Query 025886
Match_columns 247
No_of_seqs 245 out of 1428
Neff 5.6
Searched_HMMs 46136
Date Fri Mar 29 10:39:58 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/025886.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/025886hhsearch_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 6.8E-23 1.5E-27 178.6 8.9 114 30-143 50-164 (198)
2 KOG0488 Transcription factor B 99.7 2.1E-17 4.6E-22 152.9 6.0 66 24-89 166-231 (309)
3 KOG0489 Transcription factor z 99.7 1.3E-17 2.7E-22 151.0 2.3 62 28-89 157-218 (261)
4 KOG0842 Transcription factor t 99.7 8.1E-17 1.8E-21 148.3 7.3 70 27-96 150-219 (307)
5 KOG0843 Transcription factor E 99.6 1.1E-16 2.3E-21 137.1 4.9 65 28-92 100-164 (197)
6 KOG0850 Transcription factor D 99.6 2.3E-16 5.1E-21 139.3 6.2 65 23-87 115-179 (245)
7 KOG0492 Transcription factor M 99.6 5.4E-16 1.2E-20 135.4 7.6 63 27-89 141-203 (246)
8 KOG0487 Transcription factor A 99.6 5.9E-16 1.3E-20 142.7 7.0 64 27-90 232-295 (308)
9 KOG0485 Transcription factor N 99.6 9.2E-16 2E-20 134.8 5.9 64 26-89 100-163 (268)
10 KOG0484 Transcription factor P 99.6 1.2E-15 2.6E-20 120.6 4.6 63 26-88 13-75 (125)
11 PF00046 Homeobox: Homeobox do 99.6 1.4E-15 3.1E-20 106.3 3.6 57 31-87 1-57 (57)
12 KOG2251 Homeobox transcription 99.5 6.2E-15 1.3E-19 129.7 5.2 66 25-90 32-97 (228)
13 KOG0494 Transcription factor C 99.5 9.1E-15 2E-19 131.4 5.5 70 27-96 137-207 (332)
14 KOG0493 Transcription factor E 99.5 2.9E-14 6.3E-19 128.3 5.3 60 31-90 247-306 (342)
15 KOG0848 Transcription factor C 99.5 1.1E-14 2.3E-19 131.4 2.5 58 32-89 201-258 (317)
16 smart00389 HOX Homeodomain. DN 99.4 7.6E-14 1.6E-18 96.7 3.7 55 32-86 2-56 (56)
17 cd00086 homeodomain Homeodomai 99.4 1E-13 2.2E-18 96.6 4.1 56 32-87 2-57 (59)
18 TIGR01565 homeo_ZF_HD homeobox 99.4 5.6E-13 1.2E-17 95.4 5.8 52 31-82 2-57 (58)
19 COG5576 Homeodomain-containing 99.4 4.2E-13 9.1E-18 113.4 5.5 63 28-90 49-111 (156)
20 KOG0486 Transcription factor P 99.3 1.5E-12 3.2E-17 119.8 5.3 63 28-90 110-172 (351)
21 KOG0491 Transcription factor B 99.3 2.3E-13 4.9E-18 115.4 -0.1 61 29-89 99-159 (194)
22 KOG3802 Transcription factor O 99.3 2.3E-12 5E-17 121.7 5.5 60 29-88 293-352 (398)
23 KOG0844 Transcription factor E 99.3 9.7E-13 2.1E-17 120.7 2.4 64 28-91 179-242 (408)
24 KOG4577 Transcription factor L 99.3 4.9E-12 1.1E-16 115.4 4.8 98 29-127 166-263 (383)
25 KOG0847 Transcription factor, 99.1 2.5E-11 5.4E-16 107.3 1.5 60 29-88 166-225 (288)
26 KOG0490 Transcription factor, 99.1 9.7E-11 2.1E-15 101.7 3.5 63 27-89 57-119 (235)
27 KOG0849 Transcription factor P 98.8 4.4E-09 9.5E-14 99.3 4.1 68 22-89 168-235 (354)
28 KOG1168 Transcription factor A 98.7 6.3E-09 1.4E-13 95.3 3.7 60 30-89 309-368 (385)
29 KOG0775 Transcription factor S 98.5 7E-08 1.5E-12 87.8 3.8 51 37-87 183-233 (304)
30 KOG0774 Transcription factor P 98.1 1.6E-06 3.6E-11 78.7 3.3 57 31-87 189-248 (334)
31 PF05920 Homeobox_KN: Homeobox 98.1 7.8E-07 1.7E-11 59.1 0.3 34 51-84 7-40 (40)
32 PF02183 HALZ: Homeobox associ 98.0 1.3E-05 2.7E-10 54.7 5.5 44 88-131 1-44 (45)
33 KOG2252 CCAAT displacement pro 97.9 6E-06 1.3E-10 81.3 3.4 58 29-86 419-476 (558)
34 KOG0490 Transcription factor, 97.7 2.7E-05 5.8E-10 67.6 3.8 66 25-90 148-213 (235)
35 KOG1146 Homeobox protein [Gene 96.8 0.0012 2.7E-08 70.8 4.7 63 28-90 901-963 (1406)
36 KOG0773 Transcription factor M 96.4 0.0036 7.9E-08 58.4 4.4 63 30-92 239-304 (342)
37 PF11569 Homez: Homeodomain le 95.0 0.0068 1.5E-07 43.2 0.1 42 41-82 9-50 (56)
38 PF02183 HALZ: Homeobox associ 93.5 0.14 3.1E-06 34.8 4.0 38 97-134 3-40 (45)
39 PF04218 CENP-B_N: CENP-B N-te 91.5 0.21 4.6E-06 34.7 3.0 47 31-82 1-47 (53)
40 KOG3623 Homeobox transcription 90.3 0.19 4.2E-06 51.9 2.6 48 42-89 568-615 (1007)
41 PRK09413 IS2 repressor TnpA; R 90.3 0.69 1.5E-05 37.1 5.3 92 34-129 10-101 (121)
42 smart00340 HALZ homeobox assoc 89.0 0.89 1.9E-05 30.7 4.1 33 89-128 2-34 (44)
43 PF10224 DUF2205: Predicted co 85.7 5 0.00011 30.6 7.1 48 85-132 16-63 (80)
44 smart00340 HALZ homeobox assoc 85.4 1.8 4E-05 29.2 4.0 29 106-134 5-33 (44)
45 PF06156 DUF972: Protein of un 80.3 9.8 0.00021 30.4 7.2 45 89-133 12-56 (107)
46 KOG0709 CREB/ATF family transc 79.5 24 0.00051 35.1 10.9 100 34-140 218-327 (472)
47 KOG3119 Basic region leucine z 79.5 8.8 0.00019 35.2 7.6 50 82-134 208-257 (269)
48 PF00170 bZIP_1: bZIP transcri 79.3 16 0.00034 25.9 7.4 39 91-129 25-63 (64)
49 KOG0483 Transcription factor H 78.2 5.4 0.00012 35.3 5.6 55 96-150 109-164 (198)
50 PF06005 DUF904: Protein of un 72.7 21 0.00046 26.5 6.8 39 89-127 15-53 (72)
51 smart00338 BRLZ basic region l 70.3 31 0.00067 24.4 7.1 37 93-129 27-63 (65)
52 KOG4196 bZIP transcription fac 69.6 40 0.00086 28.1 8.3 86 35-133 22-115 (135)
53 PRK13169 DNA replication intia 69.4 21 0.00045 28.8 6.5 44 89-132 12-55 (110)
54 PF14775 NYD-SP28_assoc: Sperm 67.6 14 0.00031 26.4 4.8 32 100-131 27-58 (60)
55 PF00170 bZIP_1: bZIP transcri 65.6 34 0.00073 24.1 6.4 34 96-129 23-56 (64)
56 KOG4571 Activating transcripti 65.3 25 0.00054 33.0 7.0 40 91-130 247-286 (294)
57 PF01527 HTH_Tnp_1: Transposas 64.3 2.1 4.5E-05 30.7 -0.2 43 32-78 2-44 (76)
58 PF04967 HTH_10: HTH DNA bindi 63.3 7.1 0.00015 27.4 2.4 38 37-74 1-40 (53)
59 KOG4571 Activating transcripti 63.0 29 0.00062 32.6 7.0 39 93-131 242-280 (294)
60 PRK14127 cell division protein 61.3 32 0.0007 27.6 6.2 45 88-132 26-70 (109)
61 PF04545 Sigma70_r4: Sigma-70, 61.2 6 0.00013 26.3 1.7 37 36-77 4-40 (50)
62 PF06005 DUF904: Protein of un 58.8 52 0.0011 24.4 6.5 43 88-130 21-63 (72)
63 cd06171 Sigma70_r4 Sigma70, re 55.9 5.1 0.00011 25.5 0.6 42 36-82 10-51 (55)
64 smart00338 BRLZ basic region l 54.6 73 0.0016 22.4 7.3 36 96-131 23-58 (65)
65 cd00569 HTH_Hin_like Helix-tur 54.5 17 0.00037 20.4 2.8 37 36-77 5-41 (42)
66 KOG3650 Predicted coiled-coil 53.4 50 0.0011 26.5 5.9 41 92-132 63-103 (120)
67 PF05377 FlaC_arch: Flagella a 52.6 52 0.0011 23.4 5.3 32 99-130 7-38 (55)
68 PRK00888 ftsB cell division pr 52.1 33 0.00071 27.1 4.8 26 102-127 37-62 (105)
69 cd04787 HTH_HMRTR_unk Helix-Tu 52.0 76 0.0017 25.6 7.1 93 33-147 35-127 (133)
70 PF06156 DUF972: Protein of un 50.7 52 0.0011 26.2 5.7 40 88-127 18-57 (107)
71 cd04781 HTH_MerR-like_sg6 Heli 50.4 1.1E+02 0.0024 24.1 7.7 37 32-81 33-69 (120)
72 PF10668 Phage_terminase: Phag 50.2 5.3 0.00011 28.9 -0.0 19 59-77 24-42 (60)
73 PF15058 Speriolin_N: Sperioli 50.1 27 0.00058 31.0 4.3 32 99-130 5-36 (200)
74 PF04899 MbeD_MobD: MbeD/MobD 49.4 76 0.0017 23.5 6.1 39 93-131 22-60 (70)
75 KOG4005 Transcription factor X 49.0 67 0.0014 29.6 6.8 36 94-129 99-134 (292)
76 PF13443 HTH_26: Cro/C1-type H 47.4 12 0.00026 25.7 1.5 40 59-98 12-51 (63)
77 PF07407 Seadorna_VP6: Seadorn 46.7 28 0.00061 33.4 4.2 28 103-130 36-63 (420)
78 PRK13729 conjugal transfer pil 46.1 98 0.0021 31.0 8.0 46 86-131 77-122 (475)
79 COG4026 Uncharacterized protei 45.0 63 0.0014 29.6 5.9 42 91-132 148-189 (290)
80 COG3074 Uncharacterized protei 45.0 91 0.002 23.5 5.8 38 94-131 34-71 (79)
81 PRK13169 DNA replication intia 44.3 73 0.0016 25.6 5.7 39 89-127 19-57 (110)
82 PF04728 LPP: Lipoprotein leuc 44.0 1.2E+02 0.0025 21.7 6.9 45 86-130 4-48 (56)
83 PF08281 Sigma70_r4_2: Sigma-7 43.4 18 0.00039 24.1 1.8 40 36-80 10-49 (54)
84 PF07334 IFP_35_N: Interferon- 42.8 1.1E+02 0.0024 23.1 6.1 26 103-128 4-29 (76)
85 KOG1146 Homeobox protein [Gene 42.1 8.3 0.00018 42.7 -0.1 59 30-88 444-502 (1406)
86 PRK10884 SH3 domain-containing 41.9 1.1E+02 0.0024 27.0 7.1 37 92-128 132-168 (206)
87 PRK15422 septal ring assembly 41.4 1.5E+02 0.0033 22.6 6.7 25 106-130 46-70 (79)
88 COG3413 Predicted DNA binding 41.3 26 0.00057 30.4 3.0 39 36-74 155-195 (215)
89 KOG2391 Vacuolar sorting prote 40.8 1E+02 0.0022 29.8 6.9 47 82-128 222-268 (365)
90 PF04977 DivIC: Septum formati 40.5 76 0.0017 22.6 4.9 25 101-125 26-50 (80)
91 KOG4343 bZIP transcription fac 40.3 66 0.0014 32.8 5.8 36 92-127 302-337 (655)
92 PRK00888 ftsB cell division pr 39.7 75 0.0016 25.0 5.1 47 73-120 16-62 (105)
93 TIGR02449 conserved hypothetic 39.2 1.1E+02 0.0023 22.5 5.4 44 89-132 11-54 (65)
94 PRK03975 tfx putative transcri 38.9 31 0.00066 28.9 2.9 45 34-84 4-48 (141)
95 TIGR02894 DNA_bind_RsfA transc 38.6 1.2E+02 0.0027 26.0 6.5 37 92-128 104-140 (161)
96 cd01106 HTH_TipAL-Mta Helix-Tu 38.3 1.5E+02 0.0032 22.6 6.5 35 33-80 35-69 (103)
97 KOG3335 Predicted coiled-coil 37.9 1.2E+02 0.0025 26.7 6.3 37 97-133 104-140 (181)
98 cd04766 HTH_HspR Helix-Turn-He 37.5 93 0.002 23.3 5.1 55 33-130 35-89 (91)
99 KOG4403 Cell surface glycoprot 37.0 73 0.0016 31.8 5.5 25 74-98 228-255 (575)
100 KOG3119 Basic region leucine z 36.1 1.2E+02 0.0025 27.9 6.5 45 91-135 207-251 (269)
101 COG4026 Uncharacterized protei 36.1 1.5E+02 0.0032 27.2 6.9 37 94-130 137-173 (290)
102 PF07716 bZIP_2: Basic region 35.9 1.4E+02 0.0031 20.3 7.2 30 98-127 24-53 (54)
103 COG4467 Regulator of replicati 35.9 1.3E+02 0.0029 24.3 5.9 42 90-131 13-54 (114)
