Query 019530
Match_columns 339
No_of_seqs 393 out of 1669
Neff 5.7
Searched_HMMs 46136
Date Fri Mar 29 02:30:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019530.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019530hhsearch_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 2.3E-25 5E-30 202.8 9.4 120 164-283 49-169 (198)
2 KOG0489 Transcription factor z 99.8 3E-19 6.6E-24 169.5 4.2 64 163-226 157-220 (261)
3 KOG0487 Transcription factor A 99.7 3.9E-18 8.5E-23 164.1 7.8 66 163-228 233-298 (308)
4 KOG0488 Transcription factor B 99.7 1.4E-17 3.1E-22 161.4 8.7 64 163-226 170-233 (309)
5 KOG0493 Transcription factor E 99.7 2.2E-17 4.8E-22 154.1 9.3 99 125-229 212-310 (342)
6 KOG0842 Transcription factor t 99.7 5.3E-18 1.2E-22 163.1 4.5 68 164-231 152-219 (307)
7 KOG0485 Transcription factor N 99.7 5.6E-17 1.2E-21 148.0 8.3 64 161-224 100-163 (268)
8 KOG0484 Transcription factor P 99.7 2.5E-17 5.3E-22 135.0 2.9 64 162-225 14-77 (125)
9 KOG0843 Transcription factor E 99.7 9.8E-17 2.1E-21 142.8 5.3 64 164-227 101-164 (197)
10 PF00046 Homeobox: Homeobox do 99.6 5E-16 1.1E-20 113.8 5.1 57 166-222 1-57 (57)
11 KOG0850 Transcription factor D 99.6 5.3E-16 1.2E-20 142.8 5.5 64 162-225 119-182 (245)
12 KOG0494 Transcription factor C 99.6 6.6E-16 1.4E-20 144.2 5.9 64 169-232 145-208 (332)
13 KOG2251 Homeobox transcription 99.6 4.9E-16 1.1E-20 142.3 4.9 66 162-227 34-99 (228)
14 KOG0492 Transcription factor M 99.6 8.9E-16 1.9E-20 139.4 6.1 62 164-225 143-204 (246)
15 KOG0848 Transcription factor C 99.6 7.3E-16 1.6E-20 144.4 3.3 61 167-227 201-261 (317)
16 PF04618 HD-ZIP_N: HD-ZIP prot 99.5 2.6E-14 5.7E-19 119.3 7.6 99 19-128 4-103 (111)
17 smart00389 HOX Homeodomain. DN 99.5 3.1E-14 6.8E-19 103.3 4.7 56 166-221 1-56 (56)
18 cd00086 homeodomain Homeodomai 99.5 4E-14 8.8E-19 103.4 5.3 58 166-223 1-58 (59)
19 KOG0844 Transcription factor E 99.5 1.9E-14 4.1E-19 137.1 4.4 64 164-227 180-243 (408)
20 KOG0491 Transcription factor B 99.5 1.4E-14 3.1E-19 127.4 1.2 64 164-227 99-162 (194)
21 COG5576 Homeodomain-containing 99.4 6.5E-14 1.4E-18 123.8 5.1 67 161-227 47-113 (156)
22 TIGR01565 homeo_ZF_HD homeobox 99.4 1E-13 2.2E-18 103.4 4.8 53 165-217 1-57 (58)
23 KOG4577 Transcription factor L 99.4 2.1E-13 4.5E-18 129.2 6.3 69 161-229 163-231 (383)
24 KOG0486 Transcription factor P 99.4 1.6E-13 3.4E-18 131.4 4.9 73 164-236 111-183 (351)
25 KOG3802 Transcription factor O 99.4 4.2E-13 9.1E-18 132.2 4.1 61 164-224 293-353 (398)
26 KOG0847 Transcription factor, 99.3 8.2E-13 1.8E-17 121.1 2.7 64 161-224 163-226 (288)
27 KOG0490 Transcription factor, 99.2 1.4E-11 3.1E-16 112.8 3.6 63 163-225 58-120 (235)
28 smart00340 HALZ homeobox assoc 99.1 6.3E-11 1.4E-15 81.8 4.7 44 223-266 1-44 (44)
29 KOG0849 Transcription factor P 98.9 9.1E-10 2E-14 109.1 4.2 64 162-225 173-236 (354)
30 KOG1168 Transcription factor A 98.9 8.3E-10 1.8E-14 105.1 2.8 62 163-224 307-368 (385)
31 KOG0775 Transcription factor S 98.7 7.9E-09 1.7E-13 97.8 4.3 50 172-221 183-232 (304)
32 KOG0774 Transcription factor P 98.4 2.1E-07 4.6E-12 87.7 3.1 58 165-222 188-248 (334)
33 PF05920 Homeobox_KN: Homeobox 98.3 3.7E-07 7.9E-12 63.2 1.9 34 186-219 7-40 (40)
34 KOG2252 CCAAT displacement pro 98.2 1.4E-06 3E-11 89.4 4.6 63 159-221 414-476 (558)
35 KOG0490 Transcription factor, 98.0 6.6E-06 1.4E-10 75.3 4.4 63 163-225 151-213 (235)
36 KOG1146 Homeobox protein [Gene 97.6 5.5E-05 1.2E-09 84.4 4.2 62 164-225 902-963 (1406)
37 PF11569 Homez: Homeodomain le 96.7 0.00083 1.8E-08 49.9 1.6 42 177-218 10-51 (56)
38 KOG0773 Transcription factor M 96.7 0.0012 2.5E-08 65.0 2.8 59 165-223 239-300 (342)
39 PF02183 HALZ: Homeobox associ 95.9 0.014 3E-07 41.5 4.3 34 223-256 1-34 (45)
40 KOG3623 Homeobox transcription 93.8 0.056 1.2E-06 58.0 3.8 48 177-224 568-615 (1007)
41 PRK09413 IS2 repressor TnpA; R 93.8 0.53 1.1E-05 39.6 9.0 79 168-250 9-101 (121)
42 PF04218 CENP-B_N: CENP-B N-te 93.3 0.14 3.1E-06 37.2 4.1 47 166-217 1-47 (53)
43 KOG4196 bZIP transcription fac 82.8 7.9 0.00017 33.6 7.9 73 170-254 22-108 (135)
44 PF02183 HALZ: Homeobox associ 80.0 4.5 9.8E-05 28.7 4.6 31 225-255 10-40 (45)
45 PRK00888 ftsB cell division pr 75.1 5.3 0.00011 33.2 4.5 47 207-254 15-61 (105)
46 PF01527 HTH_Tnp_1: Transposas 73.0 1.2 2.5E-05 33.7 0.1 47 167-217 2-48 (76)
47 PF04545 Sigma70_r4: Sigma-70, 68.3 6.9 0.00015 27.3 3.2 45 171-220 4-48 (50)
48 KOG3119 Basic region leucine z 68.2 11 0.00024 36.2 5.7 31 228-258 223-253 (269)
49 cd06171 Sigma70_r4 Sigma70, re 65.6 4.8 0.0001 27.0 1.9 44 171-219 10-53 (55)
50 PF13443 HTH_26: Cro/C1-type H 58.3 7.2 0.00016 28.3 1.8 39 194-232 12-50 (63)
51 KOG1146 Homeobox protein [Gene 58.0 13 0.00028 43.1 4.5 65 164-228 704-768 (1406)
52 KOG4571 Activating transcripti 56.5 22 0.00048 34.8 5.3 27 228-254 256-282 (294)
53 cd00569 HTH_Hin_like Helix-tur 55.8 18 0.00039 21.4 3.2 38 171-213 5-42 (42)
54 PF04967 HTH_10: HTH DNA bindi 55.4 12 0.00027 27.4 2.6 39 172-210 1-41 (53)
55 PF06156 DUF972: Protein of un 54.7 37 0.00081 28.4 5.8 35 222-256 17-51 (107)
56 KOG4403 Cell surface glycoprot 54.4 23 0.00051 36.6 5.3 26 210-235 229-257 (575)
57 PF00170 bZIP_1: bZIP transcri 53.6 53 0.0011 24.3 5.9 27 228-254 34-60 (64)
58 PRK03975 tfx putative transcri 53.5 25 0.00054 30.9 4.7 49 169-223 4-52 (141)
59 KOG4005 Transcription factor X 52.8 27 0.00058 33.5 5.0 8 214-221 82-89 (292)
60 PF07716 bZIP_2: Basic region 52.7 50 0.0011 23.7 5.5 28 227-254 25-52 (54)
61 KOG3335 Predicted coiled-coil 50.8 59 0.0013 29.7 6.7 50 205-254 84-133 (181)
62 cd04787 HTH_HMRTR_unk Helix-Tu 50.4 72 0.0016 27.1 7.0 71 169-254 36-106 (133)
63 PF08281 Sigma70_r4_2: Sigma-7 49.2 26 0.00055 24.6 3.5 42 172-218 11-52 (54)
64 PF12824 MRP-L20: Mitochondria 48.3 93 0.002 27.9 7.6 66 168-237 82-147 (164)
65 PF09607 BrkDBD: Brinker DNA-b 47.6 22 0.00047 26.8 2.9 44 169-214 3-47 (58)
66 PF00170 bZIP_1: bZIP transcri 47.6 75 0.0016 23.5 5.9 31 225-255 24-54 (64)
67 COG2963 Transposase and inacti 47.6 1.2E+02 0.0026 24.7 7.8 46 169-218 5-51 (116)
68 cd04781 HTH_MerR-like_sg6 Heli 46.1 1.3E+02 0.0029 24.9 7.9 69 168-255 34-102 (120)
69 KOG3755 SATB1 matrix attachmen 44.2 8.3 0.00018 41.3 0.3 45 181-225 708-759 (769)
70 KOG4571 Activating transcripti 44.2 53 0.0012 32.2 5.8 31 224-254 245-275 (294)
71 cd01106 HTH_TipAL-Mta Helix-Tu 43.7 1.3E+02 0.0029 24.1 7.4 64 169-253 36-99 (103)
72 smart00338 BRLZ basic region l 43.6 86 0.0019 23.2 5.7 25 230-254 29-53 (65)
73 PF10668 Phage_terminase: Phag 43.2 10 0.00023 28.6 0.7 19 195-213 25-43 (60)
74 COG3413 Predicted DNA binding 42.7 29 0.00064 31.7 3.7 49 171-221 155-205 (215)
75 PF00196 GerE: Bacterial regul 42.4 30 0.00065 24.8 3.0 46 171-222 3-48 (58)
76 cd04766 HTH_HspR Helix-Turn-He 42.1 70 0.0015 25.2 5.3 20 195-214 4-23 (91)
77 PRK13169 DNA replication intia 41.7 59 0.0013 27.4 5.0 33 223-255 18-50 (110)
78 TIGR02209 ftsL_broad cell divi 40.3 75 0.0016 24.5 5.2 31 224-254 28-58 (85)
79 PF01166 TSC22: TSC-22/dip/bun 39.5 62 0.0013 24.4 4.2 31 226-256 13-43 (59)
80 smart00338 BRLZ basic region l 37.8 1.2E+02 0.0026 22.3 5.8 34 223-256 29-62 (65)
81 PF00424 REV: REV protein (ant 37.1 45 0.00097 27.3 3.4 37 177-227 14-50 (91)
82 PHA02955 hypothetical protein; 36.6 41 0.00088 31.6 3.6 42 174-215 60-102 (213)
83 PF04977 DivIC: Septum formati 36.2 88 0.0019 23.4 4.9 30 224-253 21-50 (80)
84 PRK04217 hypothetical protein; 35.5 62 0.0013 27.2 4.2 46 171-221 42-87 (110)
85 smart00421 HTH_LUXR helix_turn 35.1 51 0.0011 22.3 3.2 41 171-217 3-43 (58)
86 cd01109 HTH_YyaN Helix-Turn-He 35.1 1.8E+02 0.0039 23.7 7.0 70 170-254 37-106 (113)
87 PRK06759 RNA polymerase factor 34.9 55 0.0012 27.4 4.0 46 171-221 106-151 (154)
88 PRK09646 RNA polymerase sigma 34.1 57 0.0012 28.9 4.1 46 171-221 142-187 (194)
89 TIGR02937 sigma70-ECF RNA poly 33.5 56 0.0012 26.3 3.7 46 171-221 110-155 (158)
90 PRK10072 putative transcriptio 33.4 36 0.00078 27.9 2.4 42 171-219 32-73 (96)
91 cd04770 HTH_HMRTR Helix-Turn-H 32.9 2.6E+02 0.0056 23.1 7.6 72 169-255 36-107 (123)
92 PRK12526 RNA polymerase sigma 32.8 61 0.0013 29.2 4.1 47 171-222 153-199 (206)
93 PRK09642 RNA polymerase sigma 32.5 68 0.0015 27.2 4.2 46 172-222 107-152 (160)
94 PRK09652 RNA polymerase sigma 32.5 58 0.0013 27.7 3.7 46 171-221 128-173 (182)
95 PF06005 DUF904: Protein of un 32.4 1.5E+02 0.0033 23.0 5.7 28 227-254 25-52 (72)
96 PRK11924 RNA polymerase sigma 31.1 74 0.0016 27.0 4.2 46 171-221 125-170 (179)
97 PRK00888 ftsB cell division pr 31.0 94 0.002 25.7 4.5 39 210-248 24-62 (105)
98 PF08280 HTH_Mga: M protein tr 30.8 47 0.001 24.2 2.5 35 175-213 6-40 (59)
99 KOG0773 Transcription factor M 30.5 74 0.0016 31.2 4.6 39 184-222 116-154 (342)
100 cd04761 HTH_MerR-SF Helix-Turn 30.4 24 0.00052 23.9 0.8 23 195-217 3-25 (49)
101 COG4367 Uncharacterized protei 30.3 45 0.00098 27.3 2.4 40 171-210 2-41 (97)
102 PF13936 HTH_38: Helix-turn-he 29.7 38 0.00083 23.3 1.7 40 170-214 3-42 (44)
103 PRK12514 RNA polymerase sigma 29.5 48 0.001 28.8 2.7 45 172-221 130-174 (179)
104 PRK13922 rod shape-determining 29.3 1E+02 0.0022 29.3 5.1 35 223-257 72-109 (276)
105 TIGR00219 mreC rod shape-deter 29.1 1.4E+02 0.0031 28.9 6.1 35 223-257 69-107 (283)
106 PF05703 Auxin_canalis: Auxin 29.0 99 0.0022 29.6 4.9 17 205-221 99-115 (242)
107 PRK00118 putative DNA-binding 28.8 3E+02 0.0064 22.9 7.1 46 172-222 18-63 (104)
108 cd04779 HTH_MerR-like_sg4 Heli 28.6 2.6E+02 0.0057 24.0 7.1 36 169-217 35-70 (134)
109 PRK09644 RNA polymerase sigma 28.1 88 0.0019 26.7 4.1 47 171-222 108-154 (165)
110 TIGR03879 near_KaiC_dom probab 28.0 16 0.00035 28.6 -0.5 33 183-215 23-55 (73)
111 PF15058 Speriolin_N: Sperioli 27.8 74 0.0016 29.5 3.6 8 228-235 20-27 (200)
112 cd04783 HTH_MerR1 Helix-Turn-H 27.6 3E+02 0.0066 22.9 7.2 69 169-254 36-104 (126)
113 PRK12512 RNA polymerase sigma 27.1 87 0.0019 27.2 4.0 47 171-222 131-177 (184)
114 PF13518 HTH_28: Helix-turn-he 26.9 40 0.00088 23.1 1.5 21 195-215 15-35 (52)
115 cd04775 HTH_Cfa-like Helix-Tur 26.4 3.3E+02 0.0072 21.9 7.0 64 169-255 36-99 (102)
116 PRK09639 RNA polymerase sigma 26.4 1.2E+02 0.0027 25.6 4.8 45 171-221 112-156 (166)
117 PRK10403 transcriptional regul 26.2 53 0.0011 28.0 2.4 47 171-223 153-199 (215)
118 PF07989 Microtub_assoc: Micro 26.2 1.3E+02 0.0029 23.4 4.4 43 209-254 21-63 (75)
119 PRK12519 RNA polymerase sigma 26.2 72 0.0016 28.0 3.3 45 172-221 142-186 (194)
120 TIGR02449 conserved hypothetic 26.1 1.7E+02 0.0037 22.4 4.8 23 230-252 10-32 (65)
121 cd06170 LuxR_C_like C-terminal 26.1 87 0.0019 21.2 3.1 36 173-214 2-37 (57)
122 PRK12515 RNA polymerase sigma 25.9 1.1E+02 0.0023 26.9 4.3 47 171-222 131-177 (189)
123 TIGR02051 MerR Hg(II)-responsi 25.7 3.2E+02 0.007 22.8 7.0 36 169-217 35-70 (124)
124 PF10226 DUF2216: Uncharacteri 25.5 1.4E+02 0.0029 27.8 4.9 34 223-256 44-77 (195)
125 PRK15369 two component system 25.5 1.3E+02 0.0028 25.2 4.7 45 171-221 149-193 (211)
126 TIGR02985 Sig70_bacteroi1 RNA 25.4 97 0.0021 25.7 3.8 45 172-221 114-158 (161)
127 PF15136 UPF0449: Uncharacteri 25.4 1.4E+02 0.0031 24.7 4.6 29 224-252 68-96 (97)
128 PRK10884 SH3 domain-containing 25.2 3.4E+02 0.0073 25.2 7.6 11 175-185 93-103 (206)
129 PF07716 bZIP_2: Basic region 24.7 2E+02 0.0043 20.6 4.8 25 225-249 30-54 (54)
130 KOG3623 Homeobox transcription 24.5 29 0.00063 38.2 0.5 58 167-224 628-685 (1007)
131 PF09726 Macoilin: Transmembra 24.5 2.5E+02 0.0054 31.0 7.5 39 218-256 543-581 (697)
