Query 024915
Match_columns 260
No_of_seqs 378 out of 1720
Neff 6.5
Searched_HMMs 46136
Date Fri Mar 29 08:27:25 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/024915.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/024915hhsearch_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 7.3E-26 1.6E-30 195.6 8.3 118 99-217 50-168 (198)
2 KOG0489 Transcription factor z 99.7 9E-19 2E-23 158.2 2.6 62 97-158 157-218 (261)
3 KOG0842 Transcription factor t 99.7 1E-17 2.2E-22 153.0 5.9 66 99-164 153-218 (307)
4 KOG0487 Transcription factor A 99.7 7.9E-18 1.7E-22 153.8 4.8 62 98-159 234-295 (308)
5 KOG4577 Transcription factor L 99.7 1.4E-17 3E-22 149.2 4.4 103 22-160 125-228 (383)
6 KOG0843 Transcription factor E 99.7 1.9E-17 4.2E-22 139.5 4.9 64 98-161 101-164 (197)
7 KOG0488 Transcription factor B 99.7 2.6E-17 5.7E-22 151.7 6.0 63 97-159 170-232 (309)
8 PF00046 Homeobox: Homeobox do 99.6 1.7E-16 3.6E-21 110.8 3.9 57 100-156 1-57 (57)
9 KOG0484 Transcription factor P 99.6 6.2E-17 1.3E-21 125.3 1.8 62 97-158 15-76 (125)
10 KOG0844 Transcription factor E 99.6 5.2E-16 1.1E-20 140.0 6.2 66 95-160 177-242 (408)
11 KOG0493 Transcription factor E 99.6 1.3E-15 2.8E-20 135.0 7.7 68 99-166 246-313 (342)
12 KOG0492 Transcription factor M 99.6 8.9E-16 1.9E-20 132.0 6.1 58 99-156 144-201 (246)
13 KOG2251 Homeobox transcription 99.6 7.1E-16 1.5E-20 133.9 5.1 65 96-160 34-98 (228)
14 KOG0850 Transcription factor D 99.6 1.1E-15 2.3E-20 133.4 6.1 63 94-156 117-179 (245)
15 KOG0485 Transcription factor N 99.6 4E-16 8.7E-21 135.0 3.4 62 97-158 102-163 (268)
16 KOG0494 Transcription factor C 99.6 1.2E-15 2.7E-20 135.0 6.2 60 101-160 143-202 (332)
17 KOG0848 Transcription factor C 99.6 8.2E-16 1.8E-20 136.6 2.2 59 101-159 201-259 (317)
18 smart00389 HOX Homeodomain. DN 99.5 1.5E-14 3.3E-19 100.1 3.7 55 101-155 2-56 (56)
19 cd00086 homeodomain Homeodomai 99.5 1.8E-14 3.9E-19 100.4 4.0 57 101-157 2-58 (59)
20 COG5576 Homeodomain-containing 99.5 3.1E-14 6.8E-19 119.3 5.8 65 96-160 48-112 (156)
21 TIGR01565 homeo_ZF_HD homeobox 99.5 4.6E-14 9.9E-19 99.5 5.6 52 100-151 2-57 (58)
22 KOG0491 Transcription factor B 99.4 2E-14 4.3E-19 119.7 0.1 60 99-158 100-159 (194)
23 KOG3802 Transcription factor O 99.4 1.7E-13 3.8E-18 128.0 5.1 60 98-157 293-352 (398)
24 KOG0486 Transcription factor P 99.4 2.9E-13 6.3E-18 122.8 5.5 67 98-164 111-177 (351)
25 KOG0847 Transcription factor, 99.3 1.2E-12 2.7E-17 113.6 2.0 63 97-159 165-227 (288)
26 smart00340 HALZ homeobox assoc 99.1 1.1E-10 2.4E-15 75.8 5.2 44 157-201 1-44 (44)
27 KOG0490 Transcription factor, 99.1 4.8E-11 1E-15 104.5 3.6 62 97-158 58-119 (235)
28 KOG1168 Transcription factor A 99.0 2.5E-10 5.4E-15 102.9 3.8 59 99-157 309-367 (385)
29 KOG0849 Transcription factor P 98.9 1.3E-09 2.9E-14 102.6 4.4 64 96-159 173-236 (354)
30 KOG0775 Transcription factor S 98.8 3.6E-09 7.9E-14 94.8 4.0 50 106-155 183-232 (304)
31 KOG0774 Transcription factor P 98.7 3.5E-08 7.6E-13 88.1 6.7 58 99-156 188-248 (334)
32 PF05920 Homeobox_KN: Homeobox 98.3 1.2E-07 2.6E-12 62.0 0.6 34 120-153 7-40 (40)
33 KOG2252 CCAAT displacement pro 98.2 1.7E-06 3.7E-11 84.3 4.4 58 98-155 419-476 (558)
34 KOG0490 Transcription factor, 98.1 3.7E-06 8.1E-11 73.5 4.4 63 97-159 151-213 (235)
35 KOG1146 Homeobox protein [Gene 97.6 4.7E-05 1E-09 80.6 4.6 62 98-159 902-963 (1406)
36 PF02183 HALZ: Homeobox associ 96.7 0.0036 7.8E-08 41.9 4.7 35 157-191 1-35 (45)
37 PF11569 Homez: Homeodomain le 96.7 0.0005 1.1E-08 48.0 0.2 42 111-152 10-51 (56)
38 KOG0773 Transcription factor M 96.6 0.0016 3.5E-08 60.9 3.2 61 99-159 239-302 (342)
39 KOG3623 Homeobox transcription 94.7 0.021 4.6E-07 58.0 2.7 48 111-158 568-615 (1007)
40 PF04218 CENP-B_N: CENP-B N-te 93.7 0.081 1.8E-06 36.4 3.2 47 100-151 1-47 (53)
41 PRK09413 IS2 repressor TnpA; R 92.9 0.97 2.1E-05 36.0 8.9 79 101-184 8-101 (121)
42 KOG4005 Transcription factor X 92.9 0.46 1E-05 42.6 7.5 8 99-106 54-61 (292)
43 PF02183 HALZ: Homeobox associ 90.0 0.96 2.1E-05 30.2 5.0 33 158-190 9-41 (45)
44 KOG4196 bZIP transcription fac 89.8 1.8 4E-05 35.3 7.3 73 104-189 22-109 (135)
45 PRK00888 ftsB cell division pr 82.6 2.8 6.2E-05 32.8 4.9 46 142-188 16-61 (105)
46 PF07716 bZIP_2: Basic region 79.3 8.6 0.00019 26.2 5.8 27 162-188 26-52 (54)
47 PF01527 HTH_Tnp_1: Transposas 78.6 0.28 6.1E-06 35.2 -2.0 44 101-149 2-46 (76)
48 KOG0709 CREB/ATF family transc 74.6 46 0.001 32.8 11.3 84 103-193 218-318 (472)
49 PF04545 Sigma70_r4: Sigma-70, 67.7 4.2 9.1E-05 26.8 1.9 39 105-148 4-42 (50)
50 PF00170 bZIP_1: bZIP transcri 66.4 31 0.00068 24.0 6.3 24 164-187 36-59 (64)
51 KOG3119 Basic region leucine z 65.9 24 0.00052 32.2 7.1 28 165-192 226-253 (269)
52 cd00569 HTH_Hin_like Helix-tur 63.5 9.6 0.00021 21.5 2.8 38 105-147 5-42 (42)
53 PF04967 HTH_10: HTH DNA bindi 63.4 6.9 0.00015 27.0 2.3 38 106-143 1-40 (53)
54 cd06171 Sigma70_r4 Sigma70, re 63.1 3.3 7.1E-05 26.4 0.7 43 105-152 10-52 (55)
55 smart00338 BRLZ basic region l 60.5 35 0.00075 23.9 5.7 22 166-187 31-52 (65)
56 KOG4571 Activating transcripti 60.1 22 0.00048 32.9 5.6 28 162-189 256-283 (294)
57 KOG3335 Predicted coiled-coil 59.5 36 0.00077 29.3 6.4 49 140-188 85-133 (181)
58 PF06156 DUF972: Protein of un 58.8 32 0.0007 27.1 5.7 35 156-190 17-51 (107)
59 KOG4403 Cell surface glycoprot 58.0 21 0.00046 34.9 5.4 31 143-173 228-261 (575)
60 TIGR02209 ftsL_broad cell divi 57.8 37 0.0008 24.8 5.7 31 158-188 28-58 (85)
61 KOG4571 Activating transcripti 57.6 28 0.00061 32.2 5.9 31 157-187 244-274 (294)
62 PF12824 MRP-L20: Mitochondria 57.5 61 0.0013 27.5 7.6 48 102-151 82-129 (164)
63 PRK03975 tfx putative transcri 57.3 14 0.00029 30.7 3.5 47 103-155 4-50 (141)
64 PF13443 HTH_26: Cro/C1-type H 55.7 6.8 0.00015 26.8 1.3 33 129-161 13-45 (63)
65 PF08281 Sigma70_r4_2: Sigma-7 54.9 9.5 0.00021 25.3 1.9 42 105-151 10-51 (54)
66 PF04977 DivIC: Septum formati 54.5 42 0.00091 23.8 5.4 30 158-187 21-50 (80)
67 PF10668 Phage_terminase: Phag 54.2 4.3 9.4E-05 28.8 0.1 19 129-147 25-43 (60)
68 PRK00118 putative DNA-binding 54.1 42 0.00092 26.3 5.7 46 105-155 17-62 (104)
69 smart00338 BRLZ basic region l 53.0 68 0.0015 22.3 6.2 35 156-190 28-62 (65)
70 cd01106 HTH_TipAL-Mta Helix-Tu 51.7 78 0.0017 24.0 6.8 64 103-187 36-99 (103)
71 PF06005 DUF904: Protein of un 51.7 71 0.0015 23.3 6.2 27 161-187 25-51 (72)
72 PF15058 Speriolin_N: Sperioli 50.9 24 0.00052 30.8 4.1 20 164-183 8-27 (200)
73 PRK13169 DNA replication intia 49.6 49 0.0011 26.3 5.4 34 157-190 18-51 (110)
74 cd04781 HTH_MerR-like_sg6 Heli 49.4 1.1E+02 0.0024 23.9 7.6 69 102-189 34-102 (120)
75 PF00170 bZIP_1: bZIP transcri 49.3 81 0.0018 21.9 6.0 29 161-189 26-54 (64)
76 cd04787 HTH_HMRTR_unk Helix-Tu 48.9 74 0.0016 25.5 6.6 70 104-188 37-106 (133)
77 PF11594 Med28: Mediator compl 48.6 16 0.00036 28.8 2.5 14 141-154 18-31 (106)
78 PF00196 GerE: Bacterial regul 47.8 14 0.00031 25.1 1.9 46 105-156 3-48 (58)
79 PRK14127 cell division protein 47.6 53 0.0012 26.0 5.3 34 157-190 33-66 (109)
80 TIGR02449 conserved hypothetic 47.4 67 0.0014 23.1 5.3 23 164-186 10-32 (65)
81 KOG1146 Homeobox protein [Gene 46.1 26 0.00057 38.7 4.3 60 99-158 705-764 (1406)
82 PF08961 DUF1875: Domain of un 45.4 7 0.00015 34.8 0.0 33 159-191 127-159 (243)
83 PF01166 TSC22: TSC-22/dip/bun 45.1 34 0.00074 24.1 3.4 30 161-190 14-43 (59)
84 PF09607 BrkDBD: Brinker DNA-b 45.0 17 0.00036 25.7 1.9 44 103-148 3-47 (58)
85 PF07716 bZIP_2: Basic region 43.1 90 0.002 21.0 5.3 24 160-183 31-54 (54)
86 cd01109 HTH_YyaN Helix-Turn-He 42.8 91 0.002 24.1 6.1 70 104-188 37-106 (113)
87 PHA02955 hypothetical protein; 42.4 32 0.0007 30.5 3.6 42 108-149 60-102 (213)
88 PRK10072 putative transcriptio 41.6 18 0.0004 27.9 1.8 42 105-153 32-73 (96)
89 PF01486 K-box: K-box region; 41.4 41 0.00089 25.7 3.8 54 124-185 46-99 (100)
90 PRK13922 rod shape-determining 41.1 62 0.0013 29.1 5.5 34 157-190 72-108 (276)
91 PF06005 DUF904: Protein of un 40.9 1.2E+02 0.0027 22.0 6.0 30 156-185 27-56 (72)
92 PF13936 HTH_38: Helix-turn-he 40.1 11 0.00023 24.6 0.3 39 104-147 3-41 (44)
93 COG3074 Uncharacterized protei 39.7 83 0.0018 23.1 4.8 32 153-184 31-62 (79)
94 COG2963 Transposase and inacti 39.2 1.6E+02 0.0034 22.6 6.9 43 103-149 5-48 (116)
95 COG3413 Predicted DNA binding 38.8 30 0.00064 30.1 2.9 38 105-142 155-194 (215)
96 KOG3584 cAMP response element 38.7 53 0.0012 30.6 4.6 28 163-190 314-341 (348)
97 PF00424 REV: REV protein (ant 38.6 39 0.00084 26.0 3.1 35 111-159 14-48 (91)
98 PRK09652 RNA polymerase sigma 38.0 23 0.00051 28.7 2.1 42 105-151 128-169 (182)
99 TIGR03752 conj_TIGR03752 integ 37.7 60 0.0013 32.1 5.1 26 105-133 41-66 (472)
100 KOG3755 SATB1 matrix attachmen 37.1 8.6 0.00019 39.0 -0.8 60 99-158 691-758 (769)
101 cd04761 HTH_MerR-SF Helix-Turn 36.9 11 0.00023 24.2 -0.1 23 129-151 3-25 (49)
102 cd04770 HTH_HMRTR Helix-Turn-H 36.8 1.2E+02 0.0027 23.6 6.0 72 103-189 36-107 (123)
103 PRK09646 RNA polymerase sigma 36.3 29 0.00062 29.2 2.4 46 105-155 142-187 (194)
104 PF13518 HTH_28: Helix-turn-he 36.2 12 0.00026 24.3 0.0 21 129-149 15-35 (52)
105 PRK00888 ftsB cell division pr 35.8 86 0.0019 24.4 4.8 39 144-182 24-62 (105)
106 PF04999 FtsL: Cell division p 35.7 1.2E+02 0.0025 22.8 5.5 45 160-204 41-89 (97)
107 PF10883 DUF2681: Protein of u 35.6 1.6E+02 0.0034 22.5 6.0 36 145-187 21-56 (87)
108 KOG3623 Homeobox transcription 35.5 17 0.00038 37.8 1.0 61 99-159 626-686 (1007)
109 PRK06759 RNA polymerase factor 35.4 35 0.00076 27.2 2.7 45 105-154 106-150 (154)
110 PRK04217 hypothetical protein; 34.8 38 0.00083 26.8 2.7 40 104-148 41-80 (110)
111 cd04769 HTH_MerR2 Helix-Turn-H 34.6 1.2E+02 0.0026 23.6 5.6 73 103-189 35-107 (116)
112 TIGR00219 mreC rod shape-deter 34.2 92 0.002 28.5 5.5 34 157-190 69-106 (283)
113 KOG4797 Transcriptional regula 34.1 1E+02 0.0022 24.6 4.9 31 160-190 66-96 (123)
114 cd04775 HTH_Cfa-like Helix-Tur 34.1 2.1E+02 0.0045 21.7 6.9 64 103-189 36-99 (102)
115 PRK10884 SH3 domain-containing 34.1 2.9E+02 0.0062 24.2 8.3 10 109-118 93-102 (206)
116 TIGR02894 DNA_bind_RsfA transc 34.0 99 0.0021 26.2 5.1 32 157-188 100-131 (161)
117 cd04783 HTH_MerR1 Helix-Turn-H 33.3 2.2E+02 0.0048 22.4 7.0 71 103-190 36-106 (126)
118 PF07334 IFP_35_N: Interferon- 33.0 58 0.0013 24.2 3.2 13 173-185 5-17 (76)
119 PF07407 Seadorna_VP6: Seadorn 32.8 64 0.0014 30.6 4.2 25 159-183 37-61 (420)
120 PF08280 HTH_Mga: M protein tr 32.7 32 0.00069 23.7 1.7 32 109-144 6-37 (59)
121 PRK12526 RNA polymerase sigma 32.1 34 0.00074 29.2 2.2 44 106-154 154-197 (206)
122 PF02796 HTH_7: Helix-turn-hel 31.7 34 0.00073 22.2 1.6 39 104-147 4-42 (45)
123 PF03980 Nnf1: Nnf1 ; InterPr 31.5 1.1E+02 0.0024 23.6 4.8 29 160-188 79-107 (109)
124 smart00421 HTH_LUXR helix_turn 31.4 39 0.00085 21.6 2.0 39 105-149 3-41 (58)
125 PRK11924 RNA polymerase sigma 31.1 35 0.00075 27.6 2.0 45 106-155 126-170 (179)
126 TIGR02051 MerR Hg(II)-responsi 31.0 1.9E+02 0.0042 22.8 6.3 69 103-188 35-103 (124)
127 PRK09642 RNA polymerase sigma 30.7 40 0.00087 27.1 2.3 45 106-155 107-151 (160)
128 TIGR02937 sigma70-ECF RNA poly 30.5 44 0.00095 25.6 2.4 45 105-154 110-154 (158)
129 cd04779 HTH_MerR-like_sg4 Heli 30.3 2.7E+02 0.0059 22.5 7.1 35 103-150 35-69 (134)
130 PRK15422 septal ring assembly 30.2 1.5E+02 0.0032 22.3 4.9 26 159-184 37-62 (79)
131 PF14775 NYD-SP28_assoc: Sperm 30.2 1.4E+02 0.003 21.0 4.6 19 172-190 37-55 (60)
132 PF10224 DUF2205: Predicted co 30.2 2.2E+02 0.0047 21.3 5.9 29 159-187 28-56 (80)
133 cd04777 HTH_MerR-like_sg1 Heli 30.1 1.5E+02 0.0032 22.7 5.3 33 105-150 36-68 (107)
134 PF11365 DUF3166: Protein of u 30.0 1.3E+02 0.0029 23.3 4.9 32 159-190 13-44 (96)
135 PF06056 Terminase_5: Putative 29.9 21 0.00045 24.9 0.4 25 129-155 16-40 (58)
136 KOG2483 Upstream transcription 29.7 1.3E+02 0.0027 27.1 5.4 38 151-188 102-139 (232)
137 PF13411 MerR_1: MerR HTH fami 29.5 18 0.0004 25.0 0.0 20 129-148 3-22 (69)
138 PRK09639 RNA polymerase sigma 29.4 44 0.00095 27.0 2.3 43 105-153 112-154 (166)
139 PF10226 DUF2216: Uncharacteri 29.3 1.4E+02 0.0029 26.2 5.3 20 171-190 58-77 (195)
140 TIGR03879 near_KaiC_dom probab 29.3 10 0.00022 28.0 -1.4 23 127-149 33-55 (73)
141 TIGR00721 tfx DNA-binding prot 29.0 1.1E+02 0.0024 25.2 4.6 45 103-153 4-48 (137)
142 PRK12512 RNA polymerase sigma 29.0 43 0.00093 27.7 2.2 46 105-155 131-176 (184)
143 PRK14127 cell division protein 28.9 1.3E+02 0.0028 23.9 4.8 34 156-189 25-58 (109)
144 COG4367 Uncharacterized protei 28.9 45 0.00097 25.6 2.0 39 105-143 2-40 (97)
145 PRK13922 rod shape-determining 28.7 1E+02 0.0023 27.6 4.9 30 154-183 76-108 (276)
146 PRK12514 RNA polymerase sigma 28.2 51 0.0011 27.1 2.6 45 106-155 130-174 (179)
147 cd01392 HTH_LacI Helix-turn-he 28.0 32 0.0007 22.3 1.1 21 131-151 2-22 (52)
148 KOG4343 bZIP transcription fac 28.0 1.3E+02 0.0028 30.4 5.6 23 166-188 314-336 (655)
149 PRK12519 RNA polymerase sigma 27.9 36 0.00078 28.4 1.6 45 106-155 142-186 (194)
150 PF14197 Cep57_CLD_2: Centroso 27.9 2.4E+02 0.0051 20.4 5.7 20 169-188 48-67 (69)
151 PF10883 DUF2681: Protein of u 27.7 1.6E+02 0.0035 22.4 4.9 22 166-187 28-49 (87)
152 PF13384 HTH_23: Homeodomain-l 27.7 18 0.00039 23.5 -0.2 21 128-148 19-39 (50)
153 PRK12538 RNA polymerase sigma 27.4 46 0.00099 29.3 2.2 28 128-155 189-216 (233)
154 cd04766 HTH_HspR Helix-Turn-He 27.2 1.7E+02 0.0036 21.7 5.0 30 103-144 36-65 (91)
155 PF08172 CASP_C: CASP C termin 27.0 1.6E+02 0.0034 26.6 5.7 37 151-187 90-126 (248)
156 cd04785 HTH_CadR-PbrR-like Hel 26.9 2.2E+02 0.0048 22.5 6.0 71 104-189 37-107 (126)
157 TIGR02989 Sig-70_gvs1 RNA poly 26.8 45 0.00098 26.6 1.9 40 105-149 111-150 (159)
158 KOG3119 Basic region leucine z 26.7 1.1E+02 0.0023 28.0 4.5 26 164-189 218-243 (269)
159 PRK09648 RNA polymerase sigma 26.6 48 0.001 27.6 2.1 40 105-149 139-178 (189)
160 TIGR02959 SigZ RNA polymerase 26.4 47 0.001 27.3 2.0 39 105-148 100-138 (170)
161 KOG1962 B-cell receptor-associ 26.2 1.2E+02 0.0025 27.1 4.5 25 163-187 181-205 (216)
162 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.0 3.3E+02 0.0071 21.6 6.8 73 103-190 36-108 (127)
163 PF00376 MerR: MerR family reg 25.9 22 0.00047 22.6 -0.1 18 130-147 3-20 (38)
164 cd01107 HTH_BmrR Helix-Turn-He 25.8 3.1E+02 0.0066 21.0 6.5 66 103-188 37-102 (108)
