Query 022964
Match_columns 289
No_of_seqs 260 out of 1546
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 07:27:19 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/022964.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/022964hhsearch_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 4.2E-23 9E-28 184.3 11.6 105 46-150 47-151 (198)
2 KOG0842 Transcription factor t 99.7 7.3E-17 1.6E-21 152.2 6.1 59 56-114 160-218 (307)
3 KOG0489 Transcription factor z 99.6 1.3E-16 2.8E-21 148.0 4.9 61 48-108 158-218 (261)
4 KOG0843 Transcription factor E 99.6 3.7E-16 8E-21 136.9 5.7 63 48-110 101-163 (197)
5 KOG0488 Transcription factor B 99.6 5.2E-16 1.1E-20 147.3 5.8 55 54-108 177-231 (309)
6 PF00046 Homeobox: Homeobox do 99.6 1.7E-15 3.7E-20 108.5 6.2 57 50-106 1-57 (57)
7 KOG0487 Transcription factor A 99.6 9.9E-16 2.1E-20 144.6 3.6 63 48-110 234-296 (308)
8 KOG0850 Transcription factor D 99.6 5.9E-15 1.3E-19 133.6 8.0 59 49-107 122-180 (245)
9 KOG0485 Transcription factor N 99.5 1.4E-14 3E-19 130.4 8.6 61 48-108 103-163 (268)
10 KOG0484 Transcription factor P 99.5 3E-15 6.5E-20 121.0 3.9 61 47-107 15-75 (125)
11 KOG0492 Transcription factor M 99.5 8.8E-15 1.9E-19 130.8 5.8 60 49-108 144-203 (246)
12 KOG4577 Transcription factor L 99.5 1E-14 2.2E-19 135.7 3.2 93 43-136 161-253 (383)
13 KOG0848 Transcription factor C 99.5 4.9E-14 1.1E-18 130.0 6.7 54 55-108 205-258 (317)
14 KOG0494 Transcription factor C 99.5 6.5E-14 1.4E-18 128.8 7.3 55 55-109 147-201 (332)
15 cd00086 homeodomain Homeodomai 99.5 1.1E-13 2.4E-18 98.7 6.3 57 51-107 2-58 (59)
16 smart00389 HOX Homeodomain. DN 99.5 1.1E-13 2.4E-18 98.2 5.8 55 51-105 2-56 (56)
17 KOG0493 Transcription factor E 99.4 4.6E-14 9.9E-19 129.9 4.3 87 53-139 250-337 (342)
18 COG5576 Homeodomain-containing 99.4 1.7E-13 3.8E-18 118.6 6.0 67 44-110 46-112 (156)
19 KOG2251 Homeobox transcription 99.4 1.2E-13 2.7E-18 124.4 4.8 63 46-108 34-96 (228)
20 KOG0844 Transcription factor E 99.3 6.9E-13 1.5E-17 124.4 3.5 63 48-110 180-242 (408)
21 TIGR01565 homeo_ZF_HD homeobox 99.3 1.4E-12 3E-17 95.6 4.3 52 50-101 2-57 (58)
22 KOG3802 Transcription factor O 99.3 1.5E-12 3.2E-17 125.9 2.4 61 48-108 293-353 (398)
23 KOG0847 Transcription factor, 99.2 3.8E-12 8.2E-17 114.9 3.5 61 48-108 166-226 (288)
24 KOG0491 Transcription factor B 99.2 5.2E-12 1.1E-16 109.6 2.7 58 51-108 102-159 (194)
25 KOG0486 Transcription factor P 99.1 3.9E-11 8.5E-16 113.0 5.2 61 48-108 111-171 (351)
26 KOG0490 Transcription factor, 99.0 2.1E-10 4.5E-15 102.3 4.3 62 47-108 58-119 (235)
27 KOG1168 Transcription factor A 98.8 2.4E-09 5.3E-14 100.3 1.8 66 43-108 303-368 (385)
28 KOG0849 Transcription factor P 98.7 1.1E-08 2.4E-13 99.1 5.0 61 48-108 175-235 (354)
29 KOG0775 Transcription factor S 98.7 1.8E-08 3.8E-13 93.8 4.4 51 56-106 183-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.3 6E-07 1.3E-11 61.1 3.5 34 70-103 7-40 (40)
31 PF02183 HALZ: Homeobox associ 98.3 1.4E-06 3E-11 60.8 5.2 44 107-150 1-44 (45)
32 KOG0774 Transcription factor P 98.2 8.6E-07 1.9E-11 82.4 2.4 60 48-107 187-249 (334)
33 KOG2252 CCAAT displacement pro 97.9 1.4E-05 3E-10 80.8 5.9 58 48-105 419-476 (558)
34 KOG0490 Transcription factor, 97.7 4E-05 8.6E-10 68.3 5.2 61 48-108 152-212 (235)
35 KOG1146 Homeobox protein [Gene 96.9 0.00084 1.8E-08 73.8 3.9 65 45-109 899-963 (1406)
36 KOG0773 Transcription factor M 96.3 0.0034 7.3E-08 60.2 3.3 61 50-110 240-303 (342)
37 PF11569 Homez: Homeodomain le 96.2 0.0034 7.4E-08 45.8 2.5 43 60-102 9-51 (56)
38 PF02183 HALZ: Homeobox associ 94.1 0.13 2.8E-06 35.9 4.9 35 116-150 3-37 (45)
39 PRK09413 IS2 repressor TnpA; R 94.1 0.33 7.2E-06 39.9 8.1 94 51-153 8-106 (121)
40 KOG3623 Homeobox transcription 93.3 0.11 2.5E-06 54.8 4.9 48 61-108 568-615 (1007)
41 PF04218 CENP-B_N: CENP-B N-te 92.4 0.31 6.7E-06 34.8 4.7 47 50-101 1-47 (53)
42 KOG4005 Transcription factor X 92.2 1.6 3.5E-05 40.8 10.3 44 110-153 103-146 (292)
43 PF00170 bZIP_1: bZIP transcri 87.2 4.7 0.0001 29.4 7.5 38 111-148 26-63 (64)
44 smart00340 HALZ homeobox assoc 86.6 1.3 2.9E-05 30.6 4.0 25 122-146 9-33 (44)
45 KOG4196 bZIP transcription fac 85.8 17 0.00037 31.0 11.1 83 54-149 22-112 (135)
46 smart00340 HALZ homeobox assoc 85.1 1.7 3.8E-05 30.1 3.9 34 107-140 1-34 (44)
47 PRK00888 ftsB cell division pr 84.9 2.2 4.9E-05 34.7 5.3 49 90-146 14-62 (105)
48 PF06005 DUF904: Protein of un 84.0 5.9 0.00013 30.3 6.9 38 110-147 17-54 (72)
49 PF06156 DUF972: Protein of un 81.4 7 0.00015 32.0 6.9 46 108-153 12-57 (107)
50 PF06005 DUF904: Protein of un 81.3 11 0.00023 28.8 7.4 46 104-149 18-63 (72)
51 PF10224 DUF2205: Predicted co 78.4 12 0.00026 29.2 7.0 45 105-149 17-61 (80)
52 PRK13169 DNA replication intia 76.9 10 0.00022 31.3 6.6 43 108-150 12-54 (110)
53 smart00338 BRLZ basic region l 76.8 23 0.00051 25.7 7.9 37 112-148 27-63 (65)
54 KOG3119 Basic region leucine z 75.7 7.9 0.00017 36.4 6.4 48 100-150 207-254 (269)
55 PF00170 bZIP_1: bZIP transcri 74.1 15 0.00033 26.7 6.2 35 107-141 29-63 (64)
56 PF13443 HTH_26: Cro/C1-type H 73.0 6.6 0.00014 27.8 4.0 41 78-118 12-52 (63)
57 cd06171 Sigma70_r4 Sigma70, re 72.1 5.4 0.00012 26.0 3.2 43 56-103 11-53 (55)
58 PF01527 HTH_Tnp_1: Transposas 72.0 2.9 6.2E-05 30.7 2.0 44 51-98 2-45 (76)
59 PF14775 NYD-SP28_assoc: Sperm 72.0 22 0.00048 26.1 6.7 31 119-149 27-57 (60)
60 KOG4343 bZIP transcription fac 70.2 18 0.00039 37.6 7.7 31 122-152 306-336 (655)
61 PF04545 Sigma70_r4: Sigma-70, 67.9 13 0.00029 25.3 4.6 41 55-100 4-44 (50)
62 cd04766 HTH_HspR Helix-Turn-He 65.4 57 0.0012 25.1 8.2 70 79-149 4-89 (91)
63 PF07407 Seadorna_VP6: Seadorn 65.0 9 0.00019 37.5 4.2 27 122-148 36-62 (420)
64 TIGR02449 conserved hypothetic 64.6 35 0.00075 25.7 6.4 44 109-152 5-48 (65)
65 KOG4571 Activating transcripti 64.5 29 0.00063 33.3 7.5 50 102-152 240-289 (294)
66 COG4467 Regulator of replicati 60.8 26 0.00057 29.0 5.6 43 108-150 12-54 (114)
67 cd00569 HTH_Hin_like Helix-tur 60.8 22 0.00048 20.4 4.2 38 55-97 5-42 (42)
68 cd01106 HTH_TipAL-Mta Helix-Tu 60.5 81 0.0018 24.8 8.8 37 52-101 35-71 (103)
69 KOG1146 Homeobox protein [Gene 59.6 18 0.00039 41.2 5.8 56 53-108 709-764 (1406)
70 PF04967 HTH_10: HTH DNA bindi 59.6 12 0.00026 26.9 3.1 40 56-95 1-42 (53)
71 smart00338 BRLZ basic region l 58.8 37 0.00081 24.6 5.8 32 109-140 31-62 (65)
72 COG4026 Uncharacterized protei 58.6 31 0.00068 32.3 6.4 23 124-146 148-170 (290)
73 KOG4403 Cell surface glycoprot 58.4 42 0.0009 34.2 7.6 64 93-156 228-326 (575)
74 KOG2391 Vacuolar sorting prote 58.3 33 0.00072 33.8 6.8 50 100-149 221-270 (365)
75 PF10668 Phage_terminase: Phag 57.7 8.6 0.00019 28.5 2.1 18 79-96 25-42 (60)
76 PF15058 Speriolin_N: Sperioli 57.0 18 0.00038 32.9 4.4 35 118-152 5-39 (200)
77 PF07716 bZIP_2: Basic region 57.0 39 0.00085 23.8 5.4 24 122-145 29-52 (54)
78 PF06156 DUF972: Protein of un 56.8 31 0.00066 28.3 5.5 40 107-146 18-57 (107)
79 PRK15422 septal ring assembly 55.7 60 0.0013 25.4 6.5 40 110-149 24-63 (79)
80 PF04899 MbeD_MobD: MbeD/MobD 55.1 46 0.001 25.3 5.8 39 112-150 22-60 (70)
81 PRK13169 DNA replication intia 54.9 35 0.00075 28.2 5.5 39 108-146 19-57 (110)
82 cd04765 HTH_MlrA-like_sg2 Heli 54.2 56 0.0012 26.0 6.5 38 52-101 35-72 (99)
83 PRK10884 SH3 domain-containing 53.9 62 0.0013 29.4 7.5 30 118-147 132-161 (206)
84 PRK14127 cell division protein 53.5 40 0.00086 27.8 5.6 30 124-153 36-65 (109)
85 KOG0709 CREB/ATF family transc 52.4 2.2E+02 0.0048 29.3 11.6 92 54-152 219-313 (472)
86 KOG0249 LAR-interacting protei 52.2 72 0.0016 34.5 8.5 51 102-152 214-264 (916)
87 KOG0483 Transcription factor H 52.1 22 0.00048 32.3 4.3 41 115-155 109-149 (198)
88 PF08281 Sigma70_r4_2: Sigma-7 51.7 37 0.00081 23.2 4.6 41 56-101 11-51 (54)
89 PF13936 HTH_38: Helix-turn-he 50.2 22 0.00048 24.1 3.1 41 53-98 2-42 (44)
90 PF05700 BCAS2: Breast carcino 49.9 76 0.0016 28.8 7.5 44 110-153 174-217 (221)
91 KOG3156 Uncharacterized membra 49.6 46 0.001 30.7 5.9 40 113-152 103-143 (220)
92 COG3074 Uncharacterized protei 49.6 98 0.0021 23.9 6.7 41 108-148 22-62 (79)
93 PRK10884 SH3 domain-containing 49.4 64 0.0014 29.3 6.9 41 109-149 130-170 (206)
94 PF04977 DivIC: Septum formati 48.4 45 0.00098 24.5 4.9 26 119-144 25-50 (80)
95 PF05377 FlaC_arch: Flagella a 47.7 65 0.0014 23.6 5.3 32 117-148 6-37 (55)
96 cd04769 HTH_MerR2 Helix-Turn-H 47.5 1.5E+02 0.0032 23.9 8.3 38 53-103 35-72 (116)
97 PF04880 NUDE_C: NUDE protein, 47.5 17 0.00036 32.2 2.7 31 125-155 24-54 (166)
98 PRK13922 rod shape-determining 46.5 41 0.0009 31.1 5.3 38 115-152 73-113 (276)
99 cd04779 HTH_MerR-like_sg4 Heli 46.2 1.8E+02 0.0039 24.5 10.3 37 52-101 34-70 (134)
100 PRK03975 tfx putative transcri 46.2 57 0.0012 28.0 5.7 48 53-106 4-51 (141)
101 PRK14127 cell division protein 45.9 50 0.0011 27.3 5.1 36 114-149 33-68 (109)
102 PF07407 Seadorna_VP6: Seadorn 45.8 40 0.00087 33.2 5.1 32 112-143 33-64 (420)
103 PF12709 Kinetocho_Slk19: Cent 45.0 1.1E+02 0.0023 24.4 6.6 42 111-152 34-76 (87)
104 PF09304 Cortex-I_coil: Cortex 44.9 96 0.0021 25.6 6.5 36 114-149 19-54 (107)
105 KOG1962 B-cell receptor-associ 44.8 55 0.0012 30.2 5.7 26 123-148 184-209 (216)
106 TIGR00219 mreC rod shape-deter 44.1 47 0.001 31.5 5.3 39 115-153 70-112 (283)
107 PF13518 HTH_28: Helix-turn-he 44.1 24 0.00052 23.7 2.5 22 78-99 14-35 (52)
108 KOG3119 Basic region leucine z 43.8 70 0.0015 30.1 6.4 43 109-151 206-248 (269)
109 PRK15422 septal ring assembly 43.4 1.2E+02 0.0027 23.7 6.6 40 110-149 31-70 (79)
110 KOG1853 LIS1-interacting prote 43.0 1.4E+02 0.003 28.6 8.1 28 127-154 159-186 (333)
111 cd04761 HTH_MerR-SF Helix-Turn 41.9 26 0.00056 23.2 2.4 23 79-101 3-25 (49)
112 PF07334 IFP_35_N: Interferon- 41.8 50 0.0011 25.7 4.2 22 129-150 4-25 (76)
113 PRK13729 conjugal transfer pil 41.2 77 0.0017 32.6 6.6 44 105-148 77-120 (475)
114 KOG4571 Activating transcripti 39.8 87 0.0019 30.2 6.3 30 125-154 248-277 (294)
115 PF01166 TSC22: TSC-22/dip/bun 39.6 44 0.00096 24.7 3.4 24 123-146 19-42 (59)
116 PF07334 IFP_35_N: Interferon- 39.0 52 0.0011 25.6 3.9 33 121-153 3-35 (76)
117 PF05377 FlaC_arch: Flagella a 38.8 1.1E+02 0.0024 22.4 5.3 38 108-145 4-41 (55)
118 KOG1962 B-cell receptor-associ 38.4 67 0.0014 29.7 5.2 39 108-146 162-200 (216)
119 PF09607 BrkDBD: Brinker DNA-b 38.3 55 0.0012 24.2 3.8 44 53-98 3-47 (58)
120 TIGR02937 sigma70-ECF RNA poly 37.8 72 0.0016 24.9 4.9 45 56-105 111-155 (158)
121 PF10224 DUF2205: Predicted co 37.8 1.9E+02 0.0041 22.6 6.9 43 105-147 24-66 (80)
122 TIGR02894 DNA_bind_RsfA transc 37.6 88 0.0019 27.6 5.6 27 121-147 107-133 (161)
123 COG2919 Septum formation initi 37.5 1.2E+02 0.0027 24.8 6.2 35 113-147 52-86 (117)
124 TIGR03752 conj_TIGR03752 integ 37.3 1.5E+02 0.0032 30.5 7.9 94 55-151 41-135 (472)
125 PRK00888 ftsB cell division pr 37.2 68 0.0015 26.0 4.6 29 111-139 34-62 (105)
126 smart00421 HTH_LUXR helix_turn 37.1 96 0.0021 20.3 4.7 42 55-102 3-44 (58)
127 PF14197 Cep57_CLD_2: Centroso 36.8 1.8E+02 0.004 21.9 7.4 21 128-148 43-63 (69)
128 PRK06759 RNA polymerase factor 36.7 86 0.0019 25.5 5.3 45 56-105 107-151 (154)
129 COG3413 Predicted DNA binding 36.7 55 0.0012 29.2 4.4 38 55-92 155-194 (215)
130 PF00038 Filament: Intermediat 36.6 2.4E+02 0.0052 26.3 8.8 58 89-146 185-251 (312)
131 PF11932 DUF3450: Protein of u 36.3 1.4E+02 0.003 27.3 7.1 27 116-142 54-80 (251)
132 PF00196 GerE: Bacterial regul 36.3 98 0.0021 21.6 4.8 47 55-107 3-49 (58)
133 PF07989 Microtub_assoc: Micro 36.2 1.4E+02 0.0031 22.8 5.9 31 122-152 40-70 (75)
134 COG4026 Uncharacterized protei 36.1 99 0.0021 29.1 5.9 38 111-148 128-165 (290)
135 PF11559 ADIP: Afadin- and alp 35.5 2.2E+02 0.0047 23.9 7.7 51 101-151 77-127 (151)
136 PF12808 Mto2_bdg: Micro-tubul 34.8 1.5E+02 0.0032 21.4 5.4 21 124-144 28-48 (52)
137 TIGR03879 near_KaiC_dom probab 34.8 16 0.00035 28.0 0.6 35 65-99 21-55 (73)
138 PF13384 HTH_23: Homeodomain-l 34.8 38 0.00082 22.8 2.4 23 76-98 17-39 (50)
139 PF14197 Cep57_CLD_2: Centroso 34.7 2E+02 0.0042 21.7 6.4 35 111-145 33-67 (69)
140 PRK09652 RNA polymerase sigma 34.6 85 0.0019 25.9 5.0 45 56-105 129-173 (182)
141 PF13411 MerR_1: MerR HTH fami 34.6 36 0.00077 24.3 2.3 21 79-99 3-23 (69)
142 PRK09642 RNA polymerase sigma 34.4 88 0.0019 25.8 5.0 46 56-106 107-152 (160)
143 PF00424 REV: REV protein (ant 34.4 46 0.00099 26.7 3.0 34 61-108 14-47 (91)
144 PF06056 Terminase_5: Putative 34.3 36 0.00079 24.7 2.3 27 78-106 15-41 (58)
145 PRK14872 rod shape-determining 34.3 54 0.0012 32.1 4.2 26 120-145 59-84 (337)
146 PRK11924 RNA polymerase sigma 34.2 54 0.0012 27.1 3.7 46 56-106 126-171 (179)
147 PF04899 MbeD_MobD: MbeD/MobD 33.9 1.9E+02 0.0042 22.0 6.3 40 110-149 27-66 (70)
148 PRK12514 RNA polymerase sigma 33.8 53 0.0011 27.7 3.6 46 56-106 130-175 (179)
149 TIGR01069 mutS2 MutS2 family p 33.7 2.2E+02 0.0048 30.9 9.0 22 74-95 480-501 (771)
150 TIGR02894 DNA_bind_RsfA transc 33.6 1.3E+02 0.0028 26.6 6.0 34 111-144 104-137 (161)
151 PF09726 Macoilin: Transmembra 33.5 4.3E+02 0.0094 28.5 11.0 32 100-131 456-487 (697)
152 PRK10072 putative transcriptio 33.5 33 0.00072 27.5 2.2 42 55-103 32-73 (96)
153 PF02796 HTH_7: Helix-turn-hel 33.4 80 0.0017 21.2 3.8 38 55-97 5-42 (45)
154 PF06637 PV-1: PV-1 protein (P 33.1 2E+02 0.0043 29.0 7.8 33 121-153 352-384 (442)
155 PF07716 bZIP_2: Basic region 33.1 1.7E+02 0.0037 20.4 7.0 27 114-140 28-54 (54)
156 PRK09646 RNA polymerase sigma 32.9 91 0.002 26.9 5.1 46 56-106 143-188 (194)
157 PRK00409 recombination and DNA 32.6 2.2E+02 0.0048 30.9 8.8 22 74-95 485-506 (782)
158 KOG4196 bZIP transcription fac 32.2 2.3E+02 0.005 24.3 7.0 52 96-147 64-117 (135)
159 cd01109 HTH_YyaN Helix-Turn-He 32.1 2.6E+02 0.0056 22.2 9.3 36 53-101 36-71 (113)
160 PF04728 LPP: Lipoprotein leuc 32.1 2.1E+02 0.0045 21.0 6.6 41 107-147 6-46 (56)
161 PF15035 Rootletin: Ciliary ro 32.1 2E+02 0.0043 25.7 7.1 41 114-154 84-124 (182)
162 PRK04217 hypothetical protein; 32.1 1.1E+02 0.0024 25.1 5.1 46 54-104 41-86 (110)
163 PF04999 FtsL: Cell division p 31.8 1.1E+02 0.0023 23.8 4.8 27 120-146 44-70 (97)
164 PF11594 Med28: Mediator compl 31.7 2.8E+02 0.0061 22.9 7.3 14 91-104 18-31 (106)
165 KOG0150 Spliceosomal protein F 31.3 1.4E+02 0.0031 29.1 6.4 61 93-153 16-77 (336)
166 TIGR02051 MerR Hg(II)-responsi 31.3 2.9E+02 0.0063 22.5 8.8 37 52-101 34-70 (124)
167 KOG4005 Transcription factor X 31.1 4.7E+02 0.01 24.9 10.2 40 114-153 100-139 (292)
168 PF04977 DivIC: Septum formati 30.7 2.1E+02 0.0046 20.8 6.2 32 108-139 21-52 (80)
169 COG2963 Transposase and inacti 30.6 2.6E+02 0.0056 22.1 7.0 42 53-98 5-47 (116)
170 PRK12526 RNA polymerase sigma 30.5 1E+02 0.0022 27.0 5.1 46 56-106 154-199 (206)
171 PRK13922 rod shape-determining 30.4 1.4E+02 0.003 27.6 6.1 31 116-146 67-97 (276)
172 TIGR02985 Sig70_bacteroi1 RNA 30.3 68 0.0015 25.9 3.6 45 56-105 114-158 (161)
173 cd04766 HTH_HspR Helix-Turn-He 30.3 2.5E+02 0.0054 21.5 6.9 35 52-98 35-69 (91)
174 PRK14872 rod shape-determining 30.2 91 0.002 30.6 5.0 20 113-132 59-78 (337)
175 KOG2391 Vacuolar sorting prote 30.1 1.6E+02 0.0034 29.2 6.5 44 109-152 223-266 (365)
176 COG3074 Uncharacterized protei 30.1 2.1E+02 0.0047 22.1 5.9 36 113-148 34-69 (79)
177 TIGR02209 ftsL_broad cell divi 30.0 1.4E+02 0.003 22.3 5.1 23 123-145 36-58 (85)
178 cd04781 HTH_MerR-like_sg6 Heli 30.0 3E+02 0.0065 22.2 8.5 36 52-100 34-69 (120)
179 cd04770 HTH_HMRTR Helix-Turn-H 29.9 2.9E+02 0.0064 22.1 9.3 38 52-102 35-72 (123)
180 PF03670 UPF0184: Uncharacteri 29.8 1.3E+02 0.0028 23.8 4.8 35 110-144 25-59 (83)
181 TIGR02449 conserved hypothetic 29.7 2.5E+02 0.0053 21.2 6.8 42 108-149 11-52 (65)
182 PRK09639 RNA polymerase sigma 29.6 1.7E+02 0.0036 24.1 5.9 45 56-106 113-157 (166)
183 PF02344 Myc-LZ: Myc leucine z 29.4 1.4E+02 0.003 19.6 4.0 21 129-149 5-25 (32)
184 PRK12512 RNA polymerase sigma 29.3 1.1E+02 0.0025 25.8 5.0 46 56-106 132-177 (184)
185 cd00093 HTH_XRE Helix-turn-hel 28.9 67 0.0015 20.2 2.8 23 79-101 15-37 (58)
186 PF08961 DUF1875: Domain of un 28.8 19 0.0004 33.5 0.0 47 98-144 113-162 (243)
187 PF08172 CASP_C: CASP C termin 28.8 1.8E+02 0.004 27.1 6.6 30 120-149 102-131 (248)
188 KOG0709 CREB/ATF family transc 28.5 1.2E+02 0.0025 31.2 5.5 73 73-146 220-300 (472)
189 PF12999 PRKCSH-like: Glucosid 28.4 2.7E+02 0.0059 24.9 7.3 23 131-153 152-174 (176)
190 cd04762 HTH_MerR-trunc Helix-T 28.4 60 0.0013 20.8 2.5 24 79-102 3-26 (49)
191 KOG3863 bZIP transcription fac 28.4 1.8E+02 0.004 30.8 7.0 34 116-149 516-549 (604)
192 TIGR02989 Sig-70_gvs1 RNA poly 28.3 1.2E+02 0.0026 24.7 4.8 44 56-104 112-155 (159)
193 PF01381 HTH_3: Helix-turn-hel 28.2 49 0.0011 22.4 2.1 23 79-101 12-34 (55)
194 COG1579 Zn-ribbon protein, pos 28.2 2.2E+02 0.0048 26.6 6.9 50 103-152 23-72 (239)
195 cd01392 HTH_LacI Helix-turn-he 28.0 64 0.0014 21.6 2.6 21 81-101 2-22 (52)
196 cd04764 HTH_MlrA-like_sg1 Heli 27.9 58 0.0013 23.3 2.5 21 79-99 3-23 (67)
197 TIGR00219 mreC rod shape-deter 27.8 1.1E+02 0.0024 28.9 5.0 15 130-144 71-85 (283)
198 PRK12530 RNA polymerase sigma 27.6 1.5E+02 0.0033 25.5 5.5 46 56-106 135-180 (189)
199 PF00376 MerR: MerR family reg 27.4 60 0.0013 21.5 2.3 19 79-97 2-20 (38)