132 TIGR02989 Sig-70_gvs1 RNA poly 24.4 99 0.0021 25.9 3.7 45 171-220 111-155 (159)
133 TIGR02959 SigZ RNA polymerase 24.1 1E+02 0.0022 26.7 3.8 46 171-221 100-145 (170)
134 PRK12546 RNA polymerase sigma 24.0 73 0.0016 28.4 2.9 46 171-221 113-158 (188)
135 cd04777 HTH_MerR-like_sg1 Heli 24.0 2.5E+02 0.0054 22.7 5.9 33 171-216 36-68 (107)
136 PF02796 HTH_7: Helix-turn-hel 23.9 77 0.0017 21.8 2.4 38 171-213 5-42 (45)
137 cd04769 HTH_MerR2 Helix-Turn-H 23.8 2.9E+02 0.0063 22.7 6.3 72 169-254 35-106 (116)
138 TIGR02948 SigW_bacill RNA poly 23.7 93 0.002 26.9 3.5 46 171-221 136-181 (187)
139 PRK12541 RNA polymerase sigma 23.5 87 0.0019 26.6 3.2 46 171-221 112-157 (161)
140 PRK09648 RNA polymerase sigma 23.5 1.1E+02 0.0023 26.8 3.9 46 171-221 139-184 (189)
141 PF06785 UPF0242: Uncharacteri 23.2 1.9E+02 0.0041 29.2 5.7 42 216-257 137-178 (401)
142 TIGR00721 tfx DNA-binding prot 23.2 2.1E+02 0.0045 25.0 5.5 48 169-222 4-51 (137)
143 PF08172 CASP_C: CASP C termin 23.1 1.8E+02 0.004 27.8 5.6 38 217-254 90-127 (248)
144 PF06005 DUF904: Protein of un 23.0 3E+02 0.0065 21.3 5.8 31 223-253 28-58 (72)
145 PF12808 Mto2_bdg: Micro-tubul 22.8 1.9E+02 0.0042 21.2 4.4 27 228-254 23-49 (52)
146 TIGR03752 conj_TIGR03752 integ 22.8 1.2E+02 0.0026 31.8 4.6 36 188-223 55-90 (472)
147 PF08961 DUF1875: Domain of un 22.7 28 0.00061 32.9 0.0 33 225-257 127-159 (243)
148 TIGR02939 RpoE_Sigma70 RNA pol 22.7 87 0.0019 27.1 3.1 45 172-221 139-183 (190)
149 PF01486 K-box: K-box region; 22.7 1.4E+02 0.003 24.0 4.1 44 207-251 56-99 (100)
150 PRK10360 DNA-binding transcrip 22.5 75 0.0016 27.0 2.6 45 171-221 137-181 (196)
151 PRK05602 RNA polymerase sigma 22.5 1.1E+02 0.0024 26.7 3.8 46 172-222 129-174 (186)
152 PF10883 DUF2681: Protein of u 22.2 2.5E+02 0.0054 22.8 5.3 37 210-253 20-56 (87)
153 PRK12538 RNA polymerase sigma 22.1 1.2E+02 0.0026 28.1 4.1 27 195-221 190-216 (233)
154 PF11594 Med28: Mediator compl 22.0 1.6E+02 0.0035 24.8 4.3 14 207-220 18-31 (106)
155 PRK14127 cell division protein 21.9 1.8E+02 0.0039 24.5 4.6 44 203-255 22-65 (109)
156 PF14197 Cep57_CLD_2: Centroso 21.6 2.7E+02 0.0058 21.4 5.2 20 235-254 48-67 (69)
157 KOG0999 Microtubule-associated 21.5 1.5E+02 0.0032 32.0 4.8 46 209-254 145-190 (772)
158 cd04784 HTH_CadR-PbrR Helix-Tu 21.5 3.9E+02 0.0085 22.2 6.8 71 169-254 36-106 (127)
159 PF05377 FlaC_arch: Flagella a 21.5 2.2E+02 0.0049 21.1 4.5 28 227-254 7-34 (55)
160 KOG3584 cAMP response element 21.4 1.4E+02 0.0029 29.6 4.3 43 214-256 298-341 (348)
161 KOG0709 CREB/ATF family transc 21.3 72 0.0016 33.3 2.6 80 170-256 219-315 (472)
162 TIGR02999 Sig-70_X6 RNA polyme 20.8 1.4E+02 0.0029 25.9 3.9 45 172-221 135-179 (183)
163 KOG3119 Basic region leucine z 20.8 1.8E+02 0.0039 28.0 5.1 35 217-254 208-242 (269)
164 PRK06930 positive control sigm 20.8 1.5E+02 0.0032 26.5 4.2 47 171-222 114-160 (170)
165 PF13411 MerR_1: MerR HTH fami 20.7 47 0.001 24.2 0.9 19 196-214 4-22 (69)
166 PRK09935 transcriptional regul 20.6 86 0.0019 26.7 2.6 46 170-221 148-193 (210)
167 PF13384 HTH_23: Homeodomain-l 20.5 45 0.00096 22.9 0.6 22 194-215 19-40 (50)
168 PRK12543 RNA polymerase sigma 20.4 1.8E+02 0.004 25.2 4.7 45 172-221 118-162 (179)
169 PRK06811 RNA polymerase factor 20.4 1E+02 0.0022 27.1 3.1 48 171-223 131-178 (189)
170 PF03980 Nnf1: Nnf1 ; InterPr 20.2 1.8E+02 0.004 23.6 4.4 29 226-254 79-107 (109)
171 PF10224 DUF2205: Predicted co 20.2 3.5E+02 0.0076 21.5 5.7 31 224-254 27-57 (80)
172 PRK12518 RNA polymerase sigma 20.1 76 0.0016 27.2 2.2 28 195-222 139-166 (175)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.92 E-value=2.3e-25 Score=202.79 Aligned_cols=120 Identities=53% Similarity=0.691 Sum_probs=111.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHH
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEEN 243 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn 243 (339)
+.++++.||+.+|+..||+.|+.+.|+.+.+|..||++|||.+|||+|||||||||||.++++.++++||.+++.|+.++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35567789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhhhCCCcccCC-CCccccCCCCCCcccCC
Q 019530 244 RRLQKELQELRALKTSQPFYMQL-PATTLTMCPSCERVATA 283 (339)
Q Consensus 244 ~~l~~e~~~lralk~s~~~~~~~-p~~~~~~c~sC~~~~~~ 283 (339)
++|++|+++|++.+.....++++ +...+.+|+.|+.+...
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 169 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQKSPENTLTMCPNSESSSSV 169 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhccCcccccccCccccccCCc
Confidence 99999999999998888888888 88899999999855443
No 2
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.76 E-value=3e-19 Score=169.46 Aligned_cols=64 Identities=30% Similarity=0.512 Sum_probs=59.8
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 226 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~ 226 (339)
.+.||.||.||.+|+.+||+.|..++|+++..|.+||..|.|++|||||||||||+||||..+.
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 3478899999999999999999999999999999999999999999999999999999976543
No 3
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.73 E-value=3.9e-18 Score=164.09 Aligned_cols=66 Identities=33% Similarity=0.497 Sum_probs=61.0
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 228 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~ 228 (339)
+..||||.-+|+.|+.+||+.|..|.|++.+.|.+|++.|+|++|||||||||||+|.||..++..
T Consensus 233 ~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~r 298 (308)
T KOG0487|consen 233 RRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRENR 298 (308)
T ss_pred cccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhhh
Confidence 456788999999999999999999999999999999999999999999999999999998765443
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.71 E-value=1.4e-17 Score=161.41 Aligned_cols=64 Identities=31% Similarity=0.478 Sum_probs=59.3
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTE 226 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~ 226 (339)
++.||.||.||..||..||+.|++.+|++..+|++||+.|||+..|||+||||||+||||...+
T Consensus 170 kK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a~ 233 (309)
T KOG0488|consen 170 KKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTAE 233 (309)
T ss_pred cccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHHh
Confidence 4566679999999999999999999999999999999999999999999999999999976544
No 5
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.71 E-value=2.2e-17 Score=154.06 Aligned_cols=99 Identities=23% Similarity=0.389 Sum_probs=75.8
Q ss_pred CcccccchhhcCCCCCCCcccccccccccCCCCCCccccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCC
Q 019530 125 SSFQMDHFCIRNGRSKRDLFDVEISHDRASSRASDDEENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNL 204 (339)
Q Consensus 125 ss~~~~~~~~~s~~~krd~~~~~~~~~~~~~~~~~~~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgL 204 (339)
+-|+.|+||++++. ....+...... +.-.+.....||.||.||.+||..|+..|+.++|++...|++||.+|+|
T Consensus 212 ~mwPAWVycTRYSD----RPSsGPR~Rk~--kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgL 285 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSD----RPSSGPRHRKP--KKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGL 285 (342)
T ss_pred cccceeeeeecccC----CCCCCcccccc--cccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCc
Confidence 56999999998762 22222211111 1111123345789999999999999999999999999999999999999
Q ss_pred CcccccchhhhhHHHHHhhhhhhhh
Q 019530 205 RPRQVEVWFQNRRARTKLKQTEVDC 229 (339)
Q Consensus 205 s~rQVqvWFQNRRaK~Krkq~~~~~ 229 (339)
.+.||||||||+|+|.||..--+..
T Consensus 286 NEsQIKIWFQNKRAKiKKsTgskn~ 310 (342)
T KOG0493|consen 286 NESQIKIWFQNKRAKIKKSTGSKNR 310 (342)
T ss_pred CHHHhhHHhhhhhhhhhhccCCCCc
Confidence 9999999999999999986544433
No 6
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.71 E-value=5.3e-18 Score=163.10 Aligned_cols=68 Identities=34% Similarity=0.532 Sum_probs=61.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHH
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEY 231 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~ 231 (339)
++||.|..|+..|+.+||+.|++++|++..+|++||..|+|+++||||||||||-|.||++.++..+.
T Consensus 152 ~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 152 KKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 44455667999999999999999999999999999999999999999999999999999888776643
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.69 E-value=5.6e-17 Score=148.04 Aligned_cols=64 Identities=30% Similarity=0.472 Sum_probs=59.7
Q ss_pred cccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 161 EENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 161 ~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
.++++||.||.|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+.
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 4456778899999999999999999999999999999999999999999999999999999754
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.66 E-value=2.5e-17 Score=134.96 Aligned_cols=64 Identities=27% Similarity=0.415 Sum_probs=59.3
Q ss_pred ccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 162 ENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 162 ~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
.++.||-||.||..||.+||+.|.+++||+...|++||.++.|++..|||||||||+|.||+..
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQEr 77 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQER 77 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHHH
Confidence 3456788999999999999999999999999999999999999999999999999999997543
No 9
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.65 E-value=9.8e-17 Score=142.82 Aligned_cols=64 Identities=34% Similarity=0.464 Sum_probs=61.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
+.||.||.|+.+||..||..|+.+.|..-.+|.+||..|+|++.||||||||||.|.||++.+.
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 6788999999999999999999999999999999999999999999999999999999987664
No 10
>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=99.62 E-value=5e-16 Score=113.76 Aligned_cols=57 Identities=46% Similarity=0.669 Sum_probs=55.2
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 166 TRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 166 kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
||+|+.|+.+|+.+|+..|..++||+..++..||.+|||+..||++||+|||.++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 578999999999999999999999999999999999999999999999999999985
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.61 E-value=5.3e-16 Score=142.78 Aligned_cols=64 Identities=28% Similarity=0.421 Sum_probs=58.5
Q ss_pred ccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 162 ENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 162 ~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
.++-||.||.|+..||..|.+.|+++.|+-..+|.+||..|||+..||||||||||.|.||..+
T Consensus 119 ~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 119 GKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 3345567999999999999999999999999999999999999999999999999999997544
No 12
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.60 E-value=6.6e-16 Score=144.19 Aligned_cols=64 Identities=27% Similarity=0.376 Sum_probs=59.0
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYL 232 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~L 232 (339)
||.||..|+.+||+.|++.+||+...|+.||.++.|.+.+|+|||||||+||||++........
