Query 019540
Match_columns 339
No_of_seqs 275 out of 1596
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:34:40 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019540.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019540hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.8 4.1E-21 8.9E-26 176.0 9.5 107 53-159 46-152 (198)
2 KOG0489 Transcription factor z 99.7 8.2E-17 1.8E-21 152.8 5.5 63 55-117 157-219 (261)
3 KOG0842 Transcription factor t 99.6 7.8E-17 1.7E-21 156.0 4.5 68 56-123 150-219 (307)
4 KOG0488 Transcription factor B 99.6 3.4E-16 7.4E-21 152.1 7.9 54 64-117 179-232 (309)
5 PF00046 Homeobox: Homeobox do 99.6 3.6E-15 7.8E-20 109.3 7.1 57 58-114 1-57 (57)
6 KOG0484 Transcription factor P 99.6 1.8E-15 3.8E-20 126.5 5.2 59 58-116 18-76 (125)
7 KOG0843 Transcription factor E 99.6 3E-15 6.5E-20 135.2 5.9 63 57-119 102-164 (197)
8 KOG0487 Transcription factor A 99.6 1.9E-15 4.2E-20 146.5 4.5 61 57-117 235-295 (308)
9 KOG0485 Transcription factor N 99.5 1.9E-14 4E-19 133.5 9.0 59 58-116 103-163 (268)
10 KOG0492 Transcription factor M 99.5 1.1E-14 2.4E-19 134.1 6.6 68 49-116 136-203 (246)
11 KOG0494 Transcription factor C 99.5 2.9E-14 6.3E-19 135.1 7.2 56 64-119 148-203 (332)
12 KOG0493 Transcription factor E 99.5 5.6E-14 1.2E-18 133.3 8.5 94 26-119 212-308 (342)
13 KOG0850 Transcription factor D 99.5 3.5E-14 7.6E-19 132.4 5.7 56 61-116 126-181 (245)
14 KOG2251 Homeobox transcription 99.5 3.2E-14 6.9E-19 131.9 5.1 61 57-117 37-97 (228)
15 KOG0848 Transcription factor C 99.5 3.7E-14 8E-19 134.7 4.2 53 64-116 206-258 (317)
16 cd00086 homeodomain Homeodomai 99.4 2.5E-13 5.5E-18 98.9 7.1 57 59-115 2-58 (59)
17 smart00389 HOX Homeodomain. DN 99.4 3.1E-13 6.8E-18 98.0 6.5 55 59-113 2-56 (56)
18 COG5576 Homeodomain-containing 99.4 4E-13 8.6E-18 119.5 5.6 65 53-117 47-111 (156)
19 KOG4577 Transcription factor L 99.3 7.3E-13 1.6E-17 127.2 3.9 91 53-144 163-253 (383)
20 TIGR01565 homeo_ZF_HD homeobox 99.3 3.7E-12 7.9E-17 96.3 4.7 52 58-109 2-57 (58)
21 KOG0844 Transcription factor E 99.2 2.3E-12 5E-17 124.6 2.6 61 58-118 182-242 (408)
22 KOG0491 Transcription factor B 99.2 3.4E-12 7.4E-17 114.3 2.8 55 63-117 106-160 (194)
23 KOG0486 Transcription factor P 99.2 6.6E-12 1.4E-16 121.6 4.9 54 64-117 119-172 (351)
24 KOG0847 Transcription factor, 99.2 5.8E-12 1.2E-16 117.3 3.8 63 54-116 164-226 (288)
25 KOG3802 Transcription factor O 99.2 7.2E-12 1.6E-16 124.5 2.5 60 57-116 294-353 (398)
26 KOG0490 Transcription factor, 99.0 1E-10 2.3E-15 105.9 3.0 61 56-116 59-119 (235)
27 KOG0849 Transcription factor P 98.8 4.5E-09 9.8E-14 104.2 5.7 59 58-116 177-235 (354)
28 KOG1168 Transcription factor A 98.6 7.2E-09 1.6E-13 100.1 1.1 65 52-116 304-368 (385)
29 KOG0775 Transcription factor S 98.6 5.1E-08 1.1E-12 93.6 4.6 51 64-114 183-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.2 2.2E-06 4.7E-11 60.3 4.0 34 78-111 7-40 (40)
31 KOG0774 Transcription factor P 98.2 8.9E-07 1.9E-11 84.8 2.4 59 57-115 188-249 (334)
32 KOG0490 Transcription factor, 97.7 2.9E-05 6.3E-10 70.4 4.2 56 61-116 157-212 (235)
33 KOG2252 CCAAT displacement pro 97.7 7.4E-05 1.6E-09 77.7 6.4 57 57-113 420-476 (558)
34 PF02183 HALZ: Homeobox associ 97.6 9.9E-05 2.2E-09 53.3 4.8 44 115-158 1-44 (45)
35 KOG1146 Homeobox protein [Gene 97.0 0.00064 1.4E-08 76.7 4.4 61 57-117 903-963 (1406)
36 PF11569 Homez: Homeodomain le 95.9 0.0071 1.5E-07 45.8 3.0 41 69-109 10-50 (56)
37 KOG0773 Transcription factor M 95.6 0.0088 1.9E-07 58.6 3.1 54 63-116 245-301 (342)
38 KOG3623 Homeobox transcription 93.2 0.14 2.9E-06 55.9 5.5 48 69-116 568-615 (1007)
39 PRK09413 IS2 repressor TnpA; R 92.9 0.83 1.8E-05 38.6 8.8 44 59-107 8-52 (121)
40 PF02183 HALZ: Homeobox associ 90.9 0.46 1E-05 34.4 4.3 36 124-159 3-38 (45)
41 PF04218 CENP-B_N: CENP-B N-te 90.1 0.73 1.6E-05 33.9 4.9 46 59-109 2-47 (53)
42 smart00340 HALZ homeobox assoc 84.2 1.6 3.6E-05 31.5 3.6 28 127-154 6-33 (44)
43 KOG4005 Transcription factor X 77.3 10 0.00022 36.9 7.5 53 106-158 82-136 (292)
44 KOG4196 bZIP transcription fac 75.6 58 0.0013 28.9 11.7 82 62-159 22-114 (135)
45 PRK00888 ftsB cell division pr 74.5 12 0.00027 31.3 6.6 70 98-175 14-86 (105)
46 PF04545 Sigma70_r4: Sigma-70, 73.5 10 0.00022 26.7 5.1 43 63-110 4-46 (50)
47 PF01527 HTH_Tnp_1: Transposas 72.2 4.7 0.0001 30.4 3.3 47 59-109 2-48 (76)
48 cd06171 Sigma70_r4 Sigma70, re 71.6 7.5 0.00016 26.0 3.9 43 64-111 11-53 (55)
49 PF00170 bZIP_1: bZIP transcri 71.5 18 0.00039 27.2 6.3 36 120-155 27-62 (64)
50 PF06005 DUF904: Protein of un 69.2 19 0.00041 28.5 6.1 36 120-155 19-54 (72)
51 PF06156 DUF972: Protein of un 67.8 18 0.0004 30.6 6.2 47 115-161 11-57 (107)
52 KOG3119 Basic region leucine z 65.8 17 0.00036 35.3 6.3 52 109-163 208-259 (269)
53 cd00569 HTH_Hin_like Helix-tur 64.5 20 0.00042 21.2 4.5 39 62-105 4-42 (42)
54 KOG1055 GABA-B ion channel rec 62.6 13 0.00029 41.4 5.4 61 106-167 740-800 (865)
55 KOG4005 Transcription factor X 62.3 24 0.00052 34.4 6.5 47 115-161 100-146 (292)
56 COG4467 Regulator of replicati 61.5 22 0.00047 30.6 5.4 43 116-158 12-54 (114)
57 PF04967 HTH_10: HTH DNA bindi 60.0 18 0.00039 27.0 4.2 40 64-103 1-42 (53)
58 PRK13169 DNA replication intia 58.8 34 0.00074 29.3 6.2 44 116-159 12-55 (110)
59 KOG0249 LAR-interacting protei 57.4 42 0.00092 37.3 8.0 54 110-163 214-267 (916)
60 PF13443 HTH_26: Cro/C1-type H 57.2 17 0.00036 26.4 3.7 34 86-119 12-45 (63)
61 PF08281 Sigma70_r4_2: Sigma-7 55.6 32 0.00069 24.3 4.8 42 64-110 11-52 (54)
62 PF10224 DUF2205: Predicted co 55.4 53 0.0011 26.6 6.5 44 114-157 18-61 (80)
63 COG4026 Uncharacterized protei 55.3 26 0.00057 33.9 5.5 28 128-155 158-185 (290)
64 smart00340 HALZ homeobox assoc 54.9 19 0.00041 26.1 3.4 32 116-147 2-33 (44)
65 cd04766 HTH_HspR Helix-Turn-He 54.7 84 0.0018 25.0 7.6 71 87-158 4-90 (91)
66 PRK03975 tfx putative transcri 51.8 38 0.00082 30.1 5.6 48 61-114 4-51 (141)
67 COG3413 Predicted DNA binding 50.6 27 0.00059 32.0 4.8 49 63-113 155-205 (215)
68 PF06005 DUF904: Protein of un 50.1 83 0.0018 24.9 6.7 44 114-157 20-63 (72)
69 KOG4571 Activating transcripti 49.1 54 0.0012 32.6 6.7 50 110-160 240-289 (294)
70 PF10668 Phage_terminase: Phag 48.0 15 0.00033 28.2 2.2 20 86-105 24-43 (60)
71 PF07716 bZIP_2: Basic region 47.9 58 0.0013 23.7 5.3 23 131-153 30-52 (54)
72 PF00170 bZIP_1: bZIP transcri 46.5 73 0.0016 23.8 5.7 30 127-156 27-56 (64)
73 cd04779 HTH_MerR-like_sg4 Heli 46.4 2E+02 0.0043 25.0 9.7 37 60-109 34-70 (134)
74 smart00338 BRLZ basic region l 45.9 1.2E+02 0.0027 22.6 7.5 36 121-156 28-63 (65)
75 PRK09642 RNA polymerase sigma 44.6 61 0.0013 27.5 5.7 28 87-114 125-152 (160)
76 cd04765 HTH_MlrA-like_sg2 Heli 44.4 94 0.002 25.4 6.5 39 60-110 35-73 (99)
77 PF09607 BrkDBD: Brinker DNA-b 43.5 49 0.0011 25.4 4.3 43 62-106 4-47 (58)
78 COG3074 Uncharacterized protei 43.4 64 0.0014 25.9 5.1 39 118-156 24-62 (79)
79 KOG4403 Cell surface glycoprot 41.1 76 0.0016 33.5 6.6 25 102-126 229-256 (575)
80 TIGR02937 sigma70-ECF RNA poly 40.8 69 0.0015 25.6 5.2 45 64-113 111-155 (158)
81 PF00196 GerE: Bacterial regul 40.8 76 0.0016 22.9 4.9 46 63-114 3-48 (58)
82 KOG0483 Transcription factor H 40.5 41 0.00088 31.6 4.2 43 123-165 109-151 (198)
83 TIGR02449 conserved hypothetic 40.3 98 0.0021 24.2 5.6 39 118-156 6-44 (65)
84 PRK06759 RNA polymerase factor 40.1 68 0.0015 26.9 5.3 45 64-113 107-151 (154)
85 PRK09652 RNA polymerase sigma 39.7 72 0.0016 27.1 5.4 45 64-113 129-173 (182)
86 PF13936 HTH_38: Helix-turn-he 39.7 44 0.00096 23.4 3.4 41 61-106 2-42 (44)
87 PF15058 Speriolin_N: Sperioli 39.2 55 0.0012 30.8 4.8 42 121-163 7-48 (200)
88 PF07407 Seadorna_VP6: Seadorn 39.1 35 0.00075 34.8 3.7 31 127-157 33-63 (420)
89 TIGR01069 mutS2 MutS2 family p 38.8 1.1E+02 0.0025 34.0 8.0 18 85-102 483-500 (771)
90 PRK09646 RNA polymerase sigma 38.5 74 0.0016 28.2 5.5 46 64-114 143-188 (194)
91 KOG3156 Uncharacterized membra 38.2 78 0.0017 30.3 5.7 47 118-164 100-147 (220)
92 cd01106 HTH_TipAL-Mta Helix-Tu 38.1 2.2E+02 0.0047 23.1 8.1 36 61-109 36-71 (103)
93 PF14775 NYD-SP28_assoc: Sperm 37.8 64 0.0014 24.6 4.2 31 128-158 28-58 (60)
94 TIGR03879 near_KaiC_dom probab 37.7 24 0.00052 28.1 2.0 35 73-107 21-55 (73)
95 PRK12526 RNA polymerase sigma 37.3 79 0.0017 28.5 5.5 29 86-114 171-199 (206)
96 PRK12514 RNA polymerase sigma 36.9 54 0.0012 28.4 4.3 46 64-114 130-175 (179)
97 smart00421 HTH_LUXR helix_turn 36.6 97 0.0021 20.9 4.8 39 64-108 4-42 (58)
98 PRK00118 putative DNA-binding 36.6 1.7E+02 0.0036 24.7 6.9 45 64-113 18-62 (104)
99 cd04761 HTH_MerR-SF Helix-Turn 36.5 37 0.0008 23.2 2.6 23 87-109 3-25 (49)
100 PRK12530 RNA polymerase sigma 35.8 1.1E+02 0.0024 27.1 6.1 46 64-114 135-180 (189)
101 PF13518 HTH_28: Helix-turn-he 35.7 49 0.0011 22.8 3.1 24 86-109 14-37 (52)
102 PRK15422 septal ring assembly 35.7 97 0.0021 25.3 5.1 37 120-156 26-62 (79)
103 PF15058 Speriolin_N: Sperioli 35.3 47 0.001 31.3 3.7 34 126-159 5-38 (200)
104 KOG1146 Homeobox protein [Gene 35.2 59 0.0013 38.4 5.2 53 64-116 712-764 (1406)
105 PRK11546 zraP zinc resistance 35.0 1.6E+02 0.0035 26.4 6.9 32 128-159 77-108 (143)
106 PRK00409 recombination and DNA 34.8 1.4E+02 0.003 33.4 7.9 17 86-102 489-505 (782)
107 PRK11924 RNA polymerase sigma 34.7 1.1E+02 0.0023 26.0 5.6 29 86-114 143-171 (179)
108 PRK12543 RNA polymerase sigma 34.4 1.6E+02 0.0034 25.7 6.8 28 87-114 136-163 (179)
109 PRK09644 RNA polymerase sigma 34.2 1.2E+02 0.0026 25.9 5.9 29 86-114 126-154 (165)
