Query 019954
Match_columns 333
No_of_seqs 321 out of 1476
Neff 5.5
Searched_HMMs 46136
Date Fri Mar 29 05:51:56 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019954.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019954hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.9 7.5E-23 1.6E-27 186.2 8.5 102 92-193 49-150 (198)
2 KOG0842 Transcription factor t 99.7 3.8E-18 8.1E-23 164.1 5.2 59 100-158 160-218 (307)
3 KOG0489 Transcription factor z 99.7 7.8E-18 1.7E-22 159.5 4.9 63 92-154 158-220 (261)
4 KOG0488 Transcription factor B 99.7 1.2E-16 2.7E-21 154.7 11.6 59 94-152 173-231 (309)
5 KOG0843 Transcription factor E 99.7 9.3E-17 2E-21 143.2 5.5 64 92-155 101-164 (197)
6 KOG0484 Transcription factor P 99.6 1.2E-16 2.6E-21 131.3 4.7 63 90-152 14-76 (125)
7 KOG0485 Transcription factor N 99.6 4.5E-16 9.8E-21 142.3 8.7 61 92-152 103-163 (268)
8 KOG0487 Transcription factor A 99.6 3.2E-16 6.9E-21 150.9 7.7 63 92-154 234-296 (308)
9 PF00046 Homeobox: Homeobox do 99.6 7.9E-16 1.7E-20 112.5 5.8 57 94-150 1-57 (57)
10 KOG0494 Transcription factor C 99.6 1.1E-15 2.3E-20 143.0 7.4 60 97-156 145-204 (332)
11 KOG0493 Transcription factor E 99.6 3E-15 6.5E-20 140.1 9.7 91 94-184 247-338 (342)
12 KOG0850 Transcription factor D 99.6 7.4E-16 1.6E-20 141.9 5.2 62 92-153 121-182 (245)
13 KOG0492 Transcription factor M 99.6 2E-15 4.4E-20 137.3 7.2 60 93-152 144-203 (246)
14 KOG0848 Transcription factor C 99.6 7E-15 1.5E-19 138.0 9.2 54 99-152 205-258 (317)
15 KOG2251 Homeobox transcription 99.5 8.8E-15 1.9E-19 134.2 4.7 65 90-154 34-98 (228)
16 cd00086 homeodomain Homeodomai 99.5 6E-14 1.3E-18 102.2 5.9 57 95-151 2-58 (59)
17 KOG4577 Transcription factor L 99.5 1.6E-14 3.4E-19 136.9 3.4 92 87-179 161-252 (383)
18 smart00389 HOX Homeodomain. DN 99.5 6.7E-14 1.4E-18 101.4 5.4 55 95-149 2-56 (56)
19 COG5576 Homeodomain-containing 99.4 1E-13 2.2E-18 122.4 5.9 67 88-154 46-112 (156)
20 KOG0844 Transcription factor E 99.4 1.2E-13 2.6E-18 131.8 3.9 63 92-154 180-242 (408)
21 TIGR01565 homeo_ZF_HD homeobox 99.4 2.8E-13 6.1E-18 101.1 4.4 53 93-145 1-57 (58)
22 KOG0491 Transcription factor B 99.4 1.1E-13 2.4E-18 122.0 2.1 63 92-154 99-161 (194)
23 KOG0847 Transcription factor, 99.3 6.9E-13 1.5E-17 121.8 3.2 62 91-152 165-226 (288)
24 KOG0486 Transcription factor P 99.3 1.8E-12 3.9E-17 124.2 5.1 64 92-155 111-174 (351)
25 KOG3802 Transcription factor O 99.3 9.1E-13 2E-17 129.9 2.8 61 92-152 293-353 (398)
26 KOG0490 Transcription factor, 99.1 2.8E-11 6.1E-16 110.4 4.5 63 90-152 57-119 (235)
27 KOG0849 Transcription factor P 98.9 1.3E-09 2.8E-14 107.8 5.6 63 90-152 173-235 (354)
28 KOG1168 Transcription factor A 98.8 1.9E-09 4.1E-14 102.8 2.2 65 88-152 304-368 (385)
29 KOG0775 Transcription factor S 98.6 3.6E-08 7.9E-13 93.5 4.3 51 100-150 183-233 (304)
30 PF05920 Homeobox_KN: Homeobox 98.3 7.1E-07 1.5E-11 61.9 3.2 34 114-147 7-40 (40)
31 PF02183 HALZ: Homeobox associ 98.3 1.7E-06 3.8E-11 61.5 5.0 44 151-194 1-44 (45)
32 KOG0774 Transcription factor P 98.3 4.5E-07 9.7E-12 85.7 2.6 60 92-151 187-249 (334)
33 KOG0490 Transcription factor, 97.9 1.4E-05 3E-10 72.8 5.0 62 92-153 152-213 (235)
34 KOG2252 CCAAT displacement pro 97.8 2.4E-05 5.2E-10 80.5 6.2 58 91-148 418-475 (558)
35 KOG1146 Homeobox protein [Gene 97.4 0.00019 4.1E-09 80.2 5.3 67 87-153 897-963 (1406)
36 PF11569 Homez: Homeodomain le 96.3 0.0024 5.1E-08 47.6 2.1 41 105-145 10-50 (56)
37 KOG0773 Transcription factor M 96.0 0.0043 9.4E-08 60.8 2.9 62 93-154 239-303 (342)
38 PRK09413 IS2 repressor TnpA; R 94.5 0.22 4.7E-06 42.0 8.0 99 95-198 8-107 (121)
39 KOG3623 Homeobox transcription 93.6 0.084 1.8E-06 56.8 4.6 48 105-152 568-615 (1007)
40 PF02183 HALZ: Homeobox associ 93.5 0.19 4.1E-06 35.8 4.8 36 160-195 3-38 (45)
41 KOG4005 Transcription factor X 93.3 1.2 2.6E-05 42.4 11.1 44 155-198 104-147 (292)
42 PF04218 CENP-B_N: CENP-B N-te 92.4 0.29 6.2E-06 35.7 4.6 47 94-145 1-47 (53)
43 smart00340 HALZ homeobox assoc 89.7 0.65 1.4E-05 32.8 4.0 25 166-190 9-33 (44)
44 smart00340 HALZ homeobox assoc 89.1 0.72 1.6E-05 32.5 3.9 34 151-184 1-34 (44)
45 KOG4196 bZIP transcription fac 87.8 17 0.00036 31.7 12.2 84 98-193 22-112 (135)
46 PF00170 bZIP_1: bZIP transcri 86.1 5.4 0.00012 29.7 7.5 38 155-192 26-63 (64)
47 PRK00888 ftsB cell division pr 85.4 1.7 3.6E-05 36.2 4.9 48 135-190 15-62 (105)
48 PF06005 DUF904: Protein of un 81.1 7.2 0.00016 30.4 6.5 37 154-190 17-53 (72)
49 PF06156 DUF972: Protein of un 80.7 7.5 0.00016 32.5 7.0 47 151-197 11-57 (107)
50 KOG3119 Basic region leucine z 76.7 8.4 0.00018 37.1 7.0 48 144-194 207-254 (269)
51 PF10224 DUF2205: Predicted co 76.3 16 0.00036 29.1 7.3 49 147-195 15-63 (80)
52 PF06005 DUF904: Protein of un 75.6 20 0.00043 28.0 7.5 48 146-193 16-63 (72)
53 smart00338 BRLZ basic region l 75.4 23 0.0005 26.3 7.7 37 156-192 27-63 (65)
54 PRK13169 DNA replication intia 74.0 14 0.0003 31.2 6.7 45 151-195 11-55 (110)
55 PF00170 bZIP_1: bZIP transcri 73.0 17 0.00036 27.1 6.4 34 152-185 30-63 (64)
56 KOG4571 Activating transcripti 72.2 17 0.00036 35.7 7.7 51 146-197 240-290 (294)
57 PF13443 HTH_26: Cro/C1-type H 71.8 5.6 0.00012 28.8 3.5 42 122-163 12-53 (63)
58 PF04545 Sigma70_r4: Sigma-70, 70.8 8.6 0.00019 26.8 4.2 44 99-147 4-47 (50)
59 PF01527 HTH_Tnp_1: Transposas 69.9 2.6 5.7E-05 31.7 1.4 44 95-142 2-45 (76)
60 cd06171 Sigma70_r4 Sigma70, re 69.8 5.3 0.00011 26.7 2.8 43 100-147 11-53 (55)
61 KOG4403 Cell surface glycoprot 67.7 22 0.00048 36.8 7.8 63 138-200 229-326 (575)
62 PF07407 Seadorna_VP6: Seadorn 66.8 7.7 0.00017 38.7 4.2 28 166-193 36-63 (420)
63 KOG4343 bZIP transcription fac 65.8 28 0.00061 36.9 8.2 41 166-206 306-346 (655)
64 COG4026 Uncharacterized protei 65.1 21 0.00046 34.0 6.6 27 167-193 147-173 (290)
65 KOG1853 LIS1-interacting prote 61.6 85 0.0019 30.6 10.0 33 172-204 160-192 (333)
66 cd04779 HTH_MerR-like_sg4 Heli 61.4 1E+02 0.0022 26.6 9.8 73 96-181 34-107 (134)
67 PF04967 HTH_10: HTH DNA bindi 60.9 17 0.00036 26.7 4.1 38 100-137 1-40 (53)
68 PF06156 DUF972: Protein of un 59.0 26 0.00057 29.3 5.5 41 150-190 17-57 (107)
69 COG4467 Regulator of replicati 57.9 39 0.00084 28.6 6.2 43 152-194 12-54 (114)
70 PF15058 Speriolin_N: Sperioli 57.7 17 0.00036 33.7 4.4 35 163-197 6-40 (200)
71 KOG0709 CREB/ATF family transc 57.6 2.5E+02 0.0054 29.5 13.9 91 98-195 219-312 (472)
72 PF12709 Kinetocho_Slk19: Cent 57.6 51 0.0011 26.8 6.7 46 154-199 33-79 (87)
73 smart00338 BRLZ basic region l 56.6 42 0.00092 24.9 5.8 30 164-193 28-57 (65)
74 PF05700 BCAS2: Breast carcino 56.5 52 0.0011 30.6 7.7 55 143-197 163-217 (221)
75 PRK10884 SH3 domain-containing 56.0 54 0.0012 30.5 7.6 31 160-190 137-167 (206)
76 TIGR02449 conserved hypothetic 56.0 59 0.0013 25.0 6.5 39 155-193 7-45 (65)
77 PRK13169 DNA replication intia 55.7 32 0.00068 29.1 5.5 40 151-190 18-57 (110)
78 KOG4343 bZIP transcription fac 55.7 32 0.00069 36.6 6.5 51 140-190 286-337 (655)
79 KOG3156 Uncharacterized membra 55.5 1.5E+02 0.0033 28.0 10.3 30 166-195 113-142 (220)
80 cd00569 HTH_Hin_like Helix-tur 55.3 24 0.00051 20.8 3.7 38 99-141 5-42 (42)
81 PF04899 MbeD_MobD: MbeD/MobD 54.8 55 0.0012 25.5 6.3 41 156-196 22-62 (70)
82 COG3413 Predicted DNA binding 54.0 18 0.00039 33.1 4.1 49 99-149 155-205 (215)
83 PRK14127 cell division protein 53.7 30 0.00064 29.2 5.0 31 167-197 35-65 (109)
84 PF14197 Cep57_CLD_2: Centroso 53.4 1E+02 0.0022 23.8 7.6 22 172-193 43-64 (69)
85 PRK03975 tfx putative transcri 53.2 37 0.00079 29.8 5.7 48 97-150 4-51 (141)
86 PF10668 Phage_terminase: Phag 52.6 9.8 0.00021 28.8 1.8 19 122-140 24-42 (60)
87 KOG0483 Transcription factor H 52.1 22 0.00048 33.0 4.3 41 160-200 110-150 (198)
88 PRK14127 cell division protein 52.0 43 0.00094 28.2 5.7 40 155-194 30-69 (109)
89 KOG0249 LAR-interacting protei 50.9 64 0.0014 35.6 8.0 51 146-196 214-264 (916)
90 PRK10884 SH3 domain-containing 49.7 74 0.0016 29.6 7.5 42 154-195 124-165 (206)
91 KOG2391 Vacuolar sorting prote 49.7 58 0.0013 32.8 7.0 50 144-193 221-270 (365)
92 PF08281 Sigma70_r4_2: Sigma-7 49.2 33 0.00072 24.0 4.0 42 100-146 11-52 (54)
93 PF04880 NUDE_C: NUDE protein, 48.3 16 0.00034 33.1 2.7 30 169-198 24-53 (166)
94 cd04769 HTH_MerR2 Helix-Turn-H 48.2 1.2E+02 0.0026 25.0 7.9 38 97-147 35-72 (116)
95 KOG1146 Homeobox protein [Gene 48.1 33 0.00071 40.0 5.7 57 96-152 708-764 (1406)
96 PF04977 DivIC: Septum formati 47.9 45 0.00098 25.0 4.9 24 165-188 27-50 (80)
97 PF14775 NYD-SP28_assoc: Sperm 47.8 1E+02 0.0022 23.1 6.6 31 163-193 27-57 (60)
98 PRK13922 rod shape-determining 47.0 37 0.0008 32.2 5.2 35 160-194 74-111 (276)
99 COG3074 Uncharacterized protei 46.4 1.1E+02 0.0024 24.0 6.7 40 152-191 22-61 (79)
100 PF10883 DUF2681: Protein of u 46.3 47 0.001 27.0 4.9 26 171-196 32-57 (87)
101 cd01106 HTH_TipAL-Mta Helix-Tu 46.1 1.6E+02 0.0034 23.7 8.1 37 96-145 35-71 (103)
102 cd04766 HTH_HspR Helix-Turn-He 45.9 1.2E+02 0.0025 23.9 7.2 34 96-141 35-68 (91)
103 KOG4196 bZIP transcription fac 45.2 1E+02 0.0023 26.9 7.1 53 140-192 64-118 (135)
104 PF07716 bZIP_2: Basic region 44.2 91 0.002 22.4 5.8 24 166-189 29-52 (54)
105 PF11932 DUF3450: Protein of u 44.2 94 0.002 29.2 7.4 34 157-190 51-84 (251)
106 COG4026 Uncharacterized protei 44.2 74 0.0016 30.5 6.5 30 160-189 133-162 (290)
107 PF10224 DUF2205: Predicted co 43.9 1.3E+02 0.0029 24.0 7.0 45 149-193 24-68 (80)
108 PF01166 TSC22: TSC-22/dip/bun 43.4 37 0.0008 25.7 3.5 29 155-190 14-42 (59)
109 TIGR01069 mutS2 MutS2 family p 43.3 1.1E+02 0.0025 33.8 8.8 21 118-138 480-500 (771)
110 TIGR02894 DNA_bind_RsfA transc 42.7 66 0.0014 29.0 5.7 27 166-192 108-134 (161)
111 TIGR00219 mreC rod shape-deter 42.7 47 0.001 32.1 5.3 39 159-197 70-112 (283)
112 PF09726 Macoilin: Transmembra 42.1 5.1E+02 0.011 28.6 14.1 30 144-173 456-485 (697)
113 PF07407 Seadorna_VP6: Seadorn 41.9 52 0.0011 33.0 5.4 32 156-187 33-64 (420)
114 KOG4571 Activating transcripti 41.2 82 0.0018 31.0 6.5 30 169-198 248-277 (294)
115 KOG3119 Basic region leucine z 41.1 80 0.0017 30.4 6.5 38 160-197 213-250 (269)
116 PF11594 Med28: Mediator compl 40.3 1.6E+02 0.0035 24.8 7.3 34 135-171 18-51 (106)
117 PF02344 Myc-LZ: Myc leucine z 40.0 70 0.0015 21.3 4.0 22 172-193 4-25 (32)
118 TIGR02937 sigma70-ECF RNA poly 39.8 54 0.0012 26.3 4.5 45 100-149 111-155 (158)
119 KOG4005 Transcription factor X 39.7 1.2E+02 0.0026 29.3 7.2 60 141-200 81-142 (292)
120 PRK00409 recombination and DNA 39.6 1.3E+02 0.0029 33.3 8.7 21 118-138 485-505 (782)
121 PF00424 REV: REV protein (ant 39.3 35 0.00076 28.0 3.1 35 105-153 14-48 (91)
122 PF15035 Rootletin: Ciliary ro 39.3 1.3E+02 0.0028 27.5 7.2 43 156-198 82-124 (182)
123 PRK15422 septal ring assembly 39.2 1.5E+02 0.0033 23.7 6.6 38 153-190 23-60 (79)
124 cd04761 HTH_MerR-SF Helix-Turn 38.0 26 0.00057 23.7 2.0 23 123-145 3-25 (49)
125 cd01109 HTH_YyaN Helix-Turn-He 37.8 2.2E+02 0.0049 23.2 8.6 36 97-145 36-71 (113)
126 PRK13729 conjugal transfer pil 37.7 90 0.002 32.7 6.6 44 149-192 77-120 (475)
127 PF07334 IFP_35_N: Interferon- 37.5 62 0.0014 25.7 4.2 27 168-194 6-32 (76)
128 PRK06759 RNA polymerase factor 37.3 70 0.0015 26.7 4.9 45 100-149 107-151 (154)
129 PF09607 BrkDBD: Brinker DNA-b 37.2 50 0.0011 24.9 3.4 44 97-142 3-47 (58)
130 COG2919 Septum formation initi 37.1 1.2E+02 0.0025 25.5 6.2 33 159-191 54-86 (117)
131 PF05377 FlaC_arch: Flagella a 37.0 1.1E+02 0.0024 22.8 5.2 28 164-191 9-36 (55)
132 PRK12514 RNA polymerase sigma 36.0 42 0.00091 29.1 3.4 46 100-150 130-175 (179)
133 PF13518 HTH_28: Helix-turn-he 35.9 37 0.00081 23.2 2.6 22 122-143 14-35 (52)
134 PF11559 ADIP: Afadin- and alp 35.9 2.2E+02 0.0047 24.5 7.9 51 144-194 76-126 (151)
135 TIGR02449 conserved hypothetic 35.7 2E+02 0.0044 22.1 7.0 42 152-193 11-52 (65)
136 cd04765 HTH_MlrA-like_sg2 Heli 35.6 75 0.0016 25.8 4.6 20 124-143 4-23 (99)
137 PF09744 Jnk-SapK_ap_N: JNK_SA 35.4 2E+02 0.0042 25.8 7.6 80 104-193 34-113 (158)
138 PRK09652 RNA polymerase sigma 35.4 69 0.0015 27.2 4.7 46 100-150 129-174 (182)
139 PRK09646 RNA polymerase sigma 35.3 69 0.0015 28.3 4.8 46 100-150 143-188 (194)
140 PRK11924 RNA polymerase sigma 35.2 44 0.00096 28.3 3.4 46 100-150 126-171 (179)
141 KOG3755 SATB1 matrix attachmen 35.1 19 0.00042 38.7 1.3 46 108-153 707-759 (769)
142 smart00421 HTH_LUXR helix_turn 35.1 73 0.0016 21.4 4.0 42 99-146 3-44 (58)
143 TIGR02051 MerR Hg(II)-responsi 35.0 2.7E+02 0.0058 23.3 8.3 37 96-145 34-70 (124)
144 PF13936 HTH_38: Helix-turn-he 34.8 44 0.00095 23.1 2.7 40 98-142 3-42 (44)
145 PRK04217 hypothetical protein; 34.5 81 0.0018 26.5 4.7 46 99-149 42-87 (110)
146 PF07716 bZIP_2: Basic region 34.4 1.7E+02 0.0038 20.9 7.1 27 158-184 28-54 (54)
147 TIGR03752 conj_TIGR03752 integ 34.3 96 0.0021 32.5 6.1 94 99-195 41-135 (472)
148 TIGR03879 near_KaiC_dom probab 34.3 15 0.00032 28.8 0.3 35 109-143 21-55 (73)
149 PHA01750 hypothetical protein 34.1 2.1E+02 0.0046 22.3 6.5 35 158-192 38-72 (75)
150 PF00196 GerE: Bacterial regul 33.9 92 0.002 22.2 4.5 46 99-150 3-48 (58)
151 PF00038 Filament: Intermediat 33.6 2.5E+02 0.0053 26.8 8.6 16 134-149 186-201 (312)
152 PF11544 Spc42p: Spindle pole 33.2 2.5E+02 0.0054 22.3 7.4 50 142-191 6-55 (76)
153 cd04787 HTH_HMRTR_unk Helix-Tu 33.2 2.9E+02 0.0064 23.3 8.1 36 97-145 36-71 (133)
154 PF14197 Cep57_CLD_2: Centroso 33.1 1.8E+02 0.0039 22.4 6.1 26 164-189 42-67 (69)
155 PF09304 Cortex-I_coil: Cortex 32.1 2E+02 0.0044 24.2 6.7 42 152-193 34-75 (107)
156 PRK09639 RNA polymerase sigma 32.1 1.2E+02 0.0026 25.6 5.7 45 100-150 113-157 (166)
157 PRK14872 rod shape-determining 32.0 64 0.0014 32.4 4.3 25 164-188 59-83 (337)
158 TIGR02985 Sig70_bacteroi1 RNA 31.7 54 0.0012 27.2 3.3 45 100-149 114-158 (161)
159 PF07989 Microtub_assoc: Micro 31.6 1.8E+02 0.0039 22.7 6.0 31 166-196 40-70 (75)
160 PF12824 MRP-L20: Mitochondria 31.5 3.7E+02 0.0079 24.2 8.7 63 96-162 82-144 (164)
161 COG3074 Uncharacterized protei 31.4 1.9E+02 0.0042 22.7 5.9 22 165-186 42-63 (79)
162 KOG3650 Predicted coiled-coil 31.4 1.7E+02 0.0037 24.5 6.0 38 156-193 64-101 (120)
163 PRK12526 RNA polymerase sigma 31.3 88 0.0019 28.1 4.9 46 100-150 154-199 (206)
164 PF07334 IFP_35_N: Interferon- 31.3 81 0.0018 25.0 4.0 27 172-198 3-29 (76)
165 PRK10072 putative transcriptio 31.3 31 0.00066 28.3 1.7 42 99-147 32-73 (96)
166 PRK13922 rod shape-determining 31.0 2.2E+02 0.0048 26.9 7.7 28 162-189 69-96 (276)
167 PF04977 DivIC: Septum formati 30.8 1.3E+02 0.0029 22.4 5.1 30 152-181 21-50 (80)
168 KOG0150 Spliceosomal protein F 30.7 1.4E+02 0.003 29.8 6.2 56 137-192 16-72 (336)
169 PRK12519 RNA polymerase sigma 30.4 78 0.0017 27.7 4.3 46 100-150 142-187 (194)
170 PRK12512 RNA polymerase sigma 30.2 93 0.002 27.0 4.7 46 100-150 132-177 (184)
171 PF04999 FtsL: Cell division p 30.2 1.1E+02 0.0025 24.2 4.9 28 164-191 44-71 (97)
172 cd04765 HTH_MlrA-like_sg2 Heli 30.1 1.8E+02 0.0038 23.6 6.0 39 95-145 34-72 (99)
173 PRK12530 RNA polymerase sigma 29.9 1.1E+02 0.0024 26.9 5.2 46 100-150 135-180 (189)
174 PF13942 Lipoprotein_20: YfhG 29.9 4.4E+02 0.0096 24.2 10.5 90 102-194 58-155 (179)
175 PTZ00361 26 proteosome regulat 29.8 1.2E+02 0.0027 31.2 6.1 47 143-189 53-101 (438)
176 KOG2391 Vacuolar sorting prote 29.5 1.7E+02 0.0036 29.7 6.6 40 154-193 224-263 (365)
177 TIGR02948 SigW_bacill RNA poly 29.5 87 0.0019 27.0 4.4 46 100-150 137-182 (187)
178 TIGR02894 DNA_bind_RsfA transc 29.4 1.8E+02 0.004 26.2 6.4 35 155-189 104-138 (161)
179 PF05377 FlaC_arch: Flagella a 29.4 1.9E+02 0.0041 21.6 5.4 38 152-189 4-41 (55)
180 PF08172 CASP_C: CASP C termin 29.2 1.8E+02 0.0038 27.8 6.7 29 166-194 104-132 (248)
181 TIGR02209 ftsL_broad cell divi 29.2 1.4E+02 0.0031 22.8 5.1 23 168-190 37-59 (85)
182 PTZ00454 26S protease regulato 29.1 1.5E+02 0.0033 30.0 6.6 32 162-193 29-60 (398)
183 PF12999 PRKCSH-like: Glucosid 29.1 2.6E+02 0.0055 25.6 7.3 23 175-197 152-174 (176)
184 cd00093 HTH_XRE Helix-turn-hel 29.1 56 0.0012 21.1 2.5 23 123-145 15-37 (58)
185 PRK09642 RNA polymerase sigma 29.1 59 0.0013 27.5 3.1 46 100-150 107-152 (160)
186 PF06210 DUF1003: Protein of u 29.0 2E+02 0.0043 24.1 6.2 45 142-197 57-101 (108)
187 TIGR03752 conj_TIGR03752 integ 28.7 2.5E+02 0.0054 29.5 8.1 36 159-194 106-141 (472)
188 PF12808 Mto2_bdg: Micro-tubul 28.7 2.1E+02 0.0044 21.1 5.4 23 167-189 27-49 (52)
189 PF06785 UPF0242: Uncharacteri 28.7 2.2E+02 0.0047 28.8 7.3 24 174-197 139-162 (401)
190 PF13411 MerR_1: MerR HTH fami 28.6 43 0.00094 24.4 2.0 21 123-143 3-23 (69)
191 KOG1853 LIS1-interacting prote 28.6 2.3E+02 0.0051 27.6 7.2 55 137-191 55-113 (333)
192 cd01392 HTH_LacI Helix-turn-he 28.3 65 0.0014 22.1 2.7 21 125-145 2-22 (52)
193 PF09304 Cortex-I_coil: Cortex 28.1 3.1E+02 0.0068 23.1 7.1 33 158-190 19-51 (107)
194 PF08961 DUF1875: Domain of un 27.8 20 0.00043 33.9 0.0 29 160-188 134-162 (243)
195 PF13384 HTH_23: Homeodomain-l 27.5 48 0.001 22.7 1.9 23 121-143 18-40 (50)
196 PF08280 HTH_Mga: M protein tr 27.3 58 0.0013 23.8 2.4 34 103-140 6-39 (59)
197 COG2433 Uncharacterized conser 27.3 1.9E+02 0.0042 31.4 7.0 40 154-193 428-467 (652)
198 COG2963 Transposase and inacti 27.2 2.5E+02 0.0054 22.8 6.5 42 97-142 5-47 (116)
199 TIGR02989 Sig-70_gvs1 RNA poly 27.2 1.1E+02 0.0024 25.6 4.5 45 100-149 112-156 (159)
200 PF11932 DUF3450: Protein of u 27.2 3E+02 0.0064 25.8 7.8 53 135-193 42-94 (251)
201 PRK09648 RNA polymerase sigma 27.1 1.1E+02 0.0025 26.6 4.7 46 100-150 140-185 (189)
202 KOG0977 Nuclear envelope prote 27.1 2E+02 0.0044 30.8 7.2 38 152-189 152-189 (546)
203 TIGR02959 SigZ RNA polymerase 26.7 1.1E+02 0.0025 26.3 4.6 46 99-149 100-145 (170)
204 cd04781 HTH_MerR-like_sg6 Heli 26.6 3.7E+02 0.008 22.2 8.0 36 96-144 34-69 (120)
205 PRK14872 rod shape-determining 26.6 1.1E+02 0.0025 30.6 5.1 23 156-178 58-80 (337)
206 PF03670 UPF0184: Uncharacteri 26.5 1.9E+02 0.0042 23.3 5.4 38 154-191 25-62 (83)
207 PRK05602 RNA polymerase sigma 26.1 1.1E+02 0.0024 26.6 4.5 46 100-150 129-174 (186)
208 cd04770 HTH_HMRTR Helix-Turn-H 26.1 3.7E+02 0.008 22.1 9.3 38 96-146 35-72 (123)
209 PF02796 HTH_7: Helix-turn-hel 26.1 98 0.0021 21.3 3.3 38 99-141 5-42 (45)
210 COG1579 Zn-ribbon protein, pos 26.1 2.6E+02 0.0057 26.7 7.1 52 145-196 21-72 (239)
211 PRK12515 RNA polymerase sigma 26.0 1.2E+02 0.0027 26.4 4.7 46 100-150 132-177 (189)
212 KOG0709 CREB/ATF family transc 25.9 1.8E+02 0.004 30.4 6.4 74 117-191 220-301 (472)
213 PRK00118 putative DNA-binding 25.8 3.9E+02 0.0084 22.2 7.6 45 100-149 18-62 (104)
214 cd04783 HTH_MerR1 Helix-Turn-H 25.6 3.9E+02 0.0085 22.2 8.4 36 97-145 36-71 (126)
215 PF02403 Seryl_tRNA_N: Seryl-t 25.5 3.6E+02 0.0077 21.7 7.7 57 142-198 37-96 (108)
216 cd06170 LuxR_C_like C-terminal 25.3 1.4E+02 0.003 20.2 4.0 36 101-142 2-37 (57)
217 TIGR02999 Sig-70_X6 RNA polyme 25.2 1.3E+02 0.0029 25.9 4.8 46 100-150 135-180 (183)
218 PRK00888 ftsB cell division pr 25.0 2.2E+02 0.0048 23.5 5.8 28 156-183 35-62 (105)
219 PF01381 HTH_3: Helix-turn-hel 24.9 48 0.001 23.0 1.5 23 123-145 12-34 (55)
220 KOG0980 Actin-binding protein 24.7 2.8E+02 0.006 31.5 7.9 82 104-188 366-450 (980)
221 PRK15422 septal ring assembly 24.7 3.3E+02 0.0071 21.8 6.3 33 157-189 34-66 (79)
222 PF06056 Terminase_5: Putative 24.6 54 0.0012 24.3 1.8 27 122-150 15-41 (58)
223 COG4467 Regulator of replicati 24.5 1.5E+02 0.0032 25.2 4.5 36 152-187 19-54 (114)
224 PRK12541 RNA polymerase sigma 24.4 1.2E+02 0.0026 25.7 4.2 46 100-150 113-158 (161)
225 PRK14086 dnaA chromosomal repl 24.4 3.6E+02 0.0079 29.3 8.6 74 118-193 524-615 (617)
226 PTZ00454 26S protease regulato 24.4 2.1E+02 0.0046 29.0 6.6 37 153-189 27-63 (398)
227 PF12325 TMF_TATA_bd: TATA ele 24.2 2.9E+02 0.0063 23.6 6.4 49 144-192 64-112 (120)
228 cd04762 HTH_MerR-trunc Helix-T 24.1 65 0.0014 21.1 2.1 24 123-146 3-26 (49)
229 PRK05431 seryl-tRNA synthetase 24.0 2.4E+02 0.0052 28.9 7.0 64 137-200 31-97 (425)
230 PRK12538 RNA polymerase sigma 23.9 1.6E+02 0.0034 27.3 5.2 29 122-150 189-217 (233)
231 KOG0977 Nuclear envelope prote 23.8 2.2E+02 0.0047 30.5 6.7 41 156-196 149-189 (546)
232 PRK09644 RNA polymerase sigma 23.8 96 0.0021 26.4 3.6 46 100-150 109-154 (165)
233 PF03980 Nnf1: Nnf1 ; InterPr 23.6 1.5E+02 0.0032 24.2 4.5 31 159-189 77-107 (109)
234 TIGR02939 RpoE_Sigma70 RNA pol 23.5 82 0.0018 27.2 3.1 46 100-150 139-184 (190)
235 TIGR02983 SigE-fam_strep RNA p 23.4 1.7E+02 0.0036 24.7 5.0 46 100-150 111-156 (162)
236 PRK12518 RNA polymerase sigma 23.2 86 0.0019 26.8 3.1 32 119-150 135-166 (175)
237 TIGR02209 ftsL_broad cell divi 23.0 2.1E+02 0.0046 21.8 5.1 33 152-184 28-60 (85)