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT~ 208 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGSTI 208 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcchh
Confidence 8889999999999999999999999999999999999999999999999999998766655333
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.60 E-value=4.9e-16 Score=142.34 Aligned_cols=66 Identities=29% Similarity=0.451 Sum_probs=61.8
Q ss_pred ccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 162 ENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 162 ~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
.++.||.||+|+..|+++||..|.++.||+...|++||.+|+|.+.+|+|||+|||+|+|+++..+
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~qq 99 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQQ 99 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhhh
Confidence 446788999999999999999999999999999999999999999999999999999999877654
No 14
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.60 E-value=8.9e-16 Score=139.41 Aligned_cols=62 Identities=31% Similarity=0.497 Sum_probs=57.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
..|+.|+.||..||..||+.|++.+|++..+|.+++..|.|++.||||||||||+|.||.|+
T Consensus 143 ~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 143 PNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 35667999999999999999999999999999999999999999999999999999997554
No 15
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.58 E-value=7.3e-16 Score=144.42 Aligned_cols=61 Identities=31% Similarity=0.525 Sum_probs=56.2
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 167 RKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 167 RkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
|-|.+||..|..+||+.|...+|+++..|.+||..|+|++|||||||||||+|+||.++++
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~nKKk 261 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDNKKK 261 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHHHHH
Confidence 4467899999999999999999999999999999999999999999999999999865443
No 16
>PF04618 HD-ZIP_N: HD-ZIP protein N terminus; InterPro: IPR006712 Homeodomain leucine zipper (HDZip) genes encode putative transcription factors that are unique to plants. This observation suggests that homeobox-leucine zipper genes evolved after the divergence of plants and animals, perhaps to mediate specific regulatory events []. This domain is the N-terminal of plant homeobox-leucine zipper proteins. Its function is unknown.; GO: 0006351 transcription, DNA-dependent, 0005634 nucleus
Probab=99.52 E-value=2.6e-14 Score=119.27 Aligned_cols=99 Identities=29% Similarity=0.407 Sum_probs=64.2
Q ss_pred CCCCCcceeeccCCCCCCCccccccCCCCCCCcccCCCCCCCCCCCCCCCCCCCCCCCCCccCCCCCCCCC-CCCCCCCC
Q 019530 19 SSKDLGFCMGLNGSSFNGKSEEKSASDHHPSPIQLDLLPFSPVPRAHHHQPSSQLRFPWLNVVSTEPGPMD-GAGGGGLD 97 (339)
Q Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~p~~~~~~~~~~~~~~~~w~~~~~~~~~~~~-~~~~~g~D 97 (339)
.+++|||+|+||++... .....+++||+|+|+.+ +......+..+....|...+.......+ ....||||
T Consensus 4 ~~d~LGLsLSLg~~~~~--------~~~~~~plql~L~P~s~-p~~~~~~~~s~~~~~~~~~~~~~~~~~~~~~flRgiD 74 (111)
T PF04618_consen 4 KKDGLGLSLSLGFAGNR--------HPSQQPPLQLNLLPSSS-PSNSHPLFSSHNQPFWSDDRMMASCDSETRSFLRGID 74 (111)
T ss_pred CCCcceeeeeccCCCCC--------CCccCCCcccccCCccc-cccccCccccccccCCcccccccccccccccccccee
Confidence 57899999999997621 12567899999999876 2222222222233333333333233233 45799999
Q ss_pred CCCCCCcccccccCcCCCCCCCCCCCCCccc
Q 019530 98 VNRFPVAMAQEEADDGTTALSSPNSTVSSFQ 128 (339)
Q Consensus 98 vn~~p~s~~~~e~~~~~~~~ssp~s~~ss~~ 128 (339)
||++|+++..|+ ||+ +++|||||++||++
T Consensus 75 VNr~p~~~~~d~-eEe-~gvSSPNStiSS~s 103 (111)
T PF04618_consen 75 VNRLPSTVEADC-EEE-AGVSSPNSTISSVS 103 (111)
T ss_pred ccCCCccccccc-ccc-ccccCCCccceecc
Confidence 999999875433 333 77999999999864
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.48 E-value=3.1e-14 Score=103.34 Aligned_cols=56 Identities=41% Similarity=0.609 Sum_probs=52.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 166 TRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 166 kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++.|+.|+.+|+.+|+..|..++||+..++..||.++||+..||++||+|||.+.|
T Consensus 1 ~k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 1 RRKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 35678899999999999999999999999999999999999999999999998864
No 18
>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=99.48 E-value=4e-14 Score=103.37 Aligned_cols=58 Identities=41% Similarity=0.635 Sum_probs=54.6
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 166 TRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 166 kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
+++|..|+..|+.+|+..|..++||+..++..||.++||+.+||++||+|||.+.|+.
T Consensus 1 ~~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 1 RRKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 3567899999999999999999999999999999999999999999999999998863
No 19
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.48 E-value=1.9e-14 Score=137.08 Aligned_cols=64 Identities=33% Similarity=0.535 Sum_probs=59.9
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
.-||-||.||.+||..||+.|-+..|.++..|.+||..|||.+..|||||||||+|+||+....
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRlam 243 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLAM 243 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhhc
Confidence 4578899999999999999999999999999999999999999999999999999999876543
No 20
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.45 E-value=1.4e-14 Score=127.43 Aligned_cols=64 Identities=31% Similarity=0.459 Sum_probs=58.8
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
+++|.|+.|+..|+..||+.|+..+|++..+|.+||..|+|+++|||.||||||+|.||.++..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~~ 162 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRNN 162 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhcc
Confidence 3456789999999999999999999999999999999999999999999999999999866544
No 21
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.45 E-value=6.5e-14 Score=123.77 Aligned_cols=67 Identities=30% Similarity=0.487 Sum_probs=61.0
Q ss_pred cccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 161 EENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 161 ~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
.....+++|+|.|.+|+.+|++.|+.++||+...|..|+..|+|+++-|||||||||++.|+.....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~~ 113 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSGK 113 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcccc
Confidence 3345678899999999999999999999999999999999999999999999999999999866544
No 22
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.44 E-value=1e-13 Score=103.37 Aligned_cols=53 Identities=11% Similarity=0.311 Sum_probs=50.7
Q ss_pred CCCCCccCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 165 LTRKKLRLSKEQSAFLEESFKEHNT----LNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 165 ~kRkRtrft~~Ql~~LE~~F~~~~~----ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
+||.||.||.+|+..|+..|+.+.| |+..++.+||..|||++++|+|||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3788999999999999999999999 9999999999999999999999999964
No 23
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.42 E-value=2.1e-13 Score=129.23 Aligned_cols=69 Identities=23% Similarity=0.380 Sum_probs=63.0
Q ss_pred cccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhh
Q 019530 161 EENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDC 229 (339)
Q Consensus 161 ~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~ 229 (339)
.+...||.||++|..||+.|+..|...+.|.+..|++|+.++||..|.|||||||||+|+||.++....
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGR 231 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcch
Confidence 344678999999999999999999999999999999999999999999999999999999986655544
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.41 E-value=1.6e-13 Score=131.37 Aligned_cols=73 Identities=25% Similarity=0.375 Sum_probs=63.5
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCC 236 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~ 236 (339)
++||.|+.||..|+.+||.+|.+++||+...|++||..++|++..|+|||.|||+||||+++.+..|.-|..+
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~~ae~~k~~f 183 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQQAELAKGGF 183 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhHHHHhhhcCC
Confidence 4456788899999999999999999999999999999999999999999999999999887766544333333
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.35 E-value=4.2e-13 Score=132.20 Aligned_cols=61 Identities=25% Similarity=0.382 Sum_probs=58.0
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
++|||||.|....+..||+.|.+|++|+..++..||.+|+|.+.+|+|||||||.|.||..
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 6778899999999999999999999999999999999999999999999999999999754
No 26
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.30 E-value=8.2e-13 Score=121.13 Aligned_cols=64 Identities=30% Similarity=0.462 Sum_probs=58.2
Q ss_pred cccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 161 EENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 161 ~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
.+++++..|.+|+..||..||+.|+..+|+--.+|.+||..+|+++.||+|||||||.||||+-
T Consensus 163 kdG~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 163 LNGQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cCccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 3445555678899999999999999999999999999999999999999999999999999864
No 27
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.17 E-value=1.4e-11 Score=112.78 Aligned_cols=63 Identities=25% Similarity=0.291 Sum_probs=59.0
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
.+.||.|+.|+..|+++||+.|+..+||+...|+.||..+++++..|+|||||||+||+++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~~ 120 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEER 120 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhhc
Confidence 456788999999999999999999999999999999999999999999999999999997653
No 28
>smart00340 HALZ homeobox associated leucin zipper.
Probab=99.14 E-value=6.3e-11 Score=81.82 Aligned_cols=44 Identities=84% Similarity=1.250 Sum_probs=41.6
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHhhhCCCcccCC
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQELRALKTSQPFYMQL 266 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lralk~s~~~~~~~ 266 (339)
+|++.||++||+||+.|.+||++|++|+++||++|.++++||++
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLralk~~~~~~m~~ 44 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRALKLSPPLYMQH 44 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcccccC
Confidence 57899999999999999999999999999999999999999864
No 29
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.90 E-value=9.1e-10 Score=109.06 Aligned_cols=64 Identities=33% Similarity=0.463 Sum_probs=59.1
Q ss_pred ccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 162 ENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 162 ~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
.++.+|+|+.|+..|+..||+.|+.++||+...|++||.++++++..|+|||+|||+|++|...
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 3456678999999999999999999999999999999999999999999999999999997653
No 30
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.88 E-value=8.3e-10 Score=105.07 Aligned_cols=62 Identities=26% Similarity=0.410 Sum_probs=57.8
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
+.+|||||.+-....+.||.+|..++.|+.+.+..||++|.|.+..|+|||+|.|.|.||.+
T Consensus 307 ~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 307 GEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 35788999999999999999999999999999999999999999999999999999999743
No 31
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.74 E-value=7.9e-09 Score=97.82 Aligned_cols=50 Identities=30% Similarity=0.545 Sum_probs=47.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
|...-...|.++|..++||++.+|.+||+.+||+..||-+||+|||+|+|
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDR 232 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDR 232 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhh
Confidence 55666789999999999999999999999999999999999999999999
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.36 E-value=2.1e-07 Score=87.73 Aligned_cols=58 Identities=36% Similarity=0.473 Sum_probs=54.6
Q ss_pred CCCCCccCCHHHHHHHHHHHh---hcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 165 LTRKKLRLSKEQSAFLEESFK---EHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 165 ~kRkRtrft~~Ql~~LE~~F~---~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.+|||.-|++.-.++|.++|. .++||+.+.+++||+++|++..||..||.|+|-++||
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 568888999999999999996 4799999999999999999999999999999999996
No 33
>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=98.28 E-value=3.7e-07 Score=63.25 Aligned_cols=34 Identities=35% Similarity=0.513 Sum_probs=29.2
Q ss_pred hcCCCCHHHHHHHHHHcCCCcccccchhhhhHHH
Q 019530 186 EHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 219 (339)
Q Consensus 186 ~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK 219 (339)
.++||+..+|.+||+++||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 5799999999999999999999999999999975
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=98.19 E-value=1.4e-06 Score=89.45 Aligned_cols=63 Identities=27% Similarity=0.348 Sum_probs=57.6
Q ss_pred CccccCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 159 DDEENGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 159 ~~~~~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++.....||.|.+||..|.+.|..+|+++++|+.+..+.|+.+|+|..+-|.+||-|-|.|.+
T Consensus 414 ~d~~~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 414 DDKMLQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred ccccccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 444556788899999999999999999999999999999999999999999999999998863
No 35
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.98 E-value=6.6e-06 Score=75.28 Aligned_cols=63 Identities=27% Similarity=0.486 Sum_probs=58.0
Q ss_pred cCCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 163 NGLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 163 ~~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
.+.++.|+.+...|+..|+..|....+|+...+..|+..+++.++.|++||||+|.+.++...
T Consensus 151 ~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 151 KKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred cccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 356678899999999999999999999999999999999999999999999999999997543
No 36
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.58 E-value=5.5e-05 Score=84.37 Aligned_cols=62 Identities=24% Similarity=0.388 Sum_probs=58.2
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~ 225 (339)
+.+++|++++..||.+|...|....|+...+.+.|-..+++.++.|+|||||-|+|.|+..+
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 56678999999999999999999999999999999999999999999999999999998654
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.69 E-value=0.00083 Score=49.85 Aligned_cols=42 Identities=24% Similarity=0.381 Sum_probs=31.4
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHH
Q 019530 177 SAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 218 (339)
Q Consensus 177 l~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRa 218 (339)
+..|+++|..++++...+...|..+.+|+..||+.||--|+.
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=96.65 E-value=0.0012 Score=64.99 Aligned_cols=59 Identities=36% Similarity=0.363 Sum_probs=49.9
Q ss_pred CCCCCccCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 165 LTRKKLRLSKEQSAFLEESFKE---HNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 165 ~kRkRtrft~~Ql~~LE~~F~~---~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
.+|++..|......+|+.+... .+||+..++..||+++||+..||.+||.|.|-|..+-
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p 300 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKP 300 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCc
Confidence 3455567999999999987543 5799999999999999999999999999999886653
No 39
>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=95.93 E-value=0.014 Score=41.53 Aligned_cols=34 Identities=41% Similarity=0.468 Sum_probs=30.7
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
+|.+.+++.|+.+|+.|..++++|++|++.|++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~ae 34 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAE 34 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4788999999999999999999999999998854
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.82 E-value=0.056 Score=58.03 Aligned_cols=48 Identities=17% Similarity=0.315 Sum_probs=45.0
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 177 SAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 177 l~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
+..|+.+|..|..|+..+...+|.+.||..+.|++||++++++...-+
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 788999999999999999999999999999999999999999887644
No 41
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=93.78 E-value=0.53 Score=39.63 Aligned_cols=79 Identities=18% Similarity=0.197 Sum_probs=47.6
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHH--------------HHhhhhhhhhHHHH
Q 019530 168 KKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR--------------TKLKQTEVDCEYLK 233 (339)
Q Consensus 168 kRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK--------------~Krkq~~~~~e~Lk 233 (339)
+|.+|+.++....-..+..+.+ ...++|.++|+++.+|..|.+--+.. ....+.+.++..|+
T Consensus 9 ~rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L~ 84 (121)
T PRK09413 9 KRRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQ 84 (121)
T ss_pred CCCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHHH
Confidence 3556877765433333333332 24568999999999999996543321 01123445566677
Q ss_pred HhhhhhHHHHHHHHHHH
Q 019530 234 RCCETLTEENRRLQKEL 250 (339)
Q Consensus 234 ~~~~~l~eEn~~l~~e~ 250 (339)
++...|..|++-|++.+
T Consensus 85 ~el~~L~~E~diLKKa~ 101 (121)
T PRK09413 85 RLLGKKTMENELLKEAV 101 (121)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 77777777777666643
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=93.25 E-value=0.14 Score=37.24 Aligned_cols=47 Identities=19% Similarity=0.316 Sum_probs=35.4
Q ss_pred CCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 166 TRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 166 kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
||+|..+|-++...+-..++... ...+||+++|+...+|..|..|+.