104 PRK14127 cell division protein 35.6 1.1E+02 0.0024 24.6 5.4 43 94-136 25-67 (109)
105 TIGR03752 conj_TIGR03752 integ 35.0 95 0.0021 31.1 6.0 27 36-65 41-67 (472)
106 PF07334 IFP_35_N: Interferon- 34.0 59 0.0013 24.6 3.4 26 109-134 3-28 (76)
107 PF12325 TMF_TATA_bd: TATA ele 33.8 1.7E+02 0.0037 23.8 6.4 44 88-131 71-114 (120)
108 PF03670 UPF0184: Uncharacteri 33.5 1.2E+02 0.0026 23.4 5.1 35 91-125 25-59 (83)
109 PRK10884 SH3 domain-containing 33.4 1.7E+02 0.0036 25.9 6.8 38 93-130 126-163 (206)
110 PHA01750 hypothetical protein 32.4 2.1E+02 0.0046 21.3 6.8 39 92-130 35-73 (75)
111 cd04770 HTH_HMRTR Helix-Turn-H 31.8 2.5E+02 0.0054 21.9 7.5 37 32-81 34-70 (123)
112 PF10224 DUF2205: Predicted co 31.4 2.3E+02 0.0051 21.5 6.5 39 88-126 26-64 (80)
113 PF12476 DUF3696: Protein of u 31.2 25 0.00055 24.0 1.0 38 193-237 6-45 (52)
114 KOG1962 B-cell receptor-associ 31.0 1.8E+02 0.0039 26.2 6.6 36 95-130 175-210 (216)
115 PF13936 HTH_38: Helix-turn-he 30.8 31 0.00066 22.7 1.3 39 34-77 2-40 (44)
116 PF09607 BrkDBD: Brinker DNA-b 30.3 38 0.00083 24.3 1.8 44 34-79 3-47 (58)
117 KOG4005 Transcription factor X 29.6 1.4E+02 0.003 27.6 5.6 44 89-132 101-144 (292)
118 PF13518 HTH_28: Helix-turn-he 29.3 18 0.00038 23.7 -0.0 22 59-80 14-35 (52)
119 PRK15422 septal ring assembly 29.2 2.6E+02 0.0057 21.3 6.7 42 88-129 14-62 (79)
120 PF04899 MbeD_MobD: MbeD/MobD 29.2 2.3E+02 0.005 21.0 5.9 41 91-131 27-67 (70)
121 PF08280 HTH_Mga: M protein tr 28.8 37 0.0008 23.6 1.5 32 40-75 6-37 (59)
122 PRK13922 rod shape-determining 28.4 1.5E+02 0.0032 26.6 5.8 36 97-132 74-112 (276)
123 cd04761 HTH_MerR-SF Helix-Turn 27.9 18 0.00039 23.3 -0.2 22 60-81 3-24 (49)
124 PF08826 DMPK_coil: DMPK coile 27.7 2.4E+02 0.0051 20.4 6.8 42 90-131 16-57 (61)
125 PF00424 REV: REV protein (ant 27.7 70 0.0015 25.0 3.0 33 42-90 14-48 (91)
126 PF10473 CENP-F_leu_zip: Leuci 27.4 3.1E+02 0.0067 22.9 7.0 37 94-130 61-97 (140)
127 KOG4286 Dystrophin-like protei 26.9 2.4E+02 0.0051 30.3 7.4 45 91-135 840-884 (966)
128 PF06056 Terminase_5: Putative 26.9 23 0.00051 25.0 0.2 27 59-87 15-41 (58)
129 KOG4196 bZIP transcription fac 26.8 3.8E+02 0.0082 22.4 7.6 42 89-130 78-119 (135)
130 PF00196 GerE: Bacterial regul 26.7 42 0.0009 22.9 1.5 44 36-85 3-46 (58)
131 KOG4343 bZIP transcription fac 26.5 1.9E+02 0.004 29.8 6.4 51 96-146 299-351 (655)
132 PF08172 CASP_C: CASP C termin 26.4 2.3E+02 0.005 25.8 6.6 30 102-131 103-132 (248)
133 KOG0150 Spliceosomal protein F 26.3 1.7E+02 0.0036 27.9 5.7 54 74-127 16-70 (336)
134 PTZ00454 26S protease regulato 26.3 2.2E+02 0.0048 27.5 6.9 46 89-134 19-64 (398)
135 COG4367 Uncharacterized protei 26.1 78 0.0017 24.8 3.0 37 36-72 2-38 (97)
136 PF11932 DUF3450: Protein of u 25.9 3E+02 0.0065 24.5 7.3 22 179-200 168-189 (251)
137 PRK06759 RNA polymerase factor 25.9 64 0.0014 25.6 2.7 39 37-80 107-145 (154)
138 PRK11924 RNA polymerase sigma 25.8 34 0.00074 27.5 1.1 28 59-86 143-170 (179)
139 PF09744 Jnk-SapK_ap_N: JNK_SA 25.5 3.2E+02 0.007 23.2 6.9 15 41-55 34-48 (158)
140 TIGR02937 sigma70-ECF RNA poly 25.5 55 0.0012 24.9 2.2 40 37-81 111-150 (158)
141 PRK00409 recombination and DNA 25.4 2.2E+02 0.0047 30.1 7.1 21 55-75 485-505 (782)
142 PRK13922 rod shape-determining 25.3 1.2E+02 0.0027 27.2 4.7 27 99-125 69-95 (276)
143 COG3416 Uncharacterized protei 25.2 2.7E+02 0.0059 25.2 6.6 35 112-146 54-88 (233)
144 PF05700 BCAS2: Breast carcino 25.1 3.2E+02 0.007 24.0 7.2 42 91-132 174-215 (221)
145 PF08172 CASP_C: CASP C termin 25.1 2.3E+02 0.005 25.8 6.3 49 82-130 90-138 (248)
146 PF15058 Speriolin_N: Sperioli 25.1 1.6E+02 0.0034 26.2 5.0 39 93-132 6-44 (200)
147 PF14197 Cep57_CLD_2: Centroso 24.9 2.8E+02 0.0061 20.3 6.9 40 91-130 25-64 (69)
148 cd01109 HTH_YyaN Helix-Turn-He 24.9 3.3E+02 0.0071 21.0 7.1 75 33-129 35-109 (113)
149 PF04977 DivIC: Septum formati 24.9 1.8E+02 0.0038 20.6 4.6 30 89-118 21-50 (80)
150 PF07716 bZIP_2: Basic region 24.7 2.3E+02 0.005 19.2 5.9 29 93-121 26-54 (54)
151 PF08961 DUF1875: Domain of un 24.3 25 0.00055 31.8 0.0 33 93-125 130-162 (243)
152 PF10473 CENP-F_leu_zip: Leuci 24.1 4E+02 0.0087 22.3 7.1 8 118-125 78-85 (140)
153 TIGR01069 mutS2 MutS2 family p 23.9 2.7E+02 0.0058 29.5 7.4 21 55-75 480-500 (771)
154 KOG3156 Uncharacterized membra 23.8 2.6E+02 0.0057 25.2 6.3 29 105-133 115-143 (220)
155 PF12709 Kinetocho_Slk19: Cent 23.7 2.4E+02 0.0052 21.9 5.3 33 97-129 47-79 (87)
156 PRK12514 RNA polymerase sigma 23.7 44 0.00096 27.4 1.4 26 60-85 148-173 (179)
157 PRK14872 rod shape-determining 23.7 1.3E+02 0.0029 28.7 4.7 26 99-124 57-82 (337)
158 cd04785 HTH_CadR-PbrR-like Hel 23.5 3.8E+02 0.0082 21.3 7.6 35 32-79 34-68 (126)
159 PF05377 FlaC_arch: Flagella a 23.5 2.8E+02 0.006 19.7 5.6 39 89-127 4-42 (55)
160 PF04880 NUDE_C: NUDE protein, 23.2 96 0.0021 26.7 3.3 41 88-129 7-47 (166)
161 PRK09646 RNA polymerase sigma 23.2 47 0.001 27.9 1.5 22 59-80 160-181 (194)
162 PHA02955 hypothetical protein; 22.9 1.1E+02 0.0024 27.5 3.7 42 39-80 60-102 (213)
163 TIGR03879 near_KaiC_dom probab 22.9 16 0.00034 27.4 -1.3 35 46-80 21-55 (73)
164 TIGR02047 CadR-PbrR Cd(II)/Pb( 22.8 4E+02 0.0086 21.2 7.2 35 32-79 34-68 (127)
165 smart00421 HTH_LUXR helix_turn 22.6 72 0.0016 20.4 2.0 38 36-79 3-40 (58)
166 PHA00728 hypothetical protein 22.5 1.5E+02 0.0033 24.6 4.2 28 106-133 5-32 (151)
167 PF13411 MerR_1: MerR HTH fami 22.5 28 0.0006 24.2 -0.1 20 60-79 3-22 (69)
168 cd04769 HTH_MerR2 Helix-Turn-H 22.5 3.4E+02 0.0073 21.2 6.2 37 33-82 34-70 (116)
169 PF07989 Microtub_assoc: Micro 22.4 1.5E+02 0.0032 22.1 3.8 24 104-127 48-71 (75)
170 PF13384 HTH_23: Homeodomain-l 22.3 25 0.00055 23.0 -0.3 23 58-80 18-40 (50)
171 PF01166 TSC22: TSC-22/dip/bun 22.3 1.4E+02 0.0031 21.5 3.5 27 93-119 15-41 (59)
172 TIGR02989 Sig-70_gvs1 RNA poly 22.1 46 0.00099 26.5 1.1 21 59-79 129-149 (159)
173 PRK09652 RNA polymerase sigma 22.0 45 0.00098 26.9 1.1 39 36-79 128-166 (182)
174 PRK09642 RNA polymerase sigma 21.9 51 0.0011 26.5 1.4 27 60-86 125-151 (160)
175 PRK04217 hypothetical protein; 21.8 77 0.0017 25.4 2.3 41 34-79 40-80 (110)
176 PF02796 HTH_7: Helix-turn-hel 21.6 52 0.0011 21.6 1.1 38 36-78 5-42 (45)
177 PF11932 DUF3450: Protein of u 21.4 3.4E+02 0.0074 24.1 6.7 13 231-243 205-217 (251)
178 COG2963 Transposase and inacti 21.2 1.1E+02 0.0023 23.7 3.1 42 34-79 5-47 (116)
179 TIGR00219 mreC rod shape-deter 21.2 2.4E+02 0.0052 25.9 5.8 17 117-133 95-111 (283)
180 PF13565 HTH_32: Homeodomain-l 21.2 2.6E+02 0.0057 19.5 4.9 32 38-69 32-64 (77)
181 TIGR02985 Sig70_bacteroi1 RNA 21.2 47 0.001 26.1 1.0 23 59-81 131-153 (161)
182 PF06216 RTBV_P46: Rice tungro 21.0 2.5E+02 0.0053 26.3 5.7 44 91-134 70-113 (389)
183 PF11594 Med28: Mediator compl 20.8 1.9E+02 0.0041 23.3 4.3 14 72-85 18-31 (106)
184 PF14197 Cep57_CLD_2: Centroso 20.6 3.2E+02 0.007 20.0 5.2 26 101-126 42-67 (69)
185 cd04783 HTH_MerR1 Helix-Turn-H 20.3 4.4E+02 0.0095 20.8 7.5 37 32-81 34-70 (126)
186 PF05812 Herpes_BLRF2: Herpesv 20.3 1.9E+02 0.0041 23.7 4.3 28 107-134 4-31 (118)
187 COG1905 NuoE NADH:ubiquinone o 20.2 1.3E+02 0.0028 25.8 3.5 36 39-74 25-60 (160)
188 TIGR02209 ftsL_broad cell divi 20.1 3.3E+02 0.0071 19.7 5.4 28 91-118 30-57 (85)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.88 E-value=6.8e-23 Score=178.58 Aligned_cols=114 Identities=46% Similarity=0.740 Sum_probs=104.6
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHH
Q 025886 30 KCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFE 109 (247)
Q Consensus 30 krr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~ 109 (247)
..+++.+|+.+|+..||..|+.+.++.+.++..||++|||+++||+|||||||||||.++++.+++.|+..|+.|..++.
T Consensus 50 ~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~~~~ 129 (198)
T KOG0483|consen 50 GKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRSEND 129 (198)
T ss_pred cccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhhhhh
Confidence 34567789999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHHHHHHHHhc-CCCCCCCCCCcc
Q 025886 110 ALKKEKQALVIQLQKTNELLQN-KPRREDQSPSER 143 (247)
Q Consensus 110 ~l~~E~~~L~~e~~~l~~~l~~-~~~~~~~sp~~~ 143 (247)
.|+.++..|..++..++..++. +...+.+||.+.
T Consensus 130 ~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (198)
T KOG0483|consen 130 RLQSEVQELVAELSSLKREMQKSPENTLTMCPNSE 164 (198)
T ss_pred HHHHHHHHHHHHHhhhhhhhccCcccccccCcccc
Confidence 9999999999999999999998 555555555544
No 2
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.69 E-value=2.1e-17 Score=152.91 Aligned_cols=66 Identities=41% Similarity=0.702 Sum_probs=62.0
Q ss_pred CCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 24 TTTRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 24 ~~~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
...+||+|+.|+.||..|+..||+.|++.+|++...|++||..|||+..||++||||||+|||+..
T Consensus 166 ~~~pkK~RksRTaFT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~ 231 (309)
