Query 023113
Match_columns 287
No_of_seqs 379 out of 1692
Neff 5.9
Searched_HMMs 46136
Date Fri Mar 29 08:32:01 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/023113.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/023113hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 5E-27 1.1E-31 208.2 12.3 121 127-247 49-169 (198)
2 PF04618 HD-ZIP_N: HD-ZIP prot 99.8 5.6E-20 1.2E-24 149.3 6.8 101 1-101 1-110 (111)
3 KOG0488 Transcription factor B 99.7 9E-18 2E-22 158.6 6.8 64 126-189 170-233 (309)
4 KOG0489 Transcription factor z 99.7 7.3E-18 1.6E-22 155.9 4.7 63 126-188 157-219 (261)
5 KOG0485 Transcription factor N 99.7 1.4E-16 3E-21 142.0 11.4 61 127-187 103-163 (268)
6 KOG0484 Transcription factor P 99.7 1.3E-17 2.8E-22 133.2 4.0 62 126-187 15-76 (125)
7 KOG0487 Transcription factor A 99.7 2.2E-17 4.8E-22 154.9 3.9 64 126-189 233-296 (308)
8 KOG0842 Transcription factor t 99.7 3.3E-17 7.1E-22 153.7 5.1 69 126-194 151-219 (307)
9 KOG0843 Transcription factor E 99.7 6.1E-17 1.3E-21 140.5 5.4 64 127-190 101-164 (197)
10 KOG2251 Homeobox transcription 99.6 1.5E-16 3.2E-21 142.1 5.2 67 123-189 32-98 (228)
11 KOG0494 Transcription factor C 99.6 4E-16 8.7E-21 142.1 6.9 69 130-198 143-211 (332)
12 PF00046 Homeobox: Homeobox do 99.6 4.5E-16 9.8E-21 111.1 5.6 57 129-185 1-57 (57)
13 KOG0850 Transcription factor D 99.6 1.8E-15 3.9E-20 135.8 7.3 61 127-187 121-181 (245)
14 KOG0492 Transcription factor M 99.6 1.1E-15 2.5E-20 135.3 5.9 61 127-187 143-203 (246)
15 KOG4577 Transcription factor L 99.5 3.2E-14 7E-19 131.4 9.7 112 124-235 163-284 (383)
16 KOG0848 Transcription factor C 99.5 6E-15 1.3E-19 134.9 3.1 57 132-188 203-259 (317)
17 cd00086 homeodomain Homeodomai 99.5 3.8E-14 8.3E-19 100.9 5.8 57 130-186 2-58 (59)
18 smart00389 HOX Homeodomain. DN 99.5 3.4E-14 7.3E-19 100.6 5.2 55 130-184 2-56 (56)
19 KOG0844 Transcription factor E 99.5 2E-14 4.3E-19 133.6 4.6 64 127-190 180-243 (408)
20 KOG0493 Transcription factor E 99.5 2.9E-14 6.4E-19 130.1 4.9 62 128-189 246-307 (342)
21 COG5576 Homeodomain-containing 99.4 1.2E-13 2.6E-18 118.9 6.1 67 123-189 46-112 (156)
22 TIGR01565 homeo_ZF_HD homeobox 99.4 1.2E-13 2.6E-18 100.3 5.0 52 129-180 2-57 (58)
23 KOG0486 Transcription factor P 99.4 1.9E-13 4E-18 127.6 5.9 65 127-191 111-175 (351)
24 KOG3802 Transcription factor O 99.4 1.6E-13 3.4E-18 131.8 4.2 66 122-187 288-353 (398)
25 KOG0491 Transcription factor B 99.4 1E-13 2.2E-18 119.1 1.5 63 127-189 99-161 (194)
26 KOG0847 Transcription factor, 99.3 1.4E-12 3E-17 116.7 2.8 61 127-187 166-226 (288)
27 smart00340 HALZ homeobox assoc 99.2 1.7E-11 3.7E-16 82.4 4.5 44 186-229 1-44 (44)
28 KOG0490 Transcription factor, 99.2 1.1E-11 2.4E-16 110.5 3.5 62 126-187 58-119 (235)
29 KOG0490 Transcription factor, 99.1 9.3E-11 2E-15 104.6 5.7 132 57-188 70-213 (235)
30 KOG0849 Transcription factor P 99.0 2.4E-10 5.2E-15 110.2 5.2 64 125-188 173-236 (354)
31 KOG1168 Transcription factor A 98.8 3.2E-09 6.9E-14 98.7 3.0 63 125-187 306-368 (385)
32 KOG0775 Transcription factor S 98.6 2.6E-08 5.6E-13 92.0 4.5 51 135-185 183-233 (304)
33 KOG0774 Transcription factor P 98.6 1.2E-07 2.5E-12 87.3 8.4 60 127-186 187-249 (334)
34 PF05920 Homeobox_KN: Homeobox 98.2 6.6E-07 1.4E-11 60.3 2.4 34 149-182 7-40 (40)
35 KOG2252 CCAAT displacement pro 97.9 1.2E-05 2.5E-10 80.7 5.2 58 127-184 419-476 (558)
36 KOG1146 Homeobox protein [Gene 97.3 0.00014 3E-09 79.2 3.6 62 127-188 902-963 (1406)
37 PF02183 HALZ: Homeobox associ 97.0 0.001 2.2E-08 46.0 4.1 36 186-221 1-36 (45)
38 PF11569 Homez: Homeodomain le 96.7 0.0011 2.3E-08 48.0 2.1 42 140-181 10-51 (56)
39 KOG0773 Transcription factor M 96.2 0.0045 9.7E-08 59.2 4.0 59 128-186 239-300 (342)
40 PRK09413 IS2 repressor TnpA; R 94.3 0.35 7.7E-06 39.6 8.7 79 131-214 9-102 (121)
41 COG5576 Homeodomain-containing 94.0 0.014 3.1E-07 50.5 -0.2 45 58-102 62-107 (156)
42 PF04218 CENP-B_N: CENP-B N-te 93.7 0.14 3.1E-06 36.2 4.5 47 129-180 1-47 (53)
43 KOG3623 Homeobox transcription 93.0 0.11 2.3E-06 54.6 4.2 48 140-187 568-615 (1007)
44 KOG4196 bZIP transcription fac 92.5 0.97 2.1E-05 38.1 8.4 74 133-218 22-109 (135)
45 smart00389 HOX Homeodomain. DN 91.9 0.0087 1.9E-07 41.7 -3.8 44 57-100 10-54 (56)
46 KOG2251 Homeobox transcription 91.0 0.057 1.2E-06 49.1 -0.4 46 58-103 48-94 (228)
47 cd00086 homeodomain Homeodomai 90.6 0.0072 1.6E-07 42.3 -5.3 45 57-101 10-55 (59)
48 PF02183 HALZ: Homeobox associ 90.6 0.6 1.3E-05 32.2 4.5 31 188-218 10-40 (45)
49 KOG0849 Transcription factor P 90.0 0.099 2.1E-06 50.8 0.3 48 57-104 186-234 (354)
50 PF00046 Homeobox: Homeobox do 86.1 0.0069 1.5E-07 42.6 -7.9 42 57-98 10-52 (57)
51 TIGR01565 homeo_ZF_HD homeobox 85.6 0.14 3.1E-06 37.2 -1.2 41 58-98 12-57 (58)
52 PRK00888 ftsB cell division pr 84.7 2 4.3E-05 34.7 4.9 47 170-217 15-61 (105)
53 PF01527 HTH_Tnp_1: Transposas 83.6 0.4 8.7E-06 35.3 0.4 47 130-180 2-48 (76)
54 KOG0775 Transcription factor S 83.0 0.57 1.2E-05 44.1 1.2 67 38-104 166-234 (304)
55 KOG3119 Basic region leucine z 80.8 4.8 0.0001 37.7 6.5 35 187-221 219-253 (269)
56 KOG0486 Transcription factor P 80.3 0.7 1.5E-05 44.3 0.8 49 58-106 123-172 (351)
57 KOG0492 Transcription factor M 77.4 0.34 7.4E-06 44.0 -2.1 54 58-111 155-209 (246)
58 KOG0494 Transcription factor C 76.0 0.43 9.2E-06 44.7 -2.0 45 58-102 152-197 (332)
59 KOG0850 Transcription factor D 75.8 0.6 1.3E-05 42.9 -1.0 44 58-101 133-177 (245)
60 KOG0843 Transcription factor E 74.2 0.63 1.4E-05 41.4 -1.3 46 58-103 113-159 (197)
61 PF04545 Sigma70_r4: Sigma-70, 74.1 5.6 0.00012 27.0 3.7 41 134-179 4-44 (50)
62 KOG0484 Transcription factor P 71.8 0.24 5.1E-06 40.4 -4.1 45 58-102 28-73 (125)
63 PF04967 HTH_10: HTH DNA bindi 71.1 4.8 0.0001 28.7 2.8 39 135-173 1-41 (53)
64 KOG0842 Transcription factor t 70.3 1.4 3.1E-05 42.2 0.0 46 58-103 164-210 (307)
65 PF00170 bZIP_1: bZIP transcri 70.3 17 0.00038 26.2 5.8 25 193-217 29-53 (64)
66 cd06171 Sigma70_r4 Sigma70, re 69.4 4.5 9.8E-05 26.3 2.4 44 134-182 10-53 (55)
67 PF07716 bZIP_2: Basic region 67.3 20 0.00044 25.1 5.5 27 191-217 26-52 (54)
68 PF06156 DUF972: Protein of un 63.9 15 0.00032 29.9 4.8 34 186-219 18-51 (107)
69 KOG3623 Homeobox transcription 63.4 1 2.3E-05 47.6 -2.5 117 59-187 568-685 (1007)
70 KOG3335 Predicted coiled-coil 62.7 33 0.00071 30.5 6.9 51 167-217 83-133 (181)
71 PF13443 HTH_26: Cro/C1-type H 61.3 7.9 0.00017 27.2 2.5 33 157-189 12-44 (63)
72 PF00170 bZIP_1: bZIP transcri 61.2 33 0.00072 24.7 5.8 35 184-218 27-61 (64)
73 cd00569 HTH_Hin_like Helix-tur 60.7 18 0.00038 20.8 3.7 38 134-176 5-42 (42)
74 smart00338 BRLZ basic region l 60.7 31 0.00067 24.8 5.6 26 192-217 28-53 (65)
75 KOG2483 Upstream transcription 60.7 74 0.0016 29.4 9.2 39 179-217 101-139 (232)
76 smart00338 BRLZ basic region l 60.3 34 0.00074 24.6 5.7 35 185-219 28-62 (65)
77 PF07716 bZIP_2: Basic region 59.6 26 0.00056 24.5 4.8 25 188-212 30-54 (54)
78 PF01166 TSC22: TSC-22/dip/bun 59.0 21 0.00045 26.1 4.2 32 189-220 13-44 (59)
79 PRK03975 tfx putative transcri 58.4 23 0.0005 30.2 5.2 48 132-185 4-51 (141)
80 KOG0493 Transcription factor E 56.6 1.3 2.8E-05 41.6 -2.9 44 58-101 257-301 (342)
81 PF10668 Phage_terminase: Phag 56.4 6 0.00013 29.0 1.1 19 158-176 25-43 (60)
82 KOG0848 Transcription factor C 55.6 2.4 5.1E-05 40.0 -1.4 45 58-102 210-255 (317)
83 PF06005 DUF904: Protein of un 55.0 42 0.00092 25.3 5.6 29 189-217 24-52 (72)
84 TIGR02209 ftsL_broad cell divi 55.0 33 0.00071 25.7 5.1 31 187-217 28-58 (85)
85 KOG4571 Activating transcripti 54.7 28 0.0006 33.2 5.5 32 188-219 253-284 (294)
86 PRK13169 DNA replication intia 54.7 27 0.00059 28.6 4.8 34 186-219 18-51 (110)
87 PF04977 DivIC: Septum formati 54.6 32 0.00069 25.2 4.9 30 187-216 21-50 (80)
88 COG3413 Predicted DNA binding 53.2 19 0.00042 32.0 4.1 49 134-184 155-205 (215)
89 KOG4571 Activating transcripti 52.4 29 0.00062 33.1 5.2 31 187-217 245-275 (294)
90 PF09607 BrkDBD: Brinker DNA-b 52.3 21 0.00046 26.0 3.4 44 132-177 3-47 (58)
91 PF14197 Cep57_CLD_2: Centroso 52.3 51 0.0011 24.7 5.6 26 192-217 42-67 (69)
92 KOG0844 Transcription factor E 52.3 4.2 9.1E-05 39.1 -0.3 45 58-102 192-237 (408)
93 PF08281 Sigma70_r4_2: Sigma-7 52.3 28 0.00061 23.6 4.0 42 135-181 11-52 (54)
94 KOG1924 RhoA GTPase effector D 51.1 2.1E+02 0.0046 31.3 11.7 27 187-213 471-497 (1102)
95 PF07407 Seadorna_VP6: Seadorn 48.3 23 0.00049 34.6 3.9 25 193-217 35-59 (420)
96 PRK13922 rod shape-determining 48.3 31 0.00068 31.8 4.8 34 186-219 72-108 (276)
97 KOG0487 Transcription factor A 47.8 2.4 5.1E-05 40.7 -2.8 45 58-102 246-291 (308)
98 cd04787 HTH_HMRTR_unk Helix-Tu 47.6 1.1E+02 0.0024 25.2 7.6 71 132-217 36-106 (133)
99 PF00196 GerE: Bacterial regul 47.6 29 0.00062 24.2 3.5 46 134-185 3-48 (58)
100 TIGR02449 conserved hypothetic 46.1 53 0.0011 24.5 4.7 25 192-216 9-33 (65)
101 PF08961 DUF1875: Domain of un 45.7 6.9 0.00015 35.9 0.0 39 183-221 122-160 (243)
102 PF06005 DUF904: Protein of un 45.7 61 0.0013 24.5 5.2 24 190-213 32-55 (72)
103 PRK14127 cell division protein 44.7 50 0.0011 27.0 4.8 44 166-218 22-65 (109)
104 PF10883 DUF2681: Protein of u 42.8 63 0.0014 25.4 5.0 38 173-217 20-57 (87)
105 KOG4005 Transcription factor X 41.8 57 0.0012 30.5 5.3 23 195-217 116-138 (292)
106 PF13936 HTH_38: Helix-turn-he 41.6 24 0.00051 23.7 2.2 40 132-176 2-41 (44)
107 PF12824 MRP-L20: Mitochondria 41.4 1.8E+02 0.0038 25.4 8.1 45 131-177 82-126 (164)
108 PF04999 FtsL: Cell division p 41.0 72 0.0016 24.7 5.2 28 190-217 42-69 (97)
109 KOG4005 Transcription factor X 40.4 58 0.0013 30.4 5.1 9 177-185 82-90 (292)
110 PRK00888 ftsB cell division pr 40.1 55 0.0012 26.3 4.4 39 173-211 24-62 (105)
111 smart00421 HTH_LUXR helix_turn 39.9 50 0.0011 21.6 3.7 41 134-180 3-43 (58)
112 cd01106 HTH_TipAL-Mta Helix-Tu 39.8 1.8E+02 0.0039 22.6 7.7 64 132-216 36-99 (103)
113 COG3074 Uncharacterized protei 39.2 88 0.0019 23.8 5.0 17 196-212 45-61 (79)
114 PRK04217 hypothetical protein; 38.7 55 0.0012 26.7 4.3 45 133-182 41-85 (110)
115 COG3074 Uncharacterized protei 38.7 72 0.0016 24.3 4.5 32 186-217 14-45 (79)
116 KOG0485 Transcription factor N 38.6 4.2 9.1E-05 37.3 -2.5 44 58-101 115-159 (268)
117 cd01109 HTH_YyaN Helix-Turn-He 38.3 1.8E+02 0.0038 23.1 7.2 71 132-217 36-106 (113)
118 KOG1146 Homeobox protein [Gene 38.2 44 0.00095 38.0 4.6 62 128-189 705-766 (1406)
119 TIGR00219 mreC rod shape-deter 38.2 57 0.0012 30.7 4.9 34 186-219 69-106 (283)
120 KOG0488 Transcription factor B 37.6 4.7 0.0001 38.6 -2.5 47 58-104 183-230 (309)
121 COG2963 Transposase and inacti 37.6 2E+02 0.0044 22.6 7.8 45 132-180 5-50 (116)
122 PRK15422 septal ring assembly 37.0 84 0.0018 24.4 4.7 26 190-215 18-43 (79)
123 cd04766 HTH_HspR Helix-Turn-He 36.5 1.4E+02 0.0031 22.7 6.1 22 158-179 4-25 (91)
124 PF01486 K-box: K-box region; 36.1 61 0.0013 25.4 4.1 44 170-214 56-99 (100)
125 PF08826 DMPK_coil: DMPK coile 35.9 1.5E+02 0.0032 21.8 5.7 27 192-218 34-60 (61)
126 PF07989 Microtub_assoc: Micro 35.8 86 0.0019 23.8 4.7 44 172-218 21-64 (75)
127 cd04761 HTH_MerR-SF Helix-Turn 35.2 23 0.0005 23.3 1.3 23 158-180 3-25 (49)
128 KOG4343 bZIP transcription fac 35.1 65 0.0014 33.4 5.0 26 192-217 311-336 (655)
129 PRK06759 RNA polymerase factor 34.9 73 0.0016 25.9 4.6 46 134-184 106-151 (154)
130 PRK00118 putative DNA-binding 34.8 1.8E+02 0.004 23.4 6.7 45 135-184 18-62 (104)
131 KOG3755 SATB1 matrix attachmen 34.5 15 0.00033 38.3 0.5 46 144-189 708-760 (769)
132 PF15058 Speriolin_N: Sperioli 34.2 52 0.0011 29.7 3.7 24 192-215 7-30 (200)
133 TIGR02937 sigma70-ECF RNA poly 34.0 66 0.0014 25.1 4.1 46 134-184 110-155 (158)
134 cd04770 HTH_HMRTR Helix-Turn-H 33.9 2.5E+02 0.0053 22.5 7.9 72 132-218 36-107 (123)
135 KOG0489 Transcription factor z 33.9 4.2 9.1E-05 37.8 -3.4 45 58-102 170-215 (261)
136 PF13518 HTH_28: Helix-turn-he 33.7 32 0.0007 22.9 1.9 22 158-179 15-36 (52)
137 PF08280 HTH_Mga: M protein tr 33.6 45 0.00097 23.6 2.7 33 138-174 6-38 (59)
138 KOG4797 Transcriptional regula 33.5 73 0.0016 26.2 4.1 33 188-220 65-97 (123)
139 PHA02955 hypothetical protein; 33.3 51 0.0011 30.1 3.6 42 137-178 60-102 (213)
140 TIGR00721 tfx DNA-binding prot 32.8 1.4E+02 0.0031 25.3 6.0 48 132-185 4-51 (137)
141 PRK12514 RNA polymerase sigma 32.7 47 0.001 28.0 3.2 46 135-185 130-175 (179)
142 TIGR03879 near_KaiC_dom probab 32.3 15 0.00033 27.9 0.0 34 145-178 22-55 (73)
143 COG4367 Uncharacterized protei 32.2 49 0.0011 26.3 2.8 40 134-173 2-41 (97)
144 PF15136 UPF0449: Uncharacteri 32.0 1.2E+02 0.0026 24.4 5.1 29 187-215 68-96 (97)
145 TIGR02051 MerR Hg(II)-responsi 31.8 2.7E+02 0.0058 22.6 7.4 70 132-218 35-104 (124)
146 PRK09646 RNA polymerase sigma 31.7 68 0.0015 27.6 4.0 46 134-184 142-187 (194)
147 COG4467 Regulator of replicati 31.5 85 0.0018 25.8 4.2 32 187-218 19-50 (114)
148 PF08172 CASP_C: CASP C termin 31.5 1E+02 0.0023 28.6 5.4 37 180-216 90-126 (248)
149 PRK13922 rod shape-determining 31.3 73 0.0016 29.4 4.4 30 191-220 70-99 (276)
150 PF12808 Mto2_bdg: Micro-tubul 30.9 1.2E+02 0.0026 21.6 4.4 28 191-218 23-50 (52)
151 PRK11924 RNA polymerase sigma 30.9 49 0.0011 27.3 2.9 46 135-185 126-171 (179)
