Query 040769
Match_columns 257
No_of_seqs 316 out of 1635
Neff 6.6
Searched_HMMs 46136
Date Fri Mar 29 11:37:30 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/040769.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/040769hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 1.7E-21 3.7E-26 167.9 11.0 99 83-181 48-146 (198)
2 KOG0489 Transcription factor z 99.8 1.4E-20 3.1E-25 169.4 2.4 65 82-146 156-220 (261)
3 KOG0487 Transcription factor A 99.8 1.3E-19 2.8E-24 164.9 4.2 65 82-146 232-296 (308)
4 KOG0488 Transcription factor B 99.8 5.6E-19 1.2E-23 162.3 5.8 65 82-146 169-233 (309)
5 KOG0848 Transcription factor C 99.8 6.3E-19 1.4E-23 155.7 5.1 92 55-146 166-260 (317)
6 KOG0843 Transcription factor E 99.7 2.8E-18 6.1E-23 144.0 4.9 66 82-147 99-164 (197)
7 KOG4577 Transcription factor L 99.7 2.3E-18 5E-23 153.6 4.3 127 81-221 163-296 (383)
8 KOG0842 Transcription factor t 99.7 4.1E-18 9E-23 155.0 5.4 64 89-152 157-220 (307)
9 KOG0850 Transcription factor D 99.7 3E-17 6.5E-22 142.5 5.1 69 76-144 113-181 (245)
10 KOG0485 Transcription factor N 99.7 2.4E-17 5.1E-22 142.0 3.7 64 82-145 101-164 (268)
11 KOG0484 Transcription factor P 99.7 9.1E-18 2E-22 129.3 0.5 65 82-146 14-78 (125)
12 KOG2251 Homeobox transcription 99.7 7.2E-17 1.6E-21 139.5 5.5 68 80-147 32-99 (228)
13 KOG0492 Transcription factor M 99.7 1.1E-16 2.4E-21 137.1 6.5 63 82-144 141-203 (246)
14 PF00046 Homeobox: Homeobox do 99.6 7.8E-17 1.7E-21 112.1 3.6 57 86-142 1-57 (57)
15 KOG0494 Transcription factor C 99.6 1.3E-16 2.8E-21 140.6 3.7 69 89-157 145-213 (332)
16 KOG0844 Transcription factor E 99.6 2.2E-16 4.9E-21 141.8 2.3 66 82-147 178-243 (408)
17 KOG0493 Transcription factor E 99.6 8E-16 1.7E-20 135.8 4.1 60 85-144 246-305 (342)
18 COG5576 Homeodomain-containing 99.5 9.2E-15 2E-19 122.1 4.8 68 79-146 45-112 (156)
19 smart00389 HOX Homeodomain. DN 99.5 8.4E-15 1.8E-19 101.1 3.8 55 87-141 2-56 (56)
20 TIGR01565 homeo_ZF_HD homeobox 99.5 1.7E-14 3.8E-19 101.2 5.4 52 86-137 2-57 (58)
21 KOG3802 Transcription factor O 99.5 9.7E-15 2.1E-19 135.9 4.9 62 83-144 292-353 (398)
22 cd00086 homeodomain Homeodomai 99.5 1.2E-14 2.6E-19 101.0 3.9 57 87-143 2-58 (59)
23 KOG0491 Transcription factor B 99.5 5.3E-15 1.2E-19 122.7 0.2 62 83-144 98-159 (194)
24 KOG0486 Transcription factor P 99.4 5.7E-14 1.2E-18 127.0 3.4 71 84-154 111-181 (351)
25 KOG0847 Transcription factor, 99.3 2.8E-13 6E-18 117.2 2.2 64 83-146 165-228 (288)
26 KOG0490 Transcription factor, 99.2 1E-11 2.2E-16 108.6 3.2 64 82-145 57-120 (235)
27 KOG1168 Transcription factor A 99.1 8E-11 1.7E-15 105.7 3.3 64 81-144 305-368 (385)
28 KOG0849 Transcription factor P 99.0 2.7E-10 5.8E-15 107.0 3.7 67 79-145 170-236 (354)
29 KOG0775 Transcription factor S 98.8 3.8E-09 8.1E-14 94.4 3.9 51 92-142 183-233 (304)
30 KOG0774 Transcription factor P 98.5 1.1E-07 2.5E-12 84.5 3.5 59 85-143 188-249 (334)
31 PF05920 Homeobox_KN: Homeobox 98.2 2.3E-07 4.9E-12 60.5 0.3 34 106-139 7-40 (40)
32 KOG2252 CCAAT displacement pro 98.0 3.6E-06 7.9E-11 81.8 3.7 59 82-140 417-475 (558)
33 KOG0490 Transcription factor, 98.0 4.5E-06 9.7E-11 72.8 3.9 65 81-145 149-213 (235)
34 KOG1146 Homeobox protein [Gene 97.6 5.2E-05 1.1E-09 80.1 4.0 64 82-145 900-963 (1406)
35 KOG0773 Transcription factor M 96.6 0.0026 5.7E-08 59.3 4.7 63 86-148 240-305 (342)
36 PF11569 Homez: Homeodomain le 96.3 0.0012 2.5E-08 46.0 0.2 43 96-138 9-51 (56)
37 PF02183 HALZ: Homeobox associ 94.9 0.073 1.6E-06 35.4 4.9 37 143-179 1-37 (45)
38 KOG3623 Homeobox transcription 94.5 0.027 5.8E-07 57.1 2.8 48 97-144 568-615 (1007)
39 smart00340 HALZ homeobox assoc 93.7 0.14 3.1E-06 33.5 4.1 33 144-176 2-34 (44)
40 PF04218 CENP-B_N: CENP-B N-te 93.3 0.12 2.5E-06 35.4 3.4 46 86-136 1-46 (53)
41 PF02183 HALZ: Homeobox associ 90.8 0.76 1.6E-05 30.6 4.9 35 144-178 9-43 (45)
42 PRK09413 IS2 repressor TnpA; R 84.3 3.4 7.4E-05 32.7 6.1 87 88-179 9-103 (121)
43 PF04967 HTH_10: HTH DNA bindi 76.4 2.4 5.2E-05 29.2 2.3 39 92-130 1-41 (53)
44 KOG3755 SATB1 matrix attachmen 74.2 1.5 3.3E-05 44.0 1.2 64 82-145 688-759 (769)
45 PF01527 HTH_Tnp_1: Transposas 73.4 3.4 7.4E-05 29.3 2.7 43 87-134 2-45 (76)
46 KOG4196 bZIP transcription fac 73.0 23 0.00051 28.8 7.5 76 90-178 22-112 (135)
47 PF04545 Sigma70_r4: Sigma-70, 70.0 3.1 6.8E-05 27.4 1.6 39 91-134 4-42 (50)
48 PF13443 HTH_26: Cro/C1-type H 69.5 3.5 7.5E-05 28.2 1.9 44 114-157 12-55 (63)
49 cd06171 Sigma70_r4 Sigma70, re 68.1 3.5 7.7E-05 26.1 1.6 43 91-138 10-52 (55)
50 cd00569 HTH_Hin_like Helix-tur 67.2 7.8 0.00017 21.9 2.9 40 89-133 3-42 (42)
51 cd01106 HTH_TipAL-Mta Helix-Tu 66.8 37 0.0008 25.8 7.3 37 88-137 35-71 (103)
52 KOG1146 Homeobox protein [Gene 61.9 9.4 0.0002 41.8 4.1 60 85-144 705-764 (1406)
53 KOG3623 Homeobox transcription 61.4 3.7 8.1E-05 42.3 1.0 60 87-146 628-687 (1007)
54 PRK00888 ftsB cell division pr 60.0 21 0.00046 27.8 4.8 47 128-175 16-62 (105)
55 PF08281 Sigma70_r4_2: Sigma-7 60.0 5.6 0.00012 26.4 1.4 41 92-137 11-51 (54)
56 PRK03975 tfx putative transcri 59.3 13 0.00027 30.8 3.6 49 89-143 4-52 (141)
57 PF00196 GerE: Bacterial regul 57.7 8.1 0.00018 26.2 1.9 46 91-142 3-48 (58)
58 PF10668 Phage_terminase: Phag 56.9 4.3 9.4E-05 28.7 0.4 20 114-133 24-43 (60)
59 cd01109 HTH_YyaN Helix-Turn-He 55.3 94 0.002 23.9 7.9 72 89-175 36-107 (113)
60 COG3413 Predicted DNA binding 53.4 10 0.00022 33.0 2.2 38 91-128 155-194 (215)
61 PRK09646 RNA polymerase sigma 51.2 14 0.00031 31.1 2.8 45 92-141 143-187 (194)
62 KOG3119 Basic region leucine z 50.5 36 0.00078 30.9 5.5 31 149-179 224-254 (269)
63 PF13936 HTH_38: Helix-turn-he 50.3 6.4 0.00014 25.6 0.4 40 89-133 2-41 (44)
64 PRK10072 putative transcriptio 48.3 16 0.00036 28.0 2.5 45 89-140 30-74 (96)
65 PRK00118 putative DNA-binding 46.3 71 0.0015 24.9 5.8 46 92-142 18-63 (104)
66 PF00170 bZIP_1: bZIP transcri 45.9 98 0.0021 21.4 6.2 29 149-177 28-56 (64)
67 PRK14127 cell division protein 45.3 78 0.0017 25.0 5.9 42 139-180 22-63 (109)
68 PRK06759 RNA polymerase factor 45.3 16 0.00034 29.2 2.1 45 92-141 107-151 (154)
69 PRK09642 RNA polymerase sigma 44.2 20 0.00043 28.9 2.5 46 92-142 107-152 (160)
70 PRK12526 RNA polymerase sigma 43.6 20 0.00043 30.6 2.6 46 92-142 154-199 (206)
71 PRK09652 RNA polymerase sigma 43.4 20 0.00043 29.1 2.4 45 92-141 129-173 (182)
72 PRK12530 RNA polymerase sigma 42.5 25 0.00055 29.5 3.0 46 92-142 135-180 (189)
73 cd04781 HTH_MerR-like_sg6 Heli 42.2 1.6E+02 0.0036 22.9 8.1 37 88-137 34-70 (120)
74 KOG4005 Transcription factor X 41.1 1E+02 0.0023 27.8 6.6 9 84-92 53-61 (292)
75 PF09607 BrkDBD: Brinker DNA-b 41.0 24 0.00053 24.7 2.2 44 89-134 3-47 (58)
76 PRK11924 RNA polymerase sigma 40.7 29 0.00062 28.0 3.0 29 114-142 143-171 (179)
77 cd04770 HTH_HMRTR Helix-Turn-H 40.4 1.7E+02 0.0038 22.7 7.5 75 88-177 35-109 (123)
78 PRK12512 RNA polymerase sigma 40.2 25 0.00053 29.1 2.6 45 92-141 132-176 (184)
79 PRK12519 RNA polymerase sigma 40.2 19 0.00042 30.0 1.9 29 114-142 159-187 (194)
80 TIGR02937 sigma70-ECF RNA poly 39.8 24 0.00051 27.1 2.3 45 92-141 111-155 (158)
81 KOG4571 Activating transcripti 39.4 76 0.0017 29.3 5.7 28 150-177 251-278 (294)
82 smart00421 HTH_LUXR helix_turn 39.0 27 0.00059 22.3 2.2 39 91-135 3-41 (58)
83 PRK04217 hypothetical protein; 39.0 27 0.00059 27.6 2.4 41 90-135 41-81 (110)
84 PF12824 MRP-L20: Mitochondria 38.8 2.4E+02 0.0052 23.8 12.3 66 88-157 82-147 (164)
85 PRK12514 RNA polymerase sigma 38.3 31 0.00068 28.3 2.9 28 114-141 147-174 (179)
86 PF02796 HTH_7: Helix-turn-hel 38.3 21 0.00045 23.1 1.4 40 89-133 3-42 (45)
87 PF08280 HTH_Mga: M protein tr 37.6 24 0.00052 24.2 1.8 33 95-131 6-38 (59)
88 PF06056 Terminase_5: Putative 37.6 15 0.00032 25.5 0.7 28 113-142 14-41 (58)
89 PRK09648 RNA polymerase sigma 37.4 27 0.00059 29.0 2.4 43 92-139 140-182 (189)
90 cd04761 HTH_MerR-SF Helix-Turn 37.3 13 0.00028 23.8 0.3 24 115-138 3-26 (49)
91 TIGR03879 near_KaiC_dom probab 37.2 7.9 0.00017 28.4 -0.8 35 102-136 22-56 (73)
92 TIGR02959 SigZ RNA polymerase 36.9 27 0.00059 28.7 2.3 38 92-134 101-138 (170)
93 PF00170 bZIP_1: bZIP transcri 36.7 1.4E+02 0.0031 20.6 6.4 35 143-177 29-63 (64)
94 cd04769 HTH_MerR2 Helix-Turn-H 36.4 1.7E+02 0.0036 22.7 6.6 75 88-176 34-108 (116)
95 TIGR02948 SigW_bacill RNA poly 35.9 27 0.00058 28.7 2.1 45 92-141 137-181 (187)
96 TIGR02989 Sig-70_gvs1 RNA poly 35.3 29 0.00063 27.7 2.2 41 92-137 112-152 (159)
97 KOG0150 Spliceosomal protein F 35.3 88 0.0019 29.2 5.4 14 129-142 16-29 (336)
98 PRK06930 positive control sigm 35.3 32 0.00068 29.0 2.4 46 92-142 115-160 (170)
99 TIGR03001 Sig-70_gmx1 RNA poly 35.1 39 0.00085 30.0 3.2 40 114-153 179-218 (244)
100 TIGR02999 Sig-70_X6 RNA polyme 35.1 32 0.00069 28.3 2.4 28 114-141 152-179 (183)
101 PRK12515 RNA polymerase sigma 35.0 40 0.00086 28.1 3.0 46 92-142 132-177 (189)
102 cd04765 HTH_MlrA-like_sg2 Heli 34.4 1.1E+02 0.0025 23.2 5.3 40 88-139 35-74 (99)
103 PRK05602 RNA polymerase sigma 34.3 30 0.00064 28.7 2.1 28 114-141 146-173 (186)
104 cd01392 HTH_LacI Helix-turn-he 34.0 29 0.00063 22.4 1.7 21 117-137 2-22 (52)
105 PRK12537 RNA polymerase sigma 33.9 40 0.00087 27.9 2.9 45 92-141 134-178 (182)
106 TIGR02985 Sig70_bacteroi1 RNA 33.6 34 0.00074 27.0 2.3 44 92-140 114-157 (161)
107 TIGR02051 MerR Hg(II)-responsi 33.4 2.4E+02 0.0052 22.2 7.4 37 88-137 34-70 (124)
108 cd04787 HTH_HMRTR_unk Helix-Tu 33.2 2.5E+02 0.0054 22.3 7.8 75 89-178 36-110 (133)
109 PRK09644 RNA polymerase sigma 33.2 41 0.00089 27.2 2.8 29 114-142 126-154 (165)
110 PF00424 REV: REV protein (ant 33.1 40 0.00087 25.8 2.4 36 97-146 14-49 (91)
111 PF13518 HTH_28: Helix-turn-he 32.8 19 0.00041 23.3 0.6 22 114-135 14-35 (52)
112 COG4367 Uncharacterized protei 32.4 39 0.00085 25.8 2.2 37 92-128 3-39 (97)
113 PF06156 DUF972: Protein of un 32.4 1.6E+02 0.0034 23.1 5.8 37 145-181 20-56 (107)
114 cd04785 HTH_CadR-PbrR-like Hel 32.1 2.5E+02 0.0054 22.1 7.8 75 88-177 35-109 (126)
115 cd04783 HTH_MerR1 Helix-Turn-H 32.1 2.5E+02 0.0054 22.0 8.0 38 88-138 35-72 (126)
116 PRK09047 RNA polymerase factor 31.6 41 0.00088 26.9 2.5 41 92-137 107-147 (161)
117 cd04779 HTH_MerR-like_sg4 Heli 31.1 2.8E+02 0.0061 22.4 8.0 37 88-137 34-70 (134)
118 PRK12538 RNA polymerase sigma 31.0 43 0.00094 29.4 2.7 27 115-141 190-216 (233)
119 PRK09639 RNA polymerase sigma 31.0 37 0.00081 27.3 2.2 44 92-141 113-156 (166)
120 cd04775 HTH_Cfa-like Helix-Tur 30.9 2.4E+02 0.0051 21.4 7.3 35 88-135 35-69 (102)
121 KOG2391 Vacuolar sorting prote 30.7 4.8E+02 0.01 24.9 10.4 25 154-178 253-277 (365)
122 PRK12543 RNA polymerase sigma 30.5 65 0.0014 26.5 3.6 28 114-141 135-162 (179)
123 TIGR02954 Sig70_famx3 RNA poly 30.5 44 0.00096 27.1 2.6 44 92-140 120-163 (169)
124 smart00338 BRLZ basic region l 30.2 1.9E+02 0.004 20.0 5.9 30 148-177 27-56 (65)