T KOG0488|consen 166 RSTPKKRRKSRTAFSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQT 231 (309)
T ss_pred cCCCcccccchhhhhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHH
Confidence 445688888999999999999999999999999999999999999999999999999999999954
No 3
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.67 E-value=1.3e-17 Score=150.97 Aligned_cols=62 Identities=32% Similarity=0.631 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
.+.||.|+.||..|+.+||+.|+.|+|++..+|++||..|.|+++||||||||||+||||..
T Consensus 157 ~~~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~ 218 (261)
T KOG0489|consen 157 GKSKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKEN 218 (261)
T ss_pred CCCCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhh
Confidence 45788899999999999999999999999999999999999999999999999999999843
No 4
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=8.1e-17 Score=148.28 Aligned_cols=70 Identities=36% Similarity=0.555 Sum_probs=64.4
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHH
Q 025886 27 RKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNI 96 (247)
Q Consensus 27 ~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~ 96 (247)
+.++||.|..|+..|+.+||+.|...+|++..+|+.||..|.|++.||||||||||-|.||+++++..+.
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~~ 219 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALEA 219 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhhc
Confidence 5567777889999999999999999999999999999999999999999999999999999887776554
No 5
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.65 E-value=1.1e-16 Score=137.07 Aligned_cols=65 Identities=34% Similarity=0.515 Sum_probs=61.4
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLER 92 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~ 92 (247)
.+.+|.||.||++|+..||..|+.++|....+|..||..|+|++.||+|||||||.|.||.+.+.
T Consensus 100 ~~~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 100 MRPKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred cCCCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 37788999999999999999999999999999999999999999999999999999999977654
No 6
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.64 E-value=2.3e-16 Score=139.33 Aligned_cols=65 Identities=34% Similarity=0.545 Sum_probs=61.3
Q ss_pred cCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 23 TTTTRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 23 s~~~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
-..+.||-||.||.++.-||..|.+.|+++.|+--.+|.+||..|||+..||||||||||.|.|+
T Consensus 115 ~Ngk~KK~RKPRTIYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KK 179 (245)
T KOG0850|consen 115 PNGKGKKVRKPRTIYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKK 179 (245)
T ss_pred cCCCcccccCCcccccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHH
Confidence 35566788899999999999999999999999999999999999999999999999999999997
No 7
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.63 E-value=5.4e-16 Score=135.41 Aligned_cols=63 Identities=33% Similarity=0.515 Sum_probs=58.6
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 27 RKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 27 ~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
.|..|+.|+.||..|+..||+.|...+|+++.+|.+++..|.|++.||+|||||||+|.||-|
T Consensus 141 hk~nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQ 203 (246)
T KOG0492|consen 141 HKPNRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQ 203 (246)
T ss_pred cCCCCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHH
Confidence 345567799999999999999999999999999999999999999999999999999999844
No 8
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.62 E-value=5.9e-16 Score=142.66 Aligned_cols=64 Identities=31% Similarity=0.484 Sum_probs=59.9
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 27 RKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 27 ~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
.+..||||..+|..|+.+||+.|-.|.|++...|.+|++.|+|++|||+|||||||+|.||...
T Consensus 232 ~~~~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~r 295 (308)
T KOG0487|consen 232 ARRGRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNR 295 (308)
T ss_pred ccccccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhh
Confidence 4667788999999999999999999999999999999999999999999999999999998654
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.60 E-value=9.2e-16 Score=134.81 Aligned_cols=64 Identities=38% Similarity=0.585 Sum_probs=60.0
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 26 TRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 26 ~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
...+|||.|++|+..|+..||..|+..+|++..+|..||.+|.|++.||+|||||||.||||+-
T Consensus 100 g~~RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 100 GDDRKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred cccccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 3457778899999999999999999999999999999999999999999999999999999953
No 10
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.58 E-value=1.2e-15 Score=120.59 Aligned_cols=63 Identities=24% Similarity=0.550 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhH
Q 025886 26 TRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSK 88 (247)
Q Consensus 26 ~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krk 88 (247)
.++|.+|-|+.||..|+..||+.|...+||+.-.|++||.++.|++..|+|||||||||.+++
T Consensus 13 ekrKQRRIRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQ 75 (125)
T KOG0484|consen 13 EKRKQRRIRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQ 75 (125)
T ss_pred HHHHhhhhhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHH
Confidence 456778889999999999999999999999999999999999999999999999999999974
No 11
>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=99.57 E-value=1.4e-15 Score=106.35 Aligned_cols=57 Identities=40% Similarity=0.659 Sum_probs=54.6
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 31 CKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 31 rr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
+++|+.||.+|+.+|+..|..++||+..++..||..|||++.+|++||+|||++.|+
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 467899999999999999999999999999999999999999999999999999985
No 12
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.53 E-value=6.2e-15 Score=129.67 Aligned_cols=66 Identities=26% Similarity=0.503 Sum_probs=62.5
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 25 TTRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 25 ~~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
..++|.||.||.|+..|+.+||.+|.+..||+...+++||.+|+|++.+|+|||+|||+|+|+.+.
T Consensus 32 ~~pRkqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 32 SGPRKQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred ccchhcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 456889999999999999999999999999999999999999999999999999999999998654
No 13
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.52 E-value=9.1e-15 Score=131.42 Aligned_cols=70 Identities=26% Similarity=0.488 Sum_probs=60.6
Q ss_pred CCCCCCC-CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHH
Q 025886 27 RKKKCKN-KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNI 96 (247)
Q Consensus 27 ~kkkrr~-Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~ 96 (247)
++++||. |+.||..|+..||+.|+..+||+...|+-||.++.|++.+|+|||||||||||++...--..+
T Consensus 137 kk~kRRh~RTiFT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek~wg~sT 207 (332)
T KOG0494|consen 137 KKKKRRHFRTIFTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEKRWGGST 207 (332)
T ss_pred cccccccccchhhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhhhcCcch
Confidence 3444444 999999999999999999999999999999999999999999999999999998655433333
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.48 E-value=2.9e-14 Score=128.32 Aligned_cols=60 Identities=37% Similarity=0.633 Sum_probs=56.9
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 31 CKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 31 rr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
||.|+.||.+||..|...|+.++|++...|.+||.+|+|.+.||+|||||+|+|.|+..-
T Consensus 247 KRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIKIWFQNKRAKiKKsTg 306 (342)
T KOG0493|consen 247 KRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIKIWFQNKRAKIKKSTG 306 (342)
T ss_pred cCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhhHHhhhhhhhhhhccC
Confidence 477999999999999999999999999999999999999999999999999999998654
No 15
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.48 E-value=1.1e-14 Score=131.35 Aligned_cols=58 Identities=40% Similarity=0.603 Sum_probs=54.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
|-|.++|..|..+||+.|...+|+++.++.+||..|+|++|||||||||||||+||..