165 PF12269 zf-CpG_bind_C: CpG bi 25.7 2.3E+02 0.0049 25.6 6.3 75 140-216 10-94 (236)
166 TIGR02985 Sig70_bacteroi1 RNA 25.6 50 0.0011 26.1 2.0 43 106-153 114-156 (161)
167 PHA00728 hypothetical protein 25.6 1.2E+02 0.0025 24.8 4.0 25 169-193 6-30 (151)
168 PRK09644 RNA polymerase sigma 25.5 59 0.0013 26.4 2.4 46 105-155 108-153 (165)
169 cd04789 HTH_Cfa Helix-Turn-Hel 25.0 2.9E+02 0.0064 20.9 6.2 63 103-188 36-98 (102)
170 cd04762 HTH_MerR-trunc Helix-T 24.9 23 0.0005 22.1 -0.1 24 129-152 3-26 (49)
171 TIGR02999 Sig-70_X6 RNA polyme 24.7 57 0.0012 26.8 2.2 45 106-155 135-179 (183)
172 PRK06811 RNA polymerase factor 24.6 51 0.0011 27.6 1.9 46 105-155 131-176 (189)
173 PF14645 Chibby: Chibby family 24.5 1.7E+02 0.0036 23.4 4.7 47 144-190 51-100 (116)
174 PF05377 FlaC_arch: Flagella a 24.4 2.5E+02 0.0054 19.5 5.0 25 163-187 16-40 (55)
175 TIGR02948 SigW_bacill RNA poly 24.1 50 0.0011 27.1 1.8 46 105-155 136-181 (187)
176 PRK12543 RNA polymerase sigma 24.1 86 0.0019 25.9 3.2 45 106-155 118-162 (179)
177 PF12808 Mto2_bdg: Micro-tubul 24.1 1.6E+02 0.0035 20.2 3.9 26 163-188 24-49 (52)
178 PF10224 DUF2205: Predicted co 24.0 1.4E+02 0.003 22.3 3.9 30 159-188 35-64 (80)
179 KOG3863 bZIP transcription fac 23.9 7E+02 0.015 25.7 10.0 43 145-187 500-544 (604)
180 cd04765 HTH_MlrA-like_sg2 Heli 23.9 1.1E+02 0.0025 23.3 3.6 35 103-149 36-70 (99)
181 cd04784 HTH_CadR-PbrR Helix-Tu 23.7 2.7E+02 0.0058 21.9 5.9 72 103-189 36-107 (127)
182 PRK12530 RNA polymerase sigma 23.6 74 0.0016 26.7 2.7 46 105-155 134-179 (189)
183 PRK12541 RNA polymerase sigma 23.5 50 0.0011 26.7 1.6 46 105-155 112-157 (161)
184 PRK12546 RNA polymerase sigma 23.5 33 0.00072 29.0 0.6 44 106-154 114-157 (188)
185 cd02413 40S_S3_KH K homology R 23.5 84 0.0018 23.3 2.7 20 129-148 56-75 (81)
186 PF13551 HTH_29: Winged helix- 23.4 88 0.0019 23.3 2.9 46 102-147 54-108 (112)
187 TIGR02939 RpoE_Sigma70 RNA pol 23.4 45 0.00098 27.5 1.4 24 128-151 156-179 (190)
188 PRK05602 RNA polymerase sigma 23.0 56 0.0012 27.1 1.9 43 106-153 129-171 (186)
189 PF04568 IATP: Mitochondrial A 23.0 3.7E+02 0.008 20.9 6.3 27 162-188 70-96 (100)
190 PRK12537 RNA polymerase sigma 22.9 73 0.0016 26.4 2.6 42 106-152 134-175 (182)
191 PF05703 Auxin_canalis: Auxin 22.9 1.2E+02 0.0025 27.6 3.9 16 139-154 99-114 (242)
192 cd04763 HTH_MlrA-like Helix-Tu 22.8 26 0.00057 24.4 -0.2 21 129-149 3-23 (68)
193 PRK15369 two component system 22.8 1.1E+02 0.0024 24.4 3.6 45 105-155 149-193 (211)
194 PF07412 Geminin: Geminin; In 22.7 1.7E+02 0.0037 25.7 4.8 30 161-190 125-154 (200)
195 COG4467 Regulator of replicati 22.6 2E+02 0.0044 22.9 4.7 32 158-189 19-50 (114)
196 TIGR03752 conj_TIGR03752 integ 22.6 2.2E+02 0.0047 28.4 6.0 17 171-187 119-135 (472)
197 PF11460 DUF3007: Protein of u 22.6 1.1E+02 0.0024 24.1 3.3 35 151-185 68-103 (104)
198 PRK12515 RNA polymerase sigma 22.5 50 0.0011 27.5 1.5 46 105-155 131-176 (189)
199 COG2944 Predicted transcriptio 22.4 67 0.0014 25.3 2.0 42 105-153 43-84 (104)
200 cd04764 HTH_MlrA-like_sg1 Heli 22.4 30 0.00066 24.0 0.1 21 129-149 3-23 (67)
201 cd06170 LuxR_C_like C-terminal 22.3 69 0.0015 20.5 1.9 36 107-148 2-37 (57)
202 PRK14872 rod shape-determining 22.3 1.6E+02 0.0034 28.0 4.8 23 157-179 60-82 (337)
203 PRK10403 transcriptional regul 22.1 47 0.001 26.9 1.3 45 105-155 153-197 (215)
204 PF13942 Lipoprotein_20: YfhG 21.9 5E+02 0.011 22.4 7.3 63 119-186 69-148 (179)
205 PF05812 Herpes_BLRF2: Herpesv 21.8 1.8E+02 0.004 23.4 4.5 25 162-186 4-28 (118)
206 PRK09047 RNA polymerase factor 21.8 69 0.0015 25.6 2.1 39 105-148 106-144 (161)
207 cd07429 Cby_like Chibby, a nuc 21.7 2.1E+02 0.0046 22.7 4.7 31 160-190 71-101 (108)
208 PRK09637 RNA polymerase sigma 21.7 63 0.0014 27.0 1.9 39 105-148 106-144 (181)
209 cd01108 HTH_CueR Helix-Turn-He 21.6 3E+02 0.0065 21.7 5.8 73 103-190 36-108 (127)
210 TIGR02043 ZntR Zn(II)-responsi 21.6 2.7E+02 0.0059 22.2 5.6 72 103-188 37-108 (131)
211 PF06667 PspB: Phage shock pro 21.6 1.2E+02 0.0027 22.3 3.2 30 167-196 41-70 (75)
212 PF04880 NUDE_C: NUDE protein, 21.5 83 0.0018 26.8 2.6 23 162-184 25-47 (166)
213 smart00027 EH Eps15 homology d 21.3 88 0.0019 23.3 2.5 43 105-147 3-50 (96)
214 COG3074 Uncharacterized protei 21.2 3.3E+02 0.0071 20.1 5.2 16 170-185 27-42 (79)
215 PF12065 DUF3545: Protein of u 21.1 1.3E+02 0.0028 21.3 3.0 22 166-188 26-47 (59)
216 cd00093 HTH_XRE Helix-turn-hel 21.0 50 0.0011 20.2 1.0 22 130-151 16-37 (58)
217 PRK06930 positive control sigm 20.8 85 0.0018 26.5 2.6 46 105-155 114-159 (170)
218 PF09006 Surfac_D-trimer: Lung 20.8 2.6E+02 0.0057 18.8 4.3 25 164-188 2-26 (46)
219 PRK09935 transcriptional regul 20.5 56 0.0012 26.6 1.4 46 104-155 148-193 (210)
220 PF07989 Microtub_assoc: Micro 20.5 1.3E+02 0.0027 22.1 3.1 16 172-187 47-62 (75)
221 PRK10884 SH3 domain-containing 20.4 3E+02 0.0065 24.1 5.9 25 161-185 139-163 (206)
222 PF10482 CtIP_N: Tumour-suppre 20.4 1.6E+02 0.0035 23.6 3.8 14 171-184 106-119 (120)
223 PRK10360 DNA-binding transcrip 20.3 56 0.0012 26.4 1.3 45 105-155 137-181 (196)
224 KOG2391 Vacuolar sorting prote 20.3 2.6E+02 0.0057 26.7 5.8 8 173-180 258-265 (365)
225 PF06210 DUF1003: Protein of u 20.1 2.9E+02 0.0063 21.7 5.3 36 148-187 57-92 (108)
226 TIGR02957 SigX4 RNA polymerase 20.1 1.3E+02 0.0027 27.2 3.7 47 105-156 108-154 (281)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.92 E-value=7.3e-26 Score=195.62 Aligned_cols=118 Identities=48% Similarity=0.652 Sum_probs=108.7
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENK 178 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~ 178 (260)
..+++.+|+.+|+..||..|+.+.++.+.++..||++|||.+|||+|||||||||||.++++.+++.|+++++.|..+|.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 45677899999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHhhhhcCCCCcCCC-CCCCCcCCCCCccccC
Q 024915 179 RLQREVQELKSMKLSGAPLYMKL-PAPTLTVCPSCDEKLD 217 (260)
Q Consensus 179 ~l~~e~~~l~~~~~~~~~~~~~~-p~~~~~~c~sc~~~~~ 217 (260)
+||.++++|.+.+.. ...++++ +..++.+|++|+....
T Consensus 130 ~Lq~e~~eL~~~~~~-~~~~~~~~~~~~~~~~~~~~~~~~ 168 (198)
T KOG0483|consen 130 RLQSEVQELVAELSS-LKREMQKSPENTLTMCPNSESSSS 168 (198)
T ss_pred HHHHHHHHHHHHHhh-hhhhhccCcccccccCccccccCC
Confidence 999999999988765 5666666 7788999999995554
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.73 E-value=9e-19 Score=158.23 Aligned_cols=62 Identities=35% Similarity=0.592 Sum_probs=58.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
.+.||.||.||..|+.+||+.|..|+|+++.+|.+||..|.|++|||||||||||+||||..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 34789999999999999999999999999999999999999999999999999999999744
No 3
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.70 E-value=1e-17 Score=152.99 Aligned_cols=66 Identities=33% Similarity=0.612 Sum_probs=58.9
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECE 164 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e 164 (260)
+||.|.-|+..|+.+||+.|++.+|++..+|+.||..|+|++.||||||||||-|.||+++++..+
T Consensus 153 kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 153 KRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred ccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 444455699999999999999999999999999999999999999999999999999877665443
No 4
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.70 E-value=7.9e-18 Score=153.80 Aligned_cols=62 Identities=34% Similarity=0.501 Sum_probs=58.3
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
..||||..+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||||||||||+|+||...
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 36788889999999999999999999999999999999999999999999999999997654
No 5
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.69 E-value=1.4e-17 Score=149.20 Aligned_cols=103 Identities=24% Similarity=0.426 Sum_probs=84.7
Q ss_pred CCCCCCCCCCccccCCC-CCCCCCccCCCCCCccccccccCCchhHhhhccccCCCCCCCCCCCCCCCCCCCCCCCCCCC
Q 024915 22 DHDHQKKNGKKLILKDD-QLLPSLTLGRRSENTLKSATKEKESTDVLQQASCMSMSMSALSSISNSKGIRDHHEDEGGSP 100 (260)
Q Consensus 22 ~~~rql~~g~e~~l~~~-~l~c~~~~~~~~~~~~~~~~~~~~~~~~~~~~s~~s~~~s~~ss~s~~~~~~~~~~~~~~~~ 100 (260)
...|||.+||||+|-|| .|.|+.||+..-.. .+ ..-+.+...|
T Consensus 125 iC~R~L~TGdEFYLmeD~rLvCK~DYE~Ak~k------------------~~------------------~~l~gd~~nK 168 (383)
T KOG4577|consen 125 ICKRQLATGDEFYLMEDARLVCKDDYETAKQK------------------HC------------------NELEGDASNK 168 (383)
T ss_pred hhhcccccCCeeEEeccceeehhhhHHHHHhc------------------cc------------------cccccccccC
Confidence 45899999999999887 69999998871000 00 0011233468
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhH
Q 024915 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~ 160 (260)
|.||.+|..|++.|+..|+..+.|-+..|++|+.++||..|+|+|||||||||+|+-+..
T Consensus 169 RPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T KOG4577|consen 169 RPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKD 228 (383)
T ss_pred CCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhh
Confidence 999999999999999999999999999999999999999999999999999999975543
No 6
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.69 E-value=1.9e-17 Score=139.48 Aligned_cols=64 Identities=34% Similarity=0.514 Sum_probs=61.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHH
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEV 161 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~ 161 (260)
+.+|.||.|+.+|+..||..|+.+.|....+|++||+.|+|++.||||||||||.|.||++.+.
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 6789999999999999999999999999999999999999999999999999999999877664
No 7
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.68 E-value=2.6e-17 Score=151.73 Aligned_cols=63 Identities=30% Similarity=0.467 Sum_probs=58.6
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
.+.|+.||.||..|+..||+.|+..+|++..+|.+||+.|||+..||++||||||+|||+...
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 456677899999999999999999999999999999999999999999999999999997543
No 8
>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=1.7e-16 Score=110.78 Aligned_cols=57 Identities=44% Similarity=0.689 Sum_probs=55.0
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 100 PRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 100 ~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
||+|+.|+.+|+.+|+..|..++||+..+++.||.++||+..+|++||+|||+++|+
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 9
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.63 E-value=6.2e-17 Score=125.26 Aligned_cols=62 Identities=31% Similarity=0.478 Sum_probs=58.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
.+.+|.|+.||..|+..||+.|.+.+||+...|++||.++.|++..|+|||||||+|.+|+.
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 45788899999999999999999999999999999999999999999999999999999643
No 10
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.62 E-value=5.2e-16 Score=140.02 Aligned_cols=66 Identities=32% Similarity=0.494 Sum_probs=61.2
Q ss_pred CCCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhH
Q 024915 95 DEGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160 (260)
Q Consensus 95 ~~~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~ 160 (260)
.++..||.||.||.+||..||+.|-+..|.++.+|.+||..|+|.+..|||||||||+|+|++.+.
T Consensus 177 a~dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 177 ADDQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred ccHHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 334478999999999999999999999999999999999999999999999999999999987764
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.61 E-value=1.3e-15 Score=134.99 Aligned_cols=68 Identities=31% Similarity=0.511 Sum_probs=61.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELL 166 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l 166 (260)
.||.||.||.+||..|+..|..++|++..+|++||.+|+|.+.||||||||+|+|.||..-.+....+
T Consensus 246 eKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~ 313 (342)
T KOG0493|consen 246 EKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLAL 313 (342)
T ss_pred hcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhh
Confidence 57889999999999999999999999999999999999999999999999999999986554443333
No 12
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.60 E-value=8.9e-16 Score=132.04 Aligned_cols=58 Identities=34% Similarity=0.595 Sum_probs=56.0
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
+|+.|+.||.+|+..||+.|++.+|++..+|.+++..|.|++.||||||||||+|.||
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKR 201 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKR 201 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHH
Confidence 6778999999999999999999999999999999999999999999999999999994
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.60 E-value=7.1e-16 Score=133.88 Aligned_cols=65 Identities=32% Similarity=0.499 Sum_probs=60.4
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhH
Q 024915 96 EGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160 (260)
Q Consensus 96 ~~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~ 160 (260)
..+.||.||+|+..|+.+||..|.+..||+...|++||.+|+|.+.+|+|||+|||+|+|+++..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 34578999999999999999999999999999999999999999999999999999999976543
No 14
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.60 E-value=1.1e-15 Score=133.41 Aligned_cols=63 Identities=27% Similarity=0.437 Sum_probs=58.2
Q ss_pred CCCCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 94 EDEGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 94 ~~~~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
....|.|+.||.++.-||..|.+.|+++.|+-..+|.+||..|||+..||||||||||.|.||
T Consensus 117 gk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 117 GKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred CCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 334456778999999999999999999999999999999999999999999999999999996
No 15
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=4e-16 Score=134.99 Aligned_cols=62 Identities=34% Similarity=0.544 Sum_probs=58.1
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
+++||.||+|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.|||++.