125 cd00093 HTH_XRE Helix-turn-hel 30.2 44 0.00095 20.5 2.0 23 115-137 15-37 (58)
126 PHA02955 hypothetical protein; 30.1 73 0.0016 28.2 3.9 43 93-135 59-102 (213)
127 TIGR02939 RpoE_Sigma70 RNA pol 30.0 32 0.0007 28.3 1.7 27 114-140 156-182 (190)
128 PRK12541 RNA polymerase sigma 30.0 35 0.00076 27.5 1.8 45 92-141 113-157 (161)
129 PRK09637 RNA polymerase sigma 29.8 42 0.00091 28.0 2.3 39 92-135 107-145 (181)
130 COG3074 Uncharacterized protei 29.7 2.2E+02 0.0048 20.8 5.6 39 139-177 31-69 (79)
131 COG2963 Transposase and inacti 29.2 77 0.0017 24.4 3.6 42 89-134 5-47 (116)
132 cd06170 LuxR_C_like C-terminal 29.2 38 0.00082 21.8 1.6 36 93-134 2-37 (57)
133 PRK12546 RNA polymerase sigma 29.1 41 0.00088 28.4 2.1 28 114-141 131-158 (188)
134 KOG0709 CREB/ATF family transc 28.7 94 0.002 30.6 4.7 78 90-174 219-299 (472)
135 PF07407 Seadorna_VP6: Seadorn 28.4 78 0.0017 29.9 4.0 29 150-178 35-63 (420)
136 PRK07037 extracytoplasmic-func 28.3 50 0.0011 26.5 2.5 21 114-134 127-147 (163)
137 PRK12547 RNA polymerase sigma 28.3 48 0.001 26.9 2.4 45 92-141 113-157 (164)
138 PF05377 FlaC_arch: Flagella a 28.2 2.1E+02 0.0045 19.9 5.6 34 145-178 5-38 (55)
139 PRK06811 RNA polymerase factor 28.1 42 0.00091 28.0 2.1 45 92-141 132-176 (189)
140 PRK13919 putative RNA polymera 27.8 54 0.0012 27.0 2.7 26 114-139 153-178 (186)
141 PRK09651 RNA polymerase sigma 27.8 46 0.001 27.3 2.2 28 114-141 137-164 (172)
142 TIGR02983 SigE-fam_strep RNA p 27.7 48 0.001 26.6 2.3 45 92-141 111-155 (162)
143 PF13384 HTH_23: Homeodomain-l 27.7 22 0.00048 23.0 0.2 23 113-135 18-40 (50)
144 PRK13890 conjugal transfer pro 27.4 42 0.00091 26.6 1.8 44 115-159 21-64 (120)
145 TIGR00721 tfx DNA-binding prot 27.3 1.1E+02 0.0025 25.0 4.4 48 89-142 4-51 (137)
146 PRK12532 RNA polymerase sigma 27.2 57 0.0012 27.2 2.7 46 92-142 137-182 (195)
147 KOG3584 cAMP response element 27.0 1.3E+02 0.0028 28.0 5.0 42 139-180 304-345 (348)
148 cd04762 HTH_MerR-trunc Helix-T 26.7 21 0.00046 22.2 -0.0 26 115-140 3-28 (49)
149 KOG3335 Predicted coiled-coil 26.7 2.7E+02 0.0058 24.0 6.6 53 128-180 87-139 (181)
150 KOG4571 Activating transcripti 26.6 1.9E+02 0.004 26.9 6.0 36 144-179 252-287 (294)
151 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.5 3.2E+02 0.007 21.5 7.8 76 88-178 35-110 (127)
152 KOG4752 Ribosomal protein L41 26.4 1.1E+02 0.0023 17.6 2.8 13 137-149 2-14 (26)
153 PRK15369 two component system 26.4 73 0.0016 25.4 3.1 45 91-141 149-193 (211)
154 PRK10403 transcriptional regul 26.3 43 0.00094 27.1 1.8 48 91-144 153-200 (215)
155 PRK12529 RNA polymerase sigma 26.2 54 0.0012 27.1 2.4 44 92-140 128-171 (178)
156 PF13411 MerR_1: MerR HTH fami 26.1 26 0.00056 24.2 0.3 22 115-136 3-24 (69)
157 PF14775 NYD-SP28_assoc: Sperm 25.9 2.2E+02 0.0048 19.8 5.1 26 154-179 33-58 (60)
158 PRK12536 RNA polymerase sigma 25.9 56 0.0012 27.0 2.4 29 114-142 147-175 (181)
159 PF07716 bZIP_2: Basic region 25.9 2.1E+02 0.0045 19.1 6.0 29 147-175 25-53 (54)
160 cd04766 HTH_HspR Helix-Turn-He 25.8 85 0.0018 23.2 3.2 23 115-137 4-26 (91)
161 cd01107 HTH_BmrR Helix-Turn-He 25.4 3.1E+02 0.0067 20.9 8.4 69 88-176 36-104 (108)
162 PRK12524 RNA polymerase sigma 25.2 57 0.0012 27.3 2.4 27 115-141 155-181 (196)
163 TIGR02952 Sig70_famx2 RNA poly 25.1 58 0.0013 26.2 2.3 37 92-133 123-159 (170)
164 PHA00542 putative Cro-like pro 24.4 1.5E+02 0.0032 21.7 4.2 35 114-148 33-67 (82)
165 cd04777 HTH_MerR-like_sg1 Heli 24.2 2.9E+02 0.0062 20.9 6.0 35 89-136 34-68 (107)
166 PRK06986 fliA flagellar biosyn 24.2 56 0.0012 28.4 2.2 46 92-142 185-230 (236)
167 PRK09645 RNA polymerase sigma 24.1 70 0.0015 25.9 2.7 39 92-135 119-157 (173)
168 KOG3863 bZIP transcription fac 23.8 2.4E+02 0.0052 28.8 6.7 36 143-178 514-549 (604)
169 PRK13169 DNA replication intia 23.6 2.8E+02 0.006 21.9 5.8 35 146-180 21-55 (110)
170 PF15058 Speriolin_N: Sperioli 23.3 1.4E+02 0.0031 26.0 4.4 33 149-181 7-45 (200)
171 TIGR02943 Sig70_famx1 RNA poly 23.2 87 0.0019 26.2 3.1 45 92-141 132-176 (188)
172 PF00376 MerR: MerR family reg 23.2 32 0.00069 21.7 0.3 19 115-133 2-20 (38)
173 cd01110 HTH_SoxR Helix-Turn-He 23.1 4E+02 0.0087 21.4 7.1 35 88-135 35-69 (139)
174 PRK12523 RNA polymerase sigma 23.1 70 0.0015 26.1 2.5 45 92-141 120-164 (172)
175 PRK12544 RNA polymerase sigma 22.5 95 0.0021 26.6 3.3 46 92-142 149-194 (206)
176 PRK12533 RNA polymerase sigma 22.2 63 0.0014 28.0 2.1 21 114-134 152-172 (216)
177 PRK12539 RNA polymerase sigma 22.1 74 0.0016 26.3 2.5 44 92-140 132-175 (184)
178 PRK09649 RNA polymerase sigma 22.1 63 0.0014 26.9 2.0 24 115-138 149-172 (185)
179 PRK10360 DNA-binding transcrip 22.1 46 0.00099 26.9 1.1 44 91-140 137-180 (196)
180 PRK09647 RNA polymerase sigma 22.1 72 0.0016 27.2 2.4 26 114-139 156-181 (203)
181 PF04297 UPF0122: Putative hel 22.0 1.7E+02 0.0038 22.7 4.3 38 92-134 18-55 (101)
182 PRK12545 RNA polymerase sigma 21.8 93 0.002 26.3 3.0 45 92-141 140-184 (201)
183 cd04784 HTH_CadR-PbrR Helix-Tu 21.7 4E+02 0.0086 20.8 7.7 36 88-136 35-70 (127)
184 TIGR02044 CueR Cu(I)-responsiv 21.7 4E+02 0.0087 20.9 7.7 35 87-134 34-68 (127)
185 PRK12542 RNA polymerase sigma 21.4 77 0.0017 26.2 2.4 45 92-141 123-167 (185)
186 PRK10100 DNA-binding transcrip 21.4 93 0.002 27.0 3.0 48 91-144 155-202 (216)
187 cd01108 HTH_CueR Helix-Turn-He 21.4 4.1E+02 0.0088 20.9 7.3 35 88-135 35-69 (127)
188 TIGR02947 SigH_actino RNA poly 21.4 40 0.00087 28.1 0.7 29 113-141 148-176 (193)
189 PRK12516 RNA polymerase sigma 21.2 78 0.0017 26.5 2.4 21 115-135 135-155 (187)
190 PRK12511 RNA polymerase sigma 21.2 76 0.0016 26.5 2.3 38 92-134 112-149 (182)
191 PRK10651 transcriptional regul 21.2 84 0.0018 25.4 2.6 48 91-144 155-202 (216)
192 PRK09935 transcriptional regul 21.1 50 0.0011 26.8 1.2 46 90-141 148-193 (210)
193 PRK11923 algU RNA polymerase s 21.1 70 0.0015 26.5 2.1 28 114-141 156-183 (193)
194 cd04763 HTH_MlrA-like Helix-Tu 21.0 36 0.00079 23.6 0.3 21 115-135 3-23 (68)
195 PRK09641 RNA polymerase sigma 20.8 74 0.0016 26.0 2.2 28 114-141 154-181 (187)
196 TIGR02607 antidote_HigA addict 20.6 1.4E+02 0.003 20.9 3.3 37 115-152 21-57 (78)
197 COG2944 Predicted transcriptio 20.5 98 0.0021 24.3 2.6 42 91-139 43-84 (104)
198 cd04764 HTH_MlrA-like_sg1 Heli 20.5 42 0.00092 23.1 0.5 21 115-135 3-23 (67)
199 PRK12522 RNA polymerase sigma 20.4 1.1E+02 0.0024 24.8 3.2 28 114-141 137-164 (173)
200 PRK08583 RNA polymerase sigma 20.3 80 0.0017 27.8 2.4 45 92-141 206-250 (257)
201 TIGR02479 FliA_WhiG RNA polyme 20.3 79 0.0017 27.2 2.3 43 92-139 176-218 (224)
202 PF08172 CASP_C: CASP C termin 20.3 2.7E+02 0.0058 25.1 5.8 44 137-180 90-133 (248)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.86 E-value=1.7e-21 Score=167.90 Aligned_cols=99 Identities=55% Similarity=0.856 Sum_probs=93.4
Q ss_pred CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHH
Q 040769 83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSRE 162 (257)
Q Consensus 83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e 162 (257)
.+..+++.||+.+|+..||+.|+.+.++.+.+|..||++|||.+|||+|||||||||||.++.+..++.|+.+++.+..+
T Consensus 48 ~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~ 127 (198)
T KOG0483|consen 48 SKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSE 127 (198)
T ss_pred cccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhh
Confidence 33557788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHhcC
Q 040769 163 KLKLQEEVMKLKRMLKEQG 181 (257)
Q Consensus 163 ~~~l~~e~~~~~~~l~~~~ 181 (257)
+++|+.++.+|...+....
T Consensus 128 ~~~Lq~e~~eL~~~~~~~~ 146 (198)
T KOG0483|consen 128 NDRLQSEVQELVAELSSLK 146 (198)
T ss_pred hhHHHHHHHHHHHHHhhhh
Confidence 9999999999998887653
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.80 E-value=1.4e-20 Score=169.43 Aligned_cols=65 Identities=37% Similarity=0.649 Sum_probs=60.3
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
.++.||.||.||..|+.+||++|..|+|+++.+|.|||..|.|+++||||||||||+||||..+.
T Consensus 156 ~~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 156 GGKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred cCCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 34578889999999999999999999999999999999999999999999999999999985543
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.77 E-value=1.3e-19 Score=164.90 Aligned_cols=65 Identities=29% Similarity=0.535 Sum_probs=60.9
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
.++.||||..+|+.|+.+||++|..|.|+++++|.+|++.|+|++|||||||||||+|+||..++
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 36677888899999999999999999999999999999999999999999999999999997754
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.76 E-value=5.6e-19 Score=162.29 Aligned_cols=65 Identities=32% Similarity=0.640 Sum_probs=59.8
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
.+++||.||.||..||..||+.|++.+|++..+|++||+.|||+..|||+||||||+||||...+
T Consensus 169 pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 169 PKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred CcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 35666778889999999999999999999999999999999999999999999999999996543
No 5
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.75 E-value=6.3e-19 Score=155.71 Aligned_cols=92 Identities=26% Similarity=0.347 Sum_probs=74.1
Q ss_pred hccCCCCCCCCCchHhhhhhccCCCCCCCCC---CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccc
Q 040769 55 AEKSSSSIGLIPAAELMEKNIHHYGSSSTSS---QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAV 131 (257)
Q Consensus 55 ~~~~s~s~~~~~~~~~~~~~~~~~~~~~~~~---~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkv 131 (257)
+..-+.+....+..+||.+..........+- -|-|-++|+.|+.+||++|..++|.++.+|.|||.-|||+||||||
T Consensus 166 ~~~nspg~~R~s~~dwmrkpa~~~~g~~~KtRTkDKYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKI 245 (317)
T KOG0848|consen 166 PLGNSPGKSRRSPYDWMRKPAQPGTGQNVKTRTKDKYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKI 245 (317)
T ss_pred cccCCCCcCCCChhhhhhcccccCCCCCceeecccceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhH
Confidence 3333555666677889998877664422222 2335669999999999999999999999999999999999999999
Q ss_pred ccccchhhhhHHHHH
Q 040769 132 WFQNRRARWKSKQLE 146 (257)
Q Consensus 132 WFQNRRak~Kr~~~~ 146 (257)
||||||+|+||..++
T Consensus 246 WFQNRRAKERK~nKK 260 (317)
T KOG0848|consen 246 WFQNRRAKERKDNKK 260 (317)
T ss_pred hhhhhhHHHHHHHHH
Confidence 999999999996644
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.73 E-value=2.8e-18 Score=143.99 Aligned_cols=66 Identities=33% Similarity=0.486 Sum_probs=62.2
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL 147 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~ 147 (257)
..+.||.||.||.+||..||..|+.+.|....+|.+||+.|+|++.||||||||||.|.||++.+.
