Query psy9869
Match_columns 111
No_of_seqs 105 out of 1054
Neff 8.0
Searched_HMMs 46136
Date Fri Aug 16 21:42:47 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy9869.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/9869hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0488|consensus 99.7 8.8E-18 1.9E-22 124.9 7.7 69 15-83 165-233 (309)
2 KOG0489|consensus 99.7 4E-18 8.7E-23 124.3 5.1 67 19-85 156-222 (261)
3 KOG0487|consensus 99.7 7.3E-18 1.6E-22 124.4 5.4 66 18-83 231-296 (308)
4 PF00046 Homeobox: Homeobox do 99.7 2.8E-17 6.2E-22 93.9 6.2 57 23-79 1-57 (57)
5 KOG0850|consensus 99.7 1.5E-17 3.3E-22 117.6 5.7 66 17-82 117-182 (245)
6 KOG0843|consensus 99.7 2.1E-17 4.5E-22 113.2 5.7 64 21-84 101-164 (197)
7 KOG0484|consensus 99.7 1.8E-17 3.9E-22 104.5 4.9 61 20-80 15-75 (125)
8 KOG2251|consensus 99.7 2.1E-17 4.5E-22 116.3 5.3 68 17-84 32-99 (228)
9 KOG0485|consensus 99.7 1.3E-16 2.8E-21 112.3 6.2 66 18-83 100-165 (268)
10 KOG0842|consensus 99.6 2.4E-16 5.3E-21 116.4 5.3 64 20-83 151-214 (307)
11 KOG0492|consensus 99.6 7E-16 1.5E-20 107.9 6.2 64 22-85 144-207 (246)
12 KOG0848|consensus 99.6 2.2E-16 4.8E-21 113.9 3.6 62 24-85 201-262 (317)
13 KOG3802|consensus 99.6 2.1E-16 4.6E-21 119.2 3.7 77 6-82 278-354 (398)
14 KOG0494|consensus 99.6 1.4E-15 3.1E-20 109.5 6.5 62 21-82 140-201 (332)
15 cd00086 homeodomain Homeodomai 99.6 7.5E-15 1.6E-19 83.9 6.5 57 24-80 2-58 (59)
16 smart00389 HOX Homeodomain. DN 99.6 6.6E-15 1.4E-19 83.5 5.9 55 24-78 2-56 (56)
17 COG5576 Homeodomain-containing 99.6 3.8E-15 8.3E-20 101.2 5.6 68 16-83 45-112 (156)
18 TIGR01565 homeo_ZF_HD homeobox 99.6 3.3E-15 7E-20 85.9 4.3 53 22-74 1-57 (58)
19 KOG0493|consensus 99.5 4.9E-15 1.1E-19 106.9 4.7 60 22-81 246-305 (342)
20 KOG0491|consensus 99.5 9.6E-15 2.1E-19 99.0 1.6 65 21-85 99-163 (194)
21 KOG0483|consensus 99.5 1.2E-13 2.7E-18 96.8 5.9 64 22-85 50-113 (198)
22 KOG0486|consensus 99.4 2E-13 4.3E-18 100.5 4.9 62 20-81 110-171 (351)
23 KOG0844|consensus 99.4 2.1E-13 4.5E-18 100.4 2.9 64 20-83 179-242 (408)
24 KOG4577|consensus 99.4 1.2E-12 2.6E-17 95.7 5.5 69 18-86 163-231 (383)
25 KOG0847|consensus 99.3 5.8E-13 1.2E-17 94.2 3.3 65 18-82 163-227 (288)
26 KOG0490|consensus 99.2 2.2E-11 4.8E-16 86.4 3.2 63 19-81 57-119 (235)
27 KOG1168|consensus 99.1 1.2E-11 2.5E-16 90.7 1.5 61 20-80 307-367 (385)
28 KOG0849|consensus 99.1 2.6E-10 5.7E-15 86.5 5.7 64 19-82 173-236 (354)
29 KOG0775|consensus 99.0 2.6E-10 5.6E-15 82.9 4.6 51 28-78 182-232 (304)
30 KOG0774|consensus 98.9 4.1E-10 8.9E-15 81.6 1.9 75 22-96 188-265 (334)
31 PF05920 Homeobox_KN: Homeobox 98.7 1.3E-08 2.9E-13 54.3 2.9 34 43-76 7-40 (40)
32 KOG2252|consensus 98.4 6.3E-07 1.4E-11 70.7 5.9 60 18-77 416-475 (558)
33 KOG0490|consensus 98.1 3.2E-06 6.9E-11 59.9 4.4 67 16-82 147-213 (235)
34 KOG1146|consensus 97.7 6.5E-05 1.4E-09 64.5 5.1 62 21-82 902-963 (1406)
35 PF11569 Homez: Homeodomain le 97.4 0.00017 3.7E-09 40.9 2.7 43 33-75 9-51 (56)
36 KOG0773|consensus 96.6 0.0026 5.7E-08 48.0 3.9 61 22-82 239-302 (342)
37 KOG3623|consensus 95.7 0.02 4.2E-07 47.5 4.7 48 34-81 568-615 (1007)
38 PF04218 CENP-B_N: CENP-B N-te 95.5 0.062 1.3E-06 29.9 5.0 47 23-74 1-47 (53)
39 PF04545 Sigma70_r4: Sigma-70, 87.3 2.1 4.5E-05 22.9 4.4 46 28-78 4-49 (50)
40 PF01527 HTH_Tnp_1: Transposas 80.7 1.9 4E-05 24.9 2.5 46 24-73 2-47 (76)
41 KOG1146|consensus 75.3 6.5 0.00014 35.2 5.0 61 21-81 704-764 (1406)
42 PF09607 BrkDBD: Brinker DNA-b 75.2 7.7 0.00017 22.1 3.8 45 25-71 2-47 (58)
43 cd06171 Sigma70_r4 Sigma70, re 73.7 5.9 0.00013 20.3 3.1 43 29-76 11-53 (55)
44 PF10668 Phage_terminase: Phag 73.4 2.1 4.6E-05 24.5 1.2 20 52-71 25-44 (60)
45 PRK03975 tfx putative transcri 68.8 31 0.00067 23.1 6.2 52 26-83 4-55 (141)
46 PF04967 HTH_10: HTH DNA bindi 68.3 13 0.00028 20.7 3.6 42 29-70 1-44 (53)
47 PF13518 HTH_28: Helix-turn-he 64.9 6.8 0.00015 20.6 2.1 23 52-74 15-37 (52)
48 cd04761 HTH_MerR-SF Helix-Turn 61.8 6.5 0.00014 20.4 1.6 23 52-74 3-25 (49)
49 KOG3755|consensus 60.8 3.7 8E-05 33.9 0.7 47 36-82 706-759 (769)
50 PF13384 HTH_23: Homeodomain-l 58.7 7.4 0.00016 20.5 1.5 23 50-72 18-40 (50)
51 PRK09480 slmA division inhibit 57.5 13 0.00028 24.9 2.8 38 38-76 20-57 (194)
52 PRK06759 RNA polymerase factor 55.7 42 0.00091 21.6 5.1 30 50-79 123-152 (154)
53 PRK10072 putative transcriptio 54.7 7.5 0.00016 24.3 1.2 41 28-75 32-72 (96)
54 PF13411 MerR_1: MerR HTH fami 54.4 9.9 0.00021 21.3 1.6 21 52-72 3-23 (69)
55 PF06056 Terminase_5: Putative 54.3 11 0.00023 21.3 1.7 20 52-71 16-35 (58)
56 PF00196 GerE: Bacterial regul 53.8 35 0.00077 18.5 4.0 46 28-79 3-48 (58)
57 cd00569 HTH_Hin_like Helix-tur 53.7 22 0.00047 16.0 3.9 37 29-70 6-42 (42)
58 PF08281 Sigma70_r4_2: Sigma-7 53.5 13 0.00028 19.9 1.9 41 29-74 11-51 (54)
59 KOG0773|consensus 53.1 34 0.00074 25.7 4.7 42 39-80 114-155 (342)
60 PRK09646 RNA polymerase sigma 52.7 36 0.00078 23.1 4.5 31 50-80 159-189 (194)
61 PRK11924 RNA polymerase sigma 51.9 23 0.00049 23.2 3.3 32 51-82 143-174 (179)
62 PRK09639 RNA polymerase sigma 50.8 46 0.001 21.7 4.7 32 51-82 129-160 (166)
63 PF00376 MerR: MerR family reg 50.6 12 0.00027 19.1 1.4 20 52-71 2-21 (38)
64 cd04762 HTH_MerR-trunc Helix-T 50.0 14 0.00031 18.6 1.7 24 52-75 3-26 (49)
65 cd04763 HTH_MlrA-like Helix-Tu 49.4 14 0.00031 20.8 1.8 21 52-72 3-23 (68)
66 PRK12526 RNA polymerase sigma 48.9 59 0.0013 22.4 5.2 32 50-81 170-201 (206)
67 PRK09644 RNA polymerase sigma 48.4 21 0.00044 23.6 2.7 34 50-83 125-158 (165)
68 PRK12514 RNA polymerase sigma 48.2 31 0.00068 23.0 3.6 30 51-80 147-176 (179)
69 PRK09642 RNA polymerase sigma 48.1 25 0.00054 22.9 3.0 30 52-81 125-154 (160)
70 PF13443 HTH_26: Cro/C1-type H 47.7 12 0.00026 20.6 1.2 24 51-74 12-35 (63)
71 COG4367 Uncharacterized protei 47.6 31 0.00066 21.5 3.0 40 28-67 2-41 (97)
72 cd04764 HTH_MlrA-like_sg1 Heli 47.2 17 0.00037 20.4 1.9 21 52-72 3-23 (67)
73 smart00595 MADF subfamily of S 47.2 45 0.00097 19.6 3.8 35 53-87 31-65 (89)
74 PF04936 DUF658: Protein of un 47.1 9.1 0.0002 26.5 0.8 35 49-83 14-48 (186)
75 TIGR03879 near_KaiC_dom probab 46.9 8.1 0.00018 23.0 0.4 32 41-72 24-55 (73)
76 PF00424 REV: REV protein (ant 46.2 71 0.0015 19.9 5.4 43 34-90 14-56 (91)
77 PRK09652 RNA polymerase sigma 45.2 59 0.0013 21.3 4.5 31 51-81 146-176 (182)
78 cd01104 HTH_MlrA-CarA Helix-Tu 44.4 19 0.00041 20.1 1.7 21 52-72 3-23 (68)
79 COG2963 Transposase and inacti 44.3 62 0.0014 20.1 4.3 44 26-73 5-49 (116)
80 PRK12519 RNA polymerase sigma 44.3 37 0.00081 22.9 3.5 34 48-81 156-189 (194)
81 TIGR02989 Sig-70_gvs1 RNA poly 44.0 68 0.0015 20.6 4.7 29 50-78 128-156 (159)
82 PRK04217 hypothetical protein; 43.9 85 0.0018 20.1 5.3 50 25-79 39-88 (110)
83 PRK12518 RNA polymerase sigma 43.6 36 0.00077 22.5 3.3 35 47-81 134-168 (175)
84 PRK12512 RNA polymerase sigma 43.5 65 0.0014 21.5 4.6 32 50-81 148-179 (184)
85 cd01392 HTH_LacI Helix-turn-he 42.4 11 0.00023 19.9 0.5 21 54-74 2-22 (52)
86 PRK09413 IS2 repressor TnpA; R 42.3 89 0.0019 19.8 8.4 45 24-72 8-52 (121)
87 PRK12543 RNA polymerase sigma 42.0 53 0.0011 21.9 4.0 35 50-84 134-168 (179)
88 TIGR02937 sigma70-ECF RNA poly 41.9 32 0.00068 21.4 2.7 29 51-79 128-156 (158)
89 TIGR02939 RpoE_Sigma70 RNA pol 40.6 37 0.00079 22.7 3.0 34 48-81 153-186 (190)
90 PF08280 HTH_Mga: M protein tr 40.4 54 0.0012 18.1 3.2 36 32-71 6-41 (59)
91 COG3413 Predicted DNA binding 40.1 61 0.0013 22.7 4.2 42 28-69 155-198 (215)
92 PRK09640 RNA polymerase sigma 40.0 42 0.0009 22.7 3.2 32 50-81 151-182 (188)
93 TIGR02985 Sig70_bacteroi1 RNA 40.0 37 0.0008 21.7 2.9 29 51-79 131-159 (161)
94 PRK09648 RNA polymerase sigma 39.5 72 0.0016 21.4 4.3 30 50-79 156-185 (189)
95 PF13936 HTH_38: Helix-turn-he 39.1 46 0.001 17.3 2.6 39 28-71 4-42 (44)
96 TIGR02950 SigM_subfam RNA poly 39.0 36 0.00078 21.9 2.7 33 47-79 119-151 (154)
97 PRK06930 positive control sigm 38.9 1.2E+02 0.0026 20.7 5.4 49 28-81 114-162 (170)
98 TIGR02948 SigW_bacill RNA poly 38.6 42 0.00091 22.3 3.0 32 49-80 152-183 (187)
99 PF01381 HTH_3: Helix-turn-hel 38.3 18 0.00039 19.2 1.0 23 52-74 12-34 (55)
100 TIGR02947 SigH_actino RNA poly 37.7 61 0.0013 21.9 3.8 36 47-82 145-180 (193)
101 PF05703 Auxin_canalis: Auxin 37.5 1.7E+02 0.0036 21.6 9.5 15 62-76 99-113 (242)
102 PRK05602 RNA polymerase sigma 37.4 47 0.001 22.3 3.2 33 51-83 146-178 (186)
103 COG2944 Predicted transcriptio 37.2 24 0.00052 22.5 1.5 41 28-75 43-83 (104)
104 smart00422 HTH_MERR helix_turn 36.5 26 0.00057 19.5 1.5 21 52-72 3-23 (70)
105 PRK11552 putative DNA-binding 36.5 39 0.00084 23.8 2.7 45 34-80 19-63 (225)
106 TIGR01764 excise DNA binding d 36.3 26 0.00057 17.7 1.4 23 52-74 4-26 (49)
107 PRK06986 fliA flagellar biosyn 35.9 68 0.0015 22.6 3.9 31 50-80 201-231 (236)
108 PRK12513 RNA polymerase sigma 35.5 57 0.0012 22.0 3.3 35 47-81 153-187 (194)
109 TIGR03070 couple_hipB transcri 35.3 23 0.00049 18.7 1.1 23 52-74 18-40 (58)
110 PRK08301 sporulation sigma fac 35.2 1E+02 0.0022 21.6 4.7 32 50-81 199-230 (234)
111 PF14549 P22_Cro: DNA-binding 35.1 28 0.00061 19.8 1.4 18 52-69 12-29 (60)
112 PRK12530 RNA polymerase sigma 34.6 62 0.0013 21.9 3.4 30 51-80 152-181 (189)
113 PRK14996 TetR family transcrip 34.5 49 0.0011 22.2 2.9 41 35-76 15-55 (192)
114 PRK12522 RNA polymerase sigma 34.3 64 0.0014 21.3 3.4 31 51-81 137-167 (173)
115 TIGR02959 SigZ RNA polymerase 34.2 1.4E+02 0.003 19.7 5.4 32 51-82 118-149 (170)
116 PF13730 HTH_36: Helix-turn-he 34.1 45 0.00098 17.7 2.2 25 48-72 24-48 (55)
117 TIGR02999 Sig-70_X6 RNA polyme 33.9 49 0.0011 22.0 2.8 29 51-79 152-180 (183)
118 TIGR02859 spore_sigH RNA polym 33.8 46 0.001 22.4 2.6 33 47-79 163-195 (198)
119 PRK12538 RNA polymerase sigma 33.4 68 0.0015 22.8 3.6 33 50-82 188-220 (233)
120 cd00093 HTH_XRE Helix-turn-hel 33.0 28 0.0006 17.3 1.2 23 52-74 15-37 (58)
121 COG1905 NuoE NADH:ubiquinone o 32.8 86 0.0019 21.5 3.8 36 31-66 25-60 (160)
122 PRK11511 DNA-binding transcrip 32.6 1E+02 0.0022 19.7 4.0 26 48-73 24-49 (127)
123 smart00027 EH Eps15 homology d 32.3 1.2E+02 0.0025 18.2 4.2 44 28-71 3-51 (96)
124 PF12728 HTH_17: Helix-turn-he 32.2 32 0.00069 18.1 1.3 24 52-75 4-27 (51)
125 PRK09641 RNA polymerase sigma 31.6 63 0.0014 21.5 3.0 31 50-80 153-183 (187)
126 PRK12515 RNA polymerase sigma 31.5 1.6E+02 0.0035 19.7 5.5 31 51-81 149-179 (189)
127 PRK09647 RNA polymerase sigma 31.3 70 0.0015 22.1 3.3 29 52-80 157-185 (203)
128 PRK12532 RNA polymerase sigma 31.3 77 0.0017 21.4 3.4 31 51-81 154-184 (195)
129 TIGR02952 Sig70_famx2 RNA poly 31.1 1.2E+02 0.0025 19.7 4.2 30 50-79 139-168 (170)
130 TIGR02983 SigE-fam_strep RNA p 30.9 59 0.0013 21.1 2.7 30 50-79 127-156 (162)
131 cd01105 HTH_GlnR-like Helix-Tu 30.9 35 0.00076 20.5 1.5 20 52-71 4-23 (88)
132 PRK11923 algU RNA polymerase s 30.8 73 0.0016 21.4 3.3 33 50-82 155-187 (193)
133 PRK06811 RNA polymerase factor 30.7 1.2E+02 0.0026 20.4 4.3 29 51-79 149-177 (189)
134 PRK09975 DNA-binding transcrip 29.9 56 0.0012 22.2 2.6 43 34-77 17-59 (213)
135 PRK08583 RNA polymerase sigma 29.5 92 0.002 22.2 3.7 29 51-79 223-251 (257)
136 cd01106 HTH_TipAL-Mta Helix-Tu 29.3 42 0.00092 20.6 1.7 23 52-74 3-25 (103)
137 TIGR02607 antidote_HigA addict 29.0 34 0.00073 19.5 1.2 23 52-74 21-43 (78)
138 PRK07408 RNA polymerase sigma 28.9 75 0.0016 22.9 3.2 32 50-81 220-251 (256)
139 PRK05657 RNA polymerase sigma 28.9 1.6E+02 0.0034 22.2 5.0 52 29-81 263-314 (325)
140 PRK12537 RNA polymerase sigma 28.7 72 0.0016 21.3 2.9 29 51-79 151-179 (182)
141 cd04774 HTH_YfmP Helix-Turn-He 28.3 47 0.001 20.4 1.8 22 52-73 3-24 (96)
142 PRK12541 RNA polymerase sigma 28.2 65 0.0014 21.0 2.6 29 51-79 130-158 (161)
143 PRK12524 RNA polymerase sigma 28.1 81 0.0017 21.4 3.1 31 51-81 154-184 (196)
144 TIGR02954 Sig70_famx3 RNA poly 28.0 73 0.0016 20.9 2.8 29 51-79 137-165 (169)
145 smart00421 HTH_LUXR helix_turn 27.9 94 0.002 15.8 4.8 43 28-76 3-45 (58)
146 PHA01976 helix-turn-helix prot 27.7 37 0.00081 18.8 1.2 23 52-74 18-40 (67)
147 KOG0150|consensus 27.7 1.2E+02 0.0026 23.2 4.0 11 66-76 16-26 (336)
148 PRK12546 RNA polymerase sigma 27.7 69 0.0015 21.8 2.7 32 51-82 131-162 (188)
149 PRK13919 putative RNA polymera 27.7 72 0.0016 21.3 2.8 29 51-79 153-181 (186)
150 cd04766 HTH_HspR Helix-Turn-He 27.7 43 0.00094 20.1 1.5 22 52-73 4-25 (91)
151 PRK12536 RNA polymerase sigma 27.4 74 0.0016 21.3 2.8 31 50-80 146-176 (181)
152 PRK12516 RNA polymerase sigma 27.4 89 0.0019 21.2 3.2 31 52-82 135-165 (187)
153 PRK08295 RNA polymerase factor 27.3 86 0.0019 21.3 3.1 32 49-80 170-201 (208)