110 cd04769 HTH_MerR2 Helix-Turn-H 34.1 2.6E+02 0.0057 23.2 7.8 38 61-111 35-72 (116)
111 PF06156 DUF972: Protein of un 33.8 91 0.002 26.4 4.9 40 115-154 18-57 (107)
112 PRK13922 rod shape-determining 33.2 78 0.0017 30.1 5.0 37 124-160 74-113 (276)
113 PRK12512 RNA polymerase sigma 32.9 1.1E+02 0.0023 26.7 5.5 46 64-114 132-177 (184)
114 PF04899 MbeD_MobD: MbeD/MobD 32.6 1.3E+02 0.0027 23.9 5.2 40 119-158 21-60 (70)
115 PRK09648 RNA polymerase sigma 32.2 1.1E+02 0.0024 26.7 5.5 45 64-113 140-184 (189)
116 PRK04217 hypothetical protein; 32.2 1.2E+02 0.0027 25.8 5.5 46 63-113 42-87 (110)
117 PF06637 PV-1: PV-1 protein (P 31.9 2.9E+02 0.0064 28.8 9.0 26 134-159 350-375 (442)
118 TIGR02985 Sig70_bacteroi1 RNA 31.8 1.2E+02 0.0026 25.0 5.5 28 86-113 131-158 (161)
119 PRK13729 conjugal transfer pil 31.5 1.1E+02 0.0024 32.5 6.0 43 114-156 78-120 (475)
120 PF05700 BCAS2: Breast carcino 31.3 1.7E+02 0.0037 27.4 6.8 54 108-161 164-217 (221)
121 TIGR02989 Sig-70_gvs1 RNA poly 31.3 1.1E+02 0.0025 25.5 5.3 43 64-111 112-154 (159)
122 PRK12519 RNA polymerase sigma 31.0 92 0.002 27.3 4.8 29 86-114 159-187 (194)
123 PRK13169 DNA replication intia 30.9 1E+02 0.0023 26.3 4.9 40 115-154 18-57 (110)
124 PRK12515 RNA polymerase sigma 30.5 1.4E+02 0.0031 26.1 5.9 28 87-114 150-177 (189)
125 PF02796 HTH_7: Helix-turn-hel 30.3 96 0.0021 21.6 3.9 37 64-105 6-42 (45)
126 PRK09639 RNA polymerase sigma 30.3 1.9E+02 0.0042 24.4 6.5 45 64-114 113-157 (166)
127 TIGR02999 Sig-70_X6 RNA polyme 30.3 1.3E+02 0.0028 26.0 5.6 27 87-113 153-179 (183)
128 PF00424 REV: REV protein (ant 30.2 68 0.0015 26.8 3.5 32 70-117 15-48 (91)
129 TIGR02948 SigW_bacill RNA poly 30.2 1.1E+02 0.0024 26.4 5.1 46 64-114 137-182 (187)
130 TIGR02959 SigZ RNA polymerase 30.2 1.2E+02 0.0027 26.2 5.4 43 64-111 101-143 (170)
131 PF00038 Filament: Intermediat 29.9 2.8E+02 0.0061 26.5 8.3 60 98-157 186-254 (312)
132 cd04770 HTH_HMRTR Helix-Turn-H 29.2 3.3E+02 0.0072 22.5 8.6 38 60-110 35-72 (123)
133 cd01109 HTH_YyaN Helix-Turn-He 28.7 3.3E+02 0.0071 22.4 8.7 36 61-109 36-71 (113)
134 PF13411 MerR_1: MerR HTH fami 28.5 52 0.0011 24.2 2.4 22 87-108 3-24 (69)
135 PF12824 MRP-L20: Mitochondria 28.5 4.5E+02 0.0098 23.8 9.0 44 61-106 83-126 (164)
136 PF07334 IFP_35_N: Interferon- 28.1 70 0.0015 25.8 3.1 25 136-160 3-27 (76)
137 TIGR00219 mreC rod shape-deter 27.9 1E+02 0.0023 30.0 5.0 18 143-160 94-111 (283)
138 PRK05602 RNA polymerase sigma 27.8 1.3E+02 0.0028 26.2 5.2 28 87-114 147-174 (186)
139 KOG1962 B-cell receptor-associ 27.6 1.4E+02 0.003 28.5 5.6 20 134-153 180-199 (216)
140 cd06170 LuxR_C_like C-terminal 27.5 1.3E+02 0.0028 20.5 4.2 36 65-106 2-37 (57)
141 PF13384 HTH_23: Homeodomain-l 27.3 57 0.0012 22.6 2.3 22 85-106 18-39 (50)
142 PRK09047 RNA polymerase factor 27.3 1.7E+02 0.0037 24.5 5.7 45 64-113 107-151 (161)
143 PF08172 CASP_C: CASP C termin 27.3 1.7E+02 0.0037 28.2 6.2 43 109-158 90-132 (248)
144 PRK06811 RNA polymerase factor 26.9 1.4E+02 0.003 26.4 5.2 47 64-115 132-178 (189)
145 TIGR02939 RpoE_Sigma70 RNA pol 26.9 1.2E+02 0.0026 26.2 4.8 28 86-113 156-183 (190)
146 PRK10072 putative transcriptio 26.9 44 0.00095 27.7 1.9 42 63-111 32-73 (96)
147 smart00338 BRLZ basic region l 26.9 1.8E+02 0.0039 21.7 5.1 27 129-155 29-55 (65)
148 PRK12541 RNA polymerase sigma 26.8 1.4E+02 0.0029 25.4 5.0 27 87-113 131-157 (161)
149 PRK10884 SH3 domain-containing 26.1 1.9E+02 0.0042 27.1 6.2 28 128-155 134-161 (206)
150 KOG4343 bZIP transcription fac 25.9 1.8E+02 0.0039 31.6 6.5 32 122-153 305-336 (655)
151 KOG3755 SATB1 matrix attachmen 25.7 31 0.00067 37.6 0.9 47 70-116 705-758 (769)
152 PF06056 Terminase_5: Putative 25.7 59 0.0013 24.5 2.2 27 86-114 15-41 (58)
153 cd04781 HTH_MerR-like_sg6 Heli 25.2 3.9E+02 0.0085 22.2 7.4 36 60-108 34-69 (120)
154 cd04762 HTH_MerR-trunc Helix-T 25.2 78 0.0017 20.9 2.6 25 87-111 3-27 (49)
155 PRK12546 RNA polymerase sigma 25.2 1.2E+02 0.0027 27.0 4.6 28 87-114 132-159 (188)
156 TIGR02943 Sig70_famx1 RNA poly 25.1 2.2E+02 0.0048 25.2 6.2 46 64-114 132-177 (188)
157 PF08280 HTH_Mga: M protein tr 25.0 1.5E+02 0.0033 21.8 4.4 35 67-105 6-40 (59)
158 PRK10884 SH3 domain-containing 24.7 2.7E+02 0.0059 26.1 6.9 37 120-156 133-169 (206)
159 PRK12538 RNA polymerase sigma 24.5 1.9E+02 0.0041 27.0 5.8 28 87-114 190-217 (233)
160 PRK12532 RNA polymerase sigma 24.4 2E+02 0.0043 25.3 5.8 28 87-114 155-182 (195)
161 PRK10403 transcriptional regul 24.1 1.2E+02 0.0026 25.5 4.2 45 64-114 154-198 (215)
162 TIGR02983 SigE-fam_strep RNA p 23.9 1.9E+02 0.0041 24.4 5.3 46 64-114 111-156 (162)
163 PRK06930 positive control sigm 23.7 2.1E+02 0.0046 25.7 5.8 46 64-114 115-160 (170)
164 PRK06986 fliA flagellar biosyn 23.5 1.3E+02 0.0029 27.6 4.6 46 64-114 185-230 (236)
165 PRK12537 RNA polymerase sigma 23.3 2E+02 0.0043 25.1 5.5 27 87-113 152-178 (182)
166 TIGR02479 FliA_WhiG RNA polyme 23.2 1.4E+02 0.003 27.2 4.6 45 64-113 176-220 (224)
167 PRK00888 ftsB cell division pr 23.1 2.5E+02 0.0054 23.5 5.7 37 104-140 26-62 (105)
168 PF04297 UPF0122: Putative hel 23.1 4.6E+02 0.01 22.1 8.5 54 64-124 18-71 (101)
169 TIGR02954 Sig70_famx3 RNA poly 23.0 1.9E+02 0.004 24.8 5.2 45 64-113 120-164 (169)
170 cd04764 HTH_MlrA-like_sg1 Heli 22.8 77 0.0017 23.4 2.4 21 87-107 3-23 (67)
171 PRK07037 extracytoplasmic-func 22.8 2.1E+02 0.0046 24.1 5.4 27 87-113 128-154 (163)
172 cd01392 HTH_LacI Helix-turn-he 22.7 1E+02 0.0023 21.2 3.0 21 89-109 2-22 (52)
173 PRK12547 RNA polymerase sigma 22.6 2.1E+02 0.0047 24.4 5.5 45 64-113 113-157 (164)
174 PRK14127 cell division protein 22.5 1.7E+02 0.0037 25.0 4.7 24 135-158 39-62 (109)
175 TIGR02952 Sig70_famx2 RNA poly 22.4 2.2E+02 0.0048 24.0 5.5 20 87-106 141-160 (170)
176 cd04763 HTH_MlrA-like Helix-Tu 22.3 88 0.0019 23.2 2.6 21 87-107 3-23 (68)
177 PRK15369 two component system 22.1 2.2E+02 0.0048 23.6 5.4 45 63-113 149-193 (211)
178 PRK12536 RNA polymerase sigma 21.9 2.2E+02 0.0049 24.7 5.6 29 86-114 147-175 (181)
179 PRK10360 DNA-binding transcrip 21.8 1.5E+02 0.0033 25.0 4.3 44 63-112 137-180 (196)
180 PRK05657 RNA polymerase sigma 21.6 1.7E+02 0.0038 28.8 5.2 50 64-114 263-312 (325)
181 TIGR02894 DNA_bind_RsfA transc 21.6 1.6E+02 0.0035 27.0 4.6 28 128-155 106-133 (161)
182 PRK09637 RNA polymerase sigma 21.6 2E+02 0.0044 25.3 5.3 25 87-111 125-149 (181)
183 KOG3863 bZIP transcription fac 21.3 7.3E+02 0.016 27.3 10.0 35 127-161 519-553 (604)
184 PRK13919 putative RNA polymera 21.3 2.4E+02 0.0051 24.5 5.6 27 87-113 154-180 (186)
185 PF12709 Kinetocho_Slk19: Cent 21.1 3E+02 0.0064 22.8 5.6 43 118-160 33-76 (87)
186 KOG0709 CREB/ATF family transc 21.0 2.7E+02 0.0059 29.5 6.6 75 64-156 242-316 (472)
187 KOG2391 Vacuolar sorting prote 20.9 2.2E+02 0.0047 29.2 5.7 42 118-159 224-265 (365)
188 KOG4571 Activating transcripti 20.9 1.9E+02 0.0042 28.8 5.3 26 135-160 250-275 (294)
189 PHA02955 hypothetical protein; 20.9 1.2E+02 0.0027 28.8 3.8 42 66-107 60-102 (213)
190 COG4026 Uncharacterized protei 20.8 2.8E+02 0.006 27.1 6.2 47 109-155 118-164 (290)
191 PRK12518 RNA polymerase sigma 20.7 1.3E+02 0.0028 25.8 3.7 29 86-114 138-166 (175)
192 PRK09651 RNA polymerase sigma 20.7 2.2E+02 0.0048 24.6 5.2 28 86-113 137-164 (172)
193 TIGR03752 conj_TIGR03752 integ 20.7 2E+02 0.0042 30.6 5.6 44 115-158 69-127 (472)
194 PF11594 Med28: Mediator compl 20.7 3.5E+02 0.0076 23.2 6.1 15 98-112 17-31 (106)
195 PRK09935 transcriptional regul 20.6 1.6E+02 0.0035 24.9 4.3 44 64-113 150-193 (210)
196 KOG4343 bZIP transcription fac 20.6 3E+02 0.0065 30.0 6.9 35 127-161 303-337 (655)
197 PRK08301 sporulation sigma fac 20.5 2E+02 0.0042 26.4 5.1 50 64-114 179-228 (234)
198 cd00093 HTH_XRE Helix-turn-hel 20.5 79 0.0017 20.4 1.9 23 87-109 15-37 (58)
199 PRK12524 RNA polymerase sigma 20.4 2.4E+02 0.0052 24.9 5.5 27 87-113 155-181 (196)
200 PF00376 MerR: MerR family reg 20.2 86 0.0019 21.5 2.0 19 88-106 3-21 (38)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.84 E-value=4.1e-21 Score=176.03 Aligned_cols=107 Identities=59% Similarity=0.900 Sum_probs=94.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHHHHhHHHHhhHHHH
Q 019540 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALK 132 (339)
Q Consensus 53 ~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~e~~~lka~~d~Lk 132 (339)
.+....+|++||+.+|+..||..|+...++.+.++..||++|||.+|||+|||||||||||.++++.+++.|+..++.|.
T Consensus 46 ~~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~ 125 (198)
T KOG0483|consen 46 NGSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLR 125 (198)
T ss_pred cccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHh
Confidence 34446678888999999999999999999999999999999999999999999999999999999999999998888888
Q ss_pred hhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 133 LNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 133 ~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
.+++.++.++..|..+...++...+..
T Consensus 126 ~~~~~Lq~e~~eL~~~~~~~~~~~~~~ 152 (198)
T KOG0483|consen 126 SENDRLQSEVQELVAELSSLKREMQKS 152 (198)
T ss_pred hhhhHHHHHHHHHHHHHhhhhhhhccC
Confidence 888888888888877777666665543
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.65 E-value=8.2e-17 Score=152.76 Aligned_cols=63 Identities=33% Similarity=0.688 Sum_probs=56.7
Q ss_pred CCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 55 ~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
++.+|.|+-||..|+.+||+.|..++|+++.+|.+||..|.|+++||||||||||+||||...