152 PRK09652 RNA polymerase sigma 30.9 49 0.0011 27.4 3.0 45 134-183 128-172 (182)
153 PF06210 DUF1003: Protein of u 30.4 1.2E+02 0.0026 24.7 5.0 37 177-217 57-93 (108)
154 PF06785 UPF0242: Uncharacteri 30.0 1.1E+02 0.0024 30.0 5.4 39 179-217 137-175 (401)
155 cd04779 HTH_MerR-like_sg4 Heli 30.0 2.9E+02 0.0062 23.1 7.4 72 132-216 35-107 (134)
156 PRK10072 putative transcriptio 29.2 29 0.00062 27.6 1.1 41 134-181 32-72 (96)
157 PF12269 zf-CpG_bind_C: CpG bi 29.0 1.8E+02 0.0038 27.1 6.3 76 169-244 10-93 (236)
158 KOG0999 Microtubule-associated 28.6 88 0.0019 32.7 4.7 44 174-217 147-190 (772)
159 PF03980 Nnf1: Nnf1 ; InterPr 28.5 99 0.0021 24.5 4.2 29 190-218 80-108 (109)
160 PF10226 DUF2216: Uncharacteri 28.3 1.1E+02 0.0024 27.5 4.7 19 199-217 57-75 (195)
161 cd04781 HTH_MerR-like_sg6 Heli 28.3 2.9E+02 0.0063 22.2 7.0 69 131-218 34-102 (120)
162 TIGR03752 conj_TIGR03752 integ 27.1 88 0.0019 31.9 4.4 10 134-143 41-50 (472)
163 cd04783 HTH_MerR1 Helix-Turn-H 27.1 3.4E+02 0.0073 21.9 7.6 70 132-218 36-105 (126)
164 cd06170 LuxR_C_like C-terminal 26.9 1.1E+02 0.0023 20.1 3.6 36 136-177 2-37 (57)
165 PF02796 HTH_7: Helix-turn-hel 26.8 74 0.0016 21.2 2.7 38 134-176 5-42 (45)
166 PF05377 FlaC_arch: Flagella a 26.6 1.6E+02 0.0035 21.3 4.5 25 192-216 16-40 (55)
167 PRK10884 SH3 domain-containing 26.5 1.8E+02 0.0038 26.3 5.8 69 137-218 99-167 (206)
168 PRK15369 two component system 26.4 1.5E+02 0.0033 24.0 5.2 47 133-185 148-194 (211)
169 PF06056 Terminase_5: Putative 26.2 38 0.00083 24.3 1.2 20 158-177 16-35 (58)
170 PF06305 DUF1049: Protein of u 26.1 68 0.0015 22.9 2.6 13 204-216 55-67 (68)
171 PF13384 HTH_23: Homeodomain-l 26.1 39 0.00084 22.5 1.2 23 156-178 18-40 (50)
172 PRK12519 RNA polymerase sigma 25.9 58 0.0013 27.8 2.6 46 135-185 142-187 (194)
173 KOG3119 Basic region leucine z 25.6 1.4E+02 0.003 28.0 5.1 37 179-218 207-243 (269)
174 PF13411 MerR_1: MerR HTH fami 25.6 41 0.00089 23.9 1.3 21 158-178 3-23 (69)
175 PF10224 DUF2205: Predicted co 25.6 1.2E+02 0.0027 23.4 4.0 22 195-216 42-63 (80)
176 PF09278 MerR-DNA-bind: MerR, 25.5 1.9E+02 0.0041 20.2 4.8 18 160-177 8-25 (65)
177 TIGR02985 Sig70_bacteroi1 RNA 25.4 71 0.0015 25.7 2.9 44 135-183 114-157 (161)
178 smart00027 EH Eps15 homology d 25.4 1.2E+02 0.0026 23.1 4.1 43 135-177 4-51 (96)
179 PF09726 Macoilin: Transmembra 25.3 1.2E+02 0.0027 32.3 5.3 38 182-219 544-581 (697)
180 PRK10403 transcriptional regul 25.3 99 0.0021 25.5 3.8 46 134-185 153-198 (215)
181 PRK12526 RNA polymerase sigma 25.3 71 0.0015 27.9 3.1 46 135-185 154-199 (206)
182 PF14775 NYD-SP28_assoc: Sperm 25.2 2.7E+02 0.0058 20.2 5.6 19 201-219 37-55 (60)
183 PRK15422 septal ring assembly 25.1 1.9E+02 0.0042 22.4 4.9 19 195-213 44-62 (79)
184 COG2919 Septum formation initi 25.0 1.7E+02 0.0036 23.8 5.0 27 191-217 58-84 (117)
185 PRK10360 DNA-binding transcrip 24.0 81 0.0018 26.0 3.1 45 134-184 137-181 (196)
186 PF11365 DUF3166: Protein of u 24.0 1.5E+02 0.0032 23.8 4.3 31 189-219 14-44 (96)
187 cd04766 HTH_HspR Helix-Turn-He 23.9 2.8E+02 0.0061 21.0 5.9 33 132-176 36-68 (91)
188 PF07407 Seadorna_VP6: Seadorn 23.6 92 0.002 30.5 3.6 28 187-214 36-63 (420)
189 KOG4403 Cell surface glycoprot 23.3 1.6E+02 0.0035 30.0 5.3 26 173-198 229-257 (575)
190 PRK14872 rod shape-determining 23.2 1.2E+02 0.0026 29.6 4.4 26 191-216 58-83 (337)
191 TIGR02989 Sig-70_gvs1 RNA poly 23.2 1.4E+02 0.0031 24.2 4.4 44 134-182 111-154 (159)
192 PRK12512 RNA polymerase sigma 23.0 97 0.0021 26.1 3.4 47 134-185 131-177 (184)
193 KOG4343 bZIP transcription fac 22.7 1.5E+02 0.0032 30.9 5.0 25 193-217 305-329 (655)
194 cd04775 HTH_Cfa-like Helix-Tur 22.7 3.7E+02 0.0081 20.9 7.5 64 132-218 36-99 (102)
195 PRK09642 RNA polymerase sigma 22.6 74 0.0016 26.1 2.5 46 135-185 107-152 (160)
196 cd08315 Death_TRAILR_DR4_DR5 D 22.5 2.1E+02 0.0045 22.5 4.9 35 140-174 3-38 (96)
197 PF11594 Med28: Mediator compl 22.4 1.8E+02 0.004 23.7 4.6 15 170-184 18-32 (106)
198 TIGR02948 SigW_bacill RNA poly 22.3 1.4E+02 0.003 25.0 4.2 46 134-184 136-181 (187)
199 cd04762 HTH_MerR-trunc Helix-T 22.1 55 0.0012 20.8 1.3 25 158-182 3-27 (49)
200 TIGR02209 ftsL_broad cell divi 21.9 1.9E+02 0.0041 21.5 4.5 41 171-211 19-59 (85)
201 cd04763 HTH_MlrA-like Helix-Tu 21.8 54 0.0012 23.5 1.3 21 158-178 3-23 (68)
202 TIGR02894 DNA_bind_RsfA transc 21.7 1.7E+02 0.0037 25.6 4.6 32 186-217 100-131 (161)
203 PRK10869 recombination and rep 21.5 5.2E+02 0.011 26.7 8.9 59 159-217 309-368 (553)
204 cd04764 HTH_MlrA-like_sg1 Heli 21.4 57 0.0012 23.2 1.4 21 158-178 3-23 (67)
205 PRK10651 transcriptional regul 21.3 1.8E+02 0.0039 24.0 4.7 46 134-185 155-200 (216)
206 PRK05602 RNA polymerase sigma 21.2 1.1E+02 0.0025 25.8 3.5 45 135-184 129-173 (186)
207 PF02591 DUF164: Putative zinc 21.2 35 0.00076 24.0 0.2 22 223-244 34-55 (56)
208 PRK06986 fliA flagellar biosyn 20.9 99 0.0022 27.6 3.2 46 135-185 185-230 (236)
209 PF13551 HTH_29: Winged helix- 20.8 1.9E+02 0.0041 22.0 4.4 44 134-177 57-109 (112)
210 PRK09648 RNA polymerase sigma 20.6 1.3E+02 0.0029 25.4 3.8 43 134-181 139-181 (189)
211 PF10224 DUF2205: Predicted co 20.6 3.2E+02 0.0069 21.1 5.4 33 186-218 26-58 (80)
212 PRK10100 DNA-binding transcrip 20.6 2.1E+02 0.0045 25.5 5.2 46 134-185 155-200 (216)
213 KOG0709 CREB/ATF family transc 20.5 2.7E+02 0.0057 28.5 6.2 81 135-238 242-329 (472)
214 PF01381 HTH_3: Helix-turn-hel 20.3 52 0.0011 22.1 1.0 23 158-180 12-34 (55)
215 PF08279 HTH_11: HTH domain; 20.3 1.1E+02 0.0023 20.8 2.5 32 139-173 2-33 (55)
216 PRK09639 RNA polymerase sigma 20.1 1.7E+02 0.0036 24.1 4.2 45 134-184 112-156 (166)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.94 E-value=5e-27 Score=208.21 Aligned_cols=121 Identities=50% Similarity=0.664 Sum_probs=114.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHH
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEEN 206 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en 206 (287)
...+++.+|+.+|+..||..|+.+.++.+.++..||++|||.++||+|||||||||||.++.+.+|++||.+++.|+.++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35667788999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHhhhcChhhhccCCCCCCCCCCCCCCCCCcC
Q 023113 207 RRLQKEVQELRSLKLSPQLYMNMNPPTTLTMCPSCERVAVS 247 (287)
Q Consensus 207 ~~l~~e~~~lr~l~~~~~~~~~~~~~~~~~~c~sc~~~~~~ 247 (287)
++|+.|+.+|++++.....++++.+..+..+|++|+.+...
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQKSPENTLTMCPNSESSSSV 169 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhccCcccccccCccccccCCc
Confidence 99999999999999999999999999999999999965554
No 2
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=99.80 E-value=5.6e-20 Score=149.29 Aligned_cols=101 Identities=58% Similarity=0.869 Sum_probs=78.3
Q ss_pred CCCCCCCccceeecCCCCCC----CCCCcccCCCCCcccc-c--cCCCCCCCCCccCCCCCCcchhhhhhhccCCCCCCC
Q 023113 1 MGEKDDGLGLSLSLGCAARN----EPSLRLNHMPLSSSQS-M--QNHHKRSPWTELFHSSDRNSDTRSFLRGIDVNQAPT 73 (287)
Q Consensus 1 ~~~~~~~~~~~~~~~~~~~~----~~p~~~~~~p~~~~~~-~--~~~~~~~~w~~~~~~~~~~~q~~~l~~~fd~n~~P~ 73 (287)
|++++|||||||||||+.++ .+|++++|+|..+... . ...+....|...+...+...+.+.|++|||||++|.
T Consensus 1 m~~~~d~LGLsLSLg~~~~~~~~~~~plql~L~P~s~p~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~flRgiDVNr~p~ 80 (111)
T PF04618_consen 1 MMEKKDGLGLSLSLGFAGNRHPSQQPPLQLNLLPSSSPSNSHPLFSSHNQPFWSDDRMMASCDSETRSFLRGIDVNRLPS 80 (111)
T ss_pred CCCCCCcceeeeeccCCCCCCCccCCCcccccCCccccccccCccccccccCCccccccccccccccccccceeccCCCc
Confidence 88888999999999999553 6799999999986211 1 112223334444444455557788999999999999
Q ss_pred cc--ccccccCCCCCCCCcccCCCCCCCCC
Q 023113 74 VA--DCEEENGVSSPNSTVSSISGKRSERE 101 (287)
Q Consensus 74 ~a--~~e~~~~~ssp~s~i~s~~~~~s~r~ 101 (287)
.+ +||++++++||||+|++.+|++++++
T Consensus 81 ~~~~d~eEe~gvSSPNStiSS~sgkr~~~~ 110 (111)
T PF04618_consen 81 TVEADCEEEAGVSSPNSTISSVSGKRSERE 110 (111)
T ss_pred cccccccccccccCCCccceeccccccccc
Confidence 88 99999999999999999999988765
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=9e-18 Score=158.62 Aligned_cols=64 Identities=31% Similarity=0.509 Sum_probs=59.7
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
+|+|+.||.||..|+..||+.|++.+|++..+|++||++|||+..||++||||||+|||++..+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 5667779999999999999999999999999999999999999999999999999999996533
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=7.3e-18 Score=155.89 Aligned_cols=63 Identities=33% Similarity=0.606 Sum_probs=59.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhh
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 188 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~ 188 (287)
++.||.||.||..|+.+||+.|..|+|++...|.+||..|.|+++||||||||||+||||...
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 367889999999999999999999999999999999999999999999999999999999543
No 5
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.69 E-value=1.4e-16 Score=141.96 Aligned_cols=61 Identities=33% Similarity=0.518 Sum_probs=57.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
++||.||.|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 5566688999999999999999999999999999999999999999999999999999953
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.69 E-value=1.3e-17 Score=133.24 Aligned_cols=62 Identities=27% Similarity=0.427 Sum_probs=59.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
++.||-|+.||..|+..||+.|.+.+||++..|++||.++.|++.+|||||||||+|.+++.
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 57788899999999999999999999999999999999999999999999999999999854
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.67 E-value=2.2e-17 Score=154.88 Aligned_cols=64 Identities=36% Similarity=0.583 Sum_probs=60.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
+..||||.-+|+.|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||+|+||...+
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 6788999999999999999999999999999999999999999999999999999999996643
No 8
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=3.3e-17 Score=153.67 Aligned_cols=69 Identities=33% Similarity=0.549 Sum_probs=62.2
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHH
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEY 194 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~ 194 (287)
+++||.|.-|+..|+.+||+.|+..+|++..+|+.||..|+|+++||||||||||-|.||++.....+.
T Consensus 151 ~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 151 RKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred ccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 455566677999999999999999999999999999999999999999999999999999887765544
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.66 E-value=6.1e-17 Score=140.55 Aligned_cols=64 Identities=36% Similarity=0.509 Sum_probs=60.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 190 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~ 190 (287)
+.||.||.||.+|+..||..|+.+.|....+|++||..|+|++.||+|||||||+|.||++.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 5788899999999999999999999999999999999999999999999999999999987663
No 10
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.64 E-value=1.5e-16 Score=142.10 Aligned_cols=67 Identities=30% Similarity=0.494 Sum_probs=62.8
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 123 GGAGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 123 ~~~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
.+.++.||.||+|+..|+++||..|.+..||+...|++||.+|+|.+.+|+|||.|||+|+|+++..
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 4456889999999999999999999999999999999999999999999999999999999997654
No 11
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.63 E-value=4e-16 Score=142.08 Aligned_cols=69 Identities=25% Similarity=0.295 Sum_probs=61.1
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHH
Q 023113 130 RKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRC 198 (287)
Q Consensus 130 rkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~ 198 (287)
+-||.||..|+..||+.|++.+||+...|+.||.++.|.+.+|+|||||||+||||++.+-.-...-.+
T Consensus 143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~mae 211 (332)
T KOG0494|consen 143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTIMAE 211 (332)
T ss_pred cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchhhhh
Confidence 338999999999999999999999999999999999999999999999999999998766554443333
No 12
>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=99.63 E-value=4.5e-16 Score=111.12 Aligned_cols=57 Identities=46% Similarity=0.676 Sum_probs=55.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 129 SRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 129 rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
||+|+.||.+|+.+|+..|..++||+..+++.||.+|||+..+|++||+|||+++|+
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 578999999999999999999999999999999999999999999999999999985
No 13
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.59 E-value=1.8e-15 Score=135.81 Aligned_cols=61 Identities=30% Similarity=0.437 Sum_probs=57.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
|.|+.||.|+.-||..|.+.|+++.|+-..+|.+||..|||+..||||||||||.|.||..