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 57888999988888777787766 477899999999999999998853
No 43
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=82.80 E-value=7.9 Score=33.61 Aligned_cols=73 Identities=27% Similarity=0.268 Sum_probs=51.1
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHH----------Hhh----hhhhhhHHHHHh
Q 019530 170 LRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRART----------KLK----QTEVDCEYLKRC 235 (339)
Q Consensus 170 trft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~----------Krk----q~~~~~e~Lk~~ 235 (339)
.+|+.++|..+- .|+.--+.-|++...|--|=|.||+-. ||- ..+.+...|.++
T Consensus 22 d~lsDd~LvsmS------------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSMS------------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHhh------------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 578888877652 222222334888888888888888633 333 344555667888
Q ss_pred hhhhHHHHHHHHHHHHHHH
Q 019530 236 CETLTEENRRLQKELQELR 254 (339)
Q Consensus 236 ~~~l~eEn~~l~~e~~~lr 254 (339)
.+.|.+||.+++.|+..++
T Consensus 90 v~~L~~e~s~~~~E~da~k 108 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYK 108 (135)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 8899999999999988877
No 44
>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=79.96 E-value=4.5 Score=28.70 Aligned_cols=31 Identities=32% Similarity=0.510 Sum_probs=27.6
Q ss_pred hhhhhHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 019530 225 TEVDCEYLKRCCETLTEENRRLQKELQELRA 255 (339)
Q Consensus 225 ~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lra 255 (339)
....++.|+..++.|..||+.|+.++..++.
T Consensus 10 LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 10 LKASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567789999999999999999999999884
No 45
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=75.08 E-value=5.3 Score=33.17 Aligned_cols=47 Identities=17% Similarity=0.294 Sum_probs=26.3
Q ss_pred ccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 207 RQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 207 rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
-++..||++.-- .+-.+.+++.+.++.+.+.+..+|+.|+.|+..|+
T Consensus 15 l~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~ 61 (105)
T PRK00888 15 LQYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLK 61 (105)
T ss_pred HHHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 345678855411 11223334455566666667777777777766665
No 46
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=73.04 E-value=1.2 Score=33.66 Aligned_cols=47 Identities=21% Similarity=0.313 Sum_probs=29.7
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 167 RKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 167 RkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
++|.+|+.++...+-..+... .....++|+++||++.+|..|-.--+
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~~----g~sv~~va~~~gi~~~~l~~W~~~~~ 48 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLES----GESVSEVAREYGISPSTLYNWRKQYR 48 (76)
T ss_dssp -SS----HHHHHHHHHHHHHH----HCHHHHHHHHHTS-HHHHHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHHC----CCceEeeecccccccccccHHHHHHh
Confidence 467789998877666655221 24567899999999999999976444
No 47
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=68.35 E-value=6.9 Score=27.35 Aligned_cols=45 Identities=11% Similarity=0.152 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRART 220 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~ 220 (339)
.++..+..+|...|-.. ..-.++|..+|++...|+.+...-..|-
T Consensus 4 ~L~~~er~vi~~~y~~~-----~t~~eIa~~lg~s~~~V~~~~~~al~kL 48 (50)
T PF04545_consen 4 QLPPREREVIRLRYFEG-----LTLEEIAERLGISRSTVRRILKRALKKL 48 (50)
T ss_dssp TS-HHHHHHHHHHHTST------SHHHHHHHHTSCHHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcCC-----CCHHHHHHHHCCcHHHHHHHHHHHHHHh
Confidence 47788999999998332 2356799999999999988776444443
No 48
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=68.19 E-value=11 Score=36.24 Aligned_cols=31 Identities=32% Similarity=0.355 Sum_probs=22.6
Q ss_pred hhHHHHHhhhhhHHHHHHHHHHHHHHHHhhh
Q 019530 228 DCEYLKRCCETLTEENRRLQKELQELRALKT 258 (339)
Q Consensus 228 ~~e~Lk~~~~~l~eEn~~l~~e~~~lralk~ 258 (339)
....|.++++.|+.+.+.|++|+..+|.++.
T Consensus 223 r~~~leken~~lr~~v~~l~~el~~~~~~~~ 253 (269)
T KOG3119|consen 223 RVAELEKENEALRTQVEQLKKELATLRRLFL 253 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3456677777778888888888888886654
No 49
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=65.61 E-value=4.8 Score=27.00 Aligned_cols=44 Identities=14% Similarity=0.174 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 219 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK 219 (339)
.++..+..++...|... ..-.++|..+|++...|..|....+.+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 46777888887776433 234678999999999999998765543
No 50
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=58.29 E-value=7.2 Score=28.25 Aligned_cols=39 Identities=13% Similarity=0.171 Sum_probs=22.9
Q ss_pred HHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHH
Q 019530 194 QKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYL 232 (339)
Q Consensus 194 ~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~L 232 (339)
...+||+.+|++..+|..|+.++..+........=+.+|
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l 50 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKAL 50 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHc
Confidence 356799999999999999999876565554444444443
No 51
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=58.00 E-value=13 Score=43.12 Aligned_cols=65 Identities=20% Similarity=0.268 Sum_probs=57.1
Q ss_pred CCCCCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhh
Q 019530 164 GLTRKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVD 228 (339)
Q Consensus 164 ~~kRkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~ 228 (339)
..++-|+.+-.+++..|-++|-.+..|+.+.+..|......+.+++.+||+|-|.|.++.+...+
T Consensus 704 ~~~~~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~v~g~ 768 (1406)
T KOG1146|consen 704 RDKLLRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQVPGD 768 (1406)
T ss_pred ccccCcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhcccCC
Confidence 44556777778999999999999999999999999999999999999999999999998773333
No 52
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=56.46 E-value=22 Score=34.79 Aligned_cols=27 Identities=26% Similarity=0.457 Sum_probs=14.5
Q ss_pred hhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 228 DCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 228 ~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
+++.|.+.++.|++.-.+|++||+.||
T Consensus 256 e~~~Le~rN~~LK~qa~~lerEI~ylK 282 (294)
T KOG4571|consen 256 ELEGLEKRNEELKDQASELEREIRYLK 282 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555556666555
No 53
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=55.77 E-value=18 Score=21.42 Aligned_cols=38 Identities=13% Similarity=0.191 Sum_probs=26.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWF 213 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWF 213 (339)
.++..+...+...|.... ...++|+.++++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 356666666666665332 35578999999988888774
No 54
>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=55.37 E-value=12 Score=27.38 Aligned_cols=39 Identities=18% Similarity=0.206 Sum_probs=31.4
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCccccc
Q 019530 172 LSKEQSAFLEESFKEHNT--LNPKQKLALAKQLNLRPRQVE 210 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~--ps~~~r~~LA~~LgLs~rQVq 210 (339)
+|..|.++|...|+..-| |-...-.+||++||++..-|.
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~ 41 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVS 41 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHH
Confidence 578999999999988755 555566899999999986543
No 55
>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=54.73 E-value=37 Score=28.36 Aligned_cols=35 Identities=40% Similarity=0.379 Sum_probs=29.5
Q ss_pred hhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 222 LKQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 222 rkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
....-.+...||.....|.+||.+|+.|++.||..
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 34566677889999999999999999999999943
No 56
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=54.43 E-value=23 Score=36.60 Aligned_cols=26 Identities=35% Similarity=0.657 Sum_probs=18.3
Q ss_pred cchh---hhhHHHHHhhhhhhhhHHHHHh
Q 019530 210 EVWF---QNRRARTKLKQTEVDCEYLKRC 235 (339)
Q Consensus 210 qvWF---QNRRaK~Krkq~~~~~e~Lk~~ 235 (339)
-+|| ||+.+|.+-++..++.+.|++.
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~a 257 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRA 257 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4687 8988888776666666665544
No 57
>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=53.63 E-value=53 Score=24.29 Aligned_cols=27 Identities=37% Similarity=0.465 Sum_probs=12.5
Q ss_pred hhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 228 DCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 228 ~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
....|...+..|..++..|..++..|.
T Consensus 34 ~~~~L~~en~~L~~~~~~L~~~~~~L~ 60 (64)
T PF00170_consen 34 KVEELESENEELKKELEQLKKEIQSLK 60 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444443
No 58
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=53.52 E-value=25 Score=30.88 Aligned_cols=49 Identities=16% Similarity=0.081 Sum_probs=37.1
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
...++..|..+|...+ .. . ...++|..||++...|+.|-++.+.+.|+.
T Consensus 4 ~~~Lt~rqreVL~lr~-~G--l---Tq~EIAe~LGiS~~tVs~ie~ra~kkLr~~ 52 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-RG--L---TQQEIADILGTSRANVSSIEKRARENIEKA 52 (141)
T ss_pred ccCCCHHHHHHHHHHH-cC--C---CHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4578999999998732 21 2 245799999999999999998777666643
No 59
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=52.81 E-value=27 Score=33.48 Aligned_cols=8 Identities=50% Similarity=0.626 Sum_probs=3.7
Q ss_pred hhhHHHHH
Q 019530 214 QNRRARTK 221 (339)
Q Consensus 214 QNRRaK~K 221 (339)
||-|-|.|
T Consensus 82 QtaRDrKK 89 (292)
T KOG4005|consen 82 QTARDRKK 89 (292)
T ss_pred hhhhhHHH
Confidence 44444444
No 60
>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=52.74 E-value=50 Score=23.71 Aligned_cols=28 Identities=32% Similarity=0.448 Sum_probs=21.4
Q ss_pred hhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 227 VDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 227 ~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
.....|......|..+|..|+.++..|+
T Consensus 25 ~~~~~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 25 QREEELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445567778888899999988888775
No 61
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=50.76 E-value=59 Score=29.75 Aligned_cols=50 Identities=24% Similarity=0.270 Sum_probs=41.4
Q ss_pred CcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 205 RPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 205 s~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
..-...+|-+-|..+.|..+.+.+.+.|....+.|..+.+++++++.+|.
T Consensus 84 g~lv~Ey~R~~~~e~~kee~~~~e~~elr~~~~~l~~~i~~~~~~~~~L~ 133 (181)
T KOG3335|consen 84 GVLVFEYWRQARKERKKEEKRKQEIMELRLKVEKLENAIAELTKFFSQLH 133 (181)
T ss_pred eeeeehhHHhhhcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455788887777778778888888899999999999999999999996
No 62
>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=50.44 E-value=72 Score=27.09 Aligned_cols=71 Identities=10% Similarity=0.067 Sum_probs=39.9
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+..++..|. .....+.+|++-.+|+.+|......... ...-.+.|+...+.+.++..+|+.
T Consensus 36 yR~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~~~l~~~~~~l~~~i~~l~~ 100 (133)
T cd04787 36 YRLYSEKDLSRLR-------------FILSARQLGFSLKDIKEILSHADQGESP--CPMVRRLIEQRLAETERRIKELLK 100 (133)
T ss_pred eeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhhhccCCCc--HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3478999998883 3345778899999999988754321100 011123344444445555444444
Q ss_pred HHHHHH
Q 019530 249 ELQELR 254 (339)
Q Consensus 249 e~~~lr 254 (339)
-...+.
T Consensus 101 ~~~~l~ 106 (133)
T cd04787 101 LRDRMQ 106 (133)
T ss_pred HHHHHH
Confidence 444343
No 63
>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=49.20 E-value=26 Score=24.59 Aligned_cols=42 Identities=14% Similarity=0.180 Sum_probs=27.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRA 218 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRa 218 (339)
++..+..++...|-. ...-.++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~~-----g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYFQ-----GMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHTS--------HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHHH-----CcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 556666666655443 335678999999999999999975443
No 64
>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=48.25 E-value=93 Score=27.95 Aligned_cols=66 Identities=24% Similarity=0.189 Sum_probs=45.1
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhh
Q 019530 168 KKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCE 237 (339)
Q Consensus 168 kRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~ 237 (339)
++..++.+++.++.+.-..+ |....+..||+++|++..-|.+-..--. .+++..+...+..+...+
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~--e~~~~~~~~le~~k~rWg 147 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK--EKKKEMEARLEAIKSRWG 147 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH--HHHHHHHHHHHHHHHhcc
Confidence 34689999999998876554 5567788999999999887776654333 333444444555555444
No 65
>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=47.65 E-value=22 Score=26.76 Aligned_cols=44 Identities=27% Similarity=0.365 Sum_probs=22.1
Q ss_pred CccCCHHH-HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhh
Q 019530 169 KLRLSKEQ-SAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQ 214 (339)
Q Consensus 169 Rtrft~~Q-l~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQ 214 (339)
|..|+... |.+++..+. +..--..+| ..|.++|+.+++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~-~~nc~~~~R-Aaarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEK-DNNCKGNQR-AAARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HH-HHHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHH-ccchhhhHH-HHHHHhCccHHHHHHHHH
Confidence 34455433 445544443 332222233 359999999999999975
No 66
>PF00170 bZIP_1: bZIP transcription factor cAMP response element binding (CREB) protein signature fos transforming protein signature jun transcription factor signature; InterPro: IPR011616 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotic are proteins that contain a basic region mediating sequence-specific DNA-binding followed by a leucine zipper region (see IPR002158 from INTERPRO) required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 2H7H_B 2OQQ_B 1S9K_E 1JNM_A 1JUN_A 1FOS_H 1A02_J 1T2K_C 1CI6_A 1DH3_C ....
Probab=47.63 E-value=75 Score=23.46 Aligned_cols=31 Identities=35% Similarity=0.446 Sum_probs=24.8
Q ss_pred hhhhhHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 019530 225 TEVDCEYLKRCCETLTEENRRLQKELQELRA 255 (339)
Q Consensus 225 ~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lra 255 (339)
.....+.|...+..|..+|..|..++..|..