T Consensus 201 KYRvVYTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 201 KYRVVYTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ceeEEecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 4577899999999999999999999999999999999999999999999999999843
No 16
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.44 E-value=7.6e-14 Score=96.66 Aligned_cols=55 Identities=40% Similarity=0.778 Sum_probs=51.7
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHh
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWK 86 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~K 86 (247)
+.|+.|+..|+.+|+..|..++||+..++..||..+||+..||++||+|||++.+
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 4567899999999999999999999999999999999999999999999998764
No 17
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.43 E-value=1e-13 Score=96.56 Aligned_cols=56 Identities=46% Similarity=0.754 Sum_probs=53.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
+.+..++..|+.+|+..|..++||+..++..||.++||++.||++||+|||++.++
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~ 57 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKR 57 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhc
Confidence 45778999999999999999999999999999999999999999999999999886
No 18
>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=5.6e-13 Score=95.37 Aligned_cols=52 Identities=15% Similarity=0.376 Sum_probs=50.0
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCC----CCHHHHHHHHHHhCCCccceeeeccchh
Q 025886 31 CKNKRRFSDEQIRSLELMFENETR----LEPRKKLQLAKELGLQPRQVAIWFQNKR 82 (247)
Q Consensus 31 rr~Rt~fT~~Ql~~LE~~F~~~~~----ps~~~r~eLA~~LgLs~rQVkiWFQNRR 82 (247)
+|.|+.||++|+..|+..|+.++| |+...+.+||..|||++++|+|||||-+
T Consensus 2 kR~RT~Ft~~Q~~~Le~~fe~~~y~~~~~~~~~r~~la~~lgl~~~vvKVWfqN~k 57 (58)
T TIGR01565 2 KRRRTKFTAEQKEKMRDFAEKLGWKLKDKRREEVREFCEEIGVTRKVFKVWMHNNK 57 (58)
T ss_pred CCCCCCCCHHHHHHHHHHHHHcCCCCCCCCHHHHHHHHHHhCCCHHHeeeecccCC
Confidence 678999999999999999999999 9999999999999999999999999964
No 19
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.38 E-value=4.2e-13 Score=113.43 Aligned_cols=63 Identities=37% Similarity=0.530 Sum_probs=58.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
...+++|++.|..|+.+|+..|+.++||+...|..|+..|+|+++-|+|||||||++.|++..
T Consensus 49 ~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~ 111 (156)
T COG5576 49 SPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRS 111 (156)
T ss_pred CcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhcc
Confidence 456677889999999999999999999999999999999999999999999999999998543
No 20
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.32 E-value=1.5e-12 Score=119.77 Aligned_cols=63 Identities=24% Similarity=0.567 Sum_probs=59.6
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
+|++|.|+.||..|+..||..|+++.||+...|++||...+|++..|+|||.|||+||++...
T Consensus 110 ~KqrrQrthFtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 110 SKQRRQRTHFTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 478889999999999999999999999999999999999999999999999999999998543
No 21
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.32 E-value=2.3e-13 Score=115.40 Aligned_cols=61 Identities=38% Similarity=0.610 Sum_probs=57.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 29 KKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 29 kkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
++++.|++|+..|+..||+.|+..+|++-.++.+||..|+|++.||+.||||||+|.|+.+
T Consensus 99 ~r~K~Rtvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~ 159 (194)
T KOG0491|consen 99 RRRKARTVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQ 159 (194)
T ss_pred HhhhhcccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHH
Confidence 4456799999999999999999999999999999999999999999999999999999854
No 22
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.30 E-value=2.3e-12 Score=121.71 Aligned_cols=60 Identities=23% Similarity=0.365 Sum_probs=57.8
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhH
Q 025886 29 KKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSK 88 (247)
Q Consensus 29 kkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krk 88 (247)
|+||+|+.|.......||++|..|++|+..++..||.+|+|....|+|||+|||.|.||.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~ 352 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRI 352 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccC
Confidence 677889999999999999999999999999999999999999999999999999999984
No 23
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.29 E-value=9.7e-13 Score=120.72 Aligned_cols=64 Identities=30% Similarity=0.504 Sum_probs=59.5
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLE 91 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e 91 (247)
..-||-|+.||.+||..||+.|-+..|.+...|.+||..|+|++..|+|||||||+|.||+.+.
T Consensus 179 dqmRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 179 DQMRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 3557789999999999999999999999999999999999999999999999999999996653
No 24
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.25 E-value=4.9e-12 Score=115.40 Aligned_cols=98 Identities=21% Similarity=0.343 Sum_probs=83.4
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHH
Q 025886 29 KKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRF 108 (247)
Q Consensus 29 kkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~ 108 (247)
..||.|+.+|+.|++-|...|...++|....|++|+.++||.-+.|+|||||||||.||-+...-...+.+.|.+++..
T Consensus 166 ~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK~s- 244 (383)
T KOG4577|consen 166 SNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMKRS- 244 (383)
T ss_pred ccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhhcc-
Confidence 3567899999999999999999999999999999999999999999999999999999988877788898988888877
Q ss_pred HHHHHHHHHHHHHHHHHHH
Q 025886 109 EALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 109 ~~l~~E~~~L~~e~~~l~~ 127 (247)
...+.|+++-..++.-...
T Consensus 245 gs~r~ekdsd~sel~~~~d 263 (383)
T KOG4577|consen 245 GSSRAEKDSDDSELSFIND 263 (383)
T ss_pred CCcccccccccCccccccc
Confidence 5556666654445544444
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.09 E-value=2.5e-11 Score=107.28 Aligned_cols=60 Identities=37% Similarity=0.694 Sum_probs=55.6
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhH
Q 025886 29 KKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSK 88 (247)
Q Consensus 29 kkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krk 88 (247)
+++..|..|+-.|+..||..|+..+|+-...+.+||..||+++.||+|||||||+|||++
T Consensus 166 ~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKk 225 (288)
T KOG0847|consen 166 QRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKK 225 (288)
T ss_pred cccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhh
Confidence 344457789999999999999999999999999999999999999999999999999984
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.05 E-value=9.7e-11 Score=101.73 Aligned_cols=63 Identities=27% Similarity=0.284 Sum_probs=59.2
Q ss_pred CCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 27 RKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 27 ~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
..++++.|+.|+..|+.+||+.|+..+||+...++.||..+++++..|+|||||||++|++..
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 456788899999999999999999999999999999999999999999999999999999844
No 27
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.78 E-value=4.4e-09 Score=99.32 Aligned_cols=68 Identities=31% Similarity=0.563 Sum_probs=61.7
Q ss_pred ccCCCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 22 TTTTTRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 22 ~s~~~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
+....+++.+|.|+.|+..|+..|+..|+.++||....|+.||.++++++..|++||+|||+++++..
T Consensus 168 p~~~~~~~~rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 168 PGYALQRGGRRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred ccccccccccccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 33445667778899999999999999999999999999999999999999999999999999999843
No 28
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.74 E-value=6.3e-09 Score=95.35 Aligned_cols=60 Identities=28% Similarity=0.450 Sum_probs=56.1
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 30 KCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 30 krr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
+||+|+.+.+.....||.+|...++|+.+.+..||.+|+|....|+|||+|.|.|.||.+
T Consensus 309 kKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 309 KKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 466789999999999999999999999999999999999999999999999999998843
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.52 E-value=7e-08 Score=87.83 Aligned_cols=51 Identities=31% Similarity=0.517 Sum_probs=46.3
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 37 FSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 37 fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
|...-..+|..+|..++||++.++.+||+.+||+..||-+||.|||.|.|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 444456799999999999999999999999999999999999999999884
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.13 E-value=1.6e-06 Score=78.70 Aligned_cols=57 Identities=32% Similarity=0.484 Sum_probs=53.2
Q ss_pred CCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 31 CKNKRRFSDEQIRSLELMFEN---ETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 31 rr~Rt~fT~~Ql~~LE~~F~~---~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
+|+|+.|+..-..+|..+|.. ++||+...+++||+++|++..||-.||.|+|-++|+
T Consensus 189 rRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK 248 (334)
T KOG0774|consen 189 RRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKK 248 (334)
T ss_pred HHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhh
Confidence 567889999999999999964 789999999999999999999999999999999987
No 31
>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=98.09 E-value=7.8e-07 Score=59.10 Aligned_cols=34 Identities=35% Similarity=0.585 Sum_probs=29.0
Q ss_pred hcCCCCHHHHHHHHHHhCCCccceeeeccchhhH
Q 025886 51 NETRLEPRKKLQLAKELGLQPRQVAIWFQNKRAR 84 (247)
Q Consensus 51 ~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK 84 (247)
.++||+..++..||.++||+..||..||-|.|.|
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 4789999999999999999999999999999875
No 32
>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=98.04 E-value=1.3e-05 Score=54.69 Aligned_cols=44 Identities=43% Similarity=0.707 Sum_probs=41.6
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
+|++++++.|+..|+.|..++++|.+||+.|++++..|+.+++.
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 47899999999999999999999999999999999999999863
No 33
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.94 E-value=6e-06 Score=81.30 Aligned_cols=58 Identities=26% Similarity=0.371 Sum_probs=53.9
Q ss_pred CCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHh
Q 025886 29 KKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWK 86 (247)
Q Consensus 29 kkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~K 86 (247)
+.||.|.+||..|..-|..+|+.+++|+.+..+.|+.+|+|....|.+||.|-|.|.+
T Consensus 419 ~~KKPRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRsl 476 (558)
T KOG2252|consen 419 QTKKPRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRSL 476 (558)
T ss_pred cCCCceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhcc
Confidence 4556699999999999999999999999999999999999999999999999888753
No 34
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.73 E-value=2.7e-05 Score=67.59 Aligned_cols=66 Identities=30% Similarity=0.604 Sum_probs=59.8
Q ss_pred CCCCCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 25 TTRKKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 25 ~~~kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
....+.++.++.+...|+..|...|...++|....+..|+..+|++++.|++||+|+|++.++...
T Consensus 148 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 148 PSNKKPRRPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccCCCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 344567778899999999999999999999999999999999999999999999999999998543
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.83 E-value=0.0012 Score=70.82 Aligned_cols=63 Identities=25% Similarity=0.413 Sum_probs=58.0
Q ss_pred CCCCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 28 KKKCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 28 kkkrr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
-.++..|++++..|+..|...|....+|...+.+.|...+++.++.|.+||||-|++.|+...