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~ 181 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLK 181 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHH
Confidence 4566699999999999999999999999999999999999999999999999999999843
No 14
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.59 E-value=1.1e-15 Score=135.28 Aligned_cols=61 Identities=33% Similarity=0.556 Sum_probs=57.6
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
..|+.|+.||..|+..||+.|++.+|+++++|.+++..|.|++.||+|||||||+|.||-|
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 3567799999999999999999999999999999999999999999999999999999955
No 15
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.53 E-value=3.2e-14 Score=131.37 Aligned_cols=112 Identities=21% Similarity=0.307 Sum_probs=84.1
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhh-
Q 023113 124 GAGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENL- 202 (287)
Q Consensus 124 ~~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l- 202 (287)
+....||.||++|..|++.|+.+|+..+.|-...|++|+.++||.-+.|||||||||||+||-++.......-+.+..+
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK 242 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK 242 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence 3346789999999999999999999999999999999999999999999999999999999877665554442222222
Q ss_pred -----HHHHHHHHHH----HHHHHhhhcChhhhccCCCCCCC
Q 023113 203 -----TEENRRLQKE----VQELRSLKLSPQLYMNMNPPTTL 235 (287)
Q Consensus 203 -----~~en~~l~~e----~~~lr~l~~~~~~~~~~~~~~~~ 235 (287)
+.|++.-..| .+.|..+...+.+|..+..++..
T Consensus 243 ~sgs~r~ekdsd~sel~~~~dslse~~~~N~lYg~l~~~~d~ 284 (383)
T KOG4577|consen 243 RSGSSRAEKDSDDSELSFINDSLSEHGSPNYLYGTLGHPTDD 284 (383)
T ss_pred ccCCcccccccccCccccccchhhhcCCccccccccCCcccC
Confidence 2333332222 23444556667778777777765
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.51 E-value=6e-15 Score=134.92 Aligned_cols=57 Identities=35% Similarity=0.593 Sum_probs=54.0
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 188 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~ 188 (287)
|..||..|.-+||+.|...+|.++..+.+||.-|||+||||||||||||||+||..+
T Consensus 203 RvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 203 RVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred eEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 667999999999999999999999999999999999999999999999999998543
No 17
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.49 E-value=3.8e-14 Score=100.88 Aligned_cols=57 Identities=42% Similarity=0.643 Sum_probs=54.1
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhh
Q 023113 130 RKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 186 (287)
Q Consensus 130 rkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krk 186 (287)
+++..|+..|+.+|+.+|..++||+..++..||.++||+..+|++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 567889999999999999999999999999999999999999999999999998863
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.49 E-value=3.4e-14 Score=100.56 Aligned_cols=55 Identities=42% Similarity=0.617 Sum_probs=52.0
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 130 RKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 130 rkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
+.|+.|+.+|+.+|+..|..++||+..++..||.++||+..+|+.||+|||++.|
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 5677899999999999999999999999999999999999999999999998764
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.48 E-value=2e-14 Score=133.61 Aligned_cols=64 Identities=30% Similarity=0.496 Sum_probs=60.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 190 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~ 190 (287)
.-||-||.||.+||..||+.|-+..|.+...|.+||..|+|.+..|||||||||+|+||+....
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 5688899999999999999999999999999999999999999999999999999999977553
No 20
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.47 E-value=2.9e-14 Score=130.09 Aligned_cols=62 Identities=31% Similarity=0.541 Sum_probs=57.5
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 128 ASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 128 ~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
.||.||.||.+||..|+..|++++|++...|.+||.+|||.+.||+|||||+|+|.||-...
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgs 307 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGS 307 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCC
Confidence 45678999999999999999999999999999999999999999999999999999985543
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.44 E-value=1.2e-13 Score=118.86 Aligned_cols=67 Identities=31% Similarity=0.583 Sum_probs=61.5
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 123 GGAGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 123 ~~~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
++.+..+++|++.|..|+.+|++.|+.++||+...|..|+..|+|+++-|++||||||++.|++...
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3344678889999999999999999999999999999999999999999999999999999987654
No 22
>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=99.44 E-value=1.2e-13 Score=100.27 Aligned_cols=52 Identities=12% Similarity=0.324 Sum_probs=50.1
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCccchhhhhhhhh
Q 023113 129 SRKKLRLSKEQSLLLEETFKEHST----LNPKQKLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 129 rrkRt~~T~~Ql~~Le~~F~~~~~----p~~~~r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
||.||.||.+|+..|+..|+.+.| |+...+.+||.+|||++++|+|||||-+
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 788999999999999999999999 9999999999999999999999999954
No 23
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.42 E-value=1.9e-13 Score=127.59 Aligned_cols=65 Identities=26% Similarity=0.425 Sum_probs=60.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 191 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~ 191 (287)
|+||.|+.||..|+..||..|+++.||+...|++||..++|++.+|+|||.|||+||++.+.-..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ 175 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQ 175 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHH
Confidence 67788999999999999999999999999999999999999999999999999999998654443
No 24
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.40 E-value=1.6e-13 Score=131.81 Aligned_cols=66 Identities=24% Similarity=0.370 Sum_probs=60.8
Q ss_pred CCCCCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 122 DGGAGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 122 ~~~~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
....+++|||||.|.......||++|.+|++|+..++..||.+|+|.+..|+|||+|||.|.||..
T Consensus 288 i~a~~RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 288 IGAQSRKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred hhccccccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 334457888999999999999999999999999999999999999999999999999999999854
No 25
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.38 E-value=1e-13 Score=119.12 Aligned_cols=63 Identities=32% Similarity=0.474 Sum_probs=58.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
++++-|+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 456679999999999999999999999999999999999999999999999999999996644
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.28 E-value=1.4e-12 Score=116.72 Aligned_cols=61 Identities=31% Similarity=0.525 Sum_probs=56.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
+++..|.+|+-.||..||..|+..+|+-..+|.+||..+|+++.||+|||||||+|||++.
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 4555677899999999999999999999999999999999999999999999999999865
No 27
>smart00340 HALZ homeobox associated leucin zipper.
Probab=99.21 E-value=1.7e-11 Score=82.44 Aligned_cols=44 Identities=86% Similarity=1.292 Sum_probs=41.7
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhhcChhhhccC
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELRSLKLSPQLYMNM 229 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~~~~~~~~~~ 229 (287)
||+++||++||++|+.|++||++|++|+++||+++.++++||++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLSPPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccC
Confidence 58899999999999999999999999999999999999999874
No 28
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.18 E-value=1.1e-11 Score=110.46 Aligned_cols=62 Identities=26% Similarity=0.271 Sum_probs=58.9
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 126 GDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 126 ~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
.+.|+.|+.|+..|+++|++.|++.+||+...|+.||..+++++..|+|||||||++|+++.
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 36788899999999999999999999999999999999999999999999999999999865
No 29
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.10 E-value=9.3e-11 Score=104.57 Aligned_cols=132 Identities=20% Similarity=0.270 Sum_probs=103.8
Q ss_pred chhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCCCc--hhhhhccCCC---------CCCCCCCC
Q 023113 57 SDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIGDE--TEAERASCSR---------GSDDEDGG 124 (287)
Q Consensus 57 ~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~~~--~~~e~~~~s~---------~~~~~~~~ 124 (287)
.|++.|.+.|+.+.||+...++.+ ..+..++..|++||+|++.+....+. .......... ........
T Consensus 70 ~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 149 (235)
T KOG0490|consen 70 SQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEERPLPEGENLPDLSGTAPPSASRDKLDKGPS 149 (235)
T ss_pred CHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhccccccccCCCCCCCCCccccccccccCCC
Confidence 399999999999999999999988 68899999999999999865543221 0000101110 11112222
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhh
Q 023113 125 AGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 188 (287)
Q Consensus 125 ~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~ 188 (287)
..+.++.++.++..|+..|...|....+|+...++.|+..+|+.++.|++||||+|++.++...
T Consensus 150 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 150 NKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 3466778899999999999999999999999999999999999999999999999999998543
No 30
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=99.02 E-value=2.4e-10 Score=110.21 Aligned_cols=64 Identities=31% Similarity=0.433 Sum_probs=59.8
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhh
Q 023113 125 AGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 188 (287)
Q Consensus 125 ~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~ 188 (287)
+++.+|+|+.|+..|+..|++.|+.++||++..|+.||.++++++.+|+|||+|||+++++...
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~~ 236 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQHR 236 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhccc
Confidence 3567788999999999999999999999999999999999999999999999999999999653
No 31
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.78 E-value=3.2e-09 Score=98.68 Aligned_cols=63 Identities=27% Similarity=0.468 Sum_probs=59.0
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 125 AGDASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 125 ~~~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
++++|||||.+-..+.+.||.+|...+.|+.+.+..||++|.|.+..|+|||+|.|.|.||..
T Consensus 306 ~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 306 GGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 457899999999999999999999999999999999999999999999999999999988843
No 32
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.64 E-value=2.6e-08 Score=92.00 Aligned_cols=51 Identities=31% Similarity=0.526 Sum_probs=47.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
|...-...|.++|..++||++.++.+||+.+||+..||-.||.|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 556668899999999999999999999999999999999999999999984
No 33
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.63 E-value=1.2e-07 Score=87.30 Aligned_cols=60 Identities=38% Similarity=0.509 Sum_probs=55.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFK---EHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 186 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krk 186 (287)
..+|||+.|++.-.++|..+|- .++||+...+++||+++|++..||-.||.|.|-+.|+.
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 3578899999999999999996 68899999999999999999999999999999999884
No 34
>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=98.24 E-value=6.6e-07 Score=60.34 Aligned_cols=34 Identities=35% Similarity=0.525 Sum_probs=29.1
Q ss_pred hcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH
Q 023113 149 EHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 182 (287)
Q Consensus 149 ~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak 182 (287)
.++||+..++..||+++||+..||..||-|.|.|
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 5789999999999999999999999999999875
No 35
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.92 E-value=1.2e-05 Score=80.70 Aligned_cols=58 Identities=26% Similarity=0.366 Sum_probs=54.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
..||.|.+||..|...|..+|+.+++|+.+..+.|+.+|||..+-|..||-|-|.|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 5677799999999999999999999999999999999999999999999999888753
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.34 E-value=0.00014 Score=79.18 Aligned_cols=62 Identities=23% Similarity=0.357 Sum_probs=57.7
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhh
Q 023113 127 DASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 188 (287)
Q Consensus 127 ~~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~ 188 (287)
.++++|++++..|+.++..+|....||...+.+.|...+++..+.|+|||||-|+|.|+...
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 45778999999999999999999999999999999999999999999999999999988543
No 37
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=97.03 E-value=0.001 Score=46.00 Aligned_cols=36 Identities=36% Similarity=0.401 Sum_probs=32.2
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhhc
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELRSLKL 221 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~~ 221 (287)
+|.+.||+.||++|+.|+.++++|++|++.|++...
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~ 36 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQ 36 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 478999999999999999999999999999986543
No 38
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.68 E-value=0.0011 Score=47.95 Aligned_cols=42 Identities=24% Similarity=0.376 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhh
Q 023113 140 SLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 181 (287)
Q Consensus 140 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRa 181 (287)
+..|+++|..++++...+...|..+.+|+..||+.||-.|+.
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 567999999999999999999999999999999999976543
No 39
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.23 E-value=0.0045 Score=59.19 Aligned_cols=59 Identities=34% Similarity=0.336 Sum_probs=48.9
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhh
Q 023113 128 ASRKKLRLSKEQSLLLEETFK---EHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 186 (287)
Q Consensus 128 ~rrkRt~~T~~Ql~~Le~~F~---~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krk 186 (287)
..|.+..+......+|+.+.. ..+||+..++..||+++||+..||..||-|.|-|..+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 344455788999999998743 35799999999999999999999999999998876553
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=94.30 E-value=0.35 Score=39.57 Aligned_cols=79 Identities=19% Similarity=0.308 Sum_probs=45.9
Q ss_pred CCccCCHHHHH-HHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH--------------HHhhhhhhhhHHH
Q 023113 131 KKLRLSKEQSL-LLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR--------------TKLKQTEVDCEYL 195 (287)
Q Consensus 131 kRt~~T~~Ql~-~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak--------------~Krkq~~~~~~~L 195 (287)
+|.+|+.++.. ++...+. +. ....++|+++||++.+|..|.+--+.. ....+.+.++..|
T Consensus 9 ~rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L 83 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKEL 83 (121)
T ss_pred CCCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHH
Confidence 35567877654 3444443 22 234578999999999999997543321 0112233445556
Q ss_pred HHHhhhhHHHHHHHHHHHH
Q 023113 196 KRCCENLTEENRRLQKEVQ 214 (287)
Q Consensus 196 k~~~e~l~~en~~l~~e~~ 214 (287)
++++..|+.|++-|++.+.
T Consensus 84 ~~el~~L~~E~diLKKa~~ 102 (121)
T PRK09413 84 QRLLGKKTMENELLKEAVE 102 (121)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 6666666666665555543
No 41
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=94.00 E-value=0.014 Score=50.48 Aligned_cols=45 Identities=13% Similarity=0.124 Sum_probs=40.8
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|+.+|.+.|++|++|+.+++.++ ..++.|+-.|++||+|++.+..
T Consensus 62 Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k 107 (156)
T COG5576 62 QLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEK 107 (156)
T ss_pred HHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHH
Confidence 99999999999999999999998 7778899999999999986544
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.69 E-value=0.14 Score=36.23 Aligned_cols=47 Identities=21% Similarity=0.356 Sum_probs=35.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhh
Q 023113 129 SRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 129 rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
+|+|..+|-++...+-..++... ....||+++|+...+|..|..|+.
T Consensus 1 krkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 1 KRKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 57888999999888888887766 467899999999999999998853
No 43
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.05 E-value=0.11 Score=54.63 Aligned_cols=48 Identities=19% Similarity=0.306 Sum_probs=44.7
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 140 SLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 140 l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
+..|..+|..|..|+..+...+|.+.||..+.|++||+++++.....+
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 788999999999999999999999999999999999999999877654
No 44
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=92.47 E-value=0.97 Score=38.06 Aligned_cols=74 Identities=27% Similarity=0.276 Sum_probs=52.8
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH----------HHhhhhhhh----hHHHHHH
Q 023113 133 LRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR----------TKLKQTEVD----CEYLKRC 198 (287)
Q Consensus 133 t~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak----------~Krkq~~~~----~~~Lk~~ 198 (287)
.+|+.+++..+ ..|+.-=+--|++...|-.|=|.||+- .|+-+.+.+ ...|.++
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 67888887665 222222233489999999999999863 444444444 4458888
Q ss_pred hhhhHHHHHHHHHHHHHHHh
Q 023113 199 CENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 199 ~e~l~~en~~l~~e~~~lr~ 218 (287)
.+.|.+||.+++.|++.++.
T Consensus 90 v~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 99999999999999988874
No 45
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=91.89 E-value=0.0087 Score=41.68 Aligned_cols=44 Identities=14% Similarity=0.152 Sum_probs=39.3
Q ss_pred chhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCC
Q 023113 57 SDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSER 100 (287)
Q Consensus 57 ~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r 100 (287)
.|..+|...|..|.||+..+++++ ..++.+...|..||.+++.+
T Consensus 10 ~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~ 54 (56)
T smart00389 10 EQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAK 54 (56)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhc
Confidence 489999999999999999999888 77888999999999988754
No 46
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=91.03 E-value=0.057 Score=49.12 Aligned_cols=46 Identities=20% Similarity=0.051 Sum_probs=42.8
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPI 103 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~ 103 (287)
|+++|...|..-.||+...+|++ ..+..|+|.|++||.|++.+-..
T Consensus 48 QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~ 94 (228)
T KOG2251|consen 48 QLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRR 94 (228)
T ss_pred HHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhH
Confidence 99999999999999999999999 77999999999999999976654
No 47
>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=90.59 E-value=0.0072 Score=42.31 Aligned_cols=45 Identities=13% Similarity=0.144 Sum_probs=39.8
Q ss_pred chhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCC
Q 023113 57 SDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSERE 101 (287)
Q Consensus 57 ~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~ 101 (287)
.|..+|...|..|+||+..+.+++ ..++.+...|..||.+++.+.
T Consensus 10 ~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~ 55 (59)
T cd00086 10 EQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKL 55 (59)
T ss_pred HHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 389999999999999999999988 778899999999999877543
No 48
>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=90.57 E-value=0.6 Score=32.22 Aligned_cols=31 Identities=35% Similarity=0.523 Sum_probs=27.9
Q ss_pred hhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 188 TEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 188 ~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
.+..++.|+.+++.|..||+.|+.+|..|+.
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4557899999999999999999999999985
No 49
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=90.02 E-value=0.099 Score=50.82 Aligned_cols=48 Identities=13% Similarity=0.084 Sum_probs=43.6
Q ss_pred chhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCC
Q 023113 57 SDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIG 104 (287)
Q Consensus 57 ~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~ 104 (287)
+|...|..+|..++||++..+|.+ ..++.++..|..||.+++.+....
T Consensus 186 ~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~ 234 (354)
T KOG0849|consen 186 SQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQ 234 (354)
T ss_pred chHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhc
Confidence 499999999999999999999999 999999999999999998765543
No 50
>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=86.07 E-value=0.0069 Score=42.63 Aligned_cols=42 Identities=14% Similarity=0.128 Sum_probs=37.5
Q ss_pred chhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCC
Q 023113 57 SDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRS 98 (287)
Q Consensus 57 ~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s 98 (287)
.|..+|...|+.|++|+..+++.+ ..++.+...|..||.|++
T Consensus 10 ~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR 52 (57)
T PF00046_consen 10 EQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRR 52 (57)
T ss_dssp HHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhccccccccccccccccccccccccCHHHhH
Confidence 399999999999999999999888 778999999999998765
No 51
>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=85.59 E-value=0.14 Score=37.20 Aligned_cols=41 Identities=2% Similarity=-0.104 Sum_probs=38.1
Q ss_pred hhhhhhhccCCCCC----CCccccccc-cCCCCCCCCcccCCCCCC
Q 023113 58 DTRSFLRGIDVNQA----PTVADCEEE-NGVSSPNSTVSSISGKRS 98 (287)
Q Consensus 58 q~~~l~~~fd~n~~----P~~a~~e~~-~~~ssp~s~i~s~~~~~s 98 (287)
|+..|...|..+.| |+...++++ ..+++++..+..||.|..