200 PF11932 DUF3450: Protein of u 27.3 2.9E+02 0.0062 25.3 7.5 45 108-152 53-97 (251)
201 PRK00118 putative DNA-binding 27.1 1.4E+02 0.0031 24.2 4.9 45 56-105 18-62 (104)
202 PTZ00454 26S protease regulato 27.1 1.7E+02 0.0038 29.0 6.5 31 114-144 32-62 (398)
203 PF10883 DUF2681: Protein of u 27.1 1.2E+02 0.0027 24.0 4.4 23 127-149 32-54 (87)
204 PRK12519 RNA polymerase sigma 26.9 1.1E+02 0.0025 26.0 4.6 30 77-106 158-187 (194)
205 KOG0977 Nuclear envelope prote 26.7 1.8E+02 0.0038 30.5 6.5 38 113-150 150-187 (546)
206 PHA01750 hypothetical protein 26.4 3E+02 0.0064 21.1 6.4 35 114-148 38-72 (75)
207 cd04763 HTH_MlrA-like Helix-Tu 26.1 64 0.0014 23.2 2.5 21 79-99 3-23 (68)
208 TIGR02047 CadR-PbrR Cd(II)/Pb( 26.1 3.7E+02 0.008 22.0 8.7 35 52-99 35-69 (127)
209 PRK09648 RNA polymerase sigma 26.0 1.4E+02 0.0031 25.3 5.1 45 56-105 140-184 (189)
210 TIGR02948 SigW_bacill RNA poly 25.8 1.3E+02 0.0028 25.3 4.7 46 56-106 137-182 (187)
211 PRK14086 dnaA chromosomal repl 25.7 3.9E+02 0.0085 28.4 9.0 60 90-149 556-615 (617)
212 COG2433 Uncharacterized conser 25.5 2.2E+02 0.0048 30.3 7.0 39 111-149 429-467 (652)
213 PF12808 Mto2_bdg: Micro-tubul 25.5 2.5E+02 0.0055 20.2 5.3 37 114-150 11-47 (52)
214 TIGR02959 SigZ RNA polymerase 25.4 1.5E+02 0.0032 25.0 5.0 43 56-103 101-143 (170)
215 PRK12515 RNA polymerase sigma 25.2 1.5E+02 0.0033 25.2 5.1 46 56-106 132-177 (189)
216 COG4467 Regulator of replicati 24.9 1.5E+02 0.0032 24.7 4.5 36 108-143 19-54 (114)
217 cd06170 LuxR_C_like C-terminal 24.6 1.2E+02 0.0026 20.0 3.5 36 57-98 2-37 (57)
218 PRK05602 RNA polymerase sigma 24.6 1.4E+02 0.0031 25.3 4.8 46 56-106 129-174 (186)
219 KOG3650 Predicted coiled-coil 24.6 2.7E+02 0.0059 22.9 5.9 31 115-145 67-97 (120)
220 KOG3755 SATB1 matrix attachmen 24.4 37 0.00081 35.9 1.2 61 49-109 691-759 (769)
221 COG1394 NtpD Archaeal/vacuolar 24.4 3.4E+02 0.0073 25.0 7.3 51 102-152 15-65 (211)
222 PF08614 ATG16: Autophagy prot 24.3 4.3E+02 0.0093 23.3 7.9 44 110-153 143-186 (194)
223 TIGR02999 Sig-70_X6 RNA polyme 24.3 1.7E+02 0.0036 24.6 5.1 29 78-106 152-180 (183)
224 PF13551 HTH_29: Winged helix- 24.1 1.6E+02 0.0035 22.5 4.6 44 55-98 57-109 (112)
225 PF13700 DUF4158: Domain of un 24.0 4E+02 0.0086 22.6 7.4 40 71-110 64-103 (166)
226 PF12325 TMF_TATA_bd: TATA ele 24.0 2.6E+02 0.0055 23.4 5.9 47 100-146 64-110 (120)
227 KOG1853 LIS1-interacting prote 23.9 1.8E+02 0.0038 27.9 5.5 34 94-127 56-89 (333)
228 PF12844 HTH_19: Helix-turn-he 23.9 1.1E+02 0.0024 21.3 3.4 37 79-116 15-51 (64)
229 COG2919 Septum formation initi 23.9 3.5E+02 0.0075 22.1 6.7 50 90-140 37-86 (117)
230 PRK09047 RNA polymerase factor 23.8 1.7E+02 0.0037 23.9 5.0 45 56-105 107-151 (161)
231 PF08961 DUF1875: Domain of un 23.8 26 0.00057 32.5 0.0 35 113-147 124-158 (243)
232 cd04783 HTH_MerR1 Helix-Turn-H 23.7 4E+02 0.0087 21.6 8.8 36 53-101 36-71 (126)
233 KOG4343 bZIP transcription fac 23.6 1E+02 0.0023 32.2 4.2 34 113-146 304-337 (655)
234 PRK09039 hypothetical protein; 23.4 3.7E+02 0.0081 26.1 7.9 45 110-154 122-166 (343)
235 cd01104 HTH_MlrA-CarA Helix-Tu 23.3 79 0.0017 22.4 2.5 20 79-98 3-22 (68)
236 PF06210 DUF1003: Protein of u 23.2 3E+02 0.0065 22.5 6.1 44 98-152 57-100 (108)
237 PTZ00361 26 proteosome regulat 23.1 2E+02 0.0043 29.1 6.1 48 99-146 53-102 (438)
238 PF08826 DMPK_coil: DMPK coile 23.1 3.2E+02 0.0069 20.2 6.5 36 113-148 20-55 (61)
239 cd04776 HTH_GnyR Helix-Turn-He 23.1 4.1E+02 0.0089 21.5 9.3 34 53-99 34-67 (118)
240 PF11544 Spc42p: Spindle pole 23.0 3.7E+02 0.008 20.9 7.1 50 98-147 6-55 (76)
241 PF03980 Nnf1: Nnf1 ; InterPr 23.0 1.6E+02 0.0034 23.4 4.4 31 115-145 77-107 (109)
242 cd04775 HTH_Cfa-like Helix-Tur 22.9 3.8E+02 0.0082 21.0 8.7 35 52-99 35-69 (102)
243 PRK12541 RNA polymerase sigma 22.8 1.6E+02 0.0034 24.3 4.6 46 56-106 113-158 (161)
244 PRK12546 RNA polymerase sigma 22.6 1.1E+02 0.0025 26.5 3.8 46 56-106 114-159 (188)
245 PF08280 HTH_Mga: M protein tr 22.6 90 0.0019 22.2 2.6 35 59-97 6-40 (59)
246 PF12709 Kinetocho_Slk19: Cent 22.6 2.4E+02 0.0052 22.5 5.2 33 114-146 45-77 (87)
247 PRK09644 RNA polymerase sigma 22.5 1.2E+02 0.0027 25.1 3.9 29 78-106 126-154 (165)
248 KOG0773 Transcription factor M 22.4 94 0.002 29.7 3.5 38 69-106 117-154 (342)
249 PRK12518 RNA polymerase sigma 22.4 1E+02 0.0022 25.7 3.4 33 74-106 134-166 (175)
250 PF04728 LPP: Lipoprotein leuc 22.4 3.2E+02 0.007 20.0 5.7 45 113-157 5-49 (56)
251 TIGR02939 RpoE_Sigma70 RNA pol 22.3 1E+02 0.0022 26.0 3.4 30 77-106 155-184 (190)
252 PF10473 CENP-F_leu_zip: Leuci 22.3 3.8E+02 0.0082 23.0 6.8 43 108-150 56-98 (140)
253 PF09304 Cortex-I_coil: Cortex 22.1 4.6E+02 0.0099 21.7 7.1 41 110-150 36-76 (107)
254 smart00787 Spc7 Spc7 kinetocho 22.0 3.5E+02 0.0075 26.1 7.3 48 95-147 133-180 (312)
255 TIGR03070 couple_hipB transcri 22.0 76 0.0016 21.2 2.1 23 79-101 18-40 (58)
256 TIGR02209 ftsL_broad cell divi 21.8 2.4E+02 0.0051 21.1 5.0 37 108-145 28-64 (85)
257 PF12718 Tropomyosin_1: Tropom 21.7 4.1E+02 0.009 22.5 7.0 51 105-155 22-72 (143)
258 cd04777 HTH_MerR-like_sg1 Heli 21.6 4E+02 0.0088 20.9 7.0 35 53-100 34-68 (107)
259 PRK12537 RNA polymerase sigma 21.1 2E+02 0.0044 24.4 5.0 45 56-105 134-178 (182)
260 PF08317 Spc7: Spc7 kinetochor 21.1 3.8E+02 0.0083 25.6 7.4 48 95-147 138-185 (325)
261 PRK12543 RNA polymerase sigma 21.0 1.9E+02 0.0041 24.5 4.8 29 78-106 135-163 (179)
262 PRK12538 RNA polymerase sigma 20.8 2.3E+02 0.005 25.6 5.6 29 78-106 189-217 (233)
263 TIGR02950 SigM_subfam RNA poly 20.8 1.2E+02 0.0025 24.7 3.3 33 73-105 118-150 (154)
264 cd04787 HTH_HMRTR_unk Helix-Tu 20.6 4.8E+02 0.01 21.4 9.5 35 53-100 36-70 (133)
265 PF11516 DUF3220: Protein of u 20.4 2E+02 0.0043 22.8 4.3 30 91-121 31-60 (106)
266 PF04880 NUDE_C: NUDE protein, 20.4 1.4E+02 0.003 26.4 3.8 17 132-148 24-40 (166)
267 TIGR02479 FliA_WhiG RNA polyme 20.3 1.4E+02 0.0031 26.4 4.0 45 56-105 176-220 (224)
268 PF11559 ADIP: Afadin- and alp 20.3 5.1E+02 0.011 21.6 7.6 13 124-136 72-84 (151)
269 PTZ00454 26S protease regulato 20.2 2.9E+02 0.0063 27.4 6.5 45 106-150 17-61 (398)
270 PF07989 Microtub_assoc: Micro 20.0 2.6E+02 0.0056 21.4 4.8 53 93-148 21-73 (75)
271 PRK06811 RNA polymerase factor 20.0 1.9E+02 0.0042 24.7 4.7 46 56-106 132-177 (189)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.89 E-value=4.2e-23 Score=184.25 Aligned_cols=105 Identities=61% Similarity=0.892 Sum_probs=95.5
Q ss_pred cCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHH
Q 022964 46 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKA 125 (289)
Q Consensus 46 ~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~ 125 (289)
.....+|++|||.+|+..||..|+.+.++.+.+|..||++|||.+|||+|||||||||||.++++.+++.|+..++.|+.
T Consensus 47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~ 126 (198)
T KOG0483|consen 47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRS 126 (198)
T ss_pred ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhh
Confidence 33456788899999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 126 DYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 126 ~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
++..|+.++..|++++..++..++.
T Consensus 127 ~~~~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 127 ENDRLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred hhhHHHHHHHHHHHHHhhhhhhhcc
Confidence 8888888888888888777766554
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.66 E-value=7.3e-17 Score=152.16 Aligned_cols=59 Identities=39% Similarity=0.579 Sum_probs=56.2
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYD 114 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~ 114 (289)
|+..|+.+||+.|++.+|++..+|+.||..|+|++.||||||||||-|.||+++++..+
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999988776544
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=1.3e-16 Score=148.04 Aligned_cols=61 Identities=38% Similarity=0.679 Sum_probs=56.8
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
..+|.|+.||..|+.+||+.|..++|++..+|.+||..|.|+++||||||||||+||||..
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 4566667799999999999999999999999999999999999999999999999999854
No 4
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.62 E-value=3.7e-16 Score=136.85 Aligned_cols=63 Identities=35% Similarity=0.499 Sum_probs=58.3
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
+.+|.|+.||.+|+..||..|+.++|....+|++||+.|+|++.||+|||||||+|.||.+.+
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e 163 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQE 163 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHH
Confidence 445566679999999999999999999999999999999999999999999999999998755
No 5
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=5.2e-16 Score=147.26 Aligned_cols=55 Identities=42% Similarity=0.683 Sum_probs=52.6
Q ss_pred CcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 54 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 54 ~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+.||..|+..||+.|++.+|++..+|++||..|||+..||++||||||+|||+..
T Consensus 177 TaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 177 TAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred hhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 3499999999999999999999999999999999999999999999999999854
No 6
>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=99.60 E-value=1.7e-15 Score=108.48 Aligned_cols=57 Identities=42% Similarity=0.636 Sum_probs=54.5
Q ss_pred CCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 50 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 50 ~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
+++|++||.+|+..|+..|..++||+..++..||.+|||+..+|++||+|||+++|+
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 467788999999999999999999999999999999999999999999999999985
No 7
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.57 E-value=9.9e-16 Score=144.60 Aligned_cols=63 Identities=37% Similarity=0.515 Sum_probs=57.3
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
..||||..+|..|+.+||+.|-.|.|++.+.|.+|++.|+|++|||+|||||||.|.||...+
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 445555569999999999999999999999999999999999999999999999999987643
No 8
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.57 E-value=5.9e-15 Score=133.56 Aligned_cols=59 Identities=34% Similarity=0.532 Sum_probs=54.2
Q ss_pred CCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHH
Q 022964 49 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 107 (289)
Q Consensus 49 ~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk 107 (289)
.||.|+.++.-||..|.+.|+++.|+.-.+|.+||..|||+..||||||||||.|.||.
T Consensus 122 ~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 122 VRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred ccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 33445569999999999999999999999999999999999999999999999999974
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.55 E-value=1.4e-14 Score=130.38 Aligned_cols=61 Identities=36% Similarity=0.609 Sum_probs=55.4
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
++||.|+.|+..|+..||..|+...|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 3444445599999999999999999999999999999999999999999999999999954
No 10
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.55 E-value=3e-15 Score=120.99 Aligned_cols=61 Identities=26% Similarity=0.451 Sum_probs=56.6
Q ss_pred CCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHH
Q 022964 47 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 107 (289)
Q Consensus 47 ~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk 107 (289)
.+++|-|+.||..|+..||+.|...+||++-.|++||.++.|++..|+|||||||||.|++
T Consensus 15 rKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 15 RKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 3556667779999999999999999999999999999999999999999999999999975
No 11
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.53 E-value=8.8e-15 Score=130.80 Aligned_cols=60 Identities=33% Similarity=0.509 Sum_probs=55.3
Q ss_pred CCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 49 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 49 ~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
.|+.|+.||..|+..||+.|+..+|+++.+|.+++..|.|++.||+|||||||+|.||.+
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 344455699999999999999999999999999999999999999999999999999865
No 12
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.49 E-value=1e-14 Score=135.72 Aligned_cols=93 Identities=24% Similarity=0.368 Sum_probs=81.0
Q ss_pred CCccCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhh
Q 022964 43 FDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNS 122 (289)
Q Consensus 43 ~~~~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~ 122 (289)
++.....+|.|+.+|+.|+..|+..|+..++|....|++|+.++||..|.|+|||||||||+||-+...-+..|.+.+.+
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrs 240 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRS 240 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHH
Confidence 33445667888889999999999999999999999999999999999999999999999999998888888889888888
Q ss_pred HHHhhHHHHHHHHH
Q 022964 123 LKADYDNLFKEKEK 136 (289)
Q Consensus 123 lk~~~~~l~~ene~ 136 (289)
.|.. ..-++|++.
T Consensus 241 mK~s-gs~r~ekds 253 (383)
T KOG4577|consen 241 MKRS-GSSRAEKDS 253 (383)
T ss_pred hhcc-CCccccccc
Confidence 8877 555555554
No 13
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.48 E-value=4.9e-14 Score=130.04 Aligned_cols=54 Identities=44% Similarity=0.586 Sum_probs=51.9
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
.+|..|..+||+.|..++|.++.+|.+||..|||++|||||||||||||+||..
T Consensus 205 VYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred EecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 399999999999999999999999999999999999999999999999999854
No 14
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.48 E-value=6.5e-14 Score=128.83 Aligned_cols=55 Identities=31% Similarity=0.527 Sum_probs=52.6
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 109 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~ 109 (289)
.||..|+..||+.|+..+||+...|+.||.++.|.+.+|+||||||||||||+..
T Consensus 147 iFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 147 IFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred hhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 3999999999999999999999999999999999999999999999999998643
No 15
>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=99.47 E-value=1.1e-13 Score=98.71 Aligned_cols=57 Identities=49% Similarity=0.728 Sum_probs=53.6
Q ss_pred CCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHH
Q 022964 51 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 107 (289)
Q Consensus 51 rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk 107 (289)
+++.+++..|+..|+..|..++||+..++..||.++||+..||++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 456679999999999999999999999999999999999999999999999998863
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.46 E-value=1.1e-13 Score=98.18 Aligned_cols=55 Identities=45% Similarity=0.764 Sum_probs=51.5
Q ss_pred CCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 51 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 51 rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
+.|.+|+.+|+..|+..|..++||+..++..||..+||+..||+.||+|||++.|
T Consensus 2 k~r~~~~~~~~~~L~~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~ 56 (56)
T smart00389 2 RKRTSFTPEQLEELEKEFQKNPYPSREEREELAAKLGLSERQVKVWFQNRRAKWK 56 (56)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHhHHHHhhccC
Confidence 4566799999999999999999999999999999999999999999999999864
No 17
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.45 E-value=4.6e-14 Score=129.93 Aligned_cols=87 Identities=30% Similarity=0.476 Sum_probs=69.0
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHH-HH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDN-LF 131 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~-l~ 131 (289)
|+-||.+||.+|+..|+.+.|++..+|.+||.+|||.+.||+|||||+|+|.||..-.+..-.|......|...-.. |+
T Consensus 250 RTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqglyNHst~~l~ 329 (342)
T KOG0493|consen 250 RTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQGLYNHSTTHLM 329 (342)
T ss_pred cccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccccccCccchhh
Confidence 44599999999999999999999999999999999999999999999999999987766666665555544433322 44
Q ss_pred HHHHHHHH
Q 022964 132 KEKEKLKA 139 (289)
Q Consensus 132 ~ene~L~~ 139 (289)
.+.++++.
T Consensus 330 a~e~k~es 337 (342)
T KOG0493|consen 330 AQEAKVES 337 (342)
T ss_pred hhhhhhhh
Confidence 44444443
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.43 E-value=1.7e-13 Score=118.58 Aligned_cols=67 Identities=36% Similarity=0.537 Sum_probs=61.2
Q ss_pred CccCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 44 DEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 44 ~~~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
+.....+++|+|.|..|+.+|++.|+.++||+...|..|+..|+|+++-|+|||||||++.|++...