154 PRK09637 RNA polymerase sigma 27.3 96 0.0021 20.9 3.3 33 50-82 123-155 (181)
155 PRK12520 RNA polymerase sigma 27.2 99 0.0022 20.8 3.4 32 51-82 149-180 (191)
156 PRK09047 RNA polymerase factor 27.2 1.8E+02 0.0038 18.7 6.0 29 52-80 125-153 (161)
157 PF00440 TetR_N: Bacterial reg 27.2 37 0.0008 17.7 1.0 34 40-74 8-41 (47)
158 TIGR02479 FliA_WhiG RNA polyme 27.2 1.7E+02 0.0038 20.3 4.8 29 51-79 193-221 (224)
159 TIGR02941 Sigma_B RNA polymera 26.9 1.5E+02 0.0033 21.0 4.5 29 51-79 223-251 (255)
160 cd04779 HTH_MerR-like_sg4 Heli 26.8 50 0.0011 21.7 1.8 24 52-75 3-26 (134)
161 PRK12547 RNA polymerase sigma 26.7 75 0.0016 20.8 2.7 30 50-79 129-158 (164)
162 PRK09638 RNA polymerase sigma 26.7 86 0.0019 20.6 3.0 33 47-79 140-172 (176)
163 PRK06288 RNA polymerase sigma 26.5 1.5E+02 0.0032 21.4 4.4 32 50-81 229-260 (268)
164 TIGR02980 SigBFG RNA polymeras 26.3 1.3E+02 0.0028 20.9 3.9 46 29-79 179-224 (227)
165 COG5484 Uncharacterized conser 25.9 42 0.0009 25.0 1.4 26 50-77 20-45 (279)
166 PF05269 Phage_CII: Bacterioph 25.9 1.1E+02 0.0023 19.0 3.0 29 51-79 25-53 (91)
167 cd04768 HTH_BmrR-like Helix-Tu 25.9 57 0.0012 19.9 1.8 23 52-74 3-25 (96)
168 TIGR02393 RpoD_Cterm RNA polym 25.6 1.9E+02 0.0041 20.4 4.7 51 29-80 177-227 (238)
169 PF01710 HTH_Tnp_IS630: Transp 25.3 50 0.0011 21.0 1.6 20 52-71 21-40 (119)
170 smart00530 HTH_XRE Helix-turn- 25.1 76 0.0016 15.4 2.0 22 52-73 13-34 (56)
171 TIGR03001 Sig-70_gmx1 RNA poly 25.0 1.1E+02 0.0024 22.0 3.4 31 51-81 179-209 (244)
172 PRK15008 HTH-type transcriptio 24.9 73 0.0016 21.9 2.4 48 34-82 24-71 (212)
173 TIGR03613 RutR pyrimidine util 24.8 70 0.0015 21.5 2.3 44 36-80 16-59 (202)
174 cd06170 LuxR_C_like C-terminal 24.7 86 0.0019 16.1 2.3 22 51-72 17-38 (57)
175 PRK07670 RNA polymerase sigma 24.6 1.3E+02 0.0028 21.5 3.7 30 50-79 218-247 (251)
176 PRK07037 extracytoplasmic-func 24.6 2E+02 0.0044 18.5 5.1 29 51-79 127-155 (163)
177 PRK09645 RNA polymerase sigma 24.5 1E+02 0.0022 20.2 3.1 30 51-80 136-165 (173)
178 COG1595 RpoE DNA-directed RNA 24.3 1E+02 0.0022 20.6 3.1 32 51-82 145-176 (182)
179 PRK12545 RNA polymerase sigma 24.3 1.1E+02 0.0024 20.9 3.3 31 51-81 157-187 (201)
180 PRK05988 formate dehydrogenase 24.3 1.6E+02 0.0035 19.8 4.0 34 33-66 25-58 (156)
181 PF12793 SgrR_N: Sugar transpo 24.2 84 0.0018 20.1 2.4 33 34-68 6-38 (115)
182 PRK07122 RNA polymerase sigma 24.2 1.3E+02 0.0029 21.8 3.8 30 50-79 232-261 (264)
183 PRK09649 RNA polymerase sigma 24.2 86 0.0019 21.1 2.6 29 51-79 148-176 (185)
184 TIGR02392 rpoH_proteo alternat 24.2 1.6E+02 0.0034 21.4 4.1 48 29-79 219-266 (270)
185 PF12244 DUF3606: Protein of u 24.1 73 0.0016 17.7 1.9 18 50-67 21-38 (57)
186 PRK12539 RNA polymerase sigma 23.7 1E+02 0.0022 20.6 2.9 31 50-80 148-178 (184)
187 PRK12531 RNA polymerase sigma 23.7 1E+02 0.0022 20.8 3.0 29 51-79 159-187 (194)
188 PF03672 UPF0154: Uncharacteri 23.6 1.6E+02 0.0035 17.0 4.4 31 35-65 20-50 (64)
189 PRK09706 transcriptional repre 23.5 46 0.00099 21.5 1.1 24 52-75 21-44 (135)
190 TIGR02943 Sig70_famx1 RNA poly 23.4 2.4E+02 0.0052 19.0 5.5 33 50-82 148-180 (188)
191 PRK11922 RNA polymerase sigma 23.4 1.1E+02 0.0025 21.4 3.2 37 46-82 162-198 (231)
192 PRK07539 NADH dehydrogenase su 23.4 1.6E+02 0.0035 19.6 3.8 34 33-66 24-57 (154)
193 PF07638 Sigma70_ECF: ECF sigm 23.0 99 0.0021 21.0 2.8 30 50-79 152-181 (185)
194 PF13542 HTH_Tnp_ISL3: Helix-t 22.9 71 0.0015 16.7 1.7 21 51-71 29-49 (52)
195 PRK12542 RNA polymerase sigma 22.9 95 0.0021 20.8 2.7 31 51-81 140-170 (185)
196 cd00592 HTH_MerR-like Helix-Tu 22.9 61 0.0013 19.6 1.5 23 52-74 3-25 (100)
197 PRK00118 putative DNA-binding 22.8 2.1E+02 0.0045 18.0 8.4 50 29-83 18-67 (104)
198 cd04780 HTH_MerR-like_sg5 Heli 22.8 60 0.0013 19.9 1.5 20 52-71 3-22 (95)
199 PF01726 LexA_DNA_bind: LexA D 22.6 1.4E+02 0.003 17.0 2.9 40 29-70 4-47 (65)
200 PRK12523 RNA polymerase sigma 22.6 99 0.0022 20.4 2.7 29 51-79 137-165 (172)
201 PF13551 HTH_29: Winged helix- 22.5 1.8E+02 0.004 17.3 5.7 44 28-71 57-109 (112)
202 PRK12535 RNA polymerase sigma 22.5 1E+02 0.0022 21.1 2.7 32 51-82 151-182 (196)
203 TIGR00721 tfx DNA-binding prot 22.3 2.5E+02 0.0053 18.7 6.0 48 26-79 4-51 (137)
204 PRK05911 RNA polymerase sigma 22.0 1.8E+02 0.004 20.9 4.1 31 50-80 222-252 (257)
205 PRK08215 sporulation sigma fac 21.9 1.4E+02 0.003 21.4 3.5 47 28-79 209-255 (258)
206 TIGR02885 spore_sigF RNA polym 21.8 2E+02 0.0043 20.1 4.2 45 29-78 184-228 (231)
207 TIGR01958 nuoE_fam NADH-quinon 21.8 1.9E+02 0.0041 19.1 3.9 34 33-66 18-51 (148)
208 cd04788 HTH_NolA-AlbR Helix-Tu 21.8 65 0.0014 19.6 1.5 22 52-73 3-24 (96)
209 PRK12534 RNA polymerase sigma 21.6 1.8E+02 0.0038 19.4 3.8 30 50-79 154-183 (187)
210 PF08452 DNAP_B_exo_N: DNA pol 21.6 27 0.00059 15.8 -0.2 9 66-74 5-13 (22)
211 cd04782 HTH_BltR Helix-Turn-He 21.5 76 0.0016 19.4 1.8 22 52-73 3-24 (97)
212 cd04775 HTH_Cfa-like Helix-Tur 21.4 67 0.0014 19.8 1.5 21 52-72 4-24 (102)
213 PRK12529 RNA polymerase sigma 21.3 2.6E+02 0.0056 18.6 4.9 29 51-79 145-173 (178)
214 PF01257 2Fe-2S_thioredx: Thio 21.2 1.5E+02 0.0032 19.5 3.3 33 34-66 16-48 (145)
215 PRK12533 RNA polymerase sigma 21.0 1.1E+02 0.0024 21.4 2.8 31 51-81 152-182 (216)
216 TIGR02394 rpoS_proteo RNA poly 21.0 3.4E+02 0.0073 19.7 5.5 32 50-81 243-274 (285)
217 PRK10668 DNA-binding transcrip 20.9 1.1E+02 0.0024 20.8 2.7 46 34-80 17-62 (215)
218 PF07022 Phage_CI_repr: Bacter 20.9 36 0.00078 19.3 0.2 20 52-71 15-35 (66)
219 PF02796 HTH_7: Helix-turn-hel 20.8 82 0.0018 16.3 1.6 37 29-70 6-42 (45)
220 cd04789 HTH_Cfa Helix-Turn-Hel 20.6 72 0.0016 19.7 1.5 21 52-72 4-24 (102)
221 PF06971 Put_DNA-bind_N: Putat 20.4 61 0.0013 17.7 1.0 18 51-68 30-47 (50)
222 TIGR02835 spore_sigmaE RNA pol 20.4 1.3E+02 0.0027 21.3 3.0 31 50-80 199-229 (234)
223 PRK12517 RNA polymerase sigma 20.3 1.6E+02 0.0034 19.9 3.4 32 51-82 146-177 (188)
224 PRK07571 bidirectional hydroge 20.3 2.1E+02 0.0046 19.6 4.0 33 34-66 39-71 (169)
225 PRK12544 RNA polymerase sigma 20.3 1.5E+02 0.0032 20.5 3.3 30 52-81 167-196 (206)
226 cd01107 HTH_BmrR Helix-Turn-He 20.2 75 0.0016 19.8 1.6 21 52-72 3-23 (108)
227 cd01109 HTH_YyaN Helix-Turn-He 20.2 75 0.0016 19.8 1.6 22 52-73 3-24 (113)
No 1
>KOG0488|consensus
Probab=99.73 E-value=8.8e-18 Score=124.92 Aligned_cols=69 Identities=41% Similarity=0.677 Sum_probs=63.5
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 15 DEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 15 ~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
..+..+++|+.|+.||..|+..||..|+...|.+..+|..||..|||+..||++||||||+|||++...
T Consensus 165 ~~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 165 QRSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred ccCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 344457777889999999999999999999999999999999999999999999999999999997765
No 2
>KOG0489|consensus
Probab=99.73 E-value=4e-18 Score=124.32 Aligned_cols=67 Identities=72% Similarity=1.034 Sum_probs=62.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869 19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85 (111)
Q Consensus 19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 85 (111)
.+..+|.|+.||..|+..||..|+.|.|.+...|.+||..|.|+++||+|||||||+|+||+++...
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~~~ 222 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKAKS 222 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcccc
Confidence 3567899999999999999999999999999999999999999999999999999999999766533
No 3
>KOG0487|consensus
Probab=99.72 E-value=7.3e-18 Score=124.44 Aligned_cols=66 Identities=55% Similarity=0.802 Sum_probs=61.8
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
..+..||+|.-+|+.|+..||..|..|.|.+...|.+|++.|+|+++||+|||||||.|+||.++.
T Consensus 231 ~~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 231 SARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 346778899999999999999999999999999999999999999999999999999999998753
No 4
>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=99.71 E-value=2.8e-17 Score=93.94 Aligned_cols=57 Identities=49% Similarity=0.701 Sum_probs=55.0
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
++.|+.|+..|+..|+.+|..++||+..++..||..+||+..+|.+||+|+|.++||
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999986
No 5
>KOG0850|consensus
Probab=99.71 E-value=1.5e-17 Score=117.56 Aligned_cols=66 Identities=41% Similarity=0.645 Sum_probs=61.3
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
+...+.|+.||-++..||..|+..|+.++|.-..||.+||..|||+..||+|||||||.|.||...
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 344566788999999999999999999999999999999999999999999999999999999766
No 6
>KOG0843|consensus
Probab=99.70 E-value=2.1e-17 Score=113.19 Aligned_cols=64 Identities=41% Similarity=0.621 Sum_probs=60.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 84 (111)
Q Consensus 21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 84 (111)
+++|.||.|+..|+..|+..|+.++|....+|+.||..|+|++.||+|||||||.|.||.+...
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 7788999999999999999999999999999999999999999999999999999999977653
No 7
>KOG0484|consensus
Probab=99.70 E-value=1.8e-17 Score=104.53 Aligned_cols=61 Identities=43% Similarity=0.636 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
++.++-|+.|+..|+..|+..|-+.+||++..+++||.++.|++..|++||||||+|+||+
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 4567889999999999999999999999999999999999999999999999999999993
No 8
>KOG2251|consensus
Probab=99.70 E-value=2.1e-17 Score=116.28 Aligned_cols=68 Identities=35% Similarity=0.502 Sum_probs=63.4
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869 17 GANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 84 (111)
Q Consensus 17 ~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 84 (111)
...++.||+||.|+..|+.+|+..|.+.+||+...+++||.+|+|.+.+|+|||+|||+|+|++++..
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 55678889999999999999999999999999999999999999999999999999999999966653
No 9
>KOG0485|consensus
Probab=99.67 E-value=1.3e-16 Score=112.29 Aligned_cols=66 Identities=39% Similarity=0.684 Sum_probs=61.5
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
.+.++|+.|++|+..|+..|+..|+...|.+..+|..||.+|.|++.||+|||||||.||||+...
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~aa 165 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYAA 165 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHhh
Confidence 345788899999999999999999999999999999999999999999999999999999996554
No 10
>KOG0842|consensus
Probab=99.64 E-value=2.4e-16 Score=116.35 Aligned_cols=64 Identities=39% Similarity=0.660 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
.++||.|-.|+..|..+||..|....|.+..||+.||..|.|+..||+|||||||=|.||..+.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~d 214 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKD 214 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhh
Confidence 4566677789999999999999999999999999999999999999999999999999995544
No 11
>KOG0492|consensus
Probab=99.63 E-value=7e-16 Score=107.87 Aligned_cols=64 Identities=44% Similarity=0.665 Sum_probs=59.0
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 85 (111)
-|+.|+.||..|+..|+.-|...+|.++.++.+++..|.|++.||+|||||||+|.||.+..+-
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~ 207 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAEL 207 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHH
Confidence 4567999999999999999999999999999999999999999999999999999999665433
No 12
>KOG0848|consensus
Probab=99.62 E-value=2.2e-16 Score=113.90 Aligned_cols=62 Identities=55% Similarity=0.827 Sum_probs=57.7
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85 (111)
Q Consensus 24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 85 (111)
+=|-++|..|.-.||+.|..++|.++..+.+||.-|||+++||+|||||||+|+||.++...
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk~ 262 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKKR 262 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHHH
Confidence 34678999999999999999999999999999999999999999999999999999887654
No 13
>KOG3802|consensus
Probab=99.62 E-value=2.1e-16 Score=119.20 Aligned_cols=77 Identities=29% Similarity=0.385 Sum_probs=70.2
Q ss_pred CCCcccccccCCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 6 SSDLMTNLEDEGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 6 s~~~~~~~~~~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
+.+..++.+.....+++||+||+|.......|+.+|..|+.|+..++..||.+|+|.+.+|+|||||||.|+||.+.