T Consensus 24 Kk~~~~~Le~~~~~L~~en~~L~~~~~~L~~ 54 (64)
T PF00170_consen 24 KKQYIEELEEKVEELESENEELKKELEQLKK 54 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3345567788889999999999999988873
No 67
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=47.58 E-value=1.2e+02 Score=24.68 Aligned_cols=46 Identities=11% Similarity=0.124 Sum_probs=34.4
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCC-CcccccchhhhhHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNL-RPRQVEVWFQNRRA 218 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgL-s~rQVqvWFQNRRa 218 (339)
|.+|+.+....+-+.+....+ ...++|+++|+ ...++..|-+.-+.
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~~~~~ 51 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRIQLQK 51 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHHHHHH
Confidence 678998887777666665554 46789999996 99999988654433
No 68
>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=46.12 E-value=1.3e+02 Score=24.91 Aligned_cols=69 Identities=17% Similarity=0.211 Sum_probs=42.8
Q ss_pred CCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHH
Q 019530 168 KKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQ 247 (339)
Q Consensus 168 kRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~ 247 (339)
.+..|+..++..|+. ....+.+|++-.+|+.++.+.... ....+.+....+.+.++.++|+
T Consensus 34 gyR~Y~~~~l~~l~~-------------I~~lr~~G~~L~eI~~~l~~~~~~------~~~~~~l~~~~~~l~~~i~~l~ 94 (120)
T cd04781 34 LRRQYDPQVLDRLAL-------------IALGRAAGFSLDEIQAMLSHDGKP------PIDRQLLKAKAAELDQQIQRLQ 94 (120)
T ss_pred CceecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccCCc------HHHHHHHHHHHHHHHHHHHHHH
Confidence 355789999988843 356788899999999888764311 1112344445555555555565
Q ss_pred HHHHHHHH
Q 019530 248 KELQELRA 255 (339)
Q Consensus 248 ~e~~~lra 255 (339)
.-...|..
T Consensus 95 ~~~~~L~~ 102 (120)
T cd04781 95 AMRELLRH 102 (120)
T ss_pred HHHHHHHH
Confidence 55555553
No 69
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=44.20 E-value=8.3 Score=41.27 Aligned_cols=45 Identities=13% Similarity=0.155 Sum_probs=29.4
Q ss_pred HHHHhhcCCCCHHHHHHHHHHcC-------CCcccccchhhhhHHHHHhhhh
Q 019530 181 EESFKEHNTLNPKQKLALAKQLN-------LRPRQVEVWFQNRRARTKLKQT 225 (339)
Q Consensus 181 E~~F~~~~~ps~~~r~~LA~~Lg-------Ls~rQVqvWFQNRRaK~Krkq~ 225 (339)
+.+|.++..+......+--.++. ...+.|+.||.|||.++|+-+.
T Consensus 708 ~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 708 HHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred hhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 44566666666555544433333 3457799999999999987543
No 70
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=44.18 E-value=53 Score=32.24 Aligned_cols=31 Identities=26% Similarity=0.293 Sum_probs=24.3
Q ss_pred hhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 224 QTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 224 q~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
+++.+.|.|.-+++.|..+|++|+.++.++-
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~le 275 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELE 275 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445667788899999999999999887554
No 71
>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=43.72 E-value=1.3e+02 Score=24.10 Aligned_cols=64 Identities=20% Similarity=0.267 Sum_probs=38.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
+..|+..++..|.... ..+.+|++..+|+.++.... ....+.++.....|.++..+|+.
T Consensus 36 ~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~--------~~~~~~l~~~~~~l~~~i~~l~~ 94 (103)
T cd01106 36 YRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS--------EDLLEALREQKELLEEKKERLDK 94 (103)
T ss_pred ceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc--------HHHHHHHHHHHHHHHHHHHHHHH
Confidence 4469999999986653 24567888888888886543 22233344444455555555554
Q ss_pred HHHHH
Q 019530 249 ELQEL 253 (339)
Q Consensus 249 e~~~l 253 (339)
.++.|
T Consensus 95 ~~~~l 99 (103)
T cd01106 95 LIKTI 99 (103)
T ss_pred HHHHH
Confidence 44443
No 72
>smart00338 BRLZ basic region leucin zipper.
Probab=43.57 E-value=86 Score=23.18 Aligned_cols=25 Identities=52% Similarity=0.719 Sum_probs=13.2
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 230 EYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 230 e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
..|...+..|..+|..|..++..|+
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~ 53 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLR 53 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555555555555555444
No 73
>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=43.23 E-value=10 Score=28.56 Aligned_cols=19 Identities=16% Similarity=0.377 Sum_probs=16.7
Q ss_pred HHHHHHHcCCCcccccchh
Q 019530 195 KLALAKQLNLRPRQVEVWF 213 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWF 213 (339)
-.+||.+||+++.+|+.|=
T Consensus 25 lkdIA~~Lgvs~~tIr~WK 43 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKWK 43 (60)
T ss_pred HHHHHHHHCCCHHHHHHHh
Confidence 3568999999999999994
No 74
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=42.68 E-value=29 Score=31.75 Aligned_cols=49 Identities=24% Similarity=0.188 Sum_probs=37.3
Q ss_pred cCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNT--LNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~--ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.+|..|+++|...|+..-| |-.....+||++||+++.- +|..=||+..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 6999999999999998644 6566668999999999854 34444555544
No 75
>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=42.42 E-value=30 Score=24.83 Aligned_cols=46 Identities=11% Similarity=0.135 Sum_probs=34.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.||..++.+|.-...-. ...++|..++++++.|+.+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G~------~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQGM------SNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTTS-------HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhcC------CcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 57888888887765432 35689999999999999998877766553
No 76
>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=42.09 E-value=70 Score=25.21 Aligned_cols=20 Identities=10% Similarity=0.222 Sum_probs=16.4
Q ss_pred HHHHHHHcCCCcccccchhh
Q 019530 195 KLALAKQLNLRPRQVEVWFQ 214 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWFQ 214 (339)
..++|+.+|++++.|+.|-+
T Consensus 4 i~e~A~~~gvs~~tLr~ye~ 23 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYER 23 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 34688999999999999964
No 77
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=41.70 E-value=59 Score=27.42 Aligned_cols=33 Identities=30% Similarity=0.238 Sum_probs=27.9
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQELRA 255 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lra 255 (339)
...-.+...||.....+.+||..|+-|++.||.
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~ 50 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRE 50 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445567788999999999999999999999994
No 78
>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=40.31 E-value=75 Score=24.46 Aligned_cols=31 Identities=32% Similarity=0.321 Sum_probs=20.2
Q ss_pred hhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 224 QTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 224 q~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
+...+...++...+.+..||.+|+.|+..+.
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHc
Confidence 3444555566666777777777777776654
No 79
>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=39.46 E-value=62 Score=24.42 Aligned_cols=31 Identities=29% Similarity=0.320 Sum_probs=27.5
Q ss_pred hhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 226 EVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 226 ~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
+++.+.||.....|.+.|..|+.|+.-||..
T Consensus 13 rEEVevLK~~I~eL~~~n~~Le~EN~~Lk~~ 43 (59)
T PF01166_consen 13 REEVEVLKEQIAELEERNSQLEEENNLLKQN 43 (59)
T ss_dssp TTSHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4577889999999999999999999999965
No 80
>smart00338 BRLZ basic region leucin zipper.
Probab=37.79 E-value=1.2e+02 Score=22.35 Aligned_cols=34 Identities=32% Similarity=0.430 Sum_probs=27.3
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
...+.....|...+..|..+...|..++..|+..
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 29 EELERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4456667788888899999999999999888743
No 81
>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=37.10 E-value=45 Score=27.29 Aligned_cols=37 Identities=19% Similarity=0.307 Sum_probs=20.8
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh
Q 019530 177 SAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV 227 (339)
Q Consensus 177 l~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~ 227 (339)
+.+.+-.|+.++||...--.. | =.|||.+|++++.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~QI 50 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQRQI 50 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHHHH
Confidence 455666688999997431111 0 158999999877654
No 82
>PHA02955 hypothetical protein; Provisional
Probab=36.59 E-value=41 Score=31.59 Aligned_cols=42 Identities=12% Similarity=0.180 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHcCCCcccccchhhh
Q 019530 174 KEQSAFLEESFKEH-NTLNPKQKLALAKQLNLRPRQVEVWFQN 215 (339)
Q Consensus 174 ~~Ql~~LE~~F~~~-~~ps~~~r~~LA~~LgLs~rQVqvWFQN 215 (339)
..|+..|-+.|.+. ..+.+++|.+++++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 45677777777766 7799999999999999999888999976
No 83
>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=36.24 E-value=88 Score=23.43 Aligned_cols=30 Identities=30% Similarity=0.446 Sum_probs=22.8
Q ss_pred hhhhhhHHHHHhhhhhHHHHHHHHHHHHHH
Q 019530 224 QTEVDCEYLKRCCETLTEENRRLQKELQEL 253 (339)
Q Consensus 224 q~~~~~e~Lk~~~~~l~eEn~~l~~e~~~l 253 (339)
+...+...++...+.+..+|+.|+.+++.+
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 344556677788888888888888888877
No 84
>PRK04217 hypothetical protein; Provisional
Probab=35.52 E-value=62 Score=27.22 Aligned_cols=46 Identities=13% Similarity=0.005 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++.+|..++...|...- ...+||+.+|++...|+..+..-|.+.|
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 577888888877764433 4567999999999999988875444443
No 85
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.15 E-value=51 Score=22.27 Aligned_cols=41 Identities=15% Similarity=0.201 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
.++..+..++...+.. + ...++|..++++...|..|.+.-+
T Consensus 3 ~l~~~e~~i~~~~~~g--~----s~~eia~~l~is~~tv~~~~~~~~ 43 (58)
T smart00421 3 SLTPREREVLRLLAEG--L----TNKEIAERLGISEKTVKTHLSNIM 43 (58)
T ss_pred CCCHHHHHHHHHHHcC--C----CHHHHHHHHCCCHHHHHHHHHHHH
Confidence 3677777777654321 1 346799999999999998887443
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=35.10 E-value=1.8e+02 Score=23.75 Aligned_cols=70 Identities=20% Similarity=0.251 Sum_probs=41.6
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHH
Q 019530 170 LRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKE 249 (339)
Q Consensus 170 trft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e 249 (339)
..|+.+++..|.. ....+.+|++-.+|+..+........ ......+.|......+.++...|+..
T Consensus 37 R~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~~ 101 (113)
T cd01109 37 RDFTEEDLEWLEF-------------IKCLRNTGMSIKDIKEYAELRREGDS--TIPERLELLEEHREELEEQIAELQET 101 (113)
T ss_pred ccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHHHccCCc--cHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4689999888844 34467789999999988876442211 01122344555555555555555555
Q ss_pred HHHHH
Q 019530 250 LQELR 254 (339)
Q Consensus 250 ~~~lr 254 (339)
+..+.
T Consensus 102 ~~~l~ 106 (113)
T cd01109 102 LAYLD 106 (113)
T ss_pred HHHHH
Confidence 44444
No 87
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=34.88 E-value=55 Score=27.41 Aligned_cols=46 Identities=15% Similarity=0.140 Sum_probs=32.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..++...|-.. ....++|..+|++...|+.|...-|.+.|
T Consensus 106 ~L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 106 VLDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 46677777776655433 23568999999999999999875554444
No 88
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=34.13 E-value=57 Score=28.91 Aligned_cols=46 Identities=13% Similarity=0.133 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|...|-.. ..-.++|+.||++...|++|...-|.+.|
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 46677777776554332 23457999999999999999865555544
No 89
>TIGR02937 sigma70-ECF RNA polymerase sigma factor, sigma-70 family. Several PFAM models hit segments of these sequences including Sigma-70 region 2 (pfam04542) and Sigma-70, region 4 (pfam04545), but not always above their respective trusted cutoffs.
Probab=33.46 E-value=56 Score=26.30 Aligned_cols=46 Identities=15% Similarity=0.218 Sum_probs=31.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..++...|-.. ....+||..+|+++..|..|...-+.|.|
T Consensus 110 ~L~~~~~~ii~~~~~~g-----~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 110 KLPEREREVLVLRYLEG-----LSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred hCCHHHHHHHhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666665554321 23458999999999999999876555544
No 90
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.35 E-value=36 Score=27.86 Aligned_cols=42 Identities=19% Similarity=0.143 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRAR 219 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK 219 (339)
+.+...+..|..... .+ ..+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~g----lT---Q~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTG----LK---IDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcC----CC---HHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 446666777654322 22 5679999999999999999987643
No 91
>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=32.91 E-value=2.6e+02 Score=23.05 Aligned_cols=72 Identities=14% Similarity=0.038 Sum_probs=42.0
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+.+++..|+. ....+.+|++-..|+..|.+...... ....-.+.|....+.+.++.++|+.
T Consensus 36 yR~Y~~~~i~~l~~-------------I~~lr~~G~sl~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~l~~ 100 (123)
T cd04770 36 YRLYGEADLARLRF-------------IRRAQALGFSLAEIRELLSLRDDGAA--PCAEVRALLEEKLAEVEAKIAELQA 100 (123)
T ss_pred CccCCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHHhhhcCCC--CHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45689999998843 34568889988888888876543210 0111123344444555555555555
Q ss_pred HHHHHHH
Q 019530 249 ELQELRA 255 (339)
Q Consensus 249 e~~~lra 255 (339)
-...|..
T Consensus 101 ~~~~l~~ 107 (123)
T cd04770 101 LRAELAG 107 (123)
T ss_pred HHHHHHH
Confidence 5444443
No 92
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=32.77 E-value=61 Score=29.17 Aligned_cols=47 Identities=21% Similarity=0.272 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.++..+..+|...|-.. ....+||..+|++...|+++..+-|.+.|+
T Consensus 153 ~L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 153 KLPEAQQTVVKGVYFQE-----LSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35666666666543222 234689999999999999888655555543
No 93
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=32.52 E-value=68 Score=27.17 Aligned_cols=46 Identities=17% Similarity=0.174 Sum_probs=31.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
++..+..++...|-... .-.++|..+|+++..|++++..-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55666666655443222 23579999999999999998765555553
No 94
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=32.50 E-value=58 Score=27.75 Aligned_cols=46 Identities=13% Similarity=0.004 Sum_probs=32.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|...|-... .-.++|..+|++...|+.|...-+.+.|
T Consensus 128 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 128 SLPEELRTAITLREIEGL-----SYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 477888888877654221 2357999999999999999885444444
No 95
>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=32.45 E-value=1.5e+02 Score=22.96 Aligned_cols=28 Identities=36% Similarity=0.483 Sum_probs=11.5
Q ss_pred hhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 227 VDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 227 ~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
.+++.|+..+..|.++|..|+.+++.++
T Consensus 25 ~e~eeLke~n~~L~~e~~~L~~en~~L~ 52 (72)
T PF06005_consen 25 MENEELKEKNNELKEENEELKEENEQLK 52 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHH
Confidence 3344444443334444444444444333
No 96
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=31.11 E-value=74 Score=27.00 Aligned_cols=46 Identities=15% Similarity=0.128 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|...|-.. ..-.+||..+|++...|+.|...-|.+.|
T Consensus 125 ~L~~~~r~i~~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 125 ALPVKQREVFLLRYVEG-----LSYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred hCCHHHHHHhhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666665554332 22468999999999999999976555555
No 97
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=30.95 E-value=94 Score=25.72 Aligned_cols=39 Identities=15% Similarity=0.101 Sum_probs=31.3
Q ss_pred cchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 210 EVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 210 qvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
.-|+..+..+.+....+++++.++..+..|..|.++|+.