238 PRK09047 RNA polymerase factor 22.9 1.6E+02 0.0034 24.7 4.7 45 100-149 107-151 (161)
239 TIGR00721 tfx DNA-binding prot 22.7 3E+02 0.0064 24.0 6.3 47 98-150 5-51 (137)
240 PF04728 LPP: Lipoprotein leuc 22.6 3.4E+02 0.0073 20.3 6.7 44 149-192 4-47 (56)
241 PRK06811 RNA polymerase factor 22.5 1.1E+02 0.0024 26.8 3.8 47 100-151 132-178 (189)
242 PRK12537 RNA polymerase sigma 22.4 1.6E+02 0.0035 25.6 4.8 46 100-150 134-179 (182)
243 PRK13729 conjugal transfer pil 22.4 3.2E+02 0.007 28.8 7.5 25 162-186 97-121 (475)
244 TIGR02950 SigM_subfam RNA poly 22.2 89 0.0019 26.0 3.0 33 117-149 118-150 (154)
245 KOG0773 Transcription factor M 22.1 91 0.002 30.5 3.4 38 113-150 117-154 (342)
246 cd04777 HTH_MerR-like_sg1 Heli 22.0 4.2E+02 0.0092 21.3 7.1 35 97-144 34-68 (107)
247 cd04763 HTH_MlrA-like Helix-Tu 22.0 70 0.0015 23.5 2.1 21 123-143 3-23 (68)
248 PF14662 CCDC155: Coiled-coil 22.0 3.8E+02 0.0081 24.9 7.1 39 154-192 101-139 (193)
249 TIGR00219 mreC rod shape-deter 22.0 2.5E+02 0.0053 27.2 6.3 16 173-188 70-85 (283)
250 PRK06986 fliA flagellar biosyn 21.9 1.1E+02 0.0024 28.0 3.8 46 100-150 185-230 (236)
251 cd04782 HTH_BltR Helix-Turn-He 21.9 4.1E+02 0.0089 21.1 7.5 35 96-143 35-69 (97)
252 PF14645 Chibby: Chibby family 21.9 2.3E+02 0.005 24.0 5.4 16 170-185 79-94 (116)
253 PRK10722 hypothetical protein; 21.9 7.3E+02 0.016 24.0 10.9 89 103-195 105-202 (247)
254 cd04764 HTH_MlrA-like_sg1 Heli 21.8 74 0.0016 23.3 2.1 21 123-143 3-23 (67)
255 PRK12543 RNA polymerase sigma 21.8 1.5E+02 0.0033 25.7 4.4 46 100-150 118-163 (179)
256 PF07888 CALCOCO1: Calcium bin 21.6 3.7E+02 0.0081 28.8 7.9 27 157-183 187-213 (546)
257 PF00376 MerR: MerR family reg 21.6 62 0.0013 21.8 1.5 18 124-141 3-20 (38)
258 smart00787 Spc7 Spc7 kinetocho 21.5 3.8E+02 0.0083 26.4 7.6 48 138-190 132-179 (312)
259 COG1394 NtpD Archaeal/vacuolar 21.5 4.1E+02 0.0089 24.9 7.4 49 145-193 14-62 (211)
260 TIGR02479 FliA_WhiG RNA polyme 21.5 1.1E+02 0.0024 27.7 3.7 46 100-150 176-221 (224)
261 PRK10403 transcriptional regul 21.4 1.1E+02 0.0024 25.8 3.4 46 99-150 153-198 (215)
262 PF04111 APG6: Autophagy prote 21.4 3.2E+02 0.0069 26.9 7.0 10 244-253 202-211 (314)
263 PF13700 DUF4158: Domain of un 21.3 4.3E+02 0.0093 23.0 7.2 42 115-156 64-105 (166)
264 cd01107 HTH_BmrR Helix-Turn-He 20.9 4.6E+02 0.0099 21.2 7.5 37 97-146 37-73 (108)
265 PRK05657 RNA polymerase sigma 20.7 1.5E+02 0.0032 29.2 4.5 51 99-150 262-312 (325)
266 TIGR02954 Sig70_famx3 RNA poly 20.7 1.8E+02 0.0039 24.8 4.6 46 100-150 120-165 (169)
267 PF04568 IATP: Mitochondrial A 20.7 4.5E+02 0.0097 21.8 6.7 25 168-192 75-99 (100)
268 PF12718 Tropomyosin_1: Tropom 20.5 4.7E+02 0.01 22.7 7.2 51 149-199 22-72 (143)
269 KOG3863 bZIP transcription fac 20.4 3.8E+02 0.0082 29.1 7.7 37 160-196 516-552 (604)
270 PF08317 Spc7: Spc7 kinetochor 20.3 4.3E+02 0.0093 25.9 7.7 47 138-189 137-183 (325)
271 PF12709 Kinetocho_Slk19: Cent 20.3 2.5E+02 0.0055 22.8 5.0 30 160-189 47-76 (87)
272 PF12844 HTH_19: Helix-turn-he 20.3 98 0.0021 22.2 2.5 37 122-159 14-50 (64)
273 smart00027 EH Eps15 homology d 20.3 1.8E+02 0.0039 22.8 4.2 43 100-142 4-51 (96)
274 PRK06930 positive control sigm 20.1 2.2E+02 0.0047 25.4 5.1 46 100-150 115-160 (170)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.88 E-value=7.5e-23 Score=186.24 Aligned_cols=102 Identities=63% Similarity=0.946 Sum_probs=92.6
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhh
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADY 171 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~ 171 (333)
...+|++||+.+|+..||+.|+...++.+.+|..||++|||.+|||+|||||||||||.++++.+|+.|+..++.|+.++
T Consensus 49 ~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~ 128 (198)
T KOG0483|consen 49 KGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEN 128 (198)
T ss_pred ccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhh
Confidence 35577888999999999999999999999999999999999999999999999999999999999999999999888888
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 019954 172 DNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 172 ~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+.|..|+..|++++..++..+.
T Consensus 129 ~~Lq~e~~eL~~~~~~~~~~~~ 150 (198)
T KOG0483|consen 129 DRLQSEVQELVAELSSLKREMQ 150 (198)
T ss_pred hHHHHHHHHHHHHHhhhhhhhc
Confidence 8888888888888777665444
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.72 E-value=3.8e-18 Score=164.06 Aligned_cols=59 Identities=39% Similarity=0.579 Sum_probs=56.6
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYD 158 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~ 158 (333)
|+..|+.+||+.|++++|++..+|+.||..|.|+++||||||||||-|.||+++++..+
T Consensus 160 FSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 160 FSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 99999999999999999999999999999999999999999999999999998776654
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.70 E-value=7.8e-18 Score=159.51 Aligned_cols=63 Identities=37% Similarity=0.647 Sum_probs=57.9
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
+.||.|+.||..|+.+||+.|..++|++..+|.+||..|.|++|||||||||||+||||..+.
T Consensus 158 ~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k~ 220 (261)
T KOG0489|consen 158 KSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENKA 220 (261)
T ss_pred CCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhcc
Confidence 456677779999999999999999999999999999999999999999999999999986533
No 4
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=1.2e-16 Score=154.67 Aligned_cols=59 Identities=39% Similarity=0.654 Sum_probs=54.5
Q ss_pred CCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 94 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 94 ~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
|+.|+.||..||..||+.|++.+|++..+|++||+.|||+..||++||||||+||||..
T Consensus 173 RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 173 RKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred ccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 33344599999999999999999999999999999999999999999999999999954
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.65 E-value=9.3e-17 Score=143.16 Aligned_cols=64 Identities=34% Similarity=0.494 Sum_probs=59.0
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEK 155 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~k 155 (333)
+.||.|+.||.+|+..||..|+.++|....+|++||..|+|++.||||||||||+|.||.+.+.
T Consensus 101 ~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 101 RPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 4556677799999999999999999999999999999999999999999999999999987663
No 6
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.64 E-value=1.2e-16 Score=131.30 Aligned_cols=63 Identities=25% Similarity=0.435 Sum_probs=58.3
Q ss_pred ccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 90 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 90 ~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
..+++|-|+.||..||..||+.|...+||++..|++||.++.|++.+|||||||||||+||+.
T Consensus 14 krKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 14 KRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred HHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 345667777899999999999999999999999999999999999999999999999999854
No 7
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.64 E-value=4.5e-16 Score=142.34 Aligned_cols=61 Identities=36% Similarity=0.609 Sum_probs=56.4
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
+|||.|+.|+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 4555666699999999999999999999999999999999999999999999999999853
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.64 E-value=3.2e-16 Score=150.89 Aligned_cols=63 Identities=37% Similarity=0.515 Sum_probs=57.1
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
.-||||..+|..|+.+||+.|..|.|++.+.|.+|++.|+|++|||||||||||+|.||..++
T Consensus 234 ~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re 296 (308)
T KOG0487|consen 234 RGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNRE 296 (308)
T ss_pred ccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhh
Confidence 344555569999999999999999999999999999999999999999999999999997643
No 9
>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=99.61 E-value=7.9e-16 Score=112.53 Aligned_cols=57 Identities=42% Similarity=0.636 Sum_probs=54.6
Q ss_pred CCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 94 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 94 ~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++|++||.+|+..|+..|..++||+..++..||.+|||+..||++||+|||+++|+
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 467888999999999999999999999999999999999999999999999999986
No 10
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.61 E-value=1.1e-15 Score=142.97 Aligned_cols=60 Identities=28% Similarity=0.481 Sum_probs=55.4
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKD 156 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke 156 (333)
|+.||..|+..||+.|+..+||+...|+-||.++.|++.+|+||||||||||||+..+--
T Consensus 145 RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg 204 (332)
T KOG0494|consen 145 RTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWG 204 (332)
T ss_pred cchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcC
Confidence 444999999999999999999999999999999999999999999999999999765533
No 11
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.60 E-value=3e-15 Score=140.09 Aligned_cols=91 Identities=29% Similarity=0.454 Sum_probs=71.2
Q ss_pred CCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHH
Q 019954 94 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDN 173 (333)
Q Consensus 94 ~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~ 173 (333)
||.|+.||.+||+.|+..|+.++|++..+|.+||.+|||.+.||+|||||+|+|.||..-.+....|..+...|...-..
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTgskn~la~~lmaqglyNHst~ 326 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTGSKNRLALHLMAQGLYNHSTT 326 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccCCCCchhhhhhccccccCccc
Confidence 45566799999999999999999999999999999999999999999999999999987666665555554443322211
Q ss_pred -HHHHHHHHHHH
Q 019954 174 -LFKEKEKLKAE 184 (333)
Q Consensus 174 -L~~Ene~L~~E 184 (333)
|.++.++++.+
T Consensus 327 ~l~a~e~k~esr 338 (342)
T KOG0493|consen 327 HLMAQEAKVESR 338 (342)
T ss_pred hhhhhhhhhhhh
Confidence 45555555444
No 12
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.60 E-value=7.4e-16 Score=141.93 Aligned_cols=62 Identities=32% Similarity=0.507 Sum_probs=56.1
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 153 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~ 153 (333)
+.||.||.|+.-||..|.+.|++++|+-..+|.+||..|||+..||||||||||.|.||...
T Consensus 121 K~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl~k 182 (245)
T KOG0850|consen 121 KVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKLKK 182 (245)
T ss_pred cccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHHHh
Confidence 34444666999999999999999999999999999999999999999999999999998543
No 13
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.59 E-value=2e-15 Score=137.26 Aligned_cols=60 Identities=33% Similarity=0.509 Sum_probs=55.3
Q ss_pred CCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 93 QPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 93 ~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
.|+.|+.||.+||..||+.|+..+|+++.+|.+++..|.|++.||||||||||||.||.|
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 344455699999999999999999999999999999999999999999999999999865
No 14
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.57 E-value=7e-15 Score=138.01 Aligned_cols=54 Identities=44% Similarity=0.586 Sum_probs=52.0
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
.+|..|..+||+.|..++|+++.+|.+||..|||++|||||||||||||+||..
T Consensus 205 VYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 205 VYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred EecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 499999999999999999999999999999999999999999999999999854
No 15
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.51 E-value=8.8e-15 Score=134.21 Aligned_cols=65 Identities=28% Similarity=0.410 Sum_probs=60.0
Q ss_pred ccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 90 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 90 ~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
..+++|.|++|+..|+.+||..|.+..||+...|++||.+|+|.+.+|+|||.|||+|+|+.+..
T Consensus 34 pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~q 98 (228)
T KOG2251|consen 34 PRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQQ 98 (228)
T ss_pred chhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhhh
Confidence 34677888899999999999999999999999999999999999999999999999999986643
No 16
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.48 E-value=6e-14 Score=102.20 Aligned_cols=57 Identities=49% Similarity=0.728 Sum_probs=53.7
Q ss_pred CCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHH
Q 019954 95 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 151 (333)
Q Consensus 95 rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krk 151 (333)
+++.+|+..|+.+|+..|..++||+..++..||.++||++.||++||+|||++.++.
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 456779999999999999999999999999999999999999999999999998863
No 17
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.48 E-value=1.6e-14 Score=136.94 Aligned_cols=92 Identities=24% Similarity=0.372 Sum_probs=79.2
Q ss_pred CccccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhh
Q 019954 87 FDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNS 166 (333)
Q Consensus 87 ~~~~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~ 166 (333)
.+.....||.|+.+|+.||+.|+.+|...++|....|++|+.++||..|.|||||||||||+||.++..-...|.+.+..
T Consensus 161 l~gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrs 240 (383)
T KOG4577|consen 161 LEGDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRS 240 (383)
T ss_pred cccccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHH
Confidence 34445667888899999999999999999999999999999999999999999999999999999888888888888887
Q ss_pred HHHhhHHHHHHHH
Q 019954 167 LKADYDNLFKEKE 179 (333)
Q Consensus 167 Lk~~~~~L~~Ene 179 (333)
+|.. ..-.+|++
T Consensus 241 mK~s-gs~r~ekd 252 (383)
T KOG4577|consen 241 MKRS-GSSRAEKD 252 (383)
T ss_pred hhcc-CCcccccc
Confidence 7766 33444443
No 18
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.47 E-value=6.7e-14 Score=101.40 Aligned_cols=55 Identities=45% Similarity=0.764 Sum_probs=51.7
Q ss_pred CCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 95 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 95 rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
+.|.+|+..|+.+|+..|..++||+..++..||..+||+..||+.||+|||++.|
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 4566799999999999999999999999999999999999999999999998864
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.44 E-value=1e-13 Score=122.40 Aligned_cols=67 Identities=36% Similarity=0.537 Sum_probs=61.4
Q ss_pred ccccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 88 DEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 88 ~~~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
+.....+++|+|.|.+|+.+|++.|+.++||+...|..|+..|+|+++-|+|||||||++.|+....
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 3445677889999999999999999999999999999999999999999999999999999987644
No 20
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.41 E-value=1.2e-13 Score=131.79 Aligned_cols=63 Identities=33% Similarity=0.515 Sum_probs=59.3
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
+.||-|+.||.+||..||+.|-+.+|.+..+|.+||..|+|++..|||||||||+|+||+++.
T Consensus 180 qmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 180 QMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 456778889999999999999999999999999999999999999999999999999998765
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=99.39 E-value=2.8e-13 Score=101.07 Aligned_cols=53 Identities=13% Similarity=0.341 Sum_probs=50.1
Q ss_pred CCCCCcccChHHHHHHHhhhhccCC----CCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 93 QPEKKRRLTVDQVQFLEKSFEVENK----LEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 93 ~~rkR~rft~~Ql~~LE~~F~~~~~----p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
++|.|+.||.+|+..||..|+.++| |+...+.+||..|||++++|+|||||-+
T Consensus 1 ~kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 1 KKRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 3678888999999999999999999 9999999999999999999999999964
No 22
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.38 E-value=1.1e-13 Score=122.04 Aligned_cols=63 Identities=33% Similarity=0.488 Sum_probs=57.4
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
+++|-|+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+..
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r~ 161 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQRN 161 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHhc
Confidence 344556679999999999999999999999999999999999999999999999999997643
No 23
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.32 E-value=6.9e-13 Score=121.78 Aligned_cols=62 Identities=34% Similarity=0.624 Sum_probs=56.4
Q ss_pred cCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 91 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 91 ~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
.+++..|..|+..|+..||+.|++.+|+-..+|.+||..+|+++.||+|||||||+||||+.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 34444555699999999999999999999999999999999999999999999999999865
No 24
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.30 E-value=1.8e-12 Score=124.24 Aligned_cols=64 Identities=27% Similarity=0.520 Sum_probs=57.6
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEK 155 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~k 155 (333)
+++|.|+-||.+|++.||..|++++||+...|++||..++|++.+|+|||.|||+||||.....
T Consensus 111 KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrErN~ 174 (351)
T KOG0486|consen 111 KQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRERNQ 174 (351)
T ss_pred hhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhhhH
Confidence 4555556699999999999999999999999999999999999999999999999999865443
No 25
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.30 E-value=9.1e-13 Score=129.87 Aligned_cols=61 Identities=28% Similarity=0.412 Sum_probs=56.7
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
+|||||+.|.......||++|.+|++|+..++..||.+|+|.+.+|+|||||||.|.||..
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 5666777799999999999999999999999999999999999999999999999999853
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.15 E-value=2.8e-11 Score=110.36 Aligned_cols=63 Identities=29% Similarity=0.345 Sum_probs=58.3
Q ss_pred ccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 90 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 90 ~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
..++++.|+.|+..|+.+||+.|+..+||+...|+.||..+++++..|+|||||||+||++..
T Consensus 57 ~~~~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 57 KFSKRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred hccccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 345677778899999999999999999999999999999999999999999999999999854
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.91 E-value=1.3e-09 Score=107.81 Aligned_cols=63 Identities=29% Similarity=0.520 Sum_probs=57.7
Q ss_pred ccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 90 YFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 90 ~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
....+|+|+.|+..|+..||+.|+.++||+...|++||.++++++..|+|||+|||+||+|..
T Consensus 173 ~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 173 QRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 344556677899999999999999999999999999999999999999999999999999854
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.80 E-value=1.9e-09 Score=102.80 Aligned_cols=65 Identities=23% Similarity=0.340 Sum_probs=59.5
Q ss_pred ccccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 88 DEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 88 ~~~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
-....+||||+.+-....+.||.+|..+++|+.+.+..||.+|.|.+..|+|||+|.|.|-||..