T Consensus 102 ~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 102 DRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 34677788999999999999999999999999999999999999999999999999999754
No 16
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.59 E-value=1.2e-15 Score=134.98 Aligned_cols=60 Identities=32% Similarity=0.460 Sum_probs=56.0
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhH
Q 024915 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~ 160 (260)
+-||.||..|+..||+.|++.+||+...|+.||.++.|.+..|+|||||||+||||+..+
T Consensus 143 h~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~ 202 (332)
T KOG0494|consen 143 HFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKR 202 (332)
T ss_pred cccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhh
Confidence 338899999999999999999999999999999999999999999999999999986543
No 17
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.56 E-value=8.2e-16 Score=136.60 Aligned_cols=59 Identities=34% Similarity=0.557 Sum_probs=55.0
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
|.|.++|..|..+||+.|..++|.+..+|.+||..|+|++|||||||||||+|+||...
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nK 259 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNK 259 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHH
Confidence 45678999999999999999999999999999999999999999999999999997543
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.50 E-value=1.5e-14 Score=100.10 Aligned_cols=55 Identities=45% Similarity=0.696 Sum_probs=52.1
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+.|++|+.+|+..|+..|..++||+..++..||..+||+..||++||+|||++.|
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 5677899999999999999999999999999999999999999999999999864
No 19
>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=99.50 E-value=1.8e-14 Score=100.39 Aligned_cols=57 Identities=42% Similarity=0.687 Sum_probs=54.0
Q ss_pred CCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHH
Q 024915 101 RKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLK 157 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~ 157 (260)
+.|..++..|+.+|+..|..++||+..++..||.++||+.++|++||+|||.+.++.
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 20
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.49 E-value=3.1e-14 Score=119.35 Aligned_cols=65 Identities=32% Similarity=0.503 Sum_probs=59.7
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhH
Q 024915 96 EGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTE 160 (260)
Q Consensus 96 ~~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~ 160 (260)
....+++|++.|.+|+.+|+..|..++||+...|..|+..|+|+++.|+|||||||++.|+....
T Consensus 48 s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 48 SSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 34467889999999999999999999999999999999999999999999999999999976543
No 21
>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=99.49 E-value=4.6e-14 Score=99.47 Aligned_cols=52 Identities=15% Similarity=0.350 Sum_probs=50.2
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCC----CCHHHHHHHHHHhCCCCcceeecccchh
Q 024915 100 PRKKLRLTKPQFATLEDTFKEHST----LSPKQKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 100 ~r~Rt~~t~~Ql~~Le~~F~~~~~----ps~~~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
+|.||.||.+|+..|+..|..++| |+..++.+||..|||++++|+|||||-+
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 9999999999999999999999999964
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.43 E-value=2e-14 Score=119.74 Aligned_cols=60 Identities=37% Similarity=0.617 Sum_probs=56.6
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
+++-|++|+..|+..||+.|+..+|++..++.+||..|+|++.|||.||||||+|.||.+
T Consensus 100 r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 100 RRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 456689999999999999999999999999999999999999999999999999999754
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.41 E-value=1.7e-13 Score=128.03 Aligned_cols=60 Identities=27% Similarity=0.411 Sum_probs=57.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHH
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLK 157 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~ 157 (260)
++|||||.|.......||++|..|++|+..++..||.+|+|.+.+|+|||+|||.|+||.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 578889999999999999999999999999999999999999999999999999999964
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.39 E-value=2.9e-13 Score=122.84 Aligned_cols=67 Identities=28% Similarity=0.468 Sum_probs=61.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHH
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECE 164 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e 164 (260)
++||.|+.||.+|+..||..|.++.||+...|++||..++|++..|+|||.|||+||+|+......|
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae 177 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAE 177 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHH
Confidence 4677889999999999999999999999999999999999999999999999999999876555433
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.27 E-value=1.2e-12 Score=113.63 Aligned_cols=63 Identities=33% Similarity=0.548 Sum_probs=57.5
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
++++..|..|+-.||..||..|++.+|+-..++.+||..+|+++.||+|||||||.||||+.-
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkhA 227 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKHA 227 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhhc
Confidence 345556778999999999999999999999999999999999999999999999999998653
No 26
>smart00340 HALZ homeobox associated leucin zipper.
Probab=99.12 E-value=1.1e-10 Score=75.80 Aligned_cols=44 Identities=73% Similarity=1.238 Sum_probs=40.2
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcCCC
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQELKSMKLSGAPLYMKL 201 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~~~~~~~~~~~~ 201 (260)
||++++||.||++|+.|.+||+||++|+++|++++.+ .++||++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~-~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLS-PPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC-CcccccC
Confidence 5789999999999999999999999999999999886 6778764
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.10 E-value=4.8e-11 Score=104.52 Aligned_cols=62 Identities=27% Similarity=0.345 Sum_probs=58.3
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
.+.+|.|+.|+..|+.+||+.|...+||+...++.||..+++++..|+|||||||++|+++.
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 34688899999999999999999999999999999999999999999999999999999754
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.99 E-value=2.5e-10 Score=102.92 Aligned_cols=59 Identities=32% Similarity=0.513 Sum_probs=56.5
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLK 157 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~ 157 (260)
+|||||.+-....+.||.+|...+.|+.+.+..||++|+|.+.+|+|||+|.|.|.||.
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm 367 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRM 367 (385)
T ss_pred cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHh
Confidence 68999999999999999999999999999999999999999999999999999999864
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.88 E-value=1.3e-09 Score=102.61 Aligned_cols=64 Identities=28% Similarity=0.504 Sum_probs=59.0
Q ss_pred CCCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 96 EGGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 96 ~~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
+.+.+|.|+.|+..|+..||+.|+.++||+...|++||.++++++..|+|||+|||+++++...
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 4446778899999999999999999999999999999999999999999999999999997653
No 30
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.80 E-value=3.6e-09 Score=94.83 Aligned_cols=50 Identities=32% Similarity=0.539 Sum_probs=47.0
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
|...-..+|.++|..++||++.++.+||+.+||+..||-.||.|||.|+|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 55566789999999999999999999999999999999999999999998
No 31
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.69 E-value=3.5e-08 Score=88.07 Aligned_cols=58 Identities=31% Similarity=0.449 Sum_probs=55.0
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 99 SPRKKLRLTKPQFATLEDTFK---EHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~---~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
.+|||+.|++.-.++|..+|. .++||+.+.+++||+++|++..||-.||.|+|.+.||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 478899999999999999996 7999999999999999999999999999999999996
No 32
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.34 E-value=1.2e-07 Score=61.97 Aligned_cols=34 Identities=32% Similarity=0.543 Sum_probs=29.3
Q ss_pred hCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 120 EHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 120 ~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
.++||+..++++||.++||+..||..||-|.|.|
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 5899999999999999999999999999999875
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.16 E-value=1.7e-06 Score=84.34 Aligned_cols=58 Identities=31% Similarity=0.394 Sum_probs=54.4
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
..||.|.+||..|...|..+|+.+++|+.++.+.|+.+|+|..+.|..||-|-|.|.+
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 3678899999999999999999999999999999999999999999999999888753
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=98.07 E-value=3.7e-06 Score=73.50 Aligned_cols=63 Identities=30% Similarity=0.533 Sum_probs=58.0
Q ss_pred CCCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 97 GGSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 97 ~~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
.+.++.|+.+...|+..|+..|...++|+...++.|+..+|++++.|++||||+|++.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 346778899999999999999999999999999999999999999999999999999997543
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.64 E-value=4.7e-05 Score=80.65 Aligned_cols=62 Identities=26% Similarity=0.426 Sum_probs=58.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 98 GSPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 98 ~~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
+.+++|++++..|+..|..+|....+|...+.+.|...+++.+|.|+|||||-|+|.|+..+
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 46788999999999999999999999999999999999999999999999999999998665
No 36
>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=96.72 E-value=0.0036 Score=41.92 Aligned_cols=35 Identities=31% Similarity=0.429 Sum_probs=31.1
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQELKSMK 191 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~~ 191 (260)
+|++.+++.|+.+++.|..++++|++|++.|++..
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev 35 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEV 35 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 47899999999999999999999999999887653
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.65 E-value=0.0005 Score=48.02 Aligned_cols=42 Identities=29% Similarity=0.503 Sum_probs=31.4
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhH
Q 024915 111 FATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152 (260)
Q Consensus 111 l~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRa 152 (260)
+..|+++|..++.+...+...|..+.+|+..||+.||--|+.
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 38
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.59 E-value=0.0016 Score=60.93 Aligned_cols=61 Identities=28% Similarity=0.229 Sum_probs=50.6
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 99 SPRKKLRLTKPQFATLEDTFK---EHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~---~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
..|.+..|......+|+.+.. ..+||+..++..||+++||+..||.+||-|.|-|..+-..
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 345556799999999997754 3689999999999999999999999999999988665433
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=94.68 E-value=0.021 Score=58.04 Aligned_cols=48 Identities=17% Similarity=0.279 Sum_probs=44.6
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 111 FATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 111 l~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
+.+|..+|..|..|+..+...+|.+.||+.+.|++||+++++....-+
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 788999999999999999999999999999999999999999877544
No 40
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.70 E-value=0.081 Score=36.37 Aligned_cols=47 Identities=19% Similarity=0.292 Sum_probs=34.4
Q ss_pred CCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchh
Q 024915 100 PRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 100 ~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
+|+|..+|-++-..+-..++... ....||+++|+...+|..|..|+.
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 47888999998777777777665 477899999999999999998853
No 41
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=92.94 E-value=0.97 Score=36.02 Aligned_cols=79 Identities=20% Similarity=0.238 Sum_probs=44.3
Q ss_pred CCCccCCHHHHH-HHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH--------------HHHHhhHHHHHH
Q 024915 101 RKKLRLTKPQFA-TLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR--------------SKLKQTEVECEL 165 (260)
Q Consensus 101 r~Rt~~t~~Ql~-~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak--------------~Kk~~~~~~~e~ 165 (260)
++|.+++.++.. ++...+. +.. ...++|.++|+++.+|..|.+-=+.. ......+.+...
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~ 82 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKE 82 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHH
Confidence 345567777644 4444443 222 34568999999999999996432210 011223344455
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 024915 166 LKRCCEKLKDENKRLQREV 184 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~ 184 (260)
|++.+..|+.|++-|++.+
T Consensus 83 L~~el~~L~~E~diLKKa~ 101 (121)
T PRK09413 83 LQRLLGKKTMENELLKEAV 101 (121)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 5555555555555555543
No 42
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=92.90 E-value=0.46 Score=42.57 Aligned_cols=8 Identities=50% Similarity=0.704 Sum_probs=4.0
Q ss_pred CCCCCccC
Q 024915 99 SPRKKLRL 106 (260)
Q Consensus 99 ~~r~Rt~~ 106 (260)
++|||.|+
T Consensus 54 ~~rKr~RL 61 (292)
T KOG4005|consen 54 PKRKRRRL 61 (292)
T ss_pred hHHHHHhh
Confidence 45555543
No 43
>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=90.05 E-value=0.96 Score=30.19 Aligned_cols=33 Identities=39% Similarity=0.498 Sum_probs=28.8
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 158 QTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 158 ~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
.+...++.|+..++.|..||+.|+.++..|...
T Consensus 9 ~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~k 41 (45)
T PF02183_consen 9 ALKASYDSLKAEYDSLKKENEKLRAEVQELKEK 41 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356788999999999999999999999998643
No 44
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=89.79 E-value=1.8 Score=35.29 Aligned_cols=73 Identities=34% Similarity=0.415 Sum_probs=51.3
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHH-hCCCCcceeecccchhH----------HHHH----HhhHHHHHHHHH
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEK-LNLRPRQVEVWFQNRRA----------RSKL----KQTEVECELLKR 168 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~-lgLs~rqVkvWFQNRRa----------k~Kk----~~~~~~~e~l~~ 168 (260)
.+|+.+++..|-. | +|=+. -|++...|-.|=|.||+ |.|+ ..++.++..|+.
T Consensus 22 d~lsDd~LvsmSV------------R-eLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSMSV------------R-ELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHhhH------------H-HHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5788888876622 2 22233 37777778888777765 2333 345566668889
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 024915 169 CCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 169 ~~~~l~~en~~l~~e~~~l~~ 189 (260)
..+.|.+||.+++.|+..++.
T Consensus 89 qv~~L~~e~s~~~~E~da~k~ 109 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKS 109 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 999999999999999888753
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=82.62 E-value=2.8 Score=32.84 Aligned_cols=46 Identities=24% Similarity=0.376 Sum_probs=26.8
Q ss_pred ceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 142 QVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 142 qVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
++..||++.=- .+-.+.+.+.+.++..++.++++|++|+.|+..|+
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 35578865411 11223344455566667777777777777777664
No 46
>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=79.32 E-value=8.6 Score=26.15 Aligned_cols=27 Identities=30% Similarity=0.534 Sum_probs=20.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 162 ECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 162 ~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
..+.+......|..+|..|+.++..|.
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 334566777888899999988888774
No 47
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=78.56 E-value=0.28 Score=35.20 Aligned_cols=44 Identities=14% Similarity=0.255 Sum_probs=27.7
Q ss_pred CCCccCCHHHHHHHHHHH-hhCCCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 101 RKKLRLTKPQFATLEDTF-KEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 101 r~Rt~~t~~Ql~~Le~~F-~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
++|.+||.++...+-..+ ... ....++|+++|+++.+|..|-+-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~g-----~sv~~va~~~gi~~~~l~~W~~~ 46 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLESG-----ESVSEVAREYGISPSTLYNWRKQ 46 (76)
T ss_dssp -SS----HHHHHHHHHHHHHHH-----CHHHHHHHHHTS-HHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHCC-----CceEeeecccccccccccHHHHH
Confidence 456789998866655554 322 45778999999999999999643
No 48
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=74.60 E-value=46 Score=32.78 Aligned_cols=84 Identities=18% Similarity=0.279 Sum_probs=50.3
Q ss_pred CccCCHHHHHHHHHH-Hhh-CCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHH---------------HHH
Q 024915 103 KLRLTKPQFATLEDT-FKE-HSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVE---------------CEL 165 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~-F~~-~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~---------------~e~ 165 (260)
-.++|.+....|.+. |.. ..+|-.+.-+++-++ |+.=.+|+|...-.++++++ +..
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKr-------vRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKR-------VRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHH-------HHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 457899988888776 322 234444444444433 34444566654322222222 335
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhhc
Q 024915 166 LKRCCEKLKDENKRLQREVQELKSMKLS 193 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~~~l~~~~~~ 193 (260)
||+..+.|..+|+.|..+++.|.++...
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v~q 318 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLVIQ 318 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHhh
Confidence 7777788888888888888888776554
No 49
>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=67.66 E-value=4.2 Score=26.85 Aligned_cols=39 Identities=15% Similarity=0.200 Sum_probs=28.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
.+++.+..+|...|-.. ..-.++|..+|++...|+.+..
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHH
Confidence 47888999999999332 2356799999999988876553
No 50
>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=66.42 E-value=31 Score=24.05 Aligned_cols=24 Identities=42% Similarity=0.537 Sum_probs=11.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 164 ELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 164 e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
+.|...++.|..++..|+.++..|
T Consensus 36 ~~L~~en~~L~~~~~~L~~~~~~L 59 (64)
T PF00170_consen 36 EELESENEELKKELEQLKKEIQSL 59 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444
No 51
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=65.86 E-value=24 Score=32.19 Aligned_cols=28 Identities=25% Similarity=0.426 Sum_probs=16.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhh
Q 024915 165 LLKRCCEKLKDENKRLQREVQELKSMKL 192 (260)
Q Consensus 165 ~l~~~~~~l~~en~~l~~e~~~l~~~~~ 192 (260)
.|.+.++.|+.+.+.|++|+..++.++.
T Consensus 226 ~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 226 ELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555666666666666666655544
No 52
>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=63.51 E-value=9.6 Score=21.53 Aligned_cols=38 Identities=13% Similarity=0.206 Sum_probs=25.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWF 147 (260)
.++.++...+...|... . ...++|+.++++...|..|.
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 45666666666666532 2 35578899999988887773
No 53
>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=63.43 E-value=6.9 Score=26.96 Aligned_cols=38 Identities=24% Similarity=0.200 Sum_probs=30.0
Q ss_pred CCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCCcce
Q 024915 106 LTKPQFATLEDTFKEHST--LSPKQKQGLAEKLNLRPRQV 143 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~--ps~~~r~~LA~~lgLs~rqV 143 (260)
+|..|..+|...|...-| |-.....+||++||+++..|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578999999999986544 54555788999999988654
No 54
>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=63.06 E-value=3.3 Score=26.41 Aligned_cols=43 Identities=16% Similarity=0.157 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRa 152 (260)
.++..+..++...|... ....++|..+|++...|..|...-+.
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~ 52 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALK 52 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHH
Confidence 46777888887777433 23567899999999999888765443
No 55
>smart00338 BRLZ basic region leucin zipper.
Probab=60.52 E-value=35 Score=23.87 Aligned_cols=22 Identities=45% Similarity=0.779 Sum_probs=12.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 024915 166 LKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~~~l 187 (260)
|....+.|..+|..|+.++..|
T Consensus 31 Le~~~~~L~~en~~L~~~~~~l 52 (65)
T smart00338 31 LERKVEQLEAENERLKKEIERL 52 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555566666666555554
No 56
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=60.12 E-value=22 Score=32.93 Aligned_cols=28 Identities=43% Similarity=0.561 Sum_probs=15.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024915 162 ECELLKRCCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 162 ~~e~l~~~~~~l~~en~~l~~e~~~l~~ 189 (260)
+++.|-+.++.|+++..+|.+|++.|+.
T Consensus 256 e~~~Le~rN~~LK~qa~~lerEI~ylKq 283 (294)
T KOG4571|consen 256 ELEGLEKRNEELKDQASELEREIRYLKQ 283 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555555556555543
No 57
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=59.52 E-value=36 Score=29.35 Aligned_cols=49 Identities=27% Similarity=0.311 Sum_probs=39.1
Q ss_pred CcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 140 PRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 140 ~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
--...+|-+-|-.+.|..+.+.+.+.|....+.|..+.+++++++.+|.
T Consensus 85 ~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~ 133 (181)
T KOG3335|consen 85 VLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLH 133 (181)
T ss_pred eeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677777777777777777888888899999999999999999994
No 58
>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=58.84 E-value=32 Score=27.07 Aligned_cols=35 Identities=37% Similarity=0.377 Sum_probs=27.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 156 LKQTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 156 k~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
...+-.+.+.||.....|.+||.+|+-|++.|+..