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 456677777777778888888888888999888888875
No 98
>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=30.79 E-value=47 Score=24.25 Aligned_cols=35 Identities=31% Similarity=0.352 Sum_probs=26.3
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchh
Q 019530 175 EQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWF 213 (339)
Q Consensus 175 ~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWF 213 (339)
.|+..|+-.|. +...+.. +||..+|++++.|+.-.
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~i 40 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKNDI 40 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHHH
Confidence 57888888888 6766655 79999999998765443
No 99
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=30.51 E-value=74 Score=31.18 Aligned_cols=39 Identities=31% Similarity=0.371 Sum_probs=35.0
Q ss_pred HhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 184 FKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 184 F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
-+.+.|++...+..|+....|+-.||.+||-|.|.+.+.
T Consensus 116 ~~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 116 HRLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 356899999999999999999999999999999988775
No 100
>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=30.40 E-value=24 Score=23.92 Aligned_cols=23 Identities=17% Similarity=0.095 Sum_probs=19.2
Q ss_pred HHHHHHHcCCCcccccchhhhhH
Q 019530 195 KLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976554
No 101
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.34 E-value=45 Score=27.26 Aligned_cols=40 Identities=23% Similarity=0.272 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCccccc
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVE 210 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVq 210 (339)
.+.++|++.-...|+.+.-++.-..+++|.+||+++.-|+
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~~le 41 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEVKLE 41 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHHHHH
Confidence 4678888888888888888888888999999999875543
No 102
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=29.74 E-value=38 Score=23.34 Aligned_cols=40 Identities=18% Similarity=0.165 Sum_probs=20.2
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhh
Q 019530 170 LRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQ 214 (339)
Q Consensus 170 trft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQ 214 (339)
..||.+|...++..++.. ....+||+.||.+..-|..|.+
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 467888888888887643 2345799999999888877664
No 103
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=29.53 E-value=48 Score=28.77 Aligned_cols=45 Identities=16% Similarity=0.330 Sum_probs=30.8
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..+..++...|-.. ....+||..+|+++..|+++...-|.+.|
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 5556666555554222 22568999999999999999875555554
No 104
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=29.34 E-value=1e+02 Score=29.29 Aligned_cols=35 Identities=26% Similarity=0.195 Sum_probs=23.5
Q ss_pred hhhhhhhHHHHHhhhhhHHHHH---HHHHHHHHHHHhh
Q 019530 223 KQTEVDCEYLKRCCETLTEENR---RLQKELQELRALK 257 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~---~l~~e~~~lralk 257 (339)
.+..++++.|+++...|..++. .+++|+++||.+.
T Consensus 72 ~~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL 109 (276)
T PRK13922 72 FDLREENEELKKELLELESRLQELEQLEAENARLRELL 109 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4556677777777777666555 5677777777553
No 105
>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=29.11 E-value=1.4e+02 Score=28.90 Aligned_cols=35 Identities=20% Similarity=0.202 Sum_probs=21.5
Q ss_pred hhhhhhhHHHHHhhhhhHHH----HHHHHHHHHHHHHhh
Q 019530 223 KQTEVDCEYLKRCCETLTEE----NRRLQKELQELRALK 257 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eE----n~~l~~e~~~lralk 257 (339)
.+..++++.|+++...+.++ .+.+++|+++||.|-
T Consensus 69 ~~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL 107 (283)
T TIGR00219 69 NNLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELL 107 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 34667777777776554222 233777888888653
No 106
>PF05703 Auxin_canalis: Auxin canalisation; InterPro: IPR008546 This domain consists of several plant proteins of unknown function.
Probab=29.00 E-value=99 Score=29.63 Aligned_cols=17 Identities=18% Similarity=0.661 Sum_probs=13.1
Q ss_pred CcccccchhhhhHHHHH
Q 019530 205 RPRQVEVWFQNRRARTK 221 (339)
Q Consensus 205 s~rQVqvWFQNRRaK~K 221 (339)
....|..||+.|+.|.|
T Consensus 99 ~~~~i~~w~~~~~~kkk 115 (242)
T PF05703_consen 99 GGKTIGRWLKDRKEKKK 115 (242)
T ss_pred ccchHHHHHHHHHHHHH
Confidence 46779999998888544
No 107
>PRK00118 putative DNA-binding protein; Validated
Probab=28.78 E-value=3e+02 Score=22.88 Aligned_cols=46 Identities=13% Similarity=0.159 Sum_probs=31.6
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
++..|..++...|.... ...+||..+|++...|..|...-|.+.|.
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr~ 63 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLED 63 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45666666655554432 24579999999999999999755555443
No 108
>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=28.58 E-value=2.6e+02 Score=24.03 Aligned_cols=36 Identities=8% Similarity=-0.053 Sum_probs=23.4
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
+..|+..++..|... ...+.+|++-..|+.++.+..
T Consensus 35 ~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 35 YRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhc
Confidence 456899998888554 223566666666666665544
No 109
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=28.11 E-value=88 Score=26.72 Aligned_cols=47 Identities=15% Similarity=0.020 Sum_probs=31.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.++..+..++...|-.. ....+||..+|++...|++|.+.-|.+.|+
T Consensus 108 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 108 TLPVIEAQAILLCDVHE-----LTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred hCCHHHHHHHHhHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35566666665433221 234689999999999999999765555553
No 110
>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=28.00 E-value=16 Score=28.61 Aligned_cols=33 Identities=12% Similarity=0.071 Sum_probs=23.9
Q ss_pred HHhhcCCCCHHHHHHHHHHcCCCcccccchhhh
Q 019530 183 SFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQN 215 (339)
Q Consensus 183 ~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQN 215 (339)
.|....|.......+||..+|+++..|+.|+.+
T Consensus 23 af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 23 AAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 344443333445678999999999999999864
No 111
>PF15058 Speriolin_N: Speriolin N terminus
Probab=27.80 E-value=74 Score=29.53 Aligned_cols=8 Identities=38% Similarity=0.426 Sum_probs=3.5
Q ss_pred hhHHHHHh
Q 019530 228 DCEYLKRC 235 (339)
Q Consensus 228 ~~e~Lk~~ 235 (339)
+|+.||+.
T Consensus 20 ENeeLKKl 27 (200)
T PF15058_consen 20 ENEELKKL 27 (200)
T ss_pred hhHHHHHH
Confidence 34444444
No 112
>cd04783 HTH_MerR1 Helix-Turn-Helix DNA binding domain of the MerR1 transcription regulator. Helix-turn-helix (HTH) transcription regulator MerR1. MerR1 transcription regulators, such as Tn21 MerR and Tn501 MerR, mediate response to mercury exposure in eubacteria. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines that define a mercury binding site. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=27.56 E-value=3e+02 Score=22.88 Aligned_cols=69 Identities=14% Similarity=0.121 Sum_probs=40.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+.+++..|. .....+.+|++-..|+.+|....... ...-.+.++...+.+.++..+|++
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~~----~~~~~~~l~~~~~~l~~~i~~L~~ 98 (126)
T cd04783 36 YRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDDGTD----CSEARELAEQKLAEVDEKIADLQR 98 (126)
T ss_pred CeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcccCCC----HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4568999998884 34557889999999999887654210 011122333444444555555554
Q ss_pred HHHHHH
Q 019530 249 ELQELR 254 (339)
Q Consensus 249 e~~~lr 254 (339)
-...|.
T Consensus 99 ~~~~l~ 104 (126)
T cd04783 99 MRASLQ 104 (126)
T ss_pred HHHHHH
Confidence 444444
No 113
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=27.08 E-value=87 Score=27.24 Aligned_cols=47 Identities=17% Similarity=0.090 Sum_probs=33.8
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.++..+..+|...|-... .-.+||..||++...|+.++..-|.+.|+
T Consensus 131 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 131 TLPPRQRDVVQSISVEGA-----SIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 466677777766644322 34579999999999999999866666553
No 114
>PF13518 HTH_28: Helix-turn-helix domain
Probab=26.88 E-value=40 Score=23.06 Aligned_cols=21 Identities=14% Similarity=0.403 Sum_probs=18.3
Q ss_pred HHHHHHHcCCCcccccchhhh
Q 019530 195 KLALAKQLNLRPRQVEVWFQN 215 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWFQN 215 (339)
..++|.++|++..+|..|.+.
T Consensus 15 ~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 15 VREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred HHHHHHHHCCCHhHHHHHHHH
Confidence 456999999999999999864
No 115
>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=26.42 E-value=3.3e+02 Score=21.87 Aligned_cols=64 Identities=19% Similarity=0.145 Sum_probs=39.1
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+..++..|... ...+++|++-..|+..+.... ..+.+....+.+.++.++|+.
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 457899999888543 234677888888777765432 123344455555666666665
Q ss_pred HHHHHHH
Q 019530 249 ELQELRA 255 (339)
Q Consensus 249 e~~~lra 255 (339)
....|..
T Consensus 93 ~~~~l~~ 99 (102)
T cd04775 93 QQQVLAA 99 (102)
T ss_pred HHHHHHH
Confidence 5555543
No 116
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=26.38 E-value=1.2e+02 Score=25.57 Aligned_cols=45 Identities=11% Similarity=0.236 Sum_probs=32.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|.-.| . .+ .-.+||..+|++...|+.+...-|.+.|
T Consensus 112 ~L~~~~r~il~l~~-~-g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr 156 (166)
T PRK09639 112 KMTERDRTVLLLRF-S-GY----SYKEIAEALGIKESSVGTTLARAKKKFR 156 (166)
T ss_pred cCCHHHHHHHHHHH-c-CC----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46777777777766 3 22 3457999999999999999865555544
No 117
>PRK10403 transcriptional regulator NarP; Provisional
Probab=26.21 E-value=53 Score=27.96 Aligned_cols=47 Identities=19% Similarity=0.256 Sum_probs=36.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
.+|..+..+|+..... ..+.+||+.++++++.|+++.+|=|.|-..+
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~~ 199 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNVR 199 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCCC
Confidence 5889999988865543 3356889999999999999998877776543
No 118
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=26.21 E-value=1.3e+02 Score=23.41 Aligned_cols=43 Identities=26% Similarity=0.311 Sum_probs=21.9
Q ss_pred ccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 209 VEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 209 VqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
++|.|-..|... ......+.+-.++..|..+...|++++++++
T Consensus 21 LrI~fLee~l~~---~~~~~~~~~~keNieLKve~~~L~~el~~~~ 63 (75)
T PF07989_consen 21 LRIYFLEERLQK---LGPESIEELLKENIELKVEVESLKRELQEKK 63 (75)
T ss_pred HHHHHHHHHHHh---cccccHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467776666552 1222333333444445556666666655555
No 119
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.18 E-value=72 Score=28.01 Aligned_cols=45 Identities=20% Similarity=0.240 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..+..+|...|-. .....++|..+|++...|+.|+..-|.+.|
T Consensus 142 L~~~~~~v~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 186 (194)
T PRK12519 142 LPESQRQVLELAYYE-----GLSQSEIAKRLGIPLGTVKARARQGLLKLR 186 (194)
T ss_pred CCHHHhhhhhhhhhc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 555566666554422 223467999999999999999975555544
No 120
>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=26.11 E-value=1.7e+02 Score=22.42 Aligned_cols=23 Identities=35% Similarity=0.359 Sum_probs=10.1
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHH
Q 019530 230 EYLKRCCETLTEENRRLQKELQE 252 (339)
Q Consensus 230 e~Lk~~~~~l~eEn~~l~~e~~~ 252 (339)
+.|-..|+.|..||..|+.++..
T Consensus 10 e~Li~~~~~L~~EN~~Lr~q~~~ 32 (65)
T TIGR02449 10 EHLLEYLERLKSENRLLRAQEKT 32 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444444444444433
No 121
>cd06170 LuxR_C_like C-terminal DNA-binding domain of LuxR-like proteins. This domain contains a helix-turn-helix motif and binds DNA. Proteins belonging to this group are response regulators; some act as transcriptional activators, others as transcriptional repressors. Many are active as homodimers. Many are two domain proteins in which the DNA binding property of the C-terminal DNA binding domain is modulated by modifications of the N-terminal domain. For example in the case of Lux R which participates in the regulation of gene expression in response to fluctuations in cell-population density (quorum-sensing), a signaling molecule, the pheromone Acyl HSL (N-acyl derivatives of homoserine lactone), binds to the N-terminal domain and leads to LuxR dimerization. For others phophorylation of the N-terminal domain leads to multimerization, for example Escherichia coli NarL and Sinorhizobium melilot FixJ. NarL controls gene expression of many respiratory-related operons when environmental
Probab=26.08 E-value=87 Score=21.22 Aligned_cols=36 Identities=14% Similarity=0.223 Sum_probs=24.9
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhh
Q 019530 173 SKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQ 214 (339)
Q Consensus 173 t~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQ 214 (339)
+..|..++...+. . ....++|+.++++...|+.|..
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 4455666654332 1 2456789999999999999886
No 122
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.92 E-value=1.1e+02 Score=26.93 Aligned_cols=47 Identities=9% Similarity=0.143 Sum_probs=32.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.++..+..+|...|-..- .-.++|..+|+++..|++.+..-|.+.|+
T Consensus 131 ~L~~~~r~vl~l~~~~~~-----s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 131 KLSPAHREIIDLVYYHEK-----SVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 467777777766543221 24579999999999999988765555553
No 123
>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=25.67 E-value=3.2e+02 Score=22.77 Aligned_cols=36 Identities=14% Similarity=0.075 Sum_probs=26.7
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRR 217 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRR 217 (339)
...|+..++..|+ ....++.+|++...|+.+|....
