similarity=0.235 Sum_probs=18.9
Q ss_pred HhhHHHhcCCCcchhhhcccchh
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR 87 (140)
...+|..+|+++..|..|..+.+
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 34678999999999999987753
No 169
>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=21.82 E-value=64 Score=23.36 Aligned_cols=34 Identities=21% Similarity=0.131 Sum_probs=25.3
Q ss_pred CHHHHhhHHHhcCCCcchhhhcccchhhHHHHHh
Q psy10638 61 VGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQH 94 (140)
Q Consensus 61 ~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~ 94 (140)
.......||..||++...|+++...-|.+.|+..
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 3345678899999999999999875555555443
No 170
>PRK10403 transcriptional regulator NarP; Provisional
Probab=21.77 E-value=1.3e+02 Score=21.01 Aligned_cols=49 Identities=24% Similarity=0.258 Sum_probs=34.8
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhH
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHL 95 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~ 95 (140)
.++..+..+|.....- .....||..++++++.|+.+..+=+.|-....+
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 4788888887654322 335678999999999999998776666544443
No 171
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.60 E-value=1.9e+02 Score=18.51 Aligned_cols=44 Identities=14% Similarity=0.209 Sum_probs=31.7
Q ss_pred CCCHHHHHHHHHHHHhc-----CCCCHHHHhhHHHhcCCCcchhhhccc
Q psy10638 41 IFTPEQLERLEAEFERQ-----QYMVGPERLYLAHTLNLTEAQVKVWFQ 84 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~-----~~p~~~~~~~La~~lgl~~~qV~vWFq 84 (140)
.++.+++..|...|... .+.+..+...+...+|++...|..+|.
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 36778888899888753 256677777766667888777777664
No 172
>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=21.37 E-value=1.3e+02 Score=23.43 Aligned_cols=49 Identities=12% Similarity=0.041 Sum_probs=33.2
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 41 IFTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 41 ~~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
.+++.+..+|..+|-. -.......||..+|++...|+....+-..|.|+
T Consensus 218 ~L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 218 SLDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred cCCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3666777777777632 112345788999999999998877655555544
No 173
>PRK06424 transcription factor; Provisional
Probab=21.36 E-value=1.9e+02 Score=20.71 Aligned_cols=25 Identities=8% Similarity=-0.039 Sum_probs=20.6
Q ss_pred HhhHHHhcCCCcchhhhcccchhhH
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRRIK 89 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR~k 89 (140)
...||..+|++...|..|..+.+.-
T Consensus 100 Q~eLA~~iGvs~stIskiE~G~~~P 124 (144)
T PRK06424 100 QADLAAKIFERKNVIASIERGDLLP 124 (144)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCCCC
Confidence 5678999999999999999876543
No 174
>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=21.16 E-value=1.2e+02 Score=21.42 Aligned_cols=44 Identities=11% Similarity=0.129 Sum_probs=26.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKW 90 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~ 90 (140)
+++.+..++...| ........||..||++...|+.=...-|.+.
T Consensus 141 L~~~~r~vi~l~~-----~~g~s~~eIA~~lgis~~~v~~~l~Ra~~~L 184 (189)
T TIGR02984 141 LPEDYREVILLRH-----LEGLSFAEVAERMDRSEGAVSMLWVRGLARL 184 (189)
T ss_pred CCHHHHHHHHHHH-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 4455555554433 2334567789999999988887554333333
No 175
>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=21.07 E-value=46 Score=24.76 Aligned_cols=34 Identities=21% Similarity=0.220 Sum_probs=28.4
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHHhHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEF 97 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~ 97 (140)
.+.+|+.-++++...|-.|..|.+...+....-.
T Consensus 16 t~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~yK 49 (186)
T PF04936_consen 16 TIDELADYFDVSRTSVSVWIKNGKDPKRAKPKYK 49 (186)
T ss_pred cHHHHHHHHccCHHHHHHHHHcCCCcccccchhh
Confidence 4677899999999999999999998877765433
No 176
>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=20.94 E-value=1.9e+02 Score=19.22 Aligned_cols=38 Identities=18% Similarity=0.371 Sum_probs=20.0
Q ss_pred HHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHHHhHHHH
Q psy10638 47 LERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQHLEFQ 98 (140)
Q Consensus 47 ~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~~~~~~ 98 (140)
+.+.+-.|..++||...-... + -.|||.+|+++.....
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 334555588999987442111 0 1478888888875443
No 177
>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=20.69 E-value=58 Score=18.23 Aligned_cols=23 Identities=9% Similarity=-0.052 Sum_probs=19.5
Q ss_pred HhhHHHhcCCCcchhhhcccchh
Q psy10638 65 RLYLAHTLNLTEAQVKVWFQNRR 87 (140)
Q Consensus 65 ~~~La~~lgl~~~qV~vWFqNrR 87 (140)
...||..+|++...|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46789999999999999987654
No 178
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=20.64 E-value=60 Score=19.28 Aligned_cols=20 Identities=5% Similarity=-0.019 Sum_probs=16.1
Q ss_pred hhHHHhcCCCcchhhhcccc
Q psy10638 66 LYLAHTLNLTEAQVKVWFQN 85 (140)
Q Consensus 66 ~~La~~lgl~~~qV~vWFqN 85 (140)
..+|..+|+++..|+.|...
T Consensus 4 ~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 4 GEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred HHHHHHHCcCHHHHHHHHHC
Confidence 45788999999999999543
No 179
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=20.30 E-value=88 Score=22.56 Aligned_cols=32 Identities=16% Similarity=0.160 Sum_probs=24.3
Q ss_pred HHHHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 62 GPERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 62 ~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
......||..||++...|+++...-+.+-|+.
T Consensus 150 g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~ 181 (188)
T PRK09640 150 ELEFQEIADIMHMGLSATKMRYKRALDKLREK 181 (188)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999986555555543
No 180
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=20.09 E-value=1.2e+02 Score=23.34 Aligned_cols=46 Identities=11% Similarity=0.102 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHhhHHHhcCCCcchhhhcccchhhHHHH
Q psy10638 42 FTPEQLERLEAEFERQQYMVGPERLYLAHTLNLTEAQVKVWFQNRRIKWRK 92 (140)
Q Consensus 42 ~s~~q~~~Le~~F~~~~~p~~~~~~~La~~lgl~~~qV~vWFqNrR~k~kk 92 (140)
+++.+..+|...|- .......||..+|++...|+.+...-+.+.|+
T Consensus 206 L~~~er~vi~l~y~-----e~~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 251 (257)
T PRK05911 206 LEEKERKVMALYYY-----EELVLKEIGKILGVSESRVSQIHSKALLKLRA 251 (257)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 55555566666553 22346778999999999998886544444443
No 181
>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=20.04 E-value=1.6e+02 Score=23.01 Aligned_cols=30 Identities=13% Similarity=0.096 Sum_probs=23.7
Q ss_pred HHhhHHHhcCCCcchhhhcccchhhHHHHH
Q psy10638 64 ERLYLAHTLNLTEAQVKVWFQNRRIKWRKQ 93 (140)
Q Consensus 64 ~~~~La~~lgl~~~qV~vWFqNrR~k~kk~ 93 (140)
...+||..||+++..|+..+..-|.+.+..
T Consensus 126 s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~~ 155 (281)
T TIGR02957 126 PYEEIASIVGKSEANCRQLVSRARRHLDAR 155 (281)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHhh
Confidence 356789999999999999987666666554
Done!