T Consensus 12 Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 12 QKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred HHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 99999999999999 999999888 889999999999999863
No 52
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=84.74 E-value=2 Score=34.75 Aligned_cols=47 Identities=17% Similarity=0.301 Sum_probs=29.7
Q ss_pred cchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 170 RQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 170 rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
-++..||++.=- .+..+.+.+.+.++++++.++.+|+.|+.+++.|+
T Consensus 15 l~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 15 LQYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 355678855411 12223344566677777788888888888887775
No 53
>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=83.56 E-value=0.4 Score=35.25 Aligned_cols=47 Identities=23% Similarity=0.362 Sum_probs=30.0
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhh
Q 023113 130 RKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 130 rkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
++|.+||.++...+-..+.. ......++|+++||++.+|..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHHHHh
Confidence 46778999887776666522 224567899999999999999975444
No 54
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=82.97 E-value=0.57 Score=44.08 Aligned_cols=67 Identities=13% Similarity=0.066 Sum_probs=48.4
Q ss_pred cCCCCCCCCCccCCC-CCCcchhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCC
Q 023113 38 QNHHKRSPWTELFHS-SDRNSDTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIG 104 (287)
Q Consensus 38 ~~~~~~~~w~~~~~~-~~~~~q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~ 104 (287)
-+|..++.|..-... +=.+.-...|..|+-+|+||+..+.-++ ...+..--.++.||.|++.|++..
T Consensus 166 KfPlPrTIWDGEet~yCFKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa~ 234 (304)
T KOG0775|consen 166 KFPLPRTIWDGEETVYCFKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRAA 234 (304)
T ss_pred cCCCCCccccCceeeeehhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhhc
Confidence 456678899884333 2223344567889999999998777666 556677777889999999887743
No 55
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=80.78 E-value=4.8 Score=37.73 Aligned_cols=35 Identities=29% Similarity=0.331 Sum_probs=26.4
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhhc
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQELRSLKL 221 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~~ 221 (287)
+.......|.++++.|+.+.+.|++|+..||.++.
T Consensus 219 e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 219 EMAHRVAELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444566888888888888888888888887654
No 56
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=80.31 E-value=0.7 Score=44.28 Aligned_cols=49 Identities=12% Similarity=0.058 Sum_probs=41.7
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCCCc
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIGDE 106 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~~~ 106 (287)
|+..|..+|..|+||+.+++|+. .-+...+..+..||.+++.+.+.-|.
T Consensus 123 qlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 123 QLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred HHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 78889999999999999999988 55788899999999999876654443
No 57
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=77.41 E-value=0.34 Score=43.97 Aligned_cols=54 Identities=17% Similarity=0.129 Sum_probs=44.9
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCCCchhhhh
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIGDETEAER 111 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~~~~~~e~ 111 (287)
|+-.|.+.|....|-+++++-+. ......+-.+.+||+||+.++....+.+.|.
T Consensus 155 QLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQeae~Ek 209 (246)
T KOG0492|consen 155 QLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQEAELEK 209 (246)
T ss_pred HHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHHHHHHH
Confidence 99999999999999999999776 6677888899999999998877655444443
No 58
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=76.04 E-value=0.43 Score=44.68 Aligned_cols=45 Identities=11% Similarity=0.102 Sum_probs=40.5
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|+..|...|.-..||+...+|-+ .....|+..|+.||+||+.+-+
T Consensus 152 Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWR 197 (332)
T KOG0494|consen 152 QLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWR 197 (332)
T ss_pred HHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhh
Confidence 88999999999999999999888 6678999999999999986554
No 59
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=75.77 E-value=0.6 Score=42.90 Aligned_cols=44 Identities=11% Similarity=0.085 Sum_probs=40.3
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSERE 101 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~ 101 (287)
|+..|.+.|..-.|-...+|-+| +.++...-.|.+||+|+|.+-
T Consensus 133 QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~ 177 (245)
T KOG0850|consen 133 QLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKF 177 (245)
T ss_pred HHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHH
Confidence 99999999999999998899888 888999999999999998654
No 60
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=74.20 E-value=0.63 Score=41.38 Aligned_cols=46 Identities=13% Similarity=0.063 Sum_probs=41.9
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPI 103 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~ 103 (287)
|+.-|...|..|.|-+.++++++ ...+..+..+.+||+|++.+...
T Consensus 113 Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr 159 (197)
T KOG0843|consen 113 QLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKR 159 (197)
T ss_pred HHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHH
Confidence 99999999999999999999999 77899999999999999976653
No 61
>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=74.07 E-value=5.6 Score=27.03 Aligned_cols=41 Identities=12% Similarity=0.168 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNR 179 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNR 179 (287)
.++..+..+|...|-.. ..-.++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHH
Confidence 47888999999998222 335688999999999998766443
No 62
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=71.84 E-value=0.24 Score=40.40 Aligned_cols=45 Identities=13% Similarity=0.089 Sum_probs=41.0
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|+..|.+.|---.||++-++|++ ..+...+..++.||+|++.+-+
T Consensus 28 QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfR 73 (125)
T KOG0484|consen 28 QLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFR 73 (125)
T ss_pred HHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHH
Confidence 99999999999999999999998 7789999999999999986544
No 63
>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=71.09 E-value=4.8 Score=28.71 Aligned_cols=39 Identities=18% Similarity=0.189 Sum_probs=31.7
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCccchh
Q 023113 135 LSKEQSLLLEETFKEHST--LNPKQKLALAKQLNLRPRQVE 173 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~--p~~~~r~~LA~~LgL~~rqVq 173 (287)
+|..|..+|...|+..-| |-...-.+||++||++..-|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 588999999999987665 555666899999999986654
No 64
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=70.34 E-value=1.4 Score=42.16 Aligned_cols=46 Identities=9% Similarity=0.021 Sum_probs=41.2
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPI 103 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~ 103 (287)
|.-.|.+-|.+.+|-+..+||.+ ..+....--|.+||+|++-+-..
T Consensus 164 QV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR 210 (307)
T KOG0842|consen 164 QVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKR 210 (307)
T ss_pred HHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhh
Confidence 88899999999999999999999 77888889999999999865543
No 65
>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=70.27 E-value=17 Score=26.15 Aligned_cols=25 Identities=40% Similarity=0.597 Sum_probs=12.1
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 193 EYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 193 ~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
..|...++.|..+|..|..++..|.
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~L~ 53 (64)
T PF00170_consen 29 EELEEKVEELESENEELKKELEQLK 53 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555544443
No 66
>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=69.44 E-value=4.5 Score=26.33 Aligned_cols=44 Identities=14% Similarity=0.166 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 182 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak 182 (287)
.++..+..++...|... ....++|..+|++...|..|...-+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777778887776422 235678999999999999998665443
No 67
>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=67.34 E-value=20 Score=25.06 Aligned_cols=27 Identities=33% Similarity=0.498 Sum_probs=21.5
Q ss_pred hhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 191 DCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 191 ~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
....|......|..+|..|+.++..|+
T Consensus 26 ~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 26 REEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445577788888999999998888775
No 68
>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=63.94 E-value=15 Score=29.86 Aligned_cols=34 Identities=38% Similarity=0.371 Sum_probs=28.4
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
.+.-.+...||.....+.+||.+|+.|++.||..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~ 51 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRER 51 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677788999999999999999999999854
No 69
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=63.36 E-value=1 Score=47.56 Aligned_cols=117 Identities=16% Similarity=0.213 Sum_probs=76.3
Q ss_pred hhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCCCchhhhhccCCCCCCCCCCCCCCCCCCCccCCH
Q 023113 59 TRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIGDETEAERASCSRGSDDEDGGAGDASRKKLRLSK 137 (287)
Q Consensus 59 ~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~~~~~~e~~~~s~~~~~~~~~~~~~rrkRt~~T~ 137 (287)
+..|...|-.|.+|+....... ..++.|-..+..||.+....+...+ +.... ..+ ...-+-++.+..
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~-----rsps~------psg-~~p~kv~sp~k~ 635 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE-----RSPSQ------PSG-ERPVKVRSPIKE 635 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc-----cCccC------CCC-CCCccccCCCCc
Confidence 3456668899999975444333 5678888889999977654433221 11110 011 122333456666
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhh
Q 023113 138 EQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 187 (287)
Q Consensus 138 ~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq 187 (287)
++-..|..+|+-+..++-.+-..++.+|-..+..|+|||++|+..-+...
T Consensus 636 ~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 636 EDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred cchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 66777888888777766666656666788889999999999998877644
No 70
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=62.74 E-value=33 Score=30.51 Aligned_cols=51 Identities=24% Similarity=0.228 Sum_probs=42.4
Q ss_pred CCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 167 LRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 167 L~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
..--...+|.+-|-.+.|..+.+.+.+.|+-..+.|..+.+++++.+++|.
T Consensus 83 gg~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~ 133 (181)
T KOG3335|consen 83 GGVLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLH 133 (181)
T ss_pred ceeeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445788888888888888888888899999999999999999999995
No 71
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=61.25 E-value=7.9 Score=27.20 Aligned_cols=33 Identities=12% Similarity=0.222 Sum_probs=20.2
Q ss_pred HHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 157 QKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 157 ~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
...+||+.+|++...|..||.++..........
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~ 44 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLE 44 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHH
Confidence 356899999999999999998875555544333
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=61.17 E-value=33 Score=24.66 Aligned_cols=35 Identities=34% Similarity=0.431 Sum_probs=29.0
Q ss_pred HhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 184 KLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 184 Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
.....+..+..|..+++.|..++..|..++..|+.
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~ 61 (64)
T PF00170_consen 27 YIEELEEKVEELESENEELKKELEQLKKEIQSLKS 61 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34556667777999999999999999999998874
No 73
>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=60.72 E-value=18 Score=20.84 Aligned_cols=38 Identities=13% Similarity=0.175 Sum_probs=26.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWF 176 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWF 176 (287)
.++.++...+...|... + ...++|+.+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 35666666666666532 2 35578999999988887773
No 74
>smart00338 BRLZ basic region leucin zipper.
Probab=60.72 E-value=31 Score=24.85 Aligned_cols=26 Identities=50% Similarity=0.690 Sum_probs=14.4
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
...|...+..|..+|..|..++..|+
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~ 53 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLR 53 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445555556666666666655554
No 75
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=60.68 E-value=74 Score=29.40 Aligned_cols=39 Identities=23% Similarity=0.383 Sum_probs=31.7
Q ss_pred hhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 179 RRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 179 RRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+|++.-.+..+.......+..+.|..|+..|++++.+|.
T Consensus 101 ~kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~ql~ 139 (232)
T KOG2483|consen 101 DKALEHIQSLERKSATQQQDIEDLSRENRKLKARLEQLS 139 (232)
T ss_pred hhHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 466666677777777788889999999999999998876
No 76
>smart00338 BRLZ basic region leucin zipper.
Probab=60.27 E-value=34 Score=24.64 Aligned_cols=35 Identities=31% Similarity=0.438 Sum_probs=29.2
Q ss_pred hhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 185 LKQTEVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 185 rkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
....+..+..|..++..|..+...|..++..|+..
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566777779999999999999999999998754
No 77
>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=59.64 E-value=26 Score=24.50 Aligned_cols=25 Identities=28% Similarity=0.359 Sum_probs=16.0
Q ss_pred hhhhhHHHHHHhhhhHHHHHHHHHH
Q 023113 188 TEVDCEYLKRCCENLTEENRRLQKE 212 (287)
Q Consensus 188 ~~~~~~~Lk~~~e~l~~en~~l~~e 212 (287)
.+..+..|..++..|..++..|+.|
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 4444555777777777777777654
No 78
>PF01166 TSC22: TSC-22/dip/bun family; InterPro: IPR000580 Several eukaryotic proteins are evolutionary related and are thought to be involved in transcriptional regulation. These proteins are highly similar in a region of about 50 residues that include a conserved leucine-zipper domain most probably involved in homo- or hetero-dimerisation. Proteins containing this signature include: Vertebrate protein TSC-22 [], a transcriptional regulator which seems to act on C-type natriuretic peptide (CNP) promoter. Mammalian protein DIP (DSIP-immunoreactive peptide) [], a protein whose function is not yet known. Drosophila protein bunched [] (gene bun) (also known as shortsighted), a probable transcription factor required for peripheral nervous system morphogenesis, eye development and oogenesis. Caenorhabditis elegans hypothetical protein T18D3.7. ; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1DIP_B.
Probab=59.03 E-value=21 Score=26.13 Aligned_cols=32 Identities=28% Similarity=0.329 Sum_probs=28.3
Q ss_pred hhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhh
Q 023113 189 EVDCEYLKRCCENLTEENRRLQKEVQELRSLK 220 (287)
Q Consensus 189 ~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~ 220 (287)
+.+.+.||.....|.+.|..|+.|+.-||...
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~~ 44 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQNA 44 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHHC
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 46788999999999999999999999998764
No 79
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=58.38 E-value=23 Score=30.21 Aligned_cols=48 Identities=15% Similarity=0.037 Sum_probs=36.0
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
...++..|..+|...+ . - ....++|..||++...|..|..+.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~-~--G---lTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-R--G---LTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-c--C---CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4578999999997743 1 1 224589999999999999999865555544
No 80
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=56.60 E-value=1.3 Score=41.61 Aligned_cols=44 Identities=9% Similarity=0.017 Sum_probs=39.3
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSERE 101 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~ 101 (287)
|+.-|-..|..|+|-+.--+.++ .+++.-++.|.+||+|.+.+-
T Consensus 257 QL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKi 301 (342)
T KOG0493|consen 257 QLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKI 301 (342)
T ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhh
Confidence 88889999999999988888888 889999999999999988543
No 81
>PF10668 Phage_terminase: Phage terminase small subunit; InterPro: IPR018925 This entry describes the terminase small subunit from Enterococcus phage phiFL1A, related proteins in other bacteriophage, and prophage regions of bacterial genomes. Packaging of double-stranded viral DNA concatemers requires interaction of the prohead with virus DNA. This process is mediated by a phage-encoded DNA recognition and terminase protein. The terminase enzymes described so far, which are hetero-oligomers composed of a small and a large subunit, do not have a significant level of sequence homology. The small terminase subunit is thought to form a nucleoprotein structure that helps to position the terminase large subunit at the packaging initiation site [].
Probab=56.38 E-value=6 Score=28.99 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=16.7
Q ss_pred HHHHHHHhCCCccchhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWF 176 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWF 176 (287)
-.+||.+||+++.+|..|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4578999999999999884
No 82
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=55.65 E-value=2.4 Score=40.00 Aligned_cols=45 Identities=11% Similarity=0.064 Sum_probs=39.4
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|.-.|...|-.++|=++.-..++ ..++..|-.|.+||+||+.+++
T Consensus 210 QRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKER 255 (317)
T KOG0848|consen 210 QRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKER 255 (317)
T ss_pred hhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHH
Confidence 77789999999999988777777 7789999999999999997765
No 83
>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=55.01 E-value=42 Score=25.32 Aligned_cols=29 Identities=34% Similarity=0.507 Sum_probs=14.5
Q ss_pred hhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 189 EVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 189 ~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+.+++.|+..+..+.++|..|+.++.+|+
T Consensus 24 q~e~eeLke~n~~L~~e~~~L~~en~~L~ 52 (72)
T PF06005_consen 24 QMENEELKEKNNELKEENEELKEENEQLK 52 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 33444445554444455555555555554
No 84
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=54.97 E-value=33 Score=25.71 Aligned_cols=31 Identities=35% Similarity=0.346 Sum_probs=23.0
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+...+...++++.+.+..||.+|+.|+..|.
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4455666677777888888888888887764
No 85
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=54.72 E-value=28 Score=33.21 Aligned_cols=32 Identities=25% Similarity=0.366 Sum_probs=20.7
Q ss_pred hhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 188 TEVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 188 ~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
...+++.|.+.|+.|++.-.+|.+||+.||.+
T Consensus 253 l~ge~~~Le~rN~~LK~qa~~lerEI~ylKql 284 (294)
T KOG4571|consen 253 LLGELEGLEKRNEELKDQASELEREIRYLKQL 284 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566666667777667777777777644
No 86
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=54.70 E-value=27 Score=28.59 Aligned_cols=34 Identities=29% Similarity=0.229 Sum_probs=27.6
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
.+.-.+...||.....+.+||..|+.|++.||..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~ 51 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRER 51 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455567778889999999999999999999854
No 87
>PF04977 DivIC: Septum formation initiator; InterPro: IPR007060 DivIC, from the spore-forming, Gram-positive bacterium Bacillus subtilis, is necessary for both vegetative and sporulation septum formation []. These proteins are mainly composed of an N-terminal coiled-coil. DivIB, DivIC and FtsL inter-depend on each other for stabilisation and localisation. The latter two form a heterodimer. DivIC is always centre cell but the other two associate with it during septation [].; GO: 0007049 cell cycle
Probab=54.61 E-value=32 Score=25.17 Aligned_cols=30 Identities=30% Similarity=0.460 Sum_probs=24.6
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
+...+...|+.+.+.++.+|+.|+.+++.|
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445567778888889999999999998888
No 88
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=53.24 E-value=19 Score=32.01 Aligned_cols=49 Identities=24% Similarity=0.174 Sum_probs=37.1
Q ss_pred cCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHST--LNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~--p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.+|..|+.+|..+|+..-| |-...-.+||++||+++.-+ |..=|||..|
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 6999999999999986654 65666689999999998654 3444555444
No 89
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=52.44 E-value=29 Score=33.15 Aligned_cols=31 Identities=26% Similarity=0.323 Sum_probs=25.3
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+++.+-+.|--+|+.|...|++|+.++++|-
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~le 275 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELE 275 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455667788899999999999999998774
No 90
>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=52.34 E-value=21 Score=26.01 Aligned_cols=44 Identities=23% Similarity=0.324 Sum_probs=22.0
Q ss_pred CccCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q 023113 132 KLRLSKEQ-SLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 132 Rt~~T~~Q-l~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQ 177 (287)
|..|+..- +.+++.++ .+..--..+| ..|+++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~-~~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAE-KDNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHH-H-TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHH-HccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 34455544 34444444 3332222333 359999999999999874
No 91
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=52.31 E-value=51 Score=24.67 Aligned_cols=26 Identities=38% Similarity=0.410 Sum_probs=17.8
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
......++..|++|++.|++|+++++
T Consensus 42 l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 42 LGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33445567777888888888877665
No 92
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=52.29 E-value=4.2 Score=39.05 Aligned_cols=45 Identities=9% Similarity=0.058 Sum_probs=35.4
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|..-|.+.|-...|-+-..+-++ +....|+.+|..||+|++.++.