T Consensus 17 l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~ 51 (107)
T PF06156_consen 17 LGQLLEELEELKKQLQELLEENARLRIENEHLRER 51 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555667778888888899999999988888544
No 59
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=58.00 E-value=21 Score=34.90 Aligned_cols=31 Identities=29% Similarity=0.523 Sum_probs=24.2
Q ss_pred eeecc---cchhHHHHHHhhHHHHHHHHHHHHHH
Q 024915 143 VEVWF---QNRRARSKLKQTEVECELLKRCCEKL 173 (260)
Q Consensus 143 VkvWF---QNRRak~Kk~~~~~~~e~l~~~~~~l 173 (260)
+-+|| ||+.+|.+-++..++.|.|++.-..|
T Consensus 228 ~gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl 261 (575)
T KOG4403|consen 228 GGCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSL 261 (575)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34688 99999999998888888887755433
No 60
>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=57.79 E-value=37 Score=24.75 Aligned_cols=31 Identities=39% Similarity=0.370 Sum_probs=23.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 158 QTEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 158 ~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+...+.+.++...+.+..||.+|+.|+..+.
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 5555666677777788888888888887763
No 61
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=57.58 E-value=28 Score=32.22 Aligned_cols=31 Identities=29% Similarity=0.345 Sum_probs=25.2
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
++.+.+.|.+--+++.|..+|++|+.++.++
T Consensus 244 qKkRae~E~l~ge~~~Le~rN~~LK~qa~~l 274 (294)
T KOG4571|consen 244 QKKRAEKEALLGELEGLEKRNEELKDQASEL 274 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445667778888999999999999999887
No 62
>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=57.47 E-value=61 Score=27.48 Aligned_cols=48 Identities=23% Similarity=0.225 Sum_probs=36.7
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchh
Q 024915 102 KKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 102 ~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
++..+|.+++..+.+.-.++ |..-.+..||+++|+++.-|.+-.+--.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~ 129 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK 129 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH
Confidence 44689999999998876654 5566788999999999877776554433
No 63
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=57.30 E-value=14 Score=30.69 Aligned_cols=47 Identities=19% Similarity=0.097 Sum_probs=34.7
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
...+++.|..+|...+ .. ....++|..||++...|+.|-++.+.+.+
T Consensus 4 ~~~Lt~rqreVL~lr~-~G-----lTq~EIAe~LGiS~~tVs~ie~ra~kkLr 50 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG-----LTQQEIADILGTSRANVSSIEKRARENIE 50 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3578999999998743 22 23567999999999999999876554444
No 64
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=55.68 E-value=6.8 Score=26.82 Aligned_cols=33 Identities=15% Similarity=0.242 Sum_probs=20.0
Q ss_pred HHHHHHHhCCCCcceeecccchhHHHHHHhhHH
Q 024915 129 KQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEV 161 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~ 161 (260)
..+||+.+|++..+|..|+.++...........
T Consensus 13 ~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ 45 (63)
T PF13443_consen 13 QKDLARKTGISRSTLSRILNGKPSNPSLDTLEK 45 (63)
T ss_dssp HHHHHHHHT--HHHHHHHHTTT-----HHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHhcccccccHHHHHH
Confidence 567899999999999999988755554433333
No 65
>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=54.90 E-value=9.5 Score=25.33 Aligned_cols=42 Identities=17% Similarity=0.157 Sum_probs=27.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchh
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
.+++.+..++...|-.. ..-.++|..+|+++..|+.|.+.-|
T Consensus 10 ~L~~~~r~i~~l~~~~g-----~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 10 QLPERQREIFLLRYFQG-----MSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp CS-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHC-----cCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 35666767776665433 4567899999999999999986433
No 66
>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=54.49 E-value=42 Score=23.84 Aligned_cols=30 Identities=37% Similarity=0.499 Sum_probs=23.2
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 158 QTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 158 ~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
+...+...++...+.+..+|+.|+.+++.+
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 444556677788888888888888888877
No 67
>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=54.21 E-value=4.3 Score=28.78 Aligned_cols=19 Identities=26% Similarity=0.518 Sum_probs=16.6
Q ss_pred HHHHHHHhCCCCcceeecc
Q 024915 129 KQGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWF 147 (260)
..+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 4578999999999999884
No 68
>PRK00118 putative DNA-binding protein; Validated
Probab=54.14 E-value=42 Score=26.29 Aligned_cols=46 Identities=17% Similarity=0.109 Sum_probs=32.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..|..++...|.... ...++|+.+|+++..|..|...-|.+.|
T Consensus 17 ~L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 17 LLTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 356777777766655432 3557999999999999988875444443
No 69
>smart00338 BRLZ basic region leucin zipper.
Probab=52.98 E-value=68 Score=22.33 Aligned_cols=35 Identities=40% Similarity=0.530 Sum_probs=26.9
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 156 LKQTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 156 k~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
...++...+.|...+..|..+...|+.++..|+..
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456666678888888999999999988888654
No 70
>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=51.74 E-value=78 Score=24.04 Aligned_cols=64 Identities=16% Similarity=0.262 Sum_probs=39.7
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
+..|+..++..|..... .+.+|++...|+.++.... ....+.+......|.++..+|+.
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 34699999988866532 3456777777777776543 22334455555566666666665
Q ss_pred HHHHH
Q 024915 183 EVQEL 187 (260)
Q Consensus 183 e~~~l 187 (260)
.++.|
T Consensus 95 ~~~~l 99 (103)
T cd01106 95 LIKTI 99 (103)
T ss_pred HHHHH
Confidence 55554
No 71
>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=51.70 E-value=71 Score=23.32 Aligned_cols=27 Identities=41% Similarity=0.530 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 161 VECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 161 ~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
.+.+.|+..+..|.++|..|+.+++.|
T Consensus 25 ~e~eeLke~n~~L~~e~~~L~~en~~L 51 (72)
T PF06005_consen 25 MENEELKEKNNELKEENEELKEENEQL 51 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHH
Confidence 333344444333333344444333333
No 72
>PF15058 Speriolin_N: Speriolin N terminus
Probab=50.90 E-value=24 Score=30.83 Aligned_cols=20 Identities=35% Similarity=0.429 Sum_probs=8.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024915 164 ELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 164 e~l~~~~~~l~~en~~l~~e 183 (260)
|.+..++++|..||++|+|+
T Consensus 8 eGlrhqierLv~ENeeLKKl 27 (200)
T PF15058_consen 8 EGLRHQIERLVRENEELKKL 27 (200)
T ss_pred HHHHHHHHHHHhhhHHHHHH
Confidence 33333444444444444433
No 73
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=49.55 E-value=49 Score=26.29 Aligned_cols=34 Identities=26% Similarity=0.221 Sum_probs=25.5
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
..+-.+.+.||.....|.+||.+|+-|++.|+..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~ 51 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRER 51 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455566678888888888888888888888544
No 74
>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=49.38 E-value=1.1e+02 Score=23.92 Aligned_cols=69 Identities=14% Similarity=0.197 Sum_probs=43.4
Q ss_pred CCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 024915 102 KKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQ 181 (260)
Q Consensus 102 ~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~ 181 (260)
....|+..++..|.. ....+.+|++-..|+.++.+... .....+.+....+.+.++-++|+
T Consensus 34 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~~~------~~~~~~~l~~~~~~l~~~i~~l~ 94 (120)
T cd04781 34 LRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHDGK------PPIDRQLLKAKAAELDQQIQRLQ 94 (120)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccCC------cHHHHHHHHHHHHHHHHHHHHHH
Confidence 345789999888853 34577778888888888766431 11123455555666666666666
Q ss_pred HHHHHHHh
Q 024915 182 REVQELKS 189 (260)
Q Consensus 182 ~e~~~l~~ 189 (260)
.....+..
T Consensus 95 ~~~~~L~~ 102 (120)
T cd04781 95 AMRELLRH 102 (120)
T ss_pred HHHHHHHH
Confidence 66655543
No 75
>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=49.27 E-value=81 Score=21.90 Aligned_cols=29 Identities=34% Similarity=0.485 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024915 161 VECELLKRCCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 161 ~~~e~l~~~~~~l~~en~~l~~e~~~l~~ 189 (260)
...+.|...+..|..+|..|+.++..|..
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~ 54 (64)
T PF00170_consen 26 QYIEELEEKVEELESENEELKKELEQLKK 54 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34456778888999999999999888854
No 76
>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=48.94 E-value=74 Score=25.51 Aligned_cols=70 Identities=9% Similarity=0.085 Sum_probs=41.7
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e 183 (260)
+.|+.+++..|.. ....+.+|++-..|+.++........ ......+.+....+.+.++..+|++.
T Consensus 37 R~Y~~~~~~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (133)
T cd04787 37 RLYSEKDLSRLRF-------------ILSARQLGFSLKDIKEILSHADQGES--PCPMVRRLIEQRLAETERRIKELLKL 101 (133)
T ss_pred eeCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhhhccCCC--cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4789999888833 33467888888888888865432111 01122344555556666666666655
Q ss_pred HHHHH
Q 024915 184 VQELK 188 (260)
Q Consensus 184 ~~~l~ 188 (260)
.+.+.
T Consensus 102 ~~~l~ 106 (133)
T cd04787 102 RDRMQ 106 (133)
T ss_pred HHHHH
Confidence 55553
No 77
>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=48.63 E-value=16 Score=28.79 Aligned_cols=14 Identities=36% Similarity=0.615 Sum_probs=11.4
Q ss_pred cceeecccchhHHH
Q 024915 141 RQVEVWFQNRRARS 154 (260)
Q Consensus 141 rqVkvWFQNRRak~ 154 (260)
||.+.||-.+|.-.
T Consensus 18 Rq~e~~FlqKr~~L 31 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHH
Confidence 67789999888765
No 78
>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=47.76 E-value=14 Score=25.05 Aligned_cols=46 Identities=15% Similarity=0.187 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
.||..++.+|.-...-. ...++|..++++++.|+.+..+=+.|..-
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 57888888887776533 36789999999999999888776666543
No 79
>PRK14127 cell division protein GpsB; Provisional
Probab=47.59 E-value=53 Score=26.02 Aligned_cols=34 Identities=29% Similarity=0.435 Sum_probs=26.6
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
.+...+++.+.+....|++++.+|+.++.++...
T Consensus 33 d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~ 66 (109)
T PRK14127 33 DDVIKDYEAFQKEIEELQQENARLKAQVDELTKQ 66 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3556677888888888888888888888888654
No 80
>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=47.36 E-value=67 Score=23.14 Aligned_cols=23 Identities=35% Similarity=0.436 Sum_probs=10.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024915 164 ELLKRCCEKLKDENKRLQREVQE 186 (260)
Q Consensus 164 e~l~~~~~~l~~en~~l~~e~~~ 186 (260)
+.|-..++.|+.||..|+.++..
T Consensus 10 e~Li~~~~~L~~EN~~Lr~q~~~ 32 (65)
T TIGR02449 10 EHLLEYLERLKSENRLLRAQEKT 32 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444455444444433
No 81
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=46.10 E-value=26 Score=38.69 Aligned_cols=60 Identities=20% Similarity=0.264 Sum_probs=54.1
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHh
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~ 158 (260)
.++-|..+-.+++..|-+.|-.+.-|+.+.+..|......+.+++.+||+|-|.|.++.+
T Consensus 705 ~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 705 DKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 455667777799999999999999999999999999999999999999999999998766
No 82
>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=45.40 E-value=7 Score=34.80 Aligned_cols=33 Identities=36% Similarity=0.436 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Q 024915 159 TEVECELLKRCCEKLKDENKRLQREVQELKSMK 191 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~~ 191 (260)
......-|++..+.|..||++|++|+++|++-+
T Consensus 127 Q~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~ 159 (243)
T PF08961_consen 127 QATKIADLRRLVEFLLAENERLRRENKQLKAEN 159 (243)
T ss_dssp ---------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445678888888888888888888886654
No 83
>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=45.08 E-value=34 Score=24.13 Aligned_cols=30 Identities=33% Similarity=0.409 Sum_probs=25.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 161 VECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 161 ~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
.+-+.||.....|.+.|..|+.|+.-|+..
T Consensus 14 EEVevLK~~I~eL~~~n~~Le~EN~~Lk~~ 43 (59)
T PF01166_consen 14 EEVEVLKEQIAELEERNSQLEEENNLLKQN 43 (59)
T ss_dssp TSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 456789999999999999999999888765
No 84
>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=45.01 E-value=17 Score=25.66 Aligned_cols=44 Identities=25% Similarity=0.341 Sum_probs=22.4
Q ss_pred CccCCHHH-HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 103 KLRLTKPQ-FATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 103 Rt~~t~~Q-l~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
|..|+... +.+++..+..+ .--..+| .-|+++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~-nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDN-NCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-T-TTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHcc-chhhhHH-HHHHHhCccHHHHHHHHH
Confidence 34566554 45555544332 2222233 349999999999998864
No 85
>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=43.12 E-value=90 Score=21.00 Aligned_cols=24 Identities=38% Similarity=0.473 Sum_probs=13.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 160 EVECELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 160 ~~~~e~l~~~~~~l~~en~~l~~e 183 (260)
+.....|...+..|..++..|+.|
T Consensus 31 e~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 31 EQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcc
Confidence 334445556666666666666553
No 86
>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=42.79 E-value=91 Score=24.09 Aligned_cols=70 Identities=19% Similarity=0.212 Sum_probs=41.6
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e 183 (260)
..|+.+++..|... ...+.+|++-..|+..+........ ......+.+....+.|.++.+.|+..
T Consensus 37 R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (113)
T cd01109 37 RDFTEEDLEWLEFI-------------KCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQET 101 (113)
T ss_pred ccCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46899998888442 3356788888888877765432211 11222345555566666666666665
Q ss_pred HHHHH
Q 024915 184 VQELK 188 (260)
Q Consensus 184 ~~~l~ 188 (260)
+..+.
T Consensus 102 ~~~l~ 106 (113)
T cd01109 102 LAYLD 106 (113)
T ss_pred HHHHH
Confidence 55543
No 87
>PHA02955 hypothetical protein; Provisional
Probab=42.44 E-value=32 Score=30.45 Aligned_cols=42 Identities=12% Similarity=0.233 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhC-CCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 108 KPQFATLEDTFKEH-STLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 108 ~~Ql~~Le~~F~~~-~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
..|+..|-+.|.+. ..+++++|.+++++||+....|..||.+
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 35667777777654 6788899999999999998878999976
No 88
>PRK10072 putative transcriptional regulator; Provisional
Probab=41.62 E-value=18 Score=27.85 Aligned_cols=42 Identities=17% Similarity=0.187 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
+.+...+..|...-..+ ..+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~glT-------Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGLK-------IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCCC-------HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 44666677775433222 6689999999999999999987653
No 89
>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=41.36 E-value=41 Score=25.65 Aligned_cols=54 Identities=30% Similarity=0.374 Sum_probs=33.7
Q ss_pred CCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 124 LSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQ 185 (260)
Q Consensus 124 ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~ 185 (260)
.+..+...|=.. +..|...=|++ |.+......+.+++....|.++|..|++++.
T Consensus 46 Ls~~eL~~LE~~-------Le~aL~~VR~r-K~~~l~~~i~~l~~ke~~l~~en~~L~~~~~ 99 (100)
T PF01486_consen 46 LSLKELQQLEQQ-------LESALKRVRSR-KDQLLMEQIEELKKKERELEEENNQLRQKIE 99 (100)
T ss_pred cchHHHHHHHHh-------hhhhHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 444444444444 44444433444 3345566777788888888999999888765
No 90
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=41.06 E-value=62 Score=29.11 Aligned_cols=34 Identities=24% Similarity=0.234 Sum_probs=21.6
Q ss_pred HhhHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHhh
Q 024915 157 KQTEVECELLKRCCEKLKDENK---RLQREVQELKSM 190 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~---~l~~e~~~l~~~ 190 (260)
++...+++.|++.+..|+.++. .+++|+++|+.+
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 4556667777777766666665 556666666544
No 91
>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=40.91 E-value=1.2e+02 Score=22.04 Aligned_cols=30 Identities=30% Similarity=0.360 Sum_probs=16.9
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 156 LKQTEVECELLKRCCEKLKDENKRLQREVQ 185 (260)
Q Consensus 156 k~~~~~~~e~l~~~~~~l~~en~~l~~e~~ 185 (260)
....+..+..+....+.|.+||.+|+.+..
T Consensus 27 ~eeLke~n~~L~~e~~~L~~en~~L~~e~~ 56 (72)
T PF06005_consen 27 NEELKEKNNELKEENEELKEENEQLKQERN 56 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 344445555555666666666666665543
No 92
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=40.07 E-value=11 Score=24.60 Aligned_cols=39 Identities=15% Similarity=0.148 Sum_probs=19.2
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecc
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWF 147 (260)
+.||.+|...++..+... .-..+||+.||.++..|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 468888888888887643 345679999999988876554
No 93
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=39.71 E-value=83 Score=23.11 Aligned_cols=32 Identities=25% Similarity=0.276 Sum_probs=16.3
Q ss_pred HHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 153 RSKLKQTEVECELLKRCCEKLKDENKRLQREV 184 (260)
Q Consensus 153 k~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~ 184 (260)
|.|...+..+...++...+.|..||+.|+.|.
T Consensus 31 KEknn~l~~e~q~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 31 KEKNNSLSQEVQNAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444555556666666665553
No 94
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=39.22 E-value=1.6e+02 Score=22.63 Aligned_cols=43 Identities=7% Similarity=0.101 Sum_probs=31.7
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCC-CCcceeecccc
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNL-RPRQVEVWFQN 149 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgL-s~rqVkvWFQN 149 (260)
|.+|+.+....+-+.+....+ -..++|+++|+ ...++..|-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~ 48 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQ 48 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHH
Confidence 678998877666555554443 46789999996 99999988653
No 95
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=38.81 E-value=30 Score=30.07 Aligned_cols=38 Identities=21% Similarity=0.194 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHhhCCC--CCHHHHHHHHHHhCCCCcc
Q 024915 105 RLTKPQFATLEDTFKEHST--LSPKQKQGLAEKLNLRPRQ 142 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~--ps~~~r~~LA~~lgLs~rq 142 (260)
.+|..|+++|...|+..=| |=.....+||++||+++..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 6999999999999985443 5555678899999998864
No 96
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=38.70 E-value=53 Score=30.57 Aligned_cols=28 Identities=29% Similarity=0.433 Sum_probs=21.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 163 CELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 163 ~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
-..|......|..+|..|-+|++.|+.|
T Consensus 314 VKCLENRVAVLENQNKaLIEELKtLKeL 341 (348)
T KOG3584|consen 314 VKCLENRVAVLENQNKALIEELKTLKEL 341 (348)
T ss_pred HHHHHhHHHHHhcccHHHHHHHHHHHHH
Confidence 3455666678999999999888887766
No 97
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=38.64 E-value=39 Score=26.00 Aligned_cols=35 Identities=23% Similarity=0.325 Sum_probs=18.9
Q ss_pred HHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 111 FATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 111 l~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
+...+-.|..|+||...--.. | =.|||.||++++.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 445566688999997542111 1 1588999987654
No 98
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=37.95 E-value=23 Score=28.72 Aligned_cols=42 Identities=14% Similarity=0.007 Sum_probs=29.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchh
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
.+++.+..+|...|-.. ....++|..+|++...|+.|...-+
T Consensus 128 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~ 169 (182)
T PRK09652 128 SLPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAR 169 (182)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHH
Confidence 46777777776655322 2345789999999999998887333
No 99
>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=37.67 E-value=60 Score=32.12 Aligned_cols=26 Identities=19% Similarity=0.161 Sum_probs=12.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLA 133 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA 133 (260)
.++++++..|.. .-..|...-|..+|
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva 66 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVA 66 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHH
Confidence 355555544433 23445444444444
No 100
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=37.12 E-value=8.6 Score=38.98 Aligned_cols=60 Identities=17% Similarity=0.278 Sum_probs=0.0
Q ss_pred CCCCCccCCHHHHHHHHHHHh-hCCCCCHHHHHHHHHHh-------CCCCcceeecccchhHHHHHHh
Q 024915 99 SPRKKLRLTKPQFATLEDTFK-EHSTLSPKQKQGLAEKL-------NLRPRQVEVWFQNRRARSKLKQ 158 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~-~~~~ps~~~r~~LA~~l-------gLs~rqVkvWFQNRRak~Kk~~ 158 (260)
.|+++-+|-.+|...+...+. .+..+......+.-+++ ....+.|+.||.|||+++|+-+
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k 758 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLK 758 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhh
No 101
>cd04761 HTH_MerR-SF Helix-Turn-Helix DNA binding domain of transcription regulators from the MerR superfamily. Helix-turn-helix (HTH) transcription regulator MerR superfamily, N-terminal domain. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription of multidrug/metal ion transporter genes and oxidative stress regulons by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=36.89 E-value=11 Score=24.25 Aligned_cols=23 Identities=13% Similarity=0.096 Sum_probs=19.0
Q ss_pred HHHHHHHhCCCCcceeecccchh
Q 024915 129 KQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976554
No 102
>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=36.85 E-value=1.2e+02 Score=23.58 Aligned_cols=72 Identities=15% Similarity=0.082 Sum_probs=42.0
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|+.. ...+.+|++-..|+..+.+..... .....-.+.+....+.+.++-++|+.