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 334555555999999999999999999999999999999999999999999999999998653
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.65 E-value=7.8e-17 Score=156.01 Aligned_cols=68 Identities=37% Similarity=0.576 Sum_probs=60.2
Q ss_pred CCCCCCCc--CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHHHHhH
Q 019540 56 HVSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGV 123 (339)
Q Consensus 56 k~krKRrR--fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~e~~~ 123 (339)
+++|||+| |+..|+.+||+.|.+.+|++..+|+.||..|.|+++||||||||||-|.||++.++.++.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 44444555 999999999999999999999999999999999999999999999999999887665433
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=3.4e-16 Score=152.12 Aligned_cols=54 Identities=43% Similarity=0.714 Sum_probs=52.5
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+||||+..
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999654
No 5
>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=99.59 E-value=3.6e-15 Score=109.27 Aligned_cols=57 Identities=42% Similarity=0.647 Sum_probs=54.0
Q ss_pred CCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++|++||.+|+.+|+..|..++||+..+++.||.+|||+..+|++||+|||+++|+
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 356777999999999999999999999999999999999999999999999999985
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.58 E-value=1.8e-15 Score=126.50 Aligned_cols=59 Identities=27% Similarity=0.509 Sum_probs=54.2
Q ss_pred CCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
++-|+.||..||..||+.|...+||+.-.|++||.+++|++.+|||||||||+|.|++.
T Consensus 18 RRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 18 RRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 33344499999999999999999999999999999999999999999999999999864
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.56 E-value=3e-15 Score=135.20 Aligned_cols=63 Identities=35% Similarity=0.491 Sum_probs=56.8
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHH
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~ 119 (339)
.+|.|+.|+.+|+..||..|+.++|..-.+|++||+.|+|++.||+|||||||+|.||.+.+.
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 344445599999999999999999999999999999999999999999999999999977543
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.56 E-value=1.9e-15 Score=146.47 Aligned_cols=61 Identities=33% Similarity=0.497 Sum_probs=55.9
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
.+|||..+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||+|.||...
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 3455555999999999999999999999999999999999999999999999999998654
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.54 E-value=1.9e-14 Score=133.52 Aligned_cols=59 Identities=42% Similarity=0.684 Sum_probs=54.5
Q ss_pred CCCCCc--CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 58 SEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 58 krKRrR--fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+|||+| |+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 344444 99999999999999999999999999999999999999999999999999964
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=1.1e-14 Score=134.14 Aligned_cols=68 Identities=29% Similarity=0.475 Sum_probs=58.0
Q ss_pred ccccCCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 49 CLEESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 49 ~~~~~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
|........++.|+.||.+||..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.||-+
T Consensus 136 C~LrKhk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 136 CTLRKHKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred chhcccCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 33333333344455599999999999999999999999999999999999999999999999999855
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.50 E-value=2.9e-14 Score=135.07 Aligned_cols=56 Identities=30% Similarity=0.542 Sum_probs=53.3
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~ 119 (339)
||..|++.||+.|+..+||+...|+.||.++.|.+.+|+|||||||+||||++...
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~w 203 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRW 203 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhc
Confidence 99999999999999999999999999999999999999999999999999876443
No 12
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.49 E-value=5.6e-14 Score=133.27 Aligned_cols=94 Identities=26% Similarity=0.401 Sum_probs=70.2
Q ss_pred CCCCCcccccccccccCCCCcCCc---cccCCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHh
Q 019540 26 SPRNNQVYSREFQTMLDGLDEEGC---LEESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVA 102 (339)
Q Consensus 26 s~r~~~~~~r~~~s~~~g~~~~~~---~~~~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVq 102 (339)
...+-+|||..|..+.......-. ..+.....||.|+-||.+||..|+..|+.++|++..+|.+||.+|||.+.||+
T Consensus 212 ~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 556677899888776443322110 01111112233444999999999999999999999999999999999999999
Q ss_pred hhhHhhHHHhhhHHHHH
Q 019540 103 VWFQNRRARWKTKQLER 119 (339)
Q Consensus 103 VWFQNRRaK~Krkq~e~ 119 (339)
|||||+|+|.||-.--+
T Consensus 292 IWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 292 IWFQNKRAKIKKSTGSK 308 (342)
T ss_pred HHhhhhhhhhhhccCCC
Confidence 99999999999865443
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.48 E-value=3.5e-14 Score=132.38 Aligned_cols=56 Identities=36% Similarity=0.605 Sum_probs=52.4
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
|+.++.-||..|.+.|++++|+--.+|.+||..|||+..||||||||||.|.||..
T Consensus 126 RTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 126 RTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 33499999999999999999999999999999999999999999999999999843
No 14
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.47 E-value=3.2e-14 Score=131.92 Aligned_cols=61 Identities=28% Similarity=0.437 Sum_probs=56.5
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
.+|.|++|+..|+++||+.|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|+++.
T Consensus 37 qRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 37 QRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred cccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 4455666999999999999999999999999999999999999999999999999998663
No 15
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.45 E-value=3.7e-14 Score=134.75 Aligned_cols=53 Identities=42% Similarity=0.626 Sum_probs=51.4
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+|..|..+||+.|...+|.++.++.+||..|||++|||||||||||+|+||..
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999854
No 16
>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=99.45 E-value=2.5e-13 Score=98.88 Aligned_cols=57 Identities=46% Similarity=0.738 Sum_probs=53.2
Q ss_pred CCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhH
Q 019540 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krk 115 (339)
+++.+++..|+.+|+..|..++||+..++..||.++||++.+|++||+|||++.++.
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 345669999999999999999999999999999999999999999999999998863
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.43 E-value=3.1e-13 Score=97.96 Aligned_cols=55 Identities=45% Similarity=0.792 Sum_probs=51.1
Q ss_pred CCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+.|.+++.+|+.+|+..|..++||+..++..||..+||+..+|+.||+|||++.|
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 3455699999999999999999999999999999999999999999999999864
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=4e-13 Score=119.47 Aligned_cols=65 Identities=32% Similarity=0.568 Sum_probs=59.7
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 53 ~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
.....+++|+|.|..|+.+|++.|+.++||+...|..|+..|+|+++-||+||||||++.|+...
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 33556778888999999999999999999999999999999999999999999999999998654
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.33 E-value=7.3e-13 Score=127.20 Aligned_cols=91 Identities=22% Similarity=0.374 Sum_probs=76.3
Q ss_pred CCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHHHHhHHHHhhHHHH
Q 019540 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALK 132 (339)
Q Consensus 53 ~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~e~~~lka~~d~Lk 132 (339)
.++..+|.|+.+|+.||+.|+.+|...++|.+..|++|+.++||..|.|||||||||||+||-+.......|.+-+..++
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK 242 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK 242 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence 44445666667999999999999999999999999999999999999999999999999999776666667888887777
Q ss_pred hhhhhhhHhHHH
Q 019540 133 LNYDSLQHDNEA 144 (339)
Q Consensus 133 ~~~dsl~~ene~ 144 (339)
.. .+-+.|++.
T Consensus 243 ~s-gs~r~ekds 253 (383)
T KOG4577|consen 243 RS-GSSRAEKDS 253 (383)
T ss_pred cc-CCccccccc
Confidence 66 445555444
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=99.28 E-value=3.7e-12 Score=96.30 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=48.6
Q ss_pred CCCCCcCCHHHHHHHHHHhhhhcC----CCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 58 SEKKRRLSVDQVKALEKNFEVENK----LEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~y----Ps~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
++.|+.||.+|+..||..|+..+| |+...+.+||..+||++++|+|||||.+
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 456667999999999999999999 9999999999999999999999999964
No 21
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.25 E-value=2.3e-12 Score=124.58 Aligned_cols=61 Identities=34% Similarity=0.554 Sum_probs=55.9
Q ss_pred CCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHH
Q 019540 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (339)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e 118 (339)
+|=|+-||.+|+..||+.|.+..|.++.+|.+||..|+|.+.-|||||||||+|+||+.+.
T Consensus 182 RRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 182 RRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3344459999999999999999999999999999999999999999999999999997764
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.23 E-value=3.4e-12 Score=114.31 Aligned_cols=55 Identities=40% Similarity=0.572 Sum_probs=52.6
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+.
T Consensus 106 vfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 106 VFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred cccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 3999999999999999999999999999999999999999999999999998653
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.23 E-value=6.6e-12 Score=121.65 Aligned_cols=54 Identities=28% Similarity=0.570 Sum_probs=52.2
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
||.+|+..||..|.+++||+...|++||.-.+|++.+|+|||.|||+|||+++.
T Consensus 119 FtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 119 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 999999999999999999999999999999999999999999999999998653
No 24
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.22 E-value=5.8e-12 Score=117.32 Aligned_cols=63 Identities=37% Similarity=0.683 Sum_probs=56.6
Q ss_pred CCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 54 GGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 54 ~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+++++..|..|+-.|+..||..|+..+|+-..+|.+||..+|+++.||+|||||||+||||+.
T Consensus 164 dG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 164 NGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred CccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 344444555599999999999999999999999999999999999999999999999999864
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.18 E-value=7.2e-12 Score=124.55 Aligned_cols=60 Identities=32% Similarity=0.439 Sum_probs=54.7
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+||||+.|.......||+.|..|++|+..++..||.+|+|...+|+|||||||.|.||..
T Consensus 294 kRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 294 KRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred ccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 444455599999999999999999999999999999999999999999999999999843
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=1e-10 Score=105.94 Aligned_cols=61 Identities=28% Similarity=0.335 Sum_probs=55.5
Q ss_pred CCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 56 k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
++++.|..|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||++|+++.
T Consensus 59 ~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 59 SKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred cccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 3444555599999999999999999999999999999999999999999999999999865
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.81 E-value=4.5e-09 Score=104.21 Aligned_cols=59 Identities=36% Similarity=0.620 Sum_probs=54.7
Q ss_pred CCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 58 krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+++|+.|+..|+..||+.|+.++||+...|++||.++++++.+|+|||+|||++|+|..
T Consensus 177 rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34455699999999999999999999999999999999999999999999999999864
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.64 E-value=7.2e-09 Score=100.11 Aligned_cols=65 Identities=28% Similarity=0.495 Sum_probs=58.2
Q ss_pred cCCCCCCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 52 ESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 52 ~~~~k~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
..++.+||||+.+.......||.+|...+.|+.+.+..||.+|+|....|+|||+|.|+|.||..
T Consensus 304 ~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 304 LPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 34455677777788899999999999999999999999999999999999999999999999854
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.57 E-value=5.1e-08 Score=93.55 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=47.8
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
|...-..+|..+|..++||++.++.+||+.+||+..||-.||+|||+|+|-
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
>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=98.18 E-value=2.2e-06 Score=60.29 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=29.0
Q ss_pred hhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 78 VENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 78 ~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
.++||+.+++.+||+++||+..||..||-|.|.|
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 4689999999999999999999999999999975
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.16 E-value=8.9e-07 Score=84.80 Aligned_cols=59 Identities=29% Similarity=0.461 Sum_probs=53.7
Q ss_pred CCCCCCcCCHHHHHHHHHHhh---hhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhH
Q 019540 57 VSEKKRRLSVDQVKALEKNFE---VENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~---~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krk 115 (339)
.+||||-|+..-.++|..+|. .++||+.+.+++||++++++..||..||.|+|-++||.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 356666799999999999997 47899999999999999999999999999999999974
No 32
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.73 E-value=2.9e-05 Score=70.44 Aligned_cols=56 Identities=34% Similarity=0.650 Sum_probs=52.3
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+..+...|+..++..|...++|+...++.|+..+|++++.|++||||+|++.++..
T Consensus 157 ~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 157 RTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 34488999999999999999999999999999999999999999999999999864
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.66 E-value=7.4e-05 Score=77.71 Aligned_cols=57 Identities=21% Similarity=0.262 Sum_probs=51.1
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
.||.|..||..|...|..+|+.+++|+.+..+.|+.+|+|..+-|.+||-|-|.|.+
T Consensus 420 ~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 420 TKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred CCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 333344499999999999999999999999999999999999999999999998853
No 34
>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=97.63 E-value=9.9e-05 Score=53.33 Aligned_cols=44 Identities=61% Similarity=0.900 Sum_probs=41.3
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
++++++++.|++.|+.|+.+++++..||+.|++|+..|+.+++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 47899999999999999999999999999999999999998864
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.99 E-value=0.00064 Score=76.70 Aligned_cols=61 Identities=28% Similarity=0.395 Sum_probs=56.2
Q ss_pred CCCCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 57 ~krKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
++.+|++++..||..+...|....+|..++.+.|...+++..+.|+|||||-|+|.|+..+
T Consensus 903 r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 903 RRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 4566777999999999999999999999999999999999999999999999999998654
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.95 E-value=0.0071 Score=45.80 Aligned_cols=41 Identities=24% Similarity=0.424 Sum_probs=31.0
Q ss_pred HHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 69 l~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
+..|+.+|...+++.......|..+.+|+..||+.||-.|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 56699999999999999999999999999999999997553
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=95.60 E-value=0.0088 Score=58.58 Aligned_cols=54 Identities=28% Similarity=0.331 Sum_probs=46.4
Q ss_pred cCCHHHHHHHHHHhhh---hcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 63 RLSVDQVKALEKNFEV---ENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~---~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
.+....+.+|+.+... .+||+...+..||+++||+..||..||-|.|-|..+-.
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~ 301 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPM 301 (342)
T ss_pred CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCch
Confidence 4889999999987443 46999999999999999999999999999988766544
No 38
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.24 E-value=0.14 Score=55.86 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=44.8
Q ss_pred HHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 69 l~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+..|..+|..+..|+.++...+|.+.||..+.|+.||+++++....-+
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 788999999999999999999999999999999999999999877644
No 39
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.87 E-value=0.83 Score=38.61 Aligned_cols=44 Identities=23% Similarity=0.434 Sum_probs=29.4
Q ss_pred CCCCcCCHHHHH-HHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHh
Q 019540 59 EKKRRLSVDQVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 59 rKRrRfT~~Ql~-~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQN 107 (339)
+++++|+.++.. ++...+. +.. ...++|+++|+++..|..|.+.