T Consensus 192 QIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDK 237 (408)
T KOG0844|consen 192 QIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDK 237 (408)
T ss_pred HHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhh
Confidence 66677777777777666565556 8899999999999999996654
No 93
>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=52.28 E-value=28 Score=23.63 Aligned_cols=42 Identities=14% Similarity=0.206 Sum_probs=27.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 181 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRa 181 (287)
++..+..++...| .....-.++|..+|+++..|+.|.+.-|.
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 5566666666554 33345678999999999999999875443
No 94
>KOG1924 consensus RhoA GTPase effector DIA/Diaphanous [Signal transduction mechanisms; Cytoskeleton]
Probab=51.15 E-value=2.1e+02 Score=31.31 Aligned_cols=27 Identities=15% Similarity=0.198 Sum_probs=11.5
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEV 213 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~ 213 (287)
+-++....+...++...-..+..+.|+
T Consensus 471 eseqkA~e~~kk~~ke~ta~qe~qael 497 (1102)
T KOG1924|consen 471 ESEQKAAELEKKFDKELTARQEAQAEL 497 (1102)
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHH
Confidence 333333444455554443344444433
No 95
>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=48.34 E-value=23 Score=34.55 Aligned_cols=25 Identities=32% Similarity=0.335 Sum_probs=13.2
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 193 EYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 193 ~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
..|+.+++.|+.||..|+.+|.+|.
T Consensus 35 ~aLr~EN~~LKkEN~~Lk~eVerLE 59 (420)
T PF07407_consen 35 FALRMENHSLKKENNDLKIEVERLE 59 (420)
T ss_pred hhHHHHhHHHHHHHHHHHHHHHHHH
Confidence 3355555555555555555555553
No 96
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=48.32 E-value=31 Score=31.83 Aligned_cols=34 Identities=26% Similarity=0.241 Sum_probs=22.7
Q ss_pred hhhhhhhHHHHHHhhhhHHHHH---HHHHHHHHHHhh
Q 023113 186 KQTEVDCEYLKRCCENLTEENR---RLQKEVQELRSL 219 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~---~l~~e~~~lr~l 219 (287)
++...+++.|++++..|+.++. .++.|+++||.+
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~l 108 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQELEQLEAENARLREL 108 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3555667777777777766665 556777777754
No 97
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=47.77 E-value=2.4 Score=40.69 Aligned_cols=45 Identities=16% Similarity=0.006 Sum_probs=39.9
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|+..|.+.|=+|.|=+..-|-++ +-+...+-.|.+||+||+.++.
T Consensus 246 QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~K 291 (308)
T KOG0487|consen 246 QTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEK 291 (308)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHh
Confidence 99999999999999987777666 7889999999999999997664
No 98
>cd04787 HTH_HMRTR_unk Helix-Turn-Helix DNA binding domain of putative Heavy Metal Resistance transcription regulators. Putative helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR), unknown subgroup. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules, such as, metal ions, drugs, and organic substrates. This subgroup lacks one of the c
Probab=47.60 E-value=1.1e+02 Score=25.18 Aligned_cols=71 Identities=10% Similarity=0.060 Sum_probs=43.8
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+..++..|.. ....+.+|++-.+|+-+|......... ...-.+.|+...+.+.++..+|+.
T Consensus 36 yR~Y~~~~~~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 36 YRLYSEKDLSRLRF-------------ILSARQLGFSLKDIKEILSHADQGESP--CPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred eeeCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhhhccCCCc--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34789999888832 244678899999999888754321110 111234556666666666666666
Q ss_pred HHHHHH
Q 023113 212 EVQELR 217 (287)
Q Consensus 212 e~~~lr 217 (287)
..+.|.
T Consensus 101 ~~~~l~ 106 (133)
T cd04787 101 LRDRMQ 106 (133)
T ss_pred HHHHHH
Confidence 555554
No 99
>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=47.58 E-value=29 Score=24.20 Aligned_cols=46 Identities=11% Similarity=0.133 Sum_probs=34.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.||..++.+|.-...-. ...++|..+|++++.|..+..+=+.|..-
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 57888888887776432 35689999999999999988776666544
No 100
>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=46.14 E-value=53 Score=24.49 Aligned_cols=25 Identities=32% Similarity=0.340 Sum_probs=11.8
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
.+.|-..|+.|+.||..|+.++..+
T Consensus 9 le~Li~~~~~L~~EN~~Lr~q~~~~ 33 (65)
T TIGR02449 9 VEHLLEYLERLKSENRLLRAQEKTW 33 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444455555555555444433
No 101
>PF08961 DUF1875: Domain of unknown function (DUF1875); InterPro: IPR015056 MIT can be found in the Nuclear receptor-binding factor 2, it has no known function. ; PDB: 2CRB_A.
Probab=45.69 E-value=6.9 Score=35.92 Aligned_cols=39 Identities=28% Similarity=0.433 Sum_probs=0.0
Q ss_pred HHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhhc
Q 023113 183 TKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRSLKL 221 (287)
Q Consensus 183 ~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~~ 221 (287)
.+..........|++..+.|.+||++|++|++.|++-+.
T Consensus 122 T~IEEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~a 160 (243)
T PF08961_consen 122 TRIEEQATKIADLRRLVEFLLAENERLRRENKQLKAENA 160 (243)
T ss_dssp ---------------------------------------
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445555667888888888888888888888876543
No 102
>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=45.68 E-value=61 Score=24.46 Aligned_cols=24 Identities=38% Similarity=0.389 Sum_probs=10.9
Q ss_pred hhhHHHHHHhhhhHHHHHHHHHHH
Q 023113 190 VDCEYLKRCCENLTEENRRLQKEV 213 (287)
Q Consensus 190 ~~~~~Lk~~~e~l~~en~~l~~e~ 213 (287)
.++..|+.+++.|.+||.+|+.+.
T Consensus 32 e~n~~L~~e~~~L~~en~~L~~e~ 55 (72)
T PF06005_consen 32 EKNNELKEENEELKEENEQLKQER 55 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444443
No 103
>PRK14127 cell division protein GpsB; Provisional
Probab=44.65 E-value=50 Score=27.03 Aligned_cols=44 Identities=27% Similarity=0.428 Sum_probs=33.9
Q ss_pred CCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 166 NLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 166 gL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
|....+|.-+. .+...+++.|..++..|++++.+|+.++.++..
T Consensus 22 GYd~~EVD~FL---------d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 22 GYDQDEVDKFL---------DDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred CCCHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56666666554 355668888888999999999999999888875
No 104
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=42.82 E-value=63 Score=25.42 Aligned_cols=38 Identities=18% Similarity=0.413 Sum_probs=25.2
Q ss_pred hhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 173 EVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 173 qvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
-+|||=++++. +++.|..+++.|+.|.....++|...+
T Consensus 20 y~~~k~~ka~~-------~~~kL~~en~qlk~Ek~~~~~qvkn~~ 57 (87)
T PF10883_consen 20 YLWWKVKKAKK-------QNAKLQKENEQLKTEKAVAETQVKNAK 57 (87)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35666555443 367777777778777777777776544
No 105
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=41.83 E-value=57 Score=30.50 Aligned_cols=23 Identities=35% Similarity=0.499 Sum_probs=9.3
Q ss_pred HHHHhhhhHHHHHHHHHHHHHHH
Q 023113 195 LKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 195 Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
|+..++.|..+|..|..++..+|
T Consensus 116 Lr~~n~~L~~~n~el~~~le~~~ 138 (292)
T KOG4005|consen 116 LRAINESLLAKNHELDSELELLR 138 (292)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHH
Confidence 33333333444444444444333
No 106
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=41.64 E-value=24 Score=23.68 Aligned_cols=40 Identities=18% Similarity=0.127 Sum_probs=19.6
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWF 176 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWF 176 (287)
...||.+|...++..++.. ....+||+.||.+..-|..+.
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 3568888888888887533 334579999999998887665
No 107
>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=41.40 E-value=1.8e+02 Score=25.41 Aligned_cols=45 Identities=24% Similarity=0.192 Sum_probs=35.7
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q 023113 131 KKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 131 kRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQ 177 (287)
++..+|.+++..+.+.-..+ |..-.+..||+++|++..-|.+=..
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~ 126 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAP 126 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcC
Confidence 45789999999998886544 5667788999999999887776553
No 108
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=40.95 E-value=72 Score=24.66 Aligned_cols=28 Identities=32% Similarity=0.489 Sum_probs=21.1
Q ss_pred hhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 190 VDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 190 ~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
.+...++++.+.+.+||..|+-|+..|.
T Consensus 42 ~~l~~l~~~~~~l~~e~~~L~lE~~~l~ 69 (97)
T PF04999_consen 42 YELQQLEKEIDQLQEENERLRLEIATLS 69 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3466677777888888888888887775
No 109
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=40.37 E-value=58 Score=30.44 Aligned_cols=9 Identities=44% Similarity=0.512 Sum_probs=4.3
Q ss_pred hhhhhHHHh
Q 023113 177 QNRRARTKL 185 (287)
Q Consensus 177 QNRRak~Kr 185 (287)
|+-|-|.|-
T Consensus 82 QtaRDrKKa 90 (292)
T KOG4005|consen 82 QTARDRKKA 90 (292)
T ss_pred hhhhhHHHH
Confidence 454554443
No 110
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=40.06 E-value=55 Score=26.33 Aligned_cols=39 Identities=15% Similarity=0.107 Sum_probs=31.2
Q ss_pred hhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 173 EVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 173 qvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
.-|+..+..+.+....+.+++.|+.+++.|..|...|+.
T Consensus 24 ~G~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 24 NGILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred CcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 345666666667777888889999999999999999976
No 111
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=39.94 E-value=50 Score=21.65 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
.++..+..++...+.. ....++|..+|++...|..|.+.-+
T Consensus 3 ~l~~~e~~i~~~~~~g------~s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLAEG------LTNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 4677787777654321 1346889999999999998876433
No 112
>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=39.79 E-value=1.8e+02 Score=22.64 Aligned_cols=64 Identities=20% Similarity=0.229 Sum_probs=39.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
+..|+..++..|..... .+.+|++-.+|+-++.... ..-...|+.....|.++..+|+.
T Consensus 36 ~R~y~~~di~~l~~i~~-------------lr~~g~~l~~i~~~~~~~~--------~~~~~~l~~~~~~l~~~i~~l~~ 94 (103)
T cd01106 36 YRLYTEEDLERLQQILF-------------LKELGFSLKEIKELLKDPS--------EDLLEALREQKELLEEKKERLDK 94 (103)
T ss_pred ceeeCHHHHHHHHHHHH-------------HHHcCCCHHHHHHHHHcCc--------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 44699999998866532 3557888888888886543 22233455555555566666655
Q ss_pred HHHHH
Q 023113 212 EVQEL 216 (287)
Q Consensus 212 e~~~l 216 (287)
.++.|
T Consensus 95 ~~~~l 99 (103)
T cd01106 95 LIKTI 99 (103)
T ss_pred HHHHH
Confidence 55444
No 113
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.17 E-value=88 Score=23.84 Aligned_cols=17 Identities=35% Similarity=0.485 Sum_probs=7.1
Q ss_pred HHHhhhhHHHHHHHHHH
Q 023113 196 KRCCENLTEENRRLQKE 212 (287)
Q Consensus 196 k~~~e~l~~en~~l~~e 212 (287)
....+.|..||+.|+.|
T Consensus 45 q~~reaL~~eneqlk~e 61 (79)
T COG3074 45 QHQREALERENEQLKEE 61 (79)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 33334444444444443
No 114
>PRK04217 hypothetical protein; Provisional
Probab=38.72 E-value=55 Score=26.71 Aligned_cols=45 Identities=13% Similarity=0.031 Sum_probs=32.5
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH
Q 023113 133 LRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 182 (287)
Q Consensus 133 t~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak 182 (287)
..++.+|..++...|...- ...+||+.+|++...|...+..-+.+
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkk 85 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKK 85 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 3578888888877764332 45679999999999998877543333
No 115
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=38.67 E-value=72 Score=24.29 Aligned_cols=32 Identities=31% Similarity=0.331 Sum_probs=19.5
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
++--.....|.-+.+.|+++|..|..|++.++
T Consensus 14 qqAvdTI~LLQmEieELKEknn~l~~e~q~~q 45 (79)
T COG3074 14 QQAIDTITLLQMEIEELKEKNNSLSQEVQNAQ 45 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHhhHhHHHHHHHH
Confidence 33333445566677777777777777766543
No 116
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=38.57 E-value=4.2 Score=37.32 Aligned_cols=44 Identities=7% Similarity=0.019 Sum_probs=38.3
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSERE 101 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~ 101 (287)
|.-.|...||..+|-+++++--+ +.....+-.|.+||+|++.+-
T Consensus 115 QV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKw 159 (268)
T KOG0485|consen 115 QVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKW 159 (268)
T ss_pred HHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHH
Confidence 77788999999999999999877 777888999999999988543
No 117
>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=38.32 E-value=1.8e+02 Score=23.10 Aligned_cols=71 Identities=18% Similarity=0.183 Sum_probs=44.1
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+.+++..|... ...+.+|++-..|+..+........ ........|....+.+.++.+.|+.
T Consensus 36 yR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (113)
T cd01109 36 IRDFTEEDLEWLEFI-------------KCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQE 100 (113)
T ss_pred CccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899888888433 3357788888888888875432211 1122345566666666666666666
Q ss_pred HHHHHH
Q 023113 212 EVQELR 217 (287)
Q Consensus 212 e~~~lr 217 (287)
.++.|.
T Consensus 101 ~~~~l~ 106 (113)
T cd01109 101 TLAYLD 106 (113)
T ss_pred HHHHHH
Confidence 665554
No 118
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=38.21 E-value=44 Score=38.03 Aligned_cols=62 Identities=18% Similarity=0.308 Sum_probs=55.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhh
Q 023113 128 ASRKKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 128 ~rrkRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~ 189 (287)
.++-+..+-.+++..|-.+|-.+.-|+.+.+.-|....+.+.+++.+||+|-|.|.++.+..
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~ 766 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVP 766 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhccc
Confidence 45556677779999999999999999999999999999999999999999999999887733
No 119
>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=38.19 E-value=57 Score=30.69 Aligned_cols=34 Identities=21% Similarity=0.211 Sum_probs=20.7
Q ss_pred hhhhhhhHHHHHHhhhhHHHH----HHHHHHHHHHHhh
Q 023113 186 KQTEVDCEYLKRCCENLTEEN----RRLQKEVQELRSL 219 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en----~~l~~e~~~lr~l 219 (287)
.+...+++.||++...+..+. +.++.|+++||++
T Consensus 69 ~~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~L 106 (283)
T TIGR00219 69 NNLEYENYKLRQELLKKNQQLEILTQNLKQENVRLREL 106 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777777765553222 2377788888854
No 120
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=37.56 E-value=4.7 Score=38.63 Aligned_cols=47 Identities=13% Similarity=0.057 Sum_probs=42.6
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREPIG 104 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~~~ 104 (287)
|+..|.+.|..--|-+++||.++ ...+..+.-|..||+||+.+-...
T Consensus 183 Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq 230 (309)
T KOG0488|consen 183 QLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQ 230 (309)
T ss_pred HHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHH
Confidence 99999999999999999999998 888999999999999998766543
No 121
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=37.56 E-value=2e+02 Score=22.61 Aligned_cols=45 Identities=13% Similarity=0.182 Sum_probs=33.5
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-Cccchhhhhhhhh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNL-RPRQVEVWFQNRR 180 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL-~~rqVqvWFQNRR 180 (287)
+.+|+.+....+-+.+....+ ....+|+++|+ ...++..|-+.-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~ 50 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQ 50 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHH
Confidence 677898887666666655554 46689999996 9999998875433
No 122
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=36.99 E-value=84 Score=24.36 Aligned_cols=26 Identities=35% Similarity=0.376 Sum_probs=13.1
Q ss_pred hhhHHHHHHhhhhHHHHHHHHHHHHH
Q 023113 190 VDCEYLKRCCENLTEENRRLQKEVQE 215 (287)
Q Consensus 190 ~~~~~Lk~~~e~l~~en~~l~~e~~~ 215 (287)
.....|+-+.+.|+++|..|..+++.
T Consensus 18 dtI~LLqmEieELKekn~~L~~e~~~ 43 (79)
T PRK15422 18 DTITLLQMEIEELKEKNNSLSQEVQN 43 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555555555554444
No 123
>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=36.49 E-value=1.4e+02 Score=22.72 Aligned_cols=22 Identities=9% Similarity=0.141 Sum_probs=17.4
Q ss_pred HHHHHHHhCCCccchhhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQNR 179 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQNR 179 (287)
..++|+.+|++.+.|+.|.+..
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~G 25 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLG 25 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 3578899999999999987543
No 124
>PF01486 K-box: K-box region; InterPro: IPR002487 MADS genes in plants encode key developmental regulators of vegetative and reproductive development. The majority of the plant MADS proteins share a stereotypical MIKC structure. It comprises (from N- to C-terminal) an N-terminal domain, which is, however, present only in a minority of proteins; a MADS domain (see PDOC00302 from PROSITEDOC, IPR002100 from INTERPRO), which is the major determinant of DNA-binding but which also performs dimerisation and accessory factor binding functions; a weakly conserved intervening (I) domain, which constitutes a key molecular determinant for the selective formation of DNA-binding dimers; a keratin-like (K-box) domain, which promotes protein dimerisation; and a C-terminal (C) domain, which is involved in transcriptional activation or in the formation of ternary or quaternary protein complexes. The 80-amino acid K-box domain was originally identified as a region with low but significant similarity to a region of keratin, which is part of the coiled-coil sequence constituting the central rod-shaped domain of keratin [, , ]. The K-box protein-protein interaction domain which mediates heterodimerization of MIKC-type MADS proteins contains several heptad repeats in which the first and the fourth positions are occupied by hydrophobic amino acids suggesting that the K-box domain forms three amphipathic alpha-helices referred to as K1, K2, and K3 [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=36.07 E-value=61 Score=25.40 Aligned_cols=44 Identities=30% Similarity=0.357 Sum_probs=28.9
Q ss_pred cchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHH
Q 023113 170 RQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQ 214 (287)
Q Consensus 170 rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~ 214 (287)
.++..|...=|++ |.+........|+.....+.++|..|+.+++
T Consensus 56 ~~Le~aL~~VR~r-K~~~l~~~i~~l~~ke~~l~~en~~L~~~~~ 99 (100)
T PF01486_consen 56 QQLESALKRVRSR-KDQLLMEQIEELKKKERELEEENNQLRQKIE 99 (100)
T ss_pred HhhhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4445555444444 3345666777788888888888888887764
No 125
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=35.88 E-value=1.5e+02 Score=21.80 Aligned_cols=27 Identities=37% Similarity=0.484 Sum_probs=17.6
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
+..-...+..|..+...|++++.++|+
T Consensus 34 LqeaE~rn~eL~~ei~~L~~e~ee~r~ 60 (61)
T PF08826_consen 34 LQEAEKRNRELEQEIERLKKEMEELRS 60 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHH-
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 333445566677788888888877764
No 126
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=35.77 E-value=86 Score=23.80 Aligned_cols=44 Identities=25% Similarity=0.319 Sum_probs=25.6
Q ss_pred hhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 172 VEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 172 VqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
++|.|-..|.. +......+.+-.++-.|+.+...|++++++++.