T Consensus 99 ~~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 99 SMRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred ccCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 347788999999999999999999999999999999999999999999999999999999988764
No 7
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.72 E-value=2.3e-18 Score=153.57 Aligned_cols=127 Identities=25% Similarity=0.348 Sum_probs=101.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH-------HHHHHHHHHHH
Q 040769 81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS-------KQLELLYDSLK 153 (257)
Q Consensus 81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr-------~~~~~~~~~l~ 153 (257)
.....||.||.+|..||+.|+..|+..++|.+..|++|+.++||..|+|+|||||||||+|| .+|.+++.++|
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK 242 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK 242 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence 45566788999999999999999999999999999999999999999999999999999998 36777788887
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccccccCCCCCcccCCCccccccccccccCCCCCCCC
Q 040769 154 QEYDAVSREKLKLQEEVMKLKRMLKEQGTSTRNMMNKQVSTGITEVSGEETVESTSVATINGSFSNKH 221 (257)
Q Consensus 154 ~~~~~~~~e~~~l~~e~~~~~~~l~~~~~~~~~~~~~~~s~~~~~~~~e~t~as~~~~~~~~s~~~~~ 221 (257)
.. +..+.|+++- +..++... .++.+.++++.+|...++.+.+ +.+ ++|+|+++|
T Consensus 243 ~s-gs~r~ekdsd-------~sel~~~~---dslse~~~~N~lYg~l~~~~d~-g~~--~~gsy~~~~ 296 (383)
T KOG4577|consen 243 RS-GSSRAEKDSD-------DSELSFIN---DSLSEHGSPNYLYGTLGHPTDD-GNP--SNGSYSFHS 296 (383)
T ss_pred cc-CCcccccccc-------cCcccccc---chhhhcCCccccccccCCcccC-CCc--CCCceeccC
Confidence 76 5556666652 33444332 2577789999999999998776 333 336776665
No 8
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=4.1e-18 Score=155.03 Aligned_cols=64 Identities=33% Similarity=0.549 Sum_probs=58.6
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSL 152 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l 152 (257)
|--||..|+-+||+.|+.++|++..+|++||..|.|+++||||||||||-|.||+++++..+.+
T Consensus 157 RVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~~ 220 (307)
T KOG0842|consen 157 RVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEAL 220 (307)
T ss_pred ccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhcc
Confidence 3339999999999999999999999999999999999999999999999999999888665443
No 9
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.68 E-value=3e-17 Score=142.54 Aligned_cols=69 Identities=30% Similarity=0.517 Sum_probs=62.0
Q ss_pred cCCCCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 76 HHYGSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 76 ~~~~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.......++.||.||.|+..||..|.+.|++++|+...+|.+||..|||+.+||||||||||.|.||..
T Consensus 113 ~~~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 113 RRPNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred eccCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 344555666677799999999999999999999999999999999999999999999999999999843
No 10
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.67 E-value=2.4e-17 Score=142.05 Aligned_cols=64 Identities=28% Similarity=0.527 Sum_probs=58.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~ 145 (257)
..++||.||.|+..|+..||..|+..+|++..+|..||++|.|+++||||||||||.||||+-.
T Consensus 101 ~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~a 164 (268)
T KOG0485|consen 101 DDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQYA 164 (268)
T ss_pred ccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHHh
Confidence 3456667888999999999999999999999999999999999999999999999999998543
No 11
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.67 E-value=9.1e-18 Score=129.34 Aligned_cols=65 Identities=31% Similarity=0.515 Sum_probs=60.0
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
.+++||-|+.||..||.+||+.|...+||+.-.|++||.++.|++..|+|||||||+|.||+...
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr~ 78 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQERA 78 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHHH
Confidence 45677789999999999999999999999999999999999999999999999999999986543
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.66 E-value=7.2e-17 Score=139.53 Aligned_cols=68 Identities=31% Similarity=0.457 Sum_probs=63.8
Q ss_pred CCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769 80 SSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL 147 (257)
Q Consensus 80 ~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~ 147 (257)
...++.||.||+|+..|+++||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|++++.+
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 35677889999999999999999999999999999999999999999999999999999999987664
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.66 E-value=1.1e-16 Score=137.10 Aligned_cols=63 Identities=33% Similarity=0.551 Sum_probs=58.4
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.+..|+.|+.||..||..||+.|+..+|+++.+|.+++..|.|+++||||||||||+|.||.+
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 344567788999999999999999999999999999999999999999999999999999855
No 14
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.65 E-value=7.8e-17 Score=112.12 Aligned_cols=57 Identities=42% Similarity=0.687 Sum_probs=55.2
Q ss_pred CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
||+|++||.+|+.+||.+|..++||+..++..||.+|||+..+|++||+|||+++||
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 15
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=1.3e-16 Score=140.63 Aligned_cols=69 Identities=36% Similarity=0.543 Sum_probs=61.8
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYD 157 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~ 157 (257)
||.||..|++.||+.|+...||+...|+-||.++.|.+.+|+|||||||+||||+++.......-++++
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~maeyg 213 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAEYG 213 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhhhc
Confidence 777999999999999999999999999999999999999999999999999999877765555545543
No 16
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.60 E-value=2.2e-16 Score=141.85 Aligned_cols=66 Identities=32% Similarity=0.527 Sum_probs=61.1
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLEL 147 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~ 147 (257)
...-||-||.||.+||..||++|.+..|.++.+|.|||..|+|.+..|||||||||+|+||+++..
T Consensus 178 ~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 178 DDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred cHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 344567799999999999999999999999999999999999999999999999999999988764
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.58 E-value=8e-16 Score=135.76 Aligned_cols=60 Identities=40% Similarity=0.687 Sum_probs=56.3
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.||.||.||.+||..|+..|+.|.|++..+|.+||.+|||.+.||||||||+|+|.||..
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsT 305 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKST 305 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhcc
Confidence 356678899999999999999999999999999999999999999999999999999854
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.52 E-value=9.2e-15 Score=122.13 Aligned_cols=68 Identities=31% Similarity=0.537 Sum_probs=62.1
Q ss_pred CCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 79 ~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
.......+++|+|.|..|+.+|++.|+.++||+...|.+|+..|+|+++.|+|||||||++.|+....
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 33456677889999999999999999999999999999999999999999999999999999986644
No 19
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.52 E-value=8.4e-15 Score=101.08 Aligned_cols=55 Identities=45% Similarity=0.837 Sum_probs=52.3
Q ss_pred CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+.|++|+.+|+.+||..|..++||+..++..||.+|||+..+|++||+|||++.|
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 5678899999999999999999999999999999999999999999999999864
No 20
>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=99.52 E-value=1.7e-14 Score=101.20 Aligned_cols=52 Identities=17% Similarity=0.373 Sum_probs=50.3
Q ss_pred CCCCCcCCHHHHHHHHHHhhhcCC----CCHHHHHHHHHHhCCCCcccccccccch
Q 040769 86 QERKKRLTSDQLESLERSFQEEIK----LDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 86 ~r~R~r~t~~Ql~~Le~~F~~~~~----p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
||.||.||.+|+..||..|+.+.| |+...+.+||.+|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 688999999999999999999999 9999999999999999999999999965
No 21
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.51 E-value=9.7e-15 Score=135.90 Aligned_cols=62 Identities=23% Similarity=0.406 Sum_probs=58.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.++|||||.|+...+..||++|.+|++|+..++..||.+|+|...+|+|||||||.|+||..
T Consensus 292 ~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 292 SRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 36788899999999999999999999999999999999999999999999999999999844
No 22
>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=99.51 E-value=1.2e-14 Score=101.03 Aligned_cols=57 Identities=42% Similarity=0.773 Sum_probs=54.2
Q ss_pred CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769 87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143 (257)
Q Consensus 87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~ 143 (257)
++|..|+..|+.+||.+|..++||+..++..||.++||+.++|++||+|||.+.++.
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 567889999999999999999999999999999999999999999999999998863
No 23
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.48 E-value=5.3e-15 Score=122.68 Aligned_cols=62 Identities=31% Similarity=0.549 Sum_probs=57.8
Q ss_pred CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.+++|-|+.|+..|+..||+.|+..+|++..+|.|||..|+|+++|||.||||||+|.||.+
T Consensus 98 ~~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 98 CRRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HHhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 44566789999999999999999999999999999999999999999999999999999855
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.43 E-value=5.7e-14 Score=126.96 Aligned_cols=71 Identities=28% Similarity=0.499 Sum_probs=63.0
Q ss_pred CCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHH
Q 040769 84 SSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQ 154 (257)
Q Consensus 84 ~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~ 154 (257)
++||.|+.||..|+.+||..|.+|.||+...|++||.-.+|++..|+|||.|||+||||++.-+..+..+.
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~ 181 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKG 181 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhc
Confidence 45667888999999999999999999999999999999999999999999999999999877666443333
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.35 E-value=2.8e-13 Score=117.20 Aligned_cols=64 Identities=33% Similarity=0.641 Sum_probs=58.6
Q ss_pred CCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 83 TSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 83 ~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
++++..|..|+..||..||+.|+..+|+-..+|.+||..||+++.||+|||||||.||||+...
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhAa 228 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHAA 228 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhcc
Confidence 4555567789999999999999999999999999999999999999999999999999997644
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.18 E-value=1e-11 Score=108.55 Aligned_cols=64 Identities=30% Similarity=0.325 Sum_probs=59.7
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~ 145 (257)
..++|+.|+.|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||+||++...
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 4566788999999999999999999999999999999999999999999999999999998653
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=99.06 E-value=8e-11 Score=105.69 Aligned_cols=64 Identities=20% Similarity=0.397 Sum_probs=59.6
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
..+.+|||||.+-.-+.+.||.+|...+.|+.+.+..||.+|+|.+.+|+|||+|.|+|.||..
T Consensus 305 ~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 305 PGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred CccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 3567788999999999999999999999999999999999999999999999999999999844
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.98 E-value=2.7e-10 Score=106.96 Aligned_cols=67 Identities=33% Similarity=0.568 Sum_probs=61.0
Q ss_pred CCCCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769 79 GSSSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 79 ~~~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~ 145 (257)
....++.+|+|+.|+..|+..||+.|+.++||+...|++||.+++|++..|+|||+|||+|++|...
T Consensus 170 ~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 170 YALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred ccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3445666777899999999999999999999999999999999999999999999999999998653
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.79 E-value=3.8e-09 Score=94.39 Aligned_cols=51 Identities=27% Similarity=0.442 Sum_probs=47.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
|...-...|..+|..++||+..++.+||+.+||+..||-.||+|||+|+|-
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 566677899999999999999999999999999999999999999999983
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.46 E-value=1.1e-07 Score=84.53 Aligned_cols=59 Identities=22% Similarity=0.465 Sum_probs=55.1
Q ss_pred CCCCCCcCCHHHHHHHHHHhh---hcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769 85 SQERKKRLTSDQLESLERSFQ---EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143 (257)
Q Consensus 85 ~~r~R~r~t~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~ 143 (257)
.+|||+.|+..-.++|..+|. .++||+.+.+++||+++|++..||-.||.|+|-+.||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 468888999999999999997 58899999999999999999999999999999999873
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=98.25 E-value=2.3e-07 Score=60.46 Aligned_cols=34 Identities=35% Similarity=0.576 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769 106 EEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 106 ~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
.++||+..++.+||.++||+..||..||-|.|.|
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 4789999999999999999999999999999865
No 32
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.03 E-value=3.6e-06 Score=81.79 Aligned_cols=59 Identities=19% Similarity=0.290 Sum_probs=54.0
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
.-..||.|.+||..|.+.|..+|+.+++|+.+..+.|+.+|+|..+.|..||-|-|.|.
T Consensus 417 ~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 417 MLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred cccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 34456778889999999999999999999999999999999999999999999988774
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.02 E-value=4.5e-06 Score=72.80 Aligned_cols=65 Identities=40% Similarity=0.627 Sum_probs=59.1
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769 81 SSTSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 81 ~~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~ 145 (257)
...+.++.|+.+...|+..|+..|....+|+...+..|+..+|+.++.|++||||+|++.++...
T Consensus 149 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 149 SNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 44556677888999999999999999999999999999999999999999999999999998553
No 34
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.58 E-value=5.2e-05 Score=80.06 Aligned_cols=64 Identities=25% Similarity=0.387 Sum_probs=58.8
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHH
Q 040769 82 STSSQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~ 145 (257)
..++++.|++++..||.+|..+|....++...+.+.|...+++..+.|+|||||-|+|.|+...
T Consensus 900 ~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 900 GMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3456778999999999999999999999999999999999999999999999999999998543
No 35
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.60 E-value=0.0026 Score=59.30 Aligned_cols=63 Identities=25% Similarity=0.367 Sum_probs=51.6
Q ss_pred CCCCCcCCHHHHHHHHHHhhh---cCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHH
Q 040769 86 QERKKRLTSDQLESLERSFQE---EIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELL 148 (257)
Q Consensus 86 ~r~R~r~t~~Ql~~Le~~F~~---~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~ 148 (257)
.|++..+......+|+.+... .+||+..++..||.++||+..||.+||-|.|-|..+--.+..
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~~ 305 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEEM 305 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHHH
Confidence 344456999999999988443 579999999999999999999999999999988776554433
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.28 E-value=0.0012 Score=46.03 Aligned_cols=43 Identities=19% Similarity=0.383 Sum_probs=31.5
Q ss_pred HHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchh
Q 040769 96 QLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138 (257)
Q Consensus 96 Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRa 138 (257)
.+..|+++|...+.+.......|..+.+|+..||+.||-.|+.
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 3466999999999999999999999999999999999976654
No 37
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=94.95 E-value=0.073 Score=35.45 Aligned_cols=37 Identities=43% Similarity=0.549 Sum_probs=28.6
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 040769 143 KQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKE 179 (257)
Q Consensus 143 ~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~ 179 (257)
++.+..|+.|+.+++.+..+.++|..|+..|+..+..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~ 37 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE 37 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3677888888888888888888888887777776653
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.47 E-value=0.027 Score=57.14 Aligned_cols=48 Identities=19% Similarity=0.273 Sum_probs=44.8
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 97 LESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 97 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
+..|+.+|..|..|+..+...||.+.||..+.|+.||++++++....+
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 778999999999999999999999999999999999999999887643
No 39
>smart00340 HALZ homeobox associated leucin zipper.