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r~ 52 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRKQ 52 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHHH
Confidence 345668877644 3333333 222 3567899999999999999754
No 40
>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=90.92 E-value=0.46 Score=34.35 Aligned_cols=36 Identities=42% Similarity=0.675 Sum_probs=32.1
Q ss_pred HHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 124 LKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 124 lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
+...|+.|+.+++++..+++.|.+|++.|++++...
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L 38 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQEL 38 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456899999999999999999999999999987654
No 41
>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=90.11 E-value=0.73 Score=33.93 Aligned_cols=46 Identities=22% Similarity=0.420 Sum_probs=32.8
Q ss_pred CCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
++|+.+|-++-..+-..++... ....||+++|++..+|..|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4566689888777777776665 477899999999999999998753
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=84.19 E-value=1.6 Score=31.47 Aligned_cols=28 Identities=36% Similarity=0.557 Sum_probs=23.7
Q ss_pred hhHHHHhhhhhhhHhHHHHHHHHHHHHH
Q 019540 127 NYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 127 ~~d~Lk~~~dsl~~ene~L~~E~~~Lk~ 154 (339)
..+.|+.+.+++..||.+|++|+++|+.
T Consensus 6 dCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 6 DCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556777889999999999999999986
No 43
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=77.27 E-value=10 Score=36.89 Aligned_cols=53 Identities=34% Similarity=0.398 Sum_probs=35.3
Q ss_pred HhhHHHhhhH--HHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 106 QNRRARWKTK--QLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 106 QNRRaK~Krk--q~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
|+-|.|.|-+ +++.+...|.+.++.|+.+++.|+..|+.|..++.+|...|..
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~ 136 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELEL 136 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 5555554433 3333444566677888888888888888888877777776653
No 44
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=75.56 E-value=58 Score=28.90 Aligned_cols=82 Identities=27% Similarity=0.329 Sum_probs=53.5
Q ss_pred CcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHH-hCCChHHHhhhhHhhHHH----------hhhHHHHHHHhHHHHhhHH
Q 019540 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQE-LGLQPRQVAVWFQNRRAR----------WKTKQLERDYGVLKANYDA 130 (339)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~-LgLserQVqVWFQNRRaK----------~Krkq~e~e~~~lka~~d~ 130 (339)
.+|+.++|..| ..| +|=+. -|++...|--|=|.||+- .||-+.. ..|.+.+..
T Consensus 22 d~lsDd~Lvsm------------SVR-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk---~eLE~~k~~ 85 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVR-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQK---HELEKEKAE 85 (135)
T ss_pred CCcCHHHHHHh------------hHH-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHH---HHHHHHHHH
Confidence 56888888776 233 33334 489999999999988863 3333322 334445556
Q ss_pred HHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 131 LKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 131 Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
|..+-+.|..|+..+..|..-++.+...-
T Consensus 86 L~qqv~~L~~e~s~~~~E~da~k~k~e~l 114 (135)
T KOG4196|consen 86 LQQQVEKLKEENSRLRRELDAYKSKYEAL 114 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66677777777777777777777765443
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=74.45 E-value=12 Score=31.31 Aligned_cols=70 Identities=26% Similarity=0.326 Sum_probs=34.6
Q ss_pred hHHHhhhhHhhHHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHH---hhhhhcccccCccccccee
Q 019540 98 PRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK---LNEENTESNISVKQEETIV 174 (339)
Q Consensus 98 erQVqVWFQNRRaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~k---l~~~~~e~~~s~k~~~~~~ 174 (339)
.-+...||+..-- . .+..+++....++.++..++++|+.|+.|+..|+.. +.+.-.+.-.-++..|.++
T Consensus 14 ~l~y~l~~g~~G~-~-------~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~~dyiEe~AR~~Lg~vk~gEivy 85 (105)
T PRK00888 14 WLQYSLWFGKNGI-L-------DYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGGQEAIEERARNELGMVKPGETFY 85 (105)
T ss_pred HHHHHHhccCCcH-H-------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcHHHHHHHHHHHcCCCCCCCEEE
Confidence 3456788864411 0 111222233344555666667777777777777652 2222222222345556666
Q ss_pred c
Q 019540 175 H 175 (339)
Q Consensus 175 s 175 (339)
.
T Consensus 86 ~ 86 (105)
T PRK00888 86 R 86 (105)
T ss_pred E
Confidence 3
No 46
>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=73.54 E-value=10 Score=26.74 Aligned_cols=43 Identities=14% Similarity=0.180 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHH
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRa 110 (339)
.+++.+..+|...|. ....-.++|..+|++...|+.+...-..
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~al~ 46 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRALK 46 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHHHH
Confidence 378888999988882 2234678999999999999887654333
No 47
>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=72.19 E-value=4.7 Score=30.40 Aligned_cols=47 Identities=23% Similarity=0.380 Sum_probs=29.7
Q ss_pred CCCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 59 rKRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
+++++||+++...+-..+... .....++|+++|+++..+..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHHh
Confidence 355679998877765555222 24577899999999999999986443
No 48
>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=71.61 E-value=7.5 Score=26.00 Aligned_cols=43 Identities=14% Similarity=0.146 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
+++.+..++...|... ....++|..+|++...|..|....+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 6777777777766422 235678999999999999998755443
No 49
>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=71.50 E-value=18 Score=27.15 Aligned_cols=36 Identities=31% Similarity=0.382 Sum_probs=23.0
Q ss_pred HHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 120 e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
....|......|..+++.|..++..|..++..|+.+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344555566666666777777777777776666654
No 50
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=69.20 E-value=19 Score=28.48 Aligned_cols=36 Identities=28% Similarity=0.422 Sum_probs=19.2
Q ss_pred HHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 120 e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
....|+..++.|+..+..+..++..|+.++.+|+..
T Consensus 19 ti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 19 TIALLQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 334444445555555555555566666666655543
No 51
>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=67.83 E-value=18 Score=30.61 Aligned_cols=47 Identities=30% Similarity=0.405 Sum_probs=37.3
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhc
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~ 161 (339)
.+.+.....+-+....|+..-..+..||..|+-||..|+..+.+..+
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34566667777777778888888888999999999999998887765
No 52
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=65.82 E-value=17 Score=35.25 Aligned_cols=52 Identities=23% Similarity=0.247 Sum_probs=34.0
Q ss_pred HHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhccc
Q 019540 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTES 163 (339)
Q Consensus 109 RaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~ 163 (339)
|.+.|+++.+ ..++.....|..+++.++.+.++|++|+..++.-+.......
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~~~~ 259 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLPKPG 259 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccc
Confidence 4555555443 334455666777788888888888888888887666544433
No 53
>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=64.46 E-value=20 Score=21.25 Aligned_cols=39 Identities=13% Similarity=0.329 Sum_probs=27.1
Q ss_pred CcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhh
Q 019540 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (339)
Q Consensus 62 rRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWF 105 (339)
+.++..+...+...|... . ...++|..+|++...|..|.
T Consensus 4 ~~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 4 PKLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred CcCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 346677666666666532 2 45678999999999888873
No 54
>KOG1055 consensus GABA-B ion channel receptor subunit GABABR1 and related subunits, G-protein coupled receptor superfamily [Inorganic ion transport and metabolism; Amino acid transport and metabolism; Signal transduction mechanisms]
Probab=62.61 E-value=13 Score=41.35 Aligned_cols=61 Identities=13% Similarity=0.079 Sum_probs=39.5
Q ss_pred HhhHHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhcccccCc
Q 019540 106 QNRRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTESNISV 167 (339)
Q Consensus 106 QNRRaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~~~s~ 167 (339)
.++|.+.++.. ....+.-.+.++.|+.+|..+++......+.+.+++.+|..+..+.....
T Consensus 740 e~q~n~~~~~s-s~~~k~~eer~~~lk~EN~~l~~~i~ekee~i~e~~~~l~~~~~~~~~~~ 800 (865)
T KOG1055|consen 740 EAQRNMKTGPS-SSVNENEEERLRLLKKENRRLRKKIMEKEERLSELKHQLQPRPRKTITEI 800 (865)
T ss_pred hhhhccccCcc-cccchhHHHHhhhhhcccHHHHHhcccchHHHHHHHHhcccccccccccC
Confidence 34455444422 12223334467788888888888888888888888888888776655444
No 55
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=62.34 E-value=24 Score=34.38 Aligned_cols=47 Identities=28% Similarity=0.374 Sum_probs=33.4
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhc
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~ 161 (339)
+.+.++...|+..++.|+..+..|..+|..|..+++.+++.|..-.+
T Consensus 100 ~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~ 146 (292)
T KOG4005|consen 100 KDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQ 146 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHH
Confidence 34566677777777778777778877777777777777776655433
No 56
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=61.52 E-value=22 Score=30.62 Aligned_cols=43 Identities=40% Similarity=0.512 Sum_probs=34.1
Q ss_pred HHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 116 q~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
..+...+.+-+....++..-.++..||..|+-||..|+..|..
T Consensus 12 ~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 4455666666677777778888888999999999999999876
No 57
>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=60.03 E-value=18 Score=27.01 Aligned_cols=40 Identities=25% Similarity=0.264 Sum_probs=32.3
Q ss_pred CCHHHHHHHHHHhhhhcC--CCHHHHHHHHHHhCCChHHHhh
Q 019540 64 LSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAV 103 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~y--Ps~~~ReeLA~~LgLserQVqV 103 (339)
+|..|.++|...|+..-| |-...-.+||.+||+++.-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 578999999999988765 5455668999999999877543
No 58
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=58.79 E-value=34 Score=29.25 Aligned_cols=44 Identities=36% Similarity=0.464 Sum_probs=33.5
Q ss_pred HHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 116 q~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
+.+.....+-+....|+..-..+..||..|+-||..|+..+.+.
T Consensus 12 ~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 12 DLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45556666666777777777788888888888888888888764
No 59
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=57.38 E-value=42 Score=37.32 Aligned_cols=54 Identities=24% Similarity=0.328 Sum_probs=45.2
Q ss_pred HHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhccc
Q 019540 110 ARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTES 163 (339)
Q Consensus 110 aK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~ 163 (339)
+..++..+.++.+.+|+.++.+.+..+.+..+++.|+.|+.+|+......+++.
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~~~~~~~m 267 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSSLEKEQEL 267 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhhhhh
Confidence 556777788899999999999999999999999999999999997555555443
No 60
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=57.15 E-value=17 Score=26.44 Aligned_cols=34 Identities=15% Similarity=0.261 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHH
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~ 119 (339)
...+||+.+|++...|..|+.++.....-....+
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ 45 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEK 45 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHH
Confidence 4568999999999999999998866655544433
No 61
>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=55.58 E-value=32 Score=24.32 Aligned_cols=42 Identities=17% Similarity=0.231 Sum_probs=26.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRa 110 (339)
+++.+..++.-.| .....-.++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 4555555555444 33445678999999999999999974443
No 62
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=55.42 E-value=53 Score=26.65 Aligned_cols=44 Identities=20% Similarity=0.266 Sum_probs=31.9
Q ss_pred hHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhh
Q 019540 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 114 rkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~ 157 (339)
+..+.++...|+...+.|....+..+.+++.|..||+-|+.-+.
T Consensus 18 k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~ 61 (80)
T PF10224_consen 18 KEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455566667777777777788888888888888888777654
No 63
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=55.30 E-value=26 Score=33.90 Aligned_cols=28 Identities=21% Similarity=0.299 Sum_probs=11.2
Q ss_pred hHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 128 YDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 128 ~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
.+.+..+...++...+.|..|+.+|.++
T Consensus 158 leele~e~ee~~erlk~le~E~s~LeE~ 185 (290)
T COG4026 158 LEELEAEYEEVQERLKRLEVENSRLEEM 185 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333343344444444444433
No 64
>smart00340 HALZ homeobox associated leucin zipper.
Probab=54.90 E-value=19 Score=26.11 Aligned_cols=32 Identities=28% Similarity=0.288 Sum_probs=27.4
Q ss_pred HHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHH
Q 019540 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLK 147 (339)
Q Consensus 116 q~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~ 147 (339)
+.+.+.+.||.-.+.|..+|..++.|.+.|+.
T Consensus 2 QTEvdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 2 QTEVDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred chHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56888899999999999999999998877764
No 65
>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=54.69 E-value=84 Score=24.96 Aligned_cols=71 Identities=21% Similarity=0.254 Sum_probs=39.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhhHH------HHHHHhHHHH----------hhHHHHhhhhhhhHhHHHHHHHHH
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKTKQ------LERDYGVLKA----------NYDALKLNYDSLQHDNEALLKEIR 150 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Krkq------~e~e~~~lka----------~~d~Lk~~~dsl~~ene~L~~E~~ 150 (339)
..++|+.+|++++.|+.|-+..--+-.+.. ...+...++. .....+. .-.+..+.+.|++++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~-~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKR-ILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHH-HHHHHHHHHHHHHHHH
Confidence 457899999999999999865432211100 0111111111 1111111 1125667777888888
Q ss_pred HHHHHhhh
Q 019540 151 ELKSKLNE 158 (339)
Q Consensus 151 ~Lk~kl~~ 158 (339)
+|+.++..
T Consensus 83 ~l~~~~~~ 90 (91)
T cd04766 83 ELRARLRR 90 (91)
T ss_pred HHHHHhcc
Confidence 88777653
No 66
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=51.78 E-value=38 Score=30.09 Aligned_cols=48 Identities=19% Similarity=0.179 Sum_probs=36.2
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
...+++.|..+|.. +. .. ....++|..||++...|+.|-+..+.+.|+
T Consensus 4 ~~~Lt~rqreVL~l-r~-~G----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRL-RE-RG----LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHH-HH-cC----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34589999999977 32 22 235689999999999999999866665554
No 67
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=50.62 E-value=27 Score=32.04 Aligned_cols=49 Identities=24% Similarity=0.239 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHhhhhcC--CCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 63 RLSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~y--Ps~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
.+|..|+++|..+|...-| |-...-.+||+++|+++.-+ |..=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~--~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL--SEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH--HHHHHHHHHH
Confidence 4999999999999988764 55556689999999998664 4444555544
No 68
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=50.13 E-value=83 Score=24.87 Aligned_cols=44 Identities=25% Similarity=0.337 Sum_probs=28.3
Q ss_pred hHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhh
Q 019540 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 114 rkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~ 157 (339)
...++.+...|+..+..|..++..+..+|..|+.+....+..+.