T Consensus 278 ~~~~~~~~e~i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~~ 354 (398)
T KOG3802|consen 278 STGSPNSIEKIGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRITP 354 (398)
T ss_pred ccCCCCCHHHhhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCCC
Confidence 45666667777777789999999999999999999999999999999999999999999999999999999999665
No 14
>KOG0494|consensus
Probab=99.61 E-value=1.4e-15 Score=109.49 Aligned_cols=62 Identities=42% Similarity=0.598 Sum_probs=57.0
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
++|+.||.||..|+..|+..|++..||+...++.|+.+++|.+..|+|||||||+||||..+
T Consensus 140 kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 140 KRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred ccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 34455899999999999999999999999999999999999999999999999999999443
No 15
>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=99.58 E-value=7.5e-15 Score=83.90 Aligned_cols=57 Identities=58% Similarity=0.832 Sum_probs=53.9
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
+.+..++..++..|+..|..++||+..++..||..+||+..+|.+||+|+|.+.++.
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 567889999999999999999999999999999999999999999999999998763
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.57 E-value=6.6e-15 Score=83.51 Aligned_cols=55 Identities=55% Similarity=0.809 Sum_probs=51.8
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78 (111)
Q Consensus 24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 78 (111)
+.|+.++..++..|+..|..++||+..++..||..+||+..+|++||+|+|.+.+
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 5677899999999999999999999999999999999999999999999998754
No 17
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.57 E-value=3.8e-15 Score=101.17 Aligned_cols=68 Identities=31% Similarity=0.505 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
.+..+..+++|.+.+..|+.+|+..|..++||+..++..|+..|+|+++.|++||||+|++.|+....
T Consensus 45 ~~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 45 QDGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred ccCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34446778889999999999999999999999999999999999999999999999999999997665
No 18
>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=99.57 E-value=3.3e-15 Score=85.86 Aligned_cols=53 Identities=19% Similarity=0.377 Sum_probs=50.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCC----CCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869 22 RRRGRQTYTRYQTLELEKEFHTNHY----LTRRRRIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~~~~~----p~~~~~~~La~~l~l~~~~V~~WFqNrR 74 (111)
+++.||.|+.+|+..|+.+|..++| |+..++..||..+||++.+|++||+|.+
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 9999999999999999999999999964
No 19
>KOG0493|consensus
Probab=99.55 E-value=4.9e-15 Score=106.85 Aligned_cols=60 Identities=50% Similarity=0.782 Sum_probs=56.5
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
-+|.|+.|+.+||..|+..|..+.|.+...|..|+..|||.+.||+|||||+|+|.||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 356799999999999999999999999999999999999999999999999999999943
No 20
>KOG0491|consensus
Probab=99.48 E-value=9.6e-15 Score=98.96 Aligned_cols=65 Identities=45% Similarity=0.690 Sum_probs=60.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85 (111)
Q Consensus 21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 85 (111)
.+++.|++|+..|+..|+..|+...|.+..++.+|+..|+|++.||+.||||||.|.||.+...+
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 45677999999999999999999999999999999999999999999999999999999776654
No 21
>KOG0483|consensus
Probab=99.46 E-value=1.2e-13 Score=96.84 Aligned_cols=64 Identities=31% Similarity=0.477 Sum_probs=58.3
Q ss_pred CCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHH
Q psy9869 22 RRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIK 85 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~ 85 (111)
...++.+++.+|...|+..|+...+..+..+..||..|||.++||.+||||||++||..+....
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d 113 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKD 113 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhh
Confidence 4567789999999999999999999999999999999999999999999999999998655443
No 22
>KOG0486|consensus
Probab=99.42 E-value=2e-13 Score=100.53 Aligned_cols=62 Identities=39% Similarity=0.579 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.++++.|+.|+..|+..|+..|.++.||+...+++||.-.+|++..|++||+|||+||||..
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 36678899999999999999999999999999999999999999999999999999999943
No 23
>KOG0844|consensus
Probab=99.38 E-value=2.1e-13 Score=100.37 Aligned_cols=64 Identities=52% Similarity=0.728 Sum_probs=58.7
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
..-||=||.|+.+|+..|++.|-+..|.+...|.+||..|+|.+..|++||||||.|+||+.-.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3456779999999999999999999999999999999999999999999999999999996543
No 24
>KOG4577|consensus
Probab=99.35 E-value=1.2e-12 Score=95.71 Aligned_cols=69 Identities=28% Similarity=0.394 Sum_probs=62.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHH
Q psy9869 18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKE 86 (111)
Q Consensus 18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~ 86 (111)
.+..-+|+|+.+++.|+..|+..|+..+.|..-.|+.|+..+||.-++|++||||||+|+||-++....
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 345678999999999999999999999999999999999999999999999999999999996665433
No 25
>KOG0847|consensus
Probab=99.34 E-value=5.8e-13 Score=94.18 Aligned_cols=65 Identities=42% Similarity=0.725 Sum_probs=60.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
-++.++..|..|+..|+..|+..|+...|+-..++.+||..+|+++.+|+|||||||.||||...
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 34667888999999999999999999999999999999999999999999999999999999544
No 26
>KOG0490|consensus
Probab=99.15 E-value=2.2e-11 Score=86.37 Aligned_cols=63 Identities=35% Similarity=0.376 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...+++.|+.|+..|+..|+..|...+||+...++.|+..+++++..|++||||+|++++++.
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 356788999999999999999999999999999999999999999999999999999999854
No 27
>KOG1168|consensus
Probab=99.15 E-value=1.2e-11 Score=90.68 Aligned_cols=61 Identities=25% Similarity=0.403 Sum_probs=58.1
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 20 GLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 20 ~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
+.++|+|+++...+.+.|+.+|...+.|+.+.+..+|.+|.|.+.+|++||||+|.|.||.
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 5688999999999999999999999999999999999999999999999999999998883
No 28
>KOG0849|consensus
Probab=99.06 E-value=2.6e-10 Score=86.52 Aligned_cols=64 Identities=30% Similarity=0.479 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 19 NGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 19 ~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
.+..++.|+.|+..|+..|+..|+.++||++..++.|+..+++++..|.+||+|+|++++|...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3556677899999999999999999999999999999999999999999999999999999653
No 29
>KOG0775|consensus
Probab=99.04 E-value=2.6e-10 Score=82.89 Aligned_cols=51 Identities=29% Similarity=0.446 Sum_probs=47.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 78 (111)
.|...-...|.++|..++||++.++.+||..+||+..||-+||+|||.++|
T Consensus 182 CFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 182 CFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred ehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 355566789999999999999999999999999999999999999999998
No 30
>KOG0774|consensus
Probab=98.92 E-value=4.1e-10 Score=81.57 Aligned_cols=75 Identities=27% Similarity=0.420 Sum_probs=64.9
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHHHHHHHHHHHH
Q psy9869 22 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQEKQAQA 96 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~~~~~~~~~ 96 (111)
.+|+|..|+..-..+|..+|. .+|||+...+++||.+||++..||.+||.|+|.+++|......++..-.....+
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~~~k~~ee~~l~~~kk~ 265 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKNMGKNQEEANLYAAKKA 265 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhhhhhhhhhhhhHhhccc
Confidence 467889999999999999995 599999999999999999999999999999999999988777766654444433
No 31
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.71 E-value=1.3e-08 Score=54.26 Aligned_cols=34 Identities=32% Similarity=0.585 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869 43 TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76 (111)
Q Consensus 43 ~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 76 (111)
.+|||+..++..|+..+||+..||..||-|.|.+
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 4899999999999999999999999999999864
No 32
>KOG2252|consensus
Probab=98.40 E-value=6.3e-07 Score=70.66 Aligned_cols=60 Identities=20% Similarity=0.232 Sum_probs=55.3
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHh
Q psy9869 18 ANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 77 (111)
Q Consensus 18 ~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 77 (111)
.....++.|.+|+..|...|...|+.+++|+.++.+.|+..|+|...-|.+||.|-|.|.
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 345567889999999999999999999999999999999999999999999999988774
No 33
>KOG0490|consensus
Probab=98.14 E-value=3.2e-06 Score=59.88 Aligned_cols=67 Identities=37% Similarity=0.502 Sum_probs=60.5
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 16 EGANGLRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 16 ~~~~~~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
.......++.++.+...++..+...|..+++|+...+..|+..+|++...|++||+|++.+.++...
T Consensus 147 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 147 GPSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3444667788999999999999999999999999999999999999999999999999999998554
No 34
>KOG1146|consensus
Probab=97.69 E-value=6.5e-05 Score=64.53 Aligned_cols=62 Identities=26% Similarity=0.304 Sum_probs=56.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
.++..|+.++..|+..|..+|....+|...+.+.|...+++..+.|.+||+|-|.+.++...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 35567999999999999999999999999999999999999999999999999999998443
No 35
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=97.39 E-value=0.00017 Score=40.93 Aligned_cols=43 Identities=19% Similarity=0.310 Sum_probs=31.2
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhh
Q psy9869 33 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 33 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
.+..|+.+|...+++.......|..+.+|+..+|+.||-.+..
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 3567999999999999999999999999999999999975543
No 36
>KOG0773|consensus
Probab=96.61 E-value=0.0026 Score=47.96 Aligned_cols=61 Identities=20% Similarity=0.316 Sum_probs=49.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHH---hcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 22 RRRGRQTYTRYQTLELEKEFH---TNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 22 ~r~~r~~~s~~q~~~L~~~F~---~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
..+....+......+|+.+.. ..+||+..++..|+..+||+..+|.+||-|.|-+.-+...
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 344555788888888887642 3689999999999999999999999999999988776544
No 37
>KOG3623|consensus
Probab=95.69 E-value=0.02 Score=47.55 Aligned_cols=48 Identities=17% Similarity=0.208 Sum_probs=44.3
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
+..|..+|..|+.|...+...++...|+....|+.||.+.++......
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 778899999999999999999999999999999999999998877644
No 38
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=95.46 E-value=0.062 Score=29.95 Aligned_cols=47 Identities=17% Similarity=0.357 Sum_probs=34.5
Q ss_pred CCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869 23 RRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 23 r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 74 (111)
+++|..+|-.+...+-..++.+. ....+|..+|++...|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 46788899988777777777666 477889999999999999998754
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=87.34 E-value=2.1 Score=22.91 Aligned_cols=46 Identities=11% Similarity=0.134 Sum_probs=32.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 78 (111)
.+++.+..++...|. ......++|..+|++...|+.+...-..+.|
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~kLR 49 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALKKLR 49 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHHHhc
Confidence 467788888888882 2234677899999999999988765554443
No 40
>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=80.72 E-value=1.9 Score=24.94 Aligned_cols=46 Identities=17% Similarity=0.293 Sum_probs=28.5
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHH
Q psy9869 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.+..|+.++...+-..+... ......++..+||+...+..|-.--
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~ 47 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQY 47 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHH
Confidence 346788888766555554222 2567788999999999999998543
No 41
>KOG1146|consensus
Probab=75.28 E-value=6.5 Score=35.21 Aligned_cols=61 Identities=18% Similarity=0.213 Sum_probs=53.3
Q ss_pred CCCCCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 21 LRRRGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 21 ~~r~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
..+..+..+-..+...|-..|-.+.-|+.....-|....+.+.+.+.+||+|-+.+.+++.
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 3455677777899999999999999999999999999999999999999999999988865
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=75.17 E-value=7.7 Score=22.13 Aligned_cols=45 Identities=18% Similarity=0.272 Sum_probs=22.1
Q ss_pred CCCCCCHHH-HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhH
Q psy9869 25 GRQTYTRYQ-TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 25 ~r~~~s~~q-~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 71 (111)
.|..|+... +.+++ +|....---... ...|.++|++...|+-|-+
T Consensus 2 ~rrsy~~~FKL~Vv~-~a~~~~nc~~~~-RAaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 2 SRRSYTAEFKLKVVE-YAEKDNNCKGNQ-RAAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ------HHHHHHHHH-HHHH-TTTTT-H-HHHHHHTTS-HHHHHHHHT
T ss_pred CccccChHHHHHHHH-HHHHccchhhhH-HHHHHHhCccHHHHHHHHH
Confidence 355677765 44444 443332211122 3349999999999999975
No 43
>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=73.75 E-value=5.9 Score=20.31 Aligned_cols=43 Identities=12% Similarity=0.097 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 76 (111)
++..+..++...|..+ .....+|..+|++...|..|...-+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 4566666666665322 235667899999999999998755443
No 44
>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=73.37 E-value=2.1 Score=24.55 Aligned_cols=20 Identities=25% Similarity=0.463 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
...||..||+++.+|+.|=.
T Consensus 25 lkdIA~~Lgvs~~tIr~WK~ 44 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWKS 44 (60)
T ss_pred HHHHHHHHCCCHHHHHHHhh
Confidence 55679999999999999964
No 45
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=68.81 E-value=31 Score=23.10 Aligned_cols=52 Identities=15% Similarity=0.067 Sum_probs=38.9
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
...+++.+..+|...+ .. ....++|..+|++...|..|..+-+.+.++....
T Consensus 4 ~~~Lt~rqreVL~lr~--~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~~~t 55 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--RG----LTQQEIADILGTSRANVSSIEKRARENIEKARET 55 (141)
T ss_pred ccCCCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888888887732 22 2356789999999999999998877777774443
No 46
>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=68.34 E-value=13 Score=20.69 Aligned_cols=42 Identities=17% Similarity=0.181 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCccchhhhh
Q psy9869 29 YTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKIWF 70 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~WF 70 (111)
+|..|..+|...|...=| |-.....+||..+|++..-|..-+
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~~L 44 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSEHL 44 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHHHH
Confidence 467889999998876544 556677889999999987765533
No 47
>PF13518 HTH_28: Helix-turn-helix domain
Probab=64.91 E-value=6.8 Score=20.64 Aligned_cols=23 Identities=17% Similarity=0.403 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
...+|..+|++...|..|.+.-+
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHHH
Confidence 55689999999999999996443
No 48
>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=61.78 E-value=6.5 Score=20.42 Aligned_cols=23 Identities=9% Similarity=0.018 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..++|..+|++...|+.|.+...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45689999999999999976543
No 49
>KOG3755|consensus
Probab=60.79 E-value=3.7 Score=33.90 Aligned_cols=47 Identities=15% Similarity=0.114 Sum_probs=30.9
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhCC-------CccchhhhhHHHhhHhhHhHH
Q psy9869 36 ELEKEFHTNHYLTRRRRIEMAHALCL-------TERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 36 ~L~~~F~~~~~p~~~~~~~La~~l~l-------~~~~V~~WFqNrR~k~kk~~~ 82 (111)
+-+.+|-.+..+......+.-..+.+ ....|+.||.+||.++++..-
T Consensus 706 v~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 706 VKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred cchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 33455666666666655555444433 345699999999999988543
No 50
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=58.67 E-value=7.4 Score=20.52 Aligned_cols=23 Identities=17% Similarity=0.335 Sum_probs=16.9
Q ss_pred HHHHHHHHHhCCCccchhhhhHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqN 72 (111)
.....+|..+|++...|..|.+.
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 34667899999999999999853
No 51
>PRK09480 slmA division inhibitor protein; Provisional
Probab=57.50 E-value=13 Score=24.92 Aligned_cols=38 Identities=11% Similarity=0.121 Sum_probs=30.1
Q ss_pred HHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869 38 EKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76 (111)
Q Consensus 38 ~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 76 (111)
...|...+. .......++...|++...+..+|.|+..-
T Consensus 20 ~~l~~~~~G-~~~ti~~Ia~~agvs~gt~Y~~F~~K~~L 57 (194)
T PRK09480 20 AQMLESPPG-ERITTAKLAARVGVSEAALYRHFPSKARM 57 (194)
T ss_pred HHHHHhcCC-CccCHHHHHHHhCCCHhHHHHHCCCHHHH
Confidence 344555545 77789999999999999999999987753
No 52
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=55.71 E-value=42 Score=21.57 Aligned_cols=30 Identities=17% Similarity=0.183 Sum_probs=23.4
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.|...-+.+.|+
T Consensus 123 ~s~~EIA~~l~is~~tV~~~~~ra~~~Lr~ 152 (154)
T PRK06759 123 KTMGEIALETEMTYYQVRWIYRQALEKMRN 152 (154)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHhh
Confidence 346778999999999999998766555543
No 53
>PRK10072 putative transcriptional regulator; Provisional
Probab=54.70 E-value=7.5 Score=24.30 Aligned_cols=41 Identities=20% Similarity=0.147 Sum_probs=29.0
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhh
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
..+...+..|..... ....+||..+|++...|..|...++.
T Consensus 32 ~~~~~eik~LR~~~g-------lTQ~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG-------LKIDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC-------CCHHHHHHHhCCCHHHHHHHHcCCCC
Confidence 346666666644322 22577899999999999999987654
No 54
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=54.38 E-value=9.9 Score=21.35 Aligned_cols=21 Identities=14% Similarity=0.232 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
..++|..+|++...|+.|=..
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999653
No 55
>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=54.30 E-value=11 Score=21.30 Aligned_cols=20 Identities=20% Similarity=0.326 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
..++|..||++...|..|-.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 45689999999999999986
No 56
>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=53.78 E-value=35 Score=18.53 Aligned_cols=46 Identities=20% Similarity=0.108 Sum_probs=31.5
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.+|+.+..+|.....- ....++|..+|+++..|..+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 4677777777655332 235678999999999999998876666543
No 57
>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=53.67 E-value=22 Score=16.02 Aligned_cols=37 Identities=16% Similarity=0.120 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhh
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 70 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 70 (111)
++......+...|. +.. ....++..+|++...|..|.
T Consensus 6 ~~~~~~~~i~~~~~-~~~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 6 LTPEQIEEARRLLA-AGE----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCHHHHHHHHHHHH-cCC----CHHHHHHHHCCCHHHHHHhC
Confidence 44555555555554 222 35567888999988888773
No 58
>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=53.51 E-value=13 Score=19.89 Aligned_cols=41 Identities=17% Similarity=0.170 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 74 (111)
+++.+..++...|- ......++|..+|++...|+.|...-+
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 34455555554433 334567789999999999999997443
No 59
>KOG0773|consensus
Probab=53.06 E-value=34 Score=25.75 Aligned_cols=42 Identities=38% Similarity=0.552 Sum_probs=35.6
Q ss_pred HHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 39 KEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 39 ~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
..-..++||+..+...++....++..+|.+||-|-+-+.+..