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 346899999888443 335777888888877776543311 01112234455555566666666666
Q ss_pred HHHHHHh
Q 024915 183 EVQELKS 189 (260)
Q Consensus 183 e~~~l~~ 189 (260)
..+.+..
T Consensus 101 ~~~~l~~ 107 (123)
T cd04770 101 LRAELAG 107 (123)
T ss_pred HHHHHHH
Confidence 5555543
No 103
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=36.29 E-value=29 Score=29.23 Aligned_cols=46 Identities=17% Similarity=0.180 Sum_probs=31.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..+..+|...|-.. ..-.++|+.||++...|++|...-|.+.|
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 46677777776654333 23567899999999999888754444333
No 104
>PF13518 HTH_28: Helix-turn-helix domain
Probab=36.21 E-value=12 Score=24.34 Aligned_cols=21 Identities=14% Similarity=0.404 Sum_probs=17.9
Q ss_pred HHHHHHHhCCCCcceeecccc
Q 024915 129 KQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQN 149 (260)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 456899999999999999853
No 105
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=35.78 E-value=86 Score=24.43 Aligned_cols=39 Identities=15% Similarity=0.113 Sum_probs=32.1
Q ss_pred eecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 144 EVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 144 kvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
.-|+..+..+.+....+.+.+.++..++.|..|..+|+.
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 346666777777788888888999999999999999987
No 106
>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=35.71 E-value=1.2e+02 Score=22.81 Aligned_cols=45 Identities=31% Similarity=0.395 Sum_probs=27.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh----cCCCCcCCCCCC
Q 024915 160 EVECELLKRCCEKLKDENKRLQREVQELKSMKL----SGAPLYMKLPAP 204 (260)
Q Consensus 160 ~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~~~----~~~~~~~~~p~~ 204 (260)
..+.+.+.+..+.|.+||.+|+-|...+..... +...+-|..|..
T Consensus 41 ~~~l~~l~~~~~~l~~e~~~L~lE~~~l~~~~rIe~iA~~~LgM~~P~~ 89 (97)
T PF04999_consen 41 FYELQQLEKEIDQLQEENERLRLEIATLSSPSRIERIAREKLGMVPPEP 89 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhhCHHHHHHHHHHcCCCCCCCC
Confidence 344566667777888888888888777644321 123455655544
No 107
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=35.59 E-value=1.6e+02 Score=22.48 Aligned_cols=36 Identities=22% Similarity=0.477 Sum_probs=19.7
Q ss_pred ecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 145 VWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 145 vWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
+|||=++++.+ ++.|...++.|..|....+.|+...
T Consensus 21 ~~~k~~ka~~~-------~~kL~~en~qlk~Ek~~~~~qvkn~ 56 (87)
T PF10883_consen 21 LWWKVKKAKKQ-------NAKLQKENEQLKTEKAVAETQVKNA 56 (87)
T ss_pred HHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56655554444 5555555555555555555555554
No 108
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=35.45 E-value=17 Score=37.77 Aligned_cols=61 Identities=16% Similarity=0.251 Sum_probs=45.7
Q ss_pred CCCCCccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhh
Q 024915 99 SPRKKLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQT 159 (260)
Q Consensus 99 ~~r~Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~ 159 (260)
+.+.++....++-..|...|..+..++..+-..++.+|...+.+|+|||++|+..-++..+
T Consensus 626 p~kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~pl 686 (1007)
T KOG3623|consen 626 PVKVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMPL 686 (1007)
T ss_pred CccccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCcc
Confidence 3455566667777778888887776666665555666888899999999999998887654
No 109
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=35.35 E-value=35 Score=27.17 Aligned_cols=45 Identities=13% Similarity=0.067 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARS 154 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~ 154 (260)
.+++.+..++...|-.. ....++|..+|++...|+.|...-|.+.
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 46666777766655433 2367899999999999998876444433
No 110
>PRK04217 hypothetical protein; Provisional
Probab=34.77 E-value=38 Score=26.80 Aligned_cols=40 Identities=13% Similarity=0.081 Sum_probs=30.0
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
..++.+|..++...|...- ...+||+.+|++...|+..+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHH
Confidence 3578888888877765332 456799999999988876654
No 111
>cd04769 HTH_MerR2 Helix-Turn-Helix DNA binding domain of MerR2-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MerR2 and related proteins. MerR2 in Bacillus cereus RC607 regulates resistance to organomercurials. The MerR family transcription regulators have been shown to mediate responses to stress including exposure to heavy metals, drugs, or oxygen radicals in eubacterial and some archaeal species. They regulate transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.58 E-value=1.2e+02 Score=23.58 Aligned_cols=73 Identities=12% Similarity=0.107 Sum_probs=43.3
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+..++..|... ...+.+|++...|+.++....... ......-.+.+....+.+.++-++|+.
T Consensus 35 yR~Y~~~d~~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~~-~~~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (116)
T cd04769 35 YRVYDAQHVECLRFI-------------KEARQLGFTLAELKAIFAGHEGRA-VLPWPHLQQALEDKKQEIRAQITELQQ 100 (116)
T ss_pred ceeeCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhccccCC-cCcHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346888888877443 235777888888887776655432 111122234555555666666666666
Q ss_pred HHHHHHh
Q 024915 183 EVQELKS 189 (260)
Q Consensus 183 e~~~l~~ 189 (260)
..+.+..
T Consensus 101 ~~~~l~~ 107 (116)
T cd04769 101 LLARLDA 107 (116)
T ss_pred HHHHHHH
Confidence 6665543
No 112
>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=34.20 E-value=92 Score=28.55 Aligned_cols=34 Identities=21% Similarity=0.197 Sum_probs=17.8
Q ss_pred HhhHHHHHHHHHHHHHHHH----HHHHHHHHHHHHHhh
Q 024915 157 KQTEVECELLKRCCEKLKD----ENKRLQREVQELKSM 190 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~----en~~l~~e~~~l~~~ 190 (260)
++...+++.|++....|.. ..+.+++|+++|+.+
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 3455666666665544422 222356666666554
No 113
>KOG4797 consensus Transcriptional regulator [Transcription]
Probab=34.14 E-value=1e+02 Score=24.58 Aligned_cols=31 Identities=35% Similarity=0.490 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 160 EVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 160 ~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
+.+-|.|+.....|.+.|.+|++|+.-|+.+
T Consensus 66 REEVe~Lk~qI~eL~er~~~Le~EN~lLk~~ 96 (123)
T KOG4797|consen 66 REEVEVLKEQIRELEERNSALERENSLLKTL 96 (123)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4566778888888888888888887777655
No 114
>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=34.13 E-value=2.1e+02 Score=21.74 Aligned_cols=64 Identities=16% Similarity=0.173 Sum_probs=40.2
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+..++..|... ...+.+|++-..|+.++.... ..+.+....+.+.++.++|+.
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 456899999888553 224667777777776665431 234555566667777777776
Q ss_pred HHHHHHh
Q 024915 183 EVQELKS 189 (260)
Q Consensus 183 e~~~l~~ 189 (260)
....+..
T Consensus 93 ~~~~l~~ 99 (102)
T cd04775 93 QQQVLAA 99 (102)
T ss_pred HHHHHHH
Confidence 6665543
No 115
>PRK10884 SH3 domain-containing protein; Provisional
Probab=34.06 E-value=2.9e+02 Score=24.24 Aligned_cols=10 Identities=20% Similarity=0.398 Sum_probs=4.9
Q ss_pred HHHHHHHHHH
Q 024915 109 PQFATLEDTF 118 (260)
Q Consensus 109 ~Ql~~Le~~F 118 (260)
.++..|++..
T Consensus 93 ~rlp~le~el 102 (206)
T PRK10884 93 TRVPDLENQV 102 (206)
T ss_pred HHHHHHHHHH
Confidence 4455555443
No 116
>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=33.99 E-value=99 Score=26.25 Aligned_cols=32 Identities=31% Similarity=0.474 Sum_probs=0.0
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 157 KQTEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+..+.+++.|+.....|..+|+.|++++..|.
T Consensus 100 ~~~~~e~~~l~~e~~~l~~~~e~Le~e~~~L~ 131 (161)
T TIGR02894 100 QALQKENERLKNQNESLQKRNEELEKELEKLR 131 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 117
>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=33.29 E-value=2.2e+02 Score=22.40 Aligned_cols=71 Identities=14% Similarity=0.144 Sum_probs=42.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|. .....+.+|++-..|+-++...... ....-.+.++...+.+.++..+|+.
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 4468999998884 3344688888888888888654421 1112233445555566666666665
Q ss_pred HHHHHHhh
Q 024915 183 EVQELKSM 190 (260)
Q Consensus 183 e~~~l~~~ 190 (260)
....+..+
T Consensus 99 ~~~~l~~~ 106 (126)
T cd04783 99 MRASLQEL 106 (126)
T ss_pred HHHHHHHH
Confidence 55555433
No 118
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=32.99 E-value=58 Score=24.21 Aligned_cols=13 Identities=46% Similarity=0.871 Sum_probs=6.4
Q ss_pred HHHHHHHHHHHHH
Q 024915 173 LKDENKRLQREVQ 185 (260)
Q Consensus 173 l~~en~~l~~e~~ 185 (260)
|.+||.+|+.+++
T Consensus 5 i~eEn~~Lk~eiq 17 (76)
T PF07334_consen 5 IQEENARLKEEIQ 17 (76)
T ss_pred HHHHHHHHHHHHH
Confidence 4445555555544
No 119
>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=32.84 E-value=64 Score=30.61 Aligned_cols=25 Identities=36% Similarity=0.369 Sum_probs=12.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 159 TEVECELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e 183 (260)
++.+++.||+.++.|+.|-++|+.+
T Consensus 37 Lr~EN~~LKkEN~~Lk~eVerLE~e 61 (420)
T PF07407_consen 37 LRMENHSLKKENNDLKIEVERLENE 61 (420)
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555555555555555433
No 120
>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=32.68 E-value=32 Score=23.68 Aligned_cols=32 Identities=34% Similarity=0.433 Sum_probs=23.8
Q ss_pred HHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCccee
Q 024915 109 PQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVE 144 (260)
Q Consensus 109 ~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVk 144 (260)
.|+..|+-.+. +...+.. +||..+|++.+.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 57888888888 6666644 79999999987654
No 121
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=32.08 E-value=34 Score=29.21 Aligned_cols=44 Identities=18% Similarity=0.239 Sum_probs=28.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARS 154 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~ 154 (260)
++..+..+|...|-.. ....++|..+|++...|+++...-|.+.
T Consensus 154 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~L 197 (206)
T PRK12526 154 LPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKL 197 (206)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5556666665443222 2356789999999999987775443333
No 122
>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=31.65 E-value=34 Score=22.19 Aligned_cols=39 Identities=15% Similarity=0.307 Sum_probs=26.4
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecc
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWF 147 (260)
..++.+|+..+...+... ....++|+.+|++...|..|+
T Consensus 4 ~~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 4 PKLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 346776777777777655 236789999999988876554
No 123
>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=31.49 E-value=1.1e+02 Score=23.55 Aligned_cols=29 Identities=34% Similarity=0.467 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 160 EVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 160 ~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
....+.|....+.+..+|..|.+++++++
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45556788888899999999999988775
No 124
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=31.35 E-value=39 Score=21.59 Aligned_cols=39 Identities=21% Similarity=0.256 Sum_probs=27.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
.++..+...+...+. . ....++|..+|++...|..|.+.
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~ 41 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSN 41 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 467777777765432 2 13577899999999999877763
No 125
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.14 E-value=35 Score=27.60 Aligned_cols=45 Identities=18% Similarity=0.120 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+++.+..++...|-.. ..-.++|..+|+++..|+.|...-|.+.|
T Consensus 126 L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 126 LPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555544322 23568999999999999988865444443
No 126
>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=30.99 E-value=1.9e+02 Score=22.77 Aligned_cols=69 Identities=14% Similarity=0.069 Sum_probs=38.2
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+..++..|+. ....+.+|++...|+.++..... .....-.+.+....+.+.++.++|+.
T Consensus 35 ~R~Y~~~~l~~l~~-------------I~~l~~~G~sl~eI~~~l~~~~~----~~~~~~~~~l~~~~~~l~~~i~~L~~ 97 (124)
T TIGR02051 35 YRRYPEETVKRLRF-------------IKRAQELGFSLEEIGGLLGLVDG----THCREMYELASRKLKSVQAKMADLLR 97 (124)
T ss_pred CEeECHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHhcccC----CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34688888888833 33467888888888888765332 00111123334444455555555554
Q ss_pred HHHHHH
Q 024915 183 EVQELK 188 (260)
Q Consensus 183 e~~~l~ 188 (260)
-...|.
T Consensus 98 ~~~~L~ 103 (124)
T TIGR02051 98 IERLLE 103 (124)
T ss_pred HHHHHH
Confidence 444443
No 127
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=30.69 E-value=40 Score=27.12 Aligned_cols=45 Identities=20% Similarity=0.172 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+++.+..++...|-.. ..-.++|..+|+++..|+++...-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5566666665544322 12467899999999999988764444433
No 128
>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=30.49 E-value=44 Score=25.64 Aligned_cols=45 Identities=18% Similarity=0.189 Sum_probs=29.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARS 154 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~ 154 (260)
.+++.+..++...|-. .....++|..+|+++..|..|...-+.+.
T Consensus 110 ~L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl 154 (158)
T TIGR02937 110 KLPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKL 154 (158)
T ss_pred hCCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 3556666666554432 12356789999999999987776544433
No 129
>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=30.35 E-value=2.7e+02 Score=22.55 Aligned_cols=35 Identities=6% Similarity=-0.056 Sum_probs=21.1
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccch
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNR 150 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNR 150 (260)
+..|+..++..|...- . .+.+|++-..|+-++.+.
T Consensus 35 ~R~Y~~~~l~~l~~I~------------~-lr~~G~sL~eI~~~l~~~ 69 (134)
T cd04779 35 YRYYDETALDRLQLIE------------H-LKGQRLSLAEIKDQLEEV 69 (134)
T ss_pred CeeECHHHHHHHHHHH------------H-HHHCCCCHHHHHHHHHhh
Confidence 4568999988885542 1 345555555555555443
No 130
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=30.21 E-value=1.5e+02 Score=22.26 Aligned_cols=26 Identities=23% Similarity=0.266 Sum_probs=12.1
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 159 TEVECELLKRCCEKLKDENKRLQREV 184 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e~ 184 (260)
...+.+.++...+.|..||..|+.|.
T Consensus 37 L~~e~~~~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 37 LSQEVQNAQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 33333333333444555566555554
No 131
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=30.19 E-value=1.4e+02 Score=20.99 Aligned_cols=19 Identities=32% Similarity=0.553 Sum_probs=10.3
Q ss_pred HHHHHHHHHHHHHHHHHhh
Q 024915 172 KLKDENKRLQREVQELKSM 190 (260)
Q Consensus 172 ~l~~en~~l~~e~~~l~~~ 190 (260)
.|..|+..|++++.+|+.+
T Consensus 37 ~l~~e~~~L~~qN~eLr~l 55 (60)
T PF14775_consen 37 ALIQEKESLEQQNEELRSL 55 (60)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 3445555666666665543
No 132
>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=30.16 E-value=2.2e+02 Score=21.30 Aligned_cols=29 Identities=31% Similarity=0.391 Sum_probs=13.3
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 159 TEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
++...+.|+...+..++||+.|..|.+-|
T Consensus 28 LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~L 56 (80)
T PF10224_consen 28 LQDSLEALSDRVEEVKEENEKLESENEYL 56 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33334444444444444555554444433
No 133
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=30.15 E-value=1.5e+02 Score=22.68 Aligned_cols=33 Identities=12% Similarity=0.015 Sum_probs=25.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccch
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNR 150 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNR 150 (260)
+|+...+..|. ....++.+|++-..|+.+|...
T Consensus 36 ~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 36 FFDEKCQDDLE-------------FILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred ccCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhc
Confidence 58888877664 3455888999999999988653
No 134
>PF11365 DUF3166: Protein of unknown function (DUF3166); InterPro: IPR021507 This eukaryotic family of proteins has no known function.
Probab=29.99 E-value=1.3e+02 Score=23.26 Aligned_cols=32 Identities=47% Similarity=0.621 Sum_probs=26.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 159 TEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
-+.+-+.+.+-...+..+|++|..|+..++..
T Consensus 13 vEEEa~LlRRkl~ele~eN~~l~~EL~kyk~~ 44 (96)
T PF11365_consen 13 VEEEAELLRRKLSELEDENKQLTEELNKYKSK 44 (96)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34566788888899999999999999998754
No 135
>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=29.89 E-value=21 Score=24.93 Aligned_cols=25 Identities=24% Similarity=0.357 Sum_probs=19.7
Q ss_pred HHHHHHHhCCCCcceeecccchhHHHH
Q 024915 129 KQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
..++|..||++.+.|..|-+ |.+|.