T Consensus 46 ~~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 46 DGSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred cCCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 3445677888999999999999999999999999999999999999999999999999999987644
No 19
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.42 E-value=1.2e-13 Score=124.40 Aligned_cols=63 Identities=29% Similarity=0.423 Sum_probs=58.6
Q ss_pred cCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 46 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 46 ~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
..+++|.|++|+..|+.+||..|.+..||+...|++||.+|+|.+.+|+|||.|||+|+|+.+
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq 96 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQ 96 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhh
Confidence 345667788899999999999999999999999999999999999999999999999999865
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.32 E-value=6.9e-13 Score=124.43 Aligned_cols=63 Identities=33% Similarity=0.515 Sum_probs=58.4
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
+.+|-|+-||.+||.+||+.|-+.+|.+..+|.+||..|+|++..|||||||||+|.||+.+-
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 456667779999999999999999999999999999999999999999999999999997654
No 21
>TIGR01565 homeo_ZF_HD homeobox domain, ZF-HD class. This model represents a class of homoebox domain that differs substantially from the typical homoebox domain described in pfam model pfam00046. It is found in both C4 and C3 plants.
Probab=99.32 E-value=1.4e-12 Score=95.60 Aligned_cols=52 Identities=13% Similarity=0.338 Sum_probs=49.5
Q ss_pred CCCCCcCCHHHHHHHHhhhhccCC----CCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 50 PEKKRRLTVDQVQFLEKSFEVENK----LEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 50 ~rkR~R~T~eQl~~LE~~F~~~~~----P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
+|.|+.||.+|+..|+..|+.++| |+...+.+||..|||+.++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 677888999999999999999999 9999999999999999999999999964
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.26 E-value=1.5e-12 Score=125.90 Aligned_cols=61 Identities=28% Similarity=0.412 Sum_probs=56.9
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
++||||+.|.......||+.|.+|++|+..++..||.+|+|...+|+|||||||.|.||..
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 5667777799999999999999999999999999999999999999999999999999853
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.24 E-value=3.8e-12 Score=114.95 Aligned_cols=61 Identities=34% Similarity=0.662 Sum_probs=55.5
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+++..|..|+..||..||..|+..+|+-..+|.+||..+||+..||+|||||||+|||++.
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 3344455699999999999999999999999999999999999999999999999999864
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.21 E-value=5.2e-12 Score=109.64 Aligned_cols=58 Identities=36% Similarity=0.531 Sum_probs=54.2
Q ss_pred CCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 51 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 51 rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
|-|+.|+..|+..||+.|+..+|++-.++.+||..|+|++.||+.||||||+|.||.+
T Consensus 102 K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 102 KARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred hhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 3455699999999999999999999999999999999999999999999999999865
No 25
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.14 E-value=3.9e-11 Score=113.05 Aligned_cols=61 Identities=28% Similarity=0.544 Sum_probs=55.8
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+++|.|+.||..|+..||..|.++.||+...|++||.-++|++..|+|||.|||+|||+..
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrE 171 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRE 171 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhh
Confidence 4445556699999999999999999999999999999999999999999999999999853
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.02 E-value=2.1e-10 Score=102.28 Aligned_cols=62 Identities=29% Similarity=0.362 Sum_probs=57.0
Q ss_pred CCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 47 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 47 ~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
..+++.|+.|+..|+..||+.|+..+||+...++.||..+++++..|++||||||++|++..
T Consensus 58 ~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 58 FSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 35566677799999999999999999999999999999999999999999999999999854
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.76 E-value=2.4e-09 Score=100.27 Aligned_cols=66 Identities=23% Similarity=0.345 Sum_probs=59.9
Q ss_pred CCccCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 43 FDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 43 ~~~~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
.-++..++|||+.+.+...+.||.+|...++|+.+.+..||++|.|....|+|||+|.|.|.||..
T Consensus 303 l~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 303 LLPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred ccCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 334556788888899999999999999999999999999999999999999999999999998843
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.72 E-value=1.1e-08 Score=99.13 Aligned_cols=61 Identities=30% Similarity=0.564 Sum_probs=56.1
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
..+|+|+.|+..|+..|+..|+.++||+...|+.||.++|++...|++||+|||+++++..
T Consensus 175 ~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 175 GGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 3445567799999999999999999999999999999999999999999999999999854
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.67 E-value=1.8e-08 Score=93.83 Aligned_cols=51 Identities=29% Similarity=0.443 Sum_probs=47.2
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
|...-...|..+|..++||++.+|.+||+.+||+..||-.||.|||.|.|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 555567899999999999999999999999999999999999999999984
No 30
>PF05920 Homeobox_KN: Homeobox KN domain; InterPro: IPR008422 This entry represents a homeobox transcription factor KN domain conserved from fungi to human and plants [].; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 3K2A_B 2LK2_A 1X2N_A 2DMN_A.
Probab=98.31 E-value=6e-07 Score=61.08 Aligned_cols=34 Identities=38% Similarity=0.556 Sum_probs=29.1
Q ss_pred ccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHH
Q 022964 70 VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 103 (289)
Q Consensus 70 ~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak 103 (289)
.++||+.+++..||.++||+..||..||-|.|.|
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 4789999999999999999999999999999975
No 31
>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=98.30 E-value=1.4e-06 Score=60.83 Aligned_cols=44 Identities=66% Similarity=0.968 Sum_probs=41.7
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 107 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 107 k~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
+|++++|+.|+..|+.|+++|++|..||+.|++|+..|+++++.
T Consensus 1 KQlE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~kl~~ 44 (45)
T PF02183_consen 1 KQLERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKEKLQM 44 (45)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcC
Confidence 47899999999999999999999999999999999999999864
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.17 E-value=8.6e-07 Score=82.36 Aligned_cols=60 Identities=28% Similarity=0.456 Sum_probs=54.8
Q ss_pred CCCCCCCcCCHHHHHHHHhhhh---ccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFE---VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 107 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~---~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk 107 (289)
..+||||-|+..-..+|..+|- .++||+.+.+++||+++|++..||..||.|+|-++|+.
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 3567788899999999999995 58899999999999999999999999999999999974
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.93 E-value=1.4e-05 Score=80.76 Aligned_cols=58 Identities=21% Similarity=0.229 Sum_probs=52.6
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
..+|.|..||..|.+.|..+|+.+++|+.+..+.|+.+|||..+.|.+||-|-|.|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 4455566799999999999999999999999999999999999999999999888763
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.75 E-value=4e-05 Score=68.29 Aligned_cols=61 Identities=31% Similarity=0.601 Sum_probs=55.1
Q ss_pred CCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 48 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 48 ~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
..++.++.++..|+..|...|...++|....+..|+..+|++.+.|++||||+|++.++..
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~ 212 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHK 212 (235)
T ss_pred ccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhc
Confidence 3444555699999999999999999999999999999999999999999999999999864
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.86 E-value=0.00084 Score=73.79 Aligned_cols=65 Identities=22% Similarity=0.378 Sum_probs=59.1
Q ss_pred ccCCCCCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHH
Q 022964 45 EYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 109 (289)
Q Consensus 45 ~~~~~~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~ 109 (289)
....++++|++++..|+..|..+|....+|...+.+.|...+++..+.|.+||||-|++.|+..+
T Consensus 899 ~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 899 DGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 34456778889999999999999999999999999999999999999999999999999998654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.25 E-value=0.0034 Score=60.17 Aligned_cols=61 Identities=30% Similarity=0.353 Sum_probs=49.7
Q ss_pred CCCCCcCCHHHHHHHHhhhhc---cCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 50 PEKKRRLTVDQVQFLEKSFEV---ENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 50 ~rkR~R~T~eQl~~LE~~F~~---~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
.|+++.+....+.+|+.+... .+||+...+..||+++||+..||.+||-|.|-|..+-..+
T Consensus 240 ~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 240 WRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 334445989999999987433 5799999999999999999999999999998887765433
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.24 E-value=0.0034 Score=45.84 Aligned_cols=43 Identities=26% Similarity=0.365 Sum_probs=31.4
Q ss_pred HHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHH
Q 022964 60 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 102 (289)
Q Consensus 60 Ql~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRa 102 (289)
.++.|+.+|...+.+.......|..+.||+..||+.||-.|+.
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~~ 51 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERMQ 51 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS-
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhcc
Confidence 3567999999999999999999999999999999999976543
No 38
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=94.13 E-value=0.13 Score=35.90 Aligned_cols=35 Identities=43% Similarity=0.587 Sum_probs=31.0
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 116 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 116 l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
+...|+.|++.|++|..+++.|+.|+..|+..+..
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~ 37 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE 37 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45678999999999999999999999999988764
No 39
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=94.07 E-value=0.33 Score=39.93 Aligned_cols=94 Identities=19% Similarity=0.211 Sum_probs=51.8
Q ss_pred CCCCcCCHHHHH-HHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHH--H--HHHhhhhhhHHH
Q 022964 51 EKKRRLTVDQVQ-FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKD--Y--DVLQNSYNSLKA 125 (289)
Q Consensus 51 rkR~R~T~eQl~-~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e--~--~~l~~~~~~lk~ 125 (289)
++|+++|.++.. ++...+. +. ....++|+++|+++.+|..|.+-=+ ....... . .........+..
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g----~sv~evA~e~gIs~~tl~~W~r~y~----~~~~~~~~~~~~~~~~~~~~~~~~ 78 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PG----MTVSLVARQHGVAASQLFLWRKQYQ----EGSLTAVAAGEQVVPASELAAAMK 78 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CC----CCHHHHHHHHCcCHHHHHHHHHHHh----hcccccccccccCCchhHHHHHHH
Confidence 445668887644 3443443 22 2356789999999999999954321 1100000 0 000001112445
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 126 DYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 126 ~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
++..|.+++.+|+.|+.=|+..+..-..
T Consensus 79 ei~~L~~el~~L~~E~diLKKa~~~~~~ 106 (121)
T PRK09413 79 QIKELQRLLGKKTMENELLKEAVEYGRA 106 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhch
Confidence 5666777777777777777776654443
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.30 E-value=0.11 Score=54.80 Aligned_cols=48 Identities=19% Similarity=0.354 Sum_probs=44.6
Q ss_pred HHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 61 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 61 l~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+..|...|..|..|+.++-..+|.+.||+.+.|+.||+++++....-.
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 778999999999999999999999999999999999999999877644
No 41
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=92.39 E-value=0.31 Score=34.75 Aligned_cols=47 Identities=21% Similarity=0.384 Sum_probs=34.5
Q ss_pred CCCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 50 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 50 ~rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
+|+|+.+|-++...+-..++... ....||+++|++..+|..|..|+.
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 46677799988887777787666 578899999999999999998753
No 42
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=92.20 E-value=1.6 Score=40.78 Aligned_cols=44 Identities=25% Similarity=0.404 Sum_probs=31.1
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..+.+.|+..++.|++.+..|+.+|.+|..++..|++.|..-.+
T Consensus 103 ~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~ 146 (292)
T KOG4005|consen 103 TEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQ 146 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHH
Confidence 34456677777777777777777888887777777777765443
No 43
>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=87.18 E-value=4.7 Score=29.41 Aligned_cols=38 Identities=26% Similarity=0.370 Sum_probs=28.2
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.....|...+..|..++..|..++..|+.++..|+..+
T Consensus 26 ~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 26 QYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34466777777888888888888888888888777654
No 44
>smart00340 HALZ homeobox associated leucin zipper.
Probab=86.57 E-value=1.3 Score=30.60 Aligned_cols=25 Identities=32% Similarity=0.402 Sum_probs=20.6
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 122 SLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 122 ~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
.||...++|..||.+|+.|+++|+.
T Consensus 9 ~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 9 LLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 5677788888899999999988874
No 45
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=85.83 E-value=17 Score=31.00 Aligned_cols=83 Identities=20% Similarity=0.251 Sum_probs=54.7
Q ss_pred CcCCHHHHHHHHhhhhccCCCCHHHHHHHHHH-hCCChhhhhhHhhhhHHHHH-------HHHHHHHHHHHhhhhhhHHH
Q 022964 54 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKD-LGLQPRQVAIWFQNRRARWK-------TKQLEKDYDVLQNSYNSLKA 125 (289)
Q Consensus 54 ~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~-LgLs~rQVkvWFQNRRak~K-------rk~~e~e~~~l~~~~~~lk~ 125 (289)
.+|+.+++..| -..+|=+. -|++...|-.|=|.||+-.- +-+.......|......|..
T Consensus 22 d~lsDd~Lvsm-------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSM-------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHh-------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56888887765 22233333 48999999999998886321 11222334456666677777
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 126 DYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 126 ~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+.+.|..|+.+++.|+..++.+..
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 777888888888888777776654
No 46
>smart00340 HALZ homeobox associated leucin zipper.
Probab=85.14 E-value=1.7 Score=30.06 Aligned_cols=34 Identities=35% Similarity=0.440 Sum_probs=30.5
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHH
Q 022964 107 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAE 140 (289)
Q Consensus 107 k~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e 140 (289)
|+++.+.+.|+...+.|..+|..|+.|.+.|++-
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4678899999999999999999999999998864
No 47
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=84.89 E-value=2.2 Score=34.65 Aligned_cols=49 Identities=20% Similarity=0.278 Sum_probs=30.6
Q ss_pred hhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 90 PRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 90 ~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
.-++..||++.-- ..+..+++....++.++..+.++|+.|+.|+..|+.
T Consensus 14 ~l~y~l~~g~~G~--------~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 14 WLQYSLWFGKNGI--------LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHhccCCcH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3456788865311 122334444556677777777788888888877766
No 48
>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=84.02 E-value=5.9 Score=30.25 Aligned_cols=38 Identities=29% Similarity=0.339 Sum_probs=20.9
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
-.-...|+..+..|+..+..|..+++.|+.++.+|+..
T Consensus 17 veti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e 54 (72)
T PF06005_consen 17 VETIALLQMENEELKEKNNELKEENEELKEENEQLKQE 54 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHH
Confidence 33445555555555555555555555555555555543
No 49
>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=81.44 E-value=7 Score=32.05 Aligned_cols=46 Identities=28% Similarity=0.442 Sum_probs=37.5
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
+.+.....+-.....||.....|..||..|+.|+..|++.|.....
T Consensus 12 ~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 12 QLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 4566667777788888999999999999999999999988875554
No 50
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=81.31 E-value=11 Score=28.85 Aligned_cols=46 Identities=26% Similarity=0.346 Sum_probs=37.3
Q ss_pred HHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 104 WKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 104 ~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
.....++.+.+.|+..+..|..++..|..+|++|+.+....+..|.
T Consensus 18 eti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~ 63 (72)
T PF06005_consen 18 ETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445677888889999999999999999999999988777776654
No 51
>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=78.39 E-value=12 Score=29.22 Aligned_cols=45 Identities=24% Similarity=0.302 Sum_probs=33.5
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 105 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 105 Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
.+..+.++...|+.....|....+..+.|+++|+.|+.-|+.-+.
T Consensus 17 ~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~ 61 (80)
T PF10224_consen 17 EKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555666777888888888888888888888888888776654
No 52
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=76.94 E-value=10 Score=31.30 Aligned_cols=43 Identities=30% Similarity=0.459 Sum_probs=33.8
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
+++.....+......||.....|..||..|+.|+..|+..|..
T Consensus 12 ~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~ 54 (110)
T PRK13169 12 DLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEE 54 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556666677777788888888888888888888888888774
No 53
>smart00338 BRLZ basic region leucin zipper.
Probab=76.85 E-value=23 Score=25.69 Aligned_cols=37 Identities=32% Similarity=0.489 Sum_probs=27.7
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 112 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 112 e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
....|......|...+..|..+...|..|+..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4456667777788888888888888888888877665
No 54
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=75.68 E-value=7.9 Score=36.45 Aligned_cols=48 Identities=29% Similarity=0.345 Sum_probs=30.7
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 100 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 100 RRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
||.|.++++.+ ..++.....|..++..|+.+++.|+.|+..|+.-+..
T Consensus 207 ~kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~ 254 (269)
T KOG3119|consen 207 RKSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQ 254 (269)
T ss_pred HHhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35556655544 3344556667777777777777777777777665543
No 55
>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=74.05 E-value=15 Score=26.69 Aligned_cols=35 Identities=31% Similarity=0.460 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHH
Q 022964 107 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEV 141 (289)
Q Consensus 107 k~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~ 141 (289)
..++.....|...+..|+..+..|..++..|+.++
T Consensus 29 ~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 29 EELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 34455555666666666666666666666666554
No 56
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=72.98 E-value=6.6 Score=27.80 Aligned_cols=41 Identities=17% Similarity=0.201 Sum_probs=24.9
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhh
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQN 118 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~ 118 (289)
....||+.+|++..+|..|+.++........+.+-...|.-
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~ 52 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNC 52 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCC
Confidence 46789999999999999999988666666655555554433
No 57
>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=72.14 E-value=5.4 Score=26.05 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=31.9
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 103 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak 103 (289)
++..+...+...|... ....++|..+|++...|..|....+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 6777777777776422 245678999999999999998755443
No 58
>PF01527 HTH_Tnp_1: Transposase; InterPro: IPR002514 Transposase proteins are necessary for efficient DNA transposition. This family consists of various Escherichia coli insertion elements and other bacterial transposases some of which are members of the IS3 family. This region includes a helix-turn-helix motif (HTH) at the N terminus followed by a leucine zipper (LZ) motif. The LZ motif has been shown to mediate oligomerisation of the transposase components in IS911 []. More information about these proteins can be found at Protein of the Month: Transposase [].; GO: 0003677 DNA binding, 0004803 transposase activity, 0006313 transposition, DNA-mediated; PDB: 2JN6_A 2RN7_A.
Probab=72.04 E-value=2.9 Score=30.74 Aligned_cols=44 Identities=18% Similarity=0.342 Sum_probs=28.2
Q ss_pred CCCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhh
Q 022964 51 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 51 rkR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
++|++||.++...+-..+. ........+|+++|+++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHHH
Confidence 4567799988776655552 2235678899999999999999964
No 59
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=72.00 E-value=22 Score=26.12 Aligned_cols=31 Identities=32% Similarity=0.430 Sum_probs=25.4
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 119 SYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 119 ~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
.|..+..+..+|..|++.|++|+.+|+.-|.
T Consensus 27 rY~~vL~~R~~l~~e~~~L~~qN~eLr~lLk 57 (60)
T PF14775_consen 27 RYNKVLLDRAALIQEKESLEQQNEELRSLLK 57 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4566777888899999999999999987664
No 60
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=70.23 E-value=18 Score=37.63 Aligned_cols=31 Identities=32% Similarity=0.381 Sum_probs=22.9
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 122 SLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 122 ~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.|.+...+|++||+.|++|++.|+.+|..-.
T Consensus 306 ~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~ 336 (655)
T KOG4343|consen 306 GLEARLQALLSENEQLKKENATLKRQLDELV 336 (655)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHh
Confidence 5667777788888888888888887776444
No 61
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=67.87 E-value=13 Score=25.27 Aligned_cols=41 Identities=15% Similarity=0.192 Sum_probs=30.5
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhh
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 100 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNR 100 (289)
.+++.+..+|...|- ....-.++|..+|++...|+.+...-
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~~a 44 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILKRA 44 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHHHH
Confidence 477888899988883 23346789999999999998886543
No 62
>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=65.45 E-value=57 Score=25.13 Aligned_cols=70 Identities=19% Similarity=0.199 Sum_probs=39.6
Q ss_pred HHHHHHHhCCChhhhhhHhhhhHHHHHHH------HHHHHHHHH------hh----hhhhHHHhhHHHHHHHHHHHHHHH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRRARWKTK------QLEKDYDVL------QN----SYNSLKADYDNLFKEKEKLKAEVL 142 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRRak~Krk------~~e~e~~~l------~~----~~~~lk~~~~~l~~ene~L~~e~~ 142 (289)
..++|+.+|++++.|+.|-+..--.-.+. =...+...+ +. ....+ ...-.|..+.+.|++++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i-~~~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGV-KRILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHH-HHHHHHHHHHHHHHHHHH
Confidence 45789999999999999975432221110 001111111 11 11111 122347778888888888
Q ss_pred HHHHHHh
Q 022964 143 KLTDKLQ 149 (289)
Q Consensus 143 ~l~~~l~ 149 (289)
+|+.+|.
T Consensus 83 ~l~~~~~ 89 (91)
T cd04766 83 ELRARLR 89 (91)
T ss_pred HHHHHhc
Confidence 8887764
No 63
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=64.99 E-value=9 Score=37.53 Aligned_cols=27 Identities=33% Similarity=0.529 Sum_probs=12.7
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 122 SLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 122 ~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.|+.+|.+|++||+.|+.|+.+|++..
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~e~ 62 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLENEM 62 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHHHh
Confidence 344444444445555555544444333
No 64
>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=64.55 E-value=35 Score=25.72 Aligned_cols=44 Identities=18% Similarity=0.205 Sum_probs=27.7
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 109 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 109 ~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
++...+.|-..+..|+.+|..|.++...+..|...|.++....-
T Consensus 5 Le~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar 48 (65)
T TIGR02449 5 LAAQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQAR 48 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555566666677777777777777777777766655443
No 65
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=64.52 E-value=29 Score=33.34 Aligned_cols=50 Identities=16% Similarity=0.268 Sum_probs=36.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 102 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 102 ak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
+|+|.|+ +.+.+.+-.....|-..|+.|+..-..|..|++.||..+...-
T Consensus 240 tRYRqKk-Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~ 289 (294)
T KOG4571|consen 240 TRYRQKK-RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVY 289 (294)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444433 3455667777788888888888888888899888888776543
No 66
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=60.82 E-value=26 Score=29.04 Aligned_cols=43 Identities=30% Similarity=0.406 Sum_probs=34.1
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
..+.....+-+....||.....|..||-.|+-|+..|++.|..
T Consensus 12 ~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 12 NLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 4455566667777788888888999999999999999888875
No 67
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=60.77 E-value=22 Score=20.43 Aligned_cols=38 Identities=16% Similarity=0.327 Sum_probs=26.3
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHh
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 97 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWF 97 (289)
.++.++...+...|.... ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~~-----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAGE-----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCCCHHHHHHhC
Confidence 366666666666665322 45678999999998888773
No 68
>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=60.50 E-value=81 Score=24.78 Aligned_cols=37 Identities=16% Similarity=0.332 Sum_probs=27.6
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
.++.|+..++..|.... ..+.+|++..+|+.++....
T Consensus 35 g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~~ 71 (103)
T cd01106 35 GYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDPS 71 (103)
T ss_pred CceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcCc
Confidence 34569999999885443 35678999999999987643
No 69
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=59.63 E-value=18 Score=41.18 Aligned_cols=56 Identities=18% Similarity=0.259 Sum_probs=51.0
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+..+-.++...|-++|-.+.-|+.+.+.-|....+.+.+++.+||+|-|.|.++..