T Consensus 114 ~~~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~~ 155 (342)
T KOG0773|consen 114 EEHRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKKE 155 (342)
T ss_pred hhhhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhc
Confidence 334568999999999999999999999999999888876663
No 60
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=52.74 E-value=36 Score=23.13 Aligned_cols=31 Identities=16% Similarity=0.206 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|+.+...-+.+.++.
T Consensus 159 ~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~~ 189 (194)
T PRK09646 159 LTYREVAERLAVPLGTVKTRMRDGLIRLRDC 189 (194)
T ss_pred CCHHHHHHHhCCChHhHHHHHHHHHHHHHHH
Confidence 3456788999999999999998777766654
No 61
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=51.88 E-value=23 Score=23.25 Aligned_cols=32 Identities=19% Similarity=0.229 Sum_probs=25.5
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|..|...-+.+.++...
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~~l~ 174 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRECLE 174 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999877777666443
No 62
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=50.77 E-value=46 Score=21.68 Aligned_cols=32 Identities=22% Similarity=0.270 Sum_probs=25.2
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|+.+...-+.+.|+...
T Consensus 129 s~~eIA~~lgis~~tV~~~i~ra~~~Lr~~l~ 160 (166)
T PRK09639 129 SYKEIAEALGIKESSVGTTLARAKKKFRKIYE 160 (166)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35668999999999999999877777766544
No 63
>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=50.56 E-value=12 Score=19.10 Aligned_cols=20 Identities=20% Similarity=0.270 Sum_probs=15.4
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
+-++|..+|++...|+.|=.
T Consensus 2 i~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 34679999999999999853
No 64
>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=49.96 E-value=14 Score=18.64 Aligned_cols=24 Identities=17% Similarity=0.433 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCccchhhhhHHHhh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
..++|..+|++...|..|......
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 456789999999999999876543
No 65
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=49.36 E-value=14 Score=20.84 Aligned_cols=21 Identities=14% Similarity=0.211 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
..++|..+|++...++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999864
No 66
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=48.91 E-value=59 Score=22.40 Aligned_cols=32 Identities=19% Similarity=0.183 Sum_probs=25.1
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.+...-+.+.++..
T Consensus 170 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 201 (206)
T PRK12526 170 LSQEQLAQQLNVPLGTVKSRLRLALAKLKVQM 201 (206)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999999987777666644
No 67
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=48.35 E-value=21 Score=23.56 Aligned_cols=34 Identities=24% Similarity=0.135 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
....++|..+|++...|+.|...-|.+.++....
T Consensus 125 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~~ 158 (165)
T PRK09644 125 LTYEEAASVLDLKLNTYKSHLFRGRKRLKALLKE 158 (165)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHh
Confidence 3456788999999999999998777777665443
No 68
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=48.19 E-value=31 Score=22.96 Aligned_cols=30 Identities=17% Similarity=0.334 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
...++|..+|++...|++++..-|.+.|+.
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~ 176 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLREC 176 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHHHH
Confidence 366789999999999999998666666653
No 69
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=48.10 E-value=25 Score=22.95 Aligned_cols=30 Identities=17% Similarity=0.130 Sum_probs=24.1
Q ss_pred HHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
..++|..+|++...|++.+..-|.+.|+..
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l 154 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKKHW 154 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 456789999999999999987777766644
No 70
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.68 E-value=12 Score=20.62 Aligned_cols=24 Identities=4% Similarity=0.170 Sum_probs=17.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHh
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR 74 (111)
....||..+|++...|..|+.++.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~ 35 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKP 35 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhccc
Confidence 466789999999999999998763
No 71
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=47.55 E-value=31 Score=21.47 Aligned_cols=40 Identities=25% Similarity=0.241 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchh
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIK 67 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~ 67 (111)
+++++|...-...|..+--.+....+++|..|++++..|.
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3566777766666666666666778889999998875543
No 72
>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=47.21 E-value=17 Score=20.37 Aligned_cols=21 Identities=5% Similarity=0.186 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
..++|..+|++...++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 456899999999999999764
No 73
>smart00595 MADF subfamily of SANT domain.
Probab=47.17 E-value=45 Score=19.63 Aligned_cols=35 Identities=23% Similarity=0.353 Sum_probs=29.0
Q ss_pred HHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHHH
Q psy9869 53 IEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKEL 87 (111)
Q Consensus 53 ~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~ 87 (111)
..++..+|.+...|+.-+.|-|..++++.......
T Consensus 31 ~~Ia~~l~~~~~~~~~kw~~LR~~y~~e~~r~~~~ 65 (89)
T smart00595 31 EEIAEELGLSVEECKKRWKNLRDRYRRELKRLQNG 65 (89)
T ss_pred HHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45788999999999999999999999977665443
No 74
>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=47.13 E-value=9.1 Score=26.50 Aligned_cols=35 Identities=11% Similarity=0.239 Sum_probs=29.4
Q ss_pred HHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 49 RRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 49 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
...+.+|+.-++++..+|-.|..|.+...+..+..
T Consensus 14 tgt~~e~~~~~~VS~~sv~~WiKNG~~~~~a~~~y 48 (186)
T PF04936_consen 14 TGTIDELADYFDVSRTSVSVWIKNGKDPKRAKPKY 48 (186)
T ss_pred cccHHHHHHHHccCHHHHHHHHHcCCCcccccchh
Confidence 34578899999999999999999999988875543
No 75
>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=46.87 E-value=8.1 Score=23.02 Aligned_cols=32 Identities=16% Similarity=0.132 Sum_probs=23.1
Q ss_pred HHhcCCCCHHHHHHHHHHhCCCccchhhhhHH
Q psy9869 41 FHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 41 F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN 72 (111)
|....+.......++|..+|++...|+.|+.+
T Consensus 24 f~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 24 AALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 33333333345678899999999999999974
No 76
>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=46.21 E-value=71 Score=19.85 Aligned_cols=43 Identities=21% Similarity=0.329 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHHHHHHHH
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAIKELNEQ 90 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~~~~~~~ 90 (111)
+...+-.|+.||||...-... + =.|||-+|++.+..+....+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI~~lseR 56 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQIRALSER 56 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHHHHHHHH
Confidence 344555688999987441111 0 158899999877766655543
No 77
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=45.21 E-value=59 Score=21.27 Aligned_cols=31 Identities=13% Similarity=0.133 Sum_probs=24.2
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|+.|...-+.+.++..
T Consensus 146 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~l 176 (182)
T PRK09652 146 SYEEIAEIMGCPIGTVRSRIFRAREALRAKL 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3557789999999999999986666666543
No 78
>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=44.42 E-value=19 Score=20.09 Aligned_cols=21 Identities=10% Similarity=0.200 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
..++|..+|++...++.|-+.
T Consensus 3 ~~eva~~~gvs~~tlr~w~~~ 23 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWERR 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 456899999999999999863
No 79
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=44.31 E-value=62 Score=20.14 Aligned_cols=44 Identities=18% Similarity=0.208 Sum_probs=33.4
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCC-CccchhhhhHHH
Q psy9869 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCL-TERQIKIWFQNR 73 (111)
Q Consensus 26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l-~~~~V~~WFqNr 73 (111)
+..|+.+....+-..+....+ ....+|..+|+ ....+..|-..-
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~ 49 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQL 49 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHH
Confidence 778999887666666655554 57788999996 999999888633
No 80
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=44.30 E-value=37 Score=22.91 Aligned_cols=34 Identities=18% Similarity=0.201 Sum_probs=26.3
Q ss_pred CHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 48 TRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 48 ~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
......++|..+|++...|+.|+..-+.+.++..
T Consensus 156 ~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 189 (194)
T PRK12519 156 EGLSQSEIAKRLGIPLGTVKARARQGLLKLRELL 189 (194)
T ss_pred cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3345667899999999999999987777766643
No 81
>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=44.04 E-value=68 Score=20.64 Aligned_cols=29 Identities=17% Similarity=0.142 Sum_probs=22.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLK 78 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~k 78 (111)
....++|..+|++...|+++...-|.+.+
T Consensus 128 ~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 128 VSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 44667899999999999998875555544
No 82
>PRK04217 hypothetical protein; Provisional
Probab=43.87 E-value=85 Score=20.06 Aligned_cols=50 Identities=10% Similarity=-0.059 Sum_probs=36.0
Q ss_pred CCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 25 GRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 25 ~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.-..++..+..++...|...- ...++|..+|++...|...+..-+.+.+.
T Consensus 39 p~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLre 88 (110)
T PRK04217 39 PPIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVAQ 88 (110)
T ss_pred CcccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345677888777766654332 46678999999999999988766655554
No 83
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=43.60 E-value=36 Score=22.49 Aligned_cols=35 Identities=23% Similarity=0.228 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.......++|..+|++...|++.+..-+.+.++..
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~~l 168 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRKFL 168 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34445678899999999999999987777777644
No 84
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=43.46 E-value=65 Score=21.49 Aligned_cols=32 Identities=16% Similarity=0.206 Sum_probs=25.5
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.++..-+.+.+...
T Consensus 148 ~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~~l 179 (184)
T PRK12512 148 ASIKETAAKLSMSEGAVRVALHRGLAALAAKF 179 (184)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHh
Confidence 34567899999999999999987777777644
No 85
>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=42.44 E-value=11 Score=19.91 Aligned_cols=21 Identities=10% Similarity=0.181 Sum_probs=18.5
Q ss_pred HHHHHhCCCccchhhhhHHHh
Q psy9869 54 EMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 54 ~La~~l~l~~~~V~~WFqNrR 74 (111)
+||..+|++...|..|+.+..
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578999999999999998774
No 86
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=42.33 E-value=89 Score=19.84 Aligned_cols=45 Identities=11% Similarity=0.161 Sum_probs=30.3
Q ss_pred CCCCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHH
Q psy9869 24 RGRQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 24 ~~r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqN 72 (111)
..+..++.++....-.....+.. ....+|..+|++...|..|..-
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 34567888775544433333332 3556799999999999999754
No 87
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=41.99 E-value=53 Score=21.94 Aligned_cols=35 Identities=20% Similarity=0.153 Sum_probs=27.7
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQAI 84 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~~ 84 (111)
....++|..+|++...|++....-+.+.|+.....
T Consensus 134 ~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l~~~ 168 (179)
T PRK12543 134 YSQEEIAQLLQIPIGTVKSRIHAALKKLRQKEQIE 168 (179)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567789999999999999988888887765543
No 88
>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=41.85 E-value=32 Score=21.44 Aligned_cols=29 Identities=24% Similarity=0.315 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|..+...-+.+.++
T Consensus 128 s~~eIA~~l~~s~~~v~~~~~~~~~kl~~ 156 (158)
T TIGR02937 128 SYKEIAEILGISVGTVKRRLKRARKKLRE 156 (158)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45678999999999999998766665554
No 89
>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=40.59 E-value=37 Score=22.68 Aligned_cols=34 Identities=6% Similarity=0.012 Sum_probs=26.0
Q ss_pred CHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 48 TRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 48 ~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....-.++|..+|++...|+++...-|.+.|+..
T Consensus 153 ~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~~l 186 (190)
T TIGR02939 153 EGLSYEDIARIMDCPVGTVRSRIFRAREAIAIRL 186 (190)
T ss_pred cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 3344677899999999999999987666666543
No 90
>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=40.42 E-value=54 Score=18.10 Aligned_cols=36 Identities=33% Similarity=0.362 Sum_probs=25.6
Q ss_pred HHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhH
Q psy9869 32 YQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 32 ~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 71 (111)
.++..|+-.+. +...+.. +|+..+|++.+.|+....
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i~ 41 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDIN 41 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHHH
Confidence 35667777777 6666644 889999999998877654
No 91
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.08 E-value=61 Score=22.67 Aligned_cols=42 Identities=14% Similarity=0.150 Sum_probs=33.9
Q ss_pred CCCHHHHHHHHHHHHhcCC--CCHHHHHHHHHHhCCCccchhhh
Q psy9869 28 TYTRYQTLELEKEFHTNHY--LTRRRRIEMAHALCLTERQIKIW 69 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~--p~~~~~~~La~~l~l~~~~V~~W 69 (111)
.+|..|+.+|...|...=| |-......||..+|+++.-+..-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~~eh 198 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTLSEH 198 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHHHHH
Confidence 6999999999999986443 66677788999999998765543
No 92
>PRK09640 RNA polymerase sigma factor SigX; Reviewed
Probab=40.02 E-value=42 Score=22.65 Aligned_cols=32 Identities=16% Similarity=0.201 Sum_probs=25.8
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+++...-+.+.|+..
T Consensus 151 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 182 (188)
T PRK09640 151 LEFQEIADIMHMGLSATKMRYKRALDKLREKF 182 (188)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44677899999999999999987777766644
No 93
>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=39.96 E-value=37 Score=21.71 Aligned_cols=29 Identities=17% Similarity=0.273 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-+.+.++
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr~ 159 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELRK 159 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35567889999999999988766655554
No 94
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=39.52 E-value=72 Score=21.42 Aligned_cols=30 Identities=17% Similarity=0.121 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.+...-+.+.|+
T Consensus 156 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 156 LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 346678999999999999988766666554
No 95
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.10 E-value=46 Score=17.29 Aligned_cols=39 Identities=13% Similarity=0.072 Sum_probs=19.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhH
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFq 71 (111)
.++..+...+...+..+ ....++|..+|++...|..+.+
T Consensus 4 ~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 4 HLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp --------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred chhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 45666666666655422 3456689999999999888775
No 96
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=38.99 E-value=36 Score=21.87 Aligned_cols=33 Identities=27% Similarity=0.240 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.......++|..+|++...|+++...-+.+.++
T Consensus 119 ~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr~ 151 (154)
T TIGR02950 119 FKEFSYKEIAELLNLSLAKVKSNLFRARKELKK 151 (154)
T ss_pred hccCcHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 344557788999999999999998766666554
No 97
>PRK06930 positive control sigma-like factor; Validated
Probab=38.93 E-value=1.2e+02 Score=20.66 Aligned_cols=49 Identities=12% Similarity=0.086 Sum_probs=32.1
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.+++.+..++...|-.+ ....++|..+|++...|+.+...-+.+.++..
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 34555555555433211 23556789999999999999987777766643
No 98
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=38.57 E-value=42 Score=22.33 Aligned_cols=32 Identities=22% Similarity=0.224 Sum_probs=24.8
Q ss_pred HHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 49 RRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 49 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
.....++|..+|++...|++++..-|.+.+..
T Consensus 152 g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T TIGR02948 152 DLSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34456789999999999999998766666653
No 99
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=38.32 E-value=18 Score=19.20 Aligned_cols=23 Identities=22% Similarity=0.280 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..+||..+|++...|..|..+.+
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 46789999999999999998744
No 100
>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=37.67 E-value=61 Score=21.88 Aligned_cols=36 Identities=14% Similarity=0.146 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
.......++|..+|++...|+++...-|.+.++...
T Consensus 145 ~~g~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l~ 180 (193)
T TIGR02947 145 VEGFAYKEIAEIMGTPIGTVMSRLHRGRKQLRKQLV 180 (193)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 334456778999999999999999877777776544
No 101
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=37.51 E-value=1.7e+02 Score=21.56 Aligned_cols=15 Identities=27% Similarity=0.663 Sum_probs=11.9
Q ss_pred CccchhhhhHHHhhH
Q psy9869 62 TERQIKIWFQNRRMK 76 (111)
Q Consensus 62 ~~~~V~~WFqNrR~k 76 (111)
....|..||+.++.|
T Consensus 99 ~~~~i~~w~~~~~~k 113 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEK 113 (242)
T ss_pred ccchHHHHHHHHHHH
Confidence 457899999988773
No 102
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=37.40 E-value=47 Score=22.26 Aligned_cols=33 Identities=15% Similarity=0.261 Sum_probs=26.3
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
...++|..+|++...|+.+...-|.+.++....
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~~ 178 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALRAQLAD 178 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHHHHHh
Confidence 356789999999999999998777777775543
No 103
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=37.23 E-value=24 Score=22.50 Aligned_cols=41 Identities=15% Similarity=0.259 Sum_probs=31.9
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhh
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
.+++.++..+...+... ...+|.-||++..-|+.|=++|+.
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~k 83 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKK 83 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcC
Confidence 37777888887765533 456799999999999999988764
No 104
>smart00422 HTH_MERR helix_turn_helix, mercury resistance.
Probab=36.50 E-value=26 Score=19.51 Aligned_cols=21 Identities=14% Similarity=0.108 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
..+++..+|++...|+.|-..
T Consensus 3 ~~eva~~~gvs~~tlr~~~~~ 23 (70)
T smart00422 3 IGEVAKLAGVSVRTLRYYERI 23 (70)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 356789999999999999643
No 105
>PRK11552 putative DNA-binding transcriptional regulator; Provisional
Probab=36.46 E-value=39 Score=23.76 Aligned_cols=45 Identities=9% Similarity=0.000 Sum_probs=36.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
+..-...|...+|- .....+|...|++..-|..+|.++..-+.--
T Consensus 19 l~aA~~lF~~~Gy~--~s~~~IA~~AGvsk~tiy~~F~sKe~L~~av 63 (225)
T PRK11552 19 IAAALAQFGEYGLH--ATTRDIAAQAGQNIAAITYYFGSKEDLYLAV 63 (225)
T ss_pred HHHHHHHHHHhCcc--CCHHHHHHHhCCCHHHHHHHcCCHHHHHHHH
Confidence 44455568888887 5688899999999999999999988865543
No 106
>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=36.32 E-value=26 Score=17.70 Aligned_cols=23 Identities=13% Similarity=0.081 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..++|..+|++...|..|....+
T Consensus 4 ~~e~a~~lgis~~ti~~~~~~g~ 26 (49)
T TIGR01764 4 VEEAAEYLGVSKDTVYRLIHEGE 26 (49)
T ss_pred HHHHHHHHCCCHHHHHHHHHcCC
Confidence 45678889999999999986554
No 107
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=35.88 E-value=68 Score=22.61 Aligned_cols=31 Identities=13% Similarity=0.165 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|+.+...-+.+.|+.