T Consensus 21 LrI~fLee~l~---~~~~~~~~~~~keNieLKve~~~L~~el~~~~~ 64 (75)
T PF07989_consen 21 LRIYFLEERLQ---KLGPESIEELLKENIELKVEVESLKRELQEKKK 64 (75)
T ss_pred HHHHHHHHHHH---hcccccHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666655554 222334444555555677777777777776653
No 127
>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=35.15 E-value=23 Score=23.29 Aligned_cols=23 Identities=17% Similarity=0.095 Sum_probs=19.3
Q ss_pred HHHHHHHhCCCccchhhhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
..++|+.+|+++..|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976554
No 128
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=35.07 E-value=65 Score=33.41 Aligned_cols=26 Identities=31% Similarity=0.377 Sum_probs=16.9
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+..|-++|+.|+.||..|+.++..|-
T Consensus 311 Lq~ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 311 LQALLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 34456677777777777777766664
No 129
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.94 E-value=73 Score=25.87 Aligned_cols=46 Identities=15% Similarity=0.169 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.++..+..++...|-.. ....++|..+|++...|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 46666777766554322 23568999999999999998865444443
No 130
>PRK00118 putative DNA-binding protein; Validated
Probab=34.80 E-value=1.8e+02 Score=23.43 Aligned_cols=45 Identities=13% Similarity=0.130 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
++..|..++...|... ....+||+.+|++...|..|...-|.+.|
T Consensus 18 L~ekqRevl~L~y~eg-----~S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLDD-----YSLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 4566666665555432 23457999999999999999875444443
No 131
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=34.53 E-value=15 Score=38.32 Aligned_cols=46 Identities=13% Similarity=0.148 Sum_probs=29.5
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhC-------CCccchhhhhhhhhhHHHhhhhh
Q 023113 144 EETFKEHSTLNPKQKLALAKQLN-------LRPRQVEVWFQNRRARTKLKQTE 189 (287)
Q Consensus 144 e~~F~~~~~p~~~~r~~LA~~Lg-------L~~rqVqvWFQNRRak~Krkq~~ 189 (287)
+.+|-++..+......+--+++. ...+-|+.||.|||+++|+-+..
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~~ 760 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKMS 760 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhcc
Confidence 34455666666554444333332 35677999999999999986544
No 132
>PF15058 Speriolin_N: Speriolin N terminus
Probab=34.18 E-value=52 Score=29.69 Aligned_cols=24 Identities=38% Similarity=0.382 Sum_probs=14.1
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQE 215 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~ 215 (287)
|+-|+..++.|..||++|++.|.=
T Consensus 7 yeGlrhqierLv~ENeeLKKlVrL 30 (200)
T PF15058_consen 7 YEGLRHQIERLVRENEELKKLVRL 30 (200)
T ss_pred hHHHHHHHHHHHhhhHHHHHHHHH
Confidence 444555666666666666665543
No 133
>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=33.97 E-value=66 Score=25.13 Aligned_cols=46 Identities=15% Similarity=0.208 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.++..+..++...|-. .....+||+.+|+++..|..+...-+.+.|
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566666666555432 223458999999999999988765544443
No 134
>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=33.90 E-value=2.5e+02 Score=22.48 Aligned_cols=72 Identities=13% Similarity=0.015 Sum_probs=43.0
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+.+++..|... ...+.+|++-..|+..|.+..... .....-...|....+.+.++.+.|+.
T Consensus 36 yR~Y~~~~i~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 36 YRLYGEADLARLRFI-------------RRAQALGFSLAEIRELLSLRDDGA--APCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred CccCCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456899999888433 346788888888888886654321 01111234455555566666666655
Q ss_pred HHHHHHh
Q 023113 212 EVQELRS 218 (287)
Q Consensus 212 e~~~lr~ 218 (287)
..+.|..
T Consensus 101 ~~~~l~~ 107 (123)
T cd04770 101 LRAELAG 107 (123)
T ss_pred HHHHHHH
Confidence 5555543
No 135
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=33.88 E-value=4.2 Score=37.83 Aligned_cols=45 Identities=9% Similarity=-0.010 Sum_probs=39.4
Q ss_pred hhhhhhhccCCCCCCCccccccc-cCCCCCCCCcccCCCCCCCCCC
Q 023113 58 DTRSFLRGIDVNQAPTVADCEEE-NGVSSPNSTVSSISGKRSEREP 102 (287)
Q Consensus 58 q~~~l~~~fd~n~~P~~a~~e~~-~~~ssp~s~i~s~~~~~s~r~~ 102 (287)
|+-.|...|..|.|-+..-+-+. ..+...+--|.+||+||+.+..
T Consensus 170 QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~K 215 (261)
T KOG0489|consen 170 QLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWK 215 (261)
T ss_pred hhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHH
Confidence 99999999999999988777776 7788889999999999986554
No 136
>PF13518 HTH_28: Helix-turn-helix domain
Probab=33.72 E-value=32 Score=22.88 Aligned_cols=22 Identities=14% Similarity=0.357 Sum_probs=18.8
Q ss_pred HHHHHHHhCCCccchhhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQNR 179 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQNR 179 (287)
..++|+++|++..+|..|.+.-
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~y 36 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKRY 36 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHHH
Confidence 4568999999999999998653
No 137
>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=33.60 E-value=45 Score=23.63 Aligned_cols=33 Identities=36% Similarity=0.419 Sum_probs=25.6
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhh
Q 023113 138 EQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEV 174 (287)
Q Consensus 138 ~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqv 174 (287)
.|+..|+-.|+ +...+.. +||..+|++++.|+.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~ 38 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKN 38 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHH
Confidence 57888888888 6666655 899999999987754
No 138
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=33.51 E-value=73 Score=26.25 Aligned_cols=33 Identities=30% Similarity=0.395 Sum_probs=26.6
Q ss_pred hhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhh
Q 023113 188 TEVDCEYLKRCCENLTEENRRLQKEVQELRSLK 220 (287)
Q Consensus 188 ~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~ 220 (287)
-+++.+.||...-.|.+.|..|+.|+.=||.+.
T Consensus 65 VREEVe~Lk~qI~eL~er~~~Le~EN~lLk~~~ 97 (123)
T KOG4797|consen 65 VREEVEVLKEQIRELEERNSALERENSLLKTLA 97 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 345677888888889999999999988888764
No 139
>PHA02955 hypothetical protein; Provisional
Probab=33.34 E-value=51 Score=30.09 Aligned_cols=42 Identities=14% Similarity=0.176 Sum_probs=34.8
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCccchhhhhhh
Q 023113 137 KEQSLLLEETFKEH-STLNPKQKLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 137 ~~Ql~~Le~~F~~~-~~p~~~~r~~LA~~LgL~~rqVqvWFQN 178 (287)
..|+..|-+.|.+. ..+..++|.+++++||+....|..||.+
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 45677777777766 6788999999999999999878888876
No 140
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=32.83 E-value=1.4e+02 Score=25.29 Aligned_cols=48 Identities=19% Similarity=0.103 Sum_probs=34.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.+.++..|..+|.-.+ .. ....++|..+|++...|..+-..-+.+.++
T Consensus 4 ~~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4678999999997742 11 235689999999999998877655555443
No 141
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=32.70 E-value=47 Score=27.95 Aligned_cols=46 Identities=11% Similarity=0.260 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
++..+..++...|- ......+||..+|+++..|+++...-|.+.|+
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 45555555554442 22235689999999999999988755555443
No 142
>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=32.34 E-value=15 Score=27.92 Aligned_cols=34 Identities=12% Similarity=0.059 Sum_probs=24.5
Q ss_pred HHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhh
Q 023113 145 ETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 145 ~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQN 178 (287)
..|.-..|.......+||..+|+++..|+.|+.+
T Consensus 22 ~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 22 AAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 3344444434445678999999999999999864
No 143
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=32.16 E-value=49 Score=26.32 Aligned_cols=40 Identities=23% Similarity=0.268 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVE 173 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVq 173 (287)
.+.++|+..-.+.|+.+--.+.-..+++|.+||+++--|+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 3667888888888888877777888899999999886554
No 144
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=32.00 E-value=1.2e+02 Score=24.35 Aligned_cols=29 Identities=21% Similarity=0.533 Sum_probs=21.5
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQE 215 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~ 215 (287)
+.+.-+..|++.|+.|+...+.|+.++.+
T Consensus 68 rLqqa~~~Lkkk~e~L~~age~Le~~i~~ 96 (97)
T PF15136_consen 68 RLQQARDQLKKKCEELRQAGEELERDIEQ 96 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33445567888888888888888887754
No 145
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=31.85 E-value=2.7e+02 Score=22.61 Aligned_cols=70 Identities=13% Similarity=0.060 Sum_probs=40.5
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+..++..|. ....++.+|++-..|+..|..... .....-...|....+.+.++...|+.
T Consensus 35 ~R~Y~~~~l~~l~-------------~I~~l~~~G~sl~eI~~~l~~~~~----~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 35 YRRYPEETVKRLR-------------FIKRAQELGFSLEEIGGLLGLVDG----THCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred CEeECHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHhcccC----CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568888888883 234468889999999888865432 00111123444445555555555555
Q ss_pred HHHHHHh
Q 023113 212 EVQELRS 218 (287)
Q Consensus 212 e~~~lr~ 218 (287)
-...|..
T Consensus 98 ~~~~L~~ 104 (124)
T TIGR02051 98 IERLLEE 104 (124)
T ss_pred HHHHHHH
Confidence 5444443
No 146
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=31.67 E-value=68 Score=27.59 Aligned_cols=46 Identities=13% Similarity=0.114 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.++..+..+|...|-.. ..-.++|+.||++...|+++...-|.+.|
T Consensus 142 ~L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr 187 (194)
T PRK09646 142 ALTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLR 187 (194)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHH
Confidence 46666766666554222 33468899999999999988855444443
No 147
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=31.50 E-value=85 Score=25.81 Aligned_cols=32 Identities=31% Similarity=0.290 Sum_probs=26.7
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
.+-.+...||+....+.+||..|+-|++.||.
T Consensus 19 ~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~ 50 (114)
T COG4467 19 VLLAELGGLKQHLGSLVEENTALRLENEKLRE 50 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHH
Confidence 34456677889999999999999999999984
No 148
>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=31.47 E-value=1e+02 Score=28.57 Aligned_cols=37 Identities=19% Similarity=0.218 Sum_probs=24.6
Q ss_pred hhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 180 RARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 180 Rak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
|-|.|..+.+.++..++.....|+.|.+.|++++.+|
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kL 126 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKL 126 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455556666666667777777777777777776554
No 149
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=31.30 E-value=73 Score=29.36 Aligned_cols=30 Identities=30% Similarity=0.305 Sum_probs=16.9
Q ss_pred hhHHHHHHhhhhHHHHHHHHHHHHHHHhhh
Q 023113 191 DCEYLKRCCENLTEENRRLQKEVQELRSLK 220 (287)
Q Consensus 191 ~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~ 220 (287)
++..++++++.|++|+..|+.++.++++++
T Consensus 70 ~~~~l~~en~~L~~e~~~l~~~~~~~~~l~ 99 (276)
T PRK13922 70 SLFDLREENEELKKELLELESRLQELEQLE 99 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555666666666666666665554433
No 150
>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi. In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].
Probab=30.94 E-value=1.2e+02 Score=21.64 Aligned_cols=28 Identities=36% Similarity=0.459 Sum_probs=20.5
Q ss_pred hhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 191 DCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 191 ~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
+....+.....|..||+.|+.++..++.
T Consensus 23 d~~~a~~rl~~l~~EN~~Lr~eL~~~r~ 50 (52)
T PF12808_consen 23 DRSAARKRLSKLEGENRLLRAELERLRS 50 (52)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4445666777888899999888876653
No 151
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=30.91 E-value=49 Score=27.29 Aligned_cols=46 Identities=15% Similarity=0.103 Sum_probs=30.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
++..+..++...|-. ...-.+||..+|++...|..|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555554422 2234689999999999999988755554443
No 152
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=30.90 E-value=49 Score=27.37 Aligned_cols=45 Identities=13% Similarity=-0.017 Sum_probs=30.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRART 183 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~ 183 (287)
.++..+..+|...|-. ...-.++|..+|++...|+.|...-+.+.
T Consensus 128 ~L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~L 172 (182)
T PRK09652 128 SLPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREAL 172 (182)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 4677777777665432 12245889999999999999887433333
No 153
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=30.43 E-value=1.2e+02 Score=24.65 Aligned_cols=37 Identities=30% Similarity=0.417 Sum_probs=21.6
Q ss_pred hhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 177 QNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 177 QNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
|||-++.-+.+-+.|++. +.....|.+.|..+++.++
T Consensus 57 QNRq~~~dr~ra~~D~~i----nl~ae~ei~~l~~~l~~l~ 93 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQI----NLKAEQEIERLHRKLDALR 93 (108)
T ss_pred hhHhHHHHHHHHHHHHHH----HHHhHHHHHHHHHHHHHHH
Confidence 787665544444445443 4445566666776666665
No 154
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=30.00 E-value=1.1e+02 Score=29.98 Aligned_cols=39 Identities=23% Similarity=0.375 Sum_probs=31.5
Q ss_pred hhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 179 RRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 179 RRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
++.+...++.+..++.++++|....+|...|-.|+.+..
T Consensus 137 ~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~l 175 (401)
T PF06785_consen 137 RHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEAL 175 (401)
T ss_pred HHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHH
Confidence 466677778888888899999999999999988876654
No 155
>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=29.99 E-value=2.9e+02 Score=23.09 Aligned_cols=72 Identities=7% Similarity=0.016 Sum_probs=36.6
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhh-HHHhhhhhhhhHHHHHHhhhhHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRA-RTKLKQTEVDCEYLKRCCENLTEENRRLQ 210 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRa-k~Krkq~~~~~~~Lk~~~e~l~~en~~l~ 210 (287)
...|+..++..|.... . .+.+|++-..|+-++.+... .....+.....+.+....+.+......|+
T Consensus 35 ~R~Y~~~~l~~l~~I~------------~-lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L~ 101 (134)
T cd04779 35 YRYYDETALDRLQLIE------------H-LKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQLK 101 (134)
T ss_pred CeeECHHHHHHHHHHH------------H-HHHCCCCHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568998888885441 2 35566666666666655432 11122233334444444444544444444
Q ss_pred HHHHHH
Q 023113 211 KEVQEL 216 (287)
Q Consensus 211 ~e~~~l 216 (287)
.-.+.+
T Consensus 102 ~~~~~l 107 (134)
T cd04779 102 PIASQT 107 (134)
T ss_pred HHHHHH
Confidence 444333
No 156
>PRK10072 putative transcriptional regulator; Provisional
Probab=29.23 E-value=29 Score=27.62 Aligned_cols=41 Identities=20% Similarity=0.127 Sum_probs=29.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 181 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRa 181 (287)
+.+...+..|..... .+ ..+||+.+|++...|..|.+.+|.
T Consensus 32 ~~~~~eik~LR~~~g----lT---Q~elA~~lGvS~~TVs~WE~G~r~ 72 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----LK---IDDFARVLGVSVAMVKEWESRRVK 72 (96)
T ss_pred cCChHHHHHHHHHcC----CC---HHHHHHHhCCCHHHHHHHHcCCCC
Confidence 446666666644322 22 568999999999999999998764
No 157
>PF12269 zf-CpG_bind_C: CpG binding protein zinc finger C terminal domain; InterPro: IPR022056 This domain family is found in eukaryotes, and is approximately 240 amino acids in length. This domain is the zinc finger domain of a CpG binding DNA methyltransferase protein. It contains a CxxC motif which forms the zinc finger and binds to DNA.
Probab=28.97 E-value=1.8e+02 Score=27.08 Aligned_cols=76 Identities=12% Similarity=0.286 Sum_probs=37.6
Q ss_pred ccchhhhhhhh-----hhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhhhcChhhhccCCCC---CCCCCCCC
Q 023113 169 PRQVEVWFQNR-----RARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRSLKLSPQLYMNMNPP---TTLTMCPS 240 (287)
Q Consensus 169 ~rqVqvWFQNR-----Rak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l~~~~~~~~~~~~~---~~~~~c~s 240 (287)
+.+|+-||.+- ..+.+..+.+.+....+.....|......|..-+..++.....+.....-..- .....|..
T Consensus 10 PqRIQEw~~~p~~A~E~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~~~~~~~~~e~~D~~~~~~Cv~ 89 (236)
T PF12269_consen 10 PQRIQEWQLSPCVAEEQNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFTVDQDEEQNDDESEDDDLSIYCVT 89 (236)
T ss_pred hHHHHHhcCCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccccccccccccceeeeeee
Confidence 77888888653 11223333333444444555556666666666666655443332111001111 11246999
Q ss_pred CCCC
Q 023113 241 CERV 244 (287)
Q Consensus 241 c~~~ 244 (287)
|+..