T Consensus 709 ~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 709 RLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred cccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 34466699999999999999999999999999999999999999999999998865
No 70
>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=59.61 E-value=12 Score=26.88 Aligned_cols=40 Identities=25% Similarity=0.282 Sum_probs=32.7
Q ss_pred CCHHHHHHHHhhhhccCC--CCHHHHHHHHHHhCCChhhhhh
Q 022964 56 LTVDQVQFLEKSFEVENK--LEPERKIQLAKDLGLQPRQVAI 95 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~--P~~~~r~~LA~~LgLs~rQVkv 95 (289)
+|..|...|...|+..-| |-...-.+||.+||++..-|..
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~~~ 42 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTVSE 42 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHHHH
Confidence 588999999999988764 6666788899999999866543
No 71
>smart00338 BRLZ basic region leucin zipper.
Probab=58.83 E-value=37 Score=24.60 Aligned_cols=32 Identities=38% Similarity=0.535 Sum_probs=15.3
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHH
Q 022964 109 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAE 140 (289)
Q Consensus 109 ~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e 140 (289)
++.....|...+..|......|..++..|+.+
T Consensus 31 Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~ 62 (65)
T smart00338 31 LERKVEQLEAENERLKKEIERLRRELEKLKSE 62 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444444444444555444444444
No 72
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=58.62 E-value=31 Score=32.25 Aligned_cols=23 Identities=30% Similarity=0.491 Sum_probs=9.0
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHH
Q 022964 124 KADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 124 k~~~~~l~~ene~L~~e~~~l~~ 146 (289)
..++..|..+++.|+.++..+++
T Consensus 148 ~~EkeeL~~eleele~e~ee~~e 170 (290)
T COG4026 148 QKEKEELLKELEELEAEYEEVQE 170 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333444444443333333
No 73
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=58.38 E-value=42 Score=34.24 Aligned_cols=64 Identities=31% Similarity=0.417 Sum_probs=40.9
Q ss_pred hhhHh---hhhHHHHHHHHHHHHHHHHhhhhhhHH----------HhhH-----------HHH-----------HHHHHH
Q 022964 93 VAIWF---QNRRARWKTKQLEKDYDVLQNSYNSLK----------ADYD-----------NLF-----------KEKEKL 137 (289)
Q Consensus 93 VkvWF---QNRRak~Krk~~e~e~~~l~~~~~~lk----------~~~~-----------~l~-----------~ene~L 137 (289)
.-+|| ||+.+|.+-.++-++.+.|+..-..|. .++. .|. .||+..
T Consensus 228 ~gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ea~rl~elreg~e~e~~ 307 (575)
T KOG4403|consen 228 GGCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENETS 307 (575)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHhhhhhhhhhhcchhHHHH
Confidence 34688 999999888777777766654433332 2211 111 256677
Q ss_pred HHHHHHHHHHHhhhhhhcc
Q 022964 138 KAEVLKLTDKLQVKEKESK 156 (289)
Q Consensus 138 ~~e~~~l~~~l~~~~~~~~ 156 (289)
+.|+..|+.+|...+++-.
T Consensus 308 rkelE~lR~~L~kAEkele 326 (575)
T KOG4403|consen 308 RKELEQLRVALEKAEKELE 326 (575)
T ss_pred HHHHHHHHHHHHHHHHHHH
Confidence 7788888888887776554
No 74
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=58.26 E-value=33 Score=33.77 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=35.4
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 100 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 100 RRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+|.+.+-.+...+.+.++..-+.|+.-...|..+++.|+.++..|+...-
T Consensus 221 ~r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~niD 270 (365)
T KOG2391|consen 221 RRREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKNID 270 (365)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhhhH
Confidence 45555666666777777777777777777777788888877777765543
No 75
>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=57.68 E-value=8.6 Score=28.48 Aligned_cols=18 Identities=22% Similarity=0.558 Sum_probs=16.3
Q ss_pred HHHHHHHhCCChhhhhhH
Q 022964 79 KIQLAKDLGLQPRQVAIW 96 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvW 96 (289)
-..||.+||+++.+|+.|
T Consensus 25 lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 25 LKDIAEKLGVSESTIRKW 42 (60)
T ss_pred HHHHHHHHCCCHHHHHHH
Confidence 457899999999999999
No 76
>PF15058 Speriolin_N: Speriolin N terminus
Probab=57.03 E-value=18 Score=32.92 Aligned_cols=35 Identities=26% Similarity=0.475 Sum_probs=25.4
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 118 NSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 118 ~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
..|+.|++..+.|..||+.||++|.-|++....+.
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLirEN~eLks 39 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLIRENHELKS 39 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHH
Confidence 34667777788888888888888777777665443
No 77
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=57.01 E-value=39 Score=23.76 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=14.5
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 122 SLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 122 ~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
.|......|..+|..|+.++..|+
T Consensus 29 ~le~~~~~L~~en~~L~~~i~~L~ 52 (54)
T PF07716_consen 29 ELEQEVQELEEENEQLRQEIAQLE 52 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 444555566666666666666654
No 78
>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=56.82 E-value=31 Score=28.28 Aligned_cols=40 Identities=23% Similarity=0.314 Sum_probs=34.8
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 107 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 107 k~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
..+-.+...|+.....|..+|..|+-||+.|+..+..+..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3566778889999999999999999999999999888876
No 79
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=55.69 E-value=60 Score=25.43 Aligned_cols=40 Identities=23% Similarity=0.346 Sum_probs=16.7
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
..+.+.|+..+..|..+...+...++.|..++.+|+....
T Consensus 24 qmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~ 63 (79)
T PRK15422 24 QMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQN 63 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3344444444444444433322223335555555554433
No 80
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=55.06 E-value=46 Score=25.34 Aligned_cols=39 Identities=23% Similarity=0.346 Sum_probs=28.6
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 112 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 112 e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
....|+..|..|...+.....++..|.+.|..|..++..
T Consensus 22 q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~ 60 (70)
T PF04899_consen 22 QQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQR 60 (70)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 345677777788888777777777777777777776654
No 81
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=54.93 E-value=35 Score=28.20 Aligned_cols=39 Identities=23% Similarity=0.301 Sum_probs=34.4
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
.+-.+...|+.....|..+|..|..||+.|+..+.++..
T Consensus 19 ~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 19 VLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 566778889999999999999999999999999988744
No 82
>cd04765 HTH_MlrA-like_sg2 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 2), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=54.24 E-value=56 Score=25.95 Aligned_cols=38 Identities=13% Similarity=0.081 Sum_probs=27.9
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
.+++|+.+++..|. ....|.+.+|++-..|+.+..+..
T Consensus 35 g~R~Yt~~di~~l~------------~I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 35 GRRYYRPKDVELLL------------LIKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred CCeeeCHHHHHHHH------------HHHHHHHHCCCCHHHHHHHHHhcc
Confidence 45569999999883 333456788999999988886543
No 83
>PRK10884 SH3 domain-containing protein; Provisional
Probab=53.86 E-value=62 Score=29.42 Aligned_cols=30 Identities=17% Similarity=0.082 Sum_probs=13.1
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 118 NSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 118 ~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
.....|+.+|..|.++.+.++.++..|+.+
T Consensus 132 ~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~ 161 (206)
T PRK10884 132 SVINGLKEENQKLKNQLIVAQKKVDAANLQ 161 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444444444444333
No 84
>PRK14127 cell division protein GpsB; Provisional
Probab=53.52 E-value=40 Score=27.83 Aligned_cols=30 Identities=30% Similarity=0.408 Sum_probs=16.2
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 124 KADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 124 k~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..+++.+..|+..|+.++.+|+.+|..-..
T Consensus 36 ~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 36 IKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555566666666666555554443
No 85
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=52.40 E-value=2.2e+02 Score=29.25 Aligned_cols=92 Identities=20% Similarity=0.296 Sum_probs=57.7
Q ss_pred CcCCHHHHHHHHhh-hhccC-CCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHH-HHHhhhhhhHHHhhHHH
Q 022964 54 RRLTVDQVQFLEKS-FEVEN-KLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDY-DVLQNSYNSLKADYDNL 130 (289)
Q Consensus 54 ~R~T~eQl~~LE~~-F~~~~-~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~-~~l~~~~~~lk~~~~~l 130 (289)
-++|.+....|.+. +-... +|--..-+++. ++|+.=.+|+|..--.+++.++| +.|...+....++|..|
T Consensus 219 L~LteeEkrLL~kEG~slPs~lPLTKaEEriL-------KrvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL 291 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKEGYSLPSKLPLTKAEERIL-------KRVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQEL 291 (472)
T ss_pred eeccHHHHHHHHhccCcCcccCCchHHHHHHH-------HHHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHH
Confidence 35888887777665 33322 34333333332 35666667776544333334444 67777777888888888
Q ss_pred HHHHHHHHHHHHHHHHHHhhhh
Q 022964 131 FKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 131 ~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.+..+.|..++..|-.+|....
T Consensus 292 ~kkV~~Le~~N~sLl~qL~klQ 313 (472)
T KOG0709|consen 292 QKKVEELELSNRSLLAQLKKLQ 313 (472)
T ss_pred HHHHHHHhhccHHHHHHHHHHH
Confidence 8888888888888777776444
No 86
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=52.21 E-value=72 Score=34.54 Aligned_cols=51 Identities=24% Similarity=0.335 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 102 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 102 ak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
|..++..+..+.+.+++.+..+....+.|...++.|+.|+.+|+...+..+
T Consensus 214 Ale~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~~~~~ 264 (916)
T KOG0249|consen 214 ALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSSLEKE 264 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhh
Confidence 556677778888888888888888999999999999999999996554444
No 87
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=52.08 E-value=22 Score=32.27 Aligned_cols=41 Identities=32% Similarity=0.517 Sum_probs=34.2
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 022964 115 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 155 (289)
Q Consensus 115 ~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~~~ 155 (289)
.+...|+.|+..++.|..++++|+.|+..|+..+.......
T Consensus 109 qlE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~ 149 (198)
T KOG0483|consen 109 QLEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKREM 149 (198)
T ss_pred hhhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhh
Confidence 45567889999999999999999999999998887555433
No 88
>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=51.68 E-value=37 Score=23.18 Aligned_cols=41 Identities=17% Similarity=0.185 Sum_probs=26.6
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
++..+...+...|- ......++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 55556666655543 344678899999999999999987444
No 89
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=50.19 E-value=22 Score=24.07 Aligned_cols=41 Identities=22% Similarity=0.209 Sum_probs=21.0
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhh
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
.+.||.++...++..+... .-..+||+.||.++.-|..+..
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 3468888888888887633 4566799999999999887764
No 90
>PF05700 BCAS2: Breast carcinoma amplified sequence 2 (BCAS2); InterPro: IPR008409 This family consists of several eukaryotic sequences of unknown function. The mammalian members of this family are annotated as breast carcinoma amplified sequence 2 (BCAS2) proteins []. BCAS2 is a putative spliceosome associated protein [].
Probab=49.86 E-value=76 Score=28.83 Aligned_cols=44 Identities=16% Similarity=0.199 Sum_probs=31.5
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..+...|......+...+-.+..+...|+.|+.+|+.+....+.
T Consensus 174 ~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~~ 217 (221)
T PF05700_consen 174 GEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELKE 217 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34445666666667777777888888888888888877665543
No 91
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=49.59 E-value=46 Score=30.69 Aligned_cols=40 Identities=25% Similarity=0.392 Sum_probs=28.5
Q ss_pred HHHHhhhhh-hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 113 YDVLQNSYN-SLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 113 ~~~l~~~~~-~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
...++.... ..+.++..|+.|+|+|+.++.++|..|...-
T Consensus 103 f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~ei 143 (220)
T KOG3156|consen 103 FAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHEI 143 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333433333 4567888899999999999999998876433
No 92
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=49.59 E-value=98 Score=23.88 Aligned_cols=41 Identities=24% Similarity=0.345 Sum_probs=22.2
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.+..+.+.|+..++.|..+...+....+.|..++.+|+...
T Consensus 22 LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e~ 62 (79)
T COG3074 22 LLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEEQ 62 (79)
T ss_pred HHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455556666666555555555555555555555555443
No 93
>PRK10884 SH3 domain-containing protein; Provisional
Probab=49.37 E-value=64 Score=29.31 Aligned_cols=41 Identities=10% Similarity=0.019 Sum_probs=28.2
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 109 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 109 ~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
.......|+..+..|+.+...++.+++.|++++..++....
T Consensus 130 ~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~~~ 170 (206)
T PRK10884 130 SDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRTII 170 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444557777777777777777777777777777776544
No 94
>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=48.44 E-value=45 Score=24.45 Aligned_cols=26 Identities=35% Similarity=0.526 Sum_probs=14.4
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 119 SYNSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 119 ~~~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
....+......+.++++.|+.++..|
T Consensus 25 ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 25 EIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 33444555555555666666666555
No 95
>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=47.74 E-value=65 Score=23.55 Aligned_cols=32 Identities=19% Similarity=0.397 Sum_probs=17.1
Q ss_pred hhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 117 QNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 117 ~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.+...++.....+++.|++.|+.++..+.+.+
T Consensus 6 En~~~~~~~~i~tvk~en~~i~~~ve~i~env 37 (55)
T PF05377_consen 6 ENELPRIESSINTVKKENEEISESVEKIEENV 37 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444455555555555666665555555443
No 96
>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=47.51 E-value=1.5e+02 Score=23.89 Aligned_cols=38 Identities=24% Similarity=0.357 Sum_probs=28.3
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 103 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak 103 (289)
.+.|+..++..|. .....+.+|++...|+..+......
T Consensus 35 yR~Y~~~d~~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~~~ 72 (116)
T cd04769 35 YRVYDAQHVECLR-------------FIKEARQLGFTLAELKAIFAGHEGR 72 (116)
T ss_pred ceeeCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhccccC
Confidence 4558888888873 3334688999999999998766543
No 97
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=47.46 E-value=17 Score=32.22 Aligned_cols=31 Identities=35% Similarity=0.460 Sum_probs=7.4
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 022964 125 ADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 155 (289)
Q Consensus 125 ~~~~~l~~ene~L~~e~~~l~~~l~~~~~~~ 155 (289)
.+.+.|+.++++|+.|+..||..|..+++..
T Consensus 24 dEKE~L~~~~QRLkDE~RDLKqEl~V~ek~~ 54 (166)
T PF04880_consen 24 DEKENLREEVQRLKDELRDLKQELIVQEKLR 54 (166)
T ss_dssp HHHHHHHHCH---------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 4567788888888888888888887666543
No 98
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=46.45 E-value=41 Score=31.12 Aligned_cols=38 Identities=29% Similarity=0.350 Sum_probs=17.7
Q ss_pred HHhhhhhhHHHhhHHHHHHHH---HHHHHHHHHHHHHhhhh
Q 022964 115 VLQNSYNSLKADYDNLFKEKE---KLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 115 ~l~~~~~~lk~~~~~l~~ene---~L~~e~~~l~~~l~~~~ 152 (289)
.+...+..|+.++..|..++. .+++|+.+|++.|....
T Consensus 73 ~l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~~ 113 (276)
T PRK13922 73 DLREENEELKKELLELESRLQELEQLEAENARLRELLNLKE 113 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcc
Confidence 334444444444444444433 44555555555554433
No 99
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=46.21 E-value=1.8e+02 Score=24.48 Aligned_cols=37 Identities=11% Similarity=0.033 Sum_probs=26.8
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
..+.|+..++..|... ...+.+|++-..|+-++.+..
T Consensus 34 g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 34 NYRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhc
Confidence 3456999999888432 235778898888888887654
No 100
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=46.21 E-value=57 Score=28.02 Aligned_cols=48 Identities=19% Similarity=0.113 Sum_probs=35.3
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...++..|...|...+ . .....++|..||++...|..|-.+.+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr~-~-----GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLRE-R-----GLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHHH-c-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4468999999987732 1 2245689999999999999998765554443
No 101
>PRK14127 cell division protein GpsB; Provisional
Probab=45.88 E-value=50 Score=27.26 Aligned_cols=36 Identities=28% Similarity=0.500 Sum_probs=28.0
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+.....|..|..++..|..++.+|+.++..++.++.
T Consensus 33 d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~ 68 (109)
T PRK14127 33 DDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVS 68 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 344445666778888888899999999998888777
No 102
>PF07407 Seadorna_VP6: Seadornavirus VP6 protein; InterPro: IPR009982 This family consists of several VP6 proteins from the Banna virus as well as a related protein VP5 from the Kadipiro virus. Members of this family are typically of around 420 residues in length. The function of this family is unknown.
Probab=45.76 E-value=40 Score=33.18 Aligned_cols=32 Identities=31% Similarity=0.402 Sum_probs=23.9
Q ss_pred HHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHH
Q 022964 112 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLK 143 (289)
Q Consensus 112 e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~ 143 (289)
+...|+.++.+||.++..|+.+.++|++++.+
T Consensus 33 e~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l~ 64 (420)
T PF07407_consen 33 ENFALRMENHSLKKENNDLKIEVERLENEMLR 64 (420)
T ss_pred hhhhHHHHhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 44567777888888888888888888777654
No 103
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=44.95 E-value=1.1e+02 Score=24.44 Aligned_cols=42 Identities=29% Similarity=0.393 Sum_probs=26.2
Q ss_pred HHHHHHhhhhh-hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 111 KDYDVLQNSYN-SLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 111 ~e~~~l~~~~~-~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.....|+.+|. ......+.|..++..|..|+.+|+.+|....
T Consensus 34 ~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~ 76 (87)
T PF12709_consen 34 TKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTER 76 (87)
T ss_pred HHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33566665555 4555566677777777777777776665443
No 104
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=44.90 E-value=96 Score=25.63 Aligned_cols=36 Identities=22% Similarity=0.296 Sum_probs=16.1
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
..|.......|.+.+.|.++++.|+.-++.|+....
T Consensus 19 a~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~q~~ 54 (107)
T PF09304_consen 19 ASLERSLEDEKTSQGELAKQKDQLRNALQSLQAQNA 54 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444444444444433
No 105
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=44.78 E-value=55 Score=30.22 Aligned_cols=26 Identities=31% Similarity=0.440 Sum_probs=10.0
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 123 LKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 123 lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
|+...+.+..|-++|.++...|++++
T Consensus 184 l~Kq~e~~~~EydrLlee~~~Lq~~i 209 (216)
T KOG1962|consen 184 LKKQSEGLQDEYDRLLEEYSKLQEQI 209 (216)
T ss_pred HHHHHHHcccHHHHHHHHHHHHHHHH
Confidence 33333333333334444444443333
No 106
>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=44.10 E-value=47 Score=31.47 Aligned_cols=39 Identities=18% Similarity=0.130 Sum_probs=22.7
Q ss_pred HHhhhhhhHHHhhHHH----HHHHHHHHHHHHHHHHHHhhhhh
Q 022964 115 VLQNSYNSLKADYDNL----FKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 115 ~l~~~~~~lk~~~~~l----~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
.++.++..|+.+...| ....+.|++|+.+|++-|..++.
T Consensus 70 ~l~~EN~~Lr~e~~~l~~~~~~~~~~l~~EN~rLr~LL~~~~~ 112 (283)
T TIGR00219 70 NLEYENYKLRQELLKKNQQLEILTQNLKQENVRLRELLNSPLS 112 (283)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCccc
Confidence 3444555555554433 22233488888888887776654
No 107
>PF13518 HTH_28: Helix-turn-helix domain
Probab=44.06 E-value=24 Score=23.69 Aligned_cols=22 Identities=18% Similarity=0.520 Sum_probs=18.7
Q ss_pred HHHHHHHHhCCChhhhhhHhhh
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQN 99 (289)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3566899999999999999753
No 108
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=43.81 E-value=70 Score=30.11 Aligned_cols=43 Identities=23% Similarity=0.290 Sum_probs=32.2
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022964 109 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 151 (289)
Q Consensus 109 ~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~ 151 (289)
.++-+..-+...+.+......|.+||+.|+.+|.+|+..+..-
T Consensus 206 ~~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~ 248 (269)
T KOG3119|consen 206 VRKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATL 248 (269)
T ss_pred HHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555566667777778889999999999999998877643
No 109
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=43.41 E-value=1.2e+02 Score=23.70 Aligned_cols=40 Identities=18% Similarity=0.284 Sum_probs=24.4
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
......|....+.++.....|..+|++|+.|...-+++|.
T Consensus 31 Kekn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~WqerLr 70 (79)
T PRK15422 31 KEKNNSLSQEVQNAQHQREELERENNHLKEQQNGWQERLQ 70 (79)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555666666666677777777777777655555443
No 110
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=43.04 E-value=1.4e+02 Score=28.59 Aligned_cols=28 Identities=29% Similarity=0.453 Sum_probs=19.6
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 022964 127 YDNLFKEKEKLKAEVLKLTDKLQVKEKE 154 (289)
Q Consensus 127 ~~~l~~ene~L~~e~~~l~~~l~~~~~~ 154 (289)
...|....++|+.|...|+..|+.+.++
T Consensus 159 ke~llesvqRLkdEardlrqelavr~kq 186 (333)
T KOG1853|consen 159 KEVLLESVQRLKDEARDLRQELAVRTKQ 186 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3446666777777777777778877765
No 111
>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=41.90 E-value=26 Score=23.17 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=19.1
Q ss_pred HHHHHHHhCCChhhhhhHhhhhH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976543
No 112
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=41.83 E-value=50 Score=25.68 Aligned_cols=22 Identities=36% Similarity=0.530 Sum_probs=11.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHhh
Q 022964 129 NLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 129 ~l~~ene~L~~e~~~l~~~l~~ 150 (289)
.|.+||.+|+.+++.|+..|+.
T Consensus 4 ei~eEn~~Lk~eiqkle~ELq~ 25 (76)
T PF07334_consen 4 EIQEENARLKEEIQKLEAELQQ 25 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555555555555555543
No 113
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=41.17 E-value=77 Score=32.55 Aligned_cols=44 Identities=18% Similarity=0.345 Sum_probs=31.1
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 105 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 105 Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
|...+++.++.+++...-+.+....+....+.|+.|+.+|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 44455666666666666566666777777788888888888887
No 114
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=39.81 E-value=87 Score=30.20 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=13.0
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 022964 125 ADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 154 (289)
Q Consensus 125 ~~~~~l~~ene~L~~e~~~l~~~l~~~~~~ 154 (289)
++.++|..|.+.|...+.+||.++...+++
T Consensus 248 ae~E~l~ge~~~Le~rN~~LK~qa~~lerE 277 (294)
T KOG4571|consen 248 AEKEALLGELEGLEKRNEELKDQASELERE 277 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444444444444444444444433
No 115
>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=39.59 E-value=44 Score=24.75 Aligned_cols=24 Identities=25% Similarity=0.261 Sum_probs=12.4
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 123 LKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 123 lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
||.....|...|..|+.|+.-||.