Probab=93.75 E-value=0.14 Score=33.46 Aligned_cols=33 Identities=30% Similarity=0.451 Sum_probs=30.0
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Q 040769 144 QLELLYDSLKQEYDAVSREKLKLQEEVMKLKRM 176 (257)
Q Consensus 144 ~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~ 176 (257)
+.+.+++.||+..+.+..||.+|+.|+++|+..
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 567889999999999999999999999998864
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.26 E-value=0.12 Score=35.44 Aligned_cols=46 Identities=22% Similarity=0.421 Sum_probs=34.8
Q ss_pred CCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769 86 QERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136 (257)
Q Consensus 86 ~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR 136 (257)
+|+|..+|-++...+-..++... ....||+++|+...+|..|..|+
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k 46 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNK 46 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhH
Confidence 47788899988887777787765 57899999999999999999884
No 41
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=90.76 E-value=0.76 Score=30.56 Aligned_cols=35 Identities=49% Similarity=0.709 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 144 QLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 144 ~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
.....++.|+.+++.+..|++.|++++..++..+.
T Consensus 9 ~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~ 43 (45)
T PF02183_consen 9 ALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQ 43 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34567899999999999999999999999998774
No 42
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=84.33 E-value=3.4 Score=32.73 Aligned_cols=87 Identities=16% Similarity=0.158 Sum_probs=50.1
Q ss_pred CCCcCCHHHHH-HHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh-------hHHHHHHHHHHHHHHhHHH
Q 040769 88 RKKRLTSDQLE-SLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW-------KSKQLELLYDSLKQEYDAV 159 (257)
Q Consensus 88 ~R~r~t~~Ql~-~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~-------Kr~~~~~~~~~l~~~~~~~ 159 (257)
+|++||.++.. ++...+... ....+||.++|++..+|..|.+-=+... +..........+..+...|
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g-----~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPG-----MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCC-----CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence 45668877644 444444432 2467889999999999999965422110 0000001122344555566
Q ss_pred HHHHHHHHHHHHHHHHHHHh
Q 040769 160 SREKLKLQEEVMKLKRMLKE 179 (257)
Q Consensus 160 ~~e~~~l~~e~~~~~~~l~~ 179 (257)
..+...|+.|+.-|+..+..
T Consensus 84 ~~el~~L~~E~diLKKa~~~ 103 (121)
T PRK09413 84 QRLLGKKTMENELLKEAVEY 103 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 66666777777666666653
No 43
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=76.43 E-value=2.4 Score=29.15 Aligned_cols=39 Identities=26% Similarity=0.266 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCCCcccc
Q 040769 92 LTSDQLESLERSFQEEIK--LDPDRKMKLARELGLQPRQIA 130 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~--p~~~~r~~LA~~LgL~~~qVk 130 (257)
+|+.|.++|...|+..-| |-.....+||.+||++...|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 588999999999987765 556667899999999986543
No 44
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=74.16 E-value=1.5 Score=43.97 Aligned_cols=64 Identities=13% Similarity=0.067 Sum_probs=44.8
Q ss_pred CCCCCCCCCcCCHHHHH-HHHHHhhhcCCCCHHHHHHHHHHhCC-------CCcccccccccchhhhhHHHH
Q 040769 82 STSSQERKKRLTSDQLE-SLERSFQEEIKLDPDRKMKLARELGL-------QPRQIAVWFQNRRARWKSKQL 145 (257)
Q Consensus 82 ~~~~~r~R~r~t~~Ql~-~Le~~F~~~~~p~~~~r~~LA~~LgL-------~~~qVkvWFQNRRak~Kr~~~ 145 (257)
..-+|+++.+|-..|.. +-+.+|.++..+......+.-.++.| ..+.|+.||.|||+++|+-+.
T Consensus 688 ~~~pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 688 LDLPKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hcccHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 34455666665444444 34566778888888877776666654 467899999999999998543
No 45
>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=73.44 E-value=3.4 Score=29.30 Aligned_cols=43 Identities=19% Similarity=0.462 Sum_probs=28.1
Q ss_pred CCCCcCCHHHHHHHHHHh-hhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 87 ERKKRLTSDQLESLERSF-QEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 87 r~R~r~t~~Ql~~Le~~F-~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
++|++||.++...+-..+ ... ....+||+++||++.+|..|-+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHH
Confidence 567889998877555554 433 4678899999999999998864
No 46
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=73.03 E-value=23 Score=28.84 Aligned_cols=76 Identities=29% Similarity=0.381 Sum_probs=49.2
Q ss_pred CcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHh-CCCCcccccccccchhhh----------hH----HHHHHHHHHHHH
Q 040769 90 KRLTSDQLESLERSFQEEIKLDPDRKMKLAREL-GLQPRQIAVWFQNRRARW----------KS----KQLELLYDSLKQ 154 (257)
Q Consensus 90 ~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~L-gL~~~qVkvWFQNRRak~----------Kr----~~~~~~~~~l~~ 154 (257)
.+|++++|..| ...+|=+.| |++...|--|=|.||+-. || .+++.....|.+
T Consensus 22 d~lsDd~Lvsm-------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSM-------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHh-------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 78999998877 233444444 788888888888887632 22 223334455666
Q ss_pred HhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 155 EYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 155 ~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
+-+.+..|+.++..|+..++....
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 667777777777777776665554
No 47
>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=69.99 E-value=3.1 Score=27.38 Aligned_cols=39 Identities=15% Similarity=0.237 Sum_probs=29.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
.+++.+..+|...|..+ ..-.+||..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 47888999999999333 3467899999999998886654
No 48
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=69.50 E-value=3.5 Score=28.23 Aligned_cols=44 Identities=16% Similarity=0.227 Sum_probs=27.4
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYD 157 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~ 157 (257)
...+||+.+|++..+|.-|+.++..+..-.........+....+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~~~ 55 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCSPE 55 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--HH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCCHH
Confidence 46789999999999999999988777777777777666654433
No 49
>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=68.14 E-value=3.5 Score=26.15 Aligned_cols=43 Identities=16% Similarity=0.182 Sum_probs=31.9
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchh
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRa 138 (257)
.++..+..+++..|... ....++|..+|++...|..|....+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 36777888887777433 24677899999999999988765443
No 50
>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=67.24 E-value=7.8 Score=21.89 Aligned_cols=40 Identities=23% Similarity=0.381 Sum_probs=27.4
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccc
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWF 133 (257)
+..++.++...+...|.... ...++|..+|++...|..|.
T Consensus 3 ~~~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 3 PPKLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CCcCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 33466777776666665332 46688999999988887763
No 51
>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=66.78 E-value=37 Score=25.80 Aligned_cols=37 Identities=22% Similarity=0.416 Sum_probs=25.4
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
.++.|+..++..|.... ..+.+|++...|+-++....
T Consensus 35 g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 35 GYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred CceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc
Confidence 35569999999995443 23556777777777776543
No 52
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=61.91 E-value=9.4 Score=41.82 Aligned_cols=60 Identities=15% Similarity=0.190 Sum_probs=54.1
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 85 SQERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 85 ~~r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.++-|..+-.+++.+|-++|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 344566677799999999999999999999999999999999999999999999999865
No 53
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=61.44 E-value=3.7 Score=42.29 Aligned_cols=60 Identities=15% Similarity=0.250 Sum_probs=46.0
Q ss_pred CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
|-|+.+..++-..|...+.-+.-++..+-..++.+|...+.+|.|||++|+...+.....
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl~ 687 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPLF 687 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCccc
Confidence 344556666667788888877777766666667778889999999999999998886544
No 54
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=60.02 E-value=21 Score=27.81 Aligned_cols=47 Identities=17% Similarity=0.210 Sum_probs=31.4
Q ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 040769 128 QIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKR 175 (257)
Q Consensus 128 qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~ 175 (257)
+...||++.-- .+-.+..+....++++.+.++.++..|+.++..++.
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 45678866422 122344455666777888888888888888888865
No 55
>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=60.00 E-value=5.6 Score=26.42 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
+++.+..++.-.|-.+ ....+||..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 5666777776665444 4678999999999999999986443
No 56
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=59.27 E-value=13 Score=30.76 Aligned_cols=49 Identities=18% Similarity=0.148 Sum_probs=38.2
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSK 143 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~ 143 (257)
...+++.|..+|+..+ .. ....+||..||++...|+.|-++.+.|.|+.
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4568999999998743 22 2467899999999999999998777666653
No 57
>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=57.74 E-value=8.1 Score=26.20 Aligned_cols=46 Identities=22% Similarity=0.237 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
.||+.++.+|.-...-. ...+||..+|++++.|+.+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888999997777654 47899999999999999887765555443
No 58
>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=56.93 E-value=4.3 Score=28.65 Aligned_cols=20 Identities=25% Similarity=0.517 Sum_probs=17.3
Q ss_pred HHHHHHHHhCCCCccccccc
Q 040769 114 RKMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWF 133 (257)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 35678999999999999884
No 59
>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=55.26 E-value=94 Score=23.94 Aligned_cols=72 Identities=21% Similarity=0.274 Sum_probs=40.1
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQE 168 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~ 168 (257)
.+.|+.+++..| ......+.+|++-..|+..+......... .......+......+..+-..++.
T Consensus 36 yR~Y~~~~l~~l-------------~~I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 36 IRDFTEEDLEWL-------------EFIKCLRNTGMSIKDIKEYAELRREGDST--IPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred CccCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHHHHccCCcc--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456999999998 34455677888888888777654332211 122233344444444444444444
Q ss_pred HHHHHHH
Q 040769 169 EVMKLKR 175 (257)
Q Consensus 169 e~~~~~~ 175 (257)
....++.
T Consensus 101 ~~~~l~~ 107 (113)
T cd01109 101 TLAYLDY 107 (113)
T ss_pred HHHHHHH
Confidence 4444443
No 60
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=53.37 E-value=10 Score=32.96 Aligned_cols=38 Identities=29% Similarity=0.306 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHhhhcCC--CCHHHHHHHHHHhCCCCcc
Q 040769 91 RLTSDQLESLERSFQEEIK--LDPDRKMKLARELGLQPRQ 128 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~--p~~~~r~~LA~~LgL~~~q 128 (257)
.+|+.|+++|...|...-| |-.....+||++||+++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 6999999999999998764 6666778999999999854
No 61
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=51.19 E-value=14 Score=31.06 Aligned_cols=45 Identities=18% Similarity=0.193 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
++..+..+|...|..+ ....+||..||++...|+++...-|.+.|
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 4555555554443322 24568999999999999887754444444
No 62
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=50.52 E-value=36 Score=30.92 Aligned_cols=31 Identities=23% Similarity=0.433 Sum_probs=17.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 040769 149 YDSLKQEYDAVSREKLKLQEEVMKLKRMLKE 179 (257)
Q Consensus 149 ~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~ 179 (257)
...|.++++.+..+.+.|+.|+..++..+..
T Consensus 224 ~~~leken~~lr~~v~~l~~el~~~~~~~~~ 254 (269)
T KOG3119|consen 224 VAELEKENEALRTQVEQLKKELATLRRLFLQ 254 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445555555555555666666555555443
No 63
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.32 E-value=6.4 Score=25.57 Aligned_cols=40 Identities=18% Similarity=0.253 Sum_probs=19.9
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccc
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWF 133 (257)
.+.+|.+|...++..+... .-..+||+.||.+...|..+.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 3568889999999887644 456779999999988876554
No 64
>PRK10072 putative transcriptional regulator; Provisional
Probab=48.30 E-value=16 Score=28.03 Aligned_cols=45 Identities=20% Similarity=0.250 Sum_probs=33.7
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
|.+.+...+..|.+.-..+ ..+||+.+|++...|..|.+.+|.-.
T Consensus 30 ~~~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~P~ 74 (96)
T PRK10072 30 QKTTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVKPS 74 (96)
T ss_pred cccCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCCCC
Confidence 3355777777775443332 67899999999999999999887543
No 65
>PRK00118 putative DNA-binding protein; Validated
Probab=46.30 E-value=71 Score=24.94 Aligned_cols=46 Identities=13% Similarity=0.164 Sum_probs=33.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
++..|..++...|..+. ...+||..+|++...|..|....|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 56667777766655442 46789999999999999998765555554
No 66
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=45.95 E-value=98 Score=21.38 Aligned_cols=29 Identities=21% Similarity=0.447 Sum_probs=14.5
Q ss_pred HHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 040769 149 YDSLKQEYDAVSREKLKLQEEVMKLKRML 177 (257)
Q Consensus 149 ~~~l~~~~~~~~~e~~~l~~e~~~~~~~l 177 (257)
...|......+..++..|..++..++..+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~ 56 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEI 56 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555555555554443
No 67
>PRK14127 cell division protein GpsB; Provisional
Probab=45.30 E-value=78 Score=24.98 Aligned_cols=42 Identities=24% Similarity=0.453 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 040769 139 RWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180 (257)
Q Consensus 139 k~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~ 180 (257)
-.....-..+.+.+-..++.+..|+..|++++.+++..+..-
T Consensus 22 GYd~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~ 63 (109)
T PRK14127 22 GYDQDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDEL 63 (109)
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334456666777777777777788888888888877777643
No 68
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=45.28 E-value=16 Score=29.19 Aligned_cols=45 Identities=11% Similarity=0.071 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++...|-.+ ....+||..||++...|+.|...-|.+-|
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 5556666665554333 24678999999999999988765444433
No 69
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.24 E-value=20 Score=28.91 Aligned_cols=46 Identities=13% Similarity=0.170 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..++...|-.. ..-.+||..||+++..|++....-|.+-|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444555554443322 135689999999999999887655555444
No 70
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=43.57 E-value=20 Score=30.59 Aligned_cols=46 Identities=17% Similarity=0.193 Sum_probs=28.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..+|...|-.+ ....+||..||++...|+++...-|.+.|+
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4444555554333222 245689999999999998877554444443
No 71
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=43.40 E-value=20 Score=29.10 Aligned_cols=45 Identities=11% Similarity=0.043 Sum_probs=30.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|...|-.+ ....+||..||++...|+.|...-|.+.|
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6667777776654322 24568999999999999988764333333
No 72
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=42.50 E-value=25 Score=29.46 Aligned_cols=46 Identities=13% Similarity=0.132 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..++.-.|-.. ....+||..||+++..|+++...-|.+-|+
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555555544332 246789999999999999987655554444
No 73
>cd04781 HTH_MerR-like_sg6 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 6) with at least two conserved cysteines present in the C-terminal portion of the protein. 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, an
Probab=42.21 E-value=1.6e+02 Score=22.89 Aligned_cols=37 Identities=16% Similarity=0.319 Sum_probs=28.6
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
..+.|+..++..| ......+.+|++-..|+..+.+..