T Consensus 304 ~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 304 LPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 34456888888899999999999999999999999999999999999999999999999999844
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.60 E-value=3.6e-08 Score=93.47 Aligned_cols=51 Identities=29% Similarity=0.443 Sum_probs=47.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
|...-..+|...|.+++||++.+|.+||+.+||+..||-.||.|||.|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 666677899999999999999999999999999999999999999999983
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=98.27 E-value=7.1e-07 Score=61.89 Aligned_cols=34 Identities=38% Similarity=0.556 Sum_probs=29.1
Q ss_pred ccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHH
Q 019954 114 VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 147 (333)
Q Consensus 114 ~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK 147 (333)
.++||+..++..||.++||+..||..||-|.|.|
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 4799999999999999999999999999999975
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=98.26 E-value=1.7e-06 Score=61.51 Aligned_cols=44 Identities=66% Similarity=0.968 Sum_probs=41.4
Q ss_pred HHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 151 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 151 kq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
+|++++|+.|+..|+.|+++|++|.+||+.|++|+..|+.++..
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 47899999999999999999999999999999999999998863
No 32
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.26 E-value=4.5e-07 Score=85.71 Aligned_cols=60 Identities=28% Similarity=0.456 Sum_probs=55.5
Q ss_pred CCCCCCcccChHHHHHHHhhhh---ccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFE---VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 151 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~---~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krk 151 (333)
..+||||.|+..-..+|..+|. .++||+.+.+++||++++++..||-.||-|+|.++||.
T Consensus 187 darRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 187 DARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 4578888899999999999996 58999999999999999999999999999999999974
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.90 E-value=1.4e-05 Score=72.84 Aligned_cols=62 Identities=31% Similarity=0.579 Sum_probs=55.9
Q ss_pred CCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHH
Q 019954 92 HQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 153 (333)
Q Consensus 92 ~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~ 153 (333)
+.++.++.+...|+..|+..|...++|+...+.+|+..+|++++.|++||||+|++.++...
T Consensus 152 ~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 152 KPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred ccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 34455666999999999999999999999999999999999999999999999999998653
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.85 E-value=2.4e-05 Score=80.54 Aligned_cols=58 Identities=21% Similarity=0.253 Sum_probs=52.7
Q ss_pred cCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHH
Q 019954 91 FHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARW 148 (333)
Q Consensus 91 ~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~ 148 (333)
...||.|..||..|.+.|..+|+.+++|+.+..+.|+.+|+|..+-|..||-|-|.|.
T Consensus 418 ~~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 418 LQTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ccCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 3445556679999999999999999999999999999999999999999999988775
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=97.39 E-value=0.00019 Score=80.21 Aligned_cols=67 Identities=21% Similarity=0.363 Sum_probs=60.5
Q ss_pred CccccCCCCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHH
Q 019954 87 FDEYFHQPEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 153 (333)
Q Consensus 87 ~~~~~~~~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~ 153 (333)
......++++|++++..||..|..+|....+|...+.+.|...+++.+|.|+|||||-|+|.|+...
T Consensus 897 ~~~~~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 897 VPDGMGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred cchhhhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 3444467788899999999999999999999999999999999999999999999999999998554
No 36
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=96.34 E-value=0.0024 Score=47.57 Aligned_cols=41 Identities=27% Similarity=0.377 Sum_probs=31.4
Q ss_pred HHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 105 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 105 l~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
++.|+++|...+++.......|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 56799999999999999999999999999999999997654
No 37
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.04 E-value=0.0043 Score=60.78 Aligned_cols=62 Identities=29% Similarity=0.375 Sum_probs=49.8
Q ss_pred CCCCCcccChHHHHHHHhhhh---ccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHH
Q 019954 93 QPEKKRRLTVDQVQFLEKSFE---VENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLE 154 (333)
Q Consensus 93 ~~rkR~rft~~Ql~~LE~~F~---~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ 154 (333)
+.|+++.|....+.+|+.... ..+||+..++..||+++||+..||..||-|.|-|..+-...
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~ 303 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIE 303 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHH
Confidence 344444699999999887743 25799999999999999999999999999999877654433
No 38
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=94.49 E-value=0.22 Score=41.95 Aligned_cols=99 Identities=18% Similarity=0.197 Sum_probs=52.7
Q ss_pred CCCcccChHHHH-HHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHH
Q 019954 95 EKKRRLTVDQVQ-FLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDN 173 (333)
Q Consensus 95 rkR~rft~~Ql~-~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~ 173 (333)
++|++|+.++.. ++...+. +.+ ...++|.++|+++.+|..|.+-=|.....................+..+...
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~ 82 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKE 82 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHH
Confidence 345668887644 3444443 222 3567899999999999999643221100000000000000011124455666
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 174 LFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 174 L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
|.+++.+|+.|+.=|+..+......
T Consensus 83 L~~el~~L~~E~diLKKa~~~~~~~ 107 (121)
T PRK09413 83 LQRLLGKKTMENELLKEAVEYGRAK 107 (121)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhchh
Confidence 7777777777777777766655443
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=93.60 E-value=0.084 Score=56.79 Aligned_cols=48 Identities=19% Similarity=0.354 Sum_probs=44.8
Q ss_pred HHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 105 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 105 l~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
+.+|..+|..|..|+.++...+|.+.||+.+.|++||+++++......
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 678999999999999999999999999999999999999999887654
No 40
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=93.48 E-value=0.19 Score=35.82 Aligned_cols=36 Identities=42% Similarity=0.552 Sum_probs=31.4
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
|...|+.|++.|+.|..+++.|+.|+..|+..+..-
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L 38 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQEL 38 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556789999999999999999999999999887643
No 41
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=93.25 E-value=1.2 Score=42.41 Aligned_cols=44 Identities=25% Similarity=0.417 Sum_probs=28.3
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
.+.+.|+..++.|++.++.|..+|.+|..++..+++.|..-.++
T Consensus 104 een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~~~~ 147 (292)
T KOG4005|consen 104 EENEILQNENDSLRAINESLLAKNHELDSELELLRQELAELKQQ 147 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhhHHH
Confidence 33455666666677777777777777777777776666654433
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=92.35 E-value=0.29 Score=35.68 Aligned_cols=47 Identities=21% Similarity=0.384 Sum_probs=34.7
Q ss_pred CCCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 94 PEKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 94 ~rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
+|+|+.+|-++-..+-..++... ....||+++|++..+|..|..||.
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 46777899988887777787666 578899999999999999998854
No 43
>smart00340 HALZ homeobox associated leucin zipper.
Probab=89.66 E-value=0.65 Score=32.76 Aligned_cols=25 Identities=32% Similarity=0.402 Sum_probs=19.8
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
.||..++.|..||.+|+.|+.+|+.
T Consensus 9 ~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 9 LLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 4666777888888889988888873
No 44
>smart00340 HALZ homeobox associated leucin zipper.
Probab=89.09 E-value=0.72 Score=32.52 Aligned_cols=34 Identities=35% Similarity=0.440 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHH
Q 019954 151 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAE 184 (333)
Q Consensus 151 kq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E 184 (333)
+|.+.+++.|+..++.|..+|..|.+|.+.|++-
T Consensus 1 KQTEvdCe~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 1 KQTEVDCELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3678899999999999999999999999999864
No 45
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=87.80 E-value=17 Score=31.73 Aligned_cols=84 Identities=19% Similarity=0.190 Sum_probs=52.8
Q ss_pred cccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH-------HHHHHHHHHHHhhhhhHHHh
Q 019954 98 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT-------KQLEKDYDVLQNSYNSLKAD 170 (333)
Q Consensus 98 ~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr-------kq~~ke~~~l~~~~~~Lk~~ 170 (333)
.+|+.++|..| ..|+.=-+.-|++...|-.|=|.||+-.-| -+.-.....|......|..+
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~qq 89 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQQ 89 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 56888887765 222222244589999999999999863221 12223334455566666677
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHh
Q 019954 171 YDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 171 ~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
.+.|..|+.+++.|+.-++.+..
T Consensus 90 v~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 90 VEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 77777777777777777766554
No 46
>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=86.06 E-value=5.4 Score=29.70 Aligned_cols=38 Identities=26% Similarity=0.370 Sum_probs=26.6
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
.....|......|..+++.|..++..|+.++..|+..+
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 34456667777777777777777777777777776543
No 47
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=85.44 E-value=1.7 Score=36.15 Aligned_cols=48 Identities=21% Similarity=0.318 Sum_probs=28.9
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 135 RQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 135 rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
-++..||++.-- ..+..++++...++.++..+.++|+.|+.|+..|+.
T Consensus 15 l~y~l~~g~~G~--------~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 15 LQYSLWFGKNGI--------LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHhccCCcH--------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 356788865311 112223344445666777777777777777777766
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=81.11 E-value=7.2 Score=30.43 Aligned_cols=37 Identities=30% Similarity=0.338 Sum_probs=19.3
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
-.-...|+..+..|+..+..|..+++.|+.|+.+|+.
T Consensus 17 veti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~ 53 (72)
T PF06005_consen 17 VETIALLQMENEELKEKNNELKEENEELKEENEQLKQ 53 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 3344445555555555555555555555555555543
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=80.67 E-value=7.5 Score=32.53 Aligned_cols=47 Identities=28% Similarity=0.436 Sum_probs=37.1
Q ss_pred HHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 151 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 151 kq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
.+++.....+-.....||..-..|.+||.+|+.|+..|++.|...++
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 35566666777777888888888999999999999999888876544
No 50
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=76.71 E-value=8.4 Score=37.07 Aligned_cols=48 Identities=29% Similarity=0.345 Sum_probs=28.3
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 144 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 144 RRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
||.|.|+++.+ ..++.....|..+++.|..+++.|+.|+..|+.-+..
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 34555554444 3344455566667777777777777777666655543
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=76.27 E-value=16 Score=29.11 Aligned_cols=49 Identities=22% Similarity=0.237 Sum_probs=35.2
Q ss_pred HHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 019954 147 RWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 147 K~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
+..+..+.++...||.....|....+....|+++|+.|+.-|...+...
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555666677777777888888888888888888887777666543
No 52
>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=75.60 E-value=20 Score=27.98 Aligned_cols=48 Identities=27% Similarity=0.335 Sum_probs=36.7
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 146 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 146 aK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+-.....++.+.+.|+..+..|..++..|..+|++|+.+-......|.
T Consensus 16 aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~ 63 (72)
T PF06005_consen 16 AVETIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455677788888888888888889999999999888776665554
No 53
>smart00338 BRLZ basic region leucin zipper.
Probab=75.38 E-value=23 Score=26.33 Aligned_cols=37 Identities=32% Similarity=0.489 Sum_probs=24.7
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
....|......|...+..|..+...|+.|+..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3455566666777777777777777777777776554
No 54
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=73.96 E-value=14 Score=31.20 Aligned_cols=45 Identities=29% Similarity=0.427 Sum_probs=34.0
Q ss_pred HHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 019954 151 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 151 kq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
.+++.....+-.....||..-..|.+||..|+.|+..|+..|...
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 345556666667777888888888888888888888888887743
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=72.96 E-value=17 Score=27.06 Aligned_cols=34 Identities=32% Similarity=0.462 Sum_probs=16.8
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEV 185 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~ 185 (333)
.++.....|...+..|+..+..|..+...|+.++
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 30 ELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3444444455555555555555555555555443
No 56
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=72.20 E-value=17 Score=35.69 Aligned_cols=51 Identities=18% Similarity=0.283 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 146 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 146 aK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
+|+|.|+ +.+.+.+-.....|-..|+.|+....+|..|++.||.-+...-+
T Consensus 240 tRYRqKk-Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~~~ 290 (294)
T KOG4571|consen 240 TRYRQKK-RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEVYK 290 (294)
T ss_pred HHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444433 45666677777888888888888888888888888887775543
No 57
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=71.78 E-value=5.6 Score=28.80 Aligned_cols=42 Identities=19% Similarity=0.214 Sum_probs=25.6
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhh
Q 019954 122 RKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNS 163 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~ 163 (333)
....||+.+|++...|..|+.++..+.....+.+-...|.-.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~~ 53 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNCS 53 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT--
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCCC
Confidence 467899999999999999999887777766666655554433
No 58
>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=70.77 E-value=8.6 Score=26.85 Aligned_cols=44 Identities=11% Similarity=0.138 Sum_probs=31.7
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 147 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK 147 (333)
.+++.+..+|...|.. ...-.++|..+|++...|+.+...-..|
T Consensus 4 ~L~~~er~vi~~~y~~-----~~t~~eIa~~lg~s~~~V~~~~~~al~k 47 (50)
T PF04545_consen 4 QLPPREREVIRLRYFE-----GLTLEEIAERLGISRSTVRRILKRALKK 47 (50)
T ss_dssp TS-HHHHHHHHHHHTS-----T-SHHHHHHHHTSCHHHHHHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhcC-----CCCHHHHHHHHCCcHHHHHHHHHHHHHH
Confidence 3678888999988832 2346789999999999998876544333
No 59
>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=69.93 E-value=2.6 Score=31.66 Aligned_cols=44 Identities=18% Similarity=0.349 Sum_probs=27.9
Q ss_pred CCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 019954 95 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 142 (333)
Q Consensus 95 rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQ 142 (333)
++|++||.++...+-..+.. .......+|+++||++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 45677999887765555421 235678899999999999999964
No 60
>cd06171 Sigma70_r4 Sigma70, region (SR) 4 refers to the most C-terminal of four conserved domains found in Escherichia coli (Ec) sigma70, the main housekeeping sigma, and related sigma-factors (SFs). A SF is a dissociable subunit of RNA polymerase, it directs bacterial or plastid core RNA polymerase to specific promoter elements located upstream of transcription initiation points. The SR4 of Ec sigma70 and other essential primary SFs contact promoter sequences located 35 base-pairs upstream of the initiation point, recognizing a 6-base-pair -35 consensus TTGACA. Sigma70 related SFs also include SFs which are dispensable for bacterial cell growth for example Ec sigmaS, SFs which activate regulons in response to a specific signal for example heat-shock Ec sigmaH, and a group of SFs which includes the extracytoplasmic function (ECF) SFs and is typified by Ec sigmaE which contains SR2 and -4 only. ECF SFs direct the transcription of genes that regulate various responses including periplas
Probab=69.85 E-value=5.3 Score=26.73 Aligned_cols=43 Identities=14% Similarity=0.125 Sum_probs=31.9
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 147 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK 147 (333)
++..+..++...|... ....++|..+|++...|..|....+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 6777777777776422 235678999999999999998765543
No 61
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=67.68 E-value=22 Score=36.81 Aligned_cols=63 Identities=32% Similarity=0.402 Sum_probs=39.9
Q ss_pred hhhh---hhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHH---------------------H-----------HHHHHHHH
Q 019954 138 AIWF---QNRRARWKTKQLEKDYDVLQNSYNSLKADYDN---------------------L-----------FKEKEKLK 182 (333)
Q Consensus 138 kvWF---QNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~---------------------L-----------~~Ene~L~ 182 (333)
-+|| |||.+|.+-.++-++.+-|+..-..|..-... | -.||+..+
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ea~rl~elreg~e~e~~r 308 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENETSR 308 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHhhhhhhhhhhcchhHHHHH
Confidence 3488 99999998888877777666543322211111 1 12566677
Q ss_pred HHHHHHHHHHhhhhhhhc
Q 019954 183 AEVLKLTDKLQVKEKESK 200 (333)
Q Consensus 183 ~E~~~l~~~l~~~~~~~~ 200 (333)
.|++.|+.+|...|++-.
T Consensus 309 kelE~lR~~L~kAEkele 326 (575)
T KOG4403|consen 309 KELEQLRVALEKAEKELE 326 (575)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 778888888877766544
No 62
>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=66.77 E-value=7.7 Score=38.70 Aligned_cols=28 Identities=32% Similarity=0.491 Sum_probs=15.4
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
.|+.+|++|++||+.|+.|+.+|++...
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 4555555555555555555555544433
No 63
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=65.78 E-value=28 Score=36.93 Aligned_cols=41 Identities=29% Similarity=0.408 Sum_probs=28.6
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCCCC
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKESKNTELPV 206 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~~~~~~~~~ 206 (333)
.|++.-..|++||+.|++|+..||.+|..-.-+-.+-+.+.
T Consensus 306 ~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kvps 346 (655)
T KOG4343|consen 306 GLEARLQALLSENEQLKKENATLKRQLDELVSENQRLKVPS 346 (655)
T ss_pred HHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCcccccCC
Confidence 66777777888888888888888888776655444444433
No 64
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=65.14 E-value=21 Score=34.00 Aligned_cols=27 Identities=33% Similarity=0.569 Sum_probs=11.7
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 167 LKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 167 Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+..++..|.+++++|++++..+++.|.
T Consensus 147 ~~~EkeeL~~eleele~e~ee~~erlk 173 (290)
T COG4026 147 LQKEKEELLKELEELEAEYEEVQERLK 173 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444443
No 65
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=61.65 E-value=85 Score=30.55 Aligned_cols=33 Identities=24% Similarity=0.470 Sum_probs=24.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhcCCCC
Q 019954 172 DNLFKEKEKLKAEVLKLTDKLQVKEKESKNTEL 204 (333)
Q Consensus 172 ~~L~~Ene~L~~E~~~l~~~l~~~~~~~~~~~~ 204 (333)
+.|..+..+|+.|...|+..|..+.++...+.+
T Consensus 160 e~llesvqRLkdEardlrqelavr~kq~E~pR~ 192 (333)
T KOG1853|consen 160 EVLLESVQRLKDEARDLRQELAVRTKQTERPRI 192 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhccCCCc
Confidence 457777888888888888888888876555443
No 66
>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=61.41 E-value=1e+02 Score=26.61 Aligned_cols=73 Identities=10% Similarity=0.114 Sum_probs=39.9
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHH-HHHHHHHHHHHHHHHhhhhhHHHhhHHH
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA-RWKTKQLEKDYDVLQNSYNSLKADYDNL 174 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRa-K~Krkq~~ke~~~l~~~~~~Lk~~~~~L 174 (333)
.+|.|+..++..|.. ....+.+|++-..|+-++.+... .....+.....+.+......+...-..|
T Consensus 34 g~R~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~~~~~~~~~~~~l~~~i~~Le~~l~~L 100 (134)
T cd04779 34 NYRYYDETALDRLQL-------------IEHLKGQRLSLAEIKDQLEEVQRSDKEQREVAQEVQLVCDQIDGLEHRLKQL 100 (134)
T ss_pred CCeeECHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHHhhccccchHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455699999988843 23347788888888888876543 1222233333444444444444433333
Q ss_pred HHHHHHH
Q 019954 175 FKEKEKL 181 (333)
Q Consensus 175 ~~Ene~L 181 (333)
..-.+.|
T Consensus 101 ~~~~~~l 107 (134)
T cd04779 101 KPIASQT 107 (134)
T ss_pred HHHHHHH
Confidence 3333333
No 67
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=60.86 E-value=17 Score=26.74 Aligned_cols=38 Identities=26% Similarity=0.311 Sum_probs=31.8
Q ss_pred cChHHHHHHHhhhhccCC--CCHHHHHHHHHHhCCCchhh
Q 019954 100 LTVDQVQFLEKSFEVENK--LEPERKIQLAKDLGLQPRQV 137 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~--p~~~~r~~LA~~LgLs~rQV 137 (333)
+|..|..+|...|+..-| |-.....+||.+||+++.-|
T Consensus 1 LT~~Q~e~L~~A~~~GYfd~PR~~tl~elA~~lgis~st~ 40 (53)
T PF04967_consen 1 LTDRQREILKAAYELGYFDVPRRITLEELAEELGISKSTV 40 (53)
T ss_pred CCHHHHHHHHHHHHcCCCCCCCcCCHHHHHHHhCCCHHHH
Confidence 578899999999987654 66777889999999998654
No 68
>PF06156 DUF972: Protein of unknown function (DUF972); InterPro: IPR010377 FUNCTION: Involved in initiation control of chromosome replication. SUBUNIT: Interacts with both DnaA and DnaN, acting as a bridge between these two proteins. SIMILARITY: Belongs to the YabA family.
Probab=58.98 E-value=26 Score=29.30 Aligned_cols=41 Identities=22% Similarity=0.296 Sum_probs=35.4
Q ss_pred HHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 150 TKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 150 rkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
...+-.+...|+.....|..+|..|..||+.|+..+.++..
T Consensus 17 l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 17 LGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34667788889999999999999999999999999888876
No 69
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=57.87 E-value=39 Score=28.64 Aligned_cols=43 Identities=30% Similarity=0.406 Sum_probs=35.3
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
.++.....+-++...||..-..|..||-.|+-|+..|++.|..
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 4455566667777888888899999999999999999998886
No 70
>PF15058 Speriolin_N: Speriolin N terminus
Probab=57.75 E-value=17 Score=33.74 Aligned_cols=35 Identities=26% Similarity=0.467 Sum_probs=25.9
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 163 SYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 163 ~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
.|+.|++..++|..||++||.+|+-|++....+..
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLirEN~eLksa 40 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLIRENHELKSA 40 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHHHH
Confidence 45667777778888888888888877776665554
No 71
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=57.64 E-value=2.5e+02 Score=29.47 Aligned_cols=91 Identities=21% Similarity=0.297 Sum_probs=54.4
Q ss_pred cccChHHHHHHHhh-hhc-cCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHH-HHHHhhhhhHHHhhHHH
Q 019954 98 RRLTVDQVQFLEKS-FEV-ENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDY-DVLQNSYNSLKADYDNL 174 (333)
Q Consensus 98 ~rft~~Ql~~LE~~-F~~-~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~-~~l~~~~~~Lk~~~~~L 174 (333)
-++|.+....|.+. +-. .++|-.+.-+++.+ +|+.=.+|+|.+--.+++.|+| +.|...+....++|..|
T Consensus 219 L~LteeEkrLL~kEG~slPs~lPLTKaEEriLK-------rvRRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqeL 291 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKEGYSLPSKLPLTKAEERILK-------RVRRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQEL 291 (472)
T ss_pred eeccHHHHHHHHhccCcCcccCCchHHHHHHHH-------HHHHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHHH
Confidence 35788887777665 322 33454444444333 5666667777654444444444 55666666677777777
Q ss_pred HHHHHHHHHHHHHHHHHHhhh
Q 019954 175 FKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 175 ~~Ene~L~~E~~~l~~~l~~~ 195 (333)
.+..++|..+++.|-.+|.-.
T Consensus 292 ~kkV~~Le~~N~sLl~qL~kl 312 (472)
T KOG0709|consen 292 QKKVEELELSNRSLLAQLKKL 312 (472)
T ss_pred HHHHHHHhhccHHHHHHHHHH
Confidence 777777777776666665533
No 72
>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=57.57 E-value=51 Score=26.83 Aligned_cols=46 Identities=30% Similarity=0.420 Sum_probs=30.4
Q ss_pred HHHHHHHHhhhh-hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 019954 154 EKDYDVLQNSYN-SLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 199 (333)
Q Consensus 154 ~ke~~~l~~~~~-~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~~ 199 (333)
+.....|+..|. +.....+.|..++..|..|+.+|+.+|.....+.
T Consensus 33 E~KV~~LKksYe~rwek~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek 79 (87)
T PF12709_consen 33 ETKVKALKKSYEARWEKKVDELENENKALKRENEQLKKKLDTEREEK 79 (87)
T ss_pred HHHHHHHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444566666654 4555666777788888888888877777555443
No 73
>smart00338 BRLZ basic region leucin zipper.
Probab=56.61 E-value=42 Score=24.86 Aligned_cols=30 Identities=30% Similarity=0.468 Sum_probs=16.7
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 164 YNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 164 ~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
...|......|..+|..|+.++..|...+.
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~l~~e~~ 57 (65)
T smart00338 28 IEELERKVEQLEAENERLKKEIERLRRELE 57 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344555555566666666666655555444
No 74
>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=56.45 E-value=52 Score=30.58 Aligned_cols=55 Identities=16% Similarity=0.243 Sum_probs=37.9
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 143 NRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 143 NRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
|+..|........+...|......+...+-.+..+...|+.|+.+|+.+....++
T Consensus 163 N~~RK~~Q~~~~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~~~ 217 (221)
T PF05700_consen 163 NRERKRRQEEAGEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAELKE 217 (221)
T ss_pred HHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3333444444445555667777777778888888899999999988887775543
No 75
>PRK10884 SH3 domain-containing protein; Provisional
Probab=56.03 E-value=54 Score=30.47 Aligned_cols=31 Identities=13% Similarity=0.056 Sum_probs=13.7
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
|+..+..|+.+...+..+++.|++++..++.
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~ 167 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQR 167 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444444444444444444444444443
No 76
>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=55.97 E-value=59 Score=24.99 Aligned_cols=39 Identities=18% Similarity=0.210 Sum_probs=20.4
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
...+.|-..+..|+.+|..|.++...+..|-..|.++..
T Consensus 7 ~kle~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne 45 (65)
T TIGR02449 7 AQVEHLLEYLERLKSENRLLRAQEKTWREERAQLLEKNE 45 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444444555555555555555555555555555444
No 77
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=55.68 E-value=32 Score=29.07 Aligned_cols=40 Identities=23% Similarity=0.284 Sum_probs=34.6
Q ss_pred HHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 151 KQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 151 kq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
..+-++...|+.....|..+|..|..||+.|+..+.++..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3566778889999999999999999999999999988743
No 78
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=55.67 E-value=32 Score=36.58 Aligned_cols=51 Identities=24% Similarity=0.377 Sum_probs=36.4
Q ss_pred hhhhhHHHHHHHHHHHHH-HHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 140 WFQNRRARWKTKQLEKDY-DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 140 WFQNRRaK~Krkq~~ke~-~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
-..||-.-.--+++.||| ..|+.....|..+++.|++||..|+.++..|..