T Consensus 901 ~~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 901 MGRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 345677999999999999999999999999999999999999999999999999999997654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.42 E-value=0.0036 Score=58.38 Aligned_cols=63 Identities=30% Similarity=0.411 Sum_probs=51.7
Q ss_pred CCCCCCCCCHHHHHHHHHHHhh---cCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHH
Q 025886 30 KCKNKRRFSDEQIRSLELMFEN---ETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLER 92 (247)
Q Consensus 30 krr~Rt~fT~~Ql~~LE~~F~~---~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~ 92 (247)
..|.+..+....+.+|+.+... .+||+...+..||.++||+..||.+||.|.|.|..+...+.
T Consensus 239 ~~r~~~~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~~~ 304 (342)
T KOG0773|consen 239 KWRPQRGLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMIEE 304 (342)
T ss_pred CCCCCCCCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchHHH
Confidence 4555668999999999977433 46999999999999999999999999999998877644433
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=94.98 E-value=0.0068 Score=43.21 Aligned_cols=42 Identities=21% Similarity=0.367 Sum_probs=31.2
Q ss_pred HHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchh
Q 025886 41 QIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKR 82 (247)
Q Consensus 41 Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRR 82 (247)
.+..|+++|...+.+.......|..+.+|+..||+.||-.|+
T Consensus 9 d~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 9 DIQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp --HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred chHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 356799999999999999999999999999999999997554
No 38
>PF02183 HALZ: Homeobox associated leucine zipper; InterPro: IPR003106 This region is a plant specific leucine zipper that is always found associated with a homeobox []. ; GO: 0003677 DNA binding, 0006355 regulation of transcription, DNA-dependent, 0005634 nucleus
Probab=93.48 E-value=0.14 Score=34.82 Aligned_cols=38 Identities=21% Similarity=0.362 Sum_probs=33.4
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 97 LQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 97 lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
+...|+.|...++.|+.++++|..++..|+.++.....
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~L~~ 40 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQELKE 40 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45679999999999999999999999999999886654
No 39
>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=91.47 E-value=0.21 Score=34.69 Aligned_cols=47 Identities=19% Similarity=0.312 Sum_probs=34.4
Q ss_pred CCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchh
Q 025886 31 CKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKR 82 (247)
Q Consensus 31 rr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRR 82 (247)
+|+|..+|.++...+-..++... ....||+.+|++..+|..|..|+.
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 45678899988887777777665 478899999999999999988753
No 40
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=90.31 E-value=0.19 Score=51.93 Aligned_cols=48 Identities=19% Similarity=0.278 Sum_probs=44.3
Q ss_pred HHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH
Q 025886 42 IRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ 89 (247)
Q Consensus 42 l~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq 89 (247)
+.+|..+|..|..|+..+...+|.+.||+.+.|+.||+++++....-.
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 778999999999999999999999999999999999999999877643
No 41
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.28 E-value=0.69 Score=37.07 Aligned_cols=92 Identities=9% Similarity=0.100 Sum_probs=48.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHHHHHH
Q 025886 34 KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFEALKK 113 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~~ 113 (247)
|++|+.+.....-.....+.. ...++|.++|+++.+|..|.+.-+.....................+..+...|++
T Consensus 10 rr~ys~EfK~~aV~~~~~~g~----sv~evA~e~gIs~~tl~~W~r~y~~~~~~~~~~~~~~~~~~~~~~~~~ei~~L~~ 85 (121)
T PRK09413 10 RRRRTTQEKIAIVQQSFEPGM----TVSLVARQHGVAASQLFLWRKQYQEGSLTAVAAGEQVVPASELAAAMKQIKELQR 85 (121)
T ss_pred CCCCCHHHHHHHHHHHHcCCC----CHHHHHHHHCcCHHHHHHHHHHHhhcccccccccccCCchhHHHHHHHHHHHHHH
Confidence 456777765443333322332 3567899999999999999543221100000000000000111224455667777
Q ss_pred HHHHHHHHHHHHHHHH
Q 025886 114 EKQALVIQLQKTNELL 129 (247)
Q Consensus 114 E~~~L~~e~~~l~~~l 129 (247)
++..|..|+.-|++.+
T Consensus 86 el~~L~~E~diLKKa~ 101 (121)
T PRK09413 86 LLGKKTMENELLKEAV 101 (121)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 7777777777777765
No 42
>smart00340 HALZ homeobox associated leucin zipper.
Probab=88.96 E-value=0.89 Score=30.72 Aligned_cols=33 Identities=30% Similarity=0.394 Sum_probs=22.9
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNEL 128 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~ 128 (247)
|.+-+++.||. .+++|..||.+|+.++++|+..
T Consensus 2 QTEvdCe~LKr-------cce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 2 QTEVDCELLKR-------CCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred chHHHHHHHHH-------HHHHHHHHHHHHHHHHHHHHhc
Confidence 45666666665 5667777777778888777754
No 43
>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=85.67 E-value=5 Score=30.57 Aligned_cols=48 Identities=21% Similarity=0.266 Sum_probs=40.8
Q ss_pred HhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 85 WKSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 85 ~Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
..+..+.++...|+..+..|....+.++.|++.|..+++-|+..|...
T Consensus 16 e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nL 63 (80)
T PF10224_consen 16 EEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNL 63 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566778888999999999999999999999999999999987654
No 44
>smart00340 HALZ homeobox associated leucin zipper.
Probab=85.38 E-value=1.8 Score=29.23 Aligned_cols=29 Identities=17% Similarity=0.129 Sum_probs=21.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 106 SRFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 106 ~~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
...+-|++=-++|..++..|+..++..+.
T Consensus 5 vdCe~LKrcce~LteeNrRL~ke~~eLra 33 (44)
T smart00340 5 VDCELLKRCCESLTEENRRLQKEVQELRA 33 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35667777778888888888888776654
No 45
>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=80.30 E-value=9.8 Score=30.39 Aligned_cols=45 Identities=24% Similarity=0.337 Sum_probs=35.3
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKP 133 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~ 133 (247)
+++.....+-..+..|+.....+.+||..|+.|+..|++.|....
T Consensus 12 ~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~ 56 (107)
T PF06156_consen 12 QLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELE 56 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456666677777777888888888899999999999999887553
No 46
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=79.54 E-value=24 Score=35.11 Aligned_cols=100 Identities=20% Similarity=0.265 Sum_probs=55.4
Q ss_pred CCCCCHHHHHHHHHH-HhhcC-CCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHH--------HHHHHHHHHHhhhh
Q 025886 34 KRRFSDEQIRSLELM-FENET-RLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQ--------LERDYNILQANFNN 103 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~-F~~~~-~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq--------~e~e~~~lk~~~~~ 103 (247)
--++|.+....|.+. +.... +|.-+.-+++-++. +.=.+|+|.+.-.+. ++..+....+....
T Consensus 218 ~L~LteeEkrLL~kEG~slPs~lPLTKaEEriLKrv-------RRKIrNK~SAQESRrkKkeYid~LE~rv~~~taeNqe 290 (472)
T KOG0709|consen 218 PLVLTEEEKRLLTKEGYSLPSKLPLTKAEERILKRV-------RRKIRNKRSAQESRRKKKEYIDGLESRVSAFTAENQE 290 (472)
T ss_pred ceeccHHHHHHHHhccCcCcccCCchHHHHHHHHHH-------HHHHHhhhhhHHHHHhHhhHHHHHhhhhhhcccCcHH
Confidence 456788888888765 33322 34433333343333 222234433222111 12222333344556
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCCC
Q 025886 104 LASRFEALKKEKQALVIQLQKTNELLQNKPRREDQSP 140 (247)
Q Consensus 104 L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~~~~~sp 140 (247)
|....+.|..+|+.|.+||.+|+.++.....+..+..
T Consensus 291 L~kkV~~Le~~N~sLl~qL~klQt~v~q~an~s~qt~ 327 (472)
T KOG0709|consen 291 LQKKVEELELSNRSLLAQLKKLQTLVIQVANKSTQTS 327 (472)
T ss_pred HHHHHHHHhhccHHHHHHHHHHHHHHhhcccchhccc
Confidence 7777778888888889999999988877666544433
No 47
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=79.47 E-value=8.8 Score=35.20 Aligned_cols=50 Identities=26% Similarity=0.336 Sum_probs=31.5
Q ss_pred hhHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 82 RARWKSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 82 RaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
|.|.++++.. ..++.....|..+++.|+.+++.|+.|+.+|+..+.....
T Consensus 208 kSR~~~k~~~---~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~~~ 257 (269)
T KOG3119|consen 208 KSRDKRKQKE---DEMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQLPK 257 (269)
T ss_pred HhhhhHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcc
Confidence 4555554444 2333344566777788888888888888888877654433
No 48
>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=79.33 E-value=16 Score=25.87 Aligned_cols=39 Identities=26% Similarity=0.239 Sum_probs=24.5
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
......|...+..|..++..|..++..|..++..|...+
T Consensus 25 k~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 25 KQYIEELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 344555566666666666777777777766666666543
No 49
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=78.22 E-value=5.4 Score=35.27 Aligned_cols=55 Identities=22% Similarity=0.352 Sum_probs=43.5
Q ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCCC-CCccccccCCC
Q 025886 96 ILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPRREDQS-PSERQCCGQVE 150 (247)
Q Consensus 96 ~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~~~~~s-p~~~~~~~~~~ 150 (247)
.+...|+.|..+++.+..+++.|+.++..|..++.........+ +.....|..++
T Consensus 109 qlE~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~~~~~~~~~~~~~~~~~~~ 164 (198)
T KOG0483|consen 109 QLEKDYESLKRQLESLRSENDRLQSEVQELVAELSSLKREMQKSPENTLTMCPNSE 164 (198)
T ss_pred hhhhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhhhhhccCcccccccCcccc
Confidence 34567899999999999999999999999999999887776663 33345554443
No 50
>PF06005 DUF904: Protein of unknown function (DUF904); InterPro: IPR009252 Cell division protein ZapB is a non-essential, abundant cell division factor that is required for proper Z-ring formation. It is recruited early to the divisome by direct interaction with FtsZ, stimulating Z-ring assembly and thereby promoting cell division earlier in the cell cycle. Its recruitment to the Z-ring requires functional FtsA or ZipA.; GO: 0000917 barrier septum formation, 0043093 cytokinesis by binary fission, 0005737 cytoplasm; PDB: 2JEE_A.
Probab=72.72 E-value=21 Score=26.51 Aligned_cols=39 Identities=21% Similarity=0.249 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
+....+..|+...+.|...+..+..++..|..++.+|+.
T Consensus 15 ~aveti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~ 53 (72)
T PF06005_consen 15 QAVETIALLQMENEELKEKNNELKEENEELKEENEQLKQ 53 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 334445555555555555555555555555555555544
No 51
>smart00338 BRLZ basic region leucin zipper.
Probab=70.34 E-value=31 Score=24.35 Aligned_cols=37 Identities=30% Similarity=0.337 Sum_probs=20.3
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
....|......|..++..|..++..|..++..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444445555555555556556666666665555544
No 52
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=69.58 E-value=40 Score=28.12 Aligned_cols=86 Identities=21% Similarity=0.243 Sum_probs=54.0
Q ss_pred CCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHH-hCCCccceeeeccchhhHHh-------hHHHHHHHHHHHHhhhhhHH
Q 025886 35 RRFSDEQIRSLELMFENETRLEPRKKLQLAKE-LGLQPRQVAIWFQNKRARWK-------SKQLERDYNILQANFNNLAS 106 (247)
Q Consensus 35 t~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~-LgLs~rQVkiWFQNRRaK~K-------rkq~e~e~~~lk~~~~~L~~ 106 (247)
.+|+.+++..|- ..+|-+. -|++...|-.|=|.||+-.- |-+.......|......|..