T Consensus 34 gyR~Y~~~~l~~l-------------~~I~~lr~~G~~L~eI~~~l~~~~ 70 (120)
T cd04781 34 LRRQYDPQVLDRL-------------ALIALGRAAGFSLDEIQAMLSHDG 70 (120)
T ss_pred CceecCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhccC
Confidence 5667999999999 455667788888888888887653
No 74
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=41.11 E-value=1e+02 Score=27.81 Aligned_cols=9 Identities=22% Similarity=0.715 Sum_probs=4.3
Q ss_pred CCCCCCCcC
Q 040769 84 SSQERKKRL 92 (257)
Q Consensus 84 ~~~r~R~r~ 92 (257)
.++|||.|+
T Consensus 53 ~~~rKr~RL 61 (292)
T KOG4005|consen 53 QPKRKRRRL 61 (292)
T ss_pred chHHHHHhh
Confidence 344555553
No 75
>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=41.01 E-value=24 Score=24.73 Aligned_cols=44 Identities=18% Similarity=0.443 Sum_probs=22.7
Q ss_pred CCcCCHH-HHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 89 KKRLTSD-QLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 89 R~r~t~~-Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
|..|+.. -|.+++.....+ .-....|. -|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-NCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-TTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc-chhhhHHH-HHHHhCccHHHHHHHHH
Confidence 4456654 445555554433 22223333 49999999999998865
No 76
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=40.65 E-value=29 Score=28.03 Aligned_cols=29 Identities=14% Similarity=0.201 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
.-.+||..+|++...|+.|...-|.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35689999999999999888655555443
No 77
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal 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=40.45 E-value=1.7e+02 Score=22.66 Aligned_cols=75 Identities=19% Similarity=0.174 Sum_probs=41.9
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQ 167 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~ 167 (257)
..+.|+.+++..| ......+.+|++-..|+..+.+...... ........+......+..+-..++
T Consensus 35 gyR~Y~~~~i~~l-------------~~I~~lr~~G~sl~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~ 99 (123)
T cd04770 35 GYRLYGEADLARL-------------RFIRRAQALGFSLAEIRELLSLRDDGAA--PCAEVRALLEEKLAEVEAKIAELQ 99 (123)
T ss_pred CCccCCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHhhhcCCC--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567999999999 3444567788888888777765443210 112223334444444444444444
Q ss_pred HHHHHHHHHH
Q 040769 168 EEVMKLKRML 177 (257)
Q Consensus 168 ~e~~~~~~~l 177 (257)
.-...++..+
T Consensus 100 ~~~~~l~~~~ 109 (123)
T cd04770 100 ALRAELAGLL 109 (123)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 78
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=40.24 E-value=25 Score=29.10 Aligned_cols=45 Identities=16% Similarity=0.108 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|.-.|-.+ ..-.+||..||++...|+.++..-|.+.|
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4555555555544332 24568999999999999988765555544
No 79
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=40.19 E-value=19 Score=30.02 Aligned_cols=29 Identities=10% Similarity=0.242 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
...+||..+|++...|+.|...-|.+.|+
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999988655544443
No 80
>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=39.75 E-value=24 Score=27.13 Aligned_cols=45 Identities=18% Similarity=0.223 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|...|-. .....+||..+|+++..|+.+...-+.|-|
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 455566665544322 234568999999999999877755444433
No 81
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=39.40 E-value=76 Score=29.34 Aligned_cols=28 Identities=18% Similarity=0.433 Sum_probs=14.8
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 040769 150 DSLKQEYDAVSREKLKLQEEVMKLKRML 177 (257)
Q Consensus 150 ~~l~~~~~~~~~e~~~l~~e~~~~~~~l 177 (257)
+.+-.+.+.+...|++|+.++.++..++
T Consensus 251 E~l~ge~~~Le~rN~~LK~qa~~lerEI 278 (294)
T KOG4571|consen 251 EALLGELEGLEKRNEELKDQASELEREI 278 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555555555555554443
No 82
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.05 E-value=27 Score=22.33 Aligned_cols=39 Identities=21% Similarity=0.286 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
.++..+..++...+. . ....+||..+|++...|..|.+.
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 467788887766432 2 25688999999999999877753
No 83
>PRK04217 hypothetical protein; Provisional
Probab=38.96 E-value=27 Score=27.56 Aligned_cols=41 Identities=12% Similarity=0.156 Sum_probs=31.2
Q ss_pred CcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 90 KRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 90 ~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
..++.+|..++...|...- ...+||+.+|++...|+..+..
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~R 81 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTS 81 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHH
Confidence 3578888888877775443 5678999999999988866643
No 84
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=38.78 E-value=2.4e+02 Score=23.78 Aligned_cols=66 Identities=20% Similarity=0.330 Sum_probs=45.4
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYD 157 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~ 157 (257)
++..+|++++.++.+.-..+ |..-.+..||+++|++..-|.+-..--. .+++..+...+..+..-+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~--e~~~~~~~~le~~k~rWg 147 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK--EKKKEMEARLEAIKSRWG 147 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH--HHHHHHHHHHHHHHHhcc
Confidence 45779999999998877654 5666788999999999987777664433 444444444444444333
No 85
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=38.35 E-value=31 Score=28.31 Aligned_cols=28 Identities=11% Similarity=0.281 Sum_probs=21.6
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
...+||..||+++..|+++...-|.+.|
T Consensus 147 s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 147 SYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 4678999999999999887765444444
No 86
>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=38.30 E-value=21 Score=23.12 Aligned_cols=40 Identities=15% Similarity=0.404 Sum_probs=27.4
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccc
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWF 133 (257)
+..++.++++.+.+.+... ....+||+.+|++...|.-++
T Consensus 3 p~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 3 PPKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 3447777777777777665 357889999999988876554
No 87
>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=37.61 E-value=24 Score=24.19 Aligned_cols=33 Identities=27% Similarity=0.336 Sum_probs=24.8
Q ss_pred HHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccc
Q 040769 95 DQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAV 131 (257)
Q Consensus 95 ~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkv 131 (257)
.|+..|+-.+. +...+.. +||..||++++.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 57888888888 6666554 899999999987653
No 88
>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=37.60 E-value=15 Score=25.54 Aligned_cols=28 Identities=25% Similarity=0.529 Sum_probs=21.7
Q ss_pred HHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 113 DRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 113 ~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
-...+||..||++.+.|..|-+ |-+|..
T Consensus 14 ~~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 14 WSIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CCHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 3467899999999999999974 444443
No 89
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=37.43 E-value=27 Score=29.02 Aligned_cols=43 Identities=23% Similarity=0.128 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
+++.|..++...|-.+ ....+||..||++...|+.+...-|.+
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~ 182 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALAR 182 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4555555555544332 246789999999999998877443333
No 90
>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=37.26 E-value=13 Score=23.75 Aligned_cols=24 Identities=17% Similarity=0.171 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCcccccccccchh
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRA 138 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRa 138 (257)
..++|+.+|++++.|+.|.++-.-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~l 26 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGLL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCC
Confidence 467899999999999999776543
No 91
>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=37.24 E-value=7.9 Score=28.41 Aligned_cols=35 Identities=11% Similarity=0.111 Sum_probs=25.5
Q ss_pred HHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769 102 RSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136 (257)
Q Consensus 102 ~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR 136 (257)
..|....+.......+||..||+++..|+.|+.+.
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~~ 56 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKGE 56 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhcC
Confidence 33444444444567899999999999999998743
No 92
>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=36.85 E-value=27 Score=28.68 Aligned_cols=38 Identities=21% Similarity=0.199 Sum_probs=25.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
+++.+..+|.-.|-.+ ....+||..||+++..|+++-.
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 5555555555544333 2456889999999988887654
No 93
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=36.73 E-value=1.4e+02 Score=20.55 Aligned_cols=35 Identities=26% Similarity=0.354 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 040769 143 KQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRML 177 (257)
Q Consensus 143 ~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l 177 (257)
...+.....|..+++.+..+...|..++..|+..+
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 29 EELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 45677788899999999999999999998887654
No 94
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. 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 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=36.38 E-value=1.7e+02 Score=22.72 Aligned_cols=75 Identities=20% Similarity=0.301 Sum_probs=42.4
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQ 167 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~ 167 (257)
..+.|+..++..| ......+.+|++-..|+..+....... ..........+......+..+-..++
T Consensus 34 ~yR~Y~~~d~~~l-------------~~I~~lr~~G~sl~eI~~~l~~~~~~~-~~~~~~~~~~l~~~~~~l~~~i~~l~ 99 (116)
T cd04769 34 NYRVYDAQHVECL-------------RFIKEARQLGFTLAELKAIFAGHEGRA-VLPWPHLQQALEDKKQEIRAQITELQ 99 (116)
T ss_pred CceeeCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhccccCC-cCcHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3566999999988 344456778888888888887665542 11112222334444444444444444
Q ss_pred HHHHHHHHH
Q 040769 168 EEVMKLKRM 176 (257)
Q Consensus 168 ~e~~~~~~~ 176 (257)
.....++..
T Consensus 100 ~~~~~l~~~ 108 (116)
T cd04769 100 QLLARLDAF 108 (116)
T ss_pred HHHHHHHHH
Confidence 444444433
No 95
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=35.90 E-value=27 Score=28.72 Aligned_cols=45 Identities=11% Similarity=0.097 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|+..|-. ...-.+||..||++...|+++...-|.+-|
T Consensus 137 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 137 LPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 555555555543322 234678999999999999988865444444
No 96
>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=35.35 E-value=29 Score=27.69 Aligned_cols=41 Identities=24% Similarity=0.216 Sum_probs=27.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
+++.+..++...|-.. ....+||..+|++...|+++...-|
T Consensus 112 L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar 152 (159)
T TIGR02989 112 LPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLR 152 (159)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHH
Confidence 5666666665544322 3567899999999999997754333
No 97
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=35.29 E-value=88 Score=29.25 Aligned_cols=14 Identities=14% Similarity=0.463 Sum_probs=11.4
Q ss_pred cccccccchhhhhH
Q 040769 129 IAVWFQNRRARWKS 142 (257)
Q Consensus 129 VkvWFQNRRak~Kr 142 (257)
++|||+|-|+-.+-
T Consensus 16 CKiWi~dN~~Sv~~ 29 (336)
T KOG0150|consen 16 CKIWIKDNPASVRF 29 (336)
T ss_pred hhhhhcCChHHHHh
Confidence 68999999886654
No 98
>PRK06930 positive control sigma-like factor; Validated
Probab=35.27 E-value=32 Score=29.04 Aligned_cols=46 Identities=11% Similarity=0.027 Sum_probs=33.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..+|.-.|..+ ..-.+||..||++...|+.+...-|.|.++
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6777777776654333 246789999999999999988766655554
No 99
>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=35.15 E-value=39 Score=29.98 Aligned_cols=40 Identities=15% Similarity=0.277 Sum_probs=30.8
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLK 153 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~ 153 (257)
...+||..||++...|+++...-|.+-|+.-..+..+.++
T Consensus 179 S~~EIA~~Lgis~~TVk~rl~RAr~~Lr~~l~~~~~~~~~ 218 (244)
T TIGR03001 179 SMDRIGAMYQVHRSTVSRWVAQARERLLERTRRRLAERLK 218 (244)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 3568999999999999999988777777765555554443
No 100
>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=35.12 E-value=32 Score=28.29 Aligned_cols=28 Identities=21% Similarity=0.208 Sum_probs=21.3
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
...+||..||+++..|++....-|.+-|
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999987765444444
No 101
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=35.00 E-value=40 Score=28.06 Aligned_cols=46 Identities=11% Similarity=0.208 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..+|+-.|-.. ....+||..+|+++..|++-...-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555554443322 245689999999999998776554444443
No 102
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), 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. 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.
Probab=34.38 E-value=1.1e+02 Score=23.16 Aligned_cols=40 Identities=15% Similarity=0.070 Sum_probs=27.3
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
.++.|+.+++..|.. ...|.+.+|++-..|+.+..+....
T Consensus 35 g~R~Yt~~di~~l~~------------I~~llr~~G~~l~~i~~~l~~~~~~ 74 (99)
T cd04765 35 GRRYYRPKDVELLLL------------IKHLLYEKGYTIEGAKQALKEDGAA 74 (99)
T ss_pred CCeeeCHHHHHHHHH------------HHHHHHHCCCCHHHHHHHHHhcccc
Confidence 466799999998833 2335567788877777777654443
No 103
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=34.31 E-value=30 Score=28.70 Aligned_cols=28 Identities=7% Similarity=0.172 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
.-.+||..||++...|+.+...-|.+.|
T Consensus 146 s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 146 SNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 3568999999999999987754444433
No 104
>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=34.01 E-value=29 Score=22.45 Aligned_cols=21 Identities=14% Similarity=0.317 Sum_probs=18.5
Q ss_pred HHHHHhCCCCcccccccccch
Q 040769 117 KLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 117 ~LA~~LgL~~~qVkvWFQNRR 137 (257)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998875
No 105
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=33.89 E-value=40 Score=27.88 Aligned_cols=45 Identities=11% Similarity=0.302 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++...|-.+ ....+||..+|++...|+++-..-|.+.|
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 4444444444443222 24568999999999999987754444333
No 106
>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=33.60 E-value=34 Score=26.99 Aligned_cols=44 Identities=16% Similarity=0.136 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
++..+..+|.-.|-.+ ....+||..+|+++..|+.+...-|.|.
T Consensus 114 L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555555555433222 2456799999999999987765444333
No 107
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=33.37 E-value=2.4e+02 Score=22.16 Aligned_cols=37 Identities=24% Similarity=0.319 Sum_probs=27.8
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
..+.|+..++..| ......+.+|++-..|+..+....
T Consensus 34 g~R~Y~~~~l~~l-------------~~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 34 GYRRYPEETVKRL-------------RFIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred CCEeECHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHhccc
Confidence 4556999999998 445557888888888888886543
No 108
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal 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. This subgroup lacks one of the c
Probab=33.20 E-value=2.5e+02 Score=22.32 Aligned_cols=75 Identities=15% Similarity=0.191 Sum_probs=42.9
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQE 168 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~ 168 (257)
.+.|+..++..| ......+.+|++-..|+-++......... .......+......+..+-..++.
T Consensus 36 yR~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 36 YRLYSEKDLSRL-------------RFILSARQLGFSLKDIKEILSHADQGESP--CPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred eeeCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhhhccCCCc--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456999999998 44555778888888888888754322111 112223334444444444445544
Q ss_pred HHHHHHHHHH
Q 040769 169 EVMKLKRMLK 178 (257)
Q Consensus 169 e~~~~~~~l~ 178 (257)
-...+...+.
T Consensus 101 ~~~~l~~~~~ 110 (133)
T cd04787 101 LRDRMQQAVS 110 (133)
T ss_pred HHHHHHHHHH
Confidence 4444444443
No 109
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=33.18 E-value=41 Score=27.23 Aligned_cols=29 Identities=21% Similarity=0.140 Sum_probs=21.9
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
...+||..||++...|++|...-|.+.|+
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999998887654444443
No 110
>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=33.12 E-value=40 Score=25.80 Aligned_cols=36 Identities=25% Similarity=0.486 Sum_probs=19.4
Q ss_pred HHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHH
Q 040769 97 LESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLE 146 (257)
Q Consensus 97 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~ 146 (257)
+.+.+-.|+.|+||...--.. | =.|||.+||+.+..
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~Q 49 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQ 49 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHH
Confidence 445566688899987441111 1 15899999986643
No 111
>PF13518 HTH_28: Helix-turn-helix domain
Probab=32.81 E-value=19 Score=23.29 Aligned_cols=22 Identities=23% Similarity=0.569 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCCccccccccc
Q 040769 114 RKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQN 135 (257)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 4567999999999999999864
No 112
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.39 E-value=39 Score=25.82 Aligned_cols=37 Identities=19% Similarity=0.278 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQ 128 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~q 128 (257)
+.++|...-...|+.+--.+.-...+||.+|++++-.