T Consensus 90 Cg~~ 93 (236)
T PF12269_consen 90 CGHE 93 (236)
T ss_pred CCCc
Confidence 9973
No 158
>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]
Probab=28.62 E-value=88 Score=32.72 Aligned_cols=44 Identities=41% Similarity=0.390 Sum_probs=26.9
Q ss_pred hhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 174 VWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 174 vWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+=-|.+|.|.-.+...-.-..|-.+|..|.+||-.|++.|..||
T Consensus 147 ~E~qR~rlr~elKe~KfRE~RllseYSELEEENIsLQKqVs~LR 190 (772)
T KOG0999|consen 147 VEDQRRRLRDELKEYKFREARLLSEYSELEEENISLQKQVSNLR 190 (772)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHh
Confidence 33466666665555444444566666667777777777666655
No 159
>PF03980 Nnf1: Nnf1 ; InterPro: IPR007128 NNF1 is an essential yeast gene required for proper spindle orientation, nucleolar and nuclear envelope structure and mRNA export [].
Probab=28.50 E-value=99 Score=24.49 Aligned_cols=29 Identities=38% Similarity=0.457 Sum_probs=24.0
Q ss_pred hhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 190 VDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 190 ~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
...+.|+...+.+..+|..|..+|.++|+
T Consensus 80 ~~~~~L~~~l~~l~~eN~~L~~~i~~~r~ 108 (109)
T PF03980_consen 80 KEREQLNARLQELEEENEALAEEIQEQRK 108 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34567888889999999999999988764
No 160
>PF10226 DUF2216: Uncharacterized conserved proteins (DUF2216); InterPro: IPR019359 Proteins in this entry are found in Metazoa and contain a coiled-coil domain. Some annotation suggests it might be PKR, the Hepatitis delta antigen-interacting protein A, but this could not be confirmed.
Probab=28.30 E-value=1.1e+02 Score=27.52 Aligned_cols=19 Identities=47% Similarity=0.648 Sum_probs=9.8
Q ss_pred hhhhHHHHHHHHHHHHHHH
Q 023113 199 CENLTEENRRLQKEVQELR 217 (287)
Q Consensus 199 ~e~l~~en~~l~~e~~~lr 217 (287)
+..|++.|++|+.++++||
T Consensus 57 IR~LKe~NqkLqedNqELR 75 (195)
T PF10226_consen 57 IRGLKEVNQKLQEDNQELR 75 (195)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555554
No 161
>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=28.28 E-value=2.9e+02 Score=22.16 Aligned_cols=69 Identities=17% Similarity=0.190 Sum_probs=43.2
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHH
Q 023113 131 KKLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQ 210 (287)
Q Consensus 131 kRt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~ 210 (287)
....|+..++..|... ...+.+|++-..|+..|.+.... ....+.+....+.+.++.++|+
T Consensus 34 gyR~Y~~~~l~~l~~I-------------~~lr~~G~~L~eI~~~l~~~~~~------~~~~~~l~~~~~~l~~~i~~l~ 94 (120)
T cd04781 34 LRRQYDPQVLDRLALI-------------ALGRAAGFSLDEIQAMLSHDGKP------PIDRQLLKAKAAELDQQIQRLQ 94 (120)
T ss_pred CceecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhccCCc------HHHHHHHHHHHHHHHHHHHHHH
Confidence 3556899998888432 45777888888888888764311 1112345555556666666666
Q ss_pred HHHHHHHh
Q 023113 211 KEVQELRS 218 (287)
Q Consensus 211 ~e~~~lr~ 218 (287)
.....|..
T Consensus 95 ~~~~~L~~ 102 (120)
T cd04781 95 AMRELLRH 102 (120)
T ss_pred HHHHHHHH
Confidence 65555543
No 162
>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=27.15 E-value=88 Score=31.88 Aligned_cols=10 Identities=40% Similarity=0.331 Sum_probs=4.6
Q ss_pred cCCHHHHHHH
Q 023113 134 RLSKEQSLLL 143 (287)
Q Consensus 134 ~~T~~Ql~~L 143 (287)
.++++++..|
T Consensus 41 ~ltpee~kal 50 (472)
T TIGR03752 41 ELSPEELKAL 50 (472)
T ss_pred cCCcchhHhc
Confidence 3455554444
No 163
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.12 E-value=3.4e+02 Score=21.93 Aligned_cols=70 Identities=14% Similarity=0.126 Sum_probs=42.5
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+.+++..|. .....+.+|++-..|+-+|...... ....-...|+...+.+.++..+|+.
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~----~~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 36 YRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDDGT----DCSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred CeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcccCC----CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999988884 3345688999999999888764421 0111123344555555566666655
Q ss_pred HHHHHHh
Q 023113 212 EVQELRS 218 (287)
Q Consensus 212 e~~~lr~ 218 (287)
-...|..
T Consensus 99 ~~~~l~~ 105 (126)
T cd04783 99 MRASLQE 105 (126)
T ss_pred HHHHHHH
Confidence 5555543
No 164
>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=26.91 E-value=1.1e+02 Score=20.13 Aligned_cols=36 Identities=14% Similarity=0.220 Sum_probs=25.0
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhh
Q 023113 136 SKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 136 T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQ 177 (287)
+..|..++...+. . ....++|+.+|++...|..|..
T Consensus 2 ~~~e~~i~~~~~~--~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE--G----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc--C----CCHHHHHHHHCCCHHHHHHHHH
Confidence 4556666655432 1 2456889999999999998875
No 165
>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=26.76 E-value=74 Score=21.21 Aligned_cols=38 Identities=29% Similarity=0.339 Sum_probs=26.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWF 176 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWF 176 (287)
.++.++++.+.+.+... ....+||+.+|++...|.-++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 46666677777777654 235689999999998887655
No 166
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=26.60 E-value=1.6e+02 Score=21.26 Aligned_cols=25 Identities=20% Similarity=0.434 Sum_probs=11.5
Q ss_pred hHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 192 CEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 192 ~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
...++++++.+.++.+.+.+-++.|
T Consensus 16 i~tvk~en~~i~~~ve~i~envk~l 40 (55)
T PF05377_consen 16 INTVKKENEEISESVEKIEENVKDL 40 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444
No 167
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.46 E-value=1.8e+02 Score=26.31 Aligned_cols=69 Identities=6% Similarity=0.043 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 137 KEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 137 ~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
..|+..|+.....-..--.....++..++.-...+|.- .+.++..|+.+.+.++.+++.|+.+++.+
T Consensus 99 e~el~~l~~~l~~~~~~~~~~~~~l~~~~~~~~~~~~~-------------L~~~n~~L~~~l~~~~~~~~~l~~~~~~~ 165 (206)
T PRK10884 99 ENQVKTLTDKLNNIDNTWNQRTAEMQQKVAQSDSVING-------------LKEENQKLKNQLIVAQKKVDAANLQLDDK 165 (206)
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH-------------HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q ss_pred Hh
Q 023113 217 RS 218 (287)
Q Consensus 217 r~ 218 (287)
+.
T Consensus 166 ~~ 167 (206)
T PRK10884 166 QR 167 (206)
T ss_pred HH
No 168
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=26.36 E-value=1.5e+02 Score=24.00 Aligned_cols=47 Identities=19% Similarity=0.195 Sum_probs=35.0
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 133 LRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 133 t~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
..+|..+..+|.- +..+ + ...++|+.++++++.|+.+.+|=+.|..-
T Consensus 148 ~~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~~ 194 (211)
T PRK15369 148 PLLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLDV 194 (211)
T ss_pred cCCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 3488888888876 4333 2 25688999999999999998876665543
No 169
>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=26.18 E-value=38 Score=24.33 Aligned_cols=20 Identities=20% Similarity=0.328 Sum_probs=17.7
Q ss_pred HHHHHHHhCCCccchhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQ 177 (287)
..+||..||++.+.|..|-+
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~ 35 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD 35 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH
Confidence 45889999999999999974
No 170
>PF06305 DUF1049: Protein of unknown function (DUF1049); InterPro: IPR010445 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=26.12 E-value=68 Score=22.93 Aligned_cols=13 Identities=38% Similarity=0.741 Sum_probs=6.5
Q ss_pred HHHHHHHHHHHHH
Q 023113 204 EENRRLQKEVQEL 216 (287)
Q Consensus 204 ~en~~l~~e~~~l 216 (287)
.+.+.+++|+++|
T Consensus 55 k~l~~le~e~~~l 67 (68)
T PF06305_consen 55 KELKKLEKELEQL 67 (68)
T ss_pred HHHHHHHHHHHhc
Confidence 3444455555544
No 171
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=26.09 E-value=39 Score=22.52 Aligned_cols=23 Identities=22% Similarity=0.333 Sum_probs=17.1
Q ss_pred HHHHHHHHHhCCCccchhhhhhh
Q 023113 156 KQKLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 156 ~~r~~LA~~LgL~~rqVqvWFQN 178 (287)
....++|+.+|++...|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 44568999999999999999754
No 172
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=25.91 E-value=58 Score=27.79 Aligned_cols=46 Identities=17% Similarity=0.209 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
++..+..++...| .......++|..+|++...|++|+..-|.+.|+
T Consensus 142 L~~~~~~v~~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAY-----YEGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 4444444444433 222335689999999999999998654444443
No 173
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=25.62 E-value=1.4e+02 Score=28.01 Aligned_cols=37 Identities=32% Similarity=0.530 Sum_probs=26.7
Q ss_pred hhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 179 RRARTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 179 RRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
||.|.|+++.. ..+......|..||+.|+.+|.+|+.
T Consensus 207 ~kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~ 243 (269)
T KOG3119|consen 207 RKSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKK 243 (269)
T ss_pred HHhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666666655 44556677788899999999988873
No 174
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=25.62 E-value=41 Score=23.85 Aligned_cols=21 Identities=19% Similarity=0.298 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQN 178 (287)
..++|+.+|++.+.|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999654
No 175
>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=25.61 E-value=1.2e+02 Score=23.41 Aligned_cols=22 Identities=36% Similarity=0.419 Sum_probs=12.1
Q ss_pred HHHHhhhhHHHHHHHHHHHHHH
Q 023113 195 LKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 195 Lk~~~e~l~~en~~l~~e~~~l 216 (287)
.+.+|+.|+.||+-|+.-|..|
T Consensus 42 Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 42 VKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555555555555555555
No 176
>PF09278 MerR-DNA-bind: MerR, DNA binding; InterPro: IPR015358 This entry represents a family of DNA-binding domains that are predominantly found in the prokaryotic transcriptional regulator MerR. They adopt a structure consisting of a core of three alpha helices, with an architecture that is similar to that of the 'winged helix' fold []. ; PDB: 3QAO_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q09_A 1Q08_B 1Q0A_B 1Q07_A ....
Probab=25.51 E-value=1.9e+02 Score=20.24 Aligned_cols=18 Identities=6% Similarity=0.206 Sum_probs=12.9
Q ss_pred HHHHHhCCCccchhhhhh
Q 023113 160 ALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 160 ~LA~~LgL~~rqVqvWFQ 177 (287)
.-++.+|++-..|+.++.
T Consensus 8 ~~~r~lGfsL~eI~~~l~ 25 (65)
T PF09278_consen 8 RRLRELGFSLEEIRELLE 25 (65)
T ss_dssp HHHHHTT--HHHHHHHHH
T ss_pred HHHHHcCCCHHHHHHHHh
Confidence 457889999999998883
No 177
>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=25.41 E-value=71 Score=25.74 Aligned_cols=44 Identities=14% Similarity=0.111 Sum_probs=27.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHH
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRART 183 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~ 183 (287)
++..+..+|...|- ......+||..+|+++..|+.+...-|.+.
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~L 157 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKEL 157 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 45555555555432 112345789999999999998775444443
No 178
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=25.39 E-value=1.2e+02 Score=23.13 Aligned_cols=43 Identities=16% Similarity=0.214 Sum_probs=32.9
Q ss_pred CCHHHHHHHHHHHhh-----cCCCCHHHHHHHHHHhCCCccchhhhhh
Q 023113 135 LSKEQSLLLEETFKE-----HSTLNPKQKLALAKQLNLRPRQVEVWFQ 177 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~-----~~~p~~~~r~~LA~~LgL~~rqVqvWFQ 177 (287)
++.+|+..|...|.. ..+.+..+...+-+.+|+++..|..+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678899999999874 3467777777776778888888777764
No 179
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=25.34 E-value=1.2e+02 Score=32.34 Aligned_cols=38 Identities=34% Similarity=0.463 Sum_probs=26.7
Q ss_pred HHHhhhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 182 RTKLKQTEVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 182 k~Krkq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
|.|+++.+.++..|+.+....++....|+.|+++||..
T Consensus 544 r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~ 581 (697)
T PF09726_consen 544 RQRRRQLESELKKLRRELKQKEEQIRELESELQELRKY 581 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44667777777778877777777777777777666643
No 180
>PRK10403 transcriptional regulator NarP; Provisional
Probab=25.34 E-value=99 Score=25.47 Aligned_cols=46 Identities=20% Similarity=0.233 Sum_probs=36.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.+|..+..+|....+. ..+.+||+.++++++.|++...|=|.|...
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 5899999988866543 335788999999999999998887776644
No 181
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=25.27 E-value=71 Score=27.89 Aligned_cols=46 Identities=22% Similarity=0.250 Sum_probs=29.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
++..+..+|...|- ......+||..+|++...|+++...-|.+.++
T Consensus 154 L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYF-----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55556566554331 22235689999999999998887655444443
No 182
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=25.22 E-value=2.7e+02 Score=20.16 Aligned_cols=19 Identities=42% Similarity=0.637 Sum_probs=13.0
Q ss_pred hhHHHHHHHHHHHHHHHhh
Q 023113 201 NLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 201 ~l~~en~~l~~e~~~lr~l 219 (287)
.+..|+++|++++.+||.+
T Consensus 37 ~l~~e~~~L~~qN~eLr~l 55 (60)
T PF14775_consen 37 ALIQEKESLEQQNEELRSL 55 (60)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3556777777777777754
No 183
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=25.11 E-value=1.9e+02 Score=22.40 Aligned_cols=19 Identities=26% Similarity=0.358 Sum_probs=9.7
Q ss_pred HHHHhhhhHHHHHHHHHHH
Q 023113 195 LKRCCENLTEENRRLQKEV 213 (287)
Q Consensus 195 Lk~~~e~l~~en~~l~~e~ 213 (287)
++...+.|..||..|+.|.
T Consensus 44 ~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 44 AQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHhhHHHHHHHHHHHHHHH
Confidence 3333444555666666554
No 184
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=24.98 E-value=1.7e+02 Score=23.85 Aligned_cols=27 Identities=22% Similarity=0.354 Sum_probs=16.4
Q ss_pred hhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 191 DCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 191 ~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+...++++++.|..++..|..++..|+
T Consensus 58 qi~~~~~e~~~L~~~~~~l~~ei~~L~ 84 (117)
T COG2919 58 QIAAQQAELEKLSARNTALEAEIKDLK 84 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344556666666666666666666554
No 185
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=24.03 E-value=81 Score=25.98 Aligned_cols=45 Identities=22% Similarity=0.249 Sum_probs=35.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.+|..+..+|+-.++. ..+.+||.+++++++.|++..++=|.|..
T Consensus 137 ~Lt~~E~~il~~l~~g------~~~~~Ia~~l~~s~~tv~~~~~~l~~Kl~ 181 (196)
T PRK10360 137 PLTKRERQVAEKLAQG------MAVKEIAAELGLSPKTVHVHRANLMEKLG 181 (196)
T ss_pred CCCHHHHHHHHHHHCC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 5888888888776653 25778999999999999988877666544
No 186
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=23.95 E-value=1.5e+02 Score=23.79 Aligned_cols=31 Identities=32% Similarity=0.541 Sum_probs=26.5
Q ss_pred hhhhHHHHHHhhhhHHHHHHHHHHHHHHHhh
Q 023113 189 EVDCEYLKRCCENLTEENRRLQKEVQELRSL 219 (287)
Q Consensus 189 ~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~l 219 (287)
+.+.+.|++....+..+|+.|..|+.+++..
T Consensus 14 EEEa~LlRRkl~ele~eN~~l~~EL~kyk~~ 44 (96)
T PF11365_consen 14 EEEAELLRRKLSELEDENKQLTEELNKYKSK 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4566778999999999999999999998853
No 187
>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=23.95 E-value=2.8e+02 Score=21.00 Aligned_cols=33 Identities=18% Similarity=0.161 Sum_probs=22.2
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhh
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWF 176 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWF 176 (287)
...|+..++..|... ..|...+|++...|+.-+
T Consensus 36 ~R~y~~~dv~~l~~i------------~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 36 TRRYSERDIERLRRI------------QRLTQELGVNLAGVKRIL 68 (91)
T ss_pred CeeECHHHHHHHHHH------------HHHHHHcCCCHHHHHHHH
Confidence 345999999888544 355555788777765544
No 188
>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=23.58 E-value=92 Score=30.50 Aligned_cols=28 Identities=25% Similarity=0.312 Sum_probs=20.3
Q ss_pred hhhhhhHHHHHHhhhhHHHHHHHHHHHH
Q 023113 187 QTEVDCEYLKRCCENLTEENRRLQKEVQ 214 (287)
Q Consensus 187 q~~~~~~~Lk~~~e~l~~en~~l~~e~~ 214 (287)
-.++++..||++++.|+.|-++|+.++.
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566778888888888887777765553
No 189
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=23.29 E-value=1.6e+02 Score=29.96 Aligned_cols=26 Identities=35% Similarity=0.657 Sum_probs=18.8
Q ss_pred hhhh---hhhhhHHHhhhhhhhhHHHHHH
Q 023113 173 EVWF---QNRRARTKLKQTEVDCEYLKRC 198 (287)
Q Consensus 173 qvWF---QNRRak~Krkq~~~~~~~Lk~~ 198 (287)
-+|| ||+.+|.+-++.-.+++-|++.