T Consensus 19 LK~~I~eL~~~n~~Le~EN~~Lk~ 42 (59)
T PF01166_consen 19 LKEQIAELEERNSQLEEENNLLKQ 42 (59)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344444455555555555555553
No 116
>PF07334 IFP_35_N: Interferon-induced 35 kDa protein (IFP 35) N-terminus; InterPro: IPR009938 This entry represents the N terminus of interferon-induced 35 kDa protein (IFP 35) (approximately 80 residues long), which contains a leucine zipper motif in an alpha helical configuration []. This group of proteins also includes N-myc-interactor (Nmi), a homologous interferon-induced protein.
Probab=39.00 E-value=52 Score=25.55 Aligned_cols=33 Identities=27% Similarity=0.418 Sum_probs=27.1
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 121 NSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 121 ~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..+..++..|..+.++|++|+++++...+.++.
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~~qIk~d 35 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKREFQIKED 35 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhhhccC
Confidence 356778888999999999999999988776663
No 117
>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=38.79 E-value=1.1e+02 Score=22.37 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=31.8
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
.++.+...+....+.++.++..+..+.++|..-+..|-
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll 41 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLL 41 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45677788888899999999999999999998886663
No 118
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=38.35 E-value=67 Score=29.65 Aligned_cols=39 Identities=26% Similarity=0.336 Sum_probs=18.2
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
.++.+.+..+...+....+..+|.+.-+.+..|..+|.+
T Consensus 162 kL~~el~~~~~~Le~~~~~~~al~Kq~e~~~~EydrLle 200 (216)
T KOG1962|consen 162 KLETELEKKQKKLEKAQKKVDALKKQSEGLQDEYDRLLE 200 (216)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHcccHHHHHHH
Confidence 333344444444444444445555555555555555543
No 119
>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=38.27 E-value=55 Score=24.16 Aligned_cols=44 Identities=20% Similarity=0.362 Sum_probs=22.2
Q ss_pred CCcCCHHH-HHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhh
Q 022964 53 KRRLTVDQ-VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 53 R~R~T~eQ-l~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
|+.|+... +.+++.++.. ..--...|. -|+++|++.++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~-~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKD-NNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHc-cchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 33455543 4455444433 222223333 49999999999999964
No 120
>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=37.85 E-value=72 Score=24.93 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=30.5
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+...+...|-. .....++|..+|+++..|..+...-+.+.|
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666665544332 234568999999999999999876555544
No 121
>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=37.77 E-value=1.9e+02 Score=22.60 Aligned_cols=43 Identities=19% Similarity=0.295 Sum_probs=35.5
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 105 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 105 Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
..+.++.....|-...+.++.+++.|..||+-|+.=+..|...
T Consensus 24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~ 66 (80)
T PF10224_consen 24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSS 66 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3446667778888899999999999999999999988888644
No 122
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=37.61 E-value=88 Score=27.63 Aligned_cols=27 Identities=33% Similarity=0.486 Sum_probs=11.1
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 121 NSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 121 ~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
..|+.+...|..+++.|+.|+..|..+
T Consensus 107 ~~l~~e~~~l~~~~e~Le~e~~~L~~~ 133 (161)
T TIGR02894 107 ERLKNQNESLQKRNEELEKELEKLRQR 133 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444333
No 123
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=37.55 E-value=1.2e+02 Score=24.82 Aligned_cols=35 Identities=26% Similarity=0.298 Sum_probs=21.0
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
+..+......+.++++.|.+++..|++|+..|+..
T Consensus 52 ~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 52 VLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 33344444456666666666666666666666655
No 124
>TIGR03752 conj_TIGR03752 integrating conjugative element protein, PFL_4705 family. Members of this protein family are found occasionally on plasmids such as the Pseudomonas putida toluene catabolic TOL plasmid pWWO_p085. Usually, however, they are found on the bacterial main chromosome in regions flanked by markers of conjugative transfer and/or transposition.
Probab=37.34 E-value=1.5e+02 Score=30.52 Aligned_cols=94 Identities=17% Similarity=0.216 Sum_probs=45.9
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhh-hHHHhhHHHHHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYN-SLKADYDNLFKE 133 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~-~lk~~~~~l~~e 133 (289)
.++++++..|.- ..-.|...-|..+|+--.|..+.-.+==+|++-+....++++....+..... .|......+.++
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~ 117 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKE 117 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHH
Confidence 356666554432 1234555555555544333333333334555555555444443333333332 344555556666
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 022964 134 KEKLKAEVLKLTDKLQVK 151 (289)
Q Consensus 134 ne~L~~e~~~l~~~l~~~ 151 (289)
.+.|+.+.++++..|..-
T Consensus 118 ~~ql~~~~~~~~~~l~~l 135 (472)
T TIGR03752 118 IEQLKSERQQLQGLIDQL 135 (472)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 666666666666655543
No 125
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=37.23 E-value=68 Score=26.00 Aligned_cols=29 Identities=34% Similarity=0.439 Sum_probs=18.3
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHH
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKA 139 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~ 139 (289)
++.+.++..+..++..+..|..+.+.|+.
T Consensus 34 ~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 34 DQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 33445555666666677777777777765
No 126
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=37.11 E-value=96 Score=20.31 Aligned_cols=42 Identities=21% Similarity=0.229 Sum_probs=29.5
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 102 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRa 102 (289)
.++..+...+...+. . ....++|..+|++...|..|.+.-+.
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~~~~~ 44 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLSNIMR 44 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHHHHHH
Confidence 367777777755432 1 24578899999999999998764433
No 127
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=36.77 E-value=1.8e+02 Score=21.86 Aligned_cols=21 Identities=33% Similarity=0.490 Sum_probs=10.4
Q ss_pred HHHHHHHHHHHHHHHHHHHHH
Q 022964 128 DNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 128 ~~l~~ene~L~~e~~~l~~~l 148 (289)
...-.++.+|+.|+..|+..|
T Consensus 43 ~~a~~e~~~Lk~E~e~L~~el 63 (69)
T PF14197_consen 43 GDAYEENNKLKEENEALRKEL 63 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334445555555555555443
No 128
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=36.72 E-value=86 Score=25.52 Aligned_cols=45 Identities=13% Similarity=0.126 Sum_probs=31.6
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
+++.+..++...|-.. ....++|..+|++...|+.|...-|.+-|
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~Lr 151 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKMR 151 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHh
Confidence 6666666665555332 34678999999999999999865444443
No 129
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=36.67 E-value=55 Score=29.21 Aligned_cols=38 Identities=24% Similarity=0.293 Sum_probs=33.2
Q ss_pred cCCHHHHHHHHhhhhccC--CCCHHHHHHHHHHhCCChhh
Q 022964 55 RLTVDQVQFLEKSFEVEN--KLEPERKIQLAKDLGLQPRQ 92 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~--~P~~~~r~~LA~~LgLs~rQ 92 (289)
.||..|+..|...|...- +|-...-..||++||+++.-
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst 194 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST 194 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH
Confidence 599999999999999876 47777888999999999855
No 130
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=36.58 E-value=2.4e+02 Score=26.27 Aligned_cols=58 Identities=16% Similarity=0.391 Sum_probs=27.3
Q ss_pred ChhhhhhHhhhhHHHHHHH---------HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 89 QPRQVAIWFQNRRARWKTK---------QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 89 s~rQVkvWFQNRRak~Krk---------~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
....+..||+.+-...+.. ....+...++.....|..+...|...|..|...+..|..
T Consensus 185 ~~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~ 251 (312)
T PF00038_consen 185 NREELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQ 251 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHH
Confidence 3567889998874333321 122233333334444444444444444444444444433
No 131
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=36.28 E-value=1.4e+02 Score=27.34 Aligned_cols=27 Identities=30% Similarity=0.418 Sum_probs=10.1
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHH
Q 022964 116 LQNSYNSLKADYDNLFKEKEKLKAEVL 142 (289)
Q Consensus 116 l~~~~~~lk~~~~~l~~ene~L~~e~~ 142 (289)
|...+..+..+.+.|...|+++...+.
T Consensus 54 L~~e~~~l~~e~e~L~~~~~~l~~~v~ 80 (251)
T PF11932_consen 54 LLAEYRQLEREIENLEVYNEQLERQVA 80 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333333333333333333
No 132
>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=36.26 E-value=98 Score=21.57 Aligned_cols=47 Identities=17% Similarity=0.196 Sum_probs=33.5
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 107 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk 107 (289)
+||..++..|.....- ....++|..+|++++.|..+..+=+.|..-.
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~~ 49 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGVK 49 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-S
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCCC
Confidence 4777888877666542 2467899999999999999987766665543
No 133
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=36.19 E-value=1.4e+02 Score=22.82 Aligned_cols=31 Identities=29% Similarity=0.212 Sum_probs=19.2
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 122 SLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 122 ~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.+..++-.|..+++.|+.|+..++..|...+
T Consensus 40 ~~~keNieLKve~~~L~~el~~~~~~l~~a~ 70 (75)
T PF07989_consen 40 ELLKENIELKVEVESLKRELQEKKKLLKEAE 70 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555666666777777666666665444
No 134
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=36.07 E-value=99 Score=29.05 Aligned_cols=38 Identities=34% Similarity=0.504 Sum_probs=15.5
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.++..++..+..++...+.+.+||+.|..++.+|..++
T Consensus 128 ~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~e~ 165 (290)
T COG4026 128 PEYMDLKEDYEELKEKLEELQKEKEELLKELEELEAEY 165 (290)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333334444444444444444444444444444333
No 135
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=35.46 E-value=2.2e+02 Score=23.89 Aligned_cols=51 Identities=22% Similarity=0.315 Sum_probs=28.2
Q ss_pred HHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 022964 101 RARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 151 (289)
Q Consensus 101 Rak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~ 151 (289)
|.+.+....+++....+.....+......+.......+.|+.+++..++..
T Consensus 77 rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~~~~~ 127 (151)
T PF11559_consen 77 RLKEQLEELERELASAEEKERQLQKQLKSLEAKLKQEKEELQKLKNQLQQR 127 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444445555555555555555555556556666666666666555433
No 136
>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=34.84 E-value=1.5e+02 Score=21.43 Aligned_cols=21 Identities=29% Similarity=0.373 Sum_probs=9.8
Q ss_pred HHhhHHHHHHHHHHHHHHHHH
Q 022964 124 KADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 124 k~~~~~l~~ene~L~~e~~~l 144 (289)
......|..||..|++++..+
T Consensus 28 ~~rl~~l~~EN~~Lr~eL~~~ 48 (52)
T PF12808_consen 28 RKRLSKLEGENRLLRAELERL 48 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 334444444555555554443
No 137
>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=34.80 E-value=16 Score=28.01 Aligned_cols=35 Identities=14% Similarity=0.221 Sum_probs=26.3
Q ss_pred HhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhh
Q 022964 65 EKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 65 E~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQN 99 (289)
+..|....+.......+||..||+++..|+.|+.+
T Consensus 21 r~af~L~R~~eGlS~kEIAe~LGIS~~TVk~~l~~ 55 (73)
T TIGR03879 21 EAAAALAREEAGKTASEIAEELGRTEQTVRNHLKG 55 (73)
T ss_pred HHHHHHHHHHcCCCHHHHHHHHCcCHHHHHHHHhc
Confidence 34455554445556789999999999999999864
No 138
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=34.80 E-value=38 Score=22.76 Aligned_cols=23 Identities=26% Similarity=0.381 Sum_probs=17.6
Q ss_pred HHHHHHHHHHhCCChhhhhhHhh
Q 022964 76 PERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 76 ~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
.....++|+.+|++...|..|.+
T Consensus 17 G~s~~~ia~~lgvs~~Tv~~w~k 39 (50)
T PF13384_consen 17 GWSIREIAKRLGVSRSTVYRWIK 39 (50)
T ss_dssp T--HHHHHHHHTS-HHHHHHHHT
T ss_pred CCCHHHHHHHHCcCHHHHHHHHH
Confidence 34567899999999999999975
No 139
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=34.73 E-value=2e+02 Score=21.71 Aligned_cols=35 Identities=20% Similarity=0.321 Sum_probs=21.1
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
.+.+..-........++..|+.|++.|+.|+..+.
T Consensus 33 ~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 33 RERDSAERQLGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34444444445556667777777777777765543
No 140
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=34.59 E-value=85 Score=25.95 Aligned_cols=45 Identities=11% Similarity=-0.045 Sum_probs=31.4
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
+++.+..+|...|-. .....++|..||++...|+.|...-|.+.|
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 777777777665432 223568899999999999999874444444
No 141
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=34.56 E-value=36 Score=24.31 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhhhhHhhh
Q 022964 79 KIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQN 99 (289)
..++|+.+|++.+.|+.|=+.
T Consensus 3 i~eva~~~gvs~~tlr~y~~~ 23 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYERE 23 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHHT
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999543
No 142
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=34.38 E-value=88 Score=25.78 Aligned_cols=46 Identities=13% Similarity=0.110 Sum_probs=30.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
+++.+..++...|-.. ..-.++|..||++...|+.....-|.+.|.
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555554443222 234688999999999999998765555554
No 143
>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=34.38 E-value=46 Score=26.74 Aligned_cols=34 Identities=32% Similarity=0.577 Sum_probs=18.7
Q ss_pred HHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHH
Q 022964 61 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 108 (289)
Q Consensus 61 l~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~ 108 (289)
+....-.|+.++||...--.. | =.|||.||++.+
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq 47 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQ 47 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHH
Confidence 445556688999987542211 1 158999999765
No 144
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=34.35 E-value=36 Score=24.68 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.5
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...+||..||++.+.|..|-+ |-+|..
T Consensus 15 ~~~eIA~~Lg~~~~TV~~W~~--r~~W~~ 41 (58)
T PF06056_consen 15 SIKEIAEELGVPRSTVYSWKD--RYKWDE 41 (58)
T ss_pred CHHHHHHHHCCChHHHHHHHH--hhCccc
Confidence 357899999999999999964 555554
No 145
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=34.32 E-value=54 Score=32.15 Aligned_cols=26 Identities=12% Similarity=-0.038 Sum_probs=13.8
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 120 YNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 120 ~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
|-.|+.+|+.|++|+..|+.++.++.
T Consensus 59 y~~L~~EN~~Lk~Ena~L~~~l~~~e 84 (337)
T PRK14872 59 ALVLETENFLLKERIALLEERLKSYE 84 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455555555555555555555443
No 146
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=34.17 E-value=54 Score=27.09 Aligned_cols=46 Identities=20% Similarity=0.189 Sum_probs=30.7
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|- ......++|..+|++...|..|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYV-----EGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555544442 22345789999999999999998765555553
No 147
>PF04899 MbeD_MobD: MbeD/MobD like ; InterPro: IPR006983 The MbeD and MobD proteins are plasmid encoded, and are involved in the plasmid mobilisation and transfer in the presence of conjugative plasmids [].
Probab=33.92 E-value=1.9e+02 Score=21.97 Aligned_cols=40 Identities=20% Similarity=0.405 Sum_probs=32.2
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+..|+.|+..+..-..++..|...+..|-.+|..|.+++.
T Consensus 27 q~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~ 66 (70)
T PF04899_consen 27 QSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLE 66 (70)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4567888888888888888888888888888888887764
No 148
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=33.81 E-value=53 Score=27.75 Aligned_cols=46 Identities=13% Similarity=0.258 Sum_probs=30.2
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+...+...|- ......++|..||++...|+++...-|.+.|+
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 45555444444442 22346789999999999999998765555544
No 149
>TIGR01069 mutS2 MutS2 family protein. Function of MutS2 is unknown. It should not be considered a DNA mismatch repair protein. It is likely a DNA mismatch binding protein of unknown cellular function.
Probab=33.74 E-value=2.2e+02 Score=30.90 Aligned_cols=22 Identities=9% Similarity=0.119 Sum_probs=16.2
Q ss_pred CCHHHHHHHHHHhCCChhhhhh
Q 022964 74 LEPERKIQLAKDLGLQPRQVAI 95 (289)
Q Consensus 74 P~~~~r~~LA~~LgLs~rQVkv 95 (289)
|....-..+|+.+||+...|..
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~~ 501 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIEQ 501 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHHH
Confidence 4455666789999999887753
No 150
>TIGR02894 DNA_bind_RsfA transcription factor, RsfA family. In a subset of endospore-forming members of the Firmcutes, members of this protein family are found, several to a genome. Two very strongly conserved sequences regions are separated by a highly variable linker region. Much of the linker region was excised from the seed alignment for this model. A characterized member is the prespore-specific transcription RsfA from Bacillus subtilis, previously called YwfN, which is controlled by sigma factor F and seems to fine-tune expression of some genes in the sigma-F regulon. A paralog in Bacillus subtilis is designated YlbO.
Probab=33.60 E-value=1.3e+02 Score=26.64 Aligned_cols=34 Identities=32% Similarity=0.437 Sum_probs=15.5
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
.+...|+.....|...+..|.+|++.|+.++..+
T Consensus 104 ~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~ 137 (161)
T TIGR02894 104 KENERLKNQNESLQKRNEELEKELEKLRQRLSTI 137 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444444444444444333
No 151
>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=33.48 E-value=4.3e+02 Score=28.48 Aligned_cols=32 Identities=22% Similarity=0.213 Sum_probs=16.5
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHH
Q 022964 100 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLF 131 (289)
Q Consensus 100 RRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~ 131 (289)
|..|---.+++++.+.|+..+..|......-+
T Consensus 456 r~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~DK 487 (697)
T PF09726_consen 456 RSLKSELSQLRQENEQLQNKLQNLVQARQQDK 487 (697)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444555555666666555555444433
No 152
>PRK10072 putative transcriptional regulator; Provisional
Probab=33.47 E-value=33 Score=27.48 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=30.3
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHH
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 103 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak 103 (289)
+.+...+..|...... ...+||+.+|++...|..|.+.+|.-
T Consensus 32 ~~~~~eik~LR~~~gl-------TQ~elA~~lGvS~~TVs~WE~G~r~P 73 (96)
T PRK10072 32 TTSFTEFEQLRKGTGL-------KIDDFARVLGVSVAMVKEWESRRVKP 73 (96)
T ss_pred cCChHHHHHHHHHcCC-------CHHHHHHHhCCCHHHHHHHHcCCCCC
Confidence 3466666666443332 26789999999999999999877643
No 153
>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=33.37 E-value=80 Score=21.24 Aligned_cols=38 Identities=16% Similarity=0.340 Sum_probs=26.5
Q ss_pred cCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHh
Q 022964 55 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 97 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWF 97 (289)
.++.+++..+...+... ....+||+.+|++...|..++
T Consensus 5 ~~~~~~~~~i~~l~~~G-----~si~~IA~~~gvsr~TvyR~l 42 (45)
T PF02796_consen 5 KLSKEQIEEIKELYAEG-----MSIAEIAKQFGVSRSTVYRYL 42 (45)
T ss_dssp SSSHCCHHHHHHHHHTT-------HHHHHHHTTS-HHHHHHHH
T ss_pred CCCHHHHHHHHHHHHCC-----CCHHHHHHHHCcCHHHHHHHH
Confidence 36776666666666654 347889999999999887765
No 154
>PF06637 PV-1: PV-1 protein (PLVAP); InterPro: IPR009538 This family consists of several PV-1 (PLVAP) proteins, which seem to be specific to mammals. PV-1 is a novel protein component of the endothelial fenestral and stomatal diaphragms []. The function of this family is unknown.
Probab=33.11 E-value=2e+02 Score=29.02 Aligned_cols=33 Identities=36% Similarity=0.429 Sum_probs=22.2
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 121 NSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 121 ~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..|+.+.+.|.+|.+..+.|+.+|+.++..+.+
T Consensus 352 aaLrkerd~L~keLeekkreleql~~q~~v~~s 384 (442)
T PF06637_consen 352 AALRKERDSLAKELEEKKRELEQLKMQLAVKTS 384 (442)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 456666677777777777777777777665553
No 155
>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=33.05 E-value=1.7e+02 Score=20.43 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=17.2
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHH
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAE 140 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e 140 (289)
..+......|...+..|..++..|+.|
T Consensus 28 ~~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 28 EELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 445566666666777777666666654
No 156
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=32.92 E-value=91 Score=26.88 Aligned_cols=46 Identities=15% Similarity=0.097 Sum_probs=31.8
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|-.. ....++|+.||++...|+.+...-|.+.|+
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 6666666665554322 345789999999999999998655555443
No 157
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=32.62 E-value=2.2e+02 Score=30.87 Aligned_cols=22 Identities=23% Similarity=0.303 Sum_probs=16.4
Q ss_pred CCHHHHHHHHHHhCCChhhhhh
Q 022964 74 LEPERKIQLAKDLGLQPRQVAI 95 (289)
Q Consensus 74 P~~~~r~~LA~~LgLs~rQVkv 95 (289)
|....-..+|+.+||+...|..
T Consensus 485 ~g~S~a~~iA~~~Glp~~ii~~ 506 (782)
T PRK00409 485 PGKSNAFEIAKRLGLPENIIEE 506 (782)
T ss_pred CCCcHHHHHHHHhCcCHHHHHH
Confidence 4455667789999999888753
No 158
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=32.16 E-value=2.3e+02 Score=24.31 Aligned_cols=52 Identities=25% Similarity=0.326 Sum_probs=40.7
Q ss_pred HhhhhHHHHH--HHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 96 WFQNRRARWK--TKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 96 WFQNRRak~K--rk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
+-||.|.|-- +..++++...|.+..+.|+.++..+..|.+-++.-...|..-
T Consensus 64 YA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~ 117 (135)
T KOG4196|consen 64 YAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNS 117 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3455555432 345678888899999999999999999999999998888744
No 159
>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=32.12 E-value=2.6e+02 Score=22.23 Aligned_cols=36 Identities=22% Similarity=0.434 Sum_probs=27.5
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
.+.|+.+++..|. .....+.+|++-.+|+..+....
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~ 71 (113)
T cd01109 36 IRDFTEEDLEWLE-------------FIKCLRNTGMSIKDIKEYAELRR 71 (113)
T ss_pred CccCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHHHHc
Confidence 4459999998883 33457889999999999887543
No 160
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=32.07 E-value=2.1e+02 Score=21.03 Aligned_cols=41 Identities=22% Similarity=0.347 Sum_probs=20.2
Q ss_pred HHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 107 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 107 k~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
.++..+...|....+.|..+...|+.+....+.|-.+...+
T Consensus 6 d~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~R 46 (56)
T PF04728_consen 6 DQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQR 46 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555555555555555555555544444444444333
No 161
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=32.06 E-value=2e+02 Score=25.66 Aligned_cols=41 Identities=24% Similarity=0.383 Sum_probs=31.2
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 154 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~~ 154 (289)
..|....+..+..|+.|..+..+|..++..+.+.|..++..