T Consensus 3 Ln~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~ 39 (97)
T COG4367 3 LNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVK 39 (97)
T ss_pred CCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHH
Confidence 5678888888888888878888899999999998743
No 113
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=32.36 E-value=1.6e+02 Score=23.12 Aligned_cols=37 Identities=24% Similarity=0.276 Sum_probs=30.2
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhcC
Q 040769 145 LELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQG 181 (257)
Q Consensus 145 ~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~~ 181 (257)
.-.....|+.....+.+||..|+.|+..|++.+....
T Consensus 20 l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~ 56 (107)
T PF06156_consen 20 LLEELEELKKQLQELLEENARLRIENEHLRERLEELE 56 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445677888888899999999999999999988653
No 114
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. 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=32.13 E-value=2.5e+02 Score=22.06 Aligned_cols=75 Identities=17% Similarity=0.170 Sum_probs=40.3
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQ 167 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~ 167 (257)
..+.|+.+++..|. .....+.+|++-..|+-.+.-.+.... ........+......+..+-..|+
T Consensus 35 g~R~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~ 99 (126)
T cd04785 35 GYRLYGAAHVERLR-------------FIRRARDLGFSLEEIRALLALSDRPDR--SCAEADAIARAHLADVRARIADLR 99 (126)
T ss_pred CccccCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHhhhhcCCC--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35569999999993 444466777777777777654322110 111122233344444444444555
Q ss_pred HHHHHHHHHH
Q 040769 168 EEVMKLKRML 177 (257)
Q Consensus 168 ~e~~~~~~~l 177 (257)
.-...++..+
T Consensus 100 ~~~~~L~~~~ 109 (126)
T cd04785 100 RLEAELKRMV 109 (126)
T ss_pred HHHHHHHHHH
Confidence 5554555444
No 115
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. 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=32.12 E-value=2.5e+02 Score=22.01 Aligned_cols=38 Identities=24% Similarity=0.326 Sum_probs=29.1
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchh
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRA 138 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRa 138 (257)
..+.|+.+++..|+ .....+.+|++-..|+-.+.....
T Consensus 35 gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~ 72 (126)
T cd04783 35 GYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDDG 72 (126)
T ss_pred CCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcccC
Confidence 35569999999993 555678899998888888876543
No 116
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=31.57 E-value=41 Score=26.89 Aligned_cols=41 Identities=15% Similarity=0.158 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
+++.+..++.-.|-.. ....+||..||++...|++....-|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~ 147 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRAT 147 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 5566666665544332 2357899999999999987665333
No 117
>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=31.15 E-value=2.8e+02 Score=22.35 Aligned_cols=37 Identities=11% Similarity=0.091 Sum_probs=22.5
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccch
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
.++.|+..++..|... ...+.+|++-..|+-++.+..
T Consensus 34 g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 34 NYRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhc
Confidence 4566999999988443 223455555555555554443
No 118
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=30.99 E-value=43 Score=29.38 Aligned_cols=27 Identities=7% Similarity=0.167 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCcccccccccchhhhh
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
..+||..||++...|++....-|.+.|
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 348899999999999877755444444
No 119
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.95 E-value=37 Score=27.30 Aligned_cols=44 Identities=14% Similarity=0.271 Sum_probs=28.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
++..+..+|.-.| .. ....+||..||++...|+.+...-|.+.|
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555555 32 24568899999999999887754444433
No 120
>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=30.87 E-value=2.4e+02 Score=21.35 Aligned_cols=35 Identities=20% Similarity=0.276 Sum_probs=23.4
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
..+.|+..++..|.. ....+++|++-..|+..+..
T Consensus 35 g~R~Y~~~dl~~l~~-------------I~~l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 35 NYRLYSEADLSRLEK-------------IVFLQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred CCeeeCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHcC
Confidence 456699999999843 33346667776666666554
No 121
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.73 E-value=4.8e+02 Score=24.86 Aligned_cols=25 Identities=16% Similarity=0.235 Sum_probs=9.3
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 154 QEYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 154 ~~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
.+.+.|+.+..++++...-|+....
T Consensus 253 ~~~etLEqq~~~L~~niDIL~~k~~ 277 (365)
T KOG2391|consen 253 AMKETLEQQLQSLQKNIDILKSKVR 277 (365)
T ss_pred HHHHHHHHHHHHHHhhhHHHHHHHH
Confidence 3333333333333333333333333
No 122
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=30.53 E-value=65 Score=26.53 Aligned_cols=28 Identities=7% Similarity=0.120 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
...+||..||++...|++....-|.+.|
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999998876654444443
No 123
>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=30.52 E-value=44 Score=27.10 Aligned_cols=44 Identities=5% Similarity=0.101 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
++..+..++...|-.+ ....+||..||++...|+++...-|.+-
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~L 163 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKL 163 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4555555555444332 2467899999999999987664433333
No 124
>smart00338 BRLZ basic region leucin zipper.
Probab=30.17 E-value=1.9e+02 Score=19.96 Aligned_cols=30 Identities=23% Similarity=0.467 Sum_probs=15.5
Q ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 040769 148 LYDSLKQEYDAVSREKLKLQEEVMKLKRML 177 (257)
Q Consensus 148 ~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l 177 (257)
....|......+..++..|..++..+...+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~ 56 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555555555555555554443
No 125
>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=30.16 E-value=44 Score=20.48 Aligned_cols=23 Identities=26% Similarity=0.380 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCCcccccccccch
Q 040769 115 KMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
..++|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35788999999999999988764
No 126
>PHA02955 hypothetical protein; Provisional
Probab=30.07 E-value=73 Score=28.16 Aligned_cols=43 Identities=9% Similarity=0.175 Sum_probs=34.2
Q ss_pred CHHHHHHHHHHhhhc-CCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 93 TSDQLESLERSFQEE-IKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 93 t~~Ql~~Le~~F~~~-~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
...++..|-+.|... ..+..++|.+++++||+....|..||.+
T Consensus 59 a~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 59 EEKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 345777776666654 5788899999999999999878888876
No 127
>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=30.05 E-value=32 Score=28.30 Aligned_cols=27 Identities=11% Similarity=0.029 Sum_probs=20.3
Q ss_pred HHHHHHHHhCCCCcccccccccchhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
.-.+||..||+++..|+++...-|.+-
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~L 182 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAI 182 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 457899999999999988775433333
No 128
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=30.01 E-value=35 Score=27.48 Aligned_cols=45 Identities=16% Similarity=0.048 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
++..|..+|.-.|-.+ ....+||..+|++...|+.+...-|.+-|
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555554443322 24568999999999998887754444443
No 129
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=29.75 E-value=42 Score=27.99 Aligned_cols=39 Identities=23% Similarity=0.191 Sum_probs=24.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
+++.+..+|...|-.+ ....+||..+|++...|+..+..
T Consensus 107 L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~R 145 (181)
T PRK09637 107 LPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQR 145 (181)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHH
Confidence 4445555554443222 24568899999999888877653
No 130
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=29.69 E-value=2.2e+02 Score=20.82 Aligned_cols=39 Identities=23% Similarity=0.273 Sum_probs=22.9
Q ss_pred hhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH
Q 040769 139 RWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRML 177 (257)
Q Consensus 139 k~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l 177 (257)
|+|.....+....+....+.+..+++.++.+...-.+.+
T Consensus 31 KEknn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerl 69 (79)
T COG3074 31 KEKNNSLSQEVQNAQHQREALERENEQLKEEQNGWQERL 69 (79)
T ss_pred HHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455555555555566666667777777766655444333
No 131
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=29.24 E-value=77 Score=24.35 Aligned_cols=42 Identities=17% Similarity=0.256 Sum_probs=31.2
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCC-CCcccccccc
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGL-QPRQIAVWFQ 134 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL-~~~qVkvWFQ 134 (257)
|++|+.+....+=..+....+ ...+||+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 778999877655555544433 57889999996 9999887765
No 132
>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=29.18 E-value=38 Score=21.76 Aligned_cols=36 Identities=17% Similarity=0.258 Sum_probs=25.5
Q ss_pred CHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 93 TSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 93 t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
+..|..++...+. . ....++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~~-~-----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE-G-----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4556666655431 1 2567889999999999998875
No 133
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=29.07 E-value=41 Score=28.37 Aligned_cols=28 Identities=18% Similarity=0.113 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
...+||..||++...|+++...-|.+.|
T Consensus 131 s~~EIA~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 131 SYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999999988764444433
No 134
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=28.74 E-value=94 Score=30.59 Aligned_cols=78 Identities=17% Similarity=0.226 Sum_probs=41.8
Q ss_pred CcCCHHHHHHHHHH-hhhc-CCCCHHHHHHHHHHhCCCCcccccccccchh-hhhHHHHHHHHHHHHHHhHHHHHHHHHH
Q 040769 90 KRLTSDQLESLERS-FQEE-IKLDPDRKMKLARELGLQPRQIAVWFQNRRA-RWKSKQLELLYDSLKQEYDAVSREKLKL 166 (257)
Q Consensus 90 ~r~t~~Ql~~Le~~-F~~~-~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRa-k~Kr~~~~~~~~~l~~~~~~~~~e~~~l 166 (257)
-++|.+....|.+. +-.. .+|-.+.-+++-+ +|+.=.+|+|. .++|++++...+.|.........+|.+|
T Consensus 219 L~LteeEkrLL~kEG~slPs~lPLTKaEEriLK-------rvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL 291 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKEGYSLPSKLPLTKAEERILK-------RVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQEL 291 (472)
T ss_pred eeccHHHHHHHHhccCcCcccCCchHHHHHHHH-------HHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHH
Confidence 34788888888776 2222 2344443333333 34444456654 4455555555566655555555555555
Q ss_pred HHHHHHHH
Q 040769 167 QEEVMKLK 174 (257)
Q Consensus 167 ~~e~~~~~ 174 (257)
+.++.++.
T Consensus 292 ~kkV~~Le 299 (472)
T KOG0709|consen 292 QKKVEELE 299 (472)
T ss_pred HHHHHHHh
Confidence 55555443
No 135
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=28.42 E-value=78 Score=29.92 Aligned_cols=29 Identities=24% Similarity=0.314 Sum_probs=18.7
Q ss_pred HHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 150 DSLKQEYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 150 ~~l~~~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
-.|+.+++.|++|++.|+.++.+|+....
T Consensus 35 ~aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 35 FALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hhHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 35666677777777777777666655544
No 136
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=28.28 E-value=50 Score=26.51 Aligned_cols=21 Identities=29% Similarity=0.583 Sum_probs=17.2
Q ss_pred HHHHHHHHhCCCCcccccccc
Q 040769 114 RKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQ 134 (257)
...+||..+|++...|+....
T Consensus 127 s~~EIA~~lgis~~tV~~~l~ 147 (163)
T PRK07037 127 TQKDIARELGVSPTLVNFMIR 147 (163)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356899999999999997644
No 137
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=28.26 E-value=48 Score=26.92 Aligned_cols=45 Identities=20% Similarity=0.059 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|.-.|... ....+||..||+++..|+++...-|.+-|
T Consensus 113 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 113 LSADQREAIILIGASG-----FSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4555555555543322 24678999999999999987754444433
No 138
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=28.16 E-value=2.1e+02 Score=19.86 Aligned_cols=34 Identities=24% Similarity=0.345 Sum_probs=22.0
Q ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 145 LELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 145 ~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
.+.....+....++++.+++.+..++.++++.++
T Consensus 5 lEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk 38 (55)
T PF05377_consen 5 LENELPRIESSINTVKKENEEISESVEKIEENVK 38 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555556667777777777777777766654
No 139
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=28.09 E-value=42 Score=27.99 Aligned_cols=45 Identities=20% Similarity=0.285 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++.-.|-.. ....+||..||++...|+...+.-|.+-|
T Consensus 132 L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 132 LEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555433222 24568899999999888876654444433
No 140
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=27.76 E-value=54 Score=27.00 Aligned_cols=26 Identities=19% Similarity=0.184 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCcccccccccchhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
.-.+||..+|++...|+.+...-|.+
T Consensus 153 s~~eIA~~lgis~~~V~~~l~ra~~~ 178 (186)
T PRK13919 153 THREAAQLLGLPLGTLKTRARRALSR 178 (186)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 35689999999999988766543333
No 141
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=27.76 E-value=46 Score=27.29 Aligned_cols=28 Identities=11% Similarity=0.214 Sum_probs=21.0
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
...+||..||++...|+++...-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4678999999999999987754444433
No 142
>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=27.72 E-value=48 Score=26.59 Aligned_cols=45 Identities=18% Similarity=0.226 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
++..+..+|...|-. ...-.+||..+|++...|+.+-..-|.+-|
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 155 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLR 155 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 344555555444422 224568999999999999987755444444
No 143
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.66 E-value=22 Score=23.00 Aligned_cols=23 Identities=17% Similarity=0.403 Sum_probs=17.4
Q ss_pred HHHHHHHHHhCCCCccccccccc
Q 040769 113 DRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 113 ~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
....+||+.||++...|..|.+.
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 45778999999999999999753
No 144
>PRK13890 conjugal transfer protein TrbA; Provisional
Probab=27.41 E-value=42 Score=26.59 Aligned_cols=44 Identities=16% Similarity=0.163 Sum_probs=32.2
Q ss_pred HHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHH
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAV 159 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~ 159 (257)
+.+||..+|++...|.-|.++++. -......+..+.+.-..+.+
T Consensus 21 q~eLA~~~Gis~~~is~iE~g~~~-ps~~~l~kIa~aL~v~~~~L 64 (120)
T PRK13890 21 KKELSERSGVSISFLSDLTTGKAN-PSLKVMEAIADALETPLPLL 64 (120)
T ss_pred HHHHHHHHCcCHHHHHHHHcCCCC-CCHHHHHHHHHHHCCCHHHH
Confidence 678999999999999999998873 45556666666665544444
No 145
>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=27.35 E-value=1.1e+02 Score=24.97 Aligned_cols=48 Identities=19% Similarity=0.149 Sum_probs=35.9
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
.+-++..|+.+|+-.+ .. ....+||..||++...|+.+-..-|.|-|+
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 4568899999997742 22 256789999999999998887666655554
No 146
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=27.22 E-value=57 Score=27.24 Aligned_cols=46 Identities=7% Similarity=0.042 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
++..+..++.-.|-.. ..-.+||..||++...|+.....-|.+-|+
T Consensus 137 L~~~~r~i~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 137 LPENTARVFTLKEILG-----FSSDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred CCHHHHHHhhhHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4445555554333222 235789999999999999877655555444
No 147
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=26.98 E-value=1.3e+02 Score=28.00 Aligned_cols=42 Identities=17% Similarity=0.192 Sum_probs=30.4
Q ss_pred hhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 040769 139 RWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180 (257)
Q Consensus 139 k~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~ 180 (257)
|+-|++++.+...|...-.-|...|..|-+|+.-||++-...