T Consensus 201 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~~ 231 (236)
T PRK06986 201 LNLKEIGAVLGVSESRVSQIHSQAIKRLRAR 231 (236)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3467789999999999999998777777664
No 108
>PRK12513 RNA polymerase sigma factor; Provisional
Probab=35.51 E-value=57 Score=22.01 Aligned_cols=35 Identities=17% Similarity=0.122 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.......++|..+|++...|+.+...-+.+.|+..
T Consensus 153 ~~g~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~l 187 (194)
T PRK12513 153 HGDLELEEIAELTGVPEETVKSRLRYALQKLRELL 187 (194)
T ss_pred ccCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34455678899999999999998877776666643
No 109
>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=35.32 E-value=23 Score=18.68 Aligned_cols=23 Identities=13% Similarity=0.059 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
...||..+|++...|..|..+++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 56789999999999999997654
No 110
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=35.18 E-value=1e+02 Score=21.61 Aligned_cols=32 Identities=28% Similarity=0.300 Sum_probs=24.8
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.+...-+.+.|+..
T Consensus 199 ~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~~l 230 (234)
T PRK08301 199 KTQKEVADMLGISQSYISRLEKRIIKRLKKEI 230 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 34667899999999999999876666666643
No 111
>PF14549 P22_Cro: DNA-binding transcriptional regulator Cro; PDB: 1RZS_A 3BD1_A 3QWS_A 2HIN_B.
Probab=35.06 E-value=28 Score=19.77 Aligned_cols=18 Identities=22% Similarity=0.569 Sum_probs=15.2
Q ss_pred HHHHHHHhCCCccchhhh
Q psy9869 52 RIEMAHALCLTERQIKIW 69 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~W 69 (111)
...||..||++..-|..|
T Consensus 12 ~~~lAkalGVs~~aVs~W 29 (60)
T PF14549_consen 12 QSKLAKALGVSPQAVSQW 29 (60)
T ss_dssp HHHHHHHHTS-HHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHh
Confidence 357899999999999999
No 112
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=34.57 E-value=62 Score=21.92 Aligned_cols=30 Identities=7% Similarity=0.221 Sum_probs=23.8
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
...++|..+|++...|+++...-|.+.|+.
T Consensus 152 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~ 181 (189)
T PRK12530 152 SSEQICQECDISTSNLHVLLYRARLQLQAC 181 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999998666666653
No 113
>PRK14996 TetR family transcriptional regulator; Provisional
Probab=34.50 E-value=49 Score=22.23 Aligned_cols=41 Identities=7% Similarity=-0.007 Sum_probs=31.8
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869 35 LELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76 (111)
Q Consensus 35 ~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 76 (111)
..-...|....|.. .....++...|++...+..+|.++..-
T Consensus 15 ~aA~~lf~e~G~~~-tSi~~Ia~~aGvsk~~lY~~F~sK~~L 55 (192)
T PRK14996 15 QAAMRVALAEGFAA-MTVRRIASEAQVAAGQVHHHFSSAGEL 55 (192)
T ss_pred HHHHHHHHhcChhh-ccHHHHHHHhCCCcHHHHHHcCCHHHH
Confidence 34445577777754 457788999999999999999887664
No 114
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=34.34 E-value=64 Score=21.33 Aligned_cols=31 Identities=13% Similarity=0.252 Sum_probs=23.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.-.++|..+|++...|+.....-+.+.++..
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~~l 167 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMREHL 167 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHH
Confidence 3566799999999999999876666666543
No 115
>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=34.24 E-value=1.4e+02 Score=19.73 Aligned_cols=32 Identities=31% Similarity=0.305 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|+++...-+.+.++...
T Consensus 118 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 149 (170)
T TIGR02959 118 SQQEIAEKLGLSLSGAKSRVQRGRKKLKELLE 149 (170)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45677899999999999998876666666443
No 116
>PF13730 HTH_36: Helix-turn-helix domain
Probab=34.09 E-value=45 Score=17.71 Aligned_cols=25 Identities=12% Similarity=0.159 Sum_probs=19.6
Q ss_pred CHHHHHHHHHHhCCCccchhhhhHH
Q psy9869 48 TRRRRIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 48 ~~~~~~~La~~l~l~~~~V~~WFqN 72 (111)
..+....|+..+|++...|..+...
T Consensus 24 ~~pS~~~la~~~g~s~~Tv~~~i~~ 48 (55)
T PF13730_consen 24 CFPSQETLAKDLGVSRRTVQRAIKE 48 (55)
T ss_pred CCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 4445788999999999888887753
No 117
>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=33.89 E-value=49 Score=21.97 Aligned_cols=29 Identities=21% Similarity=0.159 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|++....-|.+.++
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35567889999999999998866666655
No 118
>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=33.77 E-value=46 Score=22.39 Aligned_cols=33 Identities=27% Similarity=0.235 Sum_probs=24.1
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.......++|..+|++...|++.+..-|.+.++
T Consensus 163 ~~~~s~~eIA~~l~~s~~tV~~~l~r~r~~L~~ 195 (198)
T TIGR02859 163 LDGKSYQEIACDLNRHVKSIDNALQRVKRKLEK 195 (198)
T ss_pred HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334456778999999999999888755555544
No 119
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=33.43 E-value=68 Score=22.81 Aligned_cols=33 Identities=15% Similarity=0.199 Sum_probs=26.2
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
....++|..+|++...|++....-+.+.|+...
T Consensus 188 ~s~~EIA~~Lgis~~tVk~~l~RAr~kLr~~l~ 220 (233)
T PRK12538 188 MSNGEIAEVMDTTVAAVESLLKRGRQQLRDLLR 220 (233)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999999999877777776544
No 120
>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=32.96 E-value=28 Score=17.34 Aligned_cols=23 Identities=22% Similarity=0.257 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
...++..+|++...|..|..+..
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 34678999999999999987653
No 121
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=32.79 E-value=86 Score=21.50 Aligned_cols=36 Identities=14% Similarity=0.052 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 31 RYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 31 ~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
..-+..|........|.+......+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 445677888888888999999999999999997654
No 122
>PRK11511 DNA-binding transcriptional activator MarA; Provisional
Probab=32.57 E-value=1e+02 Score=19.68 Aligned_cols=26 Identities=4% Similarity=0.077 Sum_probs=21.4
Q ss_pred CHHHHHHHHHHhCCCccchhhhhHHH
Q psy9869 48 TRRRRIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 48 ~~~~~~~La~~l~l~~~~V~~WFqNr 73 (111)
.......||..+|++...+..+|+.-
T Consensus 24 ~~~sl~~lA~~~g~S~~~l~r~Fk~~ 49 (127)
T PRK11511 24 SPLSLEKVSERSGYSKWHLQRMFKKE 49 (127)
T ss_pred CCCCHHHHHHHHCcCHHHHHHHHHHH
Confidence 33567889999999999999999754
No 123
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=32.30 E-value=1.2e+02 Score=18.20 Aligned_cols=44 Identities=9% Similarity=0.092 Sum_probs=32.2
Q ss_pred CCCHHHHHHHHHHHHh-----cCCCCHHHHHHHHHHhCCCccchhhhhH
Q psy9869 28 TYTRYQTLELEKEFHT-----NHYLTRRRRIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~-----~~~p~~~~~~~La~~l~l~~~~V~~WFq 71 (111)
.++..++..+...|.. +.+.+..+...+...+|++...|..+|.
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 4577788888888854 4467777777777778888777777764
No 124
>PF12728 HTH_17: Helix-turn-helix domain
Probab=32.24 E-value=32 Score=18.09 Aligned_cols=24 Identities=17% Similarity=0.378 Sum_probs=18.6
Q ss_pred HHHHHHHhCCCccchhhhhHHHhh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
..++|..||++...|..|.....-
T Consensus 4 ~~e~a~~l~is~~tv~~~~~~g~i 27 (51)
T PF12728_consen 4 VKEAAELLGISRSTVYRWIRQGKI 27 (51)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 456788899999999999865543
No 125
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=31.59 E-value=63 Score=21.45 Aligned_cols=31 Identities=23% Similarity=0.234 Sum_probs=24.1
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|++....-|.+.++.
T Consensus 153 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~~ 183 (187)
T PRK09641 153 LSLKEISEILDLPVGTVKTRIHRGREALRKQ 183 (187)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999887777766653
No 126
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=31.47 E-value=1.6e+02 Score=19.67 Aligned_cols=31 Identities=19% Similarity=0.205 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|++-+..-|.+.++..
T Consensus 149 s~~eIA~~lgis~~tV~~~l~Rar~~Lr~~l 179 (189)
T PRK12515 149 SVEEVGEIVGIPESTVKTRMFYARKKLAELL 179 (189)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3566788999999999998877776666643
No 127
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=31.33 E-value=70 Score=22.15 Aligned_cols=29 Identities=17% Similarity=0.224 Sum_probs=22.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
..++|..+|++...|+.+...-|.+.++.
T Consensus 157 ~~EIA~~Lgis~~tV~~~l~RArk~Lr~~ 185 (203)
T PRK09647 157 YEEIAATLGVKLGTVRSRIHRGRQQLRAA 185 (203)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998666666653
No 128
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=31.29 E-value=77 Score=21.43 Aligned_cols=31 Identities=10% Similarity=0.155 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|+.....-|.+.|+..
T Consensus 154 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 184 (195)
T PRK12532 154 SSDEIQQMCGISTSNYHTIMHRARESLRQCL 184 (195)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777777654
No 129
>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=31.12 E-value=1.2e+02 Score=19.70 Aligned_cols=30 Identities=30% Similarity=0.176 Sum_probs=21.7
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+....--+.+.|+
T Consensus 139 ~s~~eIA~~l~is~~tv~~~l~ra~~~Lr~ 168 (170)
T TIGR02952 139 LPIAEVARILGKTEGAVKILQFRAIKKLAR 168 (170)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345677889999999999887655555443
No 130
>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=30.89 E-value=59 Score=21.11 Aligned_cols=30 Identities=17% Similarity=0.242 Sum_probs=23.7
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.+...-+.+.++
T Consensus 127 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 127 LSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 335667899999999999998877766665
No 131
>cd01105 HTH_GlnR-like Helix-Turn-Helix DNA binding domain of GlnR-like transcription regulators. Helix-turn-helix (HTH) transcription regulator GlnR and related proteins, N-terminal domain. The GlnR and TnrA (also known as ScgR) proteins have been shown to regulate expression of glutamine synthetase as well as several genes involved in nitrogen metabolism. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=30.88 E-value=35 Score=20.49 Aligned_cols=20 Identities=20% Similarity=0.376 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
..++|..+|++...++.|-.
T Consensus 4 i~evA~~~gvs~~tLR~ye~ 23 (88)
T cd01105 4 IGEVSKLTGVSPRQLRYWEE 23 (88)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999953
No 132
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=30.85 E-value=73 Score=21.42 Aligned_cols=33 Identities=12% Similarity=0.118 Sum_probs=26.1
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
....++|..+|++...|++....-|.+.|+...
T Consensus 155 ~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~~l~ 187 (193)
T PRK11923 155 LSYEDIASVMQCPVGTVRSRIFRAREAIDKALQ 187 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 335678999999999999999877777776554
No 133
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=30.67 E-value=1.2e+02 Score=20.43 Aligned_cols=29 Identities=34% Similarity=0.365 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|++....-+.+.++
T Consensus 149 s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 149 KIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35677889999999999888755555555
No 134
>PRK09975 DNA-binding transcriptional regulator EnvR; Provisional
Probab=29.94 E-value=56 Score=22.20 Aligned_cols=43 Identities=16% Similarity=0.108 Sum_probs=32.1
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHh
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKL 77 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~ 77 (111)
+......|...+|... ....+|...|++..-+..+|.++-.-.
T Consensus 17 l~aa~~lf~~~G~~~~-ti~~Ia~~agvsk~t~Y~~F~sKe~Ll 59 (213)
T PRK09975 17 IETAIAQFALRGVSNT-TLNDIADAANVTRGAIYWHFENKTQLF 59 (213)
T ss_pred HHHHHHHHHHcCcccC-CHHHHHHHcCCCHHHHHHHcCCHHHHH
Confidence 3444455777776654 477789999999999999998877643
No 135
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=29.51 E-value=92 Score=22.23 Aligned_cols=29 Identities=14% Similarity=0.190 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.|...-+.+.|+
T Consensus 223 s~~eIA~~l~is~~tV~~~~~ra~~kLr~ 251 (257)
T PRK08583 223 SQKETGERLGISQMHVSRLQRQAIKKLRE 251 (257)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35778999999999999998766666554
No 136
>cd01106 HTH_TipAL-Mta Helix-Turn-Helix DNA binding domain of the transcription regulators TipAL, Mta, and SkgA. Helix-turn-helix (HTH) TipAL, Mta, and SkgA transcription regulators, and related proteins, N-terminal domain. TipAL regulates resistance to and activation by numerous cyclic thiopeptide antibiotics, such as thiostrepton. Mta is a global transcriptional regulator; the N-terminal DNA-binding domain of Mta interacts directly with the promoters of mta, bmr, blt, and ydfK, and induces transcription of these multidrug-efflux transport genes. SkgA has been shown to control stationary-phase expression of catalase-peroxidase in Caulobacter crescentus. These proteins are comprised of distinct domains that harbor an N-terminal active (DNA-binding) site and a regulatory (effector-binding) site. The conserved N-terminal domain of these transcription regulators contains winged HTH motifs that mediate DNA binding. These proteins share the N-terminal DNA binding domain with other transcrip
Probab=29.28 E-value=42 Score=20.63 Aligned_cols=23 Identities=13% Similarity=0.021 Sum_probs=18.5
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..++|..+|++...++.|.....
T Consensus 3 i~eva~~~gvs~~tlR~ye~~Gl 25 (103)
T cd01106 3 VGEVAKLTGVSVRTLHYYDEIGL 25 (103)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45678999999999999976544
No 137
>TIGR02607 antidote_HigA addiction module antidote protein, HigA family. Members of this family form a distinct clade within the larger family HTH_3 of helix-turn-helix proteins, described by Pfam model pfam01381. Members of this clade are strictly bacterial and nearly always shorter than 110 amino acids. This family includes the characterized member HigA, without which the killer protein HigB cannot be cloned. The hig (host inhibition of growth) system is noted to be unusual in that killer protein is uncoded by the upstream member of the gene pair.
Probab=29.03 E-value=34 Score=19.52 Aligned_cols=23 Identities=22% Similarity=0.265 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
...||..+|++...|..|..+++
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~ 43 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRR 43 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 46789999999999999997654
No 138
>PRK07408 RNA polymerase sigma factor SigF; Reviewed
Probab=28.93 E-value=75 Score=22.90 Aligned_cols=32 Identities=19% Similarity=0.140 Sum_probs=25.0
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.+...-+.+.|+..
T Consensus 220 ~s~~eIA~~lgvs~~~V~~~~~ra~~kLr~~l 251 (256)
T PRK07408 220 LTQKEAAERLGISPVTVSRRVKKGLDQLKKLL 251 (256)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHh
Confidence 45677899999999999999876666666543
No 139
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=28.91 E-value=1.6e+02 Score=22.24 Aligned_cols=52 Identities=13% Similarity=0.104 Sum_probs=34.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
++..+..+|...|... +.......++|..+|++...|+.+...-+.+.|+..
T Consensus 263 L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~~l 314 (325)
T PRK05657 263 LNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLREIL 314 (325)
T ss_pred CCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 4444445555444221 223345678899999999999999987777777644
No 140
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=28.67 E-value=72 Score=21.34 Aligned_cols=29 Identities=21% Similarity=0.369 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-+.+.|+
T Consensus 151 s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 151 SHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 35677899999999999998765555544
No 141
>cd04774 HTH_YfmP Helix-Turn-Helix DNA binding domain of the YfmP transcription regulator. Helix-turn-helix (HTH) transcription regulator, YfmP, and related proteins; N-terminal domain. YfmP regulates the multidrug efflux protein, YfmO, and indirectly regulates the expression of the Bacillus subtilis copZA operon encoding a metallochaperone, CopZ, and a CPx-type ATPase efflux protein, CopA. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=28.25 E-value=47 Score=20.38 Aligned_cols=22 Identities=32% Similarity=0.299 Sum_probs=18.1
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.++|..+|++...++.|....
T Consensus 3 I~e~a~~~gvs~~tLR~ye~~G 24 (96)
T cd04774 3 VDEVAKRLGLTKRTLKYYEEIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997643
No 142
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=28.18 E-value=65 Score=20.97 Aligned_cols=29 Identities=24% Similarity=0.225 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-|.+.++
T Consensus 130 s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 130 SYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35667889999999999988765555544
No 143
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=28.12 E-value=81 Score=21.41 Aligned_cols=31 Identities=10% Similarity=0.097 Sum_probs=24.5
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
.-.++|..+|++...|+.++..-+.+.++..