T Consensus 286 mIKNResA~~SRkKKKEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 286 MIKNRESACQSRKKKKEYMLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 445554333222333444 567888899999999999999999999888765
No 79
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=55.51 E-value=1.5e+02 Score=28.00 Aligned_cols=30 Identities=33% Similarity=0.482 Sum_probs=25.7
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
..+.++..|.+|+|+|+.+++++|.+|...
T Consensus 113 ~e~sEF~~lr~e~EklkndlEk~ks~lr~e 142 (220)
T KOG3156|consen 113 IERSEFANLRAENEKLKNDLEKLKSSLRHE 142 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456788999999999999999999988754
No 80
>cd00569 HTH_Hin_like Helix-turn-helix domain of Hin and related proteins, a family of DNA-binding domains unique to bacteria and represented by the Hin protein of Salmonella. The basic HTH domain is a simple fold comprised of three core helices that form a right-handed helical bundle. The principal DNA-protein interface is formed by the third helix, the recognition helix, inserting itself into the major groove of the DNA. A diverse array of HTH domains participate in a variety of functions that depend on their DNA-binding properties. HTH_Hin represents one of the simplest versions of the HTH domains; the characterization of homologous relationships between various sequence-diverse HTH domain families remains difficult. The Hin recombinase induces the site-specific inversion of a chromosomal DNA segment containing a promoter, which controls the alternate expression of two genes by reversibly switching orientation. The Hin recombinase consists of a single polypeptide chain containing a D
Probab=55.29 E-value=24 Score=20.82 Aligned_cols=38 Identities=16% Similarity=0.329 Sum_probs=26.2
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhh
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 141 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWF 141 (333)
.++..+...+...|... + ....+|..+|++...|..|.
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~~ 42 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRYL 42 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHhC
Confidence 36666666666666532 2 45678999999998888773
No 81
>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=54.75 E-value=55 Score=25.48 Aligned_cols=41 Identities=22% Similarity=0.314 Sum_probs=29.8
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
....|+..|..|...+..-..++..|.+.|..|..++..-.
T Consensus 22 q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls 62 (70)
T PF04899_consen 22 QQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLS 62 (70)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHH
Confidence 34567777778888887777788888888877777766443
No 82
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=54.01 E-value=18 Score=33.13 Aligned_cols=49 Identities=27% Similarity=0.279 Sum_probs=38.3
Q ss_pred ccChHHHHHHHhhhhccC--CCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVEN--KLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~--~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
.+|..|+++|..+|...- +|-.....+||++||+++.- +|.-=|||..|
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~K 205 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAERK 205 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHHH
Confidence 599999999999999765 47777888999999999854 44444555444
No 83
>PRK14127 cell division protein GpsB; Provisional
Probab=53.72 E-value=30 Score=29.20 Aligned_cols=31 Identities=29% Similarity=0.414 Sum_probs=17.8
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 167 LKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 167 Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
+-.+++.|.+|+..|+.++.+|+.+|.....
T Consensus 35 V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~ 65 (109)
T PRK14127 35 VIKDYEAFQKEIEELQQENARLKAQVDELTK 65 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555566666666666666666654444
No 84
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=53.41 E-value=1e+02 Score=23.77 Aligned_cols=22 Identities=32% Similarity=0.493 Sum_probs=11.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 019954 172 DNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 172 ~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
.....++.+|++|+..|+..|.
T Consensus 43 ~~a~~e~~~Lk~E~e~L~~el~ 64 (69)
T PF14197_consen 43 GDAYEENNKLKEENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555555555555544
No 85
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=53.21 E-value=37 Score=29.83 Aligned_cols=48 Identities=19% Similarity=0.129 Sum_probs=36.1
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
...+++.|..+|...+ . .....++|..||++...|+.|-++.|.+.|+
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 4468999999997732 1 2235689999999999999999866655554
No 86
>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=52.63 E-value=9.8 Score=28.77 Aligned_cols=19 Identities=21% Similarity=0.576 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCchhhhhh
Q 019954 122 RKIQLAKDLGLQPRQVAIW 140 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvW 140 (333)
.-..||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3567899999999999999
No 87
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=52.10 E-value=22 Score=32.97 Aligned_cols=41 Identities=32% Similarity=0.541 Sum_probs=33.4
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKESK 200 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~~~ 200 (333)
+...|+.||..++.|..++++|+.|+..|+..+........
T Consensus 110 lE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~~ 150 (198)
T KOG0483|consen 110 LEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKREMQ 150 (198)
T ss_pred hhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhc
Confidence 44567899999999999999999999999988875544433
No 88
>PRK14127 cell division protein GpsB; Provisional
Probab=51.96 E-value=43 Score=28.21 Aligned_cols=40 Identities=30% Similarity=0.468 Sum_probs=29.6
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
.+.+.+-..|..|..++..|..++.+|+.++.+++.++..
T Consensus 30 ~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~ 69 (109)
T PRK14127 30 KFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSV 69 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 3344445556667778888888889999998888887773
No 89
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=50.90 E-value=64 Score=35.59 Aligned_cols=51 Identities=24% Similarity=0.335 Sum_probs=38.9
Q ss_pred HHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 146 ARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 146 aK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
|+.++..+..+.+.+++++..+....+.|...++.|+.|+.+|+......+
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 456666777777778888888888888888888999999988886444433
No 90
>PRK10884 SH3 domain-containing protein; Provisional
Probab=49.72 E-value=74 Score=29.56 Aligned_cols=42 Identities=17% Similarity=0.098 Sum_probs=26.7
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhh
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
....+........|+.+|..|.++.+.++.|+..|+.++...
T Consensus 124 ~~~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~ 165 (206)
T PRK10884 124 QQKVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLDDK 165 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444555566677777777777777777777666555433
No 91
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=49.70 E-value=58 Score=32.77 Aligned_cols=50 Identities=20% Similarity=0.336 Sum_probs=33.6
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 144 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 144 RRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+|++.+-.+...+.+.|+..-+.|+.-...|.+++++|+.|+..|+....
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 45555555666666777777777777777777777777777776655443
No 92
>PF08281 Sigma70_r4_2: Sigma-70, region 4; InterPro: IPR013249 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors are involved in binding to the -35 promoter element via a helix-turn-helix motif [].; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2LFW_A 1OR7_B 2H27_D 2O8X_B.
Probab=49.23 E-value=33 Score=24.00 Aligned_cols=42 Identities=17% Similarity=0.177 Sum_probs=26.9
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 146 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRa 146 (333)
+++.+..++.-.|- ....-.++|..+|+++..|+.|.+.-|.
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~~ 52 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRARK 52 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHHh
Confidence 45555555555443 3345678999999999999999975443
No 93
>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=48.25 E-value=16 Score=33.07 Aligned_cols=30 Identities=37% Similarity=0.478 Sum_probs=7.2
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 169 ADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 169 ~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
.+.+.|+.++++|++|+..||..|..+++.
T Consensus 24 dEKE~L~~~~QRLkDE~RDLKqEl~V~ek~ 53 (166)
T PF04880_consen 24 DEKENLREEVQRLKDELRDLKQELIVQEKL 53 (166)
T ss_dssp HHHHHHHHCH--------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 356778888888888888888888655543
No 94
>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=48.23 E-value=1.2e+02 Score=24.98 Aligned_cols=38 Identities=24% Similarity=0.357 Sum_probs=28.3
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 147 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK 147 (333)
.|.|+..++..|. .....+.+|++..+|+..+......
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 4558998888873 3344688999999999998766543
No 95
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=48.08 E-value=33 Score=39.99 Aligned_cols=57 Identities=18% Similarity=0.243 Sum_probs=51.6
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHH
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQ 152 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq 152 (333)
-|..+-.+++..|-+.|-.+.-|+.+.+..|....+.+.|++.+||+|-|.|.++.+
T Consensus 708 ~~~~~~~~aa~~l~~a~~~~~sps~k~~~civcd~~st~~l~~l~~h~~~~rs~ke~ 764 (1406)
T KOG1146|consen 708 LRLTILPEAAMILGRAYMQDNSPSLKVFDCIVCDVFSTDRLDQLWFHNTRERSRKEQ 764 (1406)
T ss_pred CcccccHHHHhhhhhcccCCCCHHHHHHHHhhhhhhhhhhHHHHhhcchhhhhhhhc
Confidence 344466699999999999999999999999999999999999999999999998866
No 96
>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=47.92 E-value=45 Score=25.03 Aligned_cols=24 Identities=38% Similarity=0.577 Sum_probs=13.2
Q ss_pred hhHHHhhHHHHHHHHHHHHHHHHH
Q 019954 165 NSLKADYDNLFKEKEKLKAEVLKL 188 (333)
Q Consensus 165 ~~Lk~~~~~L~~Ene~L~~E~~~l 188 (333)
..|......+.++++.|+.++..|
T Consensus 27 ~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 27 AELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHh
Confidence 344445555555556666665555
No 97
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=47.77 E-value=1e+02 Score=23.13 Aligned_cols=31 Identities=32% Similarity=0.430 Sum_probs=24.3
Q ss_pred hhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 163 SYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 163 ~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
.|..+..+...|..|++.|+.|+.+|+.-|.
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 4556667777888899999999998887664
No 98
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=46.99 E-value=37 Score=32.19 Aligned_cols=35 Identities=26% Similarity=0.342 Sum_probs=15.1
Q ss_pred HHhhhhhHHHhhHHHHHHHH---HHHHHHHHHHHHHhh
Q 019954 160 LQNSYNSLKADYDNLFKEKE---KLKAEVLKLTDKLQV 194 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene---~L~~E~~~l~~~l~~ 194 (333)
+++++..|++++..|..++. .|++|+.+|+..|..
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~ 111 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEAENARLRELLNL 111 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Confidence 33334444444444433333 444555555544443
No 99
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=46.38 E-value=1.1e+02 Score=24.03 Aligned_cols=40 Identities=25% Similarity=0.367 Sum_probs=20.9
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
.+..+.+.|+..++.|..+-..+....+.|+.|+.+|+..
T Consensus 22 LLQmEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~e 61 (79)
T COG3074 22 LLQMEIEELKEKNNSLSQEVQNAQHQREALERENEQLKEE 61 (79)
T ss_pred HHHHHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445555566666555555544444455555555555443
No 100
>PF10883 DUF2681: Protein of unknown function (DUF2681); InterPro: IPR020274 This entry contains membrane proteins with no known function.
Probab=46.28 E-value=47 Score=26.97 Aligned_cols=26 Identities=27% Similarity=0.285 Sum_probs=12.4
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 171 YDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 171 ~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
+..|.+||+.|+.|..-...++.+..
T Consensus 32 ~~kL~~en~qlk~Ek~~~~~qvkn~~ 57 (87)
T PF10883_consen 32 NAKLQKENEQLKTEKAVAETQVKNAK 57 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33455555555555444444444433
No 101
>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=46.09 E-value=1.6e+02 Score=23.70 Aligned_cols=37 Identities=16% Similarity=0.332 Sum_probs=27.3
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
.++.|+..++..|.... ..+.+|++..+|+-+++...
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 34678999999999887643
No 102
>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=45.92 E-value=1.2e+02 Score=23.89 Aligned_cols=34 Identities=21% Similarity=0.331 Sum_probs=23.1
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhh
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 141 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWF 141 (333)
..++|+..++..|.. ...|...+|++...|+.-+
T Consensus 35 g~R~y~~~dv~~l~~------------i~~L~~d~g~~l~~i~~~l 68 (91)
T cd04766 35 GTRRYSERDIERLRR------------IQRLTQELGVNLAGVKRIL 68 (91)
T ss_pred CCeeECHHHHHHHHH------------HHHHHHHcCCCHHHHHHHH
Confidence 345699999998843 3445556888887765544
No 103
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=45.24 E-value=1e+02 Score=26.89 Aligned_cols=53 Identities=25% Similarity=0.332 Sum_probs=42.9
Q ss_pred hhhhhHHHH--HHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 140 WFQNRRARW--KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 140 WFQNRRaK~--Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
+-||.|.|- -+..++++...|.++.+.|+.++..+..|.+-++.....|..-.
T Consensus 64 YA~sCR~KRv~Qk~eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~ 118 (135)
T KOG4196|consen 64 YAQSCRVKRVQQKHELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSA 118 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 445666653 34567888899999999999999999999999999998887544
No 104
>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=44.23 E-value=91 Score=22.35 Aligned_cols=24 Identities=29% Similarity=0.512 Sum_probs=14.4
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.|......|..+|..|+.++..|+
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 105
>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=44.17 E-value=94 Score=29.17 Aligned_cols=34 Identities=24% Similarity=0.296 Sum_probs=13.8
Q ss_pred HHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 157 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 157 ~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
...+...|..|+.+.+.|...+++|...+..++.
T Consensus 51 ~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~ 84 (251)
T PF11932_consen 51 KQELLAEYRQLEREIENLEVYNEQLERQVASQEQ 84 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444444444444444444333333
No 106
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=44.16 E-value=74 Score=30.45 Aligned_cols=30 Identities=40% Similarity=0.584 Sum_probs=11.1
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
++..|..+|...+.+.+||+.|..++.+|.
T Consensus 133 ~ke~~ee~kekl~E~~~EkeeL~~eleele 162 (290)
T COG4026 133 LKEDYEELKEKLEELQKEKEELLKELEELE 162 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333333333333333333333
No 107
>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=43.94 E-value=1.3e+02 Score=23.98 Aligned_cols=45 Identities=18% Similarity=0.268 Sum_probs=37.2
Q ss_pred HHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 149 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 149 Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
..+.++.....|-...+.++.+++.|..||+-|+.=+..|...-.
T Consensus 24 ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm~~s~ 68 (80)
T PF10224_consen 24 EILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLMSSSS 68 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhh
Confidence 445667778888889999999999999999999999888866543
No 108
>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=43.42 E-value=37 Score=25.67 Aligned_cols=29 Identities=21% Similarity=0.294 Sum_probs=14.9
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
.+.+.|+..+..| ...|..|+.|+.-||.
T Consensus 14 EEVevLK~~I~eL-------~~~n~~Le~EN~~Lk~ 42 (59)
T PF01166_consen 14 EEVEVLKEQIAEL-------EERNSQLEEENNLLKQ 42 (59)
T ss_dssp TSHHHHHHHHHHH-------HHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHH-------HHHHHHHHHHHHHHHh
Confidence 4455555555544 4444555555555543
No 109
>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=43.34 E-value=1.1e+02 Score=33.79 Aligned_cols=21 Identities=10% Similarity=0.154 Sum_probs=15.7
Q ss_pred CCHHHHHHHHHHhCCCchhhh
Q 019954 118 LEPERKIQLAKDLGLQPRQVA 138 (333)
Q Consensus 118 p~~~~r~~LA~~LgLs~rQVk 138 (333)
|....=..+|+.+||++..|.
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 444566678999999987764
No 110
>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=42.74 E-value=66 Score=28.99 Aligned_cols=27 Identities=37% Similarity=0.524 Sum_probs=11.4
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
.|+.+...|.++++.|+.|+..|..++
T Consensus 108 ~l~~e~~~l~~~~e~Le~e~~~L~~~~ 134 (161)
T TIGR02894 108 RLKNQNESLQKRNEELEKELEKLRQRL 134 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444333
No 111
>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=42.69 E-value=47 Score=32.13 Aligned_cols=39 Identities=18% Similarity=0.130 Sum_probs=21.9
Q ss_pred HHHhhhhhHHHhhHHH----HHHHHHHHHHHHHHHHHHhhhhh
Q 019954 159 VLQNSYNSLKADYDNL----FKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 159 ~l~~~~~~Lk~~~~~L----~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
.+++++..|+.+...| ....+.|+.|+++|+.-|..++.
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 22233477888888877766543
No 112
>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=42.11 E-value=5.1e+02 Score=28.55 Aligned_cols=30 Identities=23% Similarity=0.308 Sum_probs=15.9
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhHH
Q 019954 144 RRARWKTKQLEKDYDVLQNSYNSLKADYDN 173 (333)
Q Consensus 144 RRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~ 173 (333)
|+.|---.+++++.+.|+..+..|......
T Consensus 456 r~lk~eL~qlr~ene~Lq~Kl~~L~~aRq~ 485 (697)
T PF09726_consen 456 RSLKSELSQLRQENEQLQNKLQNLVQARQQ 485 (697)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444445555556666666655555444433
No 113
>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=41.91 E-value=52 Score=33.03 Aligned_cols=32 Identities=31% Similarity=0.402 Sum_probs=24.8
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHH
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLK 187 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~ 187 (333)
+...|+.++.+||+++..|..|.++|++|+.+
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 44567788888888888888888888777654
No 114
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=41.16 E-value=82 Score=30.98 Aligned_cols=30 Identities=30% Similarity=0.345 Sum_probs=12.5
Q ss_pred HhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 169 ADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 169 ~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
++.+.|.-|-+.|..++.+||..+...+++
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 334444444444444444444444433333
No 115
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=41.10 E-value=80 Score=30.41 Aligned_cols=38 Identities=21% Similarity=0.293 Sum_probs=28.2
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
-+...+.....-.-|.+||+.|+.+|.+|+..+.....
T Consensus 213 ~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~~~ 250 (269)
T KOG3119|consen 213 RKQKEDEMAHRVAELEKENEALRTQVEQLKKELATLRR 250 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444566666677999999999999999988875543
No 116
>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=40.30 E-value=1.6e+02 Score=24.80 Aligned_cols=34 Identities=29% Similarity=0.421 Sum_probs=21.0
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhh
Q 019954 135 RQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADY 171 (333)
Q Consensus 135 rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~ 171 (333)
||.+.||-.+|.-.. .-+....++...+.||.+.
T Consensus 18 Rq~e~~FlqKr~~LS---~~kpe~~lkEEi~eLK~El 51 (106)
T PF11594_consen 18 RQMEAFFLQKRFELS---AYKPEQVLKEEINELKEEL 51 (106)
T ss_pred HHHHHHHHHHHHHHH---hcCHHHHHHHHHHHHHHHH
Confidence 688999999888763 2334445555555555333
No 117
>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=39.99 E-value=70 Score=21.30 Aligned_cols=22 Identities=36% Similarity=0.536 Sum_probs=14.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHh
Q 019954 172 DNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 172 ~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
..|..|++.|+..-++|+.+|.
T Consensus 4 qkL~sekeqLrrr~eqLK~kLe 25 (32)
T PF02344_consen 4 QKLISEKEQLRRRREQLKHKLE 25 (32)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 4566667777776666666654
No 118
>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=39.84 E-value=54 Score=26.30 Aligned_cols=45 Identities=16% Similarity=0.158 Sum_probs=31.3
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
++..|..++...|-. .....++|..+|+++..|+.|...-+.|.|
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 566666666554432 234568999999999999998876555544
No 119
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=39.69 E-value=1.2e+02 Score=29.26 Aligned_cols=60 Identities=25% Similarity=0.247 Sum_probs=30.7
Q ss_pred hhhhHHHHHHHHHHHH--HHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 019954 141 FQNRRARWKTKQLEKD--YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKESK 200 (333)
Q Consensus 141 FQNRRaK~Krkq~~ke--~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~~~ 200 (333)
-|+-|-|.|-+..+.+ ..-|-..+..|..+++.|.+.|+.|-.+..+|...|....++..
T Consensus 81 AQtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~ 142 (292)
T KOG4005|consen 81 AQTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELA 142 (292)
T ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 3555554443332222 23344455555666666666666666666666666664444333
No 120
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=39.65 E-value=1.3e+02 Score=33.29 Aligned_cols=21 Identities=24% Similarity=0.360 Sum_probs=15.8
Q ss_pred CCHHHHHHHHHHhCCCchhhh
Q 019954 118 LEPERKIQLAKDLGLQPRQVA 138 (333)
Q Consensus 118 p~~~~r~~LA~~LgLs~rQVk 138 (333)
|....=..+|+.+||++..|.
T Consensus 485 ~g~S~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 485 PGKSNAFEIAKRLGLPENIIE 505 (782)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 344466778999999988774
No 121
>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=39.34 E-value=35 Score=27.98 Aligned_cols=35 Identities=31% Similarity=0.540 Sum_probs=19.0
Q ss_pred HHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHH
Q 019954 105 VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQL 153 (333)
Q Consensus 105 l~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~ 153 (333)
+.+..-.|+.++||...--.. | =.|||.+||+.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~-a-------------RRnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQ-A-------------RRNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HH-H-------------HHHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccc-c-------------ccchhhhHHHHHH
Confidence 445566688999997441111 1 1589999997653
No 122
>PF15035 Rootletin: Ciliary rootlet component, centrosome cohesion
Probab=39.34 E-value=1.3e+02 Score=27.45 Aligned_cols=43 Identities=23% Similarity=0.332 Sum_probs=33.8
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
-...|+.+.+..+..|+.|..+..+|..++.+++..|..++..
T Consensus 82 vN~lLReQLEq~~~~N~~L~~dl~klt~~~~~l~~eL~~ke~~ 124 (182)
T PF15035_consen 82 VNALLREQLEQARKANEALQEDLQKLTQDWERLRDELEQKEAE 124 (182)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455666777778888889999999999988888888877753
No 123
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=39.24 E-value=1.5e+02 Score=23.72 Aligned_cols=38 Identities=26% Similarity=0.394 Sum_probs=16.4
Q ss_pred HHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 153 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 153 ~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
+..+.+.|+..+..|..+.+.+...++.|..|+.+|+.
T Consensus 23 LqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~ 60 (79)
T PRK15422 23 LQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKE 60 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHH
Confidence 34444445554444444443322223334444444443
No 124
>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=38.02 E-value=26 Score=23.68 Aligned_cols=23 Identities=22% Similarity=0.170 Sum_probs=19.1
Q ss_pred HHHHHHHhCCCchhhhhhhhhhH
Q 019954 123 KIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
..++|+.+|++++.|+.|.++-.
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 45789999999999999976543
No 125
>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=37.75 E-value=2.2e+02 Score=23.16 Aligned_cols=36 Identities=22% Similarity=0.434 Sum_probs=27.5
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
.|.|+..++..|. .....+.+|++-.+|+..+....
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 4569999988883 34456789999999999887643
No 126
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=37.73 E-value=90 Score=32.73 Aligned_cols=44 Identities=18% Similarity=0.345 Sum_probs=29.1
Q ss_pred HHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 149 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 149 Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
|...++++++.+++...-+.+....+....+.|++|+.+|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 34455566666665555555666667777777888888887777
No 127
>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=37.46 E-value=62 Score=25.67 Aligned_cols=27 Identities=26% Similarity=0.369 Sum_probs=12.5
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 168 KADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 168 k~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
..++..|..+.++|++|+.+++...++
T Consensus 6 ~eEn~~Lk~eiqkle~ELq~~~~~~qI 32 (76)
T PF07334_consen 6 QEENARLKEEIQKLEAELQQNKREFQI 32 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhh
Confidence 334444444445555555444444333
No 128
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=37.29 E-value=70 Score=26.72 Aligned_cols=45 Identities=13% Similarity=0.126 Sum_probs=32.6
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
+++.+..++...|-.. ....++|..+|++...|+.|...-|.+.|
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 6777777776555433 23678999999999999999876555544
No 129
>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=37.17 E-value=50 Score=24.91 Aligned_cols=44 Identities=20% Similarity=0.363 Sum_probs=21.9
Q ss_pred CcccChHH-HHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 019954 97 KRRLTVDQ-VQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 142 (333)
Q Consensus 97 R~rft~~Q-l~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQ 142 (333)
|+.|+... |.+++.+...+. --...|. -|+++|+++++|+-|-+
T Consensus 3 rrsy~~~FKL~Vv~~a~~~~n-c~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 3 RRSYTAEFKLKVVEYAEKDNN-CKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp -----HHHHHHHHHHHHH-TT-TTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred ccccChHHHHHHHHHHHHccc-hhhhHHH-HHHHhCccHHHHHHHHH
Confidence 34465543 445554443322 2222333 49999999999999964
No 130
>COG2919 Septum formation initiator [Cell division and chromosome partitioning]
Probab=37.14 E-value=1.2e+02 Score=25.53 Aligned_cols=33 Identities=27% Similarity=0.367 Sum_probs=20.0
Q ss_pred HHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 159 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 159 ~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
.+......+.++++.|.+++..|++|+..|+..
T Consensus 54 ~l~~qi~~~~~e~~~L~~~~~~l~~ei~~L~dg 86 (117)
T COG2919 54 QLQRQIAAQQAELEKLSARNTALEAEIKDLKDG 86 (117)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccc
Confidence 333344455666666666667777776666655
No 131
>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=36.98 E-value=1.1e+02 Score=22.83 Aligned_cols=28 Identities=18% Similarity=0.364 Sum_probs=13.9
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 164 YNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 164 ~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
..++...-.+++.|++.|+.++.++.+.