T Consensus 304 RECRRKKKEYVKCLENRVAVLENQNKaLIEELKtLKeLYc~k 345 (348)
T KOG3584|consen 304 RECRRKKKEYVKCLENRVAVLENQNKALIEELKTLKELYCHK 345 (348)
T ss_pred HHHHHhHhHHHHHHHhHHHHHhcccHHHHHHHHHHHHHhhcc
Confidence 444445555667776777777788889999999998876644
No 148
>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=26.73 E-value=21 Score=22.20 Aligned_cols=26 Identities=19% Similarity=0.452 Sum_probs=21.4
Q ss_pred HHHHHHHhCCCCcccccccccchhhh
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
..++|+.||++.+.|..|.++.+...
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~~ 28 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLKA 28 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCCc
Confidence 46889999999999999987766543
No 149
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=26.71 E-value=2.7e+02 Score=24.00 Aligned_cols=53 Identities=17% Similarity=0.226 Sum_probs=39.1
Q ss_pred ccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 040769 128 QIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180 (257)
Q Consensus 128 qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~ 180 (257)
...+|-+-|-.+.|..+.+.....|+...+.+..+-+.++.++..|.+.+...
T Consensus 87 v~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~~~l~~~ 139 (181)
T KOG3335|consen 87 VFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLHSKLNKP 139 (181)
T ss_pred eehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCc
Confidence 34567777766777677777778888888888888888888888887666644
No 150
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=26.61 E-value=1.9e+02 Score=26.85 Aligned_cols=36 Identities=19% Similarity=0.299 Sum_probs=28.3
Q ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHh
Q 040769 144 QLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKE 179 (257)
Q Consensus 144 ~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~ 179 (257)
........|.+.++.|+.--.++..|++.+|..+-+
T Consensus 252 ~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e 287 (294)
T KOG4571|consen 252 ALLGELEGLEKRNEELKDQASELEREIRYLKQLILE 287 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456788888889988888999999998887654
No 151
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.51 E-value=3.2e+02 Score=21.52 Aligned_cols=76 Identities=17% Similarity=0.159 Sum_probs=42.8
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQ 167 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~ 167 (257)
..+.|+..++..| ......+.+|++-..|+-.+.....-.. ........+......+..+-..|+
T Consensus 35 gyR~Y~~~~l~~l-------------~~I~~lr~lG~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~ 99 (127)
T TIGR02047 35 NYRVYTVGHVERL-------------AFIRNCRTLDMSLAEIRQLLRYQDKPEK--SCSDVNALLDEHISHVRARIIKLQ 99 (127)
T ss_pred CCCcCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHHhhhCCCC--CHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567999999998 3445567888888888877753222111 111222334444555555555555
Q ss_pred HHHHHHHHHHH
Q 040769 168 EEVMKLKRMLK 178 (257)
Q Consensus 168 ~e~~~~~~~l~ 178 (257)
.....++..+.
T Consensus 100 ~~~~~L~~~~~ 110 (127)
T TIGR02047 100 ALIEQLVDLRG 110 (127)
T ss_pred HHHHHHHHHHH
Confidence 55555554443
No 152
>KOG4752 consensus Ribosomal protein L41 [Translation, ribosomal structure and biogenesis]
Probab=26.37 E-value=1.1e+02 Score=17.58 Aligned_cols=13 Identities=38% Similarity=0.882 Sum_probs=8.4
Q ss_pred hhhhhHHHHHHHH
Q 040769 137 RARWKSKQLELLY 149 (257)
Q Consensus 137 Rak~Kr~~~~~~~ 149 (257)
|+||+++......
T Consensus 2 r~kwrkkrmrrlk 14 (26)
T KOG4752|consen 2 RAKWRKKRMRRLK 14 (26)
T ss_pred chHHHHHHHHHHH
Confidence 6788877665443
No 153
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.36 E-value=73 Score=25.40 Aligned_cols=45 Identities=16% Similarity=0.179 Sum_probs=34.5
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
.+|..+.++|+- +..+. ...+||+.++++++.|+.+.++=|.|-.
T Consensus 149 ~lt~~e~~vl~l-~~~g~-----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEGY-----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 489989888876 43332 3578999999999999999887665554
No 154
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.30 E-value=43 Score=27.07 Aligned_cols=48 Identities=19% Similarity=0.235 Sum_probs=36.7
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.+|..+..+|+..... ..+.+||+.++++++.|++..+|=|.|-....
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~~ 200 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVRS 200 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 4899999998766543 34678899999999999998887766655433
No 155
>PRK12529 RNA polymerase sigma factor; Provisional
Probab=26.23 E-value=54 Score=27.06 Aligned_cols=44 Identities=7% Similarity=0.114 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
+++.|..++.-.|-.+ ....+||..||+++..|+.....-+.+.
T Consensus 128 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~rAl~~~ 171 (178)
T PRK12529 128 LRPRVKQAFLMATLDG-----MKQKDIAQALDIALPTVKKYIHQAYVTC 171 (178)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5566666555544332 2456899999999999998776444443
No 156
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=26.08 E-value=26 Score=24.15 Aligned_cols=22 Identities=18% Similarity=0.372 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCCcccccccccc
Q 040769 115 KMKLARELGLQPRQIAVWFQNR 136 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNR 136 (257)
..++|+.+|++.++|+.|=+.-
T Consensus 3 i~eva~~~gvs~~tlr~y~~~g 24 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYEREG 24 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHTT
T ss_pred HHHHHHHHCcCHHHHHHHHHhc
Confidence 3579999999999999996543
No 157
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=25.95 E-value=2.2e+02 Score=19.81 Aligned_cols=26 Identities=27% Similarity=0.403 Sum_probs=20.5
Q ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHh
Q 040769 154 QEYDAVSREKLKLQEEVMKLKRMLKE 179 (257)
Q Consensus 154 ~~~~~~~~e~~~l~~e~~~~~~~l~~ 179 (257)
.+...+..|+++|++|..+|+..|+.
T Consensus 33 ~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 33 LDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34556778889999999999988764
No 158
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=25.90 E-value=56 Score=26.97 Aligned_cols=29 Identities=14% Similarity=0.087 Sum_probs=21.7
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
...+||..||++...|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999877554444443
No 159
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=25.87 E-value=2.1e+02 Score=19.09 Aligned_cols=29 Identities=28% Similarity=0.436 Sum_probs=19.8
Q ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Q 040769 147 LLYDSLKQEYDAVSREKLKLQEEVMKLKR 175 (257)
Q Consensus 147 ~~~~~l~~~~~~~~~e~~~l~~e~~~~~~ 175 (257)
.....+......+..++..|..++..|+.
T Consensus 25 ~~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 25 QREEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455666777777788888777776653
No 160
>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=25.82 E-value=85 Score=23.21 Aligned_cols=23 Identities=13% Similarity=0.157 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCCcccccccccch
Q 040769 115 KMKLARELGLQPRQIAVWFQNRR 137 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRR 137 (257)
..++|+.+|++.+.|+.|-+..-
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gl 26 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGL 26 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 46789999999999999976543
No 161
>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=25.36 E-value=3.1e+02 Score=20.90 Aligned_cols=69 Identities=22% Similarity=0.310 Sum_probs=40.4
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHHHHHhHHHHHHHHHHH
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSLKQEYDAVSREKLKLQ 167 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~ 167 (257)
..+.|+..++..|. .....+.+|++-..|+-.+..... ......+......+..+-..++
T Consensus 36 gyR~Y~~~~i~~l~-------------~I~~lr~~G~sl~~i~~l~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~ 95 (108)
T cd01107 36 GYRYYSAEQLERLN-------------RIKYLRDLGFPLEEIKEILDADND-------DELRKLLREKLAELEAEIEELQ 95 (108)
T ss_pred CccccCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcCCH-------HHHHHHHHHHHHHHHHHHHHHH
Confidence 35569999999883 344456688888888877776543 2233334444444444444444
Q ss_pred HHHHHHHHH
Q 040769 168 EEVMKLKRM 176 (257)
Q Consensus 168 ~e~~~~~~~ 176 (257)
.....++..
T Consensus 96 ~~~~~l~~~ 104 (108)
T cd01107 96 RILRLLEDR 104 (108)
T ss_pred HHHHHHHHH
Confidence 444444443
No 162
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=25.18 E-value=57 Score=27.35 Aligned_cols=27 Identities=4% Similarity=0.054 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCcccccccccchhhhh
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
-.+||..||++...|+.+...-|.+.|
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALA 181 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 458999999999999988754343333
No 163
>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=25.12 E-value=58 Score=26.15 Aligned_cols=37 Identities=22% Similarity=0.235 Sum_probs=23.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWF 133 (257)
+++.+..+|.-.|-.. ..-.+||..||++...|+...
T Consensus 123 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tv~~~l 159 (170)
T TIGR02952 123 LTPKQQHVIALRFGQN-----LPIAEVARILGKTEGAVKILQ 159 (170)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHH
Confidence 4455555554433222 245689999999998888655
No 164
>PHA00542 putative Cro-like protein
Probab=24.40 E-value=1.5e+02 Score=21.70 Aligned_cols=35 Identities=14% Similarity=0.174 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhhHHHHHHH
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWKSKQLELL 148 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~ 148 (257)
...+||+.+|++...|.-|...+...-+.......
T Consensus 33 Tq~elA~~lgIs~~tIsr~e~g~~~~p~~~~l~ki 67 (82)
T PHA00542 33 SQEQIADATDVSQPTICRIYSGRHKDPRYSVVEKL 67 (82)
T ss_pred CHHHHHHHHCcCHHHHHHHHcCCCCCCCHHHHHHH
Confidence 45679999999999999999877433333344433
No 165
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), 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=24.21 E-value=2.9e+02 Score=20.94 Aligned_cols=35 Identities=14% Similarity=0.155 Sum_probs=28.1
Q ss_pred CCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769 89 KKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136 (257)
Q Consensus 89 R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR 136 (257)
..+|+..++..| .....++.+|++-..|+-+|...
T Consensus 34 ~r~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 34 QYFFDEKCQDDL-------------EFILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred ccccCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHhc
Confidence 346999988877 46677889999999999988764
No 166
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=24.19 E-value=56 Score=28.41 Aligned_cols=46 Identities=17% Similarity=0.217 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.+..+|...|... ....+||..+|++...|+.+...-|.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4455555555544322 245789999999999999888766555554
No 167
>PRK09645 RNA polymerase sigma factor SigL; Provisional
Probab=24.12 E-value=70 Score=25.95 Aligned_cols=39 Identities=18% Similarity=0.301 Sum_probs=25.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
+++.+..+|.-.|-.+ ....+||..||+++..|+.....
T Consensus 119 L~~~~r~vl~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~r 157 (173)
T PRK09645 119 LSPEHRAVLVRSYYRG-----WSTAQIAADLGIPEGTVKSRLHY 157 (173)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHH
Confidence 4555555555544322 23568999999999999876643
No 168
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=23.82 E-value=2.4e+02 Score=28.79 Aligned_cols=36 Identities=25% Similarity=0.300 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Q 040769 143 KQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLK 178 (257)
Q Consensus 143 ~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~ 178 (257)
.+.+...+.|+.+...|..|...+...+..++..+.
T Consensus 514 ~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls 549 (604)
T KOG3863|consen 514 LNLEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLS 549 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555566666666666666666555555554443
No 169
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=23.62 E-value=2.8e+02 Score=21.89 Aligned_cols=35 Identities=26% Similarity=0.224 Sum_probs=28.3
Q ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 040769 146 ELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180 (257)
Q Consensus 146 ~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~ 180 (257)
-.....|+.....+.+||..|+.|+..|++.+...
T Consensus 21 ~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 21 LKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33456778888888999999999999999988853
No 170
>PF15058 Speriolin_N: Speriolin N terminus
Probab=23.34 E-value=1.4e+02 Score=26.00 Aligned_cols=33 Identities=27% Similarity=0.429 Sum_probs=20.2
Q ss_pred HHHHHHHhHHHHHHHHHHHHH------HHHHHHHHHhcC
Q 040769 149 YDSLKQEYDAVSREKLKLQEE------VMKLKRMLKEQG 181 (257)
Q Consensus 149 ~~~l~~~~~~~~~e~~~l~~e------~~~~~~~l~~~~ 181 (257)
|+.+++..+.+..||++|+++ .+++|..|.+..
T Consensus 7 yeGlrhqierLv~ENeeLKKlVrLirEN~eLksaL~ea~ 45 (200)
T PF15058_consen 7 YEGLRHQIERLVRENEELKKLVRLIRENHELKSALGEAC 45 (200)
T ss_pred hHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 555666667777777766654 455566655543
No 171
>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=23.21 E-value=87 Score=26.15 Aligned_cols=45 Identities=11% Similarity=0.062 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|.-.|-.+ ....+||..||++...|++....-|.+-|
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tvk~rl~Rar~~Lr 176 (188)
T TIGR02943 132 LPEQTARVFMMREVLG-----FESDEICQELEISTSNCHVLLYRARLSLR 176 (188)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 4555656665554333 25678999999999999876654443333
No 172
>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=23.17 E-value=32 Score=21.68 Aligned_cols=19 Identities=26% Similarity=0.455 Sum_probs=14.8
Q ss_pred HHHHHHHhCCCCccccccc
Q 040769 115 KMKLARELGLQPRQIAVWF 133 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWF 133 (257)
..++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999998884
No 173
>cd01110 HTH_SoxR Helix-Turn-Helix DNA binding domain of the SoxR transcription regulator. Helix-turn-helix (HTH) transcriptional regulator SoxR. The global regulator, SoxR, up-regulates gene expression of another transcription activator, SoxS, which directly stimulates the oxidative stress regulon genes in E. coli. The soxRS response renders the bacterial cell resistant to superoxide-generating agents, macrophage-generated nitric oxide, organic solvents, and antibiotics. The SoxR proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the unusually long spacer between the -35 and -10 promoter elements. They also harbor a regulatory C-terminal domain containing an iron-sulfur center.
Probab=23.15 E-value=4e+02 Score=21.43 Aligned_cols=35 Identities=29% Similarity=0.426 Sum_probs=24.0
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
..+.|+.+++..|. .....+.+|++...|+-.+.+
T Consensus 35 g~R~Y~~~dl~~l~-------------~I~~lr~~G~sl~eI~~~l~~ 69 (139)
T cd01110 35 NQRRYPRDVLRRIA-------------FIKVAQRLGLSLAEIAEALAT 69 (139)
T ss_pred CCeEECHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHHH
Confidence 35569999999883 344456777777777766653
No 174
>PRK12523 RNA polymerase sigma factor; Reviewed
Probab=23.14 E-value=70 Score=26.09 Aligned_cols=45 Identities=11% Similarity=0.148 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++.-.|-.. ..-.+||..||++...|+++...-+.+.+
T Consensus 120 Lp~~~r~v~~L~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~~~ 164 (172)
T PRK12523 120 LSSKARAAFLYNRLDG-----MGHAEIAERLGVSVSRVRQYLAQGLRQCY 164 (172)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4455555554443222 24568999999999999988765444443
No 175
>PRK12544 RNA polymerase sigma factor; Provisional
Probab=22.53 E-value=95 Score=26.55 Aligned_cols=46 Identities=13% Similarity=0.107 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhH
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKS 142 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr 142 (257)
+++.|..++.-.|-.+ ....+||..+|++...|++....-|.+-|+
T Consensus 149 L~~~~r~v~~L~~~~g-----~s~~EIAe~lgis~~tV~~~l~RAr~~Lr~ 194 (206)
T PRK12544 149 LPAKYARVFMMREFIE-----LETNEICHAVDLSVSNLNVLLYRARLRLRE 194 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4555555555544332 235789999999999999877655555444
No 176
>PRK12533 RNA polymerase sigma factor; Provisional
Probab=22.19 E-value=63 Score=28.04 Aligned_cols=21 Identities=5% Similarity=-0.023 Sum_probs=16.4
Q ss_pred HHHHHHHHhCCCCcccccccc
Q 040769 114 RKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQ 134 (257)
...+||..||+++..|++...