T Consensus 35 ~R~Y~~~~l~~l~-------------~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 35 YRRYPEETVKRLR-------------FIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred CEeECHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHhccc
Confidence 4568898888883 33457888999999988886543
No 124
>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=25.54 E-value=1.4e+02 Score=27.76 Aligned_cols=34 Identities=32% Similarity=0.331 Sum_probs=0.0
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
+.....+...-.++..|++.|++|+.++++||.+
T Consensus 44 ~evNrrlQ~hl~EIR~LKe~NqkLqedNqELRdL 77 (195)
T PF10226_consen 44 KEVNRRLQQHLNEIRGLKEVNQKLQEDNQELRDL 77 (195)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 125
>PRK15369 two component system sensor kinase SsrB; Provisional
Probab=25.47 E-value=1.3e+02 Score=25.16 Aligned_cols=45 Identities=20% Similarity=0.204 Sum_probs=34.6
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.+|..+..+|+- +..+ + ...++|+.++++++.|+.|.+|=|.|..
T Consensus 149 ~lt~~e~~vl~l-~~~g-~----~~~~Ia~~l~~s~~tv~~~~~~~~~kl~ 193 (211)
T PRK15369 149 LLTPRERQILKL-ITEG-Y----TNRDIAEQLSISIKTVETHRLNMMRKLD 193 (211)
T ss_pred CCCHHHHHHHHH-HHCC-C----CHHHHHHHhCCCHHHHHHHHHHHHHHhC
Confidence 488888888876 4333 2 2568899999999999999988666654
No 126
>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=25.43 E-value=97 Score=25.66 Aligned_cols=45 Identities=18% Similarity=0.155 Sum_probs=29.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..+..+|...|-.. ....++|..+|+++..|+.+...-|.|.|
T Consensus 114 L~~~~r~il~l~~~~~-----~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFEG-----KSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 4556666666544321 12457999999999999998875555544
No 127
>PF15136 UPF0449: Uncharacterised protein family UPF0449
Probab=25.40 E-value=1.4e+02 Score=24.66 Aligned_cols=29 Identities=21% Similarity=0.518 Sum_probs=20.1
Q ss_pred hhhhhhHHHHHhhhhhHHHHHHHHHHHHH
Q 019530 224 QTEVDCEYLKRCCETLTEENRRLQKELQE 252 (339)
Q Consensus 224 q~~~~~e~Lk~~~~~l~eEn~~l~~e~~~ 252 (339)
+.++-+..|++.|+.|..-.+.|++++.+
T Consensus 68 rLqqa~~~Lkkk~e~L~~age~Le~~i~~ 96 (97)
T PF15136_consen 68 RLQQARDQLKKKCEELRQAGEELERDIEQ 96 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34444566777788888888888877654
No 128
>PRK10884 SH3 domain-containing protein; Provisional
Probab=25.25 E-value=3.4e+02 Score=25.23 Aligned_cols=11 Identities=27% Similarity=0.250 Sum_probs=5.3
Q ss_pred HHHHHHHHHHh
Q 019530 175 EQSAFLEESFK 185 (339)
Q Consensus 175 ~Ql~~LE~~F~ 185 (339)
.++..|++...
T Consensus 93 ~rlp~le~el~ 103 (206)
T PRK10884 93 TRVPDLENQVK 103 (206)
T ss_pred HHHHHHHHHHH
Confidence 44555554443
No 129
>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=24.67 E-value=2e+02 Score=20.55 Aligned_cols=25 Identities=28% Similarity=0.349 Sum_probs=14.9
Q ss_pred hhhhhHHHHHhhhhhHHHHHHHHHH
Q 019530 225 TEVDCEYLKRCCETLTEENRRLQKE 249 (339)
Q Consensus 225 ~~~~~e~Lk~~~~~l~eEn~~l~~e 249 (339)
.+.....|...+..|..++..|+.|
T Consensus 30 le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 30 LEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 3444455666666666666666553
No 130
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=24.49 E-value=29 Score=38.23 Aligned_cols=58 Identities=17% Similarity=0.295 Sum_probs=46.4
Q ss_pred CCCccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhh
Q 019530 167 RKKLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQ 224 (339)
Q Consensus 167 RkRtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq 224 (339)
|-++.+..++-..|...|..+..++..+-..++.+|...+..|+|||++|+..-+...
T Consensus 628 kv~sp~k~~dq~ql~~a~elq~s~~n~~~pl~~t~~~n~~pv~ev~dhsrsstpsp~p 685 (1007)
T KOG3623|consen 628 KVRSPIKEEDQQQLKQAYELQASPSNDEFPLIATRLQNDPPVVEVWDHSRSSTPSPMP 685 (1007)
T ss_pred cccCCCCccchhhhHhhhhcccCccCcccchhhhhccCCCcchhhcccCCCCCCCCCc
Confidence 4456666777778888888888877777767777788899999999999999887654
No 131
>PF09726 Macoilin: Transmembrane protein; InterPro: IPR019130 This entry represents the multi-pass transmembrane protein Macoilin, which is highly conserved in eukaryotes. ; GO: 0016021 integral to membrane
Probab=24.46 E-value=2.5e+02 Score=30.96 Aligned_cols=39 Identities=36% Similarity=0.464 Sum_probs=29.6
Q ss_pred HHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 218 ARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 218 aK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
.|.|+++.+.++..|+++.....++...+..|+++||..
T Consensus 543 ~r~r~~~lE~E~~~lr~elk~kee~~~~~e~~~~~lr~~ 581 (697)
T PF09726_consen 543 CRQRRRQLESELKKLRRELKQKEEQIRELESELQELRKY 581 (697)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455667777788888888877778888888888777755
No 132
>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=24.41 E-value=99 Score=25.94 Aligned_cols=45 Identities=24% Similarity=0.250 Sum_probs=30.7
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRART 220 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~ 220 (339)
.++..+..++...|-.. ..-.++|..+|++...|+++...-|.+.
T Consensus 111 ~L~~~~r~v~~l~~~~g-----~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 111 KLPERQRELLQLRYQRG-----VSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred HCCHHHHHHHHHHHhcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 46777777776644322 2346799999999999998876444443
No 133
>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=24.07 E-value=1e+02 Score=26.69 Aligned_cols=46 Identities=20% Similarity=0.163 Sum_probs=31.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|.-.|-... ...+||..+|+++..|+++...-|.+.|
T Consensus 100 ~L~~~~r~v~~l~~~~g~-----s~~eIA~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 100 ELPDEYREAIRLTELEGL-----SQQEIAEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 466777777766553322 3467999999999999988864444433
No 134
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=24.01 E-value=73 Score=28.42 Aligned_cols=46 Identities=20% Similarity=0.016 Sum_probs=31.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|.-.|-.. ....++|..||++...|++++..-|.+.|
T Consensus 113 ~Lp~~~r~v~~L~~~~g-----~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr 158 (188)
T PRK12546 113 QLPDEQREALILVGASG-----FSYEEAAEMCGVAVGTVKSRANRARARLA 158 (188)
T ss_pred hCCHHHhHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 35666666665543321 22457999999999999999986555554
No 135
>cd04777 HTH_MerR-like_sg1 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 1), N-terminal domain. Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=24.00 E-value=2.5e+02 Score=22.67 Aligned_cols=33 Identities=15% Similarity=0.121 Sum_probs=26.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNR 216 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNR 216 (339)
+|+.+.+..|. ....++.+|++-..|+.+|...
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 58888887764 3466889999999999999753
No 136
>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=23.89 E-value=77 Score=21.79 Aligned_cols=38 Identities=29% Similarity=0.354 Sum_probs=26.4
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWF 213 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWF 213 (339)
.++.+|++.+.+.+... + ...+||+.+|++...|.-|+
T Consensus 5 ~~~~~~~~~i~~l~~~G-~----si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-M----SIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-C----CHHHHHHHHCcCHHHHHHHH
Confidence 46676777777777665 2 36679999999988877655
No 137
>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=23.80 E-value=2.9e+02 Score=22.69 Aligned_cols=72 Identities=15% Similarity=0.099 Sum_probs=40.5
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+..++..|... ...+.+|++..+|+.+|....... ......-.+.|....+.+.++..+++.
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 456888888887443 346778888888888887655432 001111123344444455555555555
Q ss_pred HHHHHH
Q 019530 249 ELQELR 254 (339)
Q Consensus 249 e~~~lr 254 (339)
..+.+.
T Consensus 101 ~~~~l~ 106 (116)
T cd04769 101 LLARLD 106 (116)
T ss_pred HHHHHH
Confidence 554444
No 138
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=23.70 E-value=93 Score=26.90 Aligned_cols=46 Identities=13% Similarity=0.149 Sum_probs=32.2
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..+..+|...|-. ...-.++|..+|+++..|+++++.-|.+.|
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 4666777776664432 223467999999999999999975555554
No 139
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=23.51 E-value=87 Score=26.57 Aligned_cols=46 Identities=20% Similarity=0.078 Sum_probs=31.3
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..|..+|.-.|-..- .-.++|..+|++...|+++...-|.+.|
T Consensus 112 ~L~~~~r~v~~l~~~~~~-----s~~eIA~~lgis~~tv~~~l~Rar~~L~ 157 (161)
T PRK12541 112 SLPLERRNVLLLRDYYGF-----SYKEIAEMTGLSLAKVKIELHRGRKETK 157 (161)
T ss_pred HCCHHHHHHhhhHHhcCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 366666666665543322 2457999999999999998875555544
No 140
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=23.50 E-value=1.1e+02 Score=26.82 Aligned_cols=46 Identities=20% Similarity=0.111 Sum_probs=32.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.++..|..++...|-.. ....+||..+|++...|+.+...-|.+.|
T Consensus 139 ~L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 139 TLPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 46677777777654442 23568999999999999998864444444
No 141
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=23.20 E-value=1.9e+02 Score=29.25 Aligned_cols=42 Identities=26% Similarity=0.389 Sum_probs=32.2
Q ss_pred hHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHhh
Q 019530 216 RRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELRALK 257 (339)
Q Consensus 216 RRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lralk 257 (339)
++.+...++.+...+.++++|....+|+..|.+|+.|..+.+
T Consensus 137 ~~~~EEn~~lqlqL~~l~~e~~Ekeeesq~LnrELaE~layq 178 (401)
T PF06785_consen 137 RHLREENQCLQLQLDALQQECGEKEEESQTLNRELAEALAYQ 178 (401)
T ss_pred HHHHHHHHHHHHhHHHHHHHHhHhHHHHHHHHHHHHHHHHHH
Confidence 455566667777788888888888889999988888776543
No 142
>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=23.17 E-value=2.1e+02 Score=24.97 Aligned_cols=48 Identities=21% Similarity=0.149 Sum_probs=35.2
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.+.++..|..+|+..+ . . . ...++|..+|++...|+.|-..-|.+-|+
T Consensus 4 ~~~Lte~qr~VL~Lr~-~-G-l---Tq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 4 KTFLTERQIKVLELRE-K-G-L---SQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred cCCCCHHHHHHHHHHH-c-C-C---CHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 4568899999998742 1 1 1 35679999999999998888765555553
No 143
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=23.07 E-value=1.8e+02 Score=27.77 Aligned_cols=38 Identities=18% Similarity=0.195 Sum_probs=26.1
Q ss_pred HHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 217 RARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 217 RaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
|-|.|-.+.++++..++.....|+.|.+.|++++..|-
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLY 127 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLY 127 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455556666676777777778888888887776554
No 144
>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=23.02 E-value=3e+02 Score=21.32 Aligned_cols=31 Identities=29% Similarity=0.319 Sum_probs=18.9
Q ss_pred hhhhhhhHHHHHhhhhhHHHHHHHHHHHHHH
Q 019530 223 KQTEVDCEYLKRCCETLTEENRRLQKELQEL 253 (339)
Q Consensus 223 kq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~l 253 (339)
...+..+..|+.....|.+||.+|+.+....
T Consensus 28 eeLke~n~~L~~e~~~L~~en~~L~~e~~~~ 58 (72)
T PF06005_consen 28 EELKEKNNELKEENEELKEENEQLKQERNAW 58 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445555666666667777777777665443
No 145
>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=22.77 E-value=1.9e+02 Score=21.21 Aligned_cols=27 Identities=37% Similarity=0.468 Sum_probs=20.2
Q ss_pred hhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 228 DCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 228 ~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
+..........|..||..|+.++.-++
T Consensus 23 d~~~a~~rl~~l~~EN~~Lr~eL~~~r 49 (52)
T PF12808_consen 23 DRSAARKRLSKLEGENRLLRAELERLR 49 (52)
T ss_pred CchhHHHHHHHHHHHHHHHHHHHHHHh
Confidence 455566777788888888888877665
No 146
>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=22.76 E-value=1.2e+02 Score=31.76 Aligned_cols=36 Identities=17% Similarity=0.181 Sum_probs=14.6
Q ss_pred CCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 188 NTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 188 ~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
..|....|..+|+.-.+..++-++==+|++.+...+
T Consensus 55 DTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~ 90 (472)
T TIGR03752 55 DTPADTLRTLVAEVKELRKRLAKLISENEALKAENE 90 (472)
T ss_pred CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444333333333233335555554433
No 147
>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=22.74 E-value=28 Score=32.92 Aligned_cols=33 Identities=33% Similarity=0.427 Sum_probs=0.0
Q ss_pred hhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHhh
Q 019530 225 TEVDCEYLKRCCETLTEENRRLQKELQELRALK 257 (339)
Q Consensus 225 ~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lralk 257 (339)
......-|++-.+.|..||++|++|++.|++-+
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 333445677788888888888888888887543
No 148
>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=22.70 E-value=87 Score=27.13 Aligned_cols=45 Identities=9% Similarity=-0.006 Sum_probs=28.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..+..++.-.|- ....-.+||..+|+++..|+++...-|.+-|
T Consensus 139 L~~~~r~v~~l~~~-----~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr 183 (190)
T TIGR02939 139 LPEDLRTAITLREL-----EGLSYEDIARIMDCPVGTVRSRIFRAREAIA 183 (190)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 44555555544332 2223468999999999999999864444444
No 149
>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=22.70 E-value=1.4e+02 Score=24.01 Aligned_cols=44 Identities=27% Similarity=0.358 Sum_probs=28.3
Q ss_pred ccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHH
Q 019530 207 RQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQ 251 (339)
Q Consensus 207 rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~ 251 (339)
.++..|...=|++.. +......+.|+.....+.++|..|++++.
T Consensus 56 ~~Le~aL~~VR~rK~-~~l~~~i~~l~~ke~~l~~en~~L~~~~~ 99 (100)
T PF01486_consen 56 QQLESALKRVRSRKD-QLLMEQIEELKKKERELEEENNQLRQKIE 99 (100)
T ss_pred HhhhhhHHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 445556554444433 44556667777777888888888887654
No 150
>PRK10360 DNA-binding transcriptional activator UhpA; Provisional
Probab=22.53 E-value=75 Score=26.99 Aligned_cols=45 Identities=22% Similarity=0.241 Sum_probs=35.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
.+|..+..+|+-..+- ..+.+||.+++++++.|++..++=|.|..