T Consensus 84 ~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~ke~~ 124 (182)
T PF15035_consen 84 ALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQKEAE 124 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44556666667888888888888888888888888877753
No 162
>PRK04217 hypothetical protein; Provisional
Probab=32.05 E-value=1.1e+02 Score=25.13 Aligned_cols=46 Identities=13% Similarity=0.027 Sum_probs=33.6
Q ss_pred CcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHH
Q 022964 54 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 104 (289)
Q Consensus 54 ~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~ 104 (289)
..++.+|..++...|...- ...+||+.+|++...|...+..-|.+.
T Consensus 41 ~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkL 86 (110)
T PRK04217 41 IFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKV 86 (110)
T ss_pred ccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHH
Confidence 3588889888877764333 467799999999999988776444333
No 163
>PF04999 FtsL: Cell division protein FtsL; InterPro: IPR007082 In Escherichia coli, nine gene products are known to be essential for assembly of the division septum. One of these, FtsL, is a bitopic membrane protein whose precise function is not understood. It has been proposed that FtsL interacts with the DivIC protein IPR007060 from INTERPRO [], however this interaction may be indirect [].; GO: 0007049 cell cycle, 0016021 integral to membrane
Probab=31.77 E-value=1.1e+02 Score=23.83 Aligned_cols=27 Identities=30% Similarity=0.538 Sum_probs=18.1
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 120 YNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 120 ~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
...+..+...|..|+++|+-|...|+.
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~~~l~~ 70 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEIATLSS 70 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 445566666777777777777777654
No 164
>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=31.72 E-value=2.8e+02 Score=22.86 Aligned_cols=14 Identities=29% Similarity=0.541 Sum_probs=11.7
Q ss_pred hhhhhHhhhhHHHH
Q 022964 91 RQVAIWFQNRRARW 104 (289)
Q Consensus 91 rQVkvWFQNRRak~ 104 (289)
||...||-.+|.-.
T Consensus 18 Rq~e~~FlqKr~~L 31 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHH
Confidence 67899999888766
No 165
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=31.34 E-value=1.4e+02 Score=29.08 Aligned_cols=61 Identities=13% Similarity=0.194 Sum_probs=39.1
Q ss_pred hhhHhhhhHHHHHHH-HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 93 VAIWFQNRRARWKTK-QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 93 VkvWFQNRRak~Krk-~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
++|||+|-|+-.+-. +..+..+.++..+..++.....-..|-.+|..+++.+..+....-.
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEaaA~~sya 77 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEAAASASYA 77 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHHHHHHHHH
Confidence 689999988766532 2333445566666666666666666677777777777666554433
No 166
>TIGR02051 MerR Hg(II)-responsive transcriptional regulator. This model represents the mercury (II) responsive transcriptional activator of the mer organomercurial resistance operon. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(8)-Cys-Pro, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=31.31 E-value=2.9e+02 Score=22.52 Aligned_cols=37 Identities=24% Similarity=0.279 Sum_probs=28.5
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
..+.|+..++..| .....++.+|++...|+..+....
T Consensus 34 g~R~Y~~~~l~~l-------------~~I~~l~~~G~sl~eI~~~l~~~~ 70 (124)
T TIGR02051 34 GYRRYPEETVKRL-------------RFIKRAQELGFSLEEIGGLLGLVD 70 (124)
T ss_pred CCEeECHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHhccc
Confidence 3455999999888 344457899999999999986543
No 167
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=31.13 E-value=4.7e+02 Score=24.86 Aligned_cols=40 Identities=23% Similarity=0.254 Sum_probs=21.7
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
..|...+..|..+++.|+.-|+.|-.++.+|...|.....
T Consensus 100 ~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~ 139 (292)
T KOG4005|consen 100 KDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQ 139 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 3444555555555555555555555555556555553333
No 168
>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=30.69 E-value=2.1e+02 Score=20.75 Aligned_cols=32 Identities=34% Similarity=0.473 Sum_probs=25.1
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKA 139 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~ 139 (289)
+...+...++..+..++.+++.|..+.+.|+.
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l~~ 52 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERLKN 52 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 44566778888888888888888888888833
No 169
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=30.57 E-value=2.6e+02 Score=22.12 Aligned_cols=42 Identities=10% Similarity=0.193 Sum_probs=31.4
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCC-ChhhhhhHhh
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGL-QPRQVAIWFQ 98 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgL-s~rQVkvWFQ 98 (289)
+++|+.+....+=..+....+ ....+|+++|+ ...++..|-+
T Consensus 5 ~r~~s~EfK~~iv~~~~~~g~----sv~~vAr~~gv~~~~~l~~W~~ 47 (116)
T COG2963 5 RKKYSPEFKLEAVALYLRGGD----TVSEVAREFGIVSATQLYKWRI 47 (116)
T ss_pred cccCCHHHHHHHHHHHHhcCc----cHHHHHHHhCCCChHHHHHHHH
Confidence 667999877666555554443 57889999996 9999998854
No 170
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=30.55 E-value=1e+02 Score=26.96 Aligned_cols=46 Identities=20% Similarity=0.157 Sum_probs=29.8
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|- ......++|..+|++...|+++..+-|.+.++
T Consensus 154 L~~~~r~vl~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYF-----QELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555544332 22345689999999999999888655555443
No 171
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=30.38 E-value=1.4e+02 Score=27.61 Aligned_cols=31 Identities=23% Similarity=0.259 Sum_probs=20.7
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 116 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 116 l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
.-..+..++++|..|++|+..|+.++.++..
T Consensus 67 ~~~~~~~l~~en~~L~~e~~~l~~~~~~~~~ 97 (276)
T PRK13922 67 SLASLFDLREENEELKKELLELESRLQELEQ 97 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566777777777777777777776643
No 172
>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=30.30 E-value=68 Score=25.92 Aligned_cols=45 Identities=16% Similarity=0.155 Sum_probs=28.9
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+...|...|- ......++|..+|+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRF-----EGKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 45555555554332 2223567899999999999988765555444
No 173
>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=30.25 E-value=2.5e+02 Score=21.46 Aligned_cols=35 Identities=20% Similarity=0.338 Sum_probs=25.1
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhh
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
..++|+..++..|.. ...|...+|++...|+.-+.
T Consensus 35 g~R~y~~~dv~~l~~------------i~~L~~d~g~~l~~i~~~l~ 69 (91)
T cd04766 35 GTRRYSERDIERLRR------------IQRLTQELGVNLAGVKRILE 69 (91)
T ss_pred CCeeECHHHHHHHHH------------HHHHHHHcCCCHHHHHHHHH
Confidence 345699999999843 44556668999888876664
No 174
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=30.21 E-value=91 Score=30.62 Aligned_cols=20 Identities=25% Similarity=0.022 Sum_probs=9.7
Q ss_pred HHHHhhhhhhHHHhhHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFK 132 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ 132 (289)
+..++.++..|+.++..|..
T Consensus 59 y~~L~~EN~~Lk~Ena~L~~ 78 (337)
T PRK14872 59 ALVLETENFLLKERIALLEE 78 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHH
Confidence 34444455555555555533
No 175
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=30.11 E-value=1.6e+02 Score=29.20 Aligned_cols=44 Identities=32% Similarity=0.284 Sum_probs=30.1
Q ss_pred HHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 109 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 109 ~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.+++.+.+....+.|++-.+.|..-+.+|+++..+|+.+++.-.
T Consensus 223 ~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~ 266 (365)
T KOG2391|consen 223 REEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQ 266 (365)
T ss_pred HHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 35566666777777777777777777777777777776666444
No 176
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=30.06 E-value=2.1e+02 Score=22.06 Aligned_cols=36 Identities=22% Similarity=0.303 Sum_probs=21.8
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
.+.|.+....+...+++|..||+.|+.|-..-++.|
T Consensus 34 nn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerl 69 (79)
T COG3074 34 NNSLSQEVQNAQHQREALERENEQLKEEQNGWQERL 69 (79)
T ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555566666777777777777655554444
No 177
>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=30.00 E-value=1.4e+02 Score=22.35 Aligned_cols=23 Identities=39% Similarity=0.497 Sum_probs=11.3
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHH
Q 022964 123 LKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 123 lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
+......+..+++.|+.|...|.
T Consensus 36 ~~~~~~~l~~en~~L~~ei~~l~ 58 (85)
T TIGR02209 36 LQLEIDKLQKEWRDLQLEVAELS 58 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHc
Confidence 33444445555555555555544
No 178
>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=29.98 E-value=3e+02 Score=22.23 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=28.7
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhh
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 100 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNR 100 (289)
..+.|+..++..|. .....+.+|++-.+|+..+.+.
T Consensus 34 gyR~Y~~~~l~~l~-------------~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 34 LRRQYDPQVLDRLA-------------LIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CceecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 34569999999883 4456889999999999999764
No 179
>cd04770 HTH_HMRTR Helix-Turn-Helix DNA binding domain of Heavy Metal Resistance transcription regulators. Helix-turn-helix (HTH) heavy metal resistance transcription regulators (HMRTR): MerR1 (mercury), CueR (copper), CadR (cadmium), PbrR (lead), ZntR (zinc), and other related proteins. These transcription regulators mediate responses to heavy metal stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=29.89 E-value=2.9e+02 Score=22.14 Aligned_cols=38 Identities=21% Similarity=0.191 Sum_probs=29.1
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHH
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 102 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRa 102 (289)
..|.|+.+++..| ......+.+|++-..|+..+.+...
T Consensus 35 gyR~Y~~~~i~~l-------------~~I~~lr~~G~sl~eI~~~l~~~~~ 72 (123)
T cd04770 35 GYRLYGEADLARL-------------RFIRRAQALGFSLAEIRELLSLRDD 72 (123)
T ss_pred CCccCCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHhhhc
Confidence 3456999999998 3444578999999999998876543
No 180
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=29.78 E-value=1.3e+02 Score=23.79 Aligned_cols=35 Identities=23% Similarity=0.470 Sum_probs=24.8
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
..+|+.+-...+.|....+.|.+.++.|..++.+|
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~L 59 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQEL 59 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 35667777777777777777777777777776655
No 181
>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=29.66 E-value=2.5e+02 Score=21.16 Aligned_cols=42 Identities=17% Similarity=0.193 Sum_probs=23.8
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
++-..++.|+..+..|+.....+..|...|...+...+.++.
T Consensus 11 ~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvE 52 (65)
T TIGR02449 11 HLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVE 52 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344445555566666666666666666666655555555444
No 182
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=29.60 E-value=1.7e+02 Score=24.14 Aligned_cols=45 Identities=16% Similarity=0.254 Sum_probs=30.7
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+...|...| .. ....+||..+|++...|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~-~g-----~s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF-SG-----YSYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH-cC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665555 22 235678999999999999998655554443
No 183
>PF02344 Myc-LZ: Myc leucine zipper domain; InterPro: IPR003327 This family consists of the leucine zipper dimerisation domain found in both cellular c-Myc proto-oncogenes and viral v-Myc oncogenes. Dimerisation via the leucine zipper motif with other basic helix-loop-helix-leucine zipper (b/HLH/lz) proteins is required for efficient DNA binding []. The Myc-Max dimer is a transactivating complex activating expression of growth related genes promoting cell proliferation. The dimerisation is facilitated via interdigitating leucine residues every 7th position of the alpha helix. Like charge repulsion of adjacent residues in this region preturbs the formation of homodimers with heterodimers being promoted by opposing charge attractions. It has been demonstrated that in transgenic mice the balance between oncogene-induced proliferation and apoptosis in a given tissue can be a critical determinant in the initiation and maintenance of the tumor [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus; PDB: 1NKP_D 1A93_A 2A93_A.
Probab=29.37 E-value=1.4e+02 Score=19.55 Aligned_cols=21 Identities=38% Similarity=0.547 Sum_probs=12.5
Q ss_pred HHHHHHHHHHHHHHHHHHHHh
Q 022964 129 NLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 129 ~l~~ene~L~~e~~~l~~~l~ 149 (289)
.|..|++.|+....+|+-+|.
T Consensus 5 kL~sekeqLrrr~eqLK~kLe 25 (32)
T PF02344_consen 5 KLISEKEQLRRRREQLKHKLE 25 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHH
Confidence 355566666666666665553
No 184
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=29.27 E-value=1.1e+02 Score=25.77 Aligned_cols=46 Identities=13% Similarity=0.042 Sum_probs=32.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|-. ...-.+||..||++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~-----g~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVE-----GASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 566666666555433 2345689999999999999998766655554
No 185
>cd00093 HTH_XRE Helix-turn-helix XRE-family like proteins. Prokaryotic DNA binding proteins belonging to the xenobiotic response element family of transcriptional regulators.
Probab=28.88 E-value=67 Score=20.20 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=19.4
Q ss_pred HHHHHHHhCCChhhhhhHhhhhH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
...+|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999988764
No 186
>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=28.85 E-value=19 Score=33.48 Aligned_cols=47 Identities=23% Similarity=0.307 Sum_probs=0.0
Q ss_pred hhhHHHHHHHHHHHH---HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 98 QNRRARWKTKQLEKD---YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 98 QNRRak~Krk~~e~e---~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
+.+..|.-+..++.. ...|+...+.|-++|+.|+.||++|++|+.+|
T Consensus 113 gsK~pKDdKT~IEEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 113 GSKAPKDDKTRIEEQATKIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp --------------------------------------------------
T ss_pred cCCCCCcchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444333322 22334444444555555555555555555555
No 187
>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=28.76 E-value=1.8e+02 Score=27.12 Aligned_cols=30 Identities=27% Similarity=0.410 Sum_probs=19.8
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 120 YNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 120 ~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
...++.....|+.|.++|++.+.+|=+|+.
T Consensus 102 lr~~~~~~~~L~~Ev~~L~~DN~kLYEKiR 131 (248)
T PF08172_consen 102 LRKQQQTISSLRREVESLRADNVKLYEKIR 131 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556666677777777777777766654
No 188
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=28.53 E-value=1.2e+02 Score=31.19 Aligned_cols=73 Identities=22% Similarity=0.278 Sum_probs=39.2
Q ss_pred CCCHHHHHHHHHH-------hCCChhhhhhHhhhhHHHHHHHHHHHHHHHHhhhh-hhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 73 KLEPERKIQLAKD-------LGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSY-NSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 73 ~P~~~~r~~LA~~-------LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~-~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
+++.+++..|.++ |-|+.++=++==+= |.|.|+|+...+-..-++.| +.|-..+..-.+||..|+..+.+|
T Consensus 220 ~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL~kkV~~L 298 (472)
T KOG0709|consen 220 VLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQELQKKVEEL 298 (472)
T ss_pred eccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHHHHHHHHH
Confidence 4556666665543 23555554444332 33444444444443333333 356666666777777777777776
Q ss_pred HH
Q 022964 145 TD 146 (289)
Q Consensus 145 ~~ 146 (289)
..
T Consensus 299 e~ 300 (472)
T KOG0709|consen 299 EL 300 (472)
T ss_pred hh
Confidence 53
No 189
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=28.39 E-value=2.7e+02 Score=24.87 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=13.9
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 022964 131 FKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 131 ~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
.+.++.++.++.+|+.+|...++
T Consensus 152 ~~~~~e~~~~l~~l~~ei~~~~~ 174 (176)
T PF12999_consen 152 KKKREELEKKLEELEKEIQAAKQ 174 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 34556666666667666665543
No 190
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=28.39 E-value=60 Score=20.76 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhhhhHhhhhHH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRRA 102 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRRa 102 (289)
..++|+.||++.+.|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 457899999999999999876554
No 191
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=28.36 E-value=1.8e+02 Score=30.75 Aligned_cols=34 Identities=18% Similarity=0.459 Sum_probs=16.8
Q ss_pred HhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 116 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 116 l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
|......|+.+...|+.|...+..++..++.+|.
T Consensus 516 LE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls 549 (604)
T KOG3863|consen 516 LEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLS 549 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444455555555555555555555555444
No 192
>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=28.31 E-value=1.2e+02 Score=24.73 Aligned_cols=44 Identities=23% Similarity=0.230 Sum_probs=29.6
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 104 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~ 104 (289)
++..+..++...|- ......++|..+|++...|+++...-|.+.
T Consensus 112 L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~L 155 (159)
T TIGR02989 112 LPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVRL 155 (159)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHH
Confidence 66666666555432 233467899999999999998875444443
No 193
>PF01381 HTH_3: Helix-turn-helix; InterPro: IPR001387 This is large family of DNA binding helix-turn helix proteins that include a bacterial plasmid copy control protein, bacterial methylases, various bacteriophage transcription control proteins and a vegetative specific protein from Dictyostelium discoideum (Slime mould).; GO: 0043565 sequence-specific DNA binding; PDB: 2AXU_A 2AWI_D 2AXV_D 2AXZ_C 2AW6_A 3KXA_C 3BS3_A 2CRO_A 1ZUG_A 3CRO_R ....
Probab=28.17 E-value=49 Score=22.42 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.3
Q ss_pred HHHHHHHhCCChhhhhhHhhhhH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
..+||+.+|+++..|..|..++|
T Consensus 12 ~~~la~~~gis~~~i~~~~~g~~ 34 (55)
T PF01381_consen 12 QKELAEKLGISRSTISRIENGKR 34 (55)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS
T ss_pred HHHHHHHhCCCcchhHHHhcCCC
Confidence 47899999999999999998854
No 194
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=28.17 E-value=2.2e+02 Score=26.63 Aligned_cols=50 Identities=20% Similarity=0.245 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 103 RWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 103 k~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
..+++...+.+...++....++.....+..+.+.|+.++.++...+..-.
T Consensus 23 ~~~~~~~~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r 72 (239)
T COG1579 23 EPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIR 72 (239)
T ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444556677777777777777777777777777777777777666444
No 195
>cd01392 HTH_LacI Helix-turn-helix (HTH) DNA binding domain of the LacI family of transcriptional regulators. HTH-DNA binding domain of the LacI (lactose operon repressor) family of bacterial transcriptional regulators and their putative homologs found in plants. The LacI family has more than 500 members distributed among almost all bacterial species. The monomeric proteins of the LacI family contain common structural features that include a small DNA-binding domain with a helix-turn-helix motif in the N-terminus, a regulatory ligand-binding domain which exhibits the type I periplasmic binding protein fold in the C-terminus for oligomerization and for effector binding, and an approximately 18-amino acid linker connecting these two functional domains. In LacI-like transcriptional regulators, the ligands are monosaccharides including lactose, ribose, fructose, xylose, arabinose, galactose/glucose, and other sugars, with a few exceptions. When the C-terminal domain of the LacI family repre
Probab=28.02 E-value=64 Score=21.62 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=18.8
Q ss_pred HHHHHhCCChhhhhhHhhhhH
Q 022964 81 QLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 81 ~LA~~LgLs~rQVkvWFQNRR 101 (289)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999998874
No 196
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=27.94 E-value=58 Score=23.30 Aligned_cols=21 Identities=10% Similarity=0.347 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhhhhhHhhh
Q 022964 79 KIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQN 99 (289)
..++|+.+|++++.++.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999765
No 197
>TIGR00219 mreC rod shape-determining protein MreC. MreC (murein formation C) is involved in the rod shape determination in E. coli, and more generally in cell shape determination of bacteria whether or not they are rod-shaped. Cells defective in MreC are round. Species with MreC include many of the Proteobacteria, Gram-positives, and spirochetes.
Probab=27.78 E-value=1.1e+02 Score=28.90 Aligned_cols=15 Identities=47% Similarity=0.443 Sum_probs=6.2
Q ss_pred HHHHHHHHHHHHHHH
Q 022964 130 LFKEKEKLKAEVLKL 144 (289)
Q Consensus 130 l~~ene~L~~e~~~l 144 (289)
+.+||++|++|+.+|
T Consensus 71 l~~EN~~Lr~e~~~l 85 (283)
T TIGR00219 71 LEYENYKLRQELLKK 85 (283)
T ss_pred HHHHHHHHHHHHHHH
Confidence 344444444444333
No 198
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=27.60 E-value=1.5e+02 Score=25.45 Aligned_cols=46 Identities=9% Similarity=0.141 Sum_probs=30.7
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..++...|-. .....++|..||+++..|+.+...-|.+.|+
T Consensus 135 Lp~~~R~v~~L~~~~-----g~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYL-----ELSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555544422 2235789999999999999998755555554
No 199
>PF00376 MerR: MerR family regulatory protein; InterPro: IPR000551 The many bacterial transcription regulation proteins which bind DNA through a 'helix-turn-helix' motif can be classified into subfamilies on the basis of sequence similarities. One of these is the MerR subfamily. MerR, which is found in many bacterial species mediates the mercuric-dependent induction of the mercury resistance operon. In the absence of mercury merR represses transcription by binding tightly, as a dimer, to the 'mer' operator region; when mercury is present the dimeric complex binds a single ion and becomes a potent transcriptional activator, while remaining bound to the mer site. Members of the family include the mercuric resistance operon regulatory protein merR; Bacillus subtilis bltR and bmrR; Bacillus glnR; Streptomyces coelicolor hspR; Bradyrhizobium japonicum nolA; Escherichia coli superoxide response regulator soxR; and Streptomyces lividans transcriptional activator tipA [, , , , , ]. Other members include hypothetical proteins from E. coli, B. subtilis and Haemophilus influenzae. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent; PDB: 3HH0_A 2DG6_A 1R8D_B 1JBG_A 2VZ4_A 2ZHH_A 2ZHG_A 1Q07_A 1Q06_A 1Q05_B ....
Probab=27.42 E-value=60 Score=21.46 Aligned_cols=19 Identities=32% Similarity=0.424 Sum_probs=15.4
Q ss_pred HHHHHHHhCCChhhhhhHh
Q 022964 79 KIQLAKDLGLQPRQVAIWF 97 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWF 97 (289)
+-++|+.+|++.+.|+.|=
T Consensus 2 i~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 2 IGEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHHCCCHHHHHHHH
Confidence 3578999999999999994
No 200
>PF11932 DUF3450: Protein of unknown function (DUF3450); InterPro: IPR016866 There is currently no experimental data for members of this group or their homologues, nor do they exhibit features indicative of any function. However, they are found in an operon along with components of a TonB transport system (typified by Vibrio cholerae TonB2 [], and are predicted to be localized to the periplasmic space. Caution: the low-complexity nature of these sequences produces spurious BLAST hits to chromosome segregation ATPases (which are much longer in length and contain canonical Walker motifs). Accordingly, some members are misidentified as such.
Probab=27.26 E-value=2.9e+02 Score=25.31 Aligned_cols=45 Identities=18% Similarity=0.301 Sum_probs=24.6
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.+..++..+....+.|...+..+......++.++.+|+.++..-.