T Consensus 20 i~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~ 63 (72)
T PF06005_consen 20 IALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566666776677777777777777777766655555443
No 69
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=49.11 E-value=54 Score=32.61 Aligned_cols=50 Identities=24% Similarity=0.358 Sum_probs=33.6
Q ss_pred HHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhh
Q 019540 110 ARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 110 aK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~ 160 (339)
+|+|.++ +.+.+.+--....|-..|+.|+.+-..|.+|++.||..+.+.-
T Consensus 240 tRYRqKk-Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~ 289 (294)
T KOG4571|consen 240 TRYRQKK-RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVY 289 (294)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444433 2333444445667777888888888899999999888776543
No 70
>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=48.04 E-value=15 Score=28.19 Aligned_cols=20 Identities=20% Similarity=0.519 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCChHHHhhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWF 105 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWF 105 (339)
.-.+||.+||+++.+|+.|=
T Consensus 24 ~lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred cHHHHHHHHCCCHHHHHHHh
Confidence 45689999999999999885
No 71
>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=47.91 E-value=58 Score=23.70 Aligned_cols=23 Identities=35% Similarity=0.547 Sum_probs=12.5
Q ss_pred HHhhhhhhhHhHHHHHHHHHHHH
Q 019540 131 LKLNYDSLQHDNEALLKEIRELK 153 (339)
Q Consensus 131 Lk~~~dsl~~ene~L~~E~~~Lk 153 (339)
|......|..+|..|..++..|+
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444455556666666655554
No 72
>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=46.49 E-value=73 Score=23.82 Aligned_cols=30 Identities=30% Similarity=0.513 Sum_probs=13.6
Q ss_pred hhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 127 NYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 127 ~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
....|......+..+|..|..++..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~ 56 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEI 56 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444433
No 73
>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=46.44 E-value=2e+02 Score=25.04 Aligned_cols=37 Identities=8% Similarity=0.082 Sum_probs=25.7
Q ss_pred CCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
..|.|+..++..|.. ....+.+|++-..|+-++.+..
T Consensus 34 g~R~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 34 NYRYYDETALDRLQL-------------IEHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCeeECHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHHhhc
Confidence 345599999998833 2234678888888888776654
No 74
>smart00338 BRLZ basic region leucin zipper.
Probab=45.87 E-value=1.2e+02 Score=22.55 Aligned_cols=36 Identities=28% Similarity=0.422 Sum_probs=23.5
Q ss_pred HhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 121 ~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
...|......|...+..|..+...|..|+..|+..+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344455566666677777777777777777776654
No 75
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=44.64 E-value=61 Score=27.45 Aligned_cols=28 Identities=14% Similarity=0.123 Sum_probs=22.3
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.++|..+|+++..|+++...-|.+-|.
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 3589999999999999988755555554
No 76
>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=44.37 E-value=94 Score=25.45 Aligned_cols=39 Identities=18% Similarity=0.082 Sum_probs=28.2
Q ss_pred CCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHH
Q 019540 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (339)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRa 110 (339)
.+|+|+.+++..|.. ...|.+.+|++-..|+-+..+...
T Consensus 35 g~R~Yt~~di~~l~~------------I~~llr~~G~~l~~i~~~l~~~~~ 73 (99)
T cd04765 35 GRRYYRPKDVELLLL------------IKHLLYEKGYTIEGAKQALKEDGA 73 (99)
T ss_pred CCeeeCHHHHHHHHH------------HHHHHHHCCCCHHHHHHHHHhccc
Confidence 355699999998833 334567889999999888865443
No 77
>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=43.47 E-value=49 Score=25.42 Aligned_cols=43 Identities=21% Similarity=0.383 Sum_probs=22.5
Q ss_pred CcCCHH-HHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhH
Q 019540 62 RRLSVD-QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 62 rRfT~~-Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQ 106 (339)
+.|+.. -|.+++.++..+. --...|. -|+++|+++++|+-|-+
T Consensus 4 rsy~~~FKL~Vv~~a~~~~n-c~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEKDNN-CKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHHH-TT-TTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHHHccc-hhhhHHH-HHHHhCccHHHHHHHHH
Confidence 335553 3555555443322 2223343 49999999999999974
No 78
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=43.43 E-value=64 Score=25.92 Aligned_cols=39 Identities=28% Similarity=0.359 Sum_probs=22.7
Q ss_pred HHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 118 e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
.-+.+.||+.+..|..+....+...+.|..|+.+||.+.
T Consensus 24 QmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 24 QMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555555555555555666666666666666654
No 79
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=41.10 E-value=76 Score=33.53 Aligned_cols=25 Identities=28% Similarity=0.618 Sum_probs=17.5
Q ss_pred hhhh---HhhHHHhhhHHHHHHHhHHHH
Q 019540 102 AVWF---QNRRARWKTKQLERDYGVLKA 126 (339)
Q Consensus 102 qVWF---QNRRaK~Krkq~e~e~~~lka 126 (339)
-+|| ||+.+|.+-.+.-++++.|+-
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~ 256 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQR 256 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHH
Confidence 5788 888888877666666555543
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=40.82 E-value=69 Score=25.63 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.|..++...|-. .....++|..+|+++..|..|...-+.+.|
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 555555555444322 223558999999999999988875555444
No 81
>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=40.78 E-value=76 Score=22.91 Aligned_cols=46 Identities=15% Similarity=0.175 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+||+.++.+|.....-. ...++|..++++++.|..+..+=+.|..-
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 47888888886654332 35689999999999999988766665543
No 82
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=40.49 E-value=41 Score=31.56 Aligned_cols=43 Identities=30% Similarity=0.499 Sum_probs=35.2
Q ss_pred HHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhccccc
Q 019540 123 VLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTESNI 165 (339)
Q Consensus 123 ~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~~~ 165 (339)
.+-..|+.|+.+++.+..++..|+.|+.+|+..+.....+...
T Consensus 109 qlE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 109 QLEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred hhhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhcc
Confidence 3344899999999999999999999999999988766544443
No 83
>TIGR02449 conserved hypothetical protein TIGR02449. Members of this family are small proteins, typically 73 amino acids in length, with single copies in each of several Proteobacteria, including Xylella fastidiosa, Pseudomonas aeruginosa, and Xanthomonas campestris. The function is unknown.
Probab=40.31 E-value=98 Score=24.23 Aligned_cols=39 Identities=18% Similarity=0.108 Sum_probs=22.5
Q ss_pred HHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 118 e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
+...+.|-..+..|+.+|..+..+...+..|...|.++.
T Consensus 6 e~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekn 44 (65)
T TIGR02449 6 AAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKN 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555666666666666666666666665554
No 84
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=40.12 E-value=68 Score=26.87 Aligned_cols=45 Identities=16% Similarity=0.127 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.+..++...|-.. ....+||..+|+++..|+.|...-|.+-|
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 5555666555444222 23568999999999999998865444443
No 85
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=39.74 E-value=72 Score=27.05 Aligned_cols=45 Identities=13% Similarity=0.016 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.+..+|.-.|-. ...-.++|..+|+++..|+.|...-|.+.|
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 666666666655422 123458999999999999999874444443
No 86
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=39.68 E-value=44 Score=23.40 Aligned_cols=41 Identities=17% Similarity=0.208 Sum_probs=20.8
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQ 106 (339)
.+.+|.+|...++..+... ....+||+.||.++.-|..|.+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 3458888888888876533 3456799999999999887764
No 87
>PF15058 Speriolin_N: Speriolin N terminus
Probab=39.24 E-value=55 Score=30.83 Aligned_cols=42 Identities=31% Similarity=0.391 Sum_probs=23.8
Q ss_pred HhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhccc
Q 019540 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTES 163 (339)
Q Consensus 121 ~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~ 163 (339)
|+.+.+.++.|-.+|..+++ ..+|.+||.+||..|.+-..+.
T Consensus 7 yeGlrhqierLv~ENeeLKK-lVrLirEN~eLksaL~ea~~~~ 48 (200)
T PF15058_consen 7 YEGLRHQIERLVRENEELKK-LVRLIRENHELKSALGEACAEP 48 (200)
T ss_pred hHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHHHHHHHHhhccc
Confidence 34444445555555555554 3345567777777776665544
No 88
>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=39.11 E-value=35 Score=34.76 Aligned_cols=31 Identities=26% Similarity=0.395 Sum_probs=20.4
Q ss_pred hhHHHHhhhhhhhHhHHHHHHHHHHHHHHhh
Q 019540 127 NYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 127 ~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~ 157 (339)
+.-+|+.+|++|++||+.|+.|+.+|++...
T Consensus 33 e~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 33 ENFALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hhhhHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445666777777777777777777766544
No 89
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=38.85 E-value=1.1e+02 Score=33.96 Aligned_cols=18 Identities=17% Similarity=0.255 Sum_probs=13.2
Q ss_pred HHHHHHHHHhCCChHHHh
Q 019540 85 ERKVKLAQELGLQPRQVA 102 (339)
Q Consensus 85 ~~ReeLA~~LgLserQVq 102 (339)
..-.++|+.+||++..|.
T Consensus 483 S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 483 SYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred cHHHHHHHHhCcCHHHHH
Confidence 344578899999888774
No 90
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=38.55 E-value=74 Score=28.20 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=30.3
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..+|.-.|-.. ..-.++|..||++...|++|...-|.+-|+
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 5556666554443222 234689999999999999988655555443
No 91
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=38.20 E-value=78 Score=30.29 Aligned_cols=47 Identities=21% Similarity=0.442 Sum_probs=34.4
Q ss_pred HHHHhHHHHh-hHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhcccc
Q 019540 118 ERDYGVLKAN-YDALKLNYDSLQHDNEALLKEIRELKSKLNEENTESN 164 (339)
Q Consensus 118 e~e~~~lka~-~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~e~~ 164 (339)
..++..++.. ....+.++..++.|+++|.-+++++|..+..+.....
T Consensus 100 ~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~ei~~~~ 147 (220)
T KOG3156|consen 100 KVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHEISKTT 147 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3445555543 3344578999999999999999999999987765443
No 92
>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=38.13 E-value=2.2e+02 Score=23.06 Aligned_cols=36 Identities=14% Similarity=0.352 Sum_probs=26.2
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
++.|+..++..|.... ..+.+|++..+++-++....
T Consensus 36 ~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 36 YRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred ceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc
Confidence 4559999999985432 34567899999988886543
No 93
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=37.81 E-value=64 Score=24.58 Aligned_cols=31 Identities=29% Similarity=0.484 Sum_probs=22.1
Q ss_pred hHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 128 YDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 128 ~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
|...-.+...+..|++.|++||.+|+.-|.+
T Consensus 28 Y~~vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 28 YNKVLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3334445666777889999999998887653
No 94
>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=37.70 E-value=24 Score=28.10 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=26.4
Q ss_pred HHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHh
Q 019540 73 EKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 73 E~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQN 107 (339)
+..|....+...-...+||..+|+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455555545556779999999999999999863
No 95
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=37.26 E-value=79 Score=28.47 Aligned_cols=29 Identities=24% Similarity=0.233 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
...+||..+|+++..|+++...-|.+.|+
T Consensus 171 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 171 SQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34589999999999999988655555444
No 96
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=36.91 E-value=54 Score=28.40 Aligned_cols=46 Identities=15% Similarity=0.294 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|- ......+||..+|+++..|+++...-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 44455444444431 22235689999999999999988755555443
No 97
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=36.59 E-value=97 Score=20.89 Aligned_cols=39 Identities=21% Similarity=0.272 Sum_probs=28.2
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNR 108 (339)
++..+..++...+ .. ....++|..+|++...|..|.+.-
T Consensus 4 l~~~e~~i~~~~~--~g----~s~~eia~~l~is~~tv~~~~~~~ 42 (58)
T smart00421 4 LTPREREVLRLLA--EG----LTNKEIAERLGISEKTVKTHLSNI 42 (58)
T ss_pred CCHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHHHH
Confidence 6777777775532 12 245789999999999999888643
No 98
>PRK00118 putative DNA-binding protein; Validated
Probab=36.58 E-value=1.7e+02 Score=24.73 Aligned_cols=45 Identities=13% Similarity=0.102 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.|..++...|.... ...+||..+|+++..|..|...-|.+.|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 55666666655444322 3457999999999999999975444444
No 99
>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=36.46 E-value=37 Score=23.16 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChHHHhhhhHhhH
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRR 109 (339)
..++|+.+|++++.|+.|.+...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999986553
No 100
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=35.75 E-value=1.1e+02 Score=27.09 Aligned_cols=46 Identities=13% Similarity=0.170 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|-. ...-.++|..+|+++..|+++...-|.+-|+
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 445555555444322 1234689999999999999998655554444
No 101
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.72 E-value=49 Score=22.81 Aligned_cols=24 Identities=25% Similarity=0.517 Sum_probs=19.7
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhH
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRR 109 (339)
...++|+++|++..+|..|.+.-+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~y~ 37 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKRYR 37 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHHHH
Confidence 355789999999999999996433
No 102
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=35.66 E-value=97 Score=25.26 Aligned_cols=37 Identities=27% Similarity=0.346 Sum_probs=17.5
Q ss_pred HHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 120 e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
+.+.+|..+..|..+.+.+....+.|..++.+||...
T Consensus 26 EieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 26 EIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444555555555543
No 103
>PF15058 Speriolin_N: Speriolin N terminus
Probab=35.26 E-value=47 Score=31.31 Aligned_cols=34 Identities=26% Similarity=0.463 Sum_probs=25.4
Q ss_pred HhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 126 ANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 126 a~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
.+|+.|.+..+.+-.||+.|+++++-+|+.+.-+
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLirEN~eLk 38 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLIRENHELK 38 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 4678888888888888888888877777765443
No 104
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=35.21 E-value=59 Score=38.38 Aligned_cols=53 Identities=17% Similarity=0.231 Sum_probs=49.3
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq 116 (339)
+-.+++..|-++|..+.-|+...+..|......+.+++.+||+|-|.|.++..
T Consensus 712 ~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 712 ILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred ccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 55699999999999999999999999999999999999999999999988765
No 105
>PRK11546 zraP zinc resistance protein; Provisional
Probab=34.96 E-value=1.6e+02 Score=26.39 Aligned_cols=32 Identities=28% Similarity=0.347 Sum_probs=18.3
Q ss_pred hHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 128 YDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 128 ~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
+++|............+|.+|+..|+.+|.+.