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~a 257 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRA 257 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4588 8999988877776676666543
No 190
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=23.25 E-value=1.2e+02 Score=29.58 Aligned_cols=26 Identities=15% Similarity=0.048 Sum_probs=14.3
Q ss_pred hhHHHHHHhhhhHHHHHHHHHHHHHH
Q 023113 191 DCEYLKRCCENLTEENRRLQKEVQEL 216 (287)
Q Consensus 191 ~~~~Lk~~~e~l~~en~~l~~e~~~l 216 (287)
++..|+.+|+.|++||..|+.++.++
T Consensus 58 ~y~~L~~EN~~Lk~Ena~L~~~l~~~ 83 (337)
T PRK14872 58 HALVLETENFLLKERIALLEERLKSY 83 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455556666666666665554443
No 191
>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=23.22 E-value=1.4e+02 Score=24.23 Aligned_cols=44 Identities=27% Similarity=0.257 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 182 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak 182 (287)
.++..+..++...|- ......++|..+|++...|+++...-|.+
T Consensus 111 ~L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~ 154 (159)
T TIGR02989 111 KLPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVR 154 (159)
T ss_pred HCCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHH
Confidence 466666666666432 22335689999999999999876544433
No 192
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=23.02 E-value=97 Score=26.14 Aligned_cols=47 Identities=17% Similarity=0.082 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.++..+..++...|-. ...-.+||..+|++...|+.++..-|.+.|.
T Consensus 131 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 3566666666665422 2234589999999999999988766655554
No 193
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=22.74 E-value=1.5e+02 Score=30.93 Aligned_cols=25 Identities=32% Similarity=0.324 Sum_probs=19.0
Q ss_pred HHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 193 EYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 193 ~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
.-|+.....|..||+.|++|+..||
T Consensus 305 ~~Le~rLq~ll~Ene~Lk~ENatLk 329 (655)
T KOG4343|consen 305 LGLEARLQALLSENEQLKKENATLK 329 (655)
T ss_pred HHHHHHHHHHHHHHHHHHhhhHHHH
Confidence 3366777778888888888887777
No 194
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.66 E-value=3.7e+02 Score=20.91 Aligned_cols=64 Identities=17% Similarity=0.130 Sum_probs=39.9
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 132 KLRLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 132 Rt~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
...|+..++..|... ...+++|++-..|+..+.... ..+.|....+.+.++...|+.
T Consensus 36 ~R~Y~~~dl~~l~~I-------------~~l~~~G~~l~ei~~~~~~~~----------~~~~l~~~~~~l~~~i~~l~~ 92 (102)
T cd04775 36 YRLYSEADLSRLEKI-------------VFLQAGGLPLEEIAGCLAQPH----------VQAILEERLQSLNREIQRLRQ 92 (102)
T ss_pred CeeeCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHcCCc----------HHHHHHHHHHHHHHHHHHHHH
Confidence 456899998888544 224667777777777665431 124455555666666666666
Q ss_pred HHHHHHh
Q 023113 212 EVQELRS 218 (287)
Q Consensus 212 e~~~lr~ 218 (287)
....|..
T Consensus 93 ~~~~l~~ 99 (102)
T cd04775 93 QQQVLAA 99 (102)
T ss_pred HHHHHHH
Confidence 6655543
No 195
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=22.61 E-value=74 Score=26.14 Aligned_cols=46 Identities=20% Similarity=0.176 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
++..+..++...|-.. ..-.++|..+|+++..|++....-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555443221 124588999999999999988755555444
No 196
>cd08315 Death_TRAILR_DR4_DR5 Death domain of Tumor necrosis factor-Related Apoptosis-Inducing Ligand Receptors. Death Domain (DD) found in Tumor necrosis factor-Related Apoptosis-Inducing Ligand (TRAIL) Receptors. In mammals, this family includes TRAILR1 (also called DR4 or TNFRSF10A) and TRAILR2 (also called DR5, TNFRSF10B, or KILLER). They function as receptors for the cytokine TRAIL and are involved in apoptosis signaling pathways. TRAIL preferentially induces apoptosis in cancer cells while exhibiting little toxicity in normal cells. DDs are protein-protein interaction domains found in a variety of domain architectures. Their common feature is that they form homodimers by self-association or heterodimers by associating with other members of the DD superfamily including CARD (Caspase activation and recruitment domain), DED (Death Effector Domain), and PYRIN. They serve as adaptors in signaling pathways and can recruit other proteins into signaling complexes.
Probab=22.50 E-value=2.1e+02 Score=22.55 Aligned_cols=35 Identities=20% Similarity=0.273 Sum_probs=24.8
Q ss_pred HHHHHHHHhhc-CCCCHHHHHHHHHHhCCCccchhh
Q 023113 140 SLLLEETFKEH-STLNPKQKLALAKQLNLRPRQVEV 174 (287)
Q Consensus 140 l~~Le~~F~~~-~~p~~~~r~~LA~~LgL~~rqVqv 174 (287)
...|..+|..- .......=..||++|||++..|..
T Consensus 3 ~~~l~~~f~~i~~~V~~~~Wk~laR~LGLse~~I~~ 38 (96)
T cd08315 3 QETLRRSFDHFIKEVPFDSWNRLMRQLGLSENEIDV 38 (96)
T ss_pred HhHHHHHHHHHHHHCCHHHHHHHHHHcCCCHHHHHH
Confidence 35677777643 344455556799999999998864
No 197
>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=22.40 E-value=1.8e+02 Score=23.70 Aligned_cols=15 Identities=33% Similarity=0.594 Sum_probs=12.1
Q ss_pred cchhhhhhhhhhHHH
Q 023113 170 RQVEVWFQNRRARTK 184 (287)
Q Consensus 170 rqVqvWFQNRRak~K 184 (287)
||.+.||-.+|.-.-
T Consensus 18 Rq~e~~FlqKr~~LS 32 (106)
T PF11594_consen 18 RQMEAFFLQKRFELS 32 (106)
T ss_pred HHHHHHHHHHHHHHH
Confidence 677999999887763
No 198
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=22.32 E-value=1.4e+02 Score=25.02 Aligned_cols=46 Identities=11% Similarity=0.167 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.++..+..++...|- ....-.++|..+|++...|+++++.-|.+.|
T Consensus 136 ~L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 136 ALPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 456666666655432 2233568899999999999998865554444
No 199
>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=22.12 E-value=55 Score=20.83 Aligned_cols=25 Identities=16% Similarity=0.432 Sum_probs=20.6
Q ss_pred HHHHHHHhCCCccchhhhhhhhhhH
Q 023113 158 KLALAKQLNLRPRQVEVWFQNRRAR 182 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQNRRak 182 (287)
..++|+.+|++.+.|..|.++..-.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~~ 27 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKLK 27 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCCC
Confidence 3578999999999999998776543
No 200
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=21.91 E-value=1.9e+02 Score=21.47 Aligned_cols=41 Identities=20% Similarity=0.303 Sum_probs=31.0
Q ss_pred chhhhhhhhhhHHHhhhhhhhhHHHHHHhhhhHHHHHHHHH
Q 023113 171 QVEVWFQNRRARTKLKQTEVDCEYLKRCCENLTEENRRLQK 211 (287)
Q Consensus 171 qVqvWFQNRRak~Krkq~~~~~~~Lk~~~e~l~~en~~l~~ 211 (287)
-|..+++.|.........+.+.+.++.+++.|..|...|..
T Consensus 19 ~v~~~~~~~~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 19 VVSAQHQTRQLNNELQKLQLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcC
Confidence 45555666766666777777888888899999888888765
No 201
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=21.79 E-value=54 Score=23.47 Aligned_cols=21 Identities=14% Similarity=0.324 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQN 178 (287)
..++|+.+|++++.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999864
No 202
>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=21.74 E-value=1.7e+02 Score=25.60 Aligned_cols=32 Identities=34% Similarity=0.486 Sum_probs=0.0
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
+....++..|+.+...|..+|+.|++++..|.
T Consensus 100 ~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~ 131 (161)
T TIGR02894 100 QALQKENERLKNQNESLQKRNEELEKELEKLR 131 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 203
>PRK10869 recombination and repair protein; Provisional
Probab=21.46 E-value=5.2e+02 Score=26.66 Aligned_cols=59 Identities=17% Similarity=0.251 Sum_probs=37.7
Q ss_pred HHHHHHhCCCccchhhhhhhhhhHHHh-hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHH
Q 023113 159 LALAKQLNLRPRQVEVWFQNRRARTKL-KQTEVDCEYLKRCCENLTEENRRLQKEVQELR 217 (287)
Q Consensus 159 ~~LA~~LgL~~rqVqvWFQNRRak~Kr-kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr 217 (287)
..|.+++|.+...|-.|++.-+.+... .......+.|+.+.+.+..+-..+-.++.+.|
T Consensus 309 ~~L~rKyg~~~~~~~~~~~~l~~eL~~L~~~e~~l~~Le~e~~~l~~~l~~~A~~LS~~R 368 (553)
T PRK10869 309 ISLARKHHVSPEELPQHHQQLLEEQQQLDDQEDDLETLALAVEKHHQQALETAQKLHQSR 368 (553)
T ss_pred HHHHHHhCCCHHHHHHHHHHHHHHHHHhhCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 367888999999999998887766554 33334455566666555555555554444444
No 204
>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=21.36 E-value=57 Score=23.19 Aligned_cols=21 Identities=5% Similarity=0.281 Sum_probs=18.3
Q ss_pred HHHHHHHhCCCccchhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQN 178 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQN 178 (287)
..++|+.+|++.+.|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999865
No 205
>PRK10651 transcriptional regulator NarL; Provisional
Probab=21.33 E-value=1.8e+02 Score=23.96 Aligned_cols=46 Identities=17% Similarity=0.259 Sum_probs=35.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.+|..+..+|+-..+- ....++|++++++++.|++..+|=|.|..-
T Consensus 155 ~Lt~rE~~vl~~l~~g------~~~~~ia~~l~is~~tV~~~~~~l~~Kl~~ 200 (216)
T PRK10651 155 QLTPRERDILKLIAQG------LPNKMIARRLDITESTVKVHVKHMLKKMKL 200 (216)
T ss_pred cCCHHHHHHHHHHHcC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 4899999999776532 124578999999999999999887777654
No 206
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=21.17 E-value=1.1e+02 Score=25.82 Aligned_cols=45 Identities=11% Similarity=0.163 Sum_probs=28.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
++..+..++...|-. ...-.+||..+|++...|+.+...-|.+.|
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 173 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALR 173 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHH
Confidence 455555555554321 222458899999999999987754444433
No 207
>PF02591 DUF164: Putative zinc ribbon domain; InterPro: IPR003743 This entry describes proteins of unknown function.
Probab=21.16 E-value=35 Score=23.97 Aligned_cols=22 Identities=27% Similarity=0.751 Sum_probs=12.8
Q ss_pred hhhhccCCCCCCCCCCCCCCCC
Q 023113 223 PQLYMNMNPPTTLTMCPSCERV 244 (287)
Q Consensus 223 ~~~~~~~~~~~~~~~c~sc~~~ 244 (287)
++.+..+.-......|++|++.
T Consensus 34 ~~~~~~i~~~~~i~~Cp~CgRi 55 (56)
T PF02591_consen 34 PQELNEIRKGDEIVFCPNCGRI 55 (56)
T ss_pred HHHHHHHHcCCCeEECcCCCcc
Confidence 3333333333455789999874
No 208
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=20.95 E-value=99 Score=27.58 Aligned_cols=46 Identities=15% Similarity=0.205 Sum_probs=32.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
+...+..++...|-. ...-.++|..+|++...|+.+...-+.+.|+
T Consensus 185 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQE-----ELNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhcc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 556666666665522 2235689999999999999988766655554
No 209
>PF13551 HTH_29: Winged helix-turn helix
Probab=20.78 E-value=1.9e+02 Score=21.99 Aligned_cols=44 Identities=23% Similarity=0.376 Sum_probs=28.2
Q ss_pred cCCHHHHHHHHHHHhhcCC-----CCHHHHHH-H-HHHh--CCCccchhhhhh
Q 023113 134 RLSKEQSLLLEETFKEHST-----LNPKQKLA-L-AKQL--NLRPRQVEVWFQ 177 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~-----p~~~~r~~-L-A~~L--gL~~rqVqvWFQ 177 (287)
.++.++...|.+.+..++. .+.....+ | .+.. .++...|..|+.
T Consensus 57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3999999999999998763 33343333 3 2222 456667766663
No 210
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=20.65 E-value=1.3e+02 Score=25.43 Aligned_cols=43 Identities=19% Similarity=0.064 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 181 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRa 181 (287)
.++..|..++...|-.. ....+||..+|++...|+.+...-|.
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~ 181 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALA 181 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 46666766776654332 33568999999999999987744333
No 211
>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=20.63 E-value=3.2e+02 Score=21.12 Aligned_cols=33 Identities=27% Similarity=0.320 Sum_probs=26.7
Q ss_pred hhhhhhhHHHHHHhhhhHHHHHHHHHHHHHHHh
Q 023113 186 KQTEVDCEYLKRCCENLTEENRRLQKEVQELRS 218 (287)
Q Consensus 186 kq~~~~~~~Lk~~~e~l~~en~~l~~e~~~lr~ 218 (287)
+.....+..|....+..++|++.|+.|++-|..
T Consensus 26 ~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~ 58 (80)
T PF10224_consen 26 LELQDSLEALSDRVEEVKEENEKLESENEYLQQ 58 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455666777888889999999999999988863
No 212
>PRK10100 DNA-binding transcriptional regulator CsgD; Provisional
Probab=20.60 E-value=2.1e+02 Score=25.52 Aligned_cols=46 Identities=13% Similarity=0.143 Sum_probs=36.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHh
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 185 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Kr 185 (287)
.+|..|.++|+-..+- ....++|++|+++++.|+.+..+-..|..-
T Consensus 155 ~Lt~rE~~Vl~l~~~G------~s~~eIA~~L~iS~~TVk~~~~~i~~Kl~v 200 (216)
T PRK10100 155 LLTHREKEILNKLRIG------ASNNEIARSLFISENTVKTHLYNLFKKIAV 200 (216)
T ss_pred CCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHhCC
Confidence 4899999999888752 224678999999999999999887766654
No 213
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=20.49 E-value=2.7e+02 Score=28.46 Aligned_cols=81 Identities=20% Similarity=0.343 Sum_probs=0.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHHhhhhhhhhHH-------HHHHhhhhHHHHH
Q 023113 135 LSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEY-------LKRCCENLTEENR 207 (287)
Q Consensus 135 ~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~Krkq~~~~~~~-------Lk~~~e~l~~en~ 207 (287)
+|+.+-++|.+. |..|..+.--.+.+ ||.|...+..+..+.. |++..+.|..+|+
T Consensus 242 LTKaEEriLKrv-----------RRKIrNK~SAQESR-------rkKkeYid~LE~rv~~~taeNqeL~kkV~~Le~~N~ 303 (472)
T KOG0709|consen 242 LTKAEERILKRV-----------RRKIRNKRSAQESR-------RKKKEYIDGLESRVSAFTAENQELQKKVEELELSNR 303 (472)
T ss_pred chHHHHHHHHHH-----------HHHHHhhhhhHHHH-------HhHhhHHHHHhhhhhhcccCcHHHHHHHHHHhhccH
Q ss_pred HHHHHHHHHHhhhcChhhhccCCCCCCCCCC
Q 023113 208 RLQKEVQELRSLKLSPQLYMNMNPPTTLTMC 238 (287)
Q Consensus 208 ~l~~e~~~lr~l~~~~~~~~~~~~~~~~~~c 238 (287)
.|..++.+|.++.. +..+-.+....|
T Consensus 304 sLl~qL~klQt~v~-----q~an~s~qt~tC 329 (472)
T KOG0709|consen 304 SLLAQLKKLQTLVI-----QVANKSTQTSTC 329 (472)
T ss_pred HHHHHHHHHHHHHh-----hcccchhccchh
No 214
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=20.30 E-value=52 Score=22.13 Aligned_cols=23 Identities=17% Similarity=0.270 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCccchhhhhhhhh
Q 023113 158 KLALAKQLNLRPRQVEVWFQNRR 180 (287)
Q Consensus 158 r~~LA~~LgL~~rqVqvWFQNRR 180 (287)
..+||+.+|++...|.-|..+++
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 36899999999999999998844
No 215
>PF08279 HTH_11: HTH domain; InterPro: IPR013196 Winged helix DNA-binding proteins share a related winged helix-turn-helix DNA-binding motif, where the "wings", or loops, are small beta-sheets. The winged helix motif consists of two wings (W1, W2), three alpha helices (H1, H2, H3) and three beta-sheets (S1, S2, S3) arranged in the order H1-S1-H2-H3-S2-W1-S3-W2 []. The DNA-recognition helix makes sequence-specific DNA contacts with the major groove of DNA, while the wings make different DNA contacts, often with the minor groove or the backbone of DNA. Several winged-helix proteins display an exposed patch of hydrophobic residues thought to mediate protein-protein interactions. This entry represents a subset of the winged helix domain superfamily which is predominantly found in bacterial proteins, though there are also some archaeal and eukaryotic examples. This domain is commonly found in the biotin (vitamin H) repressor protein BirA which regulates transcription of the biotin operon []. It is also found in other proteins including regulators of amino acid biosynthsis such as LysM [], and regulators of carbohydrate metabolisms such as LicR and FrvR [, ].; PDB: 1HXD_B 2EWN_B 1BIA_A 1BIB_A 1J5Y_A 3V7S_A 3V7C_A 3RKW_A 3RIR_A 3RKX_A ....
Probab=20.26 E-value=1.1e+02 Score=20.77 Aligned_cols=32 Identities=19% Similarity=0.343 Sum_probs=20.5
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchh
Q 023113 139 QSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVE 173 (287)
Q Consensus 139 Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVq 173 (287)
|..+|...++...+.+ ..+||.+||++.+-|.
T Consensus 2 ~~~il~~L~~~~~~it---~~eLa~~l~vS~rTi~ 33 (55)
T PF08279_consen 2 QKQILKLLLESKEPIT---AKELAEELGVSRRTIR 33 (55)
T ss_dssp HHHHHHHHHHTTTSBE---HHHHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHcCCCcC---HHHHHHHhCCCHHHHH
Confidence 3455555555555544 4478999999987764
No 216
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=20.09 E-value=1.7e+02 Score=24.07 Aligned_cols=45 Identities=11% Similarity=0.233 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccchhhhhhhhhhHHH
Q 023113 134 RLSKEQSLLLEETFKEHSTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 184 (287)
Q Consensus 134 ~~T~~Ql~~Le~~F~~~~~p~~~~r~~LA~~LgL~~rqVqvWFQNRRak~K 184 (287)
.++..+..+|.-.| . . ..-.+||..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~il~l~~-~-g----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF-S-G----YSYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH-c-C----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46666777776666 2 2 23457899999999999988754444333
Done!