T Consensus 22 d~lsDd~LvsmS-------------VReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~eLE~~k~~L~q 88 (135)
T KOG4196|consen 22 DRLSDDELVSMS-------------VRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHELEKEKAELQQ 88 (135)
T ss_pred CCcCHHHHHHhh-------------HHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 678888877652 1223333 37888888888888875321 11223333444445556777
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 025886 107 RFEALKKEKQALVIQLQKTNELLQNKP 133 (247)
Q Consensus 107 ~~~~l~~E~~~L~~e~~~l~~~l~~~~ 133 (247)
+.+.|..|+..+..++..++.+.....
T Consensus 89 qv~~L~~e~s~~~~E~da~k~k~e~l~ 115 (135)
T KOG4196|consen 89 QVEKLKEENSRLRRELDAYKSKYEALQ 115 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 778888888888888887777765443
No 53
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=69.43 E-value=21 Score=28.78 Aligned_cols=44 Identities=25% Similarity=0.382 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
+++.....+-..+..|+.....+.+||..|+.|+..|++.|...
T Consensus 12 ~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 12 DLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 45566666677777777888888888888888888888888754
No 54
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=67.62 E-value=14 Score=26.41 Aligned_cols=32 Identities=28% Similarity=0.341 Sum_probs=26.4
Q ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 100 NFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 100 ~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
.|..+..+..++..|+++|..|+.+|+.+|++
T Consensus 27 rY~~vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 27 RYNKVLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 35556667788889999999999999999874
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=65.58 E-value=34 Score=24.15 Aligned_cols=34 Identities=18% Similarity=0.296 Sum_probs=17.4
Q ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 96 ILQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 96 ~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
.-+.....|......|..++..|..++..|...+
T Consensus 23 RKk~~~~~Le~~~~~L~~en~~L~~~~~~L~~~~ 56 (64)
T PF00170_consen 23 RKKQYIEELEEKVEELESENEELKKELEQLKKEI 56 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555555555555555555444
No 56
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=65.27 E-value=25 Score=32.96 Aligned_cols=40 Identities=20% Similarity=0.302 Sum_probs=23.6
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
+.+.+.+-.+...|..+++.|+.....|..|++-|+..|.
T Consensus 247 Rae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~ 286 (294)
T KOG4571|consen 247 RAEKEALLGELEGLEKRNEELKDQASELEREIRYLKQLIL 286 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555556666666666666666666666666554
No 57
>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=64.31 E-value=2.1 Score=30.69 Aligned_cols=43 Identities=21% Similarity=0.339 Sum_probs=27.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeec
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWF 78 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWF 78 (247)
++|+.||+++...+-..+. .......++|+++||++.++..|-
T Consensus 2 ~~r~~ys~e~K~~~v~~~~----~~g~sv~~va~~~gi~~~~l~~W~ 44 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYL----ESGESVSEVAREYGISPSTLYNWR 44 (76)
T ss_dssp -SS----HHHHHHHHHHHH----HHHCHHHHHHHHHTS-HHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHH----HCCCceEeeecccccccccccHHH
Confidence 3567899988777666552 223567889999999999999885
No 58
>PF04967 HTH_10: HTH DNA binding domain; InterPro: IPR007050 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. This entry represents the HTH DNA binding domain found in Halobacterium salinarium (Halobacterium halobium) and described as a putative bacterio-opsin activator.
Probab=63.30 E-value=7.1 Score=27.37 Aligned_cols=38 Identities=26% Similarity=0.262 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCccce
Q 025886 37 FSDEQIRSLELMFENETR--LEPRKKLQLAKELGLQPRQV 74 (247)
Q Consensus 37 fT~~Ql~~LE~~F~~~~~--ps~~~r~eLA~~LgLs~rQV 74 (247)
+|+.|..+|...|...-| |-.....+||..||+++.-|
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 588999999999987665 55556788999999998654
No 59
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=62.95 E-value=29 Score=32.57 Aligned_cols=39 Identities=18% Similarity=0.143 Sum_probs=31.5
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
-...-+..-+.|..+.+.|.+.|+.|+.++..|...|+-
T Consensus 242 YRqKkRae~E~l~ge~~~Le~rN~~LK~qa~~lerEI~y 280 (294)
T KOG4571|consen 242 YRQKKRAEKEALLGELEGLEKRNEELKDQASELEREIRY 280 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344556777888888999999999999999998888764
No 60
>PRK14127 cell division protein GpsB; Provisional
Probab=61.29 E-value=32 Score=27.64 Aligned_cols=45 Identities=11% Similarity=0.252 Sum_probs=30.6
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
..-..+...+-..|+.+..+...|+.++..|+.++..++..+..+
T Consensus 26 ~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~~~~ 70 (109)
T PRK14127 26 DEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQVSVG 70 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhccc
Confidence 344555666666677777777777777777777777777766543
No 61
>PF04545 Sigma70_r4: Sigma-70, region 4; InterPro: IPR007630 The bacterial core RNA polymerase complex, which consists of five subunits, is sufficient for transcription elongation and termination but is unable to initiate transcription. Transcription initiation from promoter elements requires a sixth, dissociable subunit called a sigma factor, which reversibly associates with the core RNA polymerase complex to form a holoenzyme []. RNA polymerase recruits alternative sigma factors as a means of switching on specific regulons. Most bacteria express a multiplicity of sigma factors. Two of these factors, sigma-70 (gene rpoD), generally known as the major or primary sigma factor, and sigma-54 (gene rpoN or ntrA) direct the transcription of a wide variety of genes. The other sigma factors, known as alternative sigma factors, are required for the transcription of specific subsets of genes. With regard to sequence similarity, sigma factors can be grouped into two classes, the sigma-54 and sigma-70 families. Sequence alignments of the sigma70 family members reveal four conserved regions that can be further divided into subregions eg. sub-region 2.2, which may be involved in the binding of the sigma factor to the core RNA polymerase; and sub-region 4.2, which seems to harbor a DNA-binding 'helix-turn-helix' motif involved in binding the conserved -35 region of promoters recognised by the major sigma factors [, ]. Region 4 of sigma-70 like sigma-factors is involved in binding to the -35 promoter element via a helix-turn-helix motif []. Due to the way Pfam works, the threshold has been set artificially high to prevent overlaps with other helix-turn-helix families. Therefore there are many false negatives.; GO: 0003677 DNA binding, 0003700 sequence-specific DNA binding transcription factor activity, 0016987 sigma factor activity, 0006352 transcription initiation, DNA-dependent, 0006355 regulation of transcription, DNA-dependent; PDB: 2P7V_B 3IYD_F 1TLH_B 1KU7_A 1RIO_H 3N97_A 1KU3_A 1RP3_C 1SC5_A 1NR3_A ....
Probab=61.18 E-value=6 Score=26.34 Aligned_cols=37 Identities=16% Similarity=0.267 Sum_probs=28.1
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeee
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIW 77 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiW 77 (247)
.+++.+..+|...| .....-.++|..+|++...|+.+
T Consensus 4 ~L~~~er~vi~~~y-----~~~~t~~eIa~~lg~s~~~V~~~ 40 (50)
T PF04545_consen 4 QLPPREREVIRLRY-----FEGLTLEEIAERLGISRSTVRRI 40 (50)
T ss_dssp TS-HHHHHHHHHHH-----TST-SHHHHHHHHTSCHHHHHHH
T ss_pred hCCHHHHHHHHHHh-----cCCCCHHHHHHHHCCcHHHHHHH
Confidence 57888999999998 33344678999999999888754
No 62
>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=58.78 E-value=52 Score=24.43 Aligned_cols=43 Identities=26% Similarity=0.255 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
..+..+...|+.....|..++..|+.+|+.|+.+-...+..|.
T Consensus 21 ~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl~ 63 (72)
T PF06005_consen 21 ALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERLR 63 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4556677777777778888888888888888877776666654
No 63
>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=55.86 E-value=5.1 Score=25.45 Aligned_cols=42 Identities=14% Similarity=0.213 Sum_probs=30.3
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchh
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKR 82 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRR 82 (247)
.+++.+..++...|... ....++|..+|++...|..|...-+
T Consensus 10 ~l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~ 51 (55)
T cd06171 10 KLPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRAL 51 (55)
T ss_pred hCCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 46777888887776422 2356789999999999988765443
No 64
>smart00338 BRLZ basic region leucin zipper.
Probab=54.55 E-value=73 Score=22.40 Aligned_cols=36 Identities=19% Similarity=0.331 Sum_probs=25.2
Q ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 96 ILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 96 ~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
.-+.....|......|..+|..|..++..|...+..
T Consensus 23 rKk~~~~~Le~~~~~L~~en~~L~~~~~~l~~e~~~ 58 (65)
T smart00338 23 RKKAEIEELERKVEQLEAENERLKKEIERLRRELEK 58 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 335566677777777777777777777777776653
No 65
>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=54.49 E-value=17 Score=20.36 Aligned_cols=37 Identities=16% Similarity=0.339 Sum_probs=24.7
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeee
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIW 77 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiW 77 (247)
.++..+...+...|... . ...++|..+|++...|..|
T Consensus 5 ~~~~~~~~~i~~~~~~~-~----s~~~ia~~~~is~~tv~~~ 41 (42)
T cd00569 5 KLTPEQIEEARRLLAAG-E----SVAEIARRLGVSRSTLYRY 41 (42)
T ss_pred cCCHHHHHHHHHHHHcC-C----CHHHHHHHHCCCHHHHHHh
Confidence 35666666666666532 2 4567889999988777665
No 66
>KOG3650 consensus Predicted coiled-coil protein [General function prediction only]
Probab=53.36 E-value=50 Score=26.45 Aligned_cols=41 Identities=22% Similarity=0.299 Sum_probs=33.8
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 92 RDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 92 ~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
...-.|+.-.+.|....+++++|+-+|+.+++-|-+.+++.
T Consensus 63 tQVLELQnTLdDLSqRVdsVKEEnLKLrSENQVLGQYIeNL 103 (120)
T KOG3650|consen 63 TQVLELQNTLDDLSQRVDSVKEENLKLRSENQVLGQYIENL 103 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhhhhhhhhhHHHHHHHHHH
Confidence 34445677788999999999999999999999998877654
No 67
>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=52.62 E-value=52 Score=23.42 Aligned_cols=32 Identities=19% Similarity=0.353 Sum_probs=18.6
Q ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 99 ANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 99 ~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
+....+.....++++|++.|...+.++++-++
T Consensus 7 n~~~~~~~~i~tvk~en~~i~~~ve~i~envk 38 (55)
T PF05377_consen 7 NELPRIESSINTVKKENEEISESVEKIEENVK 38 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444555566666666666666666665543
No 68
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=52.06 E-value=33 Score=27.11 Aligned_cols=26 Identities=12% Similarity=0.139 Sum_probs=12.5
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 102 NNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 102 ~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
..+..++..++.+|+.|..++..|+.