T Consensus 77 LnALl~~~~pD~~kI~aL~kEI~~Lr~kL~e~ 108 (143)
T PRK11546 77 YNALLTANPPDSSKINAVAKEMENLRQSLDEL 108 (143)
T ss_pred HHHHHcCCCCCHHHHHHHHHHHHHHHHHHHHH
Confidence 33343333444444566777777777776654
No 106
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=34.83 E-value=1.4e+02 Score=33.36 Aligned_cols=17 Identities=24% Similarity=0.466 Sum_probs=13.2
Q ss_pred HHHHHHHHhCCChHHHh
Q 019540 86 RKVKLAQELGLQPRQVA 102 (339)
Q Consensus 86 ~ReeLA~~LgLserQVq 102 (339)
.-.++|+.+||++..|.
T Consensus 489 ~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 489 NAFEIAKRLGLPENIIE 505 (782)
T ss_pred HHHHHHHHhCcCHHHHH
Confidence 44578999999988874
No 107
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.69 E-value=1.1e+02 Score=25.97 Aligned_cols=29 Identities=17% Similarity=0.212 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
.-.+||..+|+++..|+.|...-|.+.|+
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999755555543
No 108
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=34.36 E-value=1.6e+02 Score=25.70 Aligned_cols=28 Identities=14% Similarity=0.141 Sum_probs=22.2
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.+||..+|+++..|++....-|.+.|+
T Consensus 136 ~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 136 QEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999888766665554
No 109
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=34.18 E-value=1.2e+02 Score=25.94 Aligned_cols=29 Identities=21% Similarity=0.135 Sum_probs=22.7
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
..+++|..+|+++..|++|.+.-|.+.|+
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999998755555544
No 110
>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=34.06 E-value=2.6e+02 Score=23.15 Aligned_cols=38 Identities=24% Similarity=0.379 Sum_probs=27.9
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
.|.|+..++..|. .....+.+|++...|+.++......
T Consensus 35 yR~Y~~~d~~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~~~ 72 (116)
T cd04769 35 YRVYDAQHVECLR-------------FIKEARQLGFTLAELKAIFAGHEGR 72 (116)
T ss_pred ceeeCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhccccC
Confidence 4559999888873 3344688999999999888765543
No 111
>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=33.81 E-value=91 Score=26.41 Aligned_cols=40 Identities=28% Similarity=0.317 Sum_probs=32.7
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHH
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~ 154 (339)
..+-.+.+.||.....|-.+|..|+.||+.|+..+.++..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4556677888888888888999999999999988877765
No 112
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=33.20 E-value=78 Score=30.10 Aligned_cols=37 Identities=24% Similarity=0.255 Sum_probs=20.0
Q ss_pred HHHhhHHHHhhhhhhhHhHH---HHHHHHHHHHHHhhhhh
Q 019540 124 LKANYDALKLNYDSLQHDNE---ALLKEIRELKSKLNEEN 160 (339)
Q Consensus 124 lka~~d~Lk~~~dsl~~ene---~L~~E~~~Lk~kl~~~~ 160 (339)
++++++.|+.++..++.+.. .+++|+++|+..|.-..
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~~ 113 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEAENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 33344444444444444443 56777777777665443
No 113
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=32.92 E-value=1.1e+02 Score=26.68 Aligned_cols=46 Identities=15% Similarity=0.042 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|-. ...-.+||..||++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 555555555544322 2234689999999999999998766655554
No 114
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=32.61 E-value=1.3e+02 Score=23.86 Aligned_cols=40 Identities=15% Similarity=0.378 Sum_probs=29.6
Q ss_pred HHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 119 RDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 119 ~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
+....|+..|..|+..+..-..++..|...+..|-.++..
T Consensus 21 ~q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~ 60 (70)
T PF04899_consen 21 KQQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQR 60 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 3445677788888888888888888888888777766554
No 115
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=32.23 E-value=1.1e+02 Score=26.75 Aligned_cols=45 Identities=24% Similarity=0.177 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.|..++...|-.. ....+||..+|++...|+.+...-|.+-|
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555543332 23568999999999999998754444433
No 116
>PRK04217 hypothetical protein; Provisional
Probab=32.18 E-value=1.2e+02 Score=25.78 Aligned_cols=46 Identities=11% Similarity=0.054 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
.++.+|..++...|...- ...+||+.+|++...|...+..-|.+.|
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 488999888876664333 4668999999999999888764444443
No 117
>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.
Probab=31.93 E-value=2.9e+02 Score=28.81 Aligned_cols=26 Identities=27% Similarity=0.447 Sum_probs=14.4
Q ss_pred hhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 134 NYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 134 ~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
+.-+++.+.+.|.+|+++.+.++.+.
T Consensus 350 EKaaLrkerd~L~keLeekkreleql 375 (442)
T PF06637_consen 350 EKAALRKERDSLAKELEEKKRELEQL 375 (442)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666666666555555444
No 118
>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=31.78 E-value=1.2e+02 Score=25.01 Aligned_cols=28 Identities=18% Similarity=0.298 Sum_probs=21.2
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
...++|..+|+++..|+.+...-|.+.|
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3457999999999999988865444443
No 119
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=31.51 E-value=1.1e+02 Score=32.48 Aligned_cols=43 Identities=19% Similarity=0.279 Sum_probs=29.0
Q ss_pred hHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 114 rkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
..+++++++.++.+.+.+......++...+.|+.|+.+|+.++
T Consensus 78 asELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 78 AAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 3455666666666555555555666767777888888888877
No 120
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=31.34 E-value=1.7e+02 Score=27.37 Aligned_cols=54 Identities=20% Similarity=0.264 Sum_probs=34.9
Q ss_pred hHHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhc
Q 019540 108 RRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 108 RRaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~ 161 (339)
+..|........++..|......+-..+-.+......|+.|+.+++.+..+..+
T Consensus 164 ~~RK~~Q~~~~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~~ 217 (221)
T PF05700_consen 164 RERKRRQEEAGEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELKE 217 (221)
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 333333333334445566666666677777888888888988888887765543
No 121
>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=31.27 E-value=1.1e+02 Score=25.53 Aligned_cols=43 Identities=23% Similarity=0.234 Sum_probs=28.0
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
+++.+..++...|- ....-.++|..+|++...|+++...-|.+
T Consensus 112 L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 112 LPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 55555555544332 22345689999999999999887544443
No 122
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=31.04 E-value=92 Score=27.33 Aligned_cols=29 Identities=14% Similarity=0.233 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
...++|..+|+++..|+.|...-|.+.|+
T Consensus 159 s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 159 SQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 34689999999999999999755554443
No 123
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=30.94 E-value=1e+02 Score=26.31 Aligned_cols=40 Identities=25% Similarity=0.389 Sum_probs=33.2
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHH
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~ 154 (339)
..+-.+.+.||+....+-.+|..|+.||+.|++.+.++..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3556678888888888899999999999999999887744
No 124
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=30.49 E-value=1.4e+02 Score=26.13 Aligned_cols=28 Identities=11% Similarity=0.162 Sum_probs=22.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.++|..+|+++..|++....-|.+.|.
T Consensus 150 ~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 150 VEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999988655555554
No 125
>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=30.35 E-value=96 Score=21.63 Aligned_cols=37 Identities=16% Similarity=0.358 Sum_probs=26.2
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWF 105 (339)
++.+|.+.+...+... + ...+||+.+|++...|.-|+
T Consensus 6 ~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 6 LSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 7777777776666655 2 46789999999999887665
No 126
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=30.30 E-value=1.9e+02 Score=24.41 Aligned_cols=45 Identities=13% Similarity=0.282 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..+|.-.| ..+ .-.+||..+|+++..|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5566666665555 222 34688999999999999988654544443
No 127
>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=30.30 E-value=1.3e+02 Score=26.00 Aligned_cols=27 Identities=26% Similarity=0.239 Sum_probs=21.1
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
-.++|..||+++..|++....-|.+-|
T Consensus 153 ~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 153 VEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 348999999999999998875554444
No 128
>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=30.24 E-value=68 Score=26.77 Aligned_cols=32 Identities=28% Similarity=0.647 Sum_probs=18.3
Q ss_pred HHHHHHhhhhcCCCHH--HHHHHHHHhCCChHHHhhhhHhhHHHhhhHHH
Q 019540 70 KALEKNFEVENKLEPE--RKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 70 ~~LE~~F~~~~yPs~~--~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~ 117 (339)
....-.|+.++||... .+.. .|||.+||+++.
T Consensus 15 RiIk~LyqsnPyP~~~GTr~aR----------------RnRRRRWR~rq~ 48 (91)
T PF00424_consen 15 RIIKILYQSNPYPSPEGTRQAR----------------RNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHTS-S--S-S-HHHH----------------HHHHHHHHHHHH
T ss_pred HHHHHHHccccCCCCCCccccc----------------cchhhhHHHHHH
Confidence 3445568889998744 1111 589999998654
No 129
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=30.22 E-value=1.1e+02 Score=26.39 Aligned_cols=46 Identities=13% Similarity=0.112 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++...|- ....-.++|..+|+++..|+++.+.-|.+.|.
T Consensus 137 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555544332 22334689999999999999998755554443
No 130
>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=30.20 E-value=1.2e+02 Score=26.22 Aligned_cols=43 Identities=19% Similarity=0.158 Sum_probs=27.0
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
+++.+..+|.-.|-.. ....++|..+|+++..|+++...-|.+
T Consensus 101 L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 101 LPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKK 143 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 5555555554443222 234689999999999998877533333
No 131
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=29.90 E-value=2.8e+02 Score=26.49 Aligned_cols=60 Identities=20% Similarity=0.490 Sum_probs=30.9
Q ss_pred hHHHhhhhHhhHHHhhhH---------HHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhh
Q 019540 98 PRQVAVWFQNRRARWKTK---------QLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 98 erQVqVWFQNRRaK~Krk---------q~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~ 157 (339)
...+..||+.+=...+.. ....+...++.....|..+-++++..+..|...+.+++..+.
T Consensus 186 ~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~ 254 (312)
T PF00038_consen 186 REELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLD 254 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHH
Confidence 567889998874333321 222233344444444555555555555555555555554444
No 132
>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=29.25 E-value=3.3e+02 Score=22.54 Aligned_cols=38 Identities=21% Similarity=0.248 Sum_probs=28.8
Q ss_pred CCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHH
Q 019540 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRA 110 (339)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRa 110 (339)
..|.|+.+++..| ......+.+|++...|+..+.....
T Consensus 35 gyR~Y~~~~i~~l-------------~~I~~lr~~G~sl~eI~~~l~~~~~ 72 (123)
T cd04770 35 GYRLYGEADLARL-------------RFIRRAQALGFSLAEIRELLSLRDD 72 (123)
T ss_pred CCccCCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHhhhc
Confidence 3455999999998 3344568899999999988876543
No 133
>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=28.74 E-value=3.3e+02 Score=22.35 Aligned_cols=36 Identities=19% Similarity=0.346 Sum_probs=27.4
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRR 109 (339)
.|.|+.+++..|. .....+.+|++..+|+..+....
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 36 IRDFTEEDLEWLE-------------FIKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred CccCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHHHHc
Confidence 4559999999882 34456789999999999887543
No 134
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.52 E-value=52 Score=24.17 Aligned_cols=22 Identities=18% Similarity=0.335 Sum_probs=18.5
Q ss_pred HHHHHHHhCCChHHHhhhhHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNR 108 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNR 108 (339)
..++|+.+|++.+.|+.|=+..
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 3578999999999999996543
No 135
>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=28.47 E-value=4.5e+02 Score=23.85 Aligned_cols=44 Identities=18% Similarity=0.220 Sum_probs=34.8
Q ss_pred CCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhH
Q 019540 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 61 RrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQ 106 (339)
...++++++..+...-..+ |..-.+..||+++|++..-|.+-..
T Consensus 83 ~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 83 KYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred cccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 3459999999988776555 4567889999999999988877654
No 136
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=28.13 E-value=70 Score=25.84 Aligned_cols=25 Identities=28% Similarity=0.553 Sum_probs=17.2
Q ss_pred hhhhHhHHHHHHHHHHHHHHhhhhh
Q 019540 136 DSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 136 dsl~~ene~L~~E~~~Lk~kl~~~~ 160 (339)
+.++.+|..|+.|++.|+++|++..
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~ 27 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNK 27 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3466677777777777777776543
No 137
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=27.95 E-value=1e+02 Score=29.98 Aligned_cols=18 Identities=28% Similarity=0.248 Sum_probs=13.6
Q ss_pred HHHHHHHHHHHHHhhhhh
Q 019540 143 EALLKEIRELKSKLNEEN 160 (339)
Q Consensus 143 e~L~~E~~~Lk~kl~~~~ 160 (339)
+.+++||++|+.-|.-..
T Consensus 94 ~~l~~EN~rLr~LL~~~~ 111 (283)
T TIGR00219 94 QNLKQENVRLRELLNSPL 111 (283)
T ss_pred HHHHHHHHHHHHHhcCcc
Confidence 348888999988777654
No 138
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=27.84 E-value=1.3e+02 Score=26.23 Aligned_cols=28 Identities=7% Similarity=0.182 Sum_probs=21.7
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.+||..+|++...|+.+...-|.+.|+
T Consensus 147 ~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 147 NIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred HHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999988655544443
No 139
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=27.61 E-value=1.4e+02 Score=28.52 Aligned_cols=20 Identities=30% Similarity=0.423 Sum_probs=7.5
Q ss_pred hhhhhhHhHHHHHHHHHHHH
Q 019540 134 NYDSLQHDNEALLKEIRELK 153 (339)
Q Consensus 134 ~~dsl~~ene~L~~E~~~Lk 153 (339)
..++++.+-+.+..|..+|.