T Consensus 154 s~~eIA~~lgis~~tV~~~l~Ra~~~Lr~~l 184 (196)
T PRK12524 154 SNPEIAEVMEIGVEAVESLTARGKRALAALL 184 (196)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567889999999999999987676666643
No 144
>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=28.05 E-value=73 Score=20.90 Aligned_cols=29 Identities=28% Similarity=0.330 Sum_probs=22.8
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+++...-+.+.++
T Consensus 137 s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 137 TIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45677999999999999988766666555
No 145
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=27.92 E-value=94 Score=15.80 Aligned_cols=43 Identities=21% Similarity=0.172 Sum_probs=28.7
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhH
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMK 76 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k 76 (111)
.++..+...+...+ ..+ ...++|..+|++...|..|...-+.+
T Consensus 3 ~l~~~e~~i~~~~~--~g~----s~~eia~~l~is~~tv~~~~~~~~~k 45 (58)
T smart00421 3 SLTPREREVLRLLA--EGL----TNKEIAERLGISEKTVKTHLSNIMRK 45 (58)
T ss_pred CCCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 35666666665432 222 45678899999999999988754443
No 146
>PHA01976 helix-turn-helix protein
Probab=27.69 E-value=37 Score=18.77 Aligned_cols=23 Identities=13% Similarity=0.125 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..+||..+|++...|..|....+
T Consensus 18 ~~~lA~~~gvs~~~v~~~e~g~~ 40 (67)
T PHA01976 18 APELSRRAGVRHSLIYDFEADKR 40 (67)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCC
Confidence 56789999999999999986554
No 147
>KOG0150|consensus
Probab=27.68 E-value=1.2e+02 Score=23.22 Aligned_cols=11 Identities=27% Similarity=0.721 Sum_probs=7.7
Q ss_pred hhhhhHHHhhH
Q psy9869 66 IKIWFQNRRMK 76 (111)
Q Consensus 66 V~~WFqNrR~k 76 (111)
+++||+|.+..
T Consensus 16 CKiWi~dN~~S 26 (336)
T KOG0150|consen 16 CKIWIKDNPAS 26 (336)
T ss_pred hhhhhcCChHH
Confidence 57888776654
No 148
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=27.68 E-value=69 Score=21.83 Aligned_cols=32 Identities=19% Similarity=0.122 Sum_probs=25.3
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|++++..-|.+.|+...
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~~l~ 162 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLAELLQ 162 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 35678999999999999999877777766443
No 149
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.67 E-value=72 Score=21.27 Aligned_cols=29 Identities=24% Similarity=0.184 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-+.+.+.
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~Lr~ 181 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSRLKE 181 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35667889999999999988765555554
No 150
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.66 E-value=43 Score=20.10 Aligned_cols=22 Identities=5% Similarity=0.006 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.++|..+|++...|+.|-...
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4568999999999999997543
No 151
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=27.40 E-value=74 Score=21.27 Aligned_cols=31 Identities=19% Similarity=0.141 Sum_probs=24.5
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|++....-|.+.++.
T Consensus 146 ~s~~EIA~~l~is~~tV~~~l~rar~~Lr~~ 176 (181)
T PRK12536 146 LSVAETAQLTGLSESAVKVGIHRGLKALAAK 176 (181)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456789999999999999998777776663
No 152
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=27.38 E-value=89 Score=21.20 Aligned_cols=31 Identities=23% Similarity=0.145 Sum_probs=24.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
..++|..||++...|+.....-+.+.++...
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~Rar~~Lr~~l~ 165 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNRARQRLQEILQ 165 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 4567899999999999999877777766544
No 153
>PRK08295 RNA polymerase factor sigma-70; Validated
Probab=27.28 E-value=86 Score=21.26 Aligned_cols=32 Identities=25% Similarity=0.194 Sum_probs=24.0
Q ss_pred HHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 49 RRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 49 ~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
.....++|..+|++...|++.+..-|.+.++.
T Consensus 170 ~~s~~EIA~~lgis~~tV~~~l~rar~~Lr~~ 201 (208)
T PRK08295 170 GKSYQEIAEELNRHVKSIDNALQRVKRKLEKY 201 (208)
T ss_pred cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 34456788999999999998887666666553
No 154
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=27.25 E-value=96 Score=20.89 Aligned_cols=33 Identities=30% Similarity=0.302 Sum_probs=25.2
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
....++|..+|++...|+..+..-|.+.++...
T Consensus 123 ~~~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 155 (181)
T PRK09637 123 LSQKEIAEKLGLSLSGAKSRVQRGRVKLKELLE 155 (181)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999999999876766666443
No 155
>PRK12520 RNA polymerase sigma factor; Provisional
Probab=27.23 E-value=99 Score=20.78 Aligned_cols=32 Identities=19% Similarity=0.325 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|++....-|.+.++...
T Consensus 149 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 180 (191)
T PRK12520 149 ETEEICQELQITATNAWVLLYRARMRLRECLD 180 (191)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 35678899999999999998877776666443
No 156
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.20 E-value=1.8e+02 Score=18.68 Aligned_cols=29 Identities=24% Similarity=0.194 Sum_probs=22.7
Q ss_pred HHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
..++|..+|++...|++....-+.+.|+.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 153 (161)
T PRK09047 125 VAETAAAMGCSEGSVKTHCSRATHALAKA 153 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 56789999999999999887666665553
No 157
>PF00440 TetR_N: Bacterial regulatory proteins, tetR family; InterPro: IPR001647 This entry represents a DNA-binding domain with a helix-turn-helix (HTH) structure that is found in several bacterial and archaeal transcriptional regulators, such as TetR, the tetracycline resistance repressor. Numerous other transcriptional regulatory proteins also contain HTH-type DNA-binding domains, and can be grouped into subfamiles based on sequence similarity. The domain represented by this entry is found in a subfamily of proteins that includes the transcriptional regulators TetR, TetC, AcrR, BetI, Bm3R1, EnvR, QacR, MtrR, TcmR, Ttk, YbiH, and YhgD [, , ]. Many of these proteins function as repressors that control the level of susceptibility to hydrophobic antibiotics and detergents. They all have similar molecular weights, ranging from 21 to 25 kDa. The helix-turn-helix motif is located in the initial third of the protein. The 3D structure of the homodimeric TetR protein complexed with 7-chloro-tetracycline-magnesium has been determined to 2.1 A resolution []. TetR folds into ten alpha-helices with connecting turns and loops. The three N-terminal alpha-helices of the repressor form the DNA-binding domain: this structural motif encompasses an HTH fold with an inverse orientation compared with that of other DNA-binding proteins.; GO: 0003677 DNA binding; PDB: 3NPI_B 3IUV_A 3CCY_A 2JK3_A 2FX0_A 2JJ7_A 2WV1_B 3BTI_D 3BR6_E 3BR5_A ....
Probab=27.19 E-value=37 Score=17.67 Aligned_cols=34 Identities=12% Similarity=0.199 Sum_probs=24.0
Q ss_pred HHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHh
Q psy9869 40 EFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 40 ~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR 74 (111)
.|...+|-. .....++..+|++...+...|.|+-
T Consensus 8 l~~~~G~~~-~s~~~Ia~~~gvs~~~~y~~f~~k~ 41 (47)
T PF00440_consen 8 LFAEKGYEA-VSIRDIARRAGVSKGSFYRYFPSKD 41 (47)
T ss_dssp HHHHHHTTT-SSHHHHHHHHTSCHHHHHHHCSSHH
T ss_pred HHHHhCHHh-CCHHHHHHHHccchhhHHHHcCCHH
Confidence 344444433 3366789999999999999998764
No 158
>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=27.19 E-value=1.7e+02 Score=20.26 Aligned_cols=29 Identities=24% Similarity=0.256 Sum_probs=22.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-+.+.|+
T Consensus 193 s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 193 NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45778999999999999888755555544
No 159
>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=26.90 E-value=1.5e+02 Score=21.03 Aligned_cols=29 Identities=17% Similarity=0.196 Sum_probs=22.2
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-+.+.|+
T Consensus 223 s~~eIA~~lgis~~~V~~~~~ra~~~Lr~ 251 (255)
T TIGR02941 223 SQKETGERLGISQMHVSRLQRQAISKLKE 251 (255)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 34678999999999999988755555544
No 160
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=26.77 E-value=50 Score=21.74 Aligned_cols=24 Identities=17% Similarity=0.194 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHhh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
+.++|..+|++...++.|.....-
T Consensus 3 I~e~a~~~gvs~~TLR~Ye~~GLl 26 (134)
T cd04779 3 IGQLAHLAGVSKRTIDYYTNLGLL 26 (134)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 456889999999999999865433
No 161
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=26.74 E-value=75 Score=20.85 Aligned_cols=30 Identities=17% Similarity=0.039 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.+...-|.+.+.
T Consensus 129 ~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 158 (164)
T PRK12547 129 FSYEDAAAICGCAVGTIKSRVSRARNRLQE 158 (164)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999998766665554
No 162
>PRK09638 RNA polymerase sigma factor SigY; Reviewed
Probab=26.66 E-value=86 Score=20.61 Aligned_cols=33 Identities=21% Similarity=0.191 Sum_probs=25.1
Q ss_pred CCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 47 LTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 47 p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.......++|..+|++...|+.+...-+.+.++
T Consensus 140 ~~g~s~~eIA~~l~is~~~V~~~l~ra~~~l~~ 172 (176)
T PRK09638 140 YYGYTYEEIAKMLNIPEGTVKSRVHHGIKQLRK 172 (176)
T ss_pred hcCCCHHHHHHHHCCChhHHHHHHHHHHHHHHH
Confidence 344556778999999999999988766666555
No 163
>PRK06288 RNA polymerase sigma factor WhiG; Reviewed
Probab=26.54 E-value=1.5e+02 Score=21.43 Aligned_cols=32 Identities=19% Similarity=0.272 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.....-+.+.|+..
T Consensus 229 ~s~~eIA~~lgis~~tV~~~~~ra~~~Lr~~l 260 (268)
T PRK06288 229 LTLKEIGKVLGVTESRISQLHTKAVLQLRAKL 260 (268)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 34567899999999999988876666666643
No 164
>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=26.27 E-value=1.3e+02 Score=20.93 Aligned_cols=46 Identities=15% Similarity=0.220 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
+++.+..++...|- ......++|..+|++...|..|...-+.+.++
T Consensus 179 L~~~~r~vl~l~y~-----~~~s~~eIA~~lgis~~~v~~~~~ra~~~Lr~ 224 (227)
T TIGR02980 179 LPERERRILLLRFF-----EDKTQSEIAERLGISQMHVSRLLRRALKKLRE 224 (227)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 44444455544442 22346678999999999999998755555443
No 165
>COG5484 Uncharacterized conserved protein [Function unknown]
Probab=25.93 E-value=42 Score=24.97 Aligned_cols=26 Identities=23% Similarity=0.349 Sum_probs=20.7
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKL 77 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~ 77 (111)
-...++|..+||++.+|+.|-+ |..|
T Consensus 20 mk~~dIAeklGvspntiksWKr--r~gW 45 (279)
T COG5484 20 MKLKDIAEKLGVSPNTIKSWKR--RDGW 45 (279)
T ss_pred ccHHHHHHHhCCChHHHHHHHH--hcCC
Confidence 3456789999999999999986 4444
No 166
>PF05269 Phage_CII: Bacteriophage CII protein; InterPro: IPR007933 The CII protein is a transcription activator, conserved in bacteriophage lambda and related phages, that plays a key role in the decision between lytic or lysogenic phage development. CII is regulated at multiple levels including transcription, translation initiation, mRNA stability, and proteolysis []. Conditions that stabilise cII favour lysogenic development. The lambda CII protein activates three specific promoters, binding to direct repeat sequences rather than the more usual inverted repeats. Structurally, CII is a homotetramer where each monomer is composed of four alpha helices and a disordered C terminus [, ]. The alpha helical region is responsible for DNA binding and multimerisation. The homotetramer has an unusual spatial arrangement that allows recognition of the direct repeat sequences.; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 1ZS4_C 1ZPQ_C 1XWR_A.
Probab=25.92 E-value=1.1e+02 Score=19.02 Aligned_cols=29 Identities=21% Similarity=0.283 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
-...+|..+|+++.+|..|..+-+.++-.
T Consensus 25 gq~~vA~~~Gv~eStISR~k~~~~~~~a~ 53 (91)
T PF05269_consen 25 GQKKVAEAMGVDESTISRWKNDFIEKMAM 53 (91)
T ss_dssp HHHHHHHHHTSSTTTHHHHHHHHHHHHHH
T ss_pred hhHHHHHHhCCCHHHHHHHHhhHHHHHHH
Confidence 34568999999999999998665555444
No 167
>cd04768 HTH_BmrR-like Helix-Turn-Helix DNA binding domain of BmrR-like transcription regulators. Helix-turn-helix (HTH) BmrR-like transcription regulators (TipAL, Mta, SkgA, BmrR, and BltR), N-terminal domain. These proteins have been shown to regulate expression of specific regulons in response to various toxic substances, antibiotics, or oxygen radicals in Bacillus subtilis, Streptomyces, and Caulobacter crescentus. They are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.87 E-value=57 Score=19.88 Aligned_cols=23 Identities=13% Similarity=0.003 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
+.++|..+|++...++.|-+...
T Consensus 3 i~eva~~~gvs~~tLRyye~~Gl 25 (96)
T cd04768 3 IGEFAKLAGVSIRTLRHYDDIGL 25 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999986533
No 168
>TIGR02393 RpoD_Cterm RNA polymerase sigma factor RpoD, C-terminal domain. This model represents the well-conserved C-terminal region of the major, essential sigma factor of most bacteria. Members of this clade show considerable variability in domain architecture and molecular weight, as well as in nomenclature: RpoD in E. coli and other Proteobacteria, SigA in Bacillus subtilis and many other Gram-positive bacteria, HrdB in Streptomyces, MysA in Mycobacterium smegmatis, etc.
Probab=25.63 E-value=1.9e+02 Score=20.41 Aligned_cols=51 Identities=14% Similarity=0.073 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
+++.+..+|...|....+ ......++|..+|++...|+.....-..|.|..
T Consensus 177 L~~~er~vl~l~ygl~~~-~~~t~~EIA~~lgis~~~V~q~~~~al~kLr~~ 227 (238)
T TIGR02393 177 LTERERKVLRMRYGLLDG-RPHTLEEVGKEFNVTRERIRQIESKALRKLRHP 227 (238)
T ss_pred CCHHHHHHHHHHhCCCCC-CCccHHHHHHHHCCCHHHHHHHHHHHHHHHhhh
Confidence 444455555555532222 234577889999999999999887666666653
No 169
>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=25.32 E-value=50 Score=20.98 Aligned_cols=20 Identities=15% Similarity=0.348 Sum_probs=17.6
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
+..+|..++++...|..||+
T Consensus 21 ~~eaa~~F~VS~~Tv~~W~k 40 (119)
T PF01710_consen 21 IREAAKRFGVSRNTVYRWLK 40 (119)
T ss_pred HHHHHHHhCcHHHHHHHHHH
Confidence 45578899999999999998
No 170
>smart00530 HTH_XRE Helix-turn-helix XRE-family like proteins.
Probab=25.13 E-value=76 Score=15.41 Aligned_cols=22 Identities=14% Similarity=0.179 Sum_probs=14.2
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
...++..+|++...|..|-.++
T Consensus 13 ~~~la~~~~i~~~~i~~~~~~~ 34 (56)
T smart00530 13 QEELAEKLGVSRSTLSRIENGK 34 (56)
T ss_pred HHHHHHHhCCCHHHHHHHHCCC
Confidence 3456677777777777776544
No 171
>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=24.97 E-value=1.1e+02 Score=22.00 Aligned_cols=31 Identities=10% Similarity=0.204 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|+.+...-+.+.++..
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l 209 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERT 209 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567899999999999999987777766643
No 172
>PRK15008 HTH-type transcriptional regulator RutR; Provisional
Probab=24.86 E-value=73 Score=21.88 Aligned_cols=48 Identities=8% Similarity=0.117 Sum_probs=35.2
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
+......|....|.... ...||...|++..-|...|.++..-..--..
T Consensus 24 L~AA~~lf~e~Gy~~~s-~~dIA~~aGvs~gtiY~hF~sKe~L~~a~~~ 71 (212)
T PRK15008 24 LSAALDTFSQFGFHGTR-LEQIAELAGVSKTNLLYYFPSKEALYIAVLR 71 (212)
T ss_pred HHHHHHHHHHhCcccCC-HHHHHHHhCcCHHHHHHHCCCHHHHHHHHHH
Confidence 33444557777776544 6678999999999999999988876555333
No 173
>TIGR03613 RutR pyrimidine utilization regulatory protein R. This protein is observed in operons extremely similar to that characterized in E. coli K-12 responsible for the import and catabolism of pyrimidines, primarily uracil. This protein is a member of the TetR family of transcriptional regulators defined by the N-teminal model pfam00440 and the C-terminal model pfam08362 (YcdC-like protein, C-terminal region).
Probab=24.78 E-value=70 Score=21.51 Aligned_cols=44 Identities=7% Similarity=0.077 Sum_probs=32.2
Q ss_pred HHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 36 ELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 36 ~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
.....|.+..|-. .....||...|++..-+..+|.++-.-..--
T Consensus 16 aA~~lf~e~G~~~-~s~~~IA~~agvs~~~lY~hF~sKe~L~~av 59 (202)
T TIGR03613 16 AALDTFSRFGFHG-TSLEQIAELAGVSKTNLLYYFPSKDALYLAV 59 (202)
T ss_pred HHHHHHHHhCccc-CCHHHHHHHhCCCHHHHHHHcCCHHHHHHHH
Confidence 3344567777655 3467789999999999999998877655443
No 174
>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=24.68 E-value=86 Score=16.09 Aligned_cols=22 Identities=27% Similarity=0.469 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCccchhhhhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqN 72 (111)
...++|..++++...|..|...
T Consensus 17 s~~eia~~l~~s~~tv~~~~~~ 38 (57)
T cd06170 17 TNKEIADILGISEKTVKTHLRN 38 (57)
T ss_pred CHHHHHHHHCCCHHHHHHHHHH
Confidence 4567788999999999999863
No 175
>PRK07670 RNA polymerase sigma factor SigD; Validated
Probab=24.58 E-value=1.3e+02 Score=21.46 Aligned_cols=30 Identities=27% Similarity=0.283 Sum_probs=23.2
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.++..-+.+.|+
T Consensus 218 ~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 247 (251)
T PRK07670 218 LTLTEIGQVLNLSTSRISQIHSKALFKLKK 247 (251)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345678999999999999998766665554
No 176
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=24.57 E-value=2e+02 Score=18.50 Aligned_cols=29 Identities=10% Similarity=0.264 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.....-+.+.++
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ra~~~lr~ 155 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIRDALVHCRK 155 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35678899999999999987666655555
No 177
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.46 E-value=1e+02 Score=20.20 Aligned_cols=30 Identities=17% Similarity=0.182 Sum_probs=23.2
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
...++|..+|++...|+.....-+.+.++.