T Consensus 9 ~~~~~~~i~tvk~en~~i~~~ve~i~en 36 (55)
T PF05377_consen 9 LPRIESSINTVKKENEEISESVEKIEEN 36 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444455555555555555555443
No 132
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=35.95 E-value=42 Score=29.05 Aligned_cols=46 Identities=13% Similarity=0.258 Sum_probs=32.0
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..++...|- ......++|..||+++..|+++...-|.+.|+
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 56666655555542 22236789999999999999998766665554
No 133
>PF13518 HTH_28: Helix-turn-helix domain
Probab=35.91 E-value=37 Score=23.22 Aligned_cols=22 Identities=18% Similarity=0.520 Sum_probs=18.8
Q ss_pred HHHHHHHHhCCCchhhhhhhhh
Q 019954 122 RKIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvWFQN 143 (333)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3556999999999999999864
No 134
>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=35.86 E-value=2.2e+02 Score=24.48 Aligned_cols=51 Identities=22% Similarity=0.300 Sum_probs=29.4
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 144 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 144 RRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
.|.+.+....+++...++.....+......+......++.|+.+++..+..
T Consensus 76 ~rL~~~~~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~~~~ 126 (151)
T PF11559_consen 76 ERLKEQLEELERELASAEEKERQLQKQLKSLEAKLKQEKEELQKLKNQLQQ 126 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555555555555555555566666666666666666666666655443
No 135
>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=35.72 E-value=2e+02 Score=22.07 Aligned_cols=42 Identities=17% Similarity=0.193 Sum_probs=24.7
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
++-.-++.|+..+..|+.....+..|...|...+...+.++.
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 444555566666666666666666666666666555555444
No 136
>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=35.64 E-value=75 Score=25.78 Aligned_cols=20 Identities=30% Similarity=0.527 Sum_probs=14.8
Q ss_pred HHHHHHhCCCchhhhhhhhh
Q 019954 124 IQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 124 ~~LA~~LgLs~rQVkvWFQN 143 (333)
.++|+.+|++++.++.|-++
T Consensus 4 ~EvA~~~gVs~~tLR~ye~~ 23 (99)
T cd04765 4 GEVAEILGLPPHVLRYWETE 23 (99)
T ss_pred HHHHHHHCcCHHHHHHHHHH
Confidence 46778888888888888554
No 137
>PF09744 Jnk-SapK_ap_N: JNK_SAPK-associated protein-1; InterPro: IPR019143 This entry represents the N-terminal 200 residues of a set of proteins conserved from yeasts to humans. Most of the proteins in this entry have a RhoGEF domain (IPR000219 from INTERPRO) at their C-terminal end.
Probab=35.43 E-value=2e+02 Score=25.76 Aligned_cols=80 Identities=23% Similarity=0.206 Sum_probs=40.3
Q ss_pred HHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHH
Q 019954 104 QVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKA 183 (333)
Q Consensus 104 Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~ 183 (333)
-+..|+.++..+........ .| + ...-+.=.|.+|-|..+++.+..+..+ -+.+..+...|....+.|+.
T Consensus 34 vLE~Le~~~~~n~~~~~e~~-~L-~-----~d~e~L~~q~~~ek~~r~~~e~~l~~~---Ed~~~~e~k~L~~~v~~Le~ 103 (158)
T PF09744_consen 34 VLELLESLASRNQEHEVELE-LL-R-----EDNEQLETQYEREKELRKQAEEELLEL---EDQWRQERKDLQSQVEQLEE 103 (158)
T ss_pred HHHHHHHHHHhhhhhhhHHH-HH-H-----HHHHHHHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHHHHHH
Confidence 35566777777664333211 11 1 112233345566666665555544422 23445555556666666666
Q ss_pred HHHHHHHHHh
Q 019954 184 EVLKLTDKLQ 193 (333)
Q Consensus 184 E~~~l~~~l~ 193 (333)
++..|..++.
T Consensus 104 e~r~L~~~~~ 113 (158)
T PF09744_consen 104 ENRQLELKLK 113 (158)
T ss_pred HHHHHHHHhh
Confidence 6666655554
No 138
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=35.39 E-value=69 Score=27.18 Aligned_cols=46 Identities=11% Similarity=-0.034 Sum_probs=32.9
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..+|...|-.. ....++|..||++...|+.|...-|.+.|+
T Consensus 129 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 174 (182)
T PRK09652 129 LPEELRTAITLREIEG-----LSYEEIAEIMGCPIGTVRSRIFRAREALRA 174 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 7778878777665322 235688999999999999998754444443
No 139
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=35.30 E-value=69 Score=28.30 Aligned_cols=46 Identities=15% Similarity=0.097 Sum_probs=33.3
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-.. ..-.++|+.||++...|+++...-|.+.|+
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 7777777776654322 345789999999999999998665555554
No 140
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=35.21 E-value=44 Score=28.31 Aligned_cols=46 Identities=17% Similarity=0.149 Sum_probs=32.0
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..+|...|-. ...-.++|..+|+++..|+.|...-|.+.|+
T Consensus 126 L~~~~r~i~~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYVE-----GLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555566665554432 2335789999999999999998766655554
No 141
>KOG3755 consensus SATB1 matrix attachment region binding protein [Transcription]
Probab=35.14 E-value=19 Score=38.65 Aligned_cols=46 Identities=15% Similarity=0.126 Sum_probs=31.2
Q ss_pred HHhhhhccCCCCHHHHHHHHHHhCC-------CchhhhhhhhhhHHHHHHHHH
Q 019954 108 LEKSFEVENKLEPERKIQLAKDLGL-------QPRQVAIWFQNRRARWKTKQL 153 (333)
Q Consensus 108 LE~~F~~~~~p~~~~r~~LA~~LgL-------s~rQVkvWFQNRRaK~Krkq~ 153 (333)
-+..|.+++.+......+--.++.| ...-|+.||.|||+++|+.+.
T Consensus 707 ~~~w~~k~~s~s~~~v~eYkee~~~~~~~e~~~~kn~~~~fk~~~ee~~~~k~ 759 (769)
T KOG3755|consen 707 KHHWKLKTRSGSWVDVAEYKEEELLMPYEEKFESKNVQFWFKVRREEEKRLKM 759 (769)
T ss_pred chhheecccCchhHHHHHhhHHhhcchhhhhhhhcchHHHHHHHHHHHhhhhc
Confidence 3555777777776555554444433 345699999999999998553
No 142
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=35.13 E-value=73 Score=21.41 Aligned_cols=42 Identities=21% Similarity=0.229 Sum_probs=29.5
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 146 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRa 146 (333)
.++..+..++...+. . ....++|..+|++...|..|.+.-+.
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 24578999999999999988764433
No 143
>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=34.98 E-value=2.7e+02 Score=23.26 Aligned_cols=37 Identities=24% Similarity=0.279 Sum_probs=28.5
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
..|.|+..++..| .....++.+|++-..|+.+|....
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 3456999999888 344557899999999999886543
No 144
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=34.83 E-value=44 Score=23.07 Aligned_cols=40 Identities=23% Similarity=0.232 Sum_probs=20.3
Q ss_pred cccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 019954 98 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 142 (333)
Q Consensus 98 ~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQ 142 (333)
+.||.+|...++..+... .-..+||+.||.++.-|..|..
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~relk 42 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRELK 42 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHHh
Confidence 458888888888776633 3456799999999988877653
No 145
>PRK04217 hypothetical protein; Provisional
Probab=34.54 E-value=81 Score=26.53 Aligned_cols=46 Identities=13% Similarity=0.042 Sum_probs=34.1
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
.++.+|..++...|...- ...+||+.+|++...|+..+..-|.+.|
T Consensus 42 ~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~RArkkLr 87 (110)
T PRK04217 42 FMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALTSARKKVA 87 (110)
T ss_pred cCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHHHHHHHHH
Confidence 488888888877764333 4677999999999999888765444443
No 146
>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=34.42 E-value=1.7e+02 Score=20.88 Aligned_cols=27 Identities=22% Similarity=0.379 Sum_probs=16.4
Q ss_pred HHHHhhhhhHHHhhHHHHHHHHHHHHH
Q 019954 158 DVLQNSYNSLKADYDNLFKEKEKLKAE 184 (333)
Q Consensus 158 ~~l~~~~~~Lk~~~~~L~~Ene~L~~E 184 (333)
..+......|...+..|..++..|+.|
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 444555666666666666666666554
No 147
>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=34.32 E-value=96 Score=32.51 Aligned_cols=94 Identities=17% Similarity=0.224 Sum_probs=48.2
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhh-hhHHHhhHHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSY-NSLKADYDNLFKE 177 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~-~~Lk~~~~~L~~E 177 (333)
.+++++++.|.-. -..|...-|..+|+.-.+..++-++==+|++.+....++++....+.++. ..|......+.++
T Consensus 41 ~ltpee~kalGie---gDTP~DTlrTlva~~k~~r~~~~~l~~~N~~l~~eN~~L~~r~~~id~~i~~av~~~~~~~~~~ 117 (472)
T TIGR03752 41 ELSPEELKALGIE---GDTPADTLRTLVAEVKELRKRLAKLISENEALKAENERLQKREQSIDQQIQQAVQSETQELTKE 117 (472)
T ss_pred cCCcchhHhcCCC---CCCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHhhhHHHHHH
Confidence 4666666555322 33455555655555444444444444456666555555544333333332 2444445555666
Q ss_pred HHHHHHHHHHHHHHHhhh
Q 019954 178 KEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 178 ne~L~~E~~~l~~~l~~~ 195 (333)
.+.|+.|..+++..|...
T Consensus 118 ~~ql~~~~~~~~~~l~~l 135 (472)
T TIGR03752 118 IEQLKSERQQLQGLIDQL 135 (472)
T ss_pred HHHHHHHHHHHHHHHHHH
Confidence 666666666665555433
No 148
>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=34.28 E-value=15 Score=28.85 Aligned_cols=35 Identities=14% Similarity=0.221 Sum_probs=26.7
Q ss_pred HhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhh
Q 019954 109 EKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 109 E~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQN 143 (333)
+..|...++...-...+||..+|+++..|+.|+.+
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 44455555555556789999999999999999864
No 149
>PHA01750 hypothetical protein
Probab=34.11 E-value=2.1e+02 Score=22.26 Aligned_cols=35 Identities=20% Similarity=0.457 Sum_probs=23.3
Q ss_pred HHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 158 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 158 ~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
+..++..+.|+.+-..+....+.|..++.+++.++
T Consensus 38 eIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~ 72 (75)
T PHA01750 38 EIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKL 72 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhh
Confidence 44556666677666666666666777777777655
No 150
>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=33.88 E-value=92 Score=22.20 Aligned_cols=46 Identities=15% Similarity=0.177 Sum_probs=33.3
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+||..++.+|.-...- ....++|..+|++++.|+.+..+=+.|..-
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~~ 48 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLGV 48 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT-
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhCC
Confidence 4778888887666543 236789999999999999998776666554
No 151
>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=33.64 E-value=2.5e+02 Score=26.80 Aligned_cols=16 Identities=13% Similarity=0.545 Sum_probs=10.8
Q ss_pred chhhhhhhhhhHHHHH
Q 019954 134 PRQVAIWFQNRRARWK 149 (333)
Q Consensus 134 ~rQVkvWFQNRRaK~K 149 (333)
...+..||+.+-...+
T Consensus 186 ~~e~e~~y~~k~~~l~ 201 (312)
T PF00038_consen 186 REELEEWYQSKLEELR 201 (312)
T ss_dssp HHHHHHHHHHHHHHHH
T ss_pred hhhhhhhccccccccc
Confidence 4578889988754433
No 152
>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=33.19 E-value=2.5e+02 Score=22.33 Aligned_cols=50 Identities=22% Similarity=0.278 Sum_probs=42.1
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 142 QNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 142 QNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
|||--+.+-...+.+.+.|......|+..-......+.+|+++...++..
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 67777777777888888999999999999888899999999998887764
No 153
>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=33.17 E-value=2.9e+02 Score=23.28 Aligned_cols=36 Identities=19% Similarity=0.249 Sum_probs=28.4
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
.|.|+..++..| ......+.+|++-.+|+-+|....
T Consensus 36 yR~Y~~~~~~~l-------------~~I~~lr~~G~sL~eI~~~l~~~~ 71 (133)
T cd04787 36 YRLYSEKDLSRL-------------RFILSARQLGFSLKDIKEILSHAD 71 (133)
T ss_pred eeeCCHHHHHHH-------------HHHHHHHHcCCCHHHHHHHHhhhc
Confidence 456999999988 345557899999999999997543
No 154
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=33.07 E-value=1.8e+02 Score=22.42 Aligned_cols=26 Identities=23% Similarity=0.326 Sum_probs=15.5
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 164 YNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 164 ~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
......++..|..|++.|+.|+..++
T Consensus 42 l~~a~~e~~~Lk~E~e~L~~el~~~r 67 (69)
T PF14197_consen 42 LGDAYEENNKLKEENEALRKELEELR 67 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 33445566666667777776655543
No 155
>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=32.11 E-value=2e+02 Score=24.23 Aligned_cols=42 Identities=26% Similarity=0.336 Sum_probs=23.7
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
.+.++.+.|+.....|...+..+.+-...|++++..+...+.
T Consensus 34 eL~kqkd~L~~~l~~L~~q~~s~~qr~~eLqaki~ea~~~le 75 (107)
T PF09304_consen 34 ELAKQKDQLRNALQSLQAQNASRNQRIAELQAKIDEARRNLE 75 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334444555555566666666666666666666655554444
No 156
>PRK09639 RNA polymerase sigma factor SigX; Provisional
Probab=32.06 E-value=1.2e+02 Score=25.58 Aligned_cols=45 Identities=16% Similarity=0.276 Sum_probs=32.2
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|.-.| ..+ .-.++|..+|++...|+.+...-|.+.|+
T Consensus 113 L~~~~r~il~l~~--~g~----s~~eIA~~lgis~~tV~~~i~ra~~~Lr~ 157 (166)
T PRK09639 113 MTERDRTVLLLRF--SGY----SYKEIAEALGIKESSVGTTLARAKKKFRK 157 (166)
T ss_pred CCHHHHHHHHHHH--cCC----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6677777776666 222 35678999999999999998655555444
No 157
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=32.04 E-value=64 Score=32.36 Aligned_cols=25 Identities=12% Similarity=-0.039 Sum_probs=13.9
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHH
Q 019954 164 YNSLKADYDNLFKEKEKLKAEVLKL 188 (333)
Q Consensus 164 ~~~Lk~~~~~L~~Ene~L~~E~~~l 188 (333)
|-.|+.+|+.|++|+.+|+.++.++
T Consensus 59 y~~L~~EN~~Lk~Ena~L~~~l~~~ 83 (337)
T PRK14872 59 ALVLETENFLLKERIALLEERLKSY 83 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4455555555666666665555553
No 158
>TIGR02985 Sig70_bacteroi1 RNA polymerase sigma-70 factor, Bacteroides expansion family 1. This group of sigma factors are members of the sigma-70 family (TIGR02937) and are found primarily in the genus Bacteroides. This family appears to have resulted from a lineage-specific expansion as B. thetaiotaomicron VPI-5482, Bacteroides forsythus ATCC 43037, Bacteroides fragilis YCH46 and Bacteroides fragilis NCTC 9343 contain 25, 12, 24 and 23 members, respectively. There are currentlyonly two known members of this family outside of the Bacteroides, in Rhodopseudomonas and Bradyrhizobium.
Probab=31.74 E-value=54 Score=27.16 Aligned_cols=45 Identities=13% Similarity=0.115 Sum_probs=30.4
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
++..+..+|...|-. .....++|..+|+++..|+.+...-|.+.|
T Consensus 114 L~~~~r~il~l~~~~-----~~~~~eIA~~lgis~~tv~~~~~ra~~~Lr 158 (161)
T TIGR02985 114 LPEQCRKIFILSRFE-----GKSYKEIAEELGISVKTVEYHISKALKELR 158 (161)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666666554432 223567899999999999988876555554
No 159
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=31.57 E-value=1.8e+02 Score=22.73 Aligned_cols=31 Identities=29% Similarity=0.212 Sum_probs=17.7
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
.+..++-.|..+++.|+.|+.+++..|...+
T Consensus 40 ~~~keNieLKve~~~L~~el~~~~~~l~~a~ 70 (75)
T PF07989_consen 40 ELLKENIELKVEVESLKRELQEKKKLLKEAE 70 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555566666666666666665555443
No 160
>PF12824 MRP-L20: Mitochondrial ribosomal protein subunit L20; InterPro: IPR024388 Ribosomes are the particles that catalyse mRNA-directed protein synthesis in all organisms. The codons of the mRNA are exposed on the ribosome to allow tRNA binding. This leads to the incorporation of amino acids into the growing polypeptide chain in accordance with the genetic information. Incoming amino acid monomers enter the ribosomal A site in the form of aminoacyl-tRNAs complexed with elongation factor Tu (EF-Tu) and GTP. The growing polypeptide chain, situated in the P site as peptidyl-tRNA, is then transferred to aminoacyl-tRNA and the new peptidyl-tRNA, extended by one residue, is translocated to the P site with the aid the elongation factor G (EF-G) and GTP as the deacylated tRNA is released from the ribosome through one or more exit sites [, ]. About 2/3 of the mass of the ribosome consists of RNA and 1/3 of protein. The proteins are named in accordance with the subunit of the ribosome which they belong to - the small (S1 to S31) and the large (L1 to L44). Usually they decorate the rRNA cores of the subunits. Many ribosomal proteins, particularly those of the large subunit, are composed of a globular, surfaced-exposed domain with long finger-like projections that extend into the rRNA core to stabilise its structure. Most of the proteins interact with multiple RNA elements, often from different domains. In the large subunit, about 1/3 of the 23S rRNA nucleotides are at least in van der Waal's contact with protein, and L22 interacts with all six domains of the 23S rRNA. Proteins S4 and S7, which initiate assembly of the 16S rRNA, are located at junctions of five and four RNA helices, respectively. In this way proteins serve to organise and stabilise the rRNA tertiary structure. While the crucial activities of decoding and peptide transfer are RNA based, proteins play an active role in functions that may have evolved to streamline the process of protein synthesis. In addition to their function in the ribosome, many ribosomal proteins have some function 'outside' the ribosome [, ]. This entry represents the essential mitochondrial ribosomal protein L20 family from fungi [].
Probab=31.54 E-value=3.7e+02 Score=24.15 Aligned_cols=63 Identities=22% Similarity=0.267 Sum_probs=42.5
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHh
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQN 162 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~ 162 (333)
++..+|.+++..+.+.-..+ |..-.+..||+++|+++.-|.+=..--. .+++..+...+.++.
T Consensus 82 k~y~Lt~e~i~Eir~LR~~D--P~~wTr~~LAkkF~~S~~fV~~v~~~~~--e~~~~~~~~le~~k~ 144 (164)
T PF12824_consen 82 KKYHLTPEDIQEIRRLRAED--PEKWTRKKLAKKFNCSPLFVSMVAPAPK--EKKKEMEARLEAIKS 144 (164)
T ss_pred ccccCCHHHHHHHHHHHHcC--chHhhHHHHHHHhCCCHHHHHHhcCCCH--HHHHHHHHHHHHHHH
Confidence 34569999999887776654 4556789999999999988877664433 333334444444444
No 161
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=31.38 E-value=1.9e+02 Score=22.75 Aligned_cols=22 Identities=27% Similarity=0.323 Sum_probs=11.1
Q ss_pred hhHHHhhHHHHHHHHHHHHHHH
Q 019954 165 NSLKADYDNLFKEKEKLKAEVL 186 (333)
Q Consensus 165 ~~Lk~~~~~L~~Ene~L~~E~~ 186 (333)
..+....+.|..||+.|+.|-.
T Consensus 42 q~~q~~reaL~~eneqlk~e~~ 63 (79)
T COG3074 42 QNAQHQREALERENEQLKEEQN 63 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555555555555543
No 162
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=31.36 E-value=1.7e+02 Score=24.53 Aligned_cols=38 Identities=26% Similarity=0.294 Sum_probs=26.9
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
..-.|+.-.++|-+..+++++||-+|+.|+.-|-..+.
T Consensus 64 QVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIe 101 (120)
T KOG3650|consen 64 QVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIE 101 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHH
Confidence 33446666777888888888888888888776654444
No 163
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=31.32 E-value=88 Score=28.06 Aligned_cols=46 Identities=20% Similarity=0.134 Sum_probs=31.5
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-. .....++|..+|++...|+++..+-|.+.|+
T Consensus 154 L~~~~r~vl~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVYFQ-----ELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 566666666544322 2345789999999999999888665555554
No 164
>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=31.31 E-value=81 Score=25.02 Aligned_cols=27 Identities=33% Similarity=0.539 Sum_probs=22.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 172 DNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 172 ~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
+.|.+||.+|+.|+.+|...|+....+
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 478999999999999998888866554
No 165
>PRK10072 putative transcriptional regulator; Provisional
Probab=31.31 E-value=31 Score=28.29 Aligned_cols=42 Identities=19% Similarity=0.251 Sum_probs=30.3
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRAR 147 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK 147 (333)
+.+...+..|...-.. ...+||+.+|++...|..|.+.+|.-
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 3466666666433322 26789999999999999999987653
No 166
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=31.00 E-value=2.2e+02 Score=26.89 Aligned_cols=28 Identities=25% Similarity=0.319 Sum_probs=19.0
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 162 NSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 162 ~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
..+..++++|..|++|+.+|+.++.++.
T Consensus 69 ~~~~~l~~en~~L~~e~~~l~~~~~~~~ 96 (276)
T PRK13922 69 ASLFDLREENEELKKELLELESRLQELE 96 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3455677777777777777777776554
No 167
>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=30.82 E-value=1.3e+02 Score=22.38 Aligned_cols=30 Identities=33% Similarity=0.472 Sum_probs=24.9
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKL 181 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L 181 (333)
++..+...++.....++.+++.|..+.+.|
T Consensus 21 ~~~~ei~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 21 QLNQEIAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445667788888888999999999999888
No 168
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=30.66 E-value=1.4e+02 Score=29.83 Aligned_cols=56 Identities=14% Similarity=0.241 Sum_probs=34.8
Q ss_pred hhhhhhhhHHHHHHHHH-HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 137 VAIWFQNRRARWKTKQL-EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 137 VkvWFQNRRaK~Krkq~-~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
++|||+|-|+-.+-..+ .+..+.++......+.....-..|-.+|..++..+..+.
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEaaA 72 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEAAA 72 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHHHH
Confidence 68999999886664433 334456666666666665555555556666665554433
No 169
>PRK12519 RNA polymerase sigma factor; Provisional
Probab=30.36 E-value=78 Score=27.71 Aligned_cols=46 Identities=24% Similarity=0.250 Sum_probs=31.4
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|- ......++|..+|++...|++|+..-|.+.|+
T Consensus 142 L~~~~~~v~~l~~~-----~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 187 (194)
T PRK12519 142 LPESQRQVLELAYY-----EGLSQSEIAKRLGIPLGTVKARARQGLLKLRE 187 (194)
T ss_pred CCHHHhhhhhhhhh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 55555555544432 23346789999999999999999765555554
No 170
>PRK12512 RNA polymerase sigma factor; Provisional
Probab=30.22 E-value=93 Score=26.98 Aligned_cols=46 Identities=13% Similarity=0.047 Sum_probs=33.8
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-.. ..-.++|..||++...|+.++..-|.+.|.
T Consensus 132 L~~~~r~v~~l~~~~g-----~s~~eIA~~l~is~~tV~~~l~ra~~~Lr~ 177 (184)
T PRK12512 132 LPPRQRDVVQSISVEG-----ASIKETAAKLSMSEGAVRVALHRGLAALAA 177 (184)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 6677777766654432 235789999999999999998776666654
No 171
>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=30.18 E-value=1.1e+02 Score=24.19 Aligned_cols=28 Identities=29% Similarity=0.512 Sum_probs=18.7
Q ss_pred hhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 164 YNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 164 ~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
...+..+...|..|+++|+-|...|+.-
T Consensus 44 l~~l~~~~~~l~~e~~~L~lE~~~l~~~ 71 (97)
T PF04999_consen 44 LQQLEKEIDQLQEENERLRLEIATLSSP 71 (97)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhCH
Confidence 3455566667777777777777776643
No 172
>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=30.10 E-value=1.8e+02 Score=23.57 Aligned_cols=39 Identities=13% Similarity=0.073 Sum_probs=27.7
Q ss_pred CCCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 95 EKKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 95 rkR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
..+|+|+.+++..|.. ...|.+.+|++-..|+.+..+..
T Consensus 34 ~g~R~Yt~~di~~l~~------------I~~llr~~G~~l~~i~~~l~~~~ 72 (99)
T cd04765 34 GGRRYYRPKDVELLLL------------IKHLLYEKGYTIEGAKQALKEDG 72 (99)
T ss_pred CCCeeeCHHHHHHHHH------------HHHHHHHCCCCHHHHHHHHHhcc
Confidence 3456699999998842 33356788999988888876533
No 173
>PRK12530 RNA polymerase sigma factor; Provisional
Probab=29.93 E-value=1.1e+02 Score=26.90 Aligned_cols=46 Identities=11% Similarity=0.171 Sum_probs=32.6
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..++.-.|-.. ....++|..||+++..|+++...-|.+.|+
T Consensus 135 Lp~~~R~v~~L~~~~g-----~s~~EIA~~lgis~~tVk~~l~RAr~~Lr~ 180 (189)
T PRK12530 135 LPAQQARVFMMREYLE-----LSSEQICQECDISTSNLHVLLYRARLQLQA 180 (189)
T ss_pred CCHHHHHHHhHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666666665554332 235789999999999999998766655554
No 174
>PF13942 Lipoprotein_20: YfhG lipoprotein
Probab=29.90 E-value=4.4e+02 Score=24.19 Aligned_cols=90 Identities=19% Similarity=0.291 Sum_probs=50.2
Q ss_pred hHHHHHHHhhhhccCCCCHHHHHHHHHHhCCC----chh----hhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHH
Q 019954 102 VDQVQFLEKSFEVENKLEPERKIQLAKDLGLQ----PRQ----VAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDN 173 (333)
Q Consensus 102 ~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs----~rQ----VkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~ 173 (333)
..|-.+-....-.+..|++.+|..+...|+-- |.+ +++|=.+.-...--..-+.-|..|++.. ..+.+.