T Consensus 16 ~~eIA~~Lg~~~~TV~~W~~--r~~W~ 40 (58)
T PF06056_consen 16 IKEIAEELGVPRSTVYSWKD--RYKWD 40 (58)
T ss_pred HHHHHHHHCCChHHHHHHHH--hhCcc
Confidence 45789999999999999974 44443
No 136
>KOG2483 consensus Upstream transcription factor 2/L-myc-2 protein [Transcription]
Probab=29.66 E-value=1.3e+02 Score=27.11 Aligned_cols=38 Identities=21% Similarity=0.360 Sum_probs=29.6
Q ss_pred hHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 151 RARSKLKQTEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 151 Rak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
|++.-.+.++..........+.|..||..|++++++|.
T Consensus 102 kA~~~i~~l~~~~~~~~~~~e~l~~e~~~l~~rl~ql~ 139 (232)
T KOG2483|consen 102 KALEHIQSLERKSATQQQDIEDLSRENRKLKARLEQLS 139 (232)
T ss_pred hHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 56655666666666677788899999999999998875
No 137
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=29.46 E-value=18 Score=25.04 Aligned_cols=20 Identities=15% Similarity=0.303 Sum_probs=17.0
Q ss_pred HHHHHHHhCCCCcceeeccc
Q 024915 129 KQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQ 148 (260)
..++|+.+|+++++|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 35789999999999999953
No 138
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.37 E-value=44 Score=26.98 Aligned_cols=43 Identities=16% Similarity=0.230 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
.++..+..+|.-.| .. ....++|..+|++...|+.+...-|.+
T Consensus 112 ~L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~ 154 (166)
T PRK09639 112 KMTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKK 154 (166)
T ss_pred cCCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 36666666666666 32 235678999999999998887533333
No 139
>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=29.29 E-value=1.4e+02 Score=26.16 Aligned_cols=20 Identities=40% Similarity=0.654 Sum_probs=10.9
Q ss_pred HHHHHHHHHHHHHHHHHHhh
Q 024915 171 EKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 171 ~~l~~en~~l~~e~~~l~~~ 190 (260)
..|++.|++||+++++|+.+
T Consensus 58 R~LKe~NqkLqedNqELRdL 77 (195)
T PF10226_consen 58 RGLKEVNQKLQEDNQELRDL 77 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34555555555555555443
No 140
>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=29.27 E-value=10 Score=27.99 Aligned_cols=23 Identities=22% Similarity=0.290 Sum_probs=19.7
Q ss_pred HHHHHHHHHhCCCCcceeecccc
Q 024915 127 KQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 127 ~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
....+||..+|+++..|+.|+.+
T Consensus 33 lS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 33 KTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred CCHHHHHHHHCcCHHHHHHHHhc
Confidence 34678999999999999999864
No 141
>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=29.05 E-value=1.1e+02 Score=25.18 Aligned_cols=45 Identities=20% Similarity=0.123 Sum_probs=31.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
.+.++..|..+|.-.+ .. ....++|..+|++...|+.|-..-|.+
T Consensus 4 ~~~Lte~qr~VL~Lr~-~G-----lTq~EIAe~LgiS~stV~~~e~ra~kk 48 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-KG-----LSQKEIAKELKTTRANVSAIEKRAMEN 48 (137)
T ss_pred cCCCCHHHHHHHHHHH-cC-----CCHHHHHHHHCcCHHHHHHHHHhHHHH
Confidence 3568999999998742 21 135679999999998887766543333
No 142
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=28.97 E-value=43 Score=27.70 Aligned_cols=46 Identities=20% Similarity=0.106 Sum_probs=31.5
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..+..++...|-.. ..-.+||..+|++...|+.++..-|.+.|
T Consensus 131 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr 176 (184)
T PRK12512 131 TLPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALA 176 (184)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 36666666666654332 23567999999999999988865555444
No 143
>PRK14127 cell division protein GpsB; Provisional
Probab=28.95 E-value=1.3e+02 Score=23.86 Aligned_cols=34 Identities=21% Similarity=0.211 Sum_probs=25.6
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024915 156 LKQTEVECELLKRCCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 156 k~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~ 189 (260)
...-..+.+.+...++.+..||.+|++++..|+.
T Consensus 25 ~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~ 58 (109)
T PRK14127 25 QDEVDKFLDDVIKDYEAFQKEIEELQQENARLKA 58 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445566777777888888888888888888853
No 144
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=28.87 E-value=45 Score=25.62 Aligned_cols=39 Identities=18% Similarity=0.244 Sum_probs=30.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcce
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQV 143 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqV 143 (260)
.+.++|...-...|..+-.......+++|..|++++-.|
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~l 40 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKL 40 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHH
Confidence 366788888777887777777788899999999987543
No 145
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=28.65 E-value=1e+02 Score=27.63 Aligned_cols=30 Identities=23% Similarity=0.226 Sum_probs=14.1
Q ss_pred HHHHhhHHHHHHHHHHHH---HHHHHHHHHHHH
Q 024915 154 SKLKQTEVECELLKRCCE---KLKDENKRLQRE 183 (260)
Q Consensus 154 ~Kk~~~~~~~e~l~~~~~---~l~~en~~l~~e 183 (260)
...++++.+...|+.... .+++||++|++.
T Consensus 76 ~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~l 108 (276)
T PRK13922 76 EENEELKKELLELESRLQELEQLEAENARLREL 108 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444332 555666665554
No 146
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=28.25 E-value=51 Score=27.11 Aligned_cols=45 Identities=18% Similarity=0.332 Sum_probs=29.4
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
++..+..++...|-.. ....++|..+|+++..|+++...-|.+.|
T Consensus 130 L~~~~r~i~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 174 (179)
T PRK12514 130 LEKDRAAAVRRAYLEG-----LSYKELAERHDVPLNTMRTWLRRSLLKLR 174 (179)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChHHHHHHHHHHHHHHH
Confidence 5555655555554222 23568999999999999888764444443
No 147
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.00 E-value=32 Score=22.31 Aligned_cols=21 Identities=10% Similarity=0.123 Sum_probs=18.1
Q ss_pred HHHHHhCCCCcceeecccchh
Q 024915 131 GLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 131 ~LA~~lgLs~rqVkvWFQNRR 151 (260)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 578899999999999998874
No 148
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=27.99 E-value=1.3e+02 Score=30.44 Aligned_cols=23 Identities=43% Similarity=0.537 Sum_probs=14.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024915 166 LKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+-..++.|+.||..|++++..+.
T Consensus 314 ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 314 LLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHhhhHHHHHHHHHHh
Confidence 33455666666666666666553
No 149
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=27.86 E-value=36 Score=28.42 Aligned_cols=45 Identities=16% Similarity=0.178 Sum_probs=28.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+++.+..++...|- ......++|..+|++...|++|+..-|.+.|
T Consensus 142 L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 44555555544432 2234567899999999999999864444333
No 150
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=27.86 E-value=2.4e+02 Score=20.37 Aligned_cols=20 Identities=45% Similarity=0.714 Sum_probs=13.3
Q ss_pred HHHHHHHHHHHHHHHHHHHH
Q 024915 169 CCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 169 ~~~~l~~en~~l~~e~~~l~ 188 (260)
.+..|+.|++.|++|++++.
T Consensus 48 e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 48 ENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 34567777777777766553
No 151
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=27.71 E-value=1.6e+02 Score=22.41 Aligned_cols=22 Identities=32% Similarity=0.360 Sum_probs=11.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHH
Q 024915 166 LKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~~~l 187 (260)
+++.++.|.+||+.|+.|....
T Consensus 28 a~~~~~kL~~en~qlk~Ek~~~ 49 (87)
T PF10883_consen 28 AKKQNAKLQKENEQLKTEKAVA 49 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555666555554443
No 152
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.65 E-value=18 Score=23.51 Aligned_cols=21 Identities=19% Similarity=0.449 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCCcceeeccc
Q 024915 128 QKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 128 ~r~~LA~~lgLs~rqVkvWFQ 148 (260)
...++|+.+|++...|..|.+
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHH
Confidence 466789999999999999975
No 153
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=27.42 E-value=46 Score=29.34 Aligned_cols=28 Identities=18% Similarity=0.262 Sum_probs=20.5
Q ss_pred HHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 128 QKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 128 ~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.-.++|..+|++...|+++...-|.+.|
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 3567899999999999887764444433
No 154
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=27.20 E-value=1.7e+02 Score=21.67 Aligned_cols=30 Identities=20% Similarity=0.290 Sum_probs=19.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCccee
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVE 144 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVk 144 (260)
...|+..++..|... ..|...+|++...|+
T Consensus 36 ~R~y~~~dv~~l~~i------------~~L~~d~g~~l~~i~ 65 (91)
T cd04766 36 TRRYSERDIERLRRI------------QRLTQELGVNLAGVK 65 (91)
T ss_pred CeeECHHHHHHHHHH------------HHHHHHcCCCHHHHH
Confidence 346999999888654 345555777766554
No 155
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=27.04 E-value=1.6e+02 Score=26.63 Aligned_cols=37 Identities=22% Similarity=0.246 Sum_probs=24.4
Q ss_pred hHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 151 RARSKLKQTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 151 Rak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
|-|.|-.+++.+...++.....|+.|.+.|+.++..|
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 4444555555555556666677888888888877666
No 156
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=26.94 E-value=2.2e+02 Score=22.46 Aligned_cols=71 Identities=11% Similarity=0.081 Sum_probs=39.1
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQRE 183 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e 183 (260)
..|+.+++..|... ...+.+|++-..|+.++.-..... .....-...+....+.+.++.++|+..
T Consensus 37 R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~~~ 101 (126)
T cd04785 37 RLYGAAHVERLRFI-------------RRARDLGFSLEEIRALLALSDRPD--RSCAEADAIARAHLADVRARIADLRRL 101 (126)
T ss_pred cccCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHhhhhcCC--CCHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 46999999888553 235677777777777765322111 011112233444555556666666555
Q ss_pred HHHHHh
Q 024915 184 VQELKS 189 (260)
Q Consensus 184 ~~~l~~ 189 (260)
...+..
T Consensus 102 ~~~L~~ 107 (126)
T cd04785 102 EAELKR 107 (126)
T ss_pred HHHHHH
Confidence 555543
No 157
>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=26.79 E-value=45 Score=26.63 Aligned_cols=40 Identities=20% Similarity=0.160 Sum_probs=28.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
.+++.+..++...|-.. ....++|..+|++...|+++...
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~R 150 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSR 150 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHH
Confidence 46777777776654322 34567999999999999977543
No 158
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=26.66 E-value=1.1e+02 Score=27.98 Aligned_cols=26 Identities=27% Similarity=0.472 Sum_probs=16.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024915 164 ELLKRCCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 164 e~l~~~~~~l~~en~~l~~e~~~l~~ 189 (260)
...|.....|..||+.|+.++.+|+.
T Consensus 218 ~e~~~r~~~leken~~lr~~v~~l~~ 243 (269)
T KOG3119|consen 218 DEMAHRVAELEKENEALRTQVEQLKK 243 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34555566677777777777776643
No 159
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.57 E-value=48 Score=27.58 Aligned_cols=40 Identities=20% Similarity=0.063 Sum_probs=28.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
.+++.|..++...|-.. ....++|..+|++...|+.+...
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~R 178 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHR 178 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHH
Confidence 46666777776655432 33678999999999999887743
No 160
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=26.44 E-value=47 Score=27.31 Aligned_cols=39 Identities=26% Similarity=0.154 Sum_probs=26.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
.+++.+..+|.-.|-.. ....++|..+|+++..|+++..
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~ 138 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQ 138 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 46666666666655332 2356789999999998876664
No 161
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=26.18 E-value=1.2e+02 Score=27.09 Aligned_cols=25 Identities=40% Similarity=0.533 Sum_probs=11.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 163 CELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 163 ~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
.+.|+++.+.+..|-.||.++.+.|
T Consensus 181 ~~al~Kq~e~~~~EydrLlee~~~L 205 (216)
T KOG1962|consen 181 VDALKKQSEGLQDEYDRLLEEYSKL 205 (216)
T ss_pred HHHHHHHHHHcccHHHHHHHHHHHH
Confidence 3344444444444444444444444
No 162
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.00 E-value=3.3e+02 Score=21.57 Aligned_cols=73 Identities=12% Similarity=0.105 Sum_probs=41.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|... ...+.+|++-..|+.++.....-.. ....-.+.+....+.+.++..+|+.
T Consensus 36 yR~Y~~~~l~~l~~I-------------~~lr~lG~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T TIGR02047 36 YRVYTVGHVERLAFI-------------RNCRTLDMSLAEIRQLLRYQDKPEK--SCSDVNALLDEHISHVRARIIKLQA 100 (127)
T ss_pred CCcCCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHhhhCCCC--CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 446899988888442 3357788888888877753211110 0112233455555666666666666
Q ss_pred HHHHHHhh
Q 024915 183 EVQELKSM 190 (260)
Q Consensus 183 e~~~l~~~ 190 (260)
....+..+
T Consensus 101 ~~~~L~~~ 108 (127)
T TIGR02047 101 LIEQLVDL 108 (127)
T ss_pred HHHHHHHH
Confidence 65555443
No 163
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=25.91 E-value=22 Score=22.58 Aligned_cols=18 Identities=22% Similarity=0.392 Sum_probs=14.3
Q ss_pred HHHHHHhCCCCcceeecc
Q 024915 130 QGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 130 ~~LA~~lgLs~rqVkvWF 147 (260)
-++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 468999999999998884
No 164
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=25.79 E-value=3.1e+02 Score=21.00 Aligned_cols=66 Identities=17% Similarity=0.186 Sum_probs=40.4
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+...+..|... ...+.+|++-..|+-++..... ..-.+.+....+.|.++-..|+.
T Consensus 37 yR~Y~~~~i~~l~~I-------------~~lr~~G~sl~~i~~l~~~~~~-------~~~~~~l~~~~~~l~~~i~~l~~ 96 (108)
T cd01107 37 YRYYSAEQLERLNRI-------------KYLRDLGFPLEEIKEILDADND-------DELRKLLREKLAELEAEIEELQR 96 (108)
T ss_pred ccccCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHhcCCH-------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 346888888887443 3356678888888877766543 23334455555566666666655
Q ss_pred HHHHHH
Q 024915 183 EVQELK 188 (260)
Q Consensus 183 e~~~l~ 188 (260)
..+.++
T Consensus 97 ~~~~l~ 102 (108)
T cd01107 97 ILRLLE 102 (108)
T ss_pred HHHHHH
Confidence 555543
No 165
>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=25.73 E-value=2.3e+02 Score=25.60 Aligned_cols=75 Identities=13% Similarity=0.267 Sum_probs=36.1
Q ss_pred Ccceeecccchh-----HHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhcCCCCcCCCCC-----CCCcCC
Q 024915 140 PRQVEVWFQNRR-----ARSKLKQTEVECELLKRCCEKLKDENKRLQREVQELKSMKLSGAPLYMKLPA-----PTLTVC 209 (260)
Q Consensus 140 ~rqVkvWFQNRR-----ak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~~~~~~~~~~~~p~-----~~~~~c 209 (260)
|.+|+-|+.+-= .|.+..+.+......+.....|......|..=+..++..... +.-.+... .....|
T Consensus 10 PqRIQEw~~~p~~A~E~~r~~Le~Ir~kq~~v~~~l~eLe~~~~el~~~i~~~k~~~~~--~~~~~~~~e~~D~~~~~~C 87 (236)
T PF12269_consen 10 PQRIQEWQLSPCVAEEQNRKLLEEIRKKQQKVRNRLQELEKRFKELEAIIARAKQFTVD--QDEEQNDDESEDDDLSIYC 87 (236)
T ss_pred hHHHHHhcCCCchhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccC--cccccccccccccceeeee
Confidence 677888886541 123333444444444455555555555555544444333221 11111111 123478
Q ss_pred CCCcccc
Q 024915 210 PSCDEKL 216 (260)
Q Consensus 210 ~sc~~~~ 216 (260)
.+|+...
T Consensus 88 v~Cg~~i 94 (236)
T PF12269_consen 88 VTCGHEI 94 (236)
T ss_pred eeCCCcC
Confidence 8888643
No 166
>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=25.62 E-value=50 Score=26.09 Aligned_cols=43 Identities=19% Similarity=0.120 Sum_probs=27.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
++..+..+|...|-.. ....++|..+|+++..|+.+...-|.+
T Consensus 114 L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~ 156 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKE 156 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4555666665544321 234568999999999998776543333
No 167
>PHA00728 hypothetical protein
Probab=25.56 E-value=1.2e+02 Score=24.77 Aligned_cols=25 Identities=32% Similarity=0.521 Sum_probs=20.0
Q ss_pred HHHHHHHHHHHHHHHHHHHHhhhhc
Q 024915 169 CCEKLKDENKRLQREVQELKSMKLS 193 (260)
Q Consensus 169 ~~~~l~~en~~l~~e~~~l~~~~~~ 193 (260)
..+.|+.||+.|++.+++|.++-++
T Consensus 6 eveql~keneelkkkla~leal~nn 30 (151)
T PHA00728 6 EVEQLKKENEELKKKLAELEALMNN 30 (151)
T ss_pred HHHHHHHhHHHHHHHHHHHHHHHcC
Confidence 3467888999999999999887554
No 168
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=25.52 E-value=59 Score=26.39 Aligned_cols=46 Identities=15% Similarity=0.031 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+++.+..++...|-.. ....++|..+|++...|++|.+.-|.+.|
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr 153 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLK 153 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35566666555433221 23678999999999999888864444433
No 169
>cd04789 HTH_Cfa Helix-Turn-Helix DNA binding domain of the Cfa transcription regulator. Putative helix-turn-helix (HTH) MerR-like transcription regulator; the N-terminal domain of Cfa, a cyclopropane fatty acid synthase and other related methyltransferases. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=25.05 E-value=2.9e+02 Score=20.94 Aligned_cols=63 Identities=14% Similarity=0.039 Sum_probs=35.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|... ...+.+|++-.+|+-++.... ..+.+....+.+.++-.+|+.
T Consensus 36 ~R~Y~~~~l~~l~~I-------------~~l~~~G~~l~ei~~~l~~~~----------~~~~l~~~~~~l~~~i~~l~~ 92 (102)
T cd04789 36 YRLYPDSDLQRLLLI-------------QQLQAGGLSLKECLACLQGKL----------TRSLLLERLSSLAEQIARKQQ 92 (102)
T ss_pred CeeCCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHcCCc----------HHHHHHHHHHHHHHHHHHHHH
Confidence 457899998888543 225666777666666554321 123444444555555555555
Q ss_pred HHHHHH
Q 024915 183 EVQELK 188 (260)
Q Consensus 183 e~~~l~ 188 (260)
....+.