T Consensus 136 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~~ 165 (173)
T PRK09645 136 STAQIAADLGIPEGTVKSRLHYALRALRLA 165 (173)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 356789999999999999887666666653
No 178
>COG1595 RpoE DNA-directed RNA polymerase specialized sigma subunit, sigma24 homolog [Transcription]
Probab=24.29 E-value=1e+02 Score=20.59 Aligned_cols=32 Identities=22% Similarity=0.347 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
.-.++|..+|++...|+.+...-+.+.++...
T Consensus 145 s~~EIA~~l~i~~~tVks~l~ra~~~l~~~l~ 176 (182)
T COG1595 145 SYEEIAEILGISVGTVKSRLHRARKKLREQLE 176 (182)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHh
Confidence 34567889999999999999877777766443
No 179
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=24.27 E-value=1.1e+02 Score=20.88 Aligned_cols=31 Identities=16% Similarity=0.280 Sum_probs=24.4
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|++....-|.+.|+..
T Consensus 157 s~~EIA~~lgis~~tVk~~l~RAr~~Lr~~l 187 (201)
T PRK12545 157 EIDDICTELTLTANHCSVLLYRARTRLRTCL 187 (201)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 3567789999999999999887777666644
No 180
>PRK05988 formate dehydrogenase subunit gamma; Validated
Probab=24.25 E-value=1.6e+02 Score=19.81 Aligned_cols=34 Identities=18% Similarity=0.093 Sum_probs=26.8
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 33 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 33 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
-+..|...=....|.+......+|..+|++...|
T Consensus 25 li~~L~~vQ~~~G~Ip~e~~~~iA~~l~v~~~~V 58 (156)
T PRK05988 25 LLPILHAIQDEFGYVPEDAVPVIAEALNLSRAEV 58 (156)
T ss_pred HHHHHHHHHHHcCCCCHHHHHHHHHHhCCCHHHH
Confidence 3555555556678999999999999999998765
No 181
>PF12793 SgrR_N: Sugar transport-related sRNA regulator N-term
Probab=24.23 E-value=84 Score=20.08 Aligned_cols=33 Identities=15% Similarity=0.076 Sum_probs=23.5
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhh
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKI 68 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~ 68 (111)
...|...|. +.+......+||..+.|+.+.++.
T Consensus 6 y~~L~~~~~--~~~~~vtl~elA~~l~cS~Rn~r~ 38 (115)
T PF12793_consen 6 YQRLWQHYG--GQPVEVTLDELAELLFCSRRNART 38 (115)
T ss_pred HHHHHHHcC--CCCcceeHHHHHHHhCCCHHHHHH
Confidence 344555555 556667788999999999887654
No 182
>PRK07122 RNA polymerase sigma factor SigF; Reviewed
Probab=24.22 E-value=1.3e+02 Score=21.78 Aligned_cols=30 Identities=7% Similarity=0.226 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.+...-+.+.|+
T Consensus 232 ~t~~EIA~~lgis~~~V~~~~~ral~kLr~ 261 (264)
T PRK07122 232 MTQTQIAERVGISQMHVSRLLAKTLARLRD 261 (264)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 345778999999999999988766665554
No 183
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=24.22 E-value=86 Score=21.14 Aligned_cols=29 Identities=14% Similarity=-0.011 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.+...-|.+.++
T Consensus 148 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 176 (185)
T PRK09649 148 SYADAAAVCGCPVGTIRSRVARARDALLA 176 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 35678999999999999988766666555
No 184
>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=24.19 E-value=1.6e+02 Score=21.38 Aligned_cols=48 Identities=17% Similarity=0.106 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
++..+..+|...|-. -......++|..+|++...|+.....-..|.|+
T Consensus 219 L~~rer~vl~l~y~~---~~~~t~~eIA~~lgvS~~~V~q~~~~Al~kLr~ 266 (270)
T TIGR02392 219 LDARSRRIIEARWLD---DDKLTLQELAAEYGVSAERIRQIEKNAMKKLKA 266 (270)
T ss_pred CCHHHHHHHHHHhcC---CCCcCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 444455555555521 112345788999999999999888766666665
No 185
>PF12244 DUF3606: Protein of unknown function (DUF3606); InterPro: IPR022037 This family of proteins is found in bacteria. Proteins in this family are typically between 58 and 85 amino acids in length. There is a single completely conserved residue G that may be functionally important.
Probab=24.13 E-value=73 Score=17.74 Aligned_cols=18 Identities=22% Similarity=0.176 Sum_probs=11.1
Q ss_pred HHHHHHHHHhCCCccchh
Q psy9869 50 RRRIEMAHALCLTERQIK 67 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~ 67 (111)
.+...++..+|++..+++
T Consensus 21 ~ev~ywa~~~gvt~~~L~ 38 (57)
T PF12244_consen 21 YEVRYWAKRFGVTEEQLR 38 (57)
T ss_pred HHHHHHHHHHCcCHHHHH
Confidence 455566777777665543
No 186
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=23.75 E-value=1e+02 Score=20.62 Aligned_cols=31 Identities=16% Similarity=0.064 Sum_probs=24.4
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|+.+...-+.+.++.
T Consensus 148 ~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~~ 178 (184)
T PRK12539 148 LSVAEAATRSGMSESAVKVSVHRGLKALAAL 178 (184)
T ss_pred CcHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 4456789999999999999997666666653
No 187
>PRK12531 RNA polymerase sigma factor; Provisional
Probab=23.73 E-value=1e+02 Score=20.85 Aligned_cols=29 Identities=14% Similarity=0.122 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.-+..-+.+.++
T Consensus 159 s~~EIA~~lgis~~tVk~rl~ra~~~Lr~ 187 (194)
T PRK12531 159 PHQQVAEMFDIPLGTVKSRLRLAVEKLRH 187 (194)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 35677899999999998887666655554
No 188
>PF03672 UPF0154: Uncharacterised protein family (UPF0154); InterPro: IPR005359 The proteins in this entry are functionally uncharacterised.
Probab=23.55 E-value=1.6e+02 Score=17.03 Aligned_cols=31 Identities=13% Similarity=0.113 Sum_probs=25.1
Q ss_pred HHHHHHHHhcCCCCHHHHHHHHHHhCCCccc
Q psy9869 35 LELEKEFHTNHYLTRRRRIEMAHALCLTERQ 65 (111)
Q Consensus 35 ~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~ 65 (111)
..++..+.+||-.+......+..+.|-.+.+
T Consensus 20 ~~~~k~l~~NPpine~mir~M~~QMG~kpSe 50 (64)
T PF03672_consen 20 KYMEKQLKENPPINEKMIRAMMMQMGRKPSE 50 (64)
T ss_pred HHHHHHHHHCCCCCHHHHHHHHHHhCCCccH
Confidence 4567777889999999999999999966543
No 189
>PRK09706 transcriptional repressor DicA; Reviewed
Probab=23.48 E-value=46 Score=21.49 Aligned_cols=24 Identities=17% Similarity=0.318 Sum_probs=20.3
Q ss_pred HHHHHHHhCCCccchhhhhHHHhh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRM 75 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~ 75 (111)
...||..+|++...|..|..+++.
T Consensus 21 q~~lA~~~gvs~~~is~~E~g~~~ 44 (135)
T PRK09706 21 QRSLAKAVKVSHVSISQWERDETE 44 (135)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 467899999999999999987653
No 190
>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=23.40 E-value=2.4e+02 Score=18.97 Aligned_cols=33 Identities=12% Similarity=0.229 Sum_probs=25.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
....++|..+|++...|+.....-|.+.++...
T Consensus 148 ~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~~l~ 180 (188)
T TIGR02943 148 FESDEICQELEISTSNCHVLLYRARLSLRACLS 180 (188)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHHHHH
Confidence 345678999999999999988777766666444
No 191
>PRK11922 RNA polymerase sigma factor; Provisional
Probab=23.38 E-value=1.1e+02 Score=21.39 Aligned_cols=37 Identities=24% Similarity=0.286 Sum_probs=28.8
Q ss_pred CCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 46 YLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 46 ~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
|.......++|..+|++...|++....-|.+.|+...
T Consensus 162 ~~~g~s~~EIAe~lgis~~tVk~~l~Rar~kLr~~l~ 198 (231)
T PRK11922 162 VVEELSVEETAQALGLPEETVKTRLHRARRLLRESLA 198 (231)
T ss_pred hhcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHH
Confidence 3445567788999999999999998877777777544
No 192
>PRK07539 NADH dehydrogenase subunit E; Validated
Probab=23.36 E-value=1.6e+02 Score=19.62 Aligned_cols=34 Identities=9% Similarity=0.028 Sum_probs=26.7
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 33 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 33 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
-+..|...=....|.+......+|..+|++...|
T Consensus 24 ll~~L~~vQ~~~g~ip~~~~~~iA~~l~v~~~~v 57 (154)
T PRK07539 24 VIPALKIVQEQRGWVPDEAIEAVADYLGMPAIDV 57 (154)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3555555556678999999999999999998764
No 193
>PF07638 Sigma70_ECF: ECF sigma factor
Probab=22.98 E-value=99 Score=21.00 Aligned_cols=30 Identities=23% Similarity=0.343 Sum_probs=22.9
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|+++..|+..+..=|...++
T Consensus 152 ls~~EIA~~lgiS~~tV~r~l~~aR~~l~~ 181 (185)
T PF07638_consen 152 LSVEEIAERLGISERTVRRRLRRARAWLRR 181 (185)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 356678899999999998888766655554
No 194
>PF13542 HTH_Tnp_ISL3: Helix-turn-helix domain of transposase family ISL3
Probab=22.95 E-value=71 Score=16.66 Aligned_cols=21 Identities=14% Similarity=0.194 Sum_probs=17.7
Q ss_pred HHHHHHHHhCCCccchhhhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFq 71 (111)
....+|..+|++...|..+|.
T Consensus 29 s~~~vA~~~~vs~~TV~ri~~ 49 (52)
T PF13542_consen 29 SFKDVARELGVSWSTVRRIFD 49 (52)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356789999999999998885
No 195
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=22.90 E-value=95 Score=20.76 Aligned_cols=31 Identities=19% Similarity=0.372 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|++....-|.+.++..
T Consensus 140 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~~l 170 (185)
T PRK12542 140 TYQEISSVMGITEANVRKQFERARKRVQNMI 170 (185)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 3567789999999999998876666666543
No 196
>cd00592 HTH_MerR-like Helix-Turn-Helix DNA binding domain of MerR-like transcription regulators. Helix-turn-helix (HTH) MerR-like transcription regulator, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.87 E-value=61 Score=19.57 Aligned_cols=23 Identities=17% Similarity=0.183 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhHHHh
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRR 74 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR 74 (111)
..+++..+|++...|+.|-....
T Consensus 3 ~~eva~~~gi~~~tlr~~~~~Gl 25 (100)
T cd00592 3 IGEVAKLLGVSVRTLRYYEEKGL 25 (100)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35678899999999999965433
No 197
>PRK00118 putative DNA-binding protein; Validated
Probab=22.78 E-value=2.1e+02 Score=18.05 Aligned_cols=50 Identities=12% Similarity=0.034 Sum_probs=34.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHhHHH
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKEIQA 83 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~~ 83 (111)
++..+..++...|... ....++|..+|++...|..|...-+.+.++.-..
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr~~~~~ 67 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLEDYEEK 67 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHH
Confidence 4555666665554432 2355689999999999999998777776664443
No 198
>cd04780 HTH_MerR-like_sg5 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 5), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=22.78 E-value=60 Score=19.86 Aligned_cols=20 Identities=15% Similarity=0.248 Sum_probs=16.4
Q ss_pred HHHHHHHhCCCccchhhhhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFq 71 (111)
+.++|..+|++...|+.|-.
T Consensus 3 I~eva~~~gvs~~tlR~Ye~ 22 (95)
T cd04780 3 MSELSKRSGVSVATIKYYLR 22 (95)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45688899999999988864
No 199
>PF01726 LexA_DNA_bind: LexA DNA binding domain; InterPro: IPR006199 This is the DNA binding domain of the LexA SOS regulon repressor which prevents expression of DNA repair proteins in bacteria. The aligned region contains a variant form of the helix-turn-helix DNA binding motif []. This domain usually at the N terminus is found associated with IPR006198 from INTERPRO the auto-proteolytic domain of LexA 3.4.21.88 from EC.; GO: 0004252 serine-type endopeptidase activity, 0006508 proteolysis; PDB: 1LEA_A 1JHH_A 3JSP_A 1JHF_A 3JSO_B 1LEB_A 3K2Z_A.
Probab=22.62 E-value=1.4e+02 Score=17.02 Aligned_cols=40 Identities=25% Similarity=0.229 Sum_probs=23.2
Q ss_pred CCHHHHHHH---HHHHHhcCCCCHHHHHHHHHHhCCC-ccchhhhh
Q psy9869 29 YTRYQTLEL---EKEFHTNHYLTRRRRIEMAHALCLT-ERQIKIWF 70 (111)
Q Consensus 29 ~s~~q~~~L---~~~F~~~~~p~~~~~~~La~~l~l~-~~~V~~WF 70 (111)
+|..|..+| ..+...+.||. ...+|+..+|+. ...|..-.
T Consensus 4 LT~rQ~~vL~~I~~~~~~~G~~P--t~rEIa~~~g~~S~~tv~~~L 47 (65)
T PF01726_consen 4 LTERQKEVLEFIREYIEENGYPP--TVREIAEALGLKSTSTVQRHL 47 (65)
T ss_dssp --HHHHHHHHHHHHHHHHHSS-----HHHHHHHHTSSSHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHHHHcCCCC--CHHHHHHHhCCCChHHHHHHH
Confidence 456665555 44456777763 567889999996 55555433
No 200
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=22.58 E-value=99 Score=20.39 Aligned_cols=29 Identities=10% Similarity=0.154 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.-.++|..+|++...|+++...-+.+.+.
T Consensus 137 s~~EIA~~lgis~~tV~~~l~ra~~~~~~ 165 (172)
T PRK12523 137 GHAEIAERLGVSVSRVRQYLAQGLRQCYI 165 (172)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35667889999999999998766666554
No 201
>PF13551 HTH_29: Winged helix-turn helix
Probab=22.52 E-value=1.8e+02 Score=17.29 Aligned_cols=44 Identities=14% Similarity=0.138 Sum_probs=29.5
Q ss_pred CCCHHHHHHHHHHHHhcC-----CCCHHHHHH-H-HHHhC--CCccchhhhhH
Q psy9869 28 TYTRYQTLELEKEFHTNH-----YLTRRRRIE-M-AHALC--LTERQIKIWFQ 71 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~-----~p~~~~~~~-L-a~~l~--l~~~~V~~WFq 71 (111)
.+++++...|...+..++ ..+...... | ....| ++...|..|++
T Consensus 57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 389999999999998776 344454444 3 33333 56677887774
No 202
>PRK12535 RNA polymerase sigma factor; Provisional
Probab=22.51 E-value=1e+02 Score=21.15 Aligned_cols=32 Identities=16% Similarity=0.032 Sum_probs=25.1
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|+++...-+.+.|+...
T Consensus 151 s~~EIAe~lgis~~tV~~~l~Rar~~Lr~~l~ 182 (196)
T PRK12535 151 TYEEAAKIADVRVGTIRSRVARARADLIAATA 182 (196)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHHHhc
Confidence 35678999999999999999877777666443
No 203
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.34 E-value=2.5e+02 Score=18.67 Aligned_cols=48 Identities=19% Similarity=0.088 Sum_probs=35.2
Q ss_pred CCCCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 26 RQTYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 26 r~~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.+.++..|..+|...+ .. ....++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4567888888887742 22 246678999999999999988766666554
No 204
>PRK05911 RNA polymerase sigma factor sigma-28; Reviewed
Probab=22.02 E-value=1.8e+02 Score=20.89 Aligned_cols=31 Identities=16% Similarity=0.194 Sum_probs=23.5
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|+.+...-+.+.|+.
T Consensus 222 ~t~~EIA~~lgis~~~V~~~~~ral~kLr~~ 252 (257)
T PRK05911 222 LVLKEIGKILGVSESRVSQIHSKALLKLRAT 252 (257)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHHH
Confidence 3467789999999999999887666655553
No 205
>PRK08215 sporulation sigma factor SigG; Reviewed
Probab=21.88 E-value=1.4e+02 Score=21.37 Aligned_cols=47 Identities=15% Similarity=0.261 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 28 TYTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 28 ~~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
.++..+..++...|.. .....++|..+|++...|...-.+-..+.|+
T Consensus 209 ~L~~~er~vi~~~~~~-----~~t~~eIA~~lgis~~~V~~~~~~al~kLr~ 255 (258)
T PRK08215 209 KLNDREKLILNLRFFQ-----GKTQMEVAEEIGISQAQVSRLEKAALKHMRK 255 (258)
T ss_pred cCCHHHHHHHHHHHhc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 3555555566665532 2346678999999999998876655544443
No 206
>TIGR02885 spore_sigF RNA polymerase sigma-F factor. Members of this protein family are the RNA polymerase sigma factor F. Sigma-F is specifically and universally a component of the Firmicutes lineage endospore formation program, and is expressed in the forespore to turn on expression of dozens of genes. It is closely homologous to sigma-G, which is also expressed in the forespore.