T Consensus 53 ~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~~~~ 97 (251)
T PF11932_consen 53 ELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIEQIE 97 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455555555555555555555555555555555555544333
No 201
>PRK00118 putative DNA-binding protein; Validated
Probab=27.12 E-value=1.4e+02 Score=24.23 Aligned_cols=45 Identities=13% Similarity=0.137 Sum_probs=31.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..|...+...|.... ...+||+.+|+++..|..|...-|.+.|
T Consensus 18 L~ekqRevl~L~y~eg~-----S~~EIAe~lGIS~~TV~r~L~RArkkLr 62 (104)
T PRK00118 18 LTEKQRNYMELYYLDDY-----SLGEIAEEFNVSRQAVYDNIKRTEKLLE 62 (104)
T ss_pred CCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 55666666655554322 3567999999999999999875544444
No 202
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=27.07 E-value=1.7e+02 Score=28.97 Aligned_cols=31 Identities=26% Similarity=0.324 Sum_probs=13.6
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKL 144 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l 144 (289)
..++.....+..+...+..+.++++.|+.+|
T Consensus 32 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (398)
T PTZ00454 32 EFLDIQEEYIKEEQKNLKRELIRAKEEVKRI 62 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444444444444
No 203
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=27.07 E-value=1.2e+02 Score=24.03 Aligned_cols=23 Identities=30% Similarity=0.342 Sum_probs=10.9
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHh
Q 022964 127 YDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 127 ~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+..|.+||+.|+.|......++.
T Consensus 32 ~~kL~~en~qlk~Ek~~~~~qvk 54 (87)
T PF10883_consen 32 NAKLQKENEQLKTEKAVAETQVK 54 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555555555444444433
No 204
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=26.94 E-value=1.1e+02 Score=26.03 Aligned_cols=30 Identities=17% Similarity=0.192 Sum_probs=23.3
Q ss_pred HHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 77 ERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 77 ~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
....++|..+|++...|+.|...-|.+.|+
T Consensus 158 ~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 158 LSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999999755554443
No 205
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=26.67 E-value=1.8e+02 Score=30.54 Aligned_cols=38 Identities=32% Similarity=0.367 Sum_probs=22.4
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
...+++.+..+++....|..++..|++|+.+|...|..
T Consensus 150 l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~ 187 (546)
T KOG0977|consen 150 LSELEAEINTLKRRIKALEDELKRLKAENSRLREELAR 187 (546)
T ss_pred hhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHH
Confidence 34455555566666666666666666666666555553
No 206
>PHA01750 hypothetical protein
Probab=26.38 E-value=3e+02 Score=21.05 Aligned_cols=35 Identities=20% Similarity=0.457 Sum_probs=23.1
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
+-.++..++|+.+...+....+.|..++..++.++
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 34455666677776666666667777777776654
No 207
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=26.14 E-value=64 Score=23.23 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=18.3
Q ss_pred HHHHHHHhCCChhhhhhHhhh
Q 022964 79 KIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQN 99 (289)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 457899999999999999764
No 208
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=26.13 E-value=3.7e+02 Score=22.04 Aligned_cols=35 Identities=20% Similarity=0.238 Sum_probs=26.9
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhh
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQN 99 (289)
..+.|+..++..|. ....++.+|++-.+|+-.+..
T Consensus 35 gyR~Y~~~~l~~l~-------------~I~~lr~lG~sL~eI~~~l~~ 69 (127)
T TIGR02047 35 NYRVYTVGHVERLA-------------FIRNCRTLDMSLAEIRQLLRY 69 (127)
T ss_pred CCCcCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHHh
Confidence 35569999998883 334478899999999988853
No 209
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=26.03 E-value=1.4e+02 Score=25.33 Aligned_cols=45 Identities=22% Similarity=0.178 Sum_probs=30.4
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+..++...|-.. ....++|..||++...|+.+...-|.+.|
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr 184 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLR 184 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 6666666666554332 34678999999999999998754444443
No 210
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=25.85 E-value=1.3e+02 Score=25.26 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=31.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
+++.+..++...|- ....-.++|..||++...|+.+.+.-|.+.|.
T Consensus 137 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~~v~~~l~Rar~~Lr~ 182 (187)
T TIGR02948 137 LPPKYRMVIVLKYM-----EDLSLKEISEILDLPVGTVKTRIHRGREALRK 182 (187)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555555332 23446788999999999999998755555443
No 211
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=25.71 E-value=3.9e+02 Score=28.42 Aligned_cols=60 Identities=13% Similarity=0.288 Sum_probs=30.6
Q ss_pred hhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 90 PRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 90 ~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
.|||.+|.+..-..+--..+-+.+..=....-.-......+++++..|+.++..|+.+|.
T Consensus 556 aRqiAMYL~r~lt~~Sl~~IG~~FgRdHSTV~~A~~kI~~~~~~d~~l~~~V~~L~~~i~ 615 (617)
T PRK14086 556 ARQIAMYLCRELTDLSLPKIGQQFGRDHTTVMHADRKIRALMAERRSIYNQVTELTNRIK 615 (617)
T ss_pred HHHHHHHHHHHHcCCCHHHHHHHhCCChhHHHHHHHHHHHHHHhCHHHHHHHHHHHHHHh
Confidence 466777776544444333333222210111111122234456677788888888888774
No 212
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=25.52 E-value=2.2e+02 Score=30.32 Aligned_cols=39 Identities=23% Similarity=0.424 Sum_probs=22.9
Q ss_pred HHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 022964 111 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 149 (289)
Q Consensus 111 ~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~ 149 (289)
+-.+.|+..+..|+.....++.++++|+.++.+++..+.
T Consensus 429 ~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~ 467 (652)
T COG2433 429 ETVERLEEENSELKRELEELKREIEKLESELERFRREVR 467 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455555666666666666666666666666555544
No 213
>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=25.47 E-value=2.5e+02 Score=20.21 Aligned_cols=37 Identities=22% Similarity=0.138 Sum_probs=28.4
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
..|++.-..-..+......+..+|..|+..|+.+|..
T Consensus 11 ~klkaerE~R~~d~~~a~~rl~~l~~EN~~Lr~eL~~ 47 (52)
T PF12808_consen 11 RKLKAEREARSLDRSAARKRLSKLEGENRLLRAELER 47 (52)
T ss_pred HHHHHhHHhccCCchhHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555555667788899999999999999998864
No 214
>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=25.44 E-value=1.5e+02 Score=25.02 Aligned_cols=43 Identities=16% Similarity=0.110 Sum_probs=27.6
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 103 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak 103 (289)
++..+..+|...|-. .....++|..||+++..|+.+-..-|.+
T Consensus 101 L~~~~r~v~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~Rar~~ 143 (170)
T TIGR02959 101 LPDEYREAIRLTELE-----GLSQQEIAEKLGLSLSGAKSRVQRGRKK 143 (170)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 555555555554422 2235688999999999998887543333
No 215
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.21 E-value=1.5e+02 Score=25.23 Aligned_cols=46 Identities=9% Similarity=0.143 Sum_probs=30.8
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|-. .....++|..+|+++..|++-...-|.+.|.
T Consensus 132 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYH-----EKSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 556666666554422 2235688999999999999888665555554
No 216
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=24.89 E-value=1.5e+02 Score=24.70 Aligned_cols=36 Identities=25% Similarity=0.245 Sum_probs=30.2
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLK 143 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~ 143 (289)
.+-++...|++...++-.+|..|+-||++|+.-+..
T Consensus 19 ~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 19 VLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 445567788888899999999999999999988776
No 217
>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=24.65 E-value=1.2e+02 Score=19.99 Aligned_cols=36 Identities=19% Similarity=0.242 Sum_probs=24.7
Q ss_pred CHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhh
Q 022964 57 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 57 T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQ 98 (289)
+..+...+...+. .....++|+.+|++...|..|..
T Consensus 2 ~~~e~~i~~~~~~------~~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLAE------GKTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHHc------CCCHHHHHHHHCCCHHHHHHHHH
Confidence 3445555544331 12567889999999999999976
No 218
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=24.63 E-value=1.4e+02 Score=25.25 Aligned_cols=46 Identities=11% Similarity=0.111 Sum_probs=29.4
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..+..+|...|- ......++|..||++...|+.+...-|.+.|+
T Consensus 129 L~~~~r~i~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYY-----QGLSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHh-----cCCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 45555555544332 22345688999999999999988655554443
No 219
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=24.61 E-value=2.7e+02 Score=22.93 Aligned_cols=31 Identities=32% Similarity=0.369 Sum_probs=20.9
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 115 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 115 ~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
.|+...+.|....++.++||-+|+.|++-|-
T Consensus 67 ELQnTLdDLSqRVdsVKEEnLKLrSENQVLG 97 (120)
T KOG3650|consen 67 ELQNTLDDLSQRVDSVKEENLKLRSENQVLG 97 (120)
T ss_pred HHHHHHHHHHHHHHHHHHhhhhhhhhhHHHH
Confidence 3555666677777777777777777766553
No 220
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=24.43 E-value=37 Score=35.87 Aligned_cols=61 Identities=13% Similarity=0.129 Sum_probs=0.0
Q ss_pred CCCCCCc-CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCh-------hhhhhHhhhhHHHHHHHHH
Q 022964 49 QPEKKRR-LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQP-------RQVAIWFQNRRARWKTKQL 109 (289)
Q Consensus 49 ~~rkR~R-~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~-------rQVkvWFQNRRak~Krk~~ 109 (289)
.|+++.+ |-..-..+-+.+|.+++.+......+--.++.+.+ .-|+.||.|||+++|+-+.
T Consensus 691 pk~~~~k~f~~~~~ev~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 691 PKKTIIKFFQNQRYEVKHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred cHHHHHHhhhcceeecchhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
No 221
>COG1394 NtpD Archaeal/vacuolar-type H+-ATPase subunit D [Energy production and conversion]
Probab=24.38 E-value=3.4e+02 Score=24.96 Aligned_cols=51 Identities=16% Similarity=0.224 Sum_probs=39.6
Q ss_pred HHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 102 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 102 ak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
.|.+-+..++-+..|+...+.|..++-++..+...++.++.+..+.....-
T Consensus 15 lk~rLkla~rg~~lLk~Krd~L~~ef~~i~~~~~~~r~e~~~~~~~a~~~~ 65 (211)
T COG1394 15 LKRRLKLARRGHKLLKLKRDALIMEFRAIVKEAKELREELEKELEEAYESL 65 (211)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344455667778889999999999999999999999999887776665433
No 222
>PF08614 ATG16: Autophagy protein 16 (ATG16); InterPro: IPR013923 Macroautophagy is a bulk degradation process induced by starvation in eukaryotic cells. In yeast, 15 Apg proteins coordinate the formation of autophagosomes. No molecule involved in autophagy has yet been identified in higher eukaryotes []. The pre-autophagosomal structure contains at least five Apg proteins: Apg1p, Apg2p, Apg5p, Aut7p/Apg8p and Apg16p. It is found in the vacuole []. The C-terminal glycine of Apg12p is conjugated to a lysine residue of Apg5p via an isopeptide bond. During autophagy, cytoplasmic components are enclosed in autophagosomes and delivered to lysosomes/vacuoles. Auotphagy protein 16 (Apg16) has been shown to be bind to Apg5 and is required for the function of the Apg12p-Apg5p conjugate []. Autophagy protein 5 (Apg5) is directly required for the import of aminopeptidase I via the cytoplasm-to-vacuole targeting pathway []. This entry represents auotphagy protein 16 (Apg16), which is required for the function of the Apg12p-Apg5p conjugate.; PDB: 3A7O_D 3A7P_B.
Probab=24.35 E-value=4.3e+02 Score=23.25 Aligned_cols=44 Identities=20% Similarity=0.332 Sum_probs=31.8
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 153 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~ 153 (289)
.+..+.++-.+..|...+..+.....+|+.|+..|-+.......
T Consensus 143 ~k~~e~l~DE~~~L~l~~~~~e~k~~~l~~En~~Lv~Rwm~~k~ 186 (194)
T PF08614_consen 143 NKANEILQDELQALQLQLNMLEEKLRKLEEENRELVERWMQRKA 186 (194)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666777777777888888888888888888877765443
No 223
>TIGR02999 Sig-70_X6 RNA polymerase sigma factor, TIGR02999 family. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found in a variety of species including Rhodopirellula baltica which encodes a paralogous group of five.
Probab=24.25 E-value=1.7e+02 Score=24.61 Aligned_cols=29 Identities=24% Similarity=0.193 Sum_probs=22.3
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...++|..||++...|++....-|.+-|+
T Consensus 152 s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 152 TVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999998755555443
No 224
>PF13551 HTH_29: Winged helix-turn helix
Probab=24.13 E-value=1.6e+02 Score=22.49 Aligned_cols=44 Identities=16% Similarity=0.230 Sum_probs=29.3
Q ss_pred cCCHHHHHHHHhhhhccCC-----CCHHHHHH-H-HHHh--CCChhhhhhHhh
Q 022964 55 RLTVDQVQFLEKSFEVENK-----LEPERKIQ-L-AKDL--GLQPRQVAIWFQ 98 (289)
Q Consensus 55 R~T~eQl~~LE~~F~~~~~-----P~~~~r~~-L-A~~L--gLs~rQVkvWFQ 98 (289)
+++.++...|...+...+. .+...... | .+.. .++...|..|+.
T Consensus 57 ~l~~~~~~~l~~~~~~~p~~g~~~~t~~~l~~~l~~~~~~~~~s~~ti~r~L~ 109 (112)
T PF13551_consen 57 RLSEEQRAQLIELLRENPPEGRSRWTLEELAEWLIEEEFGIDVSPSTIRRILK 109 (112)
T ss_pred CCCHHHHHHHHHHHHHCCCCCCCcccHHHHHHHHHHhccCccCCHHHHHHHHH
Confidence 3899999999999987763 33444333 4 3333 467777777764
No 225
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=24.04 E-value=4e+02 Score=22.62 Aligned_cols=40 Identities=23% Similarity=0.385 Sum_probs=29.6
Q ss_pred cCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHHHHHH
Q 022964 71 ENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 110 (289)
Q Consensus 71 ~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e 110 (289)
..-+......-||++||+.+..+.......+++.+..+.-
T Consensus 64 ~~~~p~~~i~~va~ql~~~~~~~~~y~~r~~T~~~h~~~I 103 (166)
T PF13700_consen 64 PEDIPKADIEYVAKQLGLPPSDLSSYAQRSRTRYRHRAEI 103 (166)
T ss_pred cccCCHHHHHHHHHHhCCchHHHHhhhhhhhHHHHHHHHH
Confidence 3345577888899999999988888887666666655433
No 226
>PF12325 TMF_TATA_bd: TATA element modulatory factor 1 TATA binding; InterPro: IPR022091 This is the C-terminal conserved coiled coil region of a family of TATA element modulatory factor 1 proteins conserved in eukaryotes []. The proteins bind to the TATA element of some RNA polymerase II promoters and repress their activity. by competing with the binding of TATA binding protein. TMF1_TATA_bd is the most conserved part of the TMFs []. TMFs are evolutionarily conserved golgins that bind Rab6, a ubiquitous ras-like GTP-binding Golgi protein, and contribute to Golgi organisation in animal [] and plant cells. The Rab6-binding domain appears to be the same region as this C-terminal family [].
Probab=23.99 E-value=2.6e+02 Score=23.37 Aligned_cols=47 Identities=28% Similarity=0.418 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 100 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 100 RRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
+-...+...++.+...++..|+.+..-++.-..+++.|+..+..||+
T Consensus 64 ~~~~~~~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~ 110 (120)
T PF12325_consen 64 RALKKEVEELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKE 110 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHH
No 227
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=23.94 E-value=1.8e+02 Score=27.90 Aligned_cols=34 Identities=9% Similarity=0.196 Sum_probs=20.7
Q ss_pred hhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhh
Q 022964 94 AIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADY 127 (289)
Q Consensus 94 kvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~ 127 (289)
++=-+||-..-+.+++..+.+.++...+.-+.++
T Consensus 56 q~etrnrdl~t~nqrl~~E~e~~Kek~e~q~~q~ 89 (333)
T KOG1853|consen 56 QLETRNRDLETRNQRLTTEQERNKEKQEDQRVQF 89 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444677777777676666666666655544443
No 228
>PF12844 HTH_19: Helix-turn-helix domain; PDB: 3LIS_B 3LFP_A 2XIU_B 2GZU_B 2XJ3_A 1UTX_A 2XI8_B 3F6W_C 3EUS_B.
Probab=23.92 E-value=1.1e+02 Score=21.33 Aligned_cols=37 Identities=22% Similarity=0.298 Sum_probs=23.8
Q ss_pred HHHHHHHhCCChhhhhhHhhhhHHHHHHHHHHHHHHHH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVL 116 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRRak~Krk~~e~e~~~l 116 (289)
...+|..+|++..+|..|-.++| .-....+.+-...+
T Consensus 15 ~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~l~~i~~~~ 51 (64)
T PF12844_consen 15 QKDLAEKLGISRSTISKIENGKR-KPSVSTLKKIAEAL 51 (64)
T ss_dssp HHHHHHHHTS-HHHHHHHHTTSS---BHHHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHCCCc-CCCHHHHHHHHHHh
Confidence 56788999999999999988876 44444444443433
No 229
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=23.87 E-value=3.5e+02 Score=22.14 Aligned_cols=50 Identities=26% Similarity=0.276 Sum_probs=34.6
Q ss_pred hhhhhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHH
Q 022964 90 PRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAE 140 (289)
Q Consensus 90 ~rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e 140 (289)
.-+.-.||...-.- ...+...+.+.+++.++.|.+.+..|.++...|+.+
T Consensus 37 ~f~~~~~~g~~~~~-~~~~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 37 LFQYLAWFGKNGAA-DVLQLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHhhHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 34555666543332 233455566688888888889999999999888888
No 230
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=23.85 E-value=1.7e+02 Score=23.86 Aligned_cols=45 Identities=11% Similarity=0.037 Sum_probs=29.3
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+..++...|-.. ....++|..||++...|++....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 107 LPARQREAFLLRYWED-----MDVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CCHHHHHHHHHHHHhc-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 5556655555544222 23568899999999999988764444443
No 231
>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=23.84 E-value=26 Score=32.54 Aligned_cols=35 Identities=20% Similarity=0.261 Sum_probs=0.0
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
.+.....+..|++-.+.|..+|++|+.|+.+|++.
T Consensus 124 IEEQ~T~I~dLrrlVe~L~aeNErLr~EnkqL~ae 158 (243)
T PF08961_consen 124 IEEQATKIADLRRLVEFLLAENERLRRENKQLKAE 158 (243)
T ss_dssp -----------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35566677788889999999999999999888754
No 232
>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=23.73 E-value=4e+02 Score=21.62 Aligned_cols=36 Identities=25% Similarity=0.310 Sum_probs=28.6
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhH
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
.+.|+..++..|. .....+.+|++-..|+-++....
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~ 71 (126)
T cd04783 36 YRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELDD 71 (126)
T ss_pred CeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhccc
Confidence 4459999999883 44557899999999999997654
No 233
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=23.61 E-value=1e+02 Score=32.25 Aligned_cols=34 Identities=24% Similarity=0.270 Sum_probs=29.0
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
...|+.....|..+++.|++||..|+.++..|..
T Consensus 304 ~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 304 MLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 4678888899999999999999999999877754
No 234
>PRK09039 hypothetical protein; Validated
Probab=23.37 E-value=3.7e+02 Score=26.10 Aligned_cols=45 Identities=18% Similarity=0.206 Sum_probs=25.2
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 154 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~~ 154 (289)
..+....+..+...+.....|..+.+.|+.++..|...|...+.+
T Consensus 122 ~~~L~~~k~~~se~~~~V~~L~~qI~aLr~Qla~le~~L~~ae~~ 166 (343)
T PRK09039 122 AQELDSEKQVSARALAQVELLNQQIAALRRQLAALEAALDASEKR 166 (343)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444445555555555566666666666666666666555443
No 235
>cd01104 HTH_MlrA-CarA Helix-Turn-Helix DNA binding domain of the transcription regulators MlrA and CarA. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A), N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA- and CarA-like proteins in this group appear to lack the long dimerization helix seen i
Probab=23.30 E-value=79 Score=22.39 Aligned_cols=20 Identities=20% Similarity=0.383 Sum_probs=17.8
Q ss_pred HHHHHHHhCCChhhhhhHhh
Q 022964 79 KIQLAKDLGLQPRQVAIWFQ 98 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQ 98 (289)
..++|+.+|++...++.|-+
T Consensus 3 ~~eva~~~gvs~~tlr~w~~ 22 (68)
T cd01104 3 IGAVARLTGVSPDTLRAWER 22 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999985
No 236
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=23.23 E-value=3e+02 Score=22.49 Aligned_cols=44 Identities=30% Similarity=0.286 Sum_probs=25.5
Q ss_pred hhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 022964 98 QNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 152 (289)
Q Consensus 98 QNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~ 152 (289)
|||-++.-+.+.+.+++. +.....|.+.|..++..+..++....
T Consensus 57 QNRq~~~dr~ra~~D~~i-----------nl~ae~ei~~l~~~l~~l~~~~~~~~ 100 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQI-----------NLKAEQEIERLHRKLDALREKLGELL 100 (108)
T ss_pred hhHhHHHHHHHHHHHHHH-----------HHHhHHHHHHHHHHHHHHHHHhHHHH
Confidence 777665555555555543 33344566667777766666665443
No 237
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=23.13 E-value=2e+02 Score=29.10 Aligned_cols=48 Identities=19% Similarity=0.117 Sum_probs=31.5
Q ss_pred hhHHHHHHHHHHHHHHHHhhhhhhHHHhhH--HHHHHHHHHHHHHHHHHH
Q 022964 99 NRRARWKTKQLEKDYDVLQNSYNSLKADYD--NLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 99 NRRak~Krk~~e~e~~~l~~~~~~lk~~~~--~l~~ene~L~~e~~~l~~ 146 (289)
+++++.|.+++++..+.|....+.++.+.. .+..+.+.++.++.+|+.
T Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 102 (438)
T PTZ00361 53 NTKCRLRLLKLERIKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLRG 102 (438)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhhC
Confidence 455566666666666767666666666653 567777777777777664
No 238
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=23.11 E-value=3.2e+02 Score=20.24 Aligned_cols=36 Identities=11% Similarity=0.261 Sum_probs=16.4
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
....+..+-.+..........|..|..++..|+..+
T Consensus 20 L~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ 55 (61)
T PF08826_consen 20 LTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEM 55 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444444444555555555555443
No 239
>cd04776 HTH_GnyR Helix-Turn-Helix DNA binding domain of the regulatory protein GnyR. Putative helix-turn-helix (HTH) regulatory protein, GnyR, and other related proteins. GnyR belongs to the gnyRDBHAL cluster, which is involved in acyclic isoprenoid degradation in Pseudomonas aeruginosa. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=23.05 E-value=4.1e+02 Score=21.53 Aligned_cols=34 Identities=18% Similarity=0.157 Sum_probs=24.0
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhh
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQN 99 (289)
.|.|+..++..|.. ...++.+|++-.+|+.-+..