T Consensus 93 ~~~~l~ 98 (102)
T cd04789 93 ARDLLA 98 (102)
T ss_pred HHHHHH
Confidence 544443
No 170
>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=24.91 E-value=23 Score=22.12 Aligned_cols=24 Identities=21% Similarity=0.477 Sum_probs=19.9
Q ss_pred HHHHHHHhCCCCcceeecccchhH
Q 024915 129 KQGLAEKLNLRPRQVEVWFQNRRA 152 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQNRRa 152 (260)
..++|+.+|++.+.|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 357899999999999999876654
No 171
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.75 E-value=57 Score=26.83 Aligned_cols=45 Identities=24% Similarity=0.158 Sum_probs=29.1
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+++.+..++.-.|-.. ..-.++|..+|+++..|++....-|.+.|
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 5555555555554322 23567899999999999988764444433
No 172
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=24.59 E-value=51 Score=27.56 Aligned_cols=46 Identities=15% Similarity=0.198 Sum_probs=29.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+++.+..++.-.|-.. ....++|+.+|++...|+...+.-|.+.|
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr 176 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQ 176 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46666666666544322 23567899999999988776654444433
No 173
>PF14645 Chibby: Chibby family
Probab=24.49 E-value=1.7e+02 Score=23.36 Aligned_cols=47 Identities=21% Similarity=0.271 Sum_probs=29.3
Q ss_pred eecccchhHHH---HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 144 EVWFQNRRARS---KLKQTEVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 144 kvWFQNRRak~---Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
..+|++-+.-. .......+...+++.+..|.+||..|+-+++-|-.+
T Consensus 51 ~l~F~dG~W~~e~~~~~~~~~~~~~l~~~n~~L~EENN~Lklk~elLlDM 100 (116)
T PF14645_consen 51 TLVFEDGQWTSESGSGTADGEENQRLRKENQQLEEENNLLKLKIELLLDM 100 (116)
T ss_pred EEEEECCEEeccCCCcccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34566554431 223344556667777888888888888877766544
No 174
>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=24.45 E-value=2.5e+02 Score=19.55 Aligned_cols=25 Identities=16% Similarity=0.416 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 163 CELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 163 ~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
-.++++.++.+.++.+.+.+-++.+
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 3344444445555555554444444
No 175
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=24.09 E-value=50 Score=27.14 Aligned_cols=46 Identities=15% Similarity=0.133 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+++.+..++...|-. ...-.++|..+|+++..|++++..-|.+.|
T Consensus 136 ~L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr 181 (187)
T TIGR02948 136 ALPPKYRMVIVLKYME-----DLSLKEISEILDLPVGTVKTRIHRGREALR 181 (187)
T ss_pred hCCHHHhHHhhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4566666666554332 233567899999999999988864444333
No 176
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=24.07 E-value=86 Score=25.87 Aligned_cols=45 Identities=9% Similarity=0.065 Sum_probs=27.7
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
+++.+..++...|-.. ....++|..+|++...|++....-|.+.|
T Consensus 118 Lp~~~r~i~~l~~~e~-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 118 LPYKLRQVIILRYLHD-----YSQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred CCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5555555555543222 23567899999999998876654444433
No 177
>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=24.06 E-value=1.6e+02 Score=20.22 Aligned_cols=26 Identities=27% Similarity=0.424 Sum_probs=18.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 163 CELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 163 ~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
..........|..||..|+.++..++
T Consensus 24 ~~~a~~rl~~l~~EN~~Lr~eL~~~r 49 (52)
T PF12808_consen 24 RSAARKRLSKLEGENRLLRAELERLR 49 (52)
T ss_pred chhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33455566788899999999887654
No 178
>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=24.05 E-value=1.4e+02 Score=22.34 Aligned_cols=30 Identities=33% Similarity=0.315 Sum_probs=23.8
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 159 TEVECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 159 ~~~~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+-...+..+..++.|..||+-|++-+..|-
T Consensus 35 L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm 64 (80)
T PF10224_consen 35 LSDRVEEVKEENEKLESENEYLQQYIGNLM 64 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455677788899999999999998884
No 179
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=23.90 E-value=7e+02 Score=25.66 Aligned_cols=43 Identities=30% Similarity=0.270 Sum_probs=23.2
Q ss_pred ecccchhHH--HHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 145 VWFQNRRAR--SKLKQTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 145 vWFQNRRak--~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
|==||+|.| ++..+++.+.+.|++..++|..|...+.+.+..+
T Consensus 500 vAAQnCRKRKLd~I~nLE~ev~~l~~eKeqLl~Er~~~d~~L~~~ 544 (604)
T KOG3863|consen 500 VAAQNCRKRKLDCILNLEDEVEKLQKEKEQLLRERDELDSTLGVM 544 (604)
T ss_pred hhccchhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445666554 3444555555556666666666555555544443
No 180
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.87 E-value=1.1e+02 Score=23.27 Aligned_cols=35 Identities=6% Similarity=-0.088 Sum_probs=23.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccc
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQN 149 (260)
+..|+.+++..|... ..|.+..|++-..|+.+..+
T Consensus 36 ~R~Yt~~di~~l~~I------------~~llr~~G~~l~~i~~~l~~ 70 (99)
T cd04765 36 RRYYRPKDVELLLLI------------KHLLYEKGYTIEGAKQALKE 70 (99)
T ss_pred CeeeCHHHHHHHHHH------------HHHHHHCCCCHHHHHHHHHh
Confidence 457999999888543 33456677777777766654
No 181
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.73 E-value=2.7e+02 Score=21.88 Aligned_cols=72 Identities=10% Similarity=0.076 Sum_probs=38.9
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|... ...+.+|++-..|+..+........ ....-.+.+....+.+.++-+.|+.
T Consensus 36 yR~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 36 YRLYDEEHLERLLFI-------------RRCRSLDMSLDEIRTLLQLQDDPEA--SCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred CeecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHhhhcCCC--cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 346899998887443 3467778888888777754322110 1112223444444555555555555
Q ss_pred HHHHHHh
Q 024915 183 EVQELKS 189 (260)
Q Consensus 183 e~~~l~~ 189 (260)
....+..
T Consensus 101 ~~~~L~~ 107 (127)
T cd04784 101 LEKQLQA 107 (127)
T ss_pred HHHHHHH
Confidence 4444433
No 182
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=23.59 E-value=74 Score=26.67 Aligned_cols=46 Identities=9% Similarity=0.079 Sum_probs=30.6
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..+..++.-.|-.. ..-.++|..+|+++..|+++...-|.+.|
T Consensus 134 ~Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr 179 (189)
T PRK12530 134 HLPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQ 179 (189)
T ss_pred hCCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666666655332 23567999999999999998764443333
No 183
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.53 E-value=50 Score=26.66 Aligned_cols=46 Identities=17% Similarity=0.041 Sum_probs=29.8
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..|..++.-.|-.. ....++|..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36666666665554322 23567899999999998887764444433
No 184
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=23.49 E-value=33 Score=29.02 Aligned_cols=44 Identities=20% Similarity=0.009 Sum_probs=28.3
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARS 154 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~ 154 (260)
+++.+..++.-.|-.. ....++|..+|++...|+++...-|.+.
T Consensus 114 Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~L 157 (188)
T PRK12546 114 LPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARL 157 (188)
T ss_pred CCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5555555555543211 2356789999999999998886444333
No 185
>cd02413 40S_S3_KH K homology RNA-binding (KH) domain of the eukaryotic 40S small ribosomal subunit protein S3. S3 is part of the head region of the 40S ribosomal subunit and is believed to interact with mRNA as it threads its way from the latch into the channel. The KH motif is a beta-alpha-alpha-beta-beta unit that folds into an alpha-beta structure with a three stranded beta-sheet interupted by two contiguous helices. In general, KH binds single-stranded RNA or DNA. It is found in a wide variety of proteins including ribosomal proteins, transcription factors and post-transcriptional modifiers of mRNA.
Probab=23.45 E-value=84 Score=23.29 Aligned_cols=20 Identities=15% Similarity=0.323 Sum_probs=17.5
Q ss_pred HHHHHHHhCCCCcceeeccc
Q 024915 129 KQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQ 148 (260)
+..|.+.++|..-||++|+.
T Consensus 56 ~~~L~k~~~~~~~~i~v~~~ 75 (81)
T cd02413 56 TSLVQKRFNFPEGSVELYAE 75 (81)
T ss_pred HHHHHHHhCCCCCeEEEEEE
Confidence 56688889999999999985
No 186
>PF13551 HTH_29: Winged helix-turn helix
Probab=23.44 E-value=88 Score=23.29 Aligned_cols=46 Identities=20% Similarity=0.343 Sum_probs=29.0
Q ss_pred CCccCCHHHHHHHHHHHhhCC-----CCCHHHHHH-H-HHHh--CCCCcceeecc
Q 024915 102 KKLRLTKPQFATLEDTFKEHS-----TLSPKQKQG-L-AEKL--NLRPRQVEVWF 147 (260)
Q Consensus 102 ~Rt~~t~~Ql~~Le~~F~~~~-----~ps~~~r~~-L-A~~l--gLs~rqVkvWF 147 (260)
.+..++.++...|.+.+..++ ..+.....+ | .+.. .+++..|..|+
T Consensus 54 ~~~~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L 108 (112)
T PF13551_consen 54 PRKRLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRIL 108 (112)
T ss_pred CCCCCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHH
Confidence 333499999999999999776 344444433 3 3333 35666666655
No 187
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=23.39 E-value=45 Score=27.49 Aligned_cols=24 Identities=13% Similarity=0.102 Sum_probs=18.9
Q ss_pred HHHHHHHHhCCCCcceeecccchh
Q 024915 128 QKQGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 128 ~r~~LA~~lgLs~rqVkvWFQNRR 151 (260)
.-.++|..+|+++..|+++...-|
T Consensus 156 s~~EIA~~lgis~~tv~~~l~rar 179 (190)
T TIGR02939 156 SYEDIARIMDCPVGTVRSRIFRAR 179 (190)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHH
Confidence 357899999999999988875333
No 188
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=23.04 E-value=56 Score=27.09 Aligned_cols=43 Identities=12% Similarity=0.111 Sum_probs=26.9
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
+++.+..++...|-.. ..-.++|..+|++...|+.+...-|.+
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~ 171 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRA 171 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHH
Confidence 4555555555443221 235678999999999998877543333
No 189
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=22.99 E-value=3.7e+02 Score=20.94 Aligned_cols=27 Identities=44% Similarity=0.574 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 162 ECELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 162 ~~e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+.|.|++.-+.|.+|....+++++++.
T Consensus 70 EkEqL~~Lk~kl~~e~~~~~k~i~~le 96 (100)
T PF04568_consen 70 EKEQLKKLKEKLKEEIEHHRKEIDELE 96 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555566666666677776663
No 190
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.90 E-value=73 Score=26.37 Aligned_cols=42 Identities=12% Similarity=0.250 Sum_probs=27.5
Q ss_pred CCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhH
Q 024915 106 LTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRA 152 (260)
Q Consensus 106 ~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRa 152 (260)
+++.+..++...|-.. ....++|..+|++...|++|...-|.
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~ 175 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLK 175 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHH
Confidence 5555555555544322 23567899999999999988764333
No 191
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=22.86 E-value=1.2e+02 Score=27.56 Aligned_cols=16 Identities=13% Similarity=0.636 Sum_probs=12.4
Q ss_pred CCcceeecccchhHHH
Q 024915 139 RPRQVEVWFQNRRARS 154 (260)
Q Consensus 139 s~rqVkvWFQNRRak~ 154 (260)
..+.|..||+.++.|.
T Consensus 99 ~~~~i~~w~~~~~~kk 114 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKK 114 (242)
T ss_pred ccchHHHHHHHHHHHH
Confidence 4678999999888743
No 192
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.76 E-value=26 Score=24.41 Aligned_cols=21 Identities=14% Similarity=0.346 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCcceeecccc
Q 024915 129 KQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQN 149 (260)
..++|+.+|++++.|+.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 193
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=22.75 E-value=1.1e+02 Score=24.35 Aligned_cols=45 Identities=22% Similarity=0.192 Sum_probs=33.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+|..+..+|+- +..+ + ...++|+.++++++.|+.|.+|=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 3333 2 2567899999999999999887665544
No 194
>PF07412 Geminin: Geminin; InterPro: IPR022786 This family contains the eukaryotic protein geminin (approximately 200 residues long). Geminin inhibits DNA replication by preventing the incorporation of MCM complex into prereplication complex, and is degraded during the mitotic phase of the cell cycle. It has been proposed that geminin inhibits DNA replication during S, G2, and M phases and that geminin destruction at the metaphase-anaphase transition permits replication in the succeeding cell cycle []. ; GO: 0008156 negative regulation of DNA replication; PDB: 1T6F_B 2LP0_B 1UII_B 2WVR_B 2ZXX_B.
Probab=22.71 E-value=1.7e+02 Score=25.74 Aligned_cols=30 Identities=33% Similarity=0.409 Sum_probs=20.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 161 VECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 161 ~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
.+++.|....+.+.+|..+|++|+.+|+.+
T Consensus 125 ~ENe~Lh~~ie~~~eEi~~lk~en~~L~el 154 (200)
T PF07412_consen 125 EENEKLHKEIEQKDEEIAKLKEENEELKEL 154 (200)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHCCHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 466677777777777777777766655443
No 195
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=22.56 E-value=2e+02 Score=22.86 Aligned_cols=32 Identities=28% Similarity=0.241 Sum_probs=24.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 024915 158 QTEVECELLKRCCEKLKDENKRLQREVQELKS 189 (260)
Q Consensus 158 ~~~~~~e~l~~~~~~l~~en~~l~~e~~~l~~ 189 (260)
.+-.+...+|+....+.+||..|+-|+..|+.
T Consensus 19 ~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~ 50 (114)
T COG4467 19 VLLAELGGLKQHLGSLVEENTALRLENEKLRE 50 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHH
Confidence 44455667888888888999999988888854
No 196
>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=22.56 E-value=2.2e+02 Score=28.36 Aligned_cols=17 Identities=41% Similarity=0.634 Sum_probs=7.7
Q ss_pred HHHHHHHHHHHHHHHHH
Q 024915 171 EKLKDENKRLQREVQEL 187 (260)
Q Consensus 171 ~~l~~en~~l~~e~~~l 187 (260)
+.|.+|..+++..+++|
T Consensus 119 ~ql~~~~~~~~~~l~~l 135 (472)
T TIGR03752 119 EQLKSERQQLQGLIDQL 135 (472)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 34444444444444444
No 197
>PF11460 DUF3007: Protein of unknown function (DUF3007); InterPro: IPR021562 This is a family of uncharacterised proteins found in bacteria and eukaryotes.
Probab=22.55 E-value=1.1e+02 Score=24.10 Aligned_cols=35 Identities=26% Similarity=0.314 Sum_probs=19.7
Q ss_pred hHHHHHHhhHHHHHHHHHHHHHHH-HHHHHHHHHHH
Q 024915 151 RARSKLKQTEVECELLKRCCEKLK-DENKRLQREVQ 185 (260)
Q Consensus 151 Rak~Kk~~~~~~~e~l~~~~~~l~-~en~~l~~e~~ 185 (260)
|.+.+........+.+++.++.|. +|.++|++|++
T Consensus 68 ~k~Ye~a~~~~~~~~lqkRle~l~~eE~~~L~~eie 103 (104)
T PF11460_consen 68 RKDYEEAVDQLTNEELQKRLEELSPEELEALQAEIE 103 (104)
T ss_pred HHHHHHHHHHHhHHHHHHHHHhCCHHHHHHHHHHhc
Confidence 344444444444555666666654 45577877764
No 198
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=22.52 E-value=50 Score=27.55 Aligned_cols=46 Identities=11% Similarity=0.182 Sum_probs=30.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.++..+..+|...|-.. ....++|..+|+++..|++....-|.+.|
T Consensus 131 ~L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 176 (189)
T PRK12515 131 KLSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLA 176 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 46666666666554322 23567899999999999877654443333
No 199
>COG2944 Predicted transcriptional regulator [Transcription]
Probab=22.43 E-value=67 Score=25.31 Aligned_cols=42 Identities=17% Similarity=0.302 Sum_probs=34.9
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRAR 153 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak 153 (260)
.++..++..+.+.+... ...+|+.||++...|+.|=|+|+.-
T Consensus 43 ~ls~~eIk~iRe~~~lS-------Q~vFA~~L~vs~~Tv~~WEqGr~kP 84 (104)
T COG2944 43 TLSPTEIKAIREKLGLS-------QPVFARYLGVSVSTVRKWEQGRKKP 84 (104)
T ss_pred CCCHHHHHHHHHHhCCC-------HHHHHHHHCCCHHHHHHHHcCCcCC
Confidence 38889999998877644 4578999999999999999998653
No 200
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=22.40 E-value=30 Score=23.97 Aligned_cols=21 Identities=10% Similarity=0.360 Sum_probs=18.0
Q ss_pred HHHHHHHhCCCCcceeecccc
Q 024915 129 KQGLAEKLNLRPRQVEVWFQN 149 (260)
Q Consensus 129 r~~LA~~lgLs~rqVkvWFQN 149 (260)
..++|+.+|+++++|+.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999765
No 201
>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=22.33 E-value=69 Score=20.53 Aligned_cols=36 Identities=17% Similarity=0.232 Sum_probs=24.4
Q ss_pred CHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 107 TKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 107 t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
+..|...+...+. . ....++|+.++++.+.|+.|..
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 4455566654331 1 2456789999999999988875
No 202
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=22.32 E-value=1.6e+02 Score=28.01 Aligned_cols=23 Identities=30% Similarity=0.163 Sum_probs=11.2
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHH
Q 024915 157 KQTEVECELLKRCCEKLKDENKR 179 (260)
Q Consensus 157 ~~~~~~~e~l~~~~~~l~~en~~ 179 (260)
.....+++.|++.+..|+.+..+
T Consensus 60 ~~L~~EN~~Lk~Ena~L~~~l~~ 82 (337)
T PRK14872 60 LVLETENFLLKERIALLEERLKS 82 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555444443
No 203
>PRK10403 transcriptional regulator NarP; Provisional
Probab=22.14 E-value=47 Score=26.89 Aligned_cols=45 Identities=20% Similarity=0.274 Sum_probs=34.4
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+|..+..+|+..... ....+||+.++++++.|++..+|=|.|-.
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~ 197 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLN 197 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcC
Confidence 5888888888765432 23567899999999999988887766654
No 204
>PF13942 Lipoprotein_20: YfhG lipoprotein
Probab=21.91 E-value=5e+02 Score=22.40 Aligned_cols=63 Identities=22% Similarity=0.491 Sum_probs=39.6
Q ss_pred hhCCCCCHHHHHHHHHHhCCC----Ccc----eeecccch---------hHHHHHHhhHHHHHHHHHHHHHHHHHHHHHH
Q 024915 119 KEHSTLSPKQKQGLAEKLNLR----PRQ----VEVWFQNR---------RARSKLKQTEVECELLKRCCEKLKDENKRLQ 181 (260)
Q Consensus 119 ~~~~~ps~~~r~~LA~~lgLs----~rq----VkvWFQNR---------Rak~Kk~~~~~~~e~l~~~~~~l~~en~~l~ 181 (260)
-.+-.|++.+|..+...|+-- |.+ +++|-.+. |+|.++-+...+.+ .+.|++++.+|+
T Consensus 69 L~~A~~T~~ERR~~~~~l~~y~~~~P~~vRPL~QlWRe~Q~lql~L~eEr~Ry~rLQqssD~~-----lD~Lr~qq~~Lq 143 (179)
T PF13942_consen 69 LANAEPTPAERRQMVDRLNSYSLQFPASVRPLLQLWREQQVLQLQLSEERARYQRLQQSSDSE-----LDALRQQQQRLQ 143 (179)
T ss_pred hcCCCCCHHHHHHHHHHHHHhhhhcCHHHhHHHHHHHHhHHHHHHHHHHHHHHHHHHHhhHHH-----HHHHHHHHHHHH
Confidence 356778888888877666411 222 56776554 55555555444433 577888888888
Q ss_pred HHHHH
Q 024915 182 REVQE 186 (260)
Q Consensus 182 ~e~~~ 186 (260)
.++..