T Consensus 37 ~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 37 AAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 33334444555555555555555543
No 69
>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=51.95 E-value=76 Score=25.59 Aligned_cols=93 Identities=12% Similarity=0.208 Sum_probs=51.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHHHHH
Q 025886 33 NKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFEALK 112 (247)
Q Consensus 33 ~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~ 112 (247)
..+.|+..++..|. .....+.+|++-.+|+-++......... ..... ..|......++
T Consensus 35 gyR~Y~~~~~~~l~-------------~I~~lr~~G~sL~eI~~~l~~~~~~~~~--~~~~~-------~~l~~~~~~l~ 92 (133)
T cd04787 35 GYRLYSEKDLSRLR-------------FILSARQLGFSLKDIKEILSHADQGESP--CPMVR-------RLIEQRLAETE 92 (133)
T ss_pred CeeeCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhhhccCCCc--HHHHH-------HHHHHHHHHHH
Confidence 45689999998884 3444678888888888777643221100 00111 22333445555
Q ss_pred HHHHHHHHHHHHHHHHHhcCCCCCCCCCCcccccc
Q 025886 113 KEKQALVIQLQKTNELLQNKPRREDQSPSERQCCG 147 (247)
Q Consensus 113 ~E~~~L~~e~~~l~~~l~~~~~~~~~sp~~~~~~~ 147 (247)
.+...|..-...|...+.......+..|.....|.
T Consensus 93 ~~i~~l~~~~~~l~~~~~~~~~~~~~~~~~~~~c~ 127 (133)
T cd04787 93 RRIKELLKLRDRMQQAVSQWQQMPDGAPDGHSICH 127 (133)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhCCCCCCCCCCcCc
Confidence 55666666556666665554444444444455554
No 70
>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=50.74 E-value=52 Score=26.24 Aligned_cols=40 Identities=20% Similarity=0.269 Sum_probs=32.8
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
..+-.+...||.....|..++..|+-||+.|+..+.++..
T Consensus 18 ~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 18 GQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3566777888888888888888899899888888887766
No 71
>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=50.41 E-value=1.1e+02 Score=24.14 Aligned_cols=37 Identities=11% Similarity=0.322 Sum_probs=27.0
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccch
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNR 81 (247)
..++.|+..++..|. .....+.+|++-.+|+..+.+.
T Consensus 33 ~gyR~Y~~~~l~~l~-------------~I~~lr~~G~~L~eI~~~l~~~ 69 (120)
T cd04781 33 GLRRQYDPQVLDRLA-------------LIALGRAAGFSLDEIQAMLSHD 69 (120)
T ss_pred CCceecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 367789999998885 3455777788877777777653
No 72
>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=50.21 E-value=5.3 Score=28.85 Aligned_cols=19 Identities=26% Similarity=0.597 Sum_probs=16.7
Q ss_pred HHHHHHHHhCCCccceeee
Q 025886 59 KKLQLAKELGLQPRQVAIW 77 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiW 77 (247)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3567899999999999988
No 73
>PF15058 Speriolin_N: Speriolin N terminus
Probab=50.06 E-value=27 Score=30.97 Aligned_cols=32 Identities=22% Similarity=0.319 Sum_probs=20.2
Q ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 99 ANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 99 ~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
.+|+-|.+..+.+..||+.|+++|.-+++.++
T Consensus 5 ~~yeGlrhqierLv~ENeeLKKlVrLirEN~e 36 (200)
T PF15058_consen 5 TNYEGLRHQIERLVRENEELKKLVRLIRENHE 36 (200)
T ss_pred cchHHHHHHHHHHHhhhHHHHHHHHHHHHHHH
Confidence 34566666666777777777776666665433
No 74
>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=49.45 E-value=76 Score=23.52 Aligned_cols=39 Identities=23% Similarity=0.328 Sum_probs=26.9
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
.-..++..|..|...+.....++..|.+++..|...+..
T Consensus 22 q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~ 60 (70)
T PF04899_consen 22 QQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQR 60 (70)
T ss_pred HHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHH
Confidence 344566777777777777777777777777777666654
No 75
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=49.00 E-value=67 Score=29.59 Aligned_cols=36 Identities=14% Similarity=0.163 Sum_probs=16.4
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 94 YNILQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 94 ~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
...|......|..+++.|+..++.|..++++|...|
T Consensus 99 i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~l 134 (292)
T KOG4005|consen 99 IKDLTEENEILQNENDSLRAINESLLAKNHELDSEL 134 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHH
Confidence 333444444445555555544444444444444333
No 76
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=47.44 E-value=12 Score=25.70 Aligned_cols=40 Identities=18% Similarity=0.218 Sum_probs=23.3
Q ss_pred HHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHH
Q 025886 59 KKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQ 98 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk 98 (247)
....||+.+|+++..|..|+.++.....-..+.+-+..+.
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~ 51 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALN 51 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcC
Confidence 4567899999999999999988765665555555444443
No 77
>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=46.74 E-value=28 Score=33.38 Aligned_cols=28 Identities=25% Similarity=0.344 Sum_probs=17.1
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 103 NLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 103 ~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
.|..++.+|++||..|+.++.+|++.+.
T Consensus 36 aLr~EN~~LKkEN~~Lk~eVerLE~e~l 63 (420)
T PF07407_consen 36 ALRMENHSLKKENNDLKIEVERLENEML 63 (420)
T ss_pred hHHHHhHHHHHHHHHHHHHHHHHHHHhh
Confidence 4555666666666666666666655554
No 78
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=46.11 E-value=98 Score=31.01 Aligned_cols=46 Identities=11% Similarity=0.180 Sum_probs=29.8
Q ss_pred hhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 86 KSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 86 Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
|...+++..+.++++.+.+......++...+.|..++..|+.++..
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql~a 122 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQVKA 122 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHHHh
Confidence 3345556666666666555566666667777777777777777743
No 79
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=45.04 E-value=63 Score=29.59 Aligned_cols=42 Identities=14% Similarity=0.357 Sum_probs=26.6
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
.++.+.|......|..+++.++....+|..++..|.+++.+.
T Consensus 148 ~~EkeeL~~eleele~e~ee~~erlk~le~E~s~LeE~~~~l 189 (290)
T COG4026 148 QKEKEELLKELEELEAEYEEVQERLKRLEVENSRLEEMLKKL 189 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 344555555666666666666666666777777777666544
No 80
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=44.98 E-value=91 Score=23.45 Aligned_cols=38 Identities=26% Similarity=0.262 Sum_probs=23.4
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 94 YNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 94 ~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
.+.|.+....+....+.|..||+.|+.+-..-++.|+.
T Consensus 34 nn~l~~e~q~~q~~reaL~~eneqlk~e~~~WQerlrs 71 (79)
T COG3074 34 NNSLSQEVQNAQHQREALERENEQLKEEQNGWQERLRA 71 (79)
T ss_pred hhHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34444445555666667777777777776666666553
No 81
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=44.26 E-value=73 Score=25.62 Aligned_cols=39 Identities=21% Similarity=0.279 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
.+-.+...||+....|..++..|+-||+.|+..+.++..
T Consensus 19 ~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 19 VLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 556777888888888999999999999999988887744
No 82
>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=44.02 E-value=1.2e+02 Score=21.71 Aligned_cols=45 Identities=29% Similarity=0.378 Sum_probs=35.6
Q ss_pred hhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 86 KSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 86 Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
|-.++..+...|....+.|......++.+.+..+.|....+++|-
T Consensus 4 kid~Ls~dVq~L~~kvdqLs~dv~~lr~~v~~ak~EAaRAN~RlD 48 (56)
T PF04728_consen 4 KIDQLSSDVQTLNSKVDQLSSDVNALRADVQAAKEEAARANQRLD 48 (56)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345667777888888888888888888888888888888877764
No 83
>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=43.44 E-value=18 Score=24.13 Aligned_cols=40 Identities=15% Similarity=0.258 Sum_probs=26.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccc
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
.+++.+..++...| .......++|..+|+++..|+.|.+.
T Consensus 10 ~L~~~~r~i~~l~~-----~~g~s~~eIa~~l~~s~~~v~~~l~r 49 (54)
T PF08281_consen 10 QLPERQREIFLLRY-----FQGMSYAEIAEILGISESTVKRRLRR 49 (54)
T ss_dssp CS-HHHHHHHHHHH-----TS---HHHHHHHCTS-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHH-----HHCcCHHHHHHHHCcCHHHHHHHHHH
Confidence 35666666666555 34455778999999999999988754
No 84
>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=42.77 E-value=1.1e+02 Score=23.13 Aligned_cols=26 Identities=27% Similarity=0.293 Sum_probs=15.7
Q ss_pred hhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 103 NLASRFEALKKEKQALVIQLQKTNEL 128 (247)
Q Consensus 103 ~L~~~~~~l~~E~~~L~~e~~~l~~~ 128 (247)
.+..++..|+.+.+.|.++|+.++..
T Consensus 4 ei~eEn~~Lk~eiqkle~ELq~~~~~ 29 (76)
T PF07334_consen 4 EIQEENARLKEEIQKLEAELQQNKRE 29 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34455566666666666666666655
No 85
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=42.05 E-value=8.3 Score=42.68 Aligned_cols=59 Identities=17% Similarity=0.089 Sum_probs=50.8
Q ss_pred CCCCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhH
Q 025886 30 KCKNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSK 88 (247)
Q Consensus 30 krr~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krk 88 (247)
.+-.+++++.-|..+|...|....+|.-.....++..|++..+.+-.||++++.++..-
T Consensus 444 ~~~~s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~ 502 (1406)
T KOG1146|consen 444 PLLESKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQN 502 (1406)
T ss_pred hhhhhhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhccc
Confidence 34457788899999999999989999999999999999999999888888877777653
No 86
>PRK10884 SH3 domain-containing protein; Provisional
Probab=41.87 E-value=1.1e+02 Score=27.02 Aligned_cols=37 Identities=19% Similarity=0.177 Sum_probs=21.1
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 92 RDYNILQANFNNLASRFEALKKEKQALVIQLQKTNEL 128 (247)
Q Consensus 92 ~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~ 128 (247)
.....|+..+..|..+...++.+++.|..++..++..
T Consensus 132 ~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~~ 168 (206)
T PRK10884 132 SVINGLKEENQKLKNQLIVAQKKVDAANLQLDDKQRT 168 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344455555566666666666666666666665543
No 87
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=41.39 E-value=1.5e+02 Score=22.57 Aligned_cols=25 Identities=32% Similarity=0.262 Sum_probs=11.8
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 106 SRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 106 ~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
+..+.|..+|+.|+.+...-+++|.
T Consensus 46 ~~r~~L~~en~qLk~E~~~WqerLr 70 (79)
T PRK15422 46 HQREELERENNHLKEQQNGWQERLQ 70 (79)
T ss_pred hhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444555555555544444443
No 88
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=41.33 E-value=26 Score=30.44 Aligned_cols=39 Identities=26% Similarity=0.334 Sum_probs=32.4
Q ss_pred CCCHHHHHHHHHHHhhcCC--CCHHHHHHHHHHhCCCccce
Q 025886 36 RFSDEQIRSLELMFENETR--LEPRKKLQLAKELGLQPRQV 74 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~--ps~~~r~eLA~~LgLs~rQV 74 (247)
.+|+.|+.+|...|...=| |-.....+||++||+++.-+
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst~ 195 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKSTL 195 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHHH
Confidence 6999999999999987654 55666788999999998553
No 89
>KOG2391 consensus Vacuolar sorting protein/ubiquitin receptor VPS23 [Posttranslational modification, protein turnover, chaperones; Intracellular trafficking, secretion, and vesicular transport]
Probab=40.79 E-value=1e+02 Score=29.77 Aligned_cols=47 Identities=21% Similarity=0.164 Sum_probs=28.0
Q ss_pred hhHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 82 RARWKSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNEL 128 (247)
Q Consensus 82 RaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~ 128 (247)
|++.+-.+...+.+.++.-.+.|..-...|+.+++.|+.|++.|+..