T Consensus 180 ~~~al~Kq~e~~~~EydrLl 199 (216)
T KOG1962|consen 180 KVDALKKQSEGLQDEYDRLL 199 (216)
T ss_pred HHHHHHHHHHHcccHHHHHH
Confidence 33333333333333333333
No 140
>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=27.48 E-value=1.3e+02 Score=20.47 Aligned_cols=36 Identities=17% Similarity=0.257 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhH
Q 019540 65 SVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 65 T~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQ 106 (339)
+..|..++...+ .. ....++|..++++...|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 455566664432 11 2456889999999999999886
No 141
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.34 E-value=57 Score=22.58 Aligned_cols=22 Identities=23% Similarity=0.412 Sum_probs=17.2
Q ss_pred HHHHHHHHHhCCChHHHhhhhH
Q 019540 85 ERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 85 ~~ReeLA~~LgLserQVqVWFQ 106 (339)
....++|+.+|++...|..|.+
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT
T ss_pred CCHHHHHHHHCcCHHHHHHHHH
Confidence 3467899999999999999975
No 142
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=27.33 E-value=1.7e+02 Score=24.51 Aligned_cols=45 Identities=13% Similarity=0.085 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.|..++.-.|-.. ..-.++|..||+++..|+++...-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555443221 12468999999999999987764444433
No 143
>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=27.29 E-value=1.7e+02 Score=28.23 Aligned_cols=43 Identities=21% Similarity=0.286 Sum_probs=21.8
Q ss_pred HHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 109 RaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
|-|.|..++|++...++.....|+ .|.+.|+++|..|=+|...
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~-------~Ev~~L~~DN~kLYEKiRy 132 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLR-------REVESLRADNVKLYEKIRY 132 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHH
Confidence 444455556666555555554444 4444555554444444433
No 144
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=26.95 E-value=1.4e+02 Score=26.35 Aligned_cols=47 Identities=15% Similarity=0.261 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krk 115 (339)
+++.+..++.-.|-. .....+||..+|++...|+...+.-|.+-|++
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 555555555443321 12346899999999999998776555554443
No 145
>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=26.94 E-value=1.2e+02 Score=26.25 Aligned_cols=28 Identities=11% Similarity=-0.010 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
.-.++|..+|+++..|++|...-|.+-|
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3468999999999999998864444443
No 146
>PRK10072 putative transcriptional regulator; Provisional
Probab=26.93 E-value=44 Score=27.73 Aligned_cols=42 Identities=24% Similarity=0.298 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
+.+...+..|..... . ...+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~g----l---TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----L---KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcC----C---CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 346666666633221 1 25689999999999999999877654
No 147
>smart00338 BRLZ basic region leucin zipper.
Probab=26.86 E-value=1.8e+02 Score=21.69 Aligned_cols=27 Identities=33% Similarity=0.543 Sum_probs=12.3
Q ss_pred HHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 129 DALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 129 d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
..|......+..+|..|..++..|+.+
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e 55 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRE 55 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444443
No 148
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=26.76 E-value=1.4e+02 Score=25.40 Aligned_cols=27 Identities=22% Similarity=0.238 Sum_probs=21.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
-.++|..+|++...|+.+...-|.+-|
T Consensus 131 ~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 131 YKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 458999999999999998864444444
No 149
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.09 E-value=1.9e+02 Score=27.10 Aligned_cols=28 Identities=14% Similarity=0.149 Sum_probs=12.3
Q ss_pred hHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 128 YDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 128 ~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
...|+.++..++.+.+.++.+++.++.+
T Consensus 134 ~~~L~~~n~~L~~~l~~~~~~~~~l~~~ 161 (206)
T PRK10884 134 INGLKEENQKLKNQLIVAQKKVDAANLQ 161 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444433
No 150
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=25.89 E-value=1.8e+02 Score=31.59 Aligned_cols=32 Identities=28% Similarity=0.351 Sum_probs=15.6
Q ss_pred hHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHH
Q 019540 122 GVLKANYDALKLNYDSLQHDNEALLKEIRELK 153 (339)
Q Consensus 122 ~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk 153 (339)
..|+++..+|-.+++.|+.||..|+.++..+.
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 34445555555555555555555544444443
No 151
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=25.73 E-value=31 Score=37.63 Aligned_cols=47 Identities=15% Similarity=0.103 Sum_probs=29.3
Q ss_pred HHHHHHhhhhcCCCHHHHHHHHHHhC-------CChHHHhhhhHhhHHHhhhHH
Q 019540 70 KALEKNFEVENKLEPERKVKLAQELG-------LQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 70 ~~LE~~F~~~~yPs~~~ReeLA~~Lg-------LserQVqVWFQNRRaK~Krkq 116 (339)
++-+.+|-.++.+......+--.++. ...+-|+.||.+||++.|+-+
T Consensus 705 ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 705 EVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred ecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
Confidence 33345566666666554443333322 245679999999999998754
No 152
>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=25.69 E-value=59 Score=24.46 Aligned_cols=27 Identities=30% Similarity=0.625 Sum_probs=22.4
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
...+||.+||++.+.|..|-+ |.+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 356899999999999999985 666665
No 153
>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=25.25 E-value=3.9e+02 Score=22.23 Aligned_cols=36 Identities=11% Similarity=0.265 Sum_probs=28.5
Q ss_pred CCCcCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhh
Q 019540 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (339)
Q Consensus 60 KRrRfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNR 108 (339)
..|.|+..++..| ......+.+|++-..|+.++...
T Consensus 34 gyR~Y~~~~l~~l-------------~~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 34 LRRQYDPQVLDRL-------------ALIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CceecCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhcc
Confidence 3455999999988 34466888999999999998764
No 154
>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=25.23 E-value=78 Score=20.86 Aligned_cols=25 Identities=20% Similarity=0.518 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
..++|+.+|++.+-|..|.++.+-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 4678999999999999999766543
No 155
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=25.17 E-value=1.2e+02 Score=27.01 Aligned_cols=28 Identities=21% Similarity=0.134 Sum_probs=22.2
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
..++|..||+++..|+++...-|.+.|+
T Consensus 132 ~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 132 YEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999998755555443
No 156
>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=25.09 E-value=2.2e+02 Score=25.15 Aligned_cols=46 Identities=13% Similarity=0.138 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|-. .....+||..+|++..-|+++...-|.+.|+
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~EIA~~lgis~~tvk~rl~Rar~~Lr~ 177 (188)
T TIGR02943 132 LPEQTARVFMMREVL-----GFESDEICQELEISTSNCHVLLYRARLSLRA 177 (188)
T ss_pred CCHHHHHHHHHHHHh-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 445555555443322 2235689999999999999887655555544
No 157
>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=25.04 E-value=1.5e+02 Score=21.75 Aligned_cols=35 Identities=23% Similarity=0.286 Sum_probs=26.2
Q ss_pred HHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhh
Q 019540 67 DQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (339)
Q Consensus 67 ~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWF 105 (339)
.|+..|+-.+. +...+.. +||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 57888888888 6655544 89999999999886544
No 158
>PRK10884 SH3 domain-containing protein; Provisional
Probab=24.70 E-value=2.7e+02 Score=26.09 Aligned_cols=37 Identities=16% Similarity=0.083 Sum_probs=23.6
Q ss_pred HHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHh
Q 019540 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 120 e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl 156 (339)
....|++.++.|+.+...++.+++.|..++..++...
T Consensus 133 ~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~~ 169 (206)
T PRK10884 133 VINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRTI 169 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344666666666666667777777777766666543
No 159
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=24.46 E-value=1.9e+02 Score=26.97 Aligned_cols=28 Identities=11% Similarity=0.183 Sum_probs=22.1
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.+||..||+++..|+++...-|.+-|+
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4589999999999999988755555543
No 160
>PRK12532 RNA polymerase sigma factor; Provisional
Probab=24.37 E-value=2e+02 Score=25.34 Aligned_cols=28 Identities=11% Similarity=0.189 Sum_probs=22.1
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
-.++|..+|+++..|+.+...-|.+.|+
T Consensus 155 ~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 182 (195)
T PRK12532 155 SDEIQQMCGISTSNYHTIMHRARESLRQ 182 (195)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4689999999999999988755555544
No 161
>PRK10403 transcriptional regulator NarP; Provisional
Probab=24.14 E-value=1.2e+02 Score=25.51 Aligned_cols=45 Identities=16% Similarity=0.189 Sum_probs=33.9
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+|..+..+|+..... ..+.+||..++++++-|+++.++=|.|-..
T Consensus 154 Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 154 LTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred CCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 788888888755432 335788999999999999988766666543
No 162
>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=23.86 E-value=1.9e+02 Score=24.42 Aligned_cols=46 Identities=17% Similarity=0.206 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|-. ...-.++|..+|++...|+.+-..-|.+-|+
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 445555555444321 2234589999999999999988755555544
No 163
>PRK06930 positive control sigma-like factor; Validated
Probab=23.66 E-value=2.1e+02 Score=25.72 Aligned_cols=46 Identities=9% Similarity=0.046 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|... ..-.++|..+|+++..|+.+...-|.+.++
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 6666666665543222 234589999999999999999766665554
No 164
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=23.52 E-value=1.3e+02 Score=27.61 Aligned_cols=46 Identities=15% Similarity=0.193 Sum_probs=31.5
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.+..++...|. ....-.++|..+|++...|+.+...-|.+.|+
T Consensus 185 L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQ-----EELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhc-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555555442 22245689999999999999998766666554
No 165
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=23.33 E-value=2e+02 Score=25.13 Aligned_cols=27 Identities=22% Similarity=0.431 Sum_probs=20.8
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
..++|..+|+++..|++|...-|.+.|
T Consensus 152 ~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 152 HAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred HHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 458999999999999998864444433
No 166
>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=23.22 E-value=1.4e+02 Score=27.19 Aligned_cols=45 Identities=18% Similarity=0.179 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.+..+|...|... ....++|..+|++...|+.|...-+.+-|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6677777776666322 23578999999999999988764444444
No 167
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=23.12 E-value=2.5e+02 Score=23.49 Aligned_cols=37 Identities=22% Similarity=0.181 Sum_probs=19.8
Q ss_pred hhHhhHHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhH
Q 019540 104 WFQNRRARWKTKQLERDYGVLKANYDALKLNYDSLQH 140 (339)
Q Consensus 104 WFQNRRaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ 140 (339)
|+..+..+.+....+++...+++.++.|..+-..++.
T Consensus 26 ~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 26 ILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3444444444445555566666666666555555554
No 168
>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=23.11 E-value=4.6e+02 Score=22.11 Aligned_cols=54 Identities=28% Similarity=0.368 Sum_probs=34.6
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHHHHhHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVL 124 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~e~~~l 124 (339)
+|..|...|+-.|..+ ---.+||..+|++..-|.-|.+ |++.+-..-+..++.+
T Consensus 18 LT~kQ~~~l~lyy~eD-----lSlsEIAe~~~iSRqaV~d~ik--r~~~~L~~yE~kL~l~ 71 (101)
T PF04297_consen 18 LTEKQREILELYYEED-----LSLSEIAEELGISRQAVYDSIK--RAEKKLEEYEEKLGLV 71 (101)
T ss_dssp S-HHHHHHHHHHCTS--------HHHHHHHCTS-HHHHHHHHH--HHHHHHHHHHHHH-HH
T ss_pred CCHHHHHHHHHHHccC-----CCHHHHHHHHCCCHHHHHHHHH--HHHHHHHHHHHHHhhH
Confidence 6788888887665443 3456899999999999999985 5555544555544444
No 169
>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=23.01 E-value=1.9e+02 Score=24.76 Aligned_cols=45 Identities=11% Similarity=0.110 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.+.+++...|-.. ....++|..||+++..|+++...-|.+-|
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr 164 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLK 164 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555554443222 23458999999999999987764444443
No 170
>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=22.85 E-value=77 Score=23.40 Aligned_cols=21 Identities=10% Similarity=0.365 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHhhhhHh
Q 019540 87 KVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQN 107 (339)
..++|+.+|++++.++.|-+.
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999875
No 171
>PRK07037 extracytoplasmic-function sigma-70 factor; Validated
Probab=22.75 E-value=2.1e+02 Score=24.14 Aligned_cols=27 Identities=22% Similarity=0.439 Sum_probs=20.3
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
..++|..+|++...|+.+...-|.+.|
T Consensus 128 ~~EIA~~lgis~~tV~~~l~ra~~~lr 154 (163)
T PRK07037 128 QKDIARELGVSPTLVNFMIRDALVHCR 154 (163)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 468999999999999987654444433
No 172
>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=22.69 E-value=1e+02 Score=21.23 Aligned_cols=21 Identities=14% Similarity=0.272 Sum_probs=18.9
Q ss_pred HHHHHhCCChHHHhhhhHhhH
Q 019540 89 KLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 89 eLA~~LgLserQVqVWFQNRR 109 (339)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 173
>PRK12547 RNA polymerase sigma factor; Provisional
Probab=22.56 E-value=2.1e+02 Score=24.43 Aligned_cols=45 Identities=20% Similarity=0.032 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
+++.+..++.-.|.. ...-.++|..+|+++..|+++...-|.+-|
T Consensus 113 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 157 (164)
T PRK12547 113 LSADQREAIILIGAS-----GFSYEDAAAICGCAVGTIKSRVSRARNRLQ 157 (164)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 555555555443322 123568999999999999998864444433
No 174
>PRK14127 cell division protein GpsB; Provisional
Probab=22.48 E-value=1.7e+02 Score=24.99 Aligned_cols=24 Identities=33% Similarity=0.588 Sum_probs=11.5
Q ss_pred hhhhhHhHHHHHHHHHHHHHHhhh
Q 019540 135 YDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 135 ~dsl~~ene~L~~E~~~Lk~kl~~ 158 (339)
++.+..++..|+.++.+|+.++.+
T Consensus 39 ye~l~~e~~~Lk~e~~~l~~~l~e 62 (109)
T PRK14127 39 YEAFQKEIEELQQENARLKAQVDE 62 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444555555555555554443
No 175
>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=22.37 E-value=2.2e+02 Score=24.02 Aligned_cols=20 Identities=20% Similarity=0.155 Sum_probs=16.9
Q ss_pred HHHHHHHhCCChHHHhhhhH
Q 019540 87 KVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQ 106 (339)
-.++|..||+++..|+....