T Consensus 58 ~W~~aFkq~ILL~~A~~T~~ERR~~~~~l~~y~~~~P~~vRPL~QlWRe~Q~lql~L~eEr~Ry~rLQqss---D~~lD~ 134 (179)
T PF13942_consen 58 SWQDAFKQSILLANAEPTPAERRQMVDRLNSYSLQFPASVRPLLQLWREQQVLQLQLSEERARYQRLQQSS---DSELDA 134 (179)
T ss_pred cHHHHHHHHHHhcCCCCCHHHHHHHHHHHHHhhhhcCHHHhHHHHHHHHhHHHHHHHHHHHHHHHHHHHhh---HHHHHH
Confidence 33333333344457789999999887777421 233 4566554443332222222233333332 234567
Q ss_pred HHHHHHHHHHHHHHHHHHHhh
Q 019954 174 LFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 174 L~~Ene~L~~E~~~l~~~l~~ 194 (333)
|.+.+.+|+.|+..-+.||..
T Consensus 135 Lr~qq~~Lq~qL~~T~RKLEn 155 (179)
T PF13942_consen 135 LRQQQQRLQYQLDTTTRKLEN 155 (179)
T ss_pred HHHHHHHHHHHHHHHHHHHhh
Confidence 788888888887777777664
No 175
>PTZ00361 26 proteosome regulatory subunit 4-like protein; Provisional
Probab=29.80 E-value=1.2e+02 Score=31.23 Aligned_cols=47 Identities=19% Similarity=0.119 Sum_probs=29.3
Q ss_pred hhHHHHHHHHHHHHHHHHHhhhhhHHHhhH--HHHHHHHHHHHHHHHHH
Q 019954 143 NRRARWKTKQLEKDYDVLQNSYNSLKADYD--NLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 143 NRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~--~L~~Ene~L~~E~~~l~ 189 (333)
+++++.|.+++++..+.|..+.+.++.+.. .+..|.+.++.|+.+|+
T Consensus 53 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 101 (438)
T PTZ00361 53 NTKCRLRLLKLERIKDYLLLEEEFITNQEAQKPAQEKNEAELKKVDDLR 101 (438)
T ss_pred chhhHHHHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHhh
Confidence 455666666666667766666666655553 45666666666666654
No 176
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=29.54 E-value=1.7e+02 Score=29.65 Aligned_cols=40 Identities=35% Similarity=0.342 Sum_probs=18.9
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+++.+.++.....||+..+.|..-..+|+++..+|..++.
T Consensus 224 eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~ 263 (365)
T KOG2391|consen 224 EEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQ 263 (365)
T ss_pred HHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHH
Confidence 3344444444444444444455544555544444444444
No 177
>TIGR02948 SigW_bacill RNA polymerase sigma-W factor. This sigma factor is restricted to certain lineages of the order Bacillales.
Probab=29.53 E-value=87 Score=27.00 Aligned_cols=46 Identities=13% Similarity=0.093 Sum_probs=32.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++...|- ....-.++|..+|+++..|+++++.-|.+.|.
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 66666666665433 23346789999999999999999766655554
No 178
>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=29.41 E-value=1.8e+02 Score=26.20 Aligned_cols=35 Identities=31% Similarity=0.424 Sum_probs=16.8
Q ss_pred HHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 155 KDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 155 ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.+...|+.....|+..+..|.+|+++|+.++..+.
T Consensus 104 ~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~ 138 (161)
T TIGR02894 104 KENERLKNQNESLQKRNEELEKELEKLRQRLSTIE 138 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444444444555555555555555544444433
No 179
>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=29.41 E-value=1.9e+02 Score=21.60 Aligned_cols=38 Identities=24% Similarity=0.420 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.++.+...+....+.++.++..+..+.++|..-+.+|-
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 45667777788888999999999999999998876653
No 180
>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=29.24 E-value=1.8e+02 Score=27.84 Aligned_cols=29 Identities=28% Similarity=0.408 Sum_probs=16.8
Q ss_pred hHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 166 SLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 166 ~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
.++.....|..|.+.|++.+.+|=+|+..
T Consensus 104 ~~~~~~~~L~~Ev~~L~~DN~kLYEKiRy 132 (248)
T PF08172_consen 104 KQQQTISSLRREVESLRADNVKLYEKIRY 132 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34445555666666666666666655553
No 181
>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=29.16 E-value=1.4e+02 Score=22.82 Aligned_cols=23 Identities=35% Similarity=0.435 Sum_probs=11.4
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHH
Q 019954 168 KADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 168 k~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
+...+.+..|+++|+.|...|..
T Consensus 37 ~~~~~~l~~en~~L~~ei~~l~~ 59 (85)
T TIGR02209 37 QLEIDKLQKEWRDLQLEVAELSR 59 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHcC
Confidence 33444455555555555555443
No 182
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=29.12 E-value=1.5e+02 Score=30.04 Aligned_cols=32 Identities=16% Similarity=0.352 Sum_probs=15.2
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 162 NSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 162 ~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
..+..|...+..+..+..+++.|+.++++++.
T Consensus 29 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 60 (398)
T PTZ00454 29 KELEFLDIQEEYIKEEQKNLKRELIRAKEEVK 60 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444444444455555555555555544443
No 183
>PF12999 PRKCSH-like: Glucosidase II beta subunit-like
Probab=29.09 E-value=2.6e+02 Score=25.61 Aligned_cols=23 Identities=22% Similarity=0.411 Sum_probs=13.0
Q ss_pred HHHHHHHHHHHHHHHHHHhhhhh
Q 019954 175 FKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 175 ~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
.+..+.++.++.+|+.+|...++
T Consensus 152 ~~~~~e~~~~l~~l~~ei~~~~~ 174 (176)
T PF12999_consen 152 KKKREELEKKLEELEKEIQAAKQ 174 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhc
Confidence 34455666666666666655443
No 184
>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=29.09 E-value=56 Score=21.09 Aligned_cols=23 Identities=22% Similarity=0.359 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhhhH
Q 019954 123 KIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
...+|+.+|+++..|..|..+++
T Consensus 15 ~~~~a~~~~~~~~~v~~~~~g~~ 37 (58)
T cd00093 15 QEELAEKLGVSRSTISRIENGKR 37 (58)
T ss_pred HHHHHHHHCCCHHHHHHHHcCCC
Confidence 35789999999999999988764
No 185
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=29.07 E-value=59 Score=27.51 Aligned_cols=46 Identities=13% Similarity=0.107 Sum_probs=31.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++...|-... .-.++|..||+++..|++....-|.+.|+
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 152 (160)
T PRK09642 107 LPENYRDVVLAHYLEEK-----SYQEIALQEKIEVKTVEMKLYRARKWIKK 152 (160)
T ss_pred CCHHHHHHHHHHHHhCC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 56666666555443222 24689999999999999998766666555
No 186
>PF06210 DUF1003: Protein of unknown function (DUF1003); InterPro: IPR010406 This entry consists of several hypothetical bacterial proteins of unknown function.
Probab=28.99 E-value=2e+02 Score=24.11 Aligned_cols=45 Identities=29% Similarity=0.288 Sum_probs=26.3
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 142 QNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 142 QNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
|||-++.-+.+.+.+++. +.....|.+.|.+++..+..++.....
T Consensus 57 QNRq~~~dr~ra~~D~~i-----------nl~ae~ei~~l~~~l~~l~~~~~~~~~ 101 (108)
T PF06210_consen 57 QNRQAARDRLRAELDYQI-----------NLKAEQEIERLHRKLDALREKLGELLE 101 (108)
T ss_pred hhHhHHHHHHHHHHHHHH-----------HHHhHHHHHHHHHHHHHHHHHhHHHHH
Confidence 677665545455555543 333445667777777777766664433
No 187
>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=28.74 E-value=2.5e+02 Score=29.52 Aligned_cols=36 Identities=19% Similarity=0.324 Sum_probs=26.5
Q ss_pred HHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhh
Q 019954 159 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQV 194 (333)
Q Consensus 159 ~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~ 194 (333)
.+......+..+.+.|..+..+++..+.+|..+|..
T Consensus 106 av~~~~~~~~~~~~ql~~~~~~~~~~l~~l~~~l~~ 141 (472)
T TIGR03752 106 AVQSETQELTKEIEQLKSERQQLQGLIDQLQRRLAG 141 (472)
T ss_pred HHHhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 344444566677778888888899999999888853
No 188
>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=28.69 E-value=2.1e+02 Score=21.12 Aligned_cols=23 Identities=26% Similarity=0.320 Sum_probs=13.2
Q ss_pred HHHhhHHHHHHHHHHHHHHHHHH
Q 019954 167 LKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 167 Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.......|..||..|++++..++
T Consensus 27 a~~rl~~l~~EN~~Lr~eL~~~r 49 (52)
T PF12808_consen 27 ARKRLSKLEGENRLLRAELERLR 49 (52)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHh
Confidence 34444556666666666665554
No 189
>PF06785 UPF0242: Uncharacterised protein family (UPF0242); InterPro: IPR009623 This is a group of proteins of unknown function.
Probab=28.66 E-value=2.2e+02 Score=28.84 Aligned_cols=24 Identities=25% Similarity=0.257 Sum_probs=12.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhhhh
Q 019954 174 LFKEKEKLKAEVLKLTDKLQVKEK 197 (333)
Q Consensus 174 L~~Ene~L~~E~~~l~~~l~~~~~ 197 (333)
+.+||.+|+.++..++.....+++
T Consensus 139 ~~EEn~~lqlqL~~l~~e~~Ekee 162 (401)
T PF06785_consen 139 LREENQCLQLQLDALQQECGEKEE 162 (401)
T ss_pred HHHHHHHHHHhHHHHHHHHhHhHH
Confidence 445555555555555544444433
No 190
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=28.60 E-value=43 Score=24.42 Aligned_cols=21 Identities=24% Similarity=0.382 Sum_probs=17.8
Q ss_pred HHHHHHHhCCCchhhhhhhhh
Q 019954 123 KIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQN 143 (333)
..++|+.+|++.+.|+.|=+.
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 191
>KOG1853 consensus LIS1-interacting protein NUDE [Cytoskeleton]
Probab=28.57 E-value=2.3e+02 Score=27.64 Aligned_cols=55 Identities=11% Similarity=0.099 Sum_probs=29.4
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhH----HHHHHHHHHHHHHHHHHHH
Q 019954 137 VAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYD----NLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 137 VkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~----~L~~Ene~L~~E~~~l~~~ 191 (333)
+++=-|||-..-+.+++..+.+.+|...+.-+..+. .|..++-.+++.-.+|+..
T Consensus 55 ~q~etrnrdl~t~nqrl~~E~e~~Kek~e~q~~q~y~q~s~Leddlsqt~aikeql~ky 113 (333)
T KOG1853|consen 55 DQLETRNRDLETRNQRLTTEQERNKEKQEDQRVQFYQQESQLEDDLSQTHAIKEQLRKY 113 (333)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344456777777777777776666666554444432 2334444444444444433
No 192
>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=28.27 E-value=65 Score=22.10 Aligned_cols=21 Identities=14% Similarity=0.286 Sum_probs=19.0
Q ss_pred HHHHHhCCCchhhhhhhhhhH
Q 019954 125 QLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 125 ~LA~~LgLs~rQVkvWFQNRR 145 (333)
+||+.+|++...|..|+.+++
T Consensus 2 ~lA~~~gvs~~tvs~~l~g~~ 22 (52)
T cd01392 2 DIARAAGVSVATVSRVLNGKP 22 (52)
T ss_pred cHHHHHCcCHHHHHHHHcCCC
Confidence 589999999999999999884
No 193
>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=28.15 E-value=3.1e+02 Score=23.14 Aligned_cols=33 Identities=24% Similarity=0.340 Sum_probs=14.5
Q ss_pred HHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 158 DVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 158 ~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
..|.......|.+.+.|.++++.|+.-+..|..
T Consensus 19 a~Le~slE~~K~S~~eL~kqkd~L~~~l~~L~~ 51 (107)
T PF09304_consen 19 ASLERSLEDEKTSQGELAKQKDQLRNALQSLQA 51 (107)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHhhHHHHHHhHHHHHHHHHHHHH
Confidence 333344444444444444444444444444443
No 194
>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=27.79 E-value=20 Score=33.95 Aligned_cols=29 Identities=34% Similarity=0.419 Sum_probs=0.0
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHH
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKL 188 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l 188 (333)
|+...+.|.++|+.|.+||++|++|..+|
T Consensus 134 LrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 134 LRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp -----------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33344445555555555555555555554
No 195
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=27.48 E-value=48 Score=22.74 Aligned_cols=23 Identities=26% Similarity=0.408 Sum_probs=17.2
Q ss_pred HHHHHHHHHhCCCchhhhhhhhh
Q 019954 121 ERKIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 121 ~~r~~LA~~LgLs~rQVkvWFQN 143 (333)
....++|+.||++.+.|..|.+.
T Consensus 18 ~s~~~ia~~lgvs~~Tv~~w~kr 40 (50)
T PF13384_consen 18 WSIREIAKRLGVSRSTVYRWIKR 40 (50)
T ss_dssp --HHHHHHHHTS-HHHHHHHHT-
T ss_pred CCHHHHHHHHCcCHHHHHHHHHH
Confidence 45678999999999999999753
No 196
>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=27.33 E-value=58 Score=23.76 Aligned_cols=34 Identities=24% Similarity=0.317 Sum_probs=25.4
Q ss_pred HHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhh
Q 019954 103 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIW 140 (333)
Q Consensus 103 ~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvW 140 (333)
.|+..|+-.+. ++..+.. +||..||++.+.|+.-
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~~~ 39 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIKND 39 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHHHH
Confidence 47788888888 6666544 8999999999887644
No 197
>COG2433 Uncharacterized conserved protein [Function unknown]
Probab=27.31 E-value=1.9e+02 Score=31.37 Aligned_cols=40 Identities=25% Similarity=0.444 Sum_probs=23.0
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
++..+.|+..+..|+.....+..++++|++++.+++..+.
T Consensus 428 ~~~ve~l~~e~~~L~~~~ee~k~eie~L~~~l~~~~r~~~ 467 (652)
T COG2433 428 EETVERLEEENSELKRELEELKREIEKLESELERFRREVR 467 (652)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555666666666666666666666666555443
No 198
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=27.22 E-value=2.5e+02 Score=22.77 Aligned_cols=42 Identities=10% Similarity=0.193 Sum_probs=31.2
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCC-Cchhhhhhhh
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGL-QPRQVAIWFQ 142 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgL-s~rQVkvWFQ 142 (333)
+++|+.+....+=..+....+ ....+|+++|+ ...++..|-+
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 677999876655555544443 57789999996 9999998864
No 199
>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=27.22 E-value=1.1e+02 Score=25.61 Aligned_cols=45 Identities=22% Similarity=0.245 Sum_probs=31.1
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
+++.+..++...|- ......++|..+|++...|+++...-|.+.|
T Consensus 112 L~~~~r~v~~l~~~-----~g~~~~eIA~~l~is~~tv~~~l~Rar~~Lr 156 (159)
T TIGR02989 112 LPERQRELLQLRYQ-----RGVSLTALAEQLGRTVNAVYKALSRLRVRLR 156 (159)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHhCCCHHHHHHHHHHHHHHHH
Confidence 66777666666443 2234678999999999999988765444443
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=27.16 E-value=3e+02 Score=25.80 Aligned_cols=53 Identities=15% Similarity=0.370 Sum_probs=26.4
Q ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 135 RQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 135 rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
..|.-|..- +..+..++..+..+.+.|+..+..+......++.++.+|+.++.
T Consensus 42 ~~id~~~~e------~~~L~~e~~~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~~qi~ 94 (251)
T PF11932_consen 42 KRIDQWDDE------KQELLAEYRQLEREIENLEVYNEQLERQVASQEQELASLEQQIE 94 (251)
T ss_pred HHHHHHHHH------HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345556543 23344445555555555555555555555555555555544444
No 201
>PRK09648 RNA polymerase sigma factor SigD; Reviewed
Probab=27.11 E-value=1.1e+02 Score=26.61 Aligned_cols=46 Identities=22% Similarity=0.178 Sum_probs=32.6
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..|..++...|-.. ....++|..+|++...|+.+...-|.+.|+
T Consensus 140 L~~~~r~i~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 185 (189)
T PRK09648 140 LPEKQREILILRVVVG-----LSAEETAEAVGSTPGAVRVAQHRALARLRA 185 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6777777776654432 346789999999999999988655544443
No 202
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=27.07 E-value=2e+02 Score=30.76 Aligned_cols=38 Identities=21% Similarity=0.423 Sum_probs=20.5
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.++.+...++..+..|..+...|.+||.+|..++.+++
T Consensus 152 ~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r 189 (546)
T KOG0977|consen 152 ELEAEINTLKRRIKALEDELKRLKAENSRLREELARAR 189 (546)
T ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence 44455555555555555555555555555555555544
No 203
>TIGR02959 SigZ RNA polymerase sigma factor, SigZ family. This family of RNA polymerase sigma factors is a member of the Sigma-70 subfamily (TIGR02937). One of these is designated as SigZ in B. subtilis (Swiss_Prot: SIGZ_BACSU). Interestingly, this group has a very sporatic distribution, B. subtilis, for instance, being the only sequenced strain of Bacilli with a member. Dechloromonas aromatica RCB appears to have two of these sigma factors. A member appears on a plasmid found in Photobacterium profundum SS9 and Vibrio fischeri ES114 (where a second one is chromosomally encoded).
Probab=26.70 E-value=1.1e+02 Score=26.33 Aligned_cols=46 Identities=17% Similarity=0.130 Sum_probs=31.2
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
.+++.+..+|.-.|-.. ....++|..+|+++..|+++.+.-|.+.|
T Consensus 100 ~L~~~~r~v~~l~~~~g-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr 145 (170)
T TIGR02959 100 ELPDEYREAIRLTELEG-----LSQQEIAEKLGLSLSGAKSRVQRGRKKLK 145 (170)
T ss_pred hCCHHHHHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 36677766666655332 23578899999999999888764444444
No 204
>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=26.64 E-value=3.7e+02 Score=22.20 Aligned_cols=36 Identities=14% Similarity=0.255 Sum_probs=28.6
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhh
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 144 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNR 144 (333)
..|.|+..++..|. .....+.+|++-.+|+..+.+.
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 45569999998883 4466888999999999998764
No 205
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=26.56 E-value=1.1e+02 Score=30.57 Aligned_cols=23 Identities=22% Similarity=0.001 Sum_probs=11.0
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHH
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEK 178 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~En 178 (333)
.|..+++++..|+.++..|..+.
T Consensus 58 ~y~~L~~EN~~Lk~Ena~L~~~l 80 (337)
T PRK14872 58 HALVLETENFLLKERIALLEERL 80 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444455555555555553333
No 206
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=26.47 E-value=1.9e+02 Score=23.32 Aligned_cols=38 Identities=21% Similarity=0.447 Sum_probs=27.2
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHH
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDK 191 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~ 191 (333)
..+|..+....+.|...-+.|.+.++.|..++.+|-+.
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~LLes 62 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQELLES 62 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHH
Confidence 35677777777777777777777777777777766443
No 207
>PRK05602 RNA polymerase sigma factor; Reviewed
Probab=26.15 E-value=1.1e+02 Score=26.60 Aligned_cols=46 Identities=11% Similarity=0.088 Sum_probs=31.4
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..+|...|-. ...-.++|..||++...|+.+...-|.+.|+
T Consensus 129 L~~~~r~i~~l~~~~-----g~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~ 174 (186)
T PRK05602 129 LPERQREAIVLQYYQ-----GLSNIEAAAVMDISVDALESLLARGRRALRA 174 (186)
T ss_pred CCHHHHHHhhHHHhc-----CCCHHHHHHHhCcCHHHHHHHHHHHHHHHHH
Confidence 566666666554322 2235689999999999999998765555554
No 208
>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=26.11 E-value=3.7e+02 Score=22.06 Aligned_cols=38 Identities=21% Similarity=0.191 Sum_probs=29.1
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHH
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 146 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRa 146 (333)
..|.|+..++..| ......+.+|++-..|+..+.+...
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 3456999999988 3445578999999999998876543
No 209
>PF02796 HTH_7: Helix-turn-helix domain of resolvase; InterPro: IPR006120 Site-specific recombination plays an important role in DNA rearrangement in prokaryotic organisms. Two types of site-specific recombination are known to occur: Recombination between inverted repeats resulting in the reversal of a DNA segment. Recombination between repeat sequences on two DNA molecules resulting in their cointegration, or between repeats on one DNA molecule resulting in the excision of a DNA fragment. Site-specific recombination is characterised by a strand exchange mechanism that requires no DNA synthesis or high energy cofactor; the phosphodiester bond energy is conserved in a phospho-protein linkage during strand cleavage and re-ligation. Two unrelated families of recombinases are currently known []. The first, called the 'phage integrase' family, groups a number of bacterial phage and yeast plasmid enzymes. The second [], called the 'resolvase' family, groups enzymes which share the following structural characteristics: an N-terminal catalytic and dimerization domain that contains a conserved serine residue involved in the transient covalent attachment to DNA IPR006119 from INTERPRO, and a C-terminal helix-turn-helix DNA-binding domain. ; GO: 0000150 recombinase activity, 0003677 DNA binding, 0006310 DNA recombination; PDB: 1ZR2_A 2GM4_B 1RES_A 1ZR4_A 1RET_A 1GDT_B 2R0Q_C 1JKP_C 1IJW_C 1JJ6_C ....
Probab=26.09 E-value=98 Score=21.26 Aligned_cols=38 Identities=16% Similarity=0.340 Sum_probs=26.1
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhh
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWF 141 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWF 141 (333)
.++.+|+..+...+... ....++|+.+|++...|..++
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 36676666666666654 237789999999998887665
No 210
>COG1579 Zn-ribbon protein, possibly nucleic acid-binding [General function prediction only]
Probab=26.05 E-value=2.6e+02 Score=26.73 Aligned_cols=52 Identities=21% Similarity=0.258 Sum_probs=34.7
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 145 RARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 145 RaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
|-..+++...+.+..++.....++.....+..+.+.|+.++.++...+....
T Consensus 21 rl~~~~~~~~~~l~k~~~e~e~~~~~~~~~~~e~e~le~qv~~~e~ei~~~r 72 (239)
T COG1579 21 RLEPRIKEIRKALKKAKAELEALNKALEALEIELEDLENQVSQLESEIQEIR 72 (239)
T ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444566677777777777777777777777777777777666665443
No 211
>PRK12515 RNA polymerase sigma factor; Provisional
Probab=25.96 E-value=1.2e+02 Score=26.44 Aligned_cols=46 Identities=11% Similarity=0.173 Sum_probs=32.5
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-.. ..-.++|..+|+++..|++-...-|.+.|+
T Consensus 132 L~~~~r~vl~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 177 (189)
T PRK12515 132 LSPAHREIIDLVYYHE-----KSVEEVGEIVGIPESTVKTRMFYARKKLAE 177 (189)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6677777766554322 235688999999999999888766655554
No 212
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=25.92 E-value=1.8e+02 Score=30.44 Aligned_cols=74 Identities=22% Similarity=0.275 Sum_probs=42.6
Q ss_pred CCCHHHHHHHHHH-------hCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhh-hhHHHhhHHHHHHHHHHHHHHHHH
Q 019954 117 KLEPERKIQLAKD-------LGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSY-NSLKADYDNLFKEKEKLKAEVLKL 188 (333)
Q Consensus 117 ~p~~~~r~~LA~~-------LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~-~~Lk~~~~~L~~Ene~L~~E~~~l 188 (333)
+++.+++..|.++ |-|++++=++-=+= |.|.|+|+..++...-+..| +.|-..+..-.+||..|+.+|.+|
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 4555666555543 34556665554443 33445555555554444443 466666677777888888777777
Q ss_pred HHH
Q 019954 189 TDK 191 (333)
Q Consensus 189 ~~~ 191 (333)
...
T Consensus 299 e~~ 301 (472)
T KOG0709|consen 299 ELS 301 (472)
T ss_pred hhc
Confidence 543
No 213
>PRK00118 putative DNA-binding protein; Validated
Probab=25.80 E-value=3.9e+02 Score=22.21 Aligned_cols=45 Identities=13% Similarity=0.137 Sum_probs=31.1
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
++..|..++...|.... ...++|..+|+++..|..|...-|.+.|
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 45666666655544422 3567999999999999999875555444
No 214
>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=25.56 E-value=3.9e+02 Score=22.18 Aligned_cols=36 Identities=25% Similarity=0.310 Sum_probs=28.7
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
.|.|+..++..|. .....+.+|++-..|+-+|....