T Consensus 152 s~~EIAe~LgiS~~tVk~~L~ 172 (216)
T PRK12533 152 SYREIAAIADVPVGTVMSRLA 172 (216)
T ss_pred CHHHHHHHHCCCHHHHHHHHH
Confidence 356889999999998876554
No 177
>PRK12539 RNA polymerase sigma factor; Provisional
Probab=22.15 E-value=74 Score=26.31 Aligned_cols=44 Identities=11% Similarity=0.018 Sum_probs=27.9
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
+++.+..+++-.|-. .....+||..||++...|+.+...-|.+.
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~L 175 (184)
T PRK12539 132 LPEKMRLAIQAVKLE-----GLSVAEAATRSGMSESAVKVSVHRGLKAL 175 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCcHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 555555555543322 23467899999999999987764433333
No 178
>PRK09649 RNA polymerase sigma factor SigC; Reviewed
Probab=22.11 E-value=63 Score=26.90 Aligned_cols=24 Identities=17% Similarity=0.028 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCCcccccccccchh
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRA 138 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRa 138 (257)
-.+||..||+++..|++....-|.
T Consensus 149 ~~EIA~~lgis~~tVk~~l~Rar~ 172 (185)
T PRK09649 149 YADAAAVCGCPVGTIRSRVARARD 172 (185)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHH
Confidence 458899999999888877643333
No 179
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.07 E-value=46 Score=26.88 Aligned_cols=44 Identities=27% Similarity=0.300 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhh
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARW 140 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~ 140 (257)
.+|+.+.++|+-.... ..+.+||..++++++.|++..++=|.|-
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl 180 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKL 180 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHh
Confidence 5888888888776653 2577889999999999988776655553
No 180
>PRK09647 RNA polymerase sigma factor SigE; Reviewed
Probab=22.06 E-value=72 Score=27.23 Aligned_cols=26 Identities=15% Similarity=0.251 Sum_probs=19.0
Q ss_pred HHHHHHHHhCCCCcccccccccchhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
...+||..||+++..|+++...-|.+
T Consensus 156 s~~EIA~~Lgis~~tV~~~l~RArk~ 181 (203)
T PRK09647 156 SYEEIAATLGVKLGTVRSRIHRGRQQ 181 (203)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 34588999999999998877543333
No 181
>PF04297 UPF0122: Putative helix-turn-helix protein, YlxM / p13 like; InterPro: IPR007394 Members of this family are predicted to contain a helix-turn-helix motif, for example residues 37-55 in Mycoplasma mycoides p13 (O05290 from SWISSPROT). Genes encoding family members are often part of operons that encode components of the SRP pathway, and this protein may regulate the expression of an operon related to the SRP pathway [].; PDB: 1S7O_A 1XSV_B.
Probab=21.96 E-value=1.7e+02 Score=22.71 Aligned_cols=38 Identities=29% Similarity=0.352 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
+|..|...|+-+|..+ --..+||..+|++..-|.-|.+
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ik 55 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIK 55 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHH
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 6888999998777655 4578899999999888887774
No 182
>PRK12545 RNA polymerase sigma factor; Provisional
Probab=21.76 E-value=93 Score=26.28 Aligned_cols=45 Identities=16% Similarity=0.085 Sum_probs=27.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++.-.|-.+ ..-.+||..||++...|++....-|.+-|
T Consensus 140 Lp~~~r~v~~L~~~eg-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr 184 (201)
T PRK12545 140 LPEQIGRVFMMREFLD-----FEIDDICTELTLTANHCSVLLYRARTRLR 184 (201)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4444444444433222 24568999999999999887654444333
No 183
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are 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 have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.70 E-value=4e+02 Score=20.82 Aligned_cols=36 Identities=19% Similarity=0.272 Sum_probs=26.7
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccc
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNR 136 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNR 136 (257)
..+.|+.+++..| ......+.+|++-..|+..+...
T Consensus 35 gyR~Y~~~~l~~l-------------~~I~~lr~~G~sL~eI~~~l~~~ 70 (127)
T cd04784 35 NYRLYDEEHLERL-------------LFIRRCRSLDMSLDEIRTLLQLQ 70 (127)
T ss_pred CCeecCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHHhh
Confidence 3567999999988 44555777888888888777643
No 184
>TIGR02044 CueR Cu(I)-responsive transcriptional regulator. This model represents the copper-, silver- and gold- (I) responsive transcriptional activator of the gamma proteobacterial copper efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X7-Cys. This family also lacks a conserved cysteine at the N-terminal end of the dimerization helix which is required for the binding of divalent metals such as zinc; here it is replaced by a serine residue.
Probab=21.70 E-value=4e+02 Score=20.87 Aligned_cols=35 Identities=20% Similarity=0.336 Sum_probs=25.6
Q ss_pred CCCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 87 ERKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 87 r~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
...+.|+.+++..| .....++.+|++-..|+..+.
T Consensus 34 ~gyR~Y~~~~l~~l-------------~~I~~lr~~G~sL~eI~~~l~ 68 (127)
T TIGR02044 34 GGYRTYTQQHLDEL-------------RLISRARQVGFSLEECKELLN 68 (127)
T ss_pred CCCeecCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHH
Confidence 34667999999998 344556778888777777664
No 185
>PRK12542 RNA polymerase sigma factor; Provisional
Probab=21.44 E-value=77 Score=26.17 Aligned_cols=45 Identities=11% Similarity=0.176 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..++.-.|-.. ..-.+||..+|++...|++....-|.+.|
T Consensus 123 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 167 (185)
T PRK12542 123 LNESNRQVFKYKVFYN-----LTYQEISSVMGITEANVRKQFERARKRVQ 167 (185)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4555555555433222 24568999999999999987654444443
No 186
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=21.44 E-value=93 Score=26.99 Aligned_cols=48 Identities=19% Similarity=0.139 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.+|+.++++|+-..+-- ...+||.+|+++++.|+.+..+-..|..-+.
T Consensus 155 ~Lt~rE~~Vl~l~~~G~------s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v~n 202 (216)
T PRK10100 155 LLTHREKEILNKLRIGA------SNNEIARSLFISENTVKTHLYNLFKKIAVKN 202 (216)
T ss_pred CCCHHHHHHHHHHHcCC------CHHHHHHHhCCCHHHHHHHHHHHHHHhCCCC
Confidence 48999999998777632 3578999999999999998877666655433
No 187
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins 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 winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.43 E-value=4.1e+02 Score=20.86 Aligned_cols=35 Identities=23% Similarity=0.343 Sum_probs=25.2
Q ss_pred CCCcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCccccccccc
Q 040769 88 RKKRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 88 ~R~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQN 135 (257)
..+.|+.+++..| ......+.+|++-..|+.++..
T Consensus 35 g~R~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~ 69 (127)
T cd01108 35 GYRVYNQRDIEEL-------------RFIRRARDLGFSLEEIRELLAL 69 (127)
T ss_pred CceecCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHHH
Confidence 4566999999988 3444456778887777777753
No 188
>TIGR02947 SigH_actino RNA polymerase sigma-70 factor, TIGR02947 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and (with the exception of a paralog in Thermobifida fusca YX) one-to-a-genome distribution, to represent a conserved family. This family is restricted to the Actinobacteria and each gene examined is followed by an anti-sigma factor in an apparent operon.
Probab=21.40 E-value=40 Score=28.11 Aligned_cols=29 Identities=10% Similarity=0.116 Sum_probs=21.9
Q ss_pred HHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 113 DRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 113 ~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
..-.+||..||++...|+++...-|.+.|
T Consensus 148 ~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 176 (193)
T TIGR02947 148 FAYKEIAEIMGTPIGTVMSRLHRGRKQLR 176 (193)
T ss_pred CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 34568999999999999988765444444
No 189
>PRK12516 RNA polymerase sigma factor; Provisional
Probab=21.24 E-value=78 Score=26.50 Aligned_cols=21 Identities=14% Similarity=-0.018 Sum_probs=16.3
Q ss_pred HHHHHHHhCCCCccccccccc
Q 040769 115 KMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQN 135 (257)
-.+||..||+++..|++....
T Consensus 135 ~~EIA~~Lgis~~tVk~~l~R 155 (187)
T PRK12516 135 YEEAAEICGCAVGTIKSRVNR 155 (187)
T ss_pred HHHHHHHHCCCHHHHHHHHHH
Confidence 458899999999888876643
No 190
>PRK12511 RNA polymerase sigma factor; Provisional
Probab=21.22 E-value=76 Score=26.50 Aligned_cols=38 Identities=18% Similarity=0.091 Sum_probs=24.8
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccc
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQ 134 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQ 134 (257)
++..+..+|+-.|-.. ..-.+||..||++...|+++..
T Consensus 112 Lp~~~R~v~~L~~~eg-----~s~~EIA~~lgis~~tV~~~l~ 149 (182)
T PRK12511 112 LPEEQRAALHLVAIEG-----LSYQEAAAVLGIPIGTLMSRIG 149 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCcCHHHHHHHHH
Confidence 4555555555543322 2356899999999998887664
No 191
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.18 E-value=84 Score=25.40 Aligned_cols=48 Identities=21% Similarity=0.203 Sum_probs=36.6
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhhHHH
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWKSKQ 144 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~ 144 (257)
.+|+.+.++|+-..+. ....+||++|+++.+.|++..++=|.|-.-+.
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~~~ 202 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKLKS 202 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCCC
Confidence 3999999999776532 13577899999999999998887777665433
No 192
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=21.13 E-value=50 Score=26.79 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=35.2
Q ss_pred CcCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 90 KRLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 90 ~r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
..+|..+..+|....+. ..+.+||.+|+++.+.|+++.++=|.|-.
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35888888888754433 45789999999999999988876666544
No 193
>PRK11923 algU RNA polymerase sigma factor AlgU; Provisional
Probab=21.06 E-value=70 Score=26.54 Aligned_cols=28 Identities=7% Similarity=-0.028 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
.-.+||..||+++..|++....-|.+-|
T Consensus 156 s~~eIA~~lgis~~tv~~~l~Rar~~Lr 183 (193)
T PRK11923 156 SYEDIASVMQCPVGTVRSRIFRAREAID 183 (193)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999876654444443
No 194
>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=21.02 E-value=36 Score=23.59 Aligned_cols=21 Identities=19% Similarity=0.415 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCccccccccc
Q 040769 115 KMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQN 135 (257)
..++|+.+|++++.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 468999999999999999864
No 195
>PRK09641 RNA polymerase sigma factor SigW; Provisional
Probab=20.83 E-value=74 Score=26.02 Aligned_cols=28 Identities=11% Similarity=0.156 Sum_probs=20.4
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
.-.+||..||++...|+.....-|.+-|
T Consensus 154 s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T PRK09641 154 SLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4568999999999988876654444443
No 196
>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=20.62 E-value=1.4e+02 Score=20.85 Aligned_cols=37 Identities=22% Similarity=0.251 Sum_probs=24.5
Q ss_pred HHHHHHHhCCCCcccccccccchhhhhHHHHHHHHHHH
Q 040769 115 KMKLARELGLQPRQIAVWFQNRRARWKSKQLELLYDSL 152 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQNRRak~Kr~~~~~~~~~l 152 (257)
..+||+.+|++...|..|...++. .......+..+.+
T Consensus 21 ~~~lA~~~gis~~tis~~~~g~~~-~~~~~~~~l~~~l 57 (78)
T TIGR02607 21 IRALAKALGVSRSTLSRIVNGRRG-ITADMALRLAKAL 57 (78)
T ss_pred HHHHHHHhCCCHHHHHHHHcCCCC-CCHHHHHHHHHHc
Confidence 457899999999999999876653 3334444444433
No 197
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=20.48 E-value=98 Score=24.28 Aligned_cols=42 Identities=19% Similarity=0.392 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769 91 RLTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 91 r~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
.++..++..+.+.+... ....|+-||++...|+-|=|+|+.-
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 38888999997777654 4678999999999999999998754
No 198
>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=20.46 E-value=42 Score=23.13 Aligned_cols=21 Identities=10% Similarity=0.365 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCCccccccccc
Q 040769 115 KMKLARELGLQPRQIAVWFQN 135 (257)
Q Consensus 115 r~~LA~~LgL~~~qVkvWFQN 135 (257)
..++|+.+|++.+.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999765
No 199
>PRK12522 RNA polymerase sigma factor; Provisional
Probab=20.39 E-value=1.1e+02 Score=24.83 Aligned_cols=28 Identities=4% Similarity=0.106 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCCcccccccccchhhhh
Q 040769 114 RKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 114 ~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
.-.+||..||++...|++....-|.+-|
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 164 (173)
T PRK12522 137 SYKEMSEILNIPIGTVKYRLNYAKKQMR 164 (173)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999887654333333
No 200
>PRK08583 RNA polymerase sigma factor SigB; Validated
Probab=20.33 E-value=80 Score=27.82 Aligned_cols=45 Identities=11% Similarity=0.220 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhhhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRARWK 141 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak~K 141 (257)
+++.+..+|.-.|-.. ....+||..||++...|+.|...-+.|.|
T Consensus 206 L~~~~r~vl~l~~~~g-----~s~~eIA~~l~is~~tV~~~~~ra~~kLr 250 (257)
T PRK08583 206 LSDREKSIIQCTFIEN-----LSQKETGERLGISQMHVSRLQRQAIKKLR 250 (257)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6667777776665332 23578999999999999887754444433
No 201
>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=20.29 E-value=79 Score=27.18 Aligned_cols=43 Identities=16% Similarity=0.194 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhhhcCCCCHHHHHHHHHHhCCCCcccccccccchhh
Q 040769 92 LTSDQLESLERSFQEEIKLDPDRKMKLARELGLQPRQIAVWFQNRRAR 139 (257)
Q Consensus 92 ~t~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~~qVkvWFQNRRak 139 (257)
+++.+..+|...|... ....+||..+|++...|+.+...-+.+
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~ 218 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKK 218 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 5666777776666333 245789999999999888766543333
No 202
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=20.28 E-value=2.7e+02 Score=25.07 Aligned_cols=44 Identities=23% Similarity=0.251 Sum_probs=33.6
Q ss_pred hhhhhHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHhc
Q 040769 137 RARWKSKQLELLYDSLKQEYDAVSREKLKLQEEVMKLKRMLKEQ 180 (257)
Q Consensus 137 Rak~Kr~~~~~~~~~l~~~~~~~~~e~~~l~~e~~~~~~~l~~~ 180 (257)
|-|.|-.+.+.....++.....++.|-++|+.+..+|-++++.-
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRyl 133 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYL 133 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445556666677777788888889999999999998888864
Done!