T Consensus 34 yR~Y~~~~l~~l~~-------------I~~lr~~G~~L~~I~~~l~~ 67 (118)
T cd04776 34 TRVYSRRDRARLKL-------------ILRGKRLGFSLEEIRELLDL 67 (118)
T ss_pred ccccCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHHh
Confidence 44599999888843 33367788888888776654
No 240
>PF11544 Spc42p: Spindle pole body component Spc42p; InterPro: IPR021611 Spc42p is a 42kDa component of the S.cerevisiae spindle body that localises to the electron dense central region of the SPB. Spc42p is a phosphoprotein which forms a polymeric layer at the periphery of the SPB central plaque. This functions during SPB duplication and also facilitates the attachment of the SPB to the nuclear membrane. ; PDB: 2Q6Q_B.
Probab=23.01 E-value=3.7e+02 Score=20.94 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=39.2
Q ss_pred hhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 98 QNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 98 QNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
||+--+.+-...+.+.+.|..-...|+.........+.+|+++...++..
T Consensus 6 qNk~L~~kL~~K~eEI~rLn~lv~sLR~KLiKYt~LnkkLq~~~~~~~~~ 55 (76)
T PF11544_consen 6 QNKELKKKLNDKQEEIDRLNILVGSLRGKLIKYTELNKKLQDQLLNLQRS 55 (76)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 56666666666777888888888888888888888888888888777653
No 241
>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=22.96 E-value=1.6e+02 Score=23.44 Aligned_cols=31 Identities=23% Similarity=0.263 Sum_probs=17.6
Q ss_pred HHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 115 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 115 ~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
.++.....|......+..+|..|..++..++
T Consensus 77 ~~~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 77 YKKKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3344444555666666666666666665554
No 242
>cd04775 HTH_Cfa-like Helix-Turn-Helix DNA binding domain of Cfa-like transcription regulators. Putative helix-turn-helix (HTH) MerR-like transcription regulators; the HTH domain of Cfa, a cyclopropane fatty acid synthase, and other related methyltransferases, as well as, the N-terminal domain of a conserved, uncharacterized ~172 a.a. protein. Based on sequence similarity of the N-terminal domain, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimil
Probab=22.90 E-value=3.8e+02 Score=21.04 Aligned_cols=35 Identities=23% Similarity=0.228 Sum_probs=26.0
Q ss_pred CCCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhh
Q 022964 52 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 99 (289)
Q Consensus 52 kR~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQN 99 (289)
..+.|+..++..|.. ....+++|++...|+..+..
T Consensus 35 g~R~Y~~~dl~~l~~-------------I~~l~~~G~~l~ei~~~~~~ 69 (102)
T cd04775 35 NYRLYSEADLSRLEK-------------IVFLQAGGLPLEEIAGCLAQ 69 (102)
T ss_pred CCeeeCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHcC
Confidence 345699999998833 33358889999999988764
No 243
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=22.76 E-value=1.6e+02 Score=24.29 Aligned_cols=46 Identities=20% Similarity=0.091 Sum_probs=29.4
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
++..|..+|...|- ......++|..+|++...|+.+...-|.+-|+
T Consensus 113 L~~~~r~v~~l~~~-----~~~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDY-----YGFSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 55555555444332 22235688999999999999988755555443
No 244
>PRK12546 RNA polymerase sigma factor; Provisional
Probab=22.61 E-value=1.1e+02 Score=26.48 Aligned_cols=46 Identities=20% Similarity=0.003 Sum_probs=30.3
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
+++.+..+|...|- ......++|..||++...|+.+...-|.+.|+
T Consensus 114 Lp~~~r~v~~L~~~-----~g~s~~EIA~~LgiS~~tVk~~l~Rar~~Lr~ 159 (188)
T PRK12546 114 LPDEQREALILVGA-----SGFSYEEAAEMCGVAVGTVKSRANRARARLAE 159 (188)
T ss_pred CCHHHhHHhhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555544332 22235688999999999999998765555554
No 245
>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=22.61 E-value=90 Score=22.22 Aligned_cols=35 Identities=23% Similarity=0.318 Sum_probs=25.6
Q ss_pred HHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHh
Q 022964 59 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 97 (289)
Q Consensus 59 eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWF 97 (289)
.|+..|+-.+. +...+.. +||..||++.+.|+.-.
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 46778888888 6655444 89999999998877554
No 246
>PF12709 Kinetocho_Slk19: Central kinetochore-associated; InterPro: IPR024312 This is a family of proteins integrally involved in the central kinetochore. Slk19 is a yeast member and it may play an important role in the timing of nuclear migration. It may also participate, directly or indirectly, in the maintenance of centromeric tensile strength during mitotic stagnation, for instance during activation of checkpoint controls, when cells need to preserve nuclear integrity until cell cycle progression can be resumed [].
Probab=22.57 E-value=2.4e+02 Score=22.46 Aligned_cols=33 Identities=18% Similarity=0.262 Sum_probs=22.2
Q ss_pred HHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 022964 114 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 146 (289)
Q Consensus 114 ~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~ 146 (289)
..+....+.|..++..+..|++.|+.++...+.
T Consensus 45 ~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~ 77 (87)
T PF12709_consen 45 ARWEKKVDELENENKALKRENEQLKKKLDTERE 77 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345666667777777777777777776654443
No 247
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=22.48 E-value=1.2e+02 Score=25.15 Aligned_cols=29 Identities=21% Similarity=0.110 Sum_probs=23.0
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...++|..||++...|+.|.+.-|.+.|+
T Consensus 126 s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 126 TYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45689999999999999998765555554
No 248
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=22.44 E-value=94 Score=29.69 Aligned_cols=38 Identities=34% Similarity=0.377 Sum_probs=33.8
Q ss_pred hccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 69 EVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 69 ~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
..++||+...+..|+...+|+..+|..||-|-|.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 45789999999999999999999999999998877665
No 249
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=22.44 E-value=1e+02 Score=25.71 Aligned_cols=33 Identities=18% Similarity=0.162 Sum_probs=25.3
Q ss_pred CCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 74 LEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 74 P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
.....-.++|..+|++...|+..+..-|.+.|+
T Consensus 134 ~~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 134 LEDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred hcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 334456789999999999999998766655554
No 250
>PF04728 LPP: Lipoprotein leucine-zipper; InterPro: IPR006817 This repeating sequence, NAKVDQLSNDV, is found in the enterobacterial outer membrane lipoprotein LPP. The outer membrane lipoprotein is the most abundant protein in an Escherichia coli cell. The messenger RNA for the lipoprotein of the E. coli outer membrane codes for a putative precursor, prolipoprotein, which has 20 additional amino acid residues extending from the amino terminus of the lipoprotein.; GO: 0019867 outer membrane; PDB: 1JCC_A 2GUV_C 2GUS_A 1JCD_A 1KFM_A 1T8Z_D 1KFN_A 1EQ7_A.
Probab=22.35 E-value=3.2e+02 Score=20.02 Aligned_cols=45 Identities=20% Similarity=0.297 Sum_probs=31.7
Q ss_pred HHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhccC
Q 022964 113 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKESKN 157 (289)
Q Consensus 113 ~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~~~~~ 157 (289)
.+.|-.....|....+.|..+...|+.++...++...-...+..|
T Consensus 5 id~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlDN 49 (56)
T PF04728_consen 5 IDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLDN 49 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445666666777777777778888888877777776666655544
No 251
>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=22.29 E-value=1e+02 Score=25.95 Aligned_cols=30 Identities=10% Similarity=-0.059 Sum_probs=22.6
Q ss_pred HHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 77 ERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 77 ~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
..-.++|..||++...|+++...-|.+-|+
T Consensus 155 ~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 155 LSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 346789999999999999988654444443
No 252
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=22.26 E-value=3.8e+02 Score=23.03 Aligned_cols=43 Identities=33% Similarity=0.469 Sum_probs=28.1
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
.+..+...+......|..+..++..|++.|..++..+++++..
T Consensus 56 ~L~~el~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~e 98 (140)
T PF10473_consen 56 TLEEELEELTSELNQLELELDTLRSEKENLDKELQKKQEKVSE 98 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455555666666667777777777777777777777666553
No 253
>PF09304 Cortex-I_coil: Cortexillin I, coiled coil; InterPro: IPR015383 This domain is predominantly found in the actin-bundling protein cortexillin I from Dictyostelium discoideum (Slime mold). The domain has a structure consisting of an 18-heptad-repeat alpha-helical coiled-coil, and is a prerequisite for the assembly of Cortexillin I []. ; PDB: 1D7M_A.
Probab=22.14 E-value=4.6e+02 Score=21.71 Aligned_cols=41 Identities=24% Similarity=0.274 Sum_probs=25.8
Q ss_pred HHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 110 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 110 e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
.++.+.|.+....|...+.+..+....|++++..+...|-.
T Consensus 36 ~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le~ 76 (107)
T PF09304_consen 36 AKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLED 76 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445566666666777777666667777766666555543
No 254
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=22.00 E-value=3.5e+02 Score=26.14 Aligned_cols=48 Identities=38% Similarity=0.638 Sum_probs=30.3
Q ss_pred hHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 95 IWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 95 vWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
.||. ||.+.++.-...|......|+.+...|.+..+.+..-+..|.++
T Consensus 133 ~WYe-----WR~kllegLk~~L~~~~~~l~~D~~~L~~~~~~l~~~~~~l~~~ 180 (312)
T smart00787 133 MWYE-----WRMKLLEGLKEGLDENLEGLKEDYKLLMKELELLNSIKPKLRDR 180 (312)
T ss_pred HHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 6885 66666777777777777777777766666554444444444333
No 255
>TIGR03070 couple_hipB transcriptional regulator, y4mF family. Members of this family belong to a clade of helix-turn-helix DNA-binding proteins, among the larger family pfam01381 (HTH_3; Helix-turn-helix). Members are similar in sequence to the HipB protein of E. coli. Genes for members of the seed alignment for this protein family were found to be closely linked to genes encoding proteins related to HipA. The HibBA operon appears to have some features in common with toxin-antitoxin post-segregational killing systems.
Probab=21.96 E-value=76 Score=21.22 Aligned_cols=23 Identities=17% Similarity=0.084 Sum_probs=20.1
Q ss_pred HHHHHHHhCCChhhhhhHhhhhH
Q 022964 79 KIQLAKDLGLQPRQVAIWFQNRR 101 (289)
Q Consensus 79 r~~LA~~LgLs~rQVkvWFQNRR 101 (289)
..+||..+|+++..|..|...++
T Consensus 18 q~~lA~~~gvs~~~vs~~e~g~~ 40 (58)
T TIGR03070 18 QADLADLAGVGLRFIRDVENGKP 40 (58)
T ss_pred HHHHHHHhCCCHHHHHHHHCCCC
Confidence 46799999999999999997764
No 256
>TIGR02209 ftsL_broad cell division protein FtsL. This model represents FtsL, both forms similar to that in E. coli and similar to that in B. subtilis. FtsL is one of the later proteins active in cell division septum formation. FtsL is small, low in complexity, and highly divergent. The scope of this model is broader than that of the Pfam model pfam04999.3 for FtsL, as this one includes FtsL from Bacillus subtilis and related species.
Probab=21.79 E-value=2.4e+02 Score=21.06 Aligned_cols=37 Identities=22% Similarity=0.348 Sum_probs=25.6
Q ss_pred HHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 022964 108 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 145 (289)
Q Consensus 108 ~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~ 145 (289)
+...+...+++....++.+++.|+.|...|... .++.
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~~-~rIe 64 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSRH-ERIE 64 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCH-HHHH
Confidence 445566677777777888888888888877763 4443
No 257
>PF12718 Tropomyosin_1: Tropomyosin like; InterPro: IPR000533 Tropomyosins [], are a family of closely related proteins present in muscle and non-muscle cells. In striated muscle, tropomyosin mediate the interactions between the troponin complex and actin so as to regulate muscle contraction []. The role of tropomyosin in smooth muscle and non-muscle tissues is not clear. Tropomyosin is an alpha-helical protein that forms a coiled-coil structure of 2 parallel helices containing 2 sets of 7 alternating actin binding sites []. There are multiple cell-specific isoforms, created by differential splicing of the messenger RNA from one gene, but the proportions of the isoforms vary between different cell types. Muscle isoforms of tropomyosin are characterised by having 284 amino acid residues and a highly conserved N-terminal region, whereas non-muscle forms are generally smaller and are heterogeneous in their N-terminal region. This entry represents tropomyosin (Tmp) 1, 2 and 3. Within the yeast Tmp1 and Tmp2, biochemical and sequence analyses indicate that Tpm2 spans four actin monomers along a filament, whereas Tpm1 spans five. Despite its shorter length, Tpm2 can compete with Tpm1 for binding to F-actin. Over-expression of Tpm2 in vivo alters the axial budding of haploids to a bipolar pattern, and this can be partially suppressed by co-over-expression of Tpm1. This suggests distinct functions for the two tropomyosins, and indicates that the ratio between them is important for correct morphogenesis [].
Probab=21.66 E-value=4.1e+02 Score=22.53 Aligned_cols=51 Identities=29% Similarity=0.403 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhc
Q 022964 105 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 155 (289)
Q Consensus 105 Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~~~~~~ 155 (289)
+.+.++.....+...+.+|...+..|..+.+++...+..++.++...++..
T Consensus 22 ~~K~le~~~~~~E~EI~sL~~K~~~lE~eld~~~~~l~~~k~~lee~~~~~ 72 (143)
T PF12718_consen 22 KVKQLEQENEQKEQEITSLQKKNQQLEEELDKLEEQLKEAKEKLEESEKRK 72 (143)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhHHHHH
Confidence 344555555556666666666677777777777777777776666555443
No 258
>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=21.57 E-value=4e+02 Score=20.89 Aligned_cols=35 Identities=17% Similarity=0.095 Sum_probs=27.5
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhh
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 100 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNR 100 (289)
.++|+...+..| .....++.+|++-..|+.+|...
T Consensus 34 ~r~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~ 68 (107)
T cd04777 34 QYFFDEKCQDDL-------------EFILELKGLGFSLIEIQKIFSYK 68 (107)
T ss_pred ccccCHHHHHHH-------------HHHHHHHHCCCCHHHHHHHHHhc
Confidence 346888888777 34556899999999999999753
No 259
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=21.11 E-value=2e+02 Score=24.36 Aligned_cols=45 Identities=13% Similarity=0.265 Sum_probs=29.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+..++...|- ......++|..+|++...|+.|-..-|.+.|
T Consensus 134 L~~~~r~i~~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 178 (182)
T PRK12537 134 LEPARRNCILHAYV-----DGCSHAEIAQRLGAPLGTVKAWIKRSLKALR 178 (182)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChhhHHHHHHHHHHHHH
Confidence 55555555444432 2224568899999999999998765444443
No 260
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=21.07 E-value=3.8e+02 Score=25.63 Aligned_cols=48 Identities=29% Similarity=0.593 Sum_probs=29.6
Q ss_pred hHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 022964 95 IWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 147 (289)
Q Consensus 95 vWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~ 147 (289)
.||. ||.+..+.-...|......|+.+...|....+.|..-+..|.++
T Consensus 138 ~WYe-----WR~~ll~gl~~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~~~ 185 (325)
T PF08317_consen 138 MWYE-----WRMQLLEGLKEGLEENLELLQEDYAKLDKQLEQLDELLPKLRER 185 (325)
T ss_pred HHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 5774 66666666677777777777777666665555544444444433
No 261
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=20.98 E-value=1.9e+02 Score=24.47 Aligned_cols=29 Identities=10% Similarity=0.094 Sum_probs=22.5
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...++|..||++...|++....-|.+.|+
T Consensus 135 s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 135 SQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999888766665554
No 262
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=20.83 E-value=2.3e+02 Score=25.58 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=22.9
Q ss_pred HHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 78 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 78 ~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
...++|..||++...|+.....-|.+.|+
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 45789999999999999998765555554
No 263
>TIGR02950 SigM_subfam RNA polymerase sigma factor, SigM family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937) and is restricted to certain lineages of the order Bacillales. This family encompasses at least two distinct sigma factors as two proteins are found in each of B. anthracis, B. subtilis subsp. subtilis str. 168, and B. lichiniformis (although these are not apparently the same two in each). One of these is designated as SigM in B. subtilis (Swiss_Prot: SIGM_BACSU) and is activated by various stressors.
Probab=20.75 E-value=1.2e+02 Score=24.68 Aligned_cols=33 Identities=18% Similarity=0.111 Sum_probs=24.8
Q ss_pred CCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 73 KLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 73 ~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
+.......++|..+|+++..|+++...-|.+.|
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 345556788999999999999998865444444
No 264
>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=20.65 E-value=4.8e+02 Score=21.43 Aligned_cols=35 Identities=20% Similarity=0.259 Sum_probs=27.9
Q ss_pred CCcCCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhh
Q 022964 53 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 100 (289)
Q Consensus 53 R~R~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNR 100 (289)
.|.|+..++..| ......+.+|++-.+|+-++...
T Consensus 36 yR~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~ 70 (133)
T cd04787 36 YRLYSEKDLSRL-------------RFILSARQLGFSLKDIKEILSHA 70 (133)
T ss_pred eeeCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhhh
Confidence 346999999988 34445789999999999999754
No 265
>PF11516 DUF3220: Protein of unknown function (DUF3120); InterPro: IPR021597 This family of proteins with unknown function appears to be restricted to Bordetella. ; PDB: 2JPF_A.
Probab=20.44 E-value=2e+02 Score=22.79 Aligned_cols=30 Identities=23% Similarity=0.306 Sum_probs=16.8
Q ss_pred hhhhhHhhhhHHHHHHHHHHHHHHHHhhhhh
Q 022964 91 RQVAIWFQNRRARWKTKQLEKDYDVLQNSYN 121 (289)
Q Consensus 91 rQVkvWFQNRRak~Krk~~e~e~~~l~~~~~ 121 (289)
..|++|.||--.-.-+ ........|++..+
T Consensus 31 gdvkvwmqnledlhtr-rpdeftarlqqstd 60 (106)
T PF11516_consen 31 GDVKVWMQNLEDLHTR-RPDEFTARLQQSTD 60 (106)
T ss_dssp HHHHHHHHHHHHHHHH--HHHHHHHHHTTTH
T ss_pred ccHHHHHHHHHHHhcc-ChHHHHHHHHHhHH
Confidence 5799999996544433 22344444444443
No 266
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=20.40 E-value=1.4e+02 Score=26.45 Aligned_cols=17 Identities=53% Similarity=0.794 Sum_probs=5.2
Q ss_pred HHHHHHHHHHHHHHHHH
Q 022964 132 KEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 132 ~ene~L~~e~~~l~~~l 148 (289)
.|++.|+.++++|++.+
T Consensus 24 dEKE~L~~~~QRLkDE~ 40 (166)
T PF04880_consen 24 DEKENLREEVQRLKDEL 40 (166)
T ss_dssp HHHHHHHHCH-------
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 44555555555555443
No 267
>TIGR02479 FliA_WhiG RNA polymerase sigma factor, FliA/WhiG family. Most members of this family are the flagellar operon sigma factor FliA, controlling transcription of bacterial flagellar genes by RNA polymerase. An exception is the sigma factor WhiG in the genus Streptomyces, involved in the production of sporulating aerial mycelium.
Probab=20.34 E-value=1.4e+02 Score=26.38 Aligned_cols=45 Identities=16% Similarity=0.161 Sum_probs=32.1
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 105 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~K 105 (289)
++..+..+|...|-.. ....++|..+|++...|+.+...-+.+.|
T Consensus 176 L~~~~r~il~l~y~~~-----~s~~eIA~~lgis~~tV~~~~~ra~~~Lr 220 (224)
T TIGR02479 176 LSEREQLVLSLYYYEE-----LNLKEIGEVLGLTESRVSQIHSQALKKLR 220 (224)
T ss_pred CCHHHHHHHHHHHhCC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 6777777777766332 24578999999999999988765444444
No 268
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=20.28 E-value=5.1e+02 Score=21.59 Aligned_cols=13 Identities=23% Similarity=0.363 Sum_probs=4.6
Q ss_pred HHhhHHHHHHHHH
Q 022964 124 KADYDNLFKEKEK 136 (289)
Q Consensus 124 k~~~~~l~~ene~ 136 (289)
...+..|....+.
T Consensus 72 ~~~~~rL~~~~~~ 84 (151)
T PF11559_consen 72 QNDVERLKEQLEE 84 (151)
T ss_pred HHHHHHHHHHHHH
Confidence 3333333333333
No 269
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=20.18 E-value=2.9e+02 Score=27.39 Aligned_cols=45 Identities=16% Similarity=0.316 Sum_probs=32.2
Q ss_pred HHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 022964 106 TKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 150 (289)
Q Consensus 106 rk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l~~ 150 (289)
.+........+...+..|...+..+..+..+++.|+.++++++..
T Consensus 17 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 61 (398)
T PTZ00454 17 ERDLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKR 61 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555566777788888888888888888888888777653
No 270
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=20.04 E-value=2.6e+02 Score=21.37 Aligned_cols=53 Identities=17% Similarity=0.206 Sum_probs=29.4
Q ss_pred hhhHhhhhHHHHHHHHHHHHHHHHhhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 022964 93 VAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 148 (289)
Q Consensus 93 VkvWFQNRRak~Krk~~e~e~~~l~~~~~~lk~~~~~l~~ene~L~~e~~~l~~~l 148 (289)
++|.|-..|.... .......+-..+-.|+.+...|..|.+.++..+.++..++
T Consensus 21 LrI~fLee~l~~~---~~~~~~~~~keNieLKve~~~L~~el~~~~~~l~~a~~~~ 73 (75)
T PF07989_consen 21 LRIYFLEERLQKL---GPESIEELLKENIELKVEVESLKRELQEKKKLLKEAEKAI 73 (75)
T ss_pred HHHHHHHHHHHhc---ccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3566665555411 1222333344444577777777777777777666665543
No 271
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=20.01 E-value=1.9e+02 Score=24.67 Aligned_cols=46 Identities=17% Similarity=0.272 Sum_probs=29.8
Q ss_pred CCHHHHHHHHhhhhccCCCCHHHHHHHHHHhCCChhhhhhHhhhhHHHHHH
Q 022964 56 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 106 (289)
Q Consensus 56 ~T~eQl~~LE~~F~~~~~P~~~~r~~LA~~LgLs~rQVkvWFQNRRak~Kr 106 (289)
+++.+..++...|-. .....++|..+|++...|+...+.-|.+.|+
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~ 177 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQK 177 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555544321 2345688999999999998887655555444
Done!