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 4459999999884 55567899999999999997654
No 215
>PF02403 Seryl_tRNA_N: Seryl-tRNA synthetase N-terminal domain; InterPro: IPR015866 The aminoacyl-tRNA synthetases (6.1.1. from EC) catalyse the attachment of an amino acid to its cognate transfer RNA molecule in a highly specific two-step reaction. These proteins differ widely in size and oligomeric state, and have limited sequence homology []. The 20 aminoacyl-tRNA synthetases are divided into two classes, I and II. Class I aminoacyl-tRNA synthetases contain a characteristic Rossman fold catalytic domain and are mostly monomeric []. Class II aminoacyl-tRNA synthetases share an anti-parallel beta-sheet fold flanked by alpha-helices [], and are mostly dimeric or multimeric, containing at least three conserved regions [, , ]. However, tRNA binding involves an alpha-helical structure that is conserved between class I and class II synthetases. In reactions catalysed by the class I aminoacyl-tRNA synthetases, the aminoacyl group is coupled to the 2'-hydroxyl of the tRNA, while, in class II reactions, the 3'-hydroxyl site is preferred. The synthetases specific for arginine, cysteine, glutamic acid, glutamine, isoleucine, leucine, methionine, tyrosine, tryptophan and valine belong to class I synthetases. The synthetases specific for alanine, asparagine, aspartic acid, glycine, histidine, lysine, phenylalanine, proline, serine, and threonine belong to class-II synthetases []. Based on their mode of binding to the tRNA acceptor stem, both classes of tRNA synthetases have been subdivided into three subclasses, designated 1a, 1b, 1c and 2a, 2b, 2c. This entry represents the N-terminal domain of Seryl-tRNA synthetase, which consists of two helices in a long alpha-hairpin. Seryl-tRNA synthetase (6.1.1.11 from EC) exists as monomer and belongs to class IIa [].; GO: 0000166 nucleotide binding, 0004828 serine-tRNA ligase activity, 0005524 ATP binding, 0006434 seryl-tRNA aminoacylation, 0005737 cytoplasm; PDB: 3QO8_A 3QO5_A 3QO7_A 3QNE_A 3LSQ_A 3LSS_A 2DQ3_B 1SET_A 1SER_A 1SRY_B ....
Probab=25.50 E-value=3.6e+02 Score=21.66 Aligned_cols=57 Identities=26% Similarity=0.388 Sum_probs=29.9
Q ss_pred hhhHHHHHHHHHHHHHHHHHhhhhhHHH---hhHHHHHHHHHHHHHHHHHHHHHhhhhhh
Q 019954 142 QNRRARWKTKQLEKDYDVLQNSYNSLKA---DYDNLFKEKEKLKAEVLKLTDKLQVKEKE 198 (333)
Q Consensus 142 QNRRaK~Krkq~~ke~~~l~~~~~~Lk~---~~~~L~~Ene~L~~E~~~l~~~l~~~~~~ 198 (333)
+.|..+.+...++.+...+......++. +.+.|.++...|+.++..+..++...+.+
T Consensus 37 ~~r~l~~~~e~lr~~rN~~sk~I~~~~~~~~~~~~l~~e~~~lk~~i~~le~~~~~~e~~ 96 (108)
T PF02403_consen 37 ERRELQQELEELRAERNELSKEIGKLKKAGEDAEELKAEVKELKEEIKELEEQLKELEEE 96 (108)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHCHTTCCTHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHhHHHHHHHHHhhCcccHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444455555555544444443 34556666666666666666555544443
No 216
>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=25.30 E-value=1.4e+02 Score=20.17 Aligned_cols=36 Identities=19% Similarity=0.261 Sum_probs=24.9
Q ss_pred ChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 019954 101 TVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQ 142 (333)
Q Consensus 101 t~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQ 142 (333)
+..|..++...+ .. ....++|+.++++.+.|+.|..
T Consensus 2 ~~~e~~i~~~~~--~~----~s~~eia~~l~~s~~tv~~~~~ 37 (57)
T cd06170 2 TPREREVLRLLA--EG----KTNKEIADILGISEKTVKTHLR 37 (57)
T ss_pred CHHHHHHHHHHH--cC----CCHHHHHHHHCCCHHHHHHHHH
Confidence 445555554433 11 2467889999999999999876
No 217
>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=25.23 E-value=1.3e+02 Score=25.86 Aligned_cols=46 Identities=22% Similarity=0.173 Sum_probs=30.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.|..++.-.|-.. ..-.++|..||+++..|++....-|.+.|+
T Consensus 135 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tVk~~l~Rar~~Lr~ 180 (183)
T TIGR02999 135 VDPRQAEVVELRFFAG-----LTVEEIAELLGVSVRTVERDWRFARAWLAD 180 (183)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 5555555555443322 235688999999999999998766655554
No 218
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=25.04 E-value=2.2e+02 Score=23.50 Aligned_cols=28 Identities=36% Similarity=0.449 Sum_probs=17.5
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHH
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKA 183 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~ 183 (333)
+.+.+++.+..++.++..|..|.+.|+.
T Consensus 35 q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 35 QVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3444555556666667777777777765
No 219
>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=24.86 E-value=48 Score=23.02 Aligned_cols=23 Identities=22% Similarity=0.382 Sum_probs=19.4
Q ss_pred HHHHHHHhCCCchhhhhhhhhhH
Q 019954 123 KIQLAKDLGLQPRQVAIWFQNRR 145 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQNRR 145 (333)
..+||+.+|+++..|.-|..++|
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 220
>KOG0980 consensus Actin-binding protein SLA2/Huntingtin-interacting protein Hip1 [Cytoskeleton]
Probab=24.72 E-value=2.8e+02 Score=31.48 Aligned_cols=82 Identities=23% Similarity=0.262 Sum_probs=34.4
Q ss_pred HHHHHHhhhhccCCCCHHHHH---HHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHH
Q 019954 104 QVQFLEKSFEVENKLEPERKI---QLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEK 180 (333)
Q Consensus 104 Ql~~LE~~F~~~~~p~~~~r~---~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~ 180 (333)
|+..|+..|...++..-+.+. +|..++-.- -..==|+-++..+....++..-.++++|+.+|.-+..|.++...
T Consensus 366 ql~~le~~~~e~q~~~qe~~~e~eqLr~elaql---~a~r~q~eka~~~~ee~e~~~l~~e~ry~klkek~t~l~~~h~~ 442 (980)
T KOG0980|consen 366 QLLALEGELQEQQREAQENREEQEQLRNELAQL---LASRTQLEKAQVLVEEAENKALAAENRYEKLKEKYTELRQEHAD 442 (980)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHH---HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 556677777766654433222 232222100 00011233333233333344444455555555555554444444
Q ss_pred HHHHHHHH
Q 019954 181 LKAEVLKL 188 (333)
Q Consensus 181 L~~E~~~l 188 (333)
|...+...
T Consensus 443 lL~K~~di 450 (980)
T KOG0980|consen 443 LLRKYDDI 450 (980)
T ss_pred HHHHHHHH
Confidence 44443333
No 221
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=24.66 E-value=3.3e+02 Score=21.83 Aligned_cols=33 Identities=15% Similarity=0.193 Sum_probs=17.7
Q ss_pred HHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 157 YDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 157 ~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
...|....+.++.....|..+|++|+.|-..-.
T Consensus 34 n~~L~~e~~~~~~~r~~L~~en~qLk~E~~~Wq 66 (79)
T PRK15422 34 NNSLSQEVQNAQHQREELERENNHLKEQQNGWQ 66 (79)
T ss_pred HHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHH
Confidence 344444455555555666666666666544433
No 222
>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=24.65 E-value=54 Score=24.30 Aligned_cols=27 Identities=26% Similarity=0.599 Sum_probs=21.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 122 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
...++|..||++.+.|..|-+ |.+|..
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 356899999999999999964 555554
No 223
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=24.49 E-value=1.5e+02 Score=25.20 Aligned_cols=36 Identities=25% Similarity=0.245 Sum_probs=29.3
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLK 187 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~ 187 (333)
.+-++...|++....|-.+|..|.-||++|+..+..
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 445566778888888999999999999999988766
No 224
>PRK12541 RNA polymerase sigma factor; Provisional
Probab=24.40 E-value=1.2e+02 Score=25.67 Aligned_cols=46 Identities=20% Similarity=0.109 Sum_probs=31.5
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..|..+|.-.|-.. ..-.++|..+|++...|+++...-|.+.|+
T Consensus 113 L~~~~r~v~~l~~~~~-----~s~~eIA~~lgis~~tv~~~l~Rar~~L~~ 158 (161)
T PRK12541 113 LPLERRNVLLLRDYYG-----FSYKEIAEMTGLSLAKVKIELHRGRKETKS 158 (161)
T ss_pred CCHHHHHHhhhHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHh
Confidence 6666666665544322 235689999999999999998766655554
No 225
>PRK14086 dnaA chromosomal replication initiation protein; Provisional
Probab=24.37 E-value=3.6e+02 Score=29.30 Aligned_cols=74 Identities=15% Similarity=0.321 Sum_probs=41.1
Q ss_pred CCHHHHHH-HHHHhCCC---------------chhhhhhhhhhHHHHHHHHHHHHHHHHHhhh--hhHHHhhHHHHHHHH
Q 019954 118 LEPERKIQ-LAKDLGLQ---------------PRQVAIWFQNRRARWKTKQLEKDYDVLQNSY--NSLKADYDNLFKEKE 179 (333)
Q Consensus 118 p~~~~r~~-LA~~LgLs---------------~rQVkvWFQNRRaK~Krkq~~ke~~~l~~~~--~~Lk~~~~~L~~Ene 179 (333)
++...... +|+.+|++ .|||.+|.+.+-..+.-.++.+.+. +..- -.-...-..+.+++.
T Consensus 524 it~d~I~~~Va~~f~v~~~dl~s~~R~~~i~~aRqiAMYL~r~lt~~Sl~~IG~~Fg--RdHSTV~~A~~kI~~~~~~d~ 601 (617)
T PRK14086 524 ITAAAIMAATADYFGLTVEDLCGTSRSRVLVTARQIAMYLCRELTDLSLPKIGQQFG--RDHTTVMHADRKIRALMAERR 601 (617)
T ss_pred CCHHHHHHHHHHHhCCCHHHHhCCCCCcccchHHHHHHHHHHHHcCCCHHHHHHHhC--CChhHHHHHHHHHHHHHHhCH
Confidence 55555554 57777755 3667777765555544444443332 1110 011112244667778
Q ss_pred HHHHHHHHHHHHHh
Q 019954 180 KLKAEVLKLTDKLQ 193 (333)
Q Consensus 180 ~L~~E~~~l~~~l~ 193 (333)
.|+.++..|+.+|.
T Consensus 602 ~l~~~V~~L~~~i~ 615 (617)
T PRK14086 602 SIYNQVTELTNRIK 615 (617)
T ss_pred HHHHHHHHHHHHHh
Confidence 88899988888774
No 226
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=24.36 E-value=2.1e+02 Score=29.02 Aligned_cols=37 Identities=30% Similarity=0.393 Sum_probs=26.0
Q ss_pred HHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 153 LEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 153 ~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
++++...++.....+..+...+..|.++++.|+.+|+
T Consensus 27 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 63 (398)
T PTZ00454 27 LEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQ 63 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445556666666777777777777788888877776
No 227
>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=24.19 E-value=2.9e+02 Score=23.55 Aligned_cols=49 Identities=27% Similarity=0.392 Sum_probs=0.0
Q ss_pred hHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 144 RRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 144 RRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
+-...+...++.++..++..|+.+..-++.-..+++.|+.-+..+|.-.
T Consensus 64 ~~~~~~~~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~my 112 (120)
T PF12325_consen 64 RALKKEVEELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMY 112 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHH
No 228
>cd04762 HTH_MerR-trunc Helix-Turn-Helix DNA binding domain of truncated MerR-like proteins. Proteins in this family mostly have a truncated helix-turn-helix (HTH) MerR-like domain. They lack a portion of the C-terminal region, called Wing 2 and the long dimerization helix that is typically present in MerR-like proteins. These truncated domains are found in response regulator receiver (REC) domain proteins (i.e., CheY), cytosine-C5 specific DNA methylases, IS607 transposase-like proteins, and RacA, a bacterial protein that anchors chromosomes to cell poles.
Probab=24.11 E-value=65 Score=21.09 Aligned_cols=24 Identities=21% Similarity=0.475 Sum_probs=20.2
Q ss_pred HHHHHHHhCCCchhhhhhhhhhHH
Q 019954 123 KIQLAKDLGLQPRQVAIWFQNRRA 146 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQNRRa 146 (333)
..++|+.||++.+.|..|.++.+.
T Consensus 3 ~~e~a~~lgvs~~tl~~~~~~g~~ 26 (49)
T cd04762 3 TKEAAELLGVSPSTLRRWVKEGKL 26 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHcCCC
Confidence 467899999999999999876554
No 229
>PRK05431 seryl-tRNA synthetase; Provisional
Probab=24.04 E-value=2.4e+02 Score=28.89 Aligned_cols=64 Identities=20% Similarity=0.261 Sum_probs=33.3
Q ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHh---hHHHHHHHHHHHHHHHHHHHHHhhhhhhhc
Q 019954 137 VAIWFQNRRARWKTKQLEKDYDVLQNSYNSLKAD---YDNLFKEKEKLKAEVLKLTDKLQVKEKESK 200 (333)
Q Consensus 137 VkvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~---~~~L~~Ene~L~~E~~~l~~~l~~~~~~~~ 200 (333)
|..+-+.|..+.+...++.+.+.+......++.. .+.|.++...|+.++..|..++..-+.+..
T Consensus 31 ~~ld~~~r~l~~~~~~lr~~rn~~sk~i~~~~~~~~~~~~l~~~~~~l~~~~~~~~~~~~~~~~~~~ 97 (425)
T PRK05431 31 LELDEERRELQTELEELQAERNALSKEIGQAKRKGEDAEALIAEVKELKEEIKALEAELDELEAELE 97 (425)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCcHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445454555555555555555554444432222 234666666666666666666665554443
No 230
>PRK12538 RNA polymerase sigma factor; Provisional
Probab=23.86 E-value=1.6e+02 Score=27.35 Aligned_cols=29 Identities=10% Similarity=0.140 Sum_probs=23.1
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 122 RKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
.-.++|..||++...|++..+.-|.+.|+
T Consensus 189 s~~EIA~~Lgis~~tVk~~l~RAr~kLr~ 217 (233)
T PRK12538 189 SNGEIAEVMDTTVAAVESLLKRGRQQLRD 217 (233)
T ss_pred CHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 35688999999999999998766665554
No 231
>KOG0977 consensus Nuclear envelope protein lamin, intermediate filament superfamily [Cell cycle control, cell division, chromosome partitioning; Nuclear structure]
Probab=23.79 E-value=2.2e+02 Score=30.54 Aligned_cols=41 Identities=29% Similarity=0.338 Sum_probs=31.2
Q ss_pred HHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 156 DYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 156 e~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
-...+++.+..+++....|..|+.+|+.|+.+|...|....
T Consensus 149 ~l~~leAe~~~~krr~~~le~e~~~Lk~en~rl~~~l~~~r 189 (546)
T KOG0977|consen 149 RLSELEAEINTLKRRIKALEDELKRLKAENSRLREELARAR 189 (546)
T ss_pred hhhhhhhHHHHHHHHHHHHHHHHHHHHHHhhhhHHHHHHHH
Confidence 34455666777788888888888888888888888887554
No 232
>PRK09644 RNA polymerase sigma factor SigM; Provisional
Probab=23.76 E-value=96 Score=26.42 Aligned_cols=46 Identities=20% Similarity=0.031 Sum_probs=31.0
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++...|- ......++|..+|++...|++|.+.-|.+.|+
T Consensus 109 L~~~~r~v~~l~~~-----~g~s~~eIA~~lgis~~tv~~~l~Rar~~Lr~ 154 (165)
T PRK09644 109 LPVIEAQAILLCDV-----HELTYEEAASVLDLKLNTYKSHLFRGRKRLKA 154 (165)
T ss_pred CCHHHHHHHHhHHH-----hcCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 55555555543322 22245789999999999999998766665554
No 233
>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=23.62 E-value=1.5e+02 Score=24.15 Aligned_cols=31 Identities=23% Similarity=0.263 Sum_probs=19.4
Q ss_pred HHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 159 VLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 159 ~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
.++.....|......+..+|..|..++..++
T Consensus 77 ~~~~~~~~L~~~l~~l~~eN~~L~~~i~~~r 107 (109)
T PF03980_consen 77 YKKKEREQLNARLQELEEENEALAEEIQEQR 107 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3344455666666677777777777766654
No 234
>TIGR02939 RpoE_Sigma70 RNA polymerase sigma factor RpoE. A sigma factor is a DNA-binding protein protein that binds to the DNA-directed RNA polymerase core to produce the holoenzyme capable of initiating transcription at specific sites. Different sigma factors act in vegetative growth, heat shock, extracytoplasmic functions (ECF), etc. This model represents the clade of sigma factors called RpoE. This protein may be called sigma-24, sigma-E factor, sigma-H factor, fecI-like sigma factor or alternative sigma factor AlgU.
Probab=23.47 E-value=82 Score=27.23 Aligned_cols=46 Identities=15% Similarity=-0.013 Sum_probs=29.6
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++.-.| .....-.++|..||+++..|+++...-|.+.|+
T Consensus 139 L~~~~r~v~~l~~-----~~~~s~~EIA~~lgis~~tv~~~l~rar~~Lr~ 184 (190)
T TIGR02939 139 LPEDLRTAITLRE-----LEGLSYEDIARIMDCPVGTVRSRIFRAREAIAI 184 (190)
T ss_pred CCHHHhhhhhhhh-----hcCCCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 4444444444332 233346789999999999999998655555443
No 235
>TIGR02983 SigE-fam_strep RNA polymerase sigma-70 factor, sigma-E family. This group of similar sigma-70 factors includes the sigE factor from Streptomyces coelicolor. The family appears to include a paralagous expansion in the Streptomycetes lineage, while related Actinomycetales have at most two representatives.
Probab=23.44 E-value=1.7e+02 Score=24.66 Aligned_cols=46 Identities=20% Similarity=0.192 Sum_probs=32.2
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-. ...-.++|..+|++...|+.+-..-|.+.|+
T Consensus 111 L~~~~r~i~~l~~~~-----g~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 156 (162)
T TIGR02983 111 LPARQRAVVVLRYYE-----DLSEAQVAEALGISVGTVKSRLSRALARLRE 156 (162)
T ss_pred CCHHHHHHhhhHHHh-----cCCHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 566666666555522 2235678999999999999988766666554
No 236
>PRK12518 RNA polymerase sigma factor; Provisional
Probab=23.19 E-value=86 Score=26.84 Aligned_cols=32 Identities=16% Similarity=0.125 Sum_probs=25.1
Q ss_pred CHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 119 EPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 119 ~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
....-.++|..+|+++..|++.+..-|.+.|+
T Consensus 135 ~g~s~~eIA~~lg~s~~tv~~~l~Rar~~L~~ 166 (175)
T PRK12518 135 EDLPQKEIAEILNIPVGTVKSRLFYARRQLRK 166 (175)
T ss_pred cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 33346789999999999999999766666655
No 237
>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=22.95 E-value=2.1e+02 Score=21.82 Aligned_cols=33 Identities=24% Similarity=0.364 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHH
Q 019954 152 QLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAE 184 (333)
Q Consensus 152 q~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E 184 (333)
+...+...+++..+.++.+++.|..|...|...
T Consensus 28 ~~~~~~~~~~~~~~~l~~en~~L~~ei~~l~~~ 60 (85)
T TIGR02209 28 QLNNELQKLQLEIDKLQKEWRDLQLEVAELSRH 60 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCH
Confidence 445566667777777888888888888887763
No 238
>PRK09047 RNA polymerase factor sigma-70; Validated
Probab=22.90 E-value=1.6e+02 Score=24.68 Aligned_cols=45 Identities=11% Similarity=0.035 Sum_probs=31.1
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
++..|..++.-.|-... .-.++|..||++...|++....-|.+.|
T Consensus 107 Lp~~~r~v~~l~~~~g~-----s~~EIA~~lgis~~tV~~~l~ra~~~Lr 151 (161)
T PRK09047 107 LPARQREAFLLRYWEDM-----DVAETAAAMGCSEGSVKTHCSRATHALA 151 (161)
T ss_pred CCHHHHHHHHHHHHhcC-----CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 67777776666543222 2578999999999999988765554444
No 239
>TIGR00721 tfx DNA-binding protein, Tfx family. Tfx from Methanobacterium thermoautotrophicum is associated with the operon for molybdenum formyl-methanofuran dehydrogenase and binds a DNA sequence near its promoter.
Probab=22.75 E-value=3e+02 Score=24.04 Aligned_cols=47 Identities=19% Similarity=0.134 Sum_probs=34.5
Q ss_pred cccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 98 RRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 98 ~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
.-++..|..+|.-.+ .. ....++|..||++...|+.|-+.-|.+.++
T Consensus 5 ~~Lte~qr~VL~Lr~--~G----lTq~EIAe~LgiS~stV~~~e~ra~kkLr~ 51 (137)
T TIGR00721 5 TFLTERQIKVLELRE--KG----LSQKEIAKELKTTRANVSAIEKRAMENIEK 51 (137)
T ss_pred CCCCHHHHHHHHHHH--cC----CCHHHHHHHHCcCHHHHHHHHHhHHHHHHH
Confidence 457888988887742 22 256789999999999998887665555553
No 240
>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=22.56 E-value=3.4e+02 Score=20.34 Aligned_cols=44 Identities=25% Similarity=0.373 Sum_probs=26.2
Q ss_pred HHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 149 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 149 Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
|..++..+...|....+.|..+...|..+....+.|..+....|
T Consensus 4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~Rl 47 (56)
T PF04728_consen 4 KIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRL 47 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455566666666666666666666666666666655554444
No 241
>PRK06811 RNA polymerase factor sigma-70; Validated
Probab=22.51 E-value=1.1e+02 Score=26.84 Aligned_cols=47 Identities=17% Similarity=0.272 Sum_probs=32.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTK 151 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krk 151 (333)
+++.+..++.-.|-. .....++|..+|++...|+...+.-|.+.|+.
T Consensus 132 L~~~~r~i~~l~~~~-----g~s~~EIAe~lgis~~~V~~~l~Ra~~~Lr~~ 178 (189)
T PRK06811 132 LEKLDREIFIRRYLL-----GEKIEEIAKKLGLTRSAIDNRLSRGRKKLQKN 178 (189)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHHc
Confidence 666676666654432 22357899999999999998877666655553
No 242
>PRK12537 RNA polymerase sigma factor; Provisional
Probab=22.43 E-value=1.6e+02 Score=25.58 Aligned_cols=46 Identities=13% Similarity=0.224 Sum_probs=31.0
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++...|-.. ....++|..+|++...|++|...-|.+.|+
T Consensus 134 L~~~~r~i~~l~~~~~-----~s~~eIA~~lgis~~tV~~~l~ra~~~Lr~ 179 (182)
T PRK12537 134 LEPARRNCILHAYVDG-----CSHAEIAQRLGAPLGTVKAWIKRSLKALRE 179 (182)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCCChhhHHHHHHHHHHHHHH
Confidence 6666666555544222 235689999999999999998755554443
No 243
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=22.42 E-value=3.2e+02 Score=28.75 Aligned_cols=25 Identities=12% Similarity=0.129 Sum_probs=11.1
Q ss_pred hhhhhHHHhhHHHHHHHHHHHHHHH
Q 019954 162 NSYNSLKADYDNLFKEKEKLKAEVL 186 (333)
Q Consensus 162 ~~~~~Lk~~~~~L~~Ene~L~~E~~ 186 (333)
.....+.+..+.|..|+..|+.++.
T Consensus 97 aq~~dle~KIkeLEaE~~~Lk~Ql~ 121 (475)
T PRK13729 97 KQRGDDQRRIEKLGQDNAALAEQVK 121 (475)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHH
Confidence 3333344444444444455544443
No 244
>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=22.21 E-value=89 Score=26.00 Aligned_cols=33 Identities=18% Similarity=0.111 Sum_probs=25.3
Q ss_pred CCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHH
Q 019954 117 KLEPERKIQLAKDLGLQPRQVAIWFQNRRARWK 149 (333)
Q Consensus 117 ~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~K 149 (333)
|.....-.++|..+|+++..|+++...-|.+.|
T Consensus 118 ~~~g~s~~eIA~~lgis~~tv~~~l~Ra~~~Lr 150 (154)
T TIGR02950 118 EFKEFSYKEIAELLNLSLAKVKSNLFRARKELK 150 (154)
T ss_pred hhccCcHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 344556788999999999999998875555544
No 245
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=22.07 E-value=91 Score=30.51 Aligned_cols=38 Identities=34% Similarity=0.377 Sum_probs=34.0
Q ss_pred hccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 113 EVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 113 ~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
..++|+....+..|+....|+-.||.+||-|.|.+.+.