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 5888888888776643 25778999999999999998887666543
No 151
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=22.47 E-value=1.1e+02 Score=26.65 Aligned_cols=46 Identities=11% Similarity=0.166 Sum_probs=30.7
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
++..+..+|...|-.. ..-.+||..+|++...|+.+...-|.+.|+
T Consensus 129 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYYQG-----LSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHhcC-----CCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 5566666665544221 124579999999999999998755555553
No 152
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=22.20 E-value=2.5e+02 Score=22.78 Aligned_cols=37 Identities=16% Similarity=0.384 Sum_probs=18.6
Q ss_pred cchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHH
Q 019530 210 EVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQEL 253 (339)
Q Consensus 210 qvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~l 253 (339)
-+|||=++++.+ ++.|..+.+.|..|..-.+.|+...
T Consensus 20 y~~~k~~ka~~~-------~~kL~~en~qlk~Ek~~~~~qvkn~ 56 (87)
T PF10883_consen 20 YLWWKVKKAKKQ-------NAKLQKENEQLKTEKAVAETQVKNA 56 (87)
T ss_pred HHHHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 467776666555 4444444444444444444444433
No 153
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=22.10 E-value=1.2e+02 Score=28.15 Aligned_cols=27 Identities=15% Similarity=0.220 Sum_probs=21.7
Q ss_pred HHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 195 KLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
-.+||..||++...|+++...-|.+.|
T Consensus 190 ~~EIA~~Lgis~~tVk~~l~RAr~kLr 216 (233)
T PRK12538 190 NGEIAEVMDTTVAAVESLLKRGRQQLR 216 (233)
T ss_pred HHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 458999999999999999875555554
No 154
>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=21.99 E-value=1.6e+02 Score=24.75 Aligned_cols=14 Identities=36% Similarity=0.634 Sum_probs=11.8
Q ss_pred ccccchhhhhHHHH
Q 019530 207 RQVEVWFQNRRART 220 (339)
Q Consensus 207 rQVqvWFQNRRaK~ 220 (339)
||.+.||-.+|.-.
T Consensus 18 Rq~e~~FlqKr~~L 31 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHH
Confidence 67799999999875
No 155
>PRK14127 cell division protein GpsB; Provisional
Probab=21.86 E-value=1.8e+02 Score=24.52 Aligned_cols=44 Identities=25% Similarity=0.404 Sum_probs=28.7
Q ss_pred CCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 019530 203 NLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELRA 255 (339)
Q Consensus 203 gLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lra 255 (339)
|....+|.-|. .+-..+.+.+..+...|.+++.+|+.++.++..
T Consensus 22 GYd~~EVD~FL---------d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 22 GYDQDEVDKFL---------DDVIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred CCCHHHHHHHH---------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555544 234456677777777788888888887777773
No 156
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=21.63 E-value=2.7e+02 Score=21.41 Aligned_cols=20 Identities=55% Similarity=0.690 Sum_probs=13.0
Q ss_pred hhhhhHHHHHHHHHHHHHHH
Q 019530 235 CCETLTEENRRLQKELQELR 254 (339)
Q Consensus 235 ~~~~l~eEn~~l~~e~~~lr 254 (339)
.+..|++|++.|++|+.+++
T Consensus 48 e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 48 ENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHhh
Confidence 34566777777777766654
No 157
>KOG0999 consensus Microtubule-associated protein Bicaudal-D [Intracellular trafficking, secretion, and vesicular transport]
Probab=21.55 E-value=1.5e+02 Score=32.03 Aligned_cols=46 Identities=37% Similarity=0.355 Sum_probs=33.5
Q ss_pred ccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 209 VEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 209 VqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
-.+=-|.+|.|.-.+...-....|-..|..|.+||-.|||+|..||
T Consensus 145 ~~~E~qR~rlr~elKe~KfRE~RllseYSELEEENIsLQKqVs~LR 190 (772)
T KOG0999|consen 145 AAVEDQRRRLRDELKEYKFREARLLSEYSELEEENISLQKQVSNLR 190 (772)
T ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHh
Confidence 3445577777777666666666677777888888888888888777
No 158
>cd04784 HTH_CadR-PbrR Helix-Turn-Helix DNA binding domain of the CadR and PbrR transcription regulators. Helix-turn-helix (HTH) CadR and PbrR transcription regulators including Pseudomonas aeruginosa CadR and Ralstonia metallidurans PbrR that regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which form a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.52 E-value=3.9e+02 Score=22.19 Aligned_cols=71 Identities=10% Similarity=0.047 Sum_probs=39.1
Q ss_pred CccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHH
Q 019530 169 KLRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEVDCEYLKRCCETLTEENRRLQK 248 (339)
Q Consensus 169 Rtrft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~ 248 (339)
...|+.+++..|.. ....+.+|++-..|+..|........ ....-...|....+.+.++..+|+.
T Consensus 36 yR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~--~~~~~~~~l~~~~~~l~~~i~~L~~ 100 (127)
T cd04784 36 YRLYDEEHLERLLF-------------IRRCRSLDMSLDEIRTLLQLQDDPEA--SCAEVNALIDEHLAHVRARIAELQA 100 (127)
T ss_pred CeecCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHhhhcCCC--cHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45689999888743 34577888888888888865332110 0111123344444444444444544
Q ss_pred HHHHHH
Q 019530 249 ELQELR 254 (339)
Q Consensus 249 e~~~lr 254 (339)
-...|.
T Consensus 101 ~~~~L~ 106 (127)
T cd04784 101 LEKQLQ 106 (127)
T ss_pred HHHHHH
Confidence 444444
No 159
>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=21.47 E-value=2.2e+02 Score=21.15 Aligned_cols=28 Identities=11% Similarity=0.317 Sum_probs=13.0
Q ss_pred hhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 227 VDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 227 ~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
.+...+.....+++.||+.+.+++.++.
T Consensus 7 n~~~~~~~~i~tvk~en~~i~~~ve~i~ 34 (55)
T PF05377_consen 7 NELPRIESSINTVKKENEEISESVEKIE 34 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444555555555555444443
No 160
>KOG3584 consensus cAMP response element binding protein and related transcription factors [Transcription]
Probab=21.40 E-value=1.4e+02 Score=29.65 Aligned_cols=43 Identities=28% Similarity=0.409 Sum_probs=24.2
Q ss_pred hhhHH-HHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 214 QNRRA-RTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 214 QNRRa-K~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lral 256 (339)
+||-+ |+-|+++++-.+.|......|.-.|.-|-+|++.|+.|
T Consensus 298 KNREAARECRRKKKEYVKCLENRVAVLENQNKaLIEELKtLKeL 341 (348)
T KOG3584|consen 298 KNREAARECRRKKKEYVKCLENRVAVLENQNKALIEELKTLKEL 341 (348)
T ss_pred hhHHHHHHHHHhHhHHHHHHHhHHHHHhcccHHHHHHHHHHHHH
Confidence 45443 33333333333445555566777777787777777755
No 161
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=21.27 E-value=72 Score=33.27 Aligned_cols=80 Identities=23% Similarity=0.329 Sum_probs=41.7
Q ss_pred ccCCHHHHHHHHHH-Hhh-cCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhhhhhh---------------hhHHH
Q 019530 170 LRLSKEQSAFLEES-FKE-HNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLKQTEV---------------DCEYL 232 (339)
Q Consensus 170 trft~~Ql~~LE~~-F~~-~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krkq~~~---------------~~e~L 232 (339)
.+++.+....|.+. |-. ..+|-.+.-+++.++ |+.=..|+|.+.-.+++++ ++..|
T Consensus 219 L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKr-------vRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL 291 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKR-------VRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQEL 291 (472)
T ss_pred eeccHHHHHHHHhccCcCcccCCchHHHHHHHHH-------HHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHH
Confidence 46788888877765 332 334444444444433 3444455554432222222 33445
Q ss_pred HHhhhhhHHHHHHHHHHHHHHHHh
Q 019530 233 KRCCETLTEENRRLQKELQELRAL 256 (339)
Q Consensus 233 k~~~~~l~eEn~~l~~e~~~lral 256 (339)
++..+.|..+|+.|..+++.|.++
T Consensus 292 ~kkV~~Le~~N~sLl~qL~klQt~ 315 (472)
T KOG0709|consen 292 QKKVEELELSNRSLLAQLKKLQTL 315 (472)
T ss_pred HHHHHHHhhccHHHHHHHHHHHHH
Confidence 555566666666666666666544
No 162
>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=20.82 E-value=1.4e+02 Score=25.86 Aligned_cols=45 Identities=22% Similarity=0.164 Sum_probs=30.2
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..|..++.-.|-... .-.++|..||+++..|++....-|.+-|
T Consensus 135 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tVk~~l~Rar~~Lr 179 (183)
T TIGR02999 135 VDPRQAEVVELRFFAGL-----TVEEIAELLGVSVRTVERDWRFARAWLA 179 (183)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 55555555555443322 2457999999999999999875555444
No 163
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=20.81 E-value=1.8e+02 Score=28.00 Aligned_cols=35 Identities=29% Similarity=0.490 Sum_probs=21.5
Q ss_pred HHHHHhhhhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 217 RARTKLKQTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 217 RaK~Krkq~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
|.|.|+++.+ ..+......|..||+.|+.+|.+|+
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~ 242 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLK 242 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444333 4456666677777777777777776
No 164
>PRK06930 positive control sigma-like factor; Validated
Probab=20.80 E-value=1.5e+02 Score=26.49 Aligned_cols=47 Identities=11% Similarity=0.060 Sum_probs=33.9
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
.++..+..+|...|.... .-.++|..+|++...|+.+...-|.+.++
T Consensus 114 ~L~~rer~V~~L~~~eg~-----s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 114 VLTEREKEVYLMHRGYGL-----SYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred hCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 477777777776543322 24579999999999999999866655553
No 165
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=20.73 E-value=47 Score=24.23 Aligned_cols=19 Identities=21% Similarity=0.350 Sum_probs=16.9
Q ss_pred HHHHHHcCCCcccccchhh
Q 019530 196 LALAKQLNLRPRQVEVWFQ 214 (339)
Q Consensus 196 ~~LA~~LgLs~rQVqvWFQ 214 (339)
.++|+.+|++.+.|+.|=+
T Consensus 4 ~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 4 KEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHCcCHHHHHHHHH
Confidence 5789999999999999954
No 166
>PRK09935 transcriptional regulator FimZ; Provisional
Probab=20.61 E-value=86 Score=26.72 Aligned_cols=46 Identities=20% Similarity=0.128 Sum_probs=35.7
Q ss_pred ccCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 170 LRLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 170 trft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
..++..+..+|+...+. ..+.+||.+|+++.+-|+++.++=|.|..
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 45888888888754433 45778999999999999999987766654
No 167
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=20.53 E-value=45 Score=22.92 Aligned_cols=22 Identities=23% Similarity=0.401 Sum_probs=17.1
Q ss_pred HHHHHHHHcCCCcccccchhhh
Q 019530 194 QKLALAKQLNLRPRQVEVWFQN 215 (339)
Q Consensus 194 ~r~~LA~~LgLs~rQVqvWFQN 215 (339)
...++|+.||++...|..|.+.
T Consensus 19 s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 19 SIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp -HHHHHHHHTS-HHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHHH
Confidence 4567999999999999999753
No 168
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.41 E-value=1.8e+02 Score=25.17 Aligned_cols=45 Identities=9% Similarity=0.098 Sum_probs=30.5
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHH
Q 019530 172 LSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTK 221 (339)
Q Consensus 172 ft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~K 221 (339)
++..+..++.-.|-... .-.+||..||++...|++....-|.+.|
T Consensus 118 Lp~~~r~i~~l~~~e~~-----s~~EIA~~lgis~~tV~~~l~ra~~~Lr 162 (179)
T PRK12543 118 LPYKLRQVIILRYLHDY-----SQEEIAQLLQIPIGTVKSRIHAALKKLR 162 (179)
T ss_pred CCHHHHHHHHHHHHccC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 55666655555433222 2457999999999999998876665555
No 169
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=20.38 E-value=1e+02 Score=27.10 Aligned_cols=48 Identities=15% Similarity=0.198 Sum_probs=33.1
Q ss_pred cCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHcCCCcccccchhhhhHHHHHhh
Q 019530 171 RLSKEQSAFLEESFKEHNTLNPKQKLALAKQLNLRPRQVEVWFQNRRARTKLK 223 (339)
Q Consensus 171 rft~~Ql~~LE~~F~~~~~ps~~~r~~LA~~LgLs~rQVqvWFQNRRaK~Krk 223 (339)
.++..+..++.-.|-.. ....+||..+|++...|++..+.-|.+.|+.
T Consensus 131 ~L~~~~r~i~~l~~~~g-----~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 131 DLEKLDREIFIRRYLLG-----EKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred hCCHHHHHHHHHHHHcc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 46677777776554322 2346799999999999998887665555543
No 170
>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=20.20 E-value=1.8e+02 Score=23.61 Aligned_cols=29 Identities=38% Similarity=0.455 Sum_probs=24.2
Q ss_pred hhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 226 EVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 226 ~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
....+.|+.....+..+|..|..+++++|
T Consensus 79 ~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 79 KKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34556788888999999999999998877
No 171
>PF10224 DUF2205: Predicted coiled-coil protein (DUF2205); InterPro: IPR019357 This entry represents a highly conserved 100 residue region which is likely to have a coiled-coil structure. The exact function is unknown.
Probab=20.17 E-value=3.5e+02 Score=21.52 Aligned_cols=31 Identities=29% Similarity=0.341 Sum_probs=15.9
Q ss_pred hhhhhhHHHHHhhhhhHHHHHHHHHHHHHHH
Q 019530 224 QTEVDCEYLKRCCETLTEENRRLQKELQELR 254 (339)
Q Consensus 224 q~~~~~e~Lk~~~~~l~eEn~~l~~e~~~lr 254 (339)
..+..+..|....+.+++|++.|..|++-|.
T Consensus 27 ~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq 57 (80)
T PF10224_consen 27 ELQDSLEALSDRVEEVKEENEKLESENEYLQ 57 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444455555555555555555555444
No 172
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=20.10 E-value=76 Score=27.25 Aligned_cols=28 Identities=18% Similarity=0.182 Sum_probs=22.9
Q ss_pred HHHHHHHcCCCcccccchhhhhHHHHHh
Q 019530 195 KLALAKQLNLRPRQVEVWFQNRRARTKL 222 (339)
Q Consensus 195 r~~LA~~LgLs~rQVqvWFQNRRaK~Kr 222 (339)
-.++|..+|+++..|++.+..-|.+.|+
T Consensus 139 ~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 139 QKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5689999999999999999766665554
Done!