T Consensus 144 ~qL~~ 148 (179)
T PF13942_consen 144 YQLDT 148 (179)
T ss_pred HHHHH
Confidence 87754
No 205
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=21.82 E-value=1.8e+02 Score=23.37 Aligned_cols=25 Identities=32% Similarity=0.402 Sum_probs=17.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 162 ECELLKRCCEKLKDENKRLQREVQE 186 (260)
Q Consensus 162 ~~e~l~~~~~~l~~en~~l~~e~~~ 186 (260)
..|.|......|+-||..|++.+.+
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~ 28 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQ 28 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 4456666777777777777776654
No 206
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=21.77 E-value=69 Score=25.57 Aligned_cols=39 Identities=13% Similarity=0.063 Sum_probs=27.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
.+++.+..++.-.|-.. ..-.++|..||++...|++...
T Consensus 106 ~Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ 144 (161)
T PRK09047 106 KLPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCS 144 (161)
T ss_pred hCCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 46667777766654332 1256789999999999887665
No 207
>cd07429 Cby_like Chibby, a nuclear inhibitor of Wnt/beta-catenin mediated transcription, and similar proteins. Chibby(Cby) is a well-conserved nuclear protein that functions as part of the Wnt/beta-catenin signaling pathway. Specifically, Cby binds directly to beta-catenin by interacting with its central region, which harbors armadillo repeats. Cby-beta-catenin interactions may also involve 14-3-3 proteins. By competing with other binding partners of beta-catenin, the Tcf/Lef transcription factors, Cby inhibits transcriptional activation. Cby has been shown to play a role in adipocyte differentiation. The C-terminal region of Cby appears to contain an alpha-helical coiled-coil motif.
Probab=21.73 E-value=2.1e+02 Score=22.65 Aligned_cols=31 Identities=29% Similarity=0.349 Sum_probs=21.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Q 024915 160 EVECELLKRCCEKLKDENKRLQREVQELKSM 190 (260)
Q Consensus 160 ~~~~e~l~~~~~~l~~en~~l~~e~~~l~~~ 190 (260)
..+...+++.+..|.+||.-|+-+++-|..+
T Consensus 71 ~~e~~rlkkk~~~LeEENNlLklKievLLDM 101 (108)
T cd07429 71 GREVLRLKKKNQQLEEENNLLKLKIEVLLDM 101 (108)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444556666778888888888777766544
No 208
>PRK09637 RNA polymerase sigma factor SigZ; Provisional
Probab=21.66 E-value=63 Score=26.99 Aligned_cols=39 Identities=26% Similarity=0.158 Sum_probs=25.0
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeeccc
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQ 148 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQ 148 (260)
.+++.+..+|...|-.. ....++|..+|++...|+.++.
T Consensus 106 ~L~~~~r~i~~l~~~~g-----~~~~EIA~~lgis~~tV~~~l~ 144 (181)
T PRK09637 106 ALPEKYAEALRLTELEG-----LSQKEIAEKLGLSLSGAKSRVQ 144 (181)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHH
Confidence 35555555555543222 2356789999999988877664
No 209
>cd01108 HTH_CueR Helix-Turn-Helix DNA binding domain of CueR-like transcription regulators. Helix-turn-helix (HTH) transcription regulators CueR and ActP, copper efflux regulators. In Bacillus subtilis, copper induced CueR regulates the copZA operon, preventing copper toxicity. In Rhizobium leguminosarum, ActP controls copper homeostasis; it detects cytoplasmic copper stress and activates transcription in response to increasing copper concentrations. These proteins are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have two conserved cysteines that define a monovalent copper ion binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements
Probab=21.62 E-value=3e+02 Score=21.72 Aligned_cols=73 Identities=14% Similarity=0.082 Sum_probs=41.2
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|... ...+.+|++-..|+.++....... .....-.+.+....+.+.++-..|+.
T Consensus 36 ~R~Y~~~~~~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~~~~--~~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd01108 36 YRVYNQRDIEELRFI-------------RRARDLGFSLEEIRELLALWRDPS--RASADVKALALEHIAELERKIAELQA 100 (127)
T ss_pred ceecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHHHhCCC--CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456899888887543 335677888888877775322110 00112234455555566666666666
Q ss_pred HHHHHHhh
Q 024915 183 EVQELKSM 190 (260)
Q Consensus 183 e~~~l~~~ 190 (260)
..+.+..+
T Consensus 101 ~~~~l~~~ 108 (127)
T cd01108 101 MRRTLQQL 108 (127)
T ss_pred HHHHHHHH
Confidence 55555443
No 210
>TIGR02043 ZntR Zn(II)-responsive transcriptional regulator. This model represents the zinc and cadmium (II) responsive transcriptional activator of the gamma proteobacterial zinc efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-Cys-X(8-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=21.62 E-value=2.7e+02 Score=22.18 Aligned_cols=72 Identities=11% Similarity=0.053 Sum_probs=38.8
Q ss_pred CccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 103 KLRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKLKQTEVECELLKRCCEKLKDENKRLQR 182 (260)
Q Consensus 103 Rt~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~ 182 (260)
...|+.+++..|... ...+.+|++...|+.++.+...... .....-.+.+....+.+.++-++|+.
T Consensus 37 yR~Y~~~~l~~l~~I-------------~~lr~~G~sl~eI~~~l~~~~~~~~-~~~~~~~~~l~~~~~~l~~~i~~L~~ 102 (131)
T TIGR02043 37 YRLYTDEDQKRLRFI-------------LKAKELGFTLDEIKELLSIKLDATE-HSCAEVKAIVDAKLELVDEKINELTK 102 (131)
T ss_pred ceecCHHHHHHHHHH-------------HHHHHcCCCHHHHHHHHHhhccCCC-CCHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456889998888543 2356778888888877764311000 01112233444444555555555555
Q ss_pred HHHHHH
Q 024915 183 EVQELK 188 (260)
Q Consensus 183 e~~~l~ 188 (260)
-...+.
T Consensus 103 ~~~~L~ 108 (131)
T TIGR02043 103 IRRSLK 108 (131)
T ss_pred HHHHHH
Confidence 444443
No 211
>PF06667 PspB: Phage shock protein B; InterPro: IPR009554 This family consists of several bacterial phage shock protein B (PspB) sequences. The phage shock protein (psp) operon is induced in response to heat, ethanol, osmotic shock and infection by filamentous bacteriophages []. Expression of the operon requires the alternative sigma factor sigma54 and the transcriptional activator PspF. In addition, PspA plays a negative regulatory role, and the integral-membrane proteins PspB and PspC play a positive one [].; GO: 0006355 regulation of transcription, DNA-dependent, 0009271 phage shock
Probab=21.59 E-value=1.2e+02 Score=22.32 Aligned_cols=30 Identities=13% Similarity=0.360 Sum_probs=23.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhcCCC
Q 024915 167 KRCCEKLKDENKRLQREVQELKSMKLSGAP 196 (260)
Q Consensus 167 ~~~~~~l~~en~~l~~e~~~l~~~~~~~~~ 196 (260)
.+..+.|.+..++|++.++.|+.+-.+..|
T Consensus 41 ~~~L~~L~~~a~rm~eRI~tLE~ILdae~P 70 (75)
T PF06667_consen 41 EQRLQELYEQAERMEERIETLERILDAEHP 70 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHcCCCC
Confidence 566778999999999999999887654444
No 212
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=21.46 E-value=83 Score=26.83 Aligned_cols=23 Identities=39% Similarity=0.540 Sum_probs=4.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024915 162 ECELLKRCCEKLKDENKRLQREV 184 (260)
Q Consensus 162 ~~e~l~~~~~~l~~en~~l~~e~ 184 (260)
+.|.|+..+++|++|.+.|+.|+
T Consensus 25 EKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 25 EKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555554
No 213
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=21.34 E-value=88 Score=23.27 Aligned_cols=43 Identities=16% Similarity=0.208 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhh-----CCCCCHHHHHHHHHHhCCCCcceeecc
Q 024915 105 RLTKPQFATLEDTFKE-----HSTLSPKQKQGLAEKLNLRPRQVEVWF 147 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~-----~~~ps~~~r~~LA~~lgLs~rqVkvWF 147 (260)
.++.+|+..|...|.. +.+.+..+...+-+.++++...|+.+|
T Consensus 3 ~ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~ 50 (96)
T smart00027 3 AISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIW 50 (96)
T ss_pred CCCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHH
Confidence 4678899999999874 345777777776666777666665555
No 214
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=21.17 E-value=3.3e+02 Score=20.05 Aligned_cols=16 Identities=50% Similarity=0.721 Sum_probs=6.9
Q ss_pred HHHHHHHHHHHHHHHH
Q 024915 170 CEKLKDENKRLQREVQ 185 (260)
Q Consensus 170 ~~~l~~en~~l~~e~~ 185 (260)
.+.|+++|..|..|++
T Consensus 27 ieELKEknn~l~~e~q 42 (79)
T COG3074 27 IEELKEKNNSLSQEVQ 42 (79)
T ss_pred HHHHHHHhhHhHHHHH
Confidence 3444444444444443
No 215
>PF12065 DUF3545: Protein of unknown function (DUF3545); InterPro: IPR021932 This family of proteins is functionally uncharacterised. This protein is found in bacteria. Proteins in this family are typically between 60 to 77 amino acids in length. This protein has two completely conserved residues (R and L) that may be functionally important.
Probab=21.06 E-value=1.3e+02 Score=21.30 Aligned_cols=22 Identities=36% Similarity=0.572 Sum_probs=16.1
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Q 024915 166 LKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 166 l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
.|+..+.+++ ..+|++|++++.
T Consensus 26 KWREIEAikD-r~rL~kEL~d~D 47 (59)
T PF12065_consen 26 KWREIEAIKD-RQRLRKELQDMD 47 (59)
T ss_pred hHHHHHHHHH-HHHHHHHHHHcc
Confidence 4677777765 568999988864
No 216
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=21.05 E-value=50 Score=20.25 Aligned_cols=22 Identities=27% Similarity=0.351 Sum_probs=17.7
Q ss_pred HHHHHHhCCCCcceeecccchh
Q 024915 130 QGLAEKLNLRPRQVEVWFQNRR 151 (260)
Q Consensus 130 ~~LA~~lgLs~rqVkvWFQNRR 151 (260)
.++|+.+|+++..|..|..+++
T Consensus 16 ~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 16 EELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHCCCHHHHHHHHcCCC
Confidence 4688888999888888887764
No 217
>PRK06930 positive control sigma-like factor; Validated
Probab=20.82 E-value=85 Score=26.50 Aligned_cols=46 Identities=13% Similarity=0.063 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+++.+..++...|... ..-.++|..+|++...|+.+...-|.+.+
T Consensus 114 ~L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr 159 (170)
T PRK06930 114 VLTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIA 159 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 47777777777655332 13567899999999999988875544444
No 218
>PF09006 Surfac_D-trimer: Lung surfactant protein D coiled-coil trimerisation; InterPro: IPR015097 This domain is found in the SFTPD family, which includes lung surfactant protein D (SFTPD), conglutinin, collectin-43 and collectin-46. It forms a triple-helical parallel coiled coil, and mediates trimerisation of the protein []. ; PDB: 4DN8_A 3G84_A 2RIE_C 3IKR_B 1B08_A 2GGX_B 2OS9_C 2ORK_B 1PWB_A 2RIA_C ....
Probab=20.78 E-value=2.6e+02 Score=18.77 Aligned_cols=25 Identities=28% Similarity=0.418 Sum_probs=20.3
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 164 ELLKRCCEKLKDENKRLQREVQELK 188 (260)
Q Consensus 164 e~l~~~~~~l~~en~~l~~e~~~l~ 188 (260)
+.|+++.+.|..+.++||..+...+
T Consensus 2 ~aLrqQv~aL~~qv~~Lq~~fs~yK 26 (46)
T PF09006_consen 2 NALRQQVEALQGQVQRLQAAFSQYK 26 (46)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4678888888888888888887774
No 219
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.52 E-value=56 Score=26.55 Aligned_cols=46 Identities=15% Similarity=0.137 Sum_probs=34.6
Q ss_pred ccCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 104 LRLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 104 t~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
..+|..+..+|...... ..+.++|.+++++.+.|+++.++=|.|..
T Consensus 148 ~~lt~re~~vl~~l~~g------~s~~eIa~~l~~s~~tv~~~~~~~~~kl~ 193 (210)
T PRK09935 148 TVLSNREVTILRYLVSG------LSNKEIADQLLLSNKTVSAHKSNIYGKLG 193 (210)
T ss_pred ccCCHHHHHHHHHHHcC------CCHHHHHHHhCCCHHHHHHHHHHHHHHcC
Confidence 35788888888754433 34778999999999999988877666544
No 220
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=20.47 E-value=1.3e+02 Score=22.14 Aligned_cols=16 Identities=50% Similarity=0.578 Sum_probs=7.8
Q ss_pred HHHHHHHHHHHHHHHH
Q 024915 172 KLKDENKRLQREVQEL 187 (260)
Q Consensus 172 ~l~~en~~l~~e~~~l 187 (260)
.|+.++..|+++++++
T Consensus 47 eLKve~~~L~~el~~~ 62 (75)
T PF07989_consen 47 ELKVEVESLKRELQEK 62 (75)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444555555554444
No 221
>PRK10884 SH3 domain-containing protein; Provisional
Probab=20.40 E-value=3e+02 Score=24.13 Aligned_cols=25 Identities=12% Similarity=0.004 Sum_probs=9.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 161 VECELLKRCCEKLKDENKRLQREVQ 185 (260)
Q Consensus 161 ~~~e~l~~~~~~l~~en~~l~~e~~ 185 (260)
.+++.|+...+.++.|++.|+.++.
T Consensus 139 ~~n~~L~~~l~~~~~~~~~l~~~~~ 163 (206)
T PRK10884 139 EENQKLKNQLIVAQKKVDAANLQLD 163 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333344444444444444433333
No 222
>PF10482 CtIP_N: Tumour-suppressor protein CtIP N-terminal domain; InterPro: IPR019518 CtIP is predominantly a nuclear protein that complexes with both BRCA1 and the BRCA1-associated RING domain protein (BARD1). At the protein level, CtIP expression varies with cell cycle progression in a pattern identical to that of BRCA1. Thus, the steady-state levels of CtIP polypeptides, which remain low in resting cells and G1 cycling cells, increase dramatically as Dividing cells traverse the G1/S boundary. CtIP can potentially modulate the functions ascribed to BRCA1 in transcriptional regulation, DNA repair, and/or cell cycle checkpoint control []. This N-terminal domain carries a coiled-coil region and is essential for homodimerisation of the protein []. The C-terminal domain is family CtIP_C and carries functionally important CxxC and RHR motifs, absence of which lead cells to grow slowly and show hypersensitivity to genotoxins [].
Probab=20.36 E-value=1.6e+02 Score=23.61 Aligned_cols=14 Identities=50% Similarity=0.845 Sum_probs=8.6
Q ss_pred HHHHHHHHHHHHHH
Q 024915 171 EKLKDENKRLQREV 184 (260)
Q Consensus 171 ~~l~~en~~l~~e~ 184 (260)
..|.+||++|+.|+
T Consensus 106 n~L~eEN~~L~eEl 119 (120)
T PF10482_consen 106 NTLKEENKKLKEEL 119 (120)
T ss_pred HhHHHHHHHHHHHh
Confidence 45666666666654
No 223
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=20.31 E-value=56 Score=26.39 Aligned_cols=45 Identities=24% Similarity=0.231 Sum_probs=33.3
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSK 155 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~K 155 (260)
.+|+.+..+|+-.... ..+.++|..++++.+.|++..++=|.|..
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 5888888887776542 24678899999999999888776665543
No 224
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=20.31 E-value=2.6e+02 Score=26.67 Aligned_cols=8 Identities=25% Similarity=0.422 Sum_probs=2.9
Q ss_pred HHHHHHHH
Q 024915 173 LKDENKRL 180 (260)
Q Consensus 173 l~~en~~l 180 (260)
|.++...|
T Consensus 258 LEqq~~~L 265 (365)
T KOG2391|consen 258 LEQQLQSL 265 (365)
T ss_pred HHHHHHHH
Confidence 33333333
No 225
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=20.12 E-value=2.9e+02 Score=21.69 Aligned_cols=36 Identities=31% Similarity=0.452 Sum_probs=16.9
Q ss_pred cchhHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Q 024915 148 QNRRARSKLKQTEVECELLKRCCEKLKDENKRLQREVQEL 187 (260)
Q Consensus 148 QNRRak~Kk~~~~~~~e~l~~~~~~l~~en~~l~~e~~~l 187 (260)
|||-++.-+.+.+.+.+. +.+...|.++|++++.++
T Consensus 57 QNRq~~~dr~ra~~D~~i----nl~ae~ei~~l~~~l~~l 92 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQI----NLKAEQEIERLHRKLDAL 92 (108)
T ss_pred hhHhHHHHHHHHHHHHHH----HHHhHHHHHHHHHHHHHH
Confidence 677665444444444442 223344444555544444
No 226
>TIGR02957 SigX4 RNA polymerase sigma-70 factor, TIGR02957 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building and bidirectional best hits, to represent a conserved family. This family is found in a limited number of bacterial lineages. This family includes apparent paralogous expansion in Streptomyces coelicolor A3(2), and multiple copies in Mycobacterium smegmatis MC2, Streptomyces avermitilis MA-4680 and Nocardia farcinica IFM10152.
Probab=20.06 E-value=1.3e+02 Score=27.16 Aligned_cols=47 Identities=11% Similarity=-0.037 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhhCCCCCHHHHHHHHHHhCCCCcceeecccchhHHHHH
Q 024915 105 RLTKPQFATLEDTFKEHSTLSPKQKQGLAEKLNLRPRQVEVWFQNRRARSKL 156 (260)
Q Consensus 105 ~~t~~Ql~~Le~~F~~~~~ps~~~r~~LA~~lgLs~rqVkvWFQNRRak~Kk 156 (260)
.+++.|..++.-.|-.. ..-.++|..+|+++..|+.++..-|.+.|.
T Consensus 108 ~L~~~~R~v~~L~~~~g-----~s~~EIA~~lg~s~~tVr~~l~RAr~~Lr~ 154 (281)
T TIGR02957 108 RLSPLERAVFVLREVFD-----YPYEEIASIVGKSEANCRQLVSRARRHLDA 154 (281)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 45666666555543222 125678999999999999999766665554
Done!