T Consensus 117 ~~~~~~~k~~~~ll~~~~~~~~~~~~~~~~~a~r~~~~ 154 (342)
T KOG0773|consen 117 RLNPYPSKLEKILLAVITKLTLTQVSTWFANARRRLKK 154 (342)
T ss_pred hhccCchHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHh
Confidence 45889999999999999999999999999998877665
No 246
>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=22.02 E-value=4.2e+02 Score=21.27 Aligned_cols=35 Identities=17% Similarity=0.095 Sum_probs=27.6
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhh
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNR 144 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNR 144 (333)
.++|+..++..| .....++.+|++-..|+-+|..+
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 446888888776 35566899999999999999753
No 247
>cd04763 HTH_MlrA-like Helix-Turn-Helix DNA binding domain of MlrA-like transcription regulators. Helix-turn-helix (HTH) transcription regulator MlrA (merR-like regulator A) and related proteins, N-terminal domain. The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. Its close homolog, CarA from Myxococcus xanthus, is involved in activation of the carotenoid biosynthesis genes by light. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen
Probab=22.02 E-value=70 Score=23.53 Aligned_cols=21 Identities=19% Similarity=0.360 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCchhhhhhhhh
Q 019954 123 KIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQN 143 (333)
..++|+.+|++++.++.|.+.
T Consensus 3 i~e~A~~~gVs~~tlr~ye~~ 23 (68)
T cd04763 3 IGEVALLTGIKPHVLRAWERE 23 (68)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999764
No 248
>PF14662 CCDC155: Coiled-coil region of CCDC155
Probab=21.98 E-value=3.8e+02 Score=24.95 Aligned_cols=39 Identities=28% Similarity=0.348 Sum_probs=16.1
Q ss_pred HHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 154 EKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 154 ~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
..+.+.|+..+..|..+.+.+......|-.+...|+.++
T Consensus 101 ~~~i~~Lqeen~kl~~e~~~lk~~~~eL~~~~~~Lq~Ql 139 (193)
T PF14662_consen 101 VAEIETLQEENGKLLAERDGLKKRSKELATEKATLQRQL 139 (193)
T ss_pred HHHHHHHHHHHhHHHHhhhhHHHHHHHHHHhhHHHHHHH
Confidence 333334444444444444444444444444444444444
No 249
>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=21.98 E-value=2.5e+02 Score=27.20 Aligned_cols=16 Identities=50% Similarity=0.495 Sum_probs=7.1
Q ss_pred HHHHHHHHHHHHHHHH
Q 019954 173 NLFKEKEKLKAEVLKL 188 (333)
Q Consensus 173 ~L~~Ene~L~~E~~~l 188 (333)
.|.+||++|+.|+.+|
T Consensus 70 ~l~~EN~~Lr~e~~~l 85 (283)
T TIGR00219 70 NLEYENYKLRQELLKK 85 (283)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3444444444444444
No 250
>PRK06986 fliA flagellar biosynthesis sigma factor; Validated
Probab=21.94 E-value=1.1e+02 Score=28.05 Aligned_cols=46 Identities=15% Similarity=0.170 Sum_probs=34.1
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|... ..-.++|..+|++...|+.+...-|.+.|+
T Consensus 185 L~~~~r~vl~l~~~~g-----~s~~EIA~~lgis~~tV~~~~~ra~~~Lr~ 230 (236)
T PRK06986 185 LPEREQLVLSLYYQEE-----LNLKEIGAVLGVSESRVSQIHSQAIKRLRA 230 (236)
T ss_pred CCHHHHHHHHhHhccC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 5666777776665322 246789999999999999999876666665
No 251
>cd04782 HTH_BltR Helix-Turn-Helix DNA binding domain of the BltR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BltR (BmrR-like transporter) of Bacillus subtilis, and related proteins; N-terminal domain. Blt, like Bmr, is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. These regulators are comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains are often unrelated and bind specific coactivator molecules. They share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=21.92 E-value=4.1e+02 Score=21.11 Aligned_cols=35 Identities=29% Similarity=0.474 Sum_probs=24.8
Q ss_pred CCcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhh
Q 019954 96 KKRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 96 kR~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQN 143 (333)
..|.|+..++..|.. ....+.+|++-..|+.-+.+
T Consensus 35 gyR~Y~~~~~~~l~~-------------I~~lr~~G~~l~eI~~~l~~ 69 (97)
T cd04782 35 GYRYYTLEQFEQLDI-------------ILLLKELGISLKEIKDYLDN 69 (97)
T ss_pred CCccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhc
Confidence 355699999888743 33467788888888776654
No 252
>PF14645 Chibby: Chibby family
Probab=21.91 E-value=2.3e+02 Score=23.95 Aligned_cols=16 Identities=25% Similarity=0.370 Sum_probs=6.2
Q ss_pred hhHHHHHHHHHHHHHH
Q 019954 170 DYDNLFKEKEKLKAEV 185 (333)
Q Consensus 170 ~~~~L~~Ene~L~~E~ 185 (333)
++..|.+||.-|+-++
T Consensus 79 ~n~~L~EENN~Lklk~ 94 (116)
T PF14645_consen 79 ENQQLEEENNLLKLKI 94 (116)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 3333344444433333
No 253
>PRK10722 hypothetical protein; Provisional
Probab=21.90 E-value=7.3e+02 Score=23.96 Aligned_cols=89 Identities=22% Similarity=0.297 Sum_probs=48.1
Q ss_pred HHHHHHHhhhhccCCCCHHHHHHHHHHhCCC----chhhhhhhhhhHHH-HHHHHHHHHHHHHHhhhhhH----HHhhHH
Q 019954 103 DQVQFLEKSFEVENKLEPERKIQLAKDLGLQ----PRQVAIWFQNRRAR-WKTKQLEKDYDVLQNSYNSL----KADYDN 173 (333)
Q Consensus 103 ~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs----~rQVkvWFQNRRaK-~Krkq~~ke~~~l~~~~~~L----k~~~~~ 173 (333)
++........-.+..++..+|..+...|.-. +..|+-=+|=-|.+ .-.-++..+ +..|.+| ..+.+.
T Consensus 105 w~~afkq~ILL~~a~~t~~err~~l~rl~~~~~~~p~~lrPL~qlwr~~Q~l~l~LaeE----r~Ry~rLQq~sD~qlD~ 180 (247)
T PRK10722 105 WQNAFKQGILLADAKITPAERRQIVERLNAYSLQIPAQVRPLYQLWRDGQALQLALAEE----RQRYQKLQQSSDSELDA 180 (247)
T ss_pred HHHHHHHHHHHcCCCCChHHHHHHHHHHhhcccccchhhhHHHHHHHHhhHHHHhHHHH----HHHHHHHhhccHHHHHH
Confidence 3333334444456677788888877766533 22333222222222 111111111 2233333 456778
Q ss_pred HHHHHHHHHHHHHHHHHHHhhh
Q 019954 174 LFKEKEKLKAEVLKLTDKLQVK 195 (333)
Q Consensus 174 L~~Ene~L~~E~~~l~~~l~~~ 195 (333)
|.+.+.+|+.++.....||..-
T Consensus 181 lrqq~~~Lq~~L~~t~rKLEnL 202 (247)
T PRK10722 181 LRQQQQRLQYQLELTTRKLENL 202 (247)
T ss_pred HHHHHHHHHHHHHHHHHHHHHH
Confidence 8888888888888888888754
No 254
>cd04764 HTH_MlrA-like_sg1 Helix-Turn-Helix DNA binding domain of putative MlrA-like transcription regulators. Putative helix-turn-helix (HTH) MlrA-like transcription regulators (subgroup 1). The MlrA protein, also known as YehV, has been shown to control cell-cell aggregation by co-regulating the expression of curli and extracellular matrix production in Escherichia coli and Salmonella typhimurium. These proteins belong to the MerR superfamily of transcription regulators that promote expression of several stress regulon genes by reconfiguring the spacer between the -35 and -10 promoter elements. Their conserved N-terminal domains contain predicted HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules. Many MlrA-like proteins in this group appear to lack the long dimerization helix seen in the N-terminal domains of typical MerR-like proteins.
Probab=21.84 E-value=74 Score=23.28 Aligned_cols=21 Identities=10% Similarity=0.347 Sum_probs=18.2
Q ss_pred HHHHHHHhCCCchhhhhhhhh
Q 019954 123 KIQLAKDLGLQPRQVAIWFQN 143 (333)
Q Consensus 123 r~~LA~~LgLs~rQVkvWFQN 143 (333)
..++|+.+|++++.++.|-++
T Consensus 3 i~evA~~~gvs~~tlR~~~~~ 23 (67)
T cd04764 3 IKEVSEIIGVKPHTLRYYEKE 23 (67)
T ss_pred HHHHHHHHCcCHHHHHHHHHh
Confidence 357899999999999999765
No 255
>PRK12543 RNA polymerase sigma factor; Provisional
Probab=21.80 E-value=1.5e+02 Score=25.69 Aligned_cols=46 Identities=11% Similarity=0.042 Sum_probs=30.9
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++.-.|-. ...-.++|..||++...|++....-|.+.|+
T Consensus 118 Lp~~~r~i~~l~~~e-----~~s~~EIA~~lgis~~tV~~~l~ra~~~Lr~ 163 (179)
T PRK12543 118 LPYKLRQVIILRYLH-----DYSQEEIAQLLQIPIGTVKSRIHAALKKLRQ 163 (179)
T ss_pred CCHHHHHHHHHHHHc-----cCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 555555555443322 2235688999999999999888766666655
No 256
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=21.65 E-value=3.7e+02 Score=28.80 Aligned_cols=27 Identities=26% Similarity=0.397 Sum_probs=10.5
Q ss_pred HHHHHhhhhhHHHhhHHHHHHHHHHHH
Q 019954 157 YDVLQNSYNSLKADYDNLFKEKEKLKA 183 (333)
Q Consensus 157 ~~~l~~~~~~Lk~~~~~L~~Ene~L~~ 183 (333)
...|+..+..+......+..|++.|..
T Consensus 187 ~e~L~~~~kel~~~~e~l~~E~~~L~~ 213 (546)
T PF07888_consen 187 MEQLKQQQKELTESSEELKEERESLKE 213 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333333333333333333
No 257
>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=21.58 E-value=62 Score=21.84 Aligned_cols=18 Identities=33% Similarity=0.486 Sum_probs=14.9
Q ss_pred HHHHHHhCCCchhhhhhh
Q 019954 124 IQLAKDLGLQPRQVAIWF 141 (333)
Q Consensus 124 ~~LA~~LgLs~rQVkvWF 141 (333)
-++|+.+|++.+.|+.|=
T Consensus 3 ~e~A~~~gvs~~tlR~ye 20 (38)
T PF00376_consen 3 GEVAKLLGVSPRTLRYYE 20 (38)
T ss_dssp HHHHHHHTS-HHHHHHHH
T ss_pred HHHHHHHCCCHHHHHHHH
Confidence 478999999999999984
No 258
>smart00787 Spc7 Spc7 kinetochore protein. This domain is found in cell division proteins which are required for kinetochore-spindle association.
Probab=21.50 E-value=3.8e+02 Score=26.42 Aligned_cols=48 Identities=38% Similarity=0.616 Sum_probs=28.1
Q ss_pred hhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHH
Q 019954 138 AIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTD 190 (333)
Q Consensus 138 kvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~ 190 (333)
++||. ||.+.++.-.+.|......|+.+...|.+..+.+..-+..|++
T Consensus 132 ~~WYe-----WR~kllegLk~~L~~~~~~l~~D~~~L~~~~~~l~~~~~~l~~ 179 (312)
T smart00787 132 KMWYE-----WRMKLLEGLKEGLDENLEGLKEDYKLLMKELELLNSIKPKLRD 179 (312)
T ss_pred HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 36986 5555566666666666666666666655555444444444433
No 259
>COG1394 NtpD Archaeal/vacuolar-type H+-ATPase subunit D [Energy production and conversion]
Probab=21.48 E-value=4.1e+02 Score=24.92 Aligned_cols=49 Identities=18% Similarity=0.296 Sum_probs=37.6
Q ss_pred HHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHh
Q 019954 145 RARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQ 193 (333)
Q Consensus 145 RaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~ 193 (333)
+.|.|-+..++-+..|+..-+.|..++-++..+...++.++.+......
T Consensus 14 ~lk~rLkla~rg~~lLk~Krd~L~~ef~~i~~~~~~~r~e~~~~~~~a~ 62 (211)
T COG1394 14 RLKRRLKLARRGHKLLKLKRDALIMEFRAIVKEAKELREELEKELEEAY 62 (211)
T ss_pred HHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555666777888888888999999999999999998887665544
No 260
>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=21.46 E-value=1.1e+02 Score=27.69 Aligned_cols=46 Identities=15% Similarity=0.160 Sum_probs=33.7
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..+|...|-... ...++|..+|++...|+.+...-+.+.|+
T Consensus 176 L~~~~r~il~l~y~~~~-----s~~eIA~~lgis~~tV~~~~~ra~~~Lr~ 221 (224)
T TIGR02479 176 LSEREQLVLSLYYYEEL-----NLKEIGEVLGLTESRVSQIHSQALKKLRA 221 (224)
T ss_pred CCHHHHHHHHHHHhCCC-----CHHHHHHHhCCCHHHHHHHHHHHHHHHHH
Confidence 67788888877764332 45789999999999999887655554443
No 261
>PRK10403 transcriptional regulator NarP; Provisional
Probab=21.36 E-value=1.1e+02 Score=25.84 Aligned_cols=46 Identities=17% Similarity=0.183 Sum_probs=35.0
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
.+|..+..+|+..... ..+.+||+.++++++.|++..+|=|.|...
T Consensus 153 ~Lt~~e~~vl~~~~~g------~s~~~ia~~l~~s~~tv~~~~~~i~~kl~~ 198 (215)
T PRK10403 153 VLTERELDVLHELAQG------LSNKQIASVLNISEQTVKVHIRNLLRKLNV 198 (215)
T ss_pred cCCHHHHHHHHHHHCC------CCHHHHHHHcCCCHHHHHHHHHHHHHHcCC
Confidence 3788888888765442 336788999999999999998877666544
No 262
>PF04111 APG6: Autophagy protein Apg6; InterPro: IPR007243 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 []. Apg6/Vps30p has two distinct functions in the autophagic process, either associated with the membrane or in a retrieval step of the carboxypeptidase Y sorting pathway [].; GO: 0006914 autophagy; PDB: 3Q8T_A 3VP7_A 4DDP_A.
Probab=21.35 E-value=3.2e+02 Score=26.88 Aligned_cols=10 Identities=20% Similarity=0.072 Sum_probs=4.1
Q ss_pred cccccccCCC
Q 019954 244 SAKSDIFDSD 253 (333)
Q Consensus 244 s~~s~~~d~~ 253 (333)
++.|-|.+-+
T Consensus 202 Gs~S~I~~~~ 211 (314)
T PF04111_consen 202 GSFSKIEKLE 211 (314)
T ss_dssp GGG-EEEECS
T ss_pred CCCCEEEEec
Confidence 3445454443
No 263
>PF13700 DUF4158: Domain of unknown function (DUF4158)
Probab=21.29 E-value=4.3e+02 Score=22.96 Aligned_cols=42 Identities=21% Similarity=0.409 Sum_probs=30.0
Q ss_pred cCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHH
Q 019954 115 ENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKD 156 (333)
Q Consensus 115 ~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke 156 (333)
..-+......-||++||+.+..+.......+++.+..+.-.+
T Consensus 64 ~~~~p~~~i~~va~ql~~~~~~~~~y~~r~~T~~~h~~~I~~ 105 (166)
T PF13700_consen 64 PEDIPKADIEYVAKQLGLPPSDLSSYAQRSRTRYRHRAEIRE 105 (166)
T ss_pred cccCCHHHHHHHHHHhCCchHHHHhhhhhhhHHHHHHHHHHH
Confidence 334556778889999999998888888766666665444333
No 264
>cd01107 HTH_BmrR Helix-Turn-Helix DNA binding domain of the BmrR transcription regulator. Helix-turn-helix (HTH) multidrug-efflux transporter transcription regulator, BmrR and YdfL of Bacillus subtilis, and related proteins; N-terminal domain. Bmr is a membrane protein which causes the efflux of a variety of toxic substances and antibiotics. BmrR is comprised of two distinct domains that harbor a regulatory (effector-binding) site and an active (DNA-binding) site. The conserved N-terminal domain contains a winged HTH motif that mediates DNA binding, while the C-terminal domain binds coactivating, toxic compounds. BmrR shares the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=20.94 E-value=4.6e+02 Score=21.25 Aligned_cols=37 Identities=19% Similarity=0.363 Sum_probs=27.4
Q ss_pred CcccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHH
Q 019954 97 KRRLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRA 146 (333)
Q Consensus 97 R~rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRa 146 (333)
.|.|+..++..|. .....+.+|++-..|+-.+.....
T Consensus 37 yR~Y~~~~i~~l~-------------~I~~lr~~G~sl~~i~~l~~~~~~ 73 (108)
T cd01107 37 YRYYSAEQLERLN-------------RIKYLRDLGFPLEEIKEILDADND 73 (108)
T ss_pred ccccCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcCCH
Confidence 4569999888873 334467789999999988876543
No 265
>PRK05657 RNA polymerase sigma factor RpoS; Validated
Probab=20.72 E-value=1.5e+02 Score=29.20 Aligned_cols=51 Identities=20% Similarity=0.253 Sum_probs=38.0
Q ss_pred ccChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 99 RLTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 99 rft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++..|..+|...|.-. +.......+||..||++...|+.+...-+.|.|+
T Consensus 262 ~L~~~~R~vl~lrygL~-~~e~~s~~EIA~~Lgis~~tV~~~~~rAl~kLr~ 312 (325)
T PRK05657 262 ELNDKQREVLARRFGLL-GYEAATLEDVAREIGLTRERVRQIQVEALRRLRE 312 (325)
T ss_pred cCCHHHHHHHHHHhccC-CCCCcCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 38888988998877332 2234456889999999999999998766655554
No 266
>TIGR02954 Sig70_famx3 RNA polymerase sigma-70 factor, TIGR02954 family. This group of sigma factors are members of the sigma-70 family (TIGR02937). They and appear by homology, tree building, bidirectional best hits and one-to-a-genome distribution, to represent a conserved family. This family is found in certain Bacillus and Clostridium species.
Probab=20.71 E-value=1.8e+02 Score=24.79 Aligned_cols=46 Identities=9% Similarity=0.053 Sum_probs=31.8
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
++..+..++...|-.. ....++|..||+++..|+++...-|.+.|+
T Consensus 120 L~~~~r~i~~l~~~~g-----~s~~eiA~~lgis~~tv~~~l~Ra~~~Lr~ 165 (169)
T TIGR02954 120 LNDKYQTAIILRYYHD-----LTIKEIAEVMNKPEGTVKTYLHRALKKLKK 165 (169)
T ss_pred CCHHHhHHHHHHHHcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 6666666665554332 235688999999999999887655555444
No 267
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=20.70 E-value=4.5e+02 Score=21.84 Aligned_cols=25 Identities=24% Similarity=0.267 Sum_probs=13.8
Q ss_pred HHhhHHHHHHHHHHHHHHHHHHHHH
Q 019954 168 KADYDNLFKEKEKLKAEVLKLTDKL 192 (333)
Q Consensus 168 k~~~~~L~~Ene~L~~E~~~l~~~l 192 (333)
+.-...|.+|....+.++.+|.+.|
T Consensus 75 ~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 75 KKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3333445555566666666665544
No 268
>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=20.49 E-value=4.7e+02 Score=22.72 Aligned_cols=51 Identities=29% Similarity=0.403 Sum_probs=32.3
Q ss_pred HHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhhhhh
Q 019954 149 KTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKEKES 199 (333)
Q Consensus 149 Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~~~~ 199 (333)
+.+.+......+...+..|...+..|..+.+++..++..++.++...++..
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 344555555555566666777777777777777777777777666555443
No 269
>KOG3863 consensus bZIP transcription factor NRF1 [Transcription]
Probab=20.40 E-value=3.8e+02 Score=29.10 Aligned_cols=37 Identities=16% Similarity=0.362 Sum_probs=24.1
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHHHHHhhhh
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLTDKLQVKE 196 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~~~l~~~~ 196 (333)
|....++|+.+-+.|+.|...+..++..++.+|...-
T Consensus 516 LE~ev~~l~~eKeqLl~Er~~~d~~L~~~kqqls~L~ 552 (604)
T KOG3863|consen 516 LEDEVEKLQKEKEQLLRERDELDSTLGVMKQQLSELY 552 (604)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4445556666667777777777777777777666443
No 270
>PF08317 Spc7: Spc7 kinetochore protein; InterPro: IPR013253 This entry consists of cell division proteins which are required for kinetochore-spindle association [].
Probab=20.35 E-value=4.3e+02 Score=25.87 Aligned_cols=47 Identities=30% Similarity=0.564 Sum_probs=26.9
Q ss_pred hhhhhhhHHHHHHHHHHHHHHHHHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 138 AIWFQNRRARWKTKQLEKDYDVLQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 138 kvWFQNRRaK~Krkq~~ke~~~l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
+.||. ||.+....-...|......|+.+...|.+..+.|..-+.+|.
T Consensus 137 ~~WYe-----WR~~ll~gl~~~L~~~~~~L~~D~~~L~~~~~~l~~~~~~l~ 183 (325)
T PF08317_consen 137 KMWYE-----WRMQLLEGLKEGLEENLELLQEDYAKLDKQLEQLDELLPKLR 183 (325)
T ss_pred HHHHH-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 35875 555555666666666666666666555555544444444443
No 271
>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=20.31 E-value=2.5e+02 Score=22.81 Aligned_cols=30 Identities=20% Similarity=0.284 Sum_probs=20.1
Q ss_pred HHhhhhhHHHhhHHHHHHHHHHHHHHHHHH
Q 019954 160 LQNSYNSLKADYDNLFKEKEKLKAEVLKLT 189 (333)
Q Consensus 160 l~~~~~~Lk~~~~~L~~Ene~L~~E~~~l~ 189 (333)
+....+.|..++..|..|++.|+.++...+
T Consensus 47 wek~v~~L~~e~~~l~~E~e~L~~~l~~e~ 76 (87)
T PF12709_consen 47 WEKKVDELENENKALKRENEQLKKKLDTER 76 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 455566677777777777777777665443
No 272
>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=20.30 E-value=98 Score=22.17 Aligned_cols=37 Identities=19% Similarity=0.260 Sum_probs=23.4
Q ss_pred HHHHHHHHhCCCchhhhhhhhhhHHHHHHHHHHHHHHH
Q 019954 122 RKIQLAKDLGLQPRQVAIWFQNRRARWKTKQLEKDYDV 159 (333)
Q Consensus 122 ~r~~LA~~LgLs~rQVkvWFQNRRaK~Krkq~~ke~~~ 159 (333)
....+|..+|++..+|.-|-.++| .-....+.+-.+.
T Consensus 14 t~~~~a~~~~i~~~~i~~~e~g~~-~~~~~~l~~i~~~ 50 (64)
T PF12844_consen 14 TQKDLAEKLGISRSTISKIENGKR-KPSVSTLKKIAEA 50 (64)
T ss_dssp -HHHHHHHHTS-HHHHHHHHTTSS---BHHHHHHHHHH
T ss_pred CHHHHHHHHCcCHHHHHHHHCCCc-CCCHHHHHHHHHH
Confidence 356788999999999999998877 4444444433333
No 273
>smart00027 EH Eps15 homology domain. Pair of EF hand motifs that recognise proteins containing Asn-Pro-Phe (NPF) sequences.
Probab=20.29 E-value=1.8e+02 Score=22.81 Aligned_cols=43 Identities=12% Similarity=0.185 Sum_probs=32.3
Q ss_pred cChHHHHHHHhhhhc-----cCCCCHHHHHHHHHHhCCCchhhhhhhh
Q 019954 100 LTVDQVQFLEKSFEV-----ENKLEPERKIQLAKDLGLQPRQVAIWFQ 142 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~-----~~~p~~~~r~~LA~~LgLs~rQVkvWFQ 142 (333)
++.+|+..|...|.. ..+.+..+...+-..+|++...|+.+|.
T Consensus 4 ls~~~~~~l~~~F~~~D~d~~G~Is~~el~~~l~~~~~~~~ev~~i~~ 51 (96)
T smart00027 4 ISPEDKAKYEQIFRSLDKNQDGTVTGAQAKPILLKSGLPQTLLAKIWN 51 (96)
T ss_pred CCHHHHHHHHHHHHHhCCCCCCeEeHHHHHHHHHHcCCCHHHHHHHHH
Confidence 678899999999875 2357777777776778888877776664
No 274
>PRK06930 positive control sigma-like factor; Validated
Probab=20.05 E-value=2.2e+02 Score=25.41 Aligned_cols=46 Identities=11% Similarity=0.035 Sum_probs=33.0
Q ss_pred cChHHHHHHHhhhhccCCCCHHHHHHHHHHhCCCchhhhhhhhhhHHHHHH
Q 019954 100 LTVDQVQFLEKSFEVENKLEPERKIQLAKDLGLQPRQVAIWFQNRRARWKT 150 (333)
Q Consensus 100 ft~~Ql~~LE~~F~~~~~p~~~~r~~LA~~LgLs~rQVkvWFQNRRaK~Kr 150 (333)
+++.+..++.-.|... ..-.++|..+|++...|+.+...-|.+.++
T Consensus 115 L~~rer~V~~L~~~eg-----~s~~EIA~~lgiS~~tVk~~l~Ra~~kLr~ 160 (170)
T PRK06930 115 LTEREKEVYLMHRGYG-----LSYSEIADYLNIKKSTVQSMIERAEKKIAR 160 (170)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHHHHH
Confidence 6777777666544322 235678999999999999998866666654
Done!