Probab=21.84 E-value=2e+02 Score=20.06 Aligned_cols=45 Identities=13% Similarity=0.165 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhh
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLK 78 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~k 78 (111)
++..+..++...|. ......++|..+|++...|..+-..-..+.|
T Consensus 184 L~~~e~~i~~~~~~-----~~~t~~eIA~~lgis~~~V~~~~~~al~~Lr 228 (231)
T TIGR02885 184 LDERERQIIMLRYF-----KDKTQTEVANMLGISQVQVSRLEKKVLKKMK 228 (231)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 34444444444442 2235777899999999888887654444433
No 207
>TIGR01958 nuoE_fam NADH-quinone oxidoreductase, E subunit. This model describes the E chain of complexes that resemble NADH-quinone oxidoreductases. The electron acceptor is a quinone, ubiquinone, in mitochondria and most bacteria, including Escherichia coli, where the recommended gene symbol is nuoB. This model does not identify proteins from chloroplast and cyanobacteria.
Probab=21.83 E-value=1.9e+02 Score=19.09 Aligned_cols=34 Identities=12% Similarity=0.031 Sum_probs=25.9
Q ss_pred HHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 33 QTLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 33 q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
-+..|...=....|.+......+|..+|++...|
T Consensus 18 li~~L~~vQ~~~G~i~~~~~~~iA~~l~~~~~~v 51 (148)
T TIGR01958 18 IMPALMIAQEQKGWVTPEAIAAVAEMLGIPPVWV 51 (148)
T ss_pred HHHHHHHHHHHhCCCCHHHHHHHHHHhCcCHHHH
Confidence 3455555545567999999999999999988654
No 208
>cd04788 HTH_NolA-AlbR Helix-Turn-Helix DNA binding domain of the transcription regulators NolA and AlbR. Helix-turn-helix (HTH) transcription regulators NolA and AlbR, N-terminal domain. In Bradyrhizobium (Arachis) sp. NC92, NolA is required for efficient nodulation of host plants. In Xanthomonas albilineans, AlbR regulates the expression of the pathotoxin, albicidin. These proteins are putatively comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.77 E-value=65 Score=19.60 Aligned_cols=22 Identities=18% Similarity=0.080 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.++|..+|++...++.|-...
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (96)
T cd04788 3 IGELARRTGLSVRTLHHYDHIG 24 (96)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4568999999999999998643
No 209
>PRK12534 RNA polymerase sigma factor; Provisional
Probab=21.64 E-value=1.8e+02 Score=19.37 Aligned_cols=30 Identities=23% Similarity=0.207 Sum_probs=21.7
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
....++|..+|++...|+.-...-|.+.|.
T Consensus 154 ~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 183 (187)
T PRK12534 154 ITYEELAARTDTPIGTVKSWIRRGLAKLKA 183 (187)
T ss_pred CCHHHHHHHhCCChhHHHHHHHHHHHHHHH
Confidence 345667889999999998877655555544
No 210
>PF08452 DNAP_B_exo_N: DNA polymerase family B exonuclease domain, N-terminal; InterPro: IPR013660 This domain is found in viral DNA polymerases to the N terminus of DNA polymerase family B exonuclease domains (IPR006133 from INTERPRO). ; GO: 0003887 DNA-directed DNA polymerase activity
Probab=21.60 E-value=27 Score=15.77 Aligned_cols=9 Identities=33% Similarity=0.796 Sum_probs=6.3
Q ss_pred hhhhhHHHh
Q psy9869 66 IKIWFQNRR 74 (111)
Q Consensus 66 V~~WFqNrR 74 (111)
+-+||-++.
T Consensus 5 CiNWFE~~g 13 (22)
T PF08452_consen 5 CINWFESRG 13 (22)
T ss_pred EeehhhhCC
Confidence 347998775
No 211
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.48 E-value=76 Score=19.35 Aligned_cols=22 Identities=9% Similarity=0.009 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.++|..+|++...++.|....
T Consensus 3 i~eva~~~gvs~~tlR~ye~~G 24 (97)
T cd04782 3 TGEFAKLCGISKQTLFHYDKIG 24 (97)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567889999999999997543
No 212
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=21.42 E-value=67 Score=19.79 Aligned_cols=21 Identities=5% Similarity=0.026 Sum_probs=17.2
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
+.++|..+|++...++.|-+.
T Consensus 4 i~eva~~~gvs~~tLR~ye~~ 24 (102)
T cd04775 4 IGQMSRKFGVSRSTLLYYESI 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456889999999999999754
No 213
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=21.32 E-value=2.6e+02 Score=18.55 Aligned_cols=29 Identities=14% Similarity=0.241 Sum_probs=22.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKK 79 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk 79 (111)
...++|..+|++...|+.....-+.+.+.
T Consensus 145 s~~EIA~~lgis~~tVk~~l~rAl~~~~~ 173 (178)
T PRK12529 145 KQKDIAQALDIALPTVKKYIHQAYVTCLS 173 (178)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35677899999999999988765555543
No 214
>PF01257 2Fe-2S_thioredx: Thioredoxin-like [2Fe-2S] ferredoxin; InterPro: IPR002023 NADH:ubiquinone oxidoreductase (complex I) (1.6.5.3 from EC) is a respiratory-chain enzyme that catalyses the transfer of two electrons from NADH to ubiquinone in a reaction that is associated with proton translocation across the membrane (NADH + ubiquinone = NAD+ + ubiquinol) []. Complex I is a major source of reactive oxygen species (ROS) that are predominantly formed by electron transfer from FMNH(2). Complex I is found in bacteria, cyanobacteria (as a NADH-plastoquinone oxidoreductase), archaea [], mitochondira, and in the hydrogenosome, a mitochondria-derived organelle. In general, the bacterial complex consists of 14 different subunits, while the mitochondrial complex contains homologues to these subunits in addition to approximately 31 additional proteins []. Mitochondrial complex I, which is located in the inner mitochondrial membrane, is the largest multimeric respiratory enzyme in the mitochondria, consisting of more than 40 subunits, one FMN co-factor and eight FeS clusters []. The assembly of mitochondrial complex I is an intricate process that requires the cooperation of the nuclear and mitochondrial genomes [, ]. Mitochondrial complex I can cycle between active and deactive forms that can be distinguished by the reactivity towards divalent cations and thiol-reactive agents. All redox prosthetic groups reside in the peripheral arm of the L-shaped structure. The NADH oxidation domain harbouring the FMN cofactor is connected via a chain of iron-sulphur clusters to the ubiquinone reduction site that is located in a large pocket formed by the PSST and 49kDa subunits of complex I []. Among the many polypeptide subunits that make up complex I, there is one with a molecular weight of 24 kDa (in mammals), which is a component of the iron-sulphur (IP) fragment of the enzyme. It seems to bind a 2Fe-2S iron-sulphur cluster. The 24 kDa subunit is nuclear encoded, as a precursor form with a transit peptide in mammals and in Neurospora crassa. There is a highly conserved region located in the central section of this subunit that contains two conserved cysteines, that are probably involved in the binding of the 2Fe-2S centre. The 24 kDa subunit is highly similar to [, ]: Subunit E of Escherichia coli NADH-ubiquinone oxidoreductase (gene nuoE) Subunit NQO2 of Paracoccus denitrificans NADH-ubiquinone oxidoreductase ; GO: 0016491 oxidoreductase activity, 0051287 NAD binding, 0055114 oxidation-reduction process; PDB: 1M2D_A 1M2A_B 1F37_B 1M2B_B 2FUG_B 3M9S_B 3IAM_B 3IAS_K 2YBB_2 3I9V_B ....
Probab=21.23 E-value=1.5e+02 Score=19.52 Aligned_cols=33 Identities=18% Similarity=0.186 Sum_probs=23.6
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
+..|...=..-.|.+......+|..+|++...|
T Consensus 16 l~~L~~~Q~~~g~i~~~~~~~iA~~l~i~~~~v 48 (145)
T PF01257_consen 16 LPILHEVQEEYGYIPEEALEEIAEALGIPPAEV 48 (145)
T ss_dssp HHHHHHHHHHHSS--HHHHHHHHHHHTS-HHHH
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHHCCCHHHH
Confidence 455655556678999999999999999998765
No 215
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=21.04 E-value=1.1e+02 Score=21.43 Aligned_cols=31 Identities=13% Similarity=0.065 Sum_probs=24.0
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
...++|..+|++...|+.+...-|.+.++..
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~RAr~~Lr~~l 182 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLARARRRLAALL 182 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 4567789999999999998876666666643
No 216
>TIGR02394 rpoS_proteo RNA polymerase sigma factor RpoS. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoS (also called sigma-38, KatF, etc.), found only in Proteobacteria. This sigma factor is induced in stationary phase (in response to the stress of nutrient limitation) and becomes the second prinicipal sigma factor at that time. RpoS is a member of the larger Sigma-70 subfamily (TIGR02937) and most closely related to RpoD (TIGR02393).
Probab=20.96 E-value=3.4e+02 Score=19.75 Aligned_cols=32 Identities=19% Similarity=0.180 Sum_probs=25.4
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
....++|..+|++...|+.+...-+.+.|+..
T Consensus 243 ~s~~EIA~~Lgis~~tVk~~l~rAlkkLr~~l 274 (285)
T TIGR02394 243 ATLEEVAAEVGLTRERVRQIQVEALKKLRRIL 274 (285)
T ss_pred ccHHHHHHHHCCCHHHHHHHHHHHHHHHHHHH
Confidence 44677899999999999999887777666644
No 217
>PRK10668 DNA-binding transcriptional repressor AcrR; Provisional
Probab=20.90 E-value=1.1e+02 Score=20.79 Aligned_cols=46 Identities=15% Similarity=0.083 Sum_probs=34.4
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
+......|.+..|-.. ....|+...|++..-+..+|.++-.-..--
T Consensus 17 l~AA~~lf~e~G~~~~-t~~~Ia~~agvs~~tlY~~F~sKe~Ll~~v 62 (215)
T PRK10668 17 LDAALRLFSQQGVSAT-SLADIAKAAGVTRGAIYWHFKNKSDLFSEI 62 (215)
T ss_pred HHHHHHHHHHcCcccC-CHHHHHHHhCCChHHHHHHCCCHHHHHHHH
Confidence 4445556877787653 367789999999999999998887764443
No 218
>PF07022 Phage_CI_repr: Bacteriophage CI repressor helix-turn-helix domain; InterPro: IPR010744 This family consists of several phage CI repressor proteins and related bacterial sequences. The CI repressor is known to function as a transcriptional switch, determining whether transcription is lytic or lysogenic [].; GO: 0003677 DNA binding, 0045892 negative regulation of transcription, DNA-dependent; PDB: 2FJR_B.
Probab=20.89 E-value=36 Score=19.29 Aligned_cols=20 Identities=20% Similarity=0.434 Sum_probs=15.3
Q ss_pred HHHHHHHhCCCccchh-hhhH
Q psy9869 52 RIEMAHALCLTERQIK-IWFQ 71 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~-~WFq 71 (111)
..+||..+|++...|. .|..
T Consensus 15 ~~~lA~~lgis~st~s~~~~~ 35 (66)
T PF07022_consen 15 DKELAERLGISKSTLSNNWKK 35 (66)
T ss_dssp CHHHHCCTT--HHHHH-HHHH
T ss_pred HHHHHHHhCcCHHHhhHHHHh
Confidence 4578999999999999 8885
No 219
>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=20.84 E-value=82 Score=16.29 Aligned_cols=37 Identities=11% Similarity=0.213 Sum_probs=22.4
Q ss_pred CCHHHHHHHHHHHHhcCCCCHHHHHHHHHHhCCCccchhhhh
Q psy9869 29 YTRYQTLELEKEFHTNHYLTRRRRIEMAHALCLTERQIKIWF 70 (111)
Q Consensus 29 ~s~~q~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V~~WF 70 (111)
++..+...+...+... .....+|..+|++...|..++
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 4444444444444433 336778999999998887765
No 220
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.58 E-value=72 Score=19.68 Aligned_cols=21 Identities=10% Similarity=0.075 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
+.++|..+|++...++.|-..
T Consensus 4 i~eva~~~gvs~~tlR~ye~~ 24 (102)
T cd04789 4 ISELAEKAGISRSTLLYYEKL 24 (102)
T ss_pred HHHHHHHHCcCHHHHHHHHHC
Confidence 456788899999988888754
No 221
>PF06971 Put_DNA-bind_N: Putative DNA-binding protein N-terminus; InterPro: IPR009718 This entry represents the C terminus (approximately 30 residues) of a number of Rex proteins. These are redox-sensing repressors that appear to be widespread among Gram-positive bacteria []. They modulate transcription in response to changes in cellular NADH/NAD(+) redox state. Rex is predicted to include a pyridine nucleotide-binding domain (Rossmann fold), and residues that might play key structural and nucleotide binding roles are highly conserved.; GO: 0045892 negative regulation of transcription, DNA-dependent, 0051775 response to redox state, 0005737 cytoplasm; PDB: 3IL2_B 3IKT_A 3IKV_B 1XCB_F 2DT5_A 2VT3_A 2VT2_A 3KEO_B 3KET_A 3KEQ_A ....
Probab=20.41 E-value=61 Score=17.70 Aligned_cols=18 Identities=33% Similarity=0.407 Sum_probs=13.0
Q ss_pred HHHHHHHHhCCCccchhh
Q psy9869 51 RRIEMAHALCLTERQIKI 68 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~ 68 (111)
.-.+||..+|++..+|+-
T Consensus 30 SS~~La~~~gi~~~qVRK 47 (50)
T PF06971_consen 30 SSQELAEALGITPAQVRK 47 (50)
T ss_dssp -HHHHHHHHTS-HHHHHH
T ss_pred CHHHHHHHHCCCHHHhcc
Confidence 356789999999988863
No 222
>TIGR02835 spore_sigmaE RNA polymerase sigma-E factor. Members of this family comprise the Firmicutes lineage endospore formation-specific sigma factor SigE, also called SpoIIGB and sigma-29. As characterized in Bacillus subtilis, this protein is synthesized as a precursor, specifically in the mother cell compartment, and must cleaved by the SpoIIGA protein to be made active.
Probab=20.40 E-value=1.3e+02 Score=21.25 Aligned_cols=31 Identities=26% Similarity=0.269 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCCccchhhhhHHHhhHhhHh
Q psy9869 50 RRRIEMAHALCLTERQIKIWFQNRRMKLKKE 80 (111)
Q Consensus 50 ~~~~~La~~l~l~~~~V~~WFqNrR~k~kk~ 80 (111)
....++|..+|++...|+.+...-+.+.|+.
T Consensus 199 ~s~~EIA~~Lgis~~tV~~~l~ra~~~LR~~ 229 (234)
T TIGR02835 199 KTQKEVADMLGISQSYISRLEKRILKRLKKE 229 (234)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 3456778899999999999887656665553
No 223
>PRK12517 RNA polymerase sigma factor; Provisional
Probab=20.35 E-value=1.6e+02 Score=19.91 Aligned_cols=32 Identities=22% Similarity=0.278 Sum_probs=24.7
Q ss_pred HHHHHHHHhCCCccchhhhhHHHhhHhhHhHH
Q psy9869 51 RRIEMAHALCLTERQIKIWFQNRRMKLKKEIQ 82 (111)
Q Consensus 51 ~~~~La~~l~l~~~~V~~WFqNrR~k~kk~~~ 82 (111)
...++|..+|++...|+++..--|.+.++...
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~l~ 177 (188)
T PRK12517 146 SGEEIAEILDLNKNTVMTRLFRARNQLKEALE 177 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999998766666666443
No 224
>PRK07571 bidirectional hydrogenase complex protein HoxE; Reviewed
Probab=20.34 E-value=2.1e+02 Score=19.61 Aligned_cols=33 Identities=24% Similarity=0.178 Sum_probs=24.9
Q ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhCCCccch
Q psy9869 34 TLELEKEFHTNHYLTRRRRIEMAHALCLTERQI 66 (111)
Q Consensus 34 ~~~L~~~F~~~~~p~~~~~~~La~~l~l~~~~V 66 (111)
+..|...=....|.+......+|..+|++...|
T Consensus 39 i~~L~~iQ~~~GyIp~e~~~~iA~~l~v~~a~V 71 (169)
T PRK07571 39 IEVLHKAQELFGYLERDLLLYVARQLKLPLSRV 71 (169)
T ss_pred HHHHHHHHHHcCCCCHHHHHHHHHHhCcCHHHH
Confidence 344444445578999999999999999988654
No 225
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=20.32 E-value=1.5e+02 Score=20.52 Aligned_cols=30 Identities=20% Similarity=0.430 Sum_probs=24.3
Q ss_pred HHHHHHHhCCCccchhhhhHHHhhHhhHhH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNRRMKLKKEI 81 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNrR~k~kk~~ 81 (111)
..++|..+|++...|+.....-|.+.|+..
T Consensus 167 ~~EIAe~lgis~~tV~~~l~RAr~~Lr~~l 196 (206)
T PRK12544 167 TNEICHAVDLSVSNLNVLLYRARLRLRECL 196 (206)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHHHH
Confidence 467899999999999999887777766644
No 226
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.25 E-value=75 Score=19.76 Aligned_cols=21 Identities=14% Similarity=0.075 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCccchhhhhHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQN 72 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqN 72 (111)
+.++|..+|++...++.|-..
T Consensus 3 i~eva~~~gis~~tlR~ye~~ 23 (108)
T cd01107 3 IGEFAKLSNLSIKALRYYDKI 23 (108)
T ss_pred HHHHHHHHCcCHHHHHHHHHc
Confidence 456889999999999999864
No 227
>cd01109 HTH_YyaN Helix-Turn-Helix DNA binding domain of the MerR-like transcription regulators YyaN and YraB. Putative helix-turn-helix (HTH) MerR-like transcription regulators of Bacillus subtilis, YyaN and YraB, and related proteins; N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=20.16 E-value=75 Score=19.84 Aligned_cols=22 Identities=14% Similarity=0.175 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCccchhhhhHHH
Q psy9869 52 RIEMAHALCLTERQIKIWFQNR 73 (111)
Q Consensus 52 ~~~La~~l~l~~~~V~~WFqNr 73 (111)
+.++|..+|++...++.|-+..
T Consensus 3 i~e~a~~~gvs~~tlr~ye~~g 24 (113)
T cd01109 3 IKEVAEKTGLSADTLRYYEKEG 24 (113)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4567888899888888886543
Done!