T Consensus 222 r~eeeme~~~aeq~slkRt~EeL~~G~~kL~~~~etLEqq~~~L~~n 268 (365)
T KOG2391|consen 222 RREEEMERLQAEQESLKRTEEELNIGKQKLVAMKETLEQQLQSLQKN 268 (365)
T ss_pred HHHHHHHHHHHHHHHHHhhHHHHHhhHHHHHHHHHHHHHHHHHHHhh
Confidence 44444444455556666666666666666666666666666666554
No 90
>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=40.49 E-value=76 Score=22.55 Aligned_cols=25 Identities=28% Similarity=0.457 Sum_probs=12.2
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHH
Q 025886 101 FNNLASRFEALKKEKQALVIQLQKT 125 (247)
Q Consensus 101 ~~~L~~~~~~l~~E~~~L~~e~~~l 125 (247)
+..+..+...++.+++.|..++..|
T Consensus 26 i~~l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 26 IAELQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3334444445555555555555554
No 91
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=40.35 E-value=66 Score=32.82 Aligned_cols=36 Identities=33% Similarity=0.252 Sum_probs=23.0
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 92 RDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 92 ~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
+-...|++....|..+++.|++||-.|+.++..|-.
T Consensus 302 Ey~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 302 EYMLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 334556666666777777777777777766655544
No 92
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=39.70 E-value=75 Score=25.04 Aligned_cols=47 Identities=19% Similarity=0.217 Sum_probs=29.4
Q ss_pred ceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHH
Q 025886 73 QVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFEALKKEKQALVI 120 (247)
Q Consensus 73 QVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~ 120 (247)
++..||++.-- .+-.++.++...+++....+..++..|+.|.+.|+.
T Consensus 16 ~y~l~~g~~G~-~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 16 QYSLWFGKNGI-LDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHhccCCcH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 44578765421 122244556666677777777788888877777765
No 93
>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=39.17 E-value=1.1e+02 Score=22.49 Aligned_cols=44 Identities=11% Similarity=0.156 Sum_probs=26.8
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
++...++.++.....|..+...+..|...|...+...+.++...
T Consensus 11 ~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~rvEam 54 (65)
T TIGR02449 11 HLLEYLERLKSENRLLRAQEKTWREERAQLLEKNEQARQKVEAM 54 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666666666666666666666665555443
No 94
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=38.92 E-value=31 Score=28.90 Aligned_cols=45 Identities=20% Similarity=0.200 Sum_probs=32.9
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhH
Q 025886 34 KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRAR 84 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK 84 (247)
...+++.|..+|...+ . .....++|..||++...|..|-.+.+.+
T Consensus 4 ~~~Lt~rqreVL~lr~--~----GlTq~EIAe~LGiS~~tVs~ie~ra~kk 48 (141)
T PRK03975 4 ESFLTERQIEVLRLRE--R----GLTQQEIADILGTSRANVSSIEKRAREN 48 (141)
T ss_pred ccCCCHHHHHHHHHHH--c----CCCHHHHHHHHCCCHHHHHHHHHHHHHH
Confidence 4578999999998732 1 2335689999999999998876643333
No 95
>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=38.65 E-value=1.2e+02 Score=26.05 Aligned_cols=37 Identities=27% Similarity=0.301 Sum_probs=20.1
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 92 RDYNILQANFNNLASRFEALKKEKQALVIQLQKTNEL 128 (247)
Q Consensus 92 ~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~ 128 (247)
.+...++.....|...++.|.+|++.|..++..+++.
T Consensus 104 ~e~~~l~~e~~~l~~~~e~Le~e~~~L~~~~~~~~eD 140 (161)
T TIGR02894 104 KENERLKNQNESLQKRNEELEKELEKLRQRLSTIEED 140 (161)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444555555555555566666666665555555443
No 96
>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=38.25 E-value=1.5e+02 Score=22.63 Aligned_cols=35 Identities=20% Similarity=0.512 Sum_probs=23.5
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccc
Q 025886 33 NKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 33 ~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
.+..|+..++..|.... ..+.+|++..+|+.++..
T Consensus 35 g~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~ 69 (103)
T cd01106 35 GYRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKD 69 (103)
T ss_pred CceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHc
Confidence 45679999999886543 234567777776666644
No 97
>KOG3335 consensus Predicted coiled-coil protein [General function prediction only]
Probab=37.89 E-value=1.2e+02 Score=26.68 Aligned_cols=37 Identities=14% Similarity=0.147 Sum_probs=27.9
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 025886 97 LQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKP 133 (247)
Q Consensus 97 lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~ 133 (247)
.++....|....+.|..+.+.+...+..|...+.++.
T Consensus 104 ~~~e~~elr~~~~~l~~~i~~~~~~~~~L~~~l~~~~ 140 (181)
T KOG3335|consen 104 RKQEIMELRLKVEKLENAIAELTKFFSQLHSKLNKPE 140 (181)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCcc
Confidence 3455556667778888888899999999987777664
No 98
>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=37.45 E-value=93 Score=23.26 Aligned_cols=55 Identities=27% Similarity=0.390 Sum_probs=34.0
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHHHHH
Q 025886 33 NKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFEALK 112 (247)
Q Consensus 33 ~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~ 112 (247)
....|+..++..|.. ...|...+|++...|+.-+ .+.
T Consensus 35 g~R~y~~~dv~~l~~------------i~~L~~d~g~~l~~i~~~l-------------------------------~l~ 71 (91)
T cd04766 35 GTRRYSERDIERLRR------------IQRLTQELGVNLAGVKRIL-------------------------------ELE 71 (91)
T ss_pred CCeeECHHHHHHHHH------------HHHHHHHcCCCHHHHHHHH-------------------------------HHH
Confidence 445789988888854 3445555777665543211 155
Q ss_pred HHHHHHHHHHHHHHHHHh
Q 025886 113 KEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 113 ~E~~~L~~e~~~l~~~l~ 130 (247)
++.+.|+.++..|++.++
T Consensus 72 ~~~~~l~~~l~~l~~~~~ 89 (91)
T cd04766 72 EELAELRAELDELRARLR 89 (91)
T ss_pred HHHHHHHHHHHHHHHHhc
Confidence 566667777777777665
No 99
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=37.03 E-value=73 Score=31.77 Aligned_cols=25 Identities=36% Similarity=0.583 Sum_probs=17.7
Q ss_pred eeeec---cchhhHHhhHHHHHHHHHHH
Q 025886 74 VAIWF---QNKRARWKSKQLERDYNILQ 98 (247)
Q Consensus 74 VkiWF---QNRRaK~Krkq~e~e~~~lk 98 (247)
.-+|| ||+.+|.+-.++-++.+.|+
T Consensus 228 ~gcw~ay~Qnk~akehv~km~kdle~Lq 255 (575)
T KOG4403|consen 228 GGCWFAYRQNKKAKEHVNKMMKDLEGLQ 255 (575)
T ss_pred hhhhhhhhhhhHHHHHHHHHHHHHHHHH
Confidence 45788 89888888766666655554
No 100
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=36.11 E-value=1.2e+02 Score=27.86 Aligned_cols=45 Identities=22% Similarity=0.287 Sum_probs=31.9
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPRR 135 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~~ 135 (247)
++.....+...+........|.+||+.|+.++..|+..+.+....
T Consensus 207 ~kSR~~~k~~~~e~~~r~~~leken~~lr~~v~~l~~el~~~~~~ 251 (269)
T KOG3119|consen 207 RKSRDKRKQKEDEMAHRVAELEKENEALRTQVEQLKKELATLRRL 251 (269)
T ss_pred HHhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444455557777778888888888888888888887765543
No 101
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=36.11 E-value=1.5e+02 Score=27.23 Aligned_cols=37 Identities=27% Similarity=0.384 Sum_probs=17.3
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 94 YNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 94 ~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
++.++..++.+..+...|.++++.|..++..+++.|.
T Consensus 137 ~ee~kekl~E~~~EkeeL~~eleele~e~ee~~erlk 173 (290)
T COG4026 137 YEELKEKLEELQKEKEELLKELEELEAEYEEVQERLK 173 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344444444444444444455555555555554443
No 102
>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=35.93 E-value=1.4e+02 Score=20.30 Aligned_cols=30 Identities=13% Similarity=0.269 Sum_probs=20.0
Q ss_pred HHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 98 QANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 98 k~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
+.....|......|..+|..|..++..|+.
T Consensus 24 k~~~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 24 KQREEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 444455556677777777777777777654
No 103
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=35.91 E-value=1.3e+02 Score=24.33 Aligned_cols=42 Identities=29% Similarity=0.403 Sum_probs=29.7
Q ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 90 LERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 90 ~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
++.....+-+....|+.....+.+||-.|+.++.+|++.|-.
T Consensus 13 le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 13 LEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 344455555556666667777788888888888888888865
No 104
>PRK14127 cell division protein GpsB; Provisional
Probab=35.57 E-value=1.1e+02 Score=24.61 Aligned_cols=43 Identities=12% Similarity=0.225 Sum_probs=34.6
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCC
Q 025886 94 YNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPRRE 136 (247)
Q Consensus 94 ~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~~~ 136 (247)
.+......+.+...++.+.+|+..|+.++..|+..|.......
T Consensus 25 ~~EVD~FLd~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~~~~~ 67 (109)
T PRK14127 25 QDEVDKFLDDVIKDYEAFQKEIEELQQENARLKAQVDELTKQV 67 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 3445567788888999999999999999999999988665533
No 105
>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=35.02 E-value=95 Score=31.06 Aligned_cols=27 Identities=15% Similarity=0.268 Sum_probs=14.0
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHH
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAK 65 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~ 65 (247)
.++++++..|.- ....|...-|..+|.
T Consensus 41 ~ltpee~kalGi---egDTP~DTlrTlva~ 67 (472)
T TIGR03752 41 ELSPEELKALGI---EGDTPADTLRTLVAE 67 (472)
T ss_pred cCCcchhHhcCC---CCCCccchHHHHHHH
Confidence 577777766642 233454444444333
No 106
>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=34.01 E-value=59 Score=24.63 Aligned_cols=26 Identities=27% Similarity=0.368 Sum_probs=21.9
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 109 EALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 109 ~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
..+.+||..|+.++++|...|+....
T Consensus 3 ~ei~eEn~~Lk~eiqkle~ELq~~~~ 28 (76)
T PF07334_consen 3 HEIQEENARLKEEIQKLEAELQQNKR 28 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 46889999999999999888886544
No 107
>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=33.83 E-value=1.7e+02 Score=23.78 Aligned_cols=44 Identities=20% Similarity