T Consensus 141 ~~eIA~~l~is~~tv~~~l~ 160 (170)
T TIGR02952 141 IAEVARILGKTEGAVKILQF 160 (170)
T ss_pred HHHHHHHHCCCHHHHHHHHH
Confidence 45899999999999988664
No 176
>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=22.28 E-value=88 Score=23.23 Aligned_cols=21 Identities=19% Similarity=0.412 Sum_probs=18.4
Q ss_pred HHHHHHHhCCChHHHhhhhHh
Q 019540 87 KVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQN 107 (339)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999864
No 177
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.06 E-value=2.2e+02 Score=23.55 Aligned_cols=45 Identities=13% Similarity=0.121 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
.+|+.+.++|.- +... + ...++|..++++++.|+.|.++=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 388888888866 3322 2 2568999999999999999887555544
No 178
>PRK12536 RNA polymerase sigma factor; Provisional
Probab=21.91 E-value=2.2e+02 Score=24.73 Aligned_cols=29 Identities=21% Similarity=0.108 Sum_probs=22.6
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
...++|..||+++..|++....-|.+.|+
T Consensus 147 s~~EIA~~l~is~~tV~~~l~rar~~Lr~ 175 (181)
T PRK12536 147 SVAETAQLTGLSESAVKVGIHRGLKALAA 175 (181)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35689999999999999988655555544
No 179
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=21.76 E-value=1.5e+02 Score=24.98 Aligned_cols=44 Identities=27% Similarity=0.268 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHh
Q 019540 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (339)
Q Consensus 63 RfT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~ 112 (339)
.+|+.+.++|+-..+. ..+.+||..++++++.|++..++=|.|-
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 3777777777665532 2577889999999999988877655553
No 180
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=21.59 E-value=1.7e+02 Score=28.83 Aligned_cols=50 Identities=22% Similarity=0.272 Sum_probs=36.7
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.|..+|...|.... .......+||..+|++...|+.+...-+.+-|+
T Consensus 263 L~~~~R~vl~lrygL~~-~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 263 LNDKQREVLARRFGLLG-YEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred CCHHHHHHHHHHhccCC-CCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 78888888887763322 233456789999999999999988755555554
No 181
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=21.57 E-value=1.6e+02 Score=26.96 Aligned_cols=28 Identities=39% Similarity=0.542 Sum_probs=12.4
Q ss_pred hHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 128 YDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 128 ~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
+..|+.+...++..++.|.+|+..|+.+
T Consensus 106 ~~~l~~e~~~l~~~~e~Le~e~~~L~~~ 133 (161)
T TIGR02894 106 NERLKNQNESLQKRNEELEKELEKLRQR 133 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444444443
No 182
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.57 E-value=2e+02 Score=25.28 Aligned_cols=25 Identities=24% Similarity=0.363 Sum_probs=19.0
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHH
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK 111 (339)
..++|..+|+++..|+.++..-|.+
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~ 149 (181)
T PRK09637 125 QKEIAEKLGLSLSGAKSRVQRGRVK 149 (181)
T ss_pred HHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 4588999999999998877633333
No 183
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=21.34 E-value=7.3e+02 Score=27.33 Aligned_cols=35 Identities=17% Similarity=0.266 Sum_probs=19.4
Q ss_pred hhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhc
Q 019540 127 NYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 127 ~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~ 161 (339)
..+.|+.+...|.+|..++.+.+.+++.++.+..+
T Consensus 519 ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~~ 553 (604)
T KOG3863|consen 519 EVEKLQKEKEQLLRERDELDSTLGVMKQQLSELYQ 553 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555555555666666666666666554443
No 184
>PRK13919 putative RNA polymerase sigma E protein; Provisional
Probab=21.25 E-value=2.4e+02 Score=24.45 Aligned_cols=27 Identities=26% Similarity=0.209 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
-.++|..+|+++..|+++...-|.+-|
T Consensus 154 ~~eIA~~lgis~~~V~~~l~ra~~~Lr 180 (186)
T PRK13919 154 HREAAQLLGLPLGTLKTRARRALSRLK 180 (186)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 458999999999999987764444333
No 185
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=21.11 E-value=3e+02 Score=22.82 Aligned_cols=43 Identities=37% Similarity=0.546 Sum_probs=24.6
Q ss_pred HHHHhHHHHhhHH-HHhhhhhhhHhHHHHHHHHHHHHHHhhhhh
Q 019540 118 ERDYGVLKANYDA-LKLNYDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 118 e~e~~~lka~~d~-Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~ 160 (339)
+.....|+.+|+. ....-+.+..++..+..|+.+|+.++....
T Consensus 33 E~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~ 76 (87)
T PF12709_consen 33 ETKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTER 76 (87)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555654443 223455666677777777777777665443
No 186
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=20.99 E-value=2.7e+02 Score=29.54 Aligned_cols=75 Identities=19% Similarity=0.301 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHH
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNE 143 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene 143 (339)
+|..+-++| ...|..|.++..-.+.+ ||.|..-..+|..+..--+.+..|+.....+..+|.
T Consensus 242 LTKaEEriL-----------KrvRRKIrNK~SAQESR-------rkKkeYid~LE~rv~~~taeNqeL~kkV~~Le~~N~ 303 (472)
T KOG0709|consen 242 LTKAEERIL-----------KRVRRKIRNKRSAQESR-------RKKKEYIDGLESRVSAFTAENQELQKKVEELELSNR 303 (472)
T ss_pred chHHHHHHH-----------HHHHHHHHhhhhhHHHH-------HhHhhHHHHHhhhhhhcccCcHHHHHHHHHHhhccH
Q ss_pred HHHHHHHHHHHHh
Q 019540 144 ALLKEIRELKSKL 156 (339)
Q Consensus 144 ~L~~E~~~Lk~kl 156 (339)
.|.++++.|+...
T Consensus 304 sLl~qL~klQt~v 316 (472)
T KOG0709|consen 304 SLLAQLKKLQTLV 316 (472)
T ss_pred HHHHHHHHHHHHH
No 187
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.88 E-value=2.2e+02 Score=29.20 Aligned_cols=42 Identities=21% Similarity=0.284 Sum_probs=25.7
Q ss_pred HHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhh
Q 019540 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 118 e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~ 159 (339)
+++.+.+.+..+.++...+.+.....+|+++.++|+.++..-
T Consensus 224 eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L 265 (365)
T KOG2391|consen 224 EEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSL 265 (365)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHH
Confidence 344555555566666666666666666666666666665544
No 188
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=20.88 E-value=1.9e+02 Score=28.82 Aligned_cols=26 Identities=31% Similarity=0.298 Sum_probs=12.2
Q ss_pred hhhhhHhHHHHHHHHHHHHHHhhhhh
Q 019540 135 YDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 135 ~dsl~~ene~L~~E~~~Lk~kl~~~~ 160 (339)
.+.+.-|.+.|.++|++||.+....+
T Consensus 250 ~E~l~ge~~~Le~rN~~LK~qa~~le 275 (294)
T KOG4571|consen 250 KEALLGELEGLEKRNEELKDQASELE 275 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444445555555555444433
No 189
>PHA02955 hypothetical protein; Provisional
Probab=20.86 E-value=1.2e+02 Score=28.84 Aligned_cols=42 Identities=7% Similarity=0.132 Sum_probs=33.3
Q ss_pred HHHHHHHHHHhhhh-cCCCHHHHHHHHHHhCCChHHHhhhhHh
Q 019540 66 VDQVKALEKNFEVE-NKLEPERKVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 66 ~~Ql~~LE~~F~~~-~yPs~~~ReeLA~~LgLserQVqVWFQN 107 (339)
..|+..|-+.|... .-+.+++|.+++++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 46677777777665 5788999999999999998777888863
No 190
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=20.80 E-value=2.8e+02 Score=27.11 Aligned_cols=47 Identities=43% Similarity=0.584 Sum_probs=21.1
Q ss_pred HHHhhhHHHHHHHhHHHHhhHHHHhhhhhhhHhHHHHHHHHHHHHHH
Q 019540 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 109 RaK~Krkq~e~e~~~lka~~d~Lk~~~dsl~~ene~L~~E~~~Lk~k 155 (339)
||-.|.-+.-.++..+|..+..++...+.++.+++.|.+++.+|..+
T Consensus 118 RAGLktL~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e 164 (290)
T COG4026 118 RAGLKTLQRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAE 164 (290)
T ss_pred HHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444433333444444444444444444444444444444444443
No 191
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.74 E-value=1.3e+02 Score=25.79 Aligned_cols=29 Identities=14% Similarity=0.163 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
.-.++|..+|+++..|++++..-|.+.|+
T Consensus 138 s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 138 PQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999988755555554
No 192
>PRK09651 RNA polymerase sigma factor FecI; Provisional
Probab=20.72 E-value=2.2e+02 Score=24.61 Aligned_cols=28 Identities=14% Similarity=0.229 Sum_probs=21.1
Q ss_pred HHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 86 RKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 86 ~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
...+||..+|++...|+++...-+.+.+
T Consensus 137 s~~EIA~~lgis~~tV~~~l~Ra~~~~~ 164 (172)
T PRK09651 137 TYSEIAHKLGVSVSSVKKYVAKATEHCL 164 (172)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 3568999999999999998854444433
No 193
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=20.70 E-value=2e+02 Score=30.63 Aligned_cols=44 Identities=34% Similarity=0.491 Sum_probs=0.0
Q ss_pred HHHHHHHhHHHHhhHHHHhhhhhhhH---------------hHHHHHHHHHHHHHHhhh
Q 019540 115 KQLERDYGVLKANYDALKLNYDSLQH---------------DNEALLKEIRELKSKLNE 158 (339)
Q Consensus 115 kq~e~e~~~lka~~d~Lk~~~dsl~~---------------ene~L~~E~~~Lk~kl~~ 158 (339)
++.+++...+...++.|+.+++.|++ +...+.+|.++|+.++++
T Consensus 69 k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~~~ql~~~~~~ 127 (472)
T TIGR03752 69 KELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKEIEQLKSERQQ 127 (472)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHHHHHHHHHHHH
No 194
>PF11594 Med28: Mediator complex subunit 28; InterPro: IPR021640 Mediator is a large complex of up to 33 proteins that is conserved from plants to fungi to humans - the number and representation of individual subunits varying with species [],[]. It is arranged into four different sections, a core, a head, a tail and a kinase-activity part, and the number of subunits within each of these is what varies with species. Overall, Mediator regulates the transcriptional activity of RNA polymerase II but it would appear that each of the four different sections has a slightly different function []. Subunit Med28 of the Mediator may function as a scaffolding protein within Mediator by maintaining the stability of a submodule within the head module, and components of this submodule act together in a gene-regulatory programme to suppress smooth muscle cell differentiation. Thus, mammalian Mediator subunit Med28 functions as a repressor of smooth muscle-cell differentiation, which could have implications for disorders associated with abnormalities in smooth muscle cell growth and differentiation, including atherosclerosis, asthma, hypertension, and smooth muscle tumours [].
Probab=20.65 E-value=3.5e+02 Score=23.20 Aligned_cols=15 Identities=27% Similarity=0.532 Sum_probs=12.1
Q ss_pred hHHHhhhhHhhHHHh
Q 019540 98 PRQVAVWFQNRRARW 112 (339)
Q Consensus 98 erQVqVWFQNRRaK~ 112 (339)
.||...||-.+|.--
T Consensus 17 aRq~e~~FlqKr~~L 31 (106)
T PF11594_consen 17 ARQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHHH
Confidence 467899999888766
No 195
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.59 E-value=1.6e+02 Score=24.86 Aligned_cols=44 Identities=20% Similarity=0.129 Sum_probs=32.7
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
++..+..+|....+. ..+.+||.+++++.+-|+++..+=|.|-.
T Consensus 150 lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 150 LSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred CCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 777777777643322 45778999999999999998876665543
No 196
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=20.58 E-value=3e+02 Score=29.98 Aligned_cols=35 Identities=31% Similarity=0.319 Sum_probs=24.7
Q ss_pred hhHHHHhhhhhhhHhHHHHHHHHHHHHHHhhhhhc
Q 019540 127 NYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 127 ~~d~Lk~~~dsl~~ene~L~~E~~~Lk~kl~~~~~ 161 (339)
....|...-.++..||+.|++||..||.+|..-..
T Consensus 303 y~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 303 YMLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 44455556667777888888888888888766544
No 197
>PRK08301 sporulation sigma factor SigE; Reviewed
Probab=20.52 E-value=2e+02 Score=26.35 Aligned_cols=50 Identities=20% Similarity=0.221 Sum_probs=31.8
Q ss_pred CCHHHHHHHHHHhhhhcCCCHHHHHHHHHHhCCChHHHhhhhHhhHHHhhh
Q 019540 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~~Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLserQVqVWFQNRRaK~Kr 114 (339)
+++.|..++.-.|... +.....-.++|..+|+++..|+.+...-|.+-|+
T Consensus 179 Lp~~~R~v~~L~y~l~-~~eg~s~~EIA~~lgis~~tVk~~~~rA~~~Lr~ 228 (234)
T PRK08301 179 LSDREKQIMELRFGLN-GGEEKTQKEVADMLGISQSYISRLEKRIIKRLKK 228 (234)
T ss_pred CCHHHHHHHHHHhccC-CCCCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666666555210 0222345689999999999999887644444443
No 198
>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=20.48 E-value=79 Score=20.42 Aligned_cols=23 Identities=22% Similarity=0.387 Sum_probs=19.6
Q ss_pred HHHHHHHhCCChHHHhhhhHhhH
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRR 109 (339)
..++|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999987764
No 199
>PRK12524 RNA polymerase sigma factor; Provisional
Probab=20.42 E-value=2.4e+02 Score=24.94 Aligned_cols=27 Identities=7% Similarity=0.081 Sum_probs=20.9
Q ss_pred HHHHHHHhCCChHHHhhhhHhhHHHhh
Q 019540 87 KVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 87 ReeLA~~LgLserQVqVWFQNRRaK~K 113 (339)
-.+||..+|++...|+.+...-|.+.|
T Consensus 155 ~~eIA~~lgis~~tV~~~l~Ra~~~Lr 181 (196)
T PRK12524 155 NPEIAEVMEIGVEAVESLTARGKRALA 181 (196)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 458999999999999998864444433
No 200
>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=20.23 E-value=86 Score=21.52 Aligned_cols=19 Identities=26% Similarity=0.483 Sum_probs=15.6
Q ss_pred HHHHHHhCCChHHHhhhhH
Q 019540 88 VKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 88 eeLA~~LgLserQVqVWFQ 106 (339)
-++|+.+|++.+.|+.|=+
T Consensus 3 ~e~A~~~gvs~~tlR~ye~ 21 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYER 21 (38)
T ss_dssp HHHHHHHTS-HHHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHHH
Confidence 4789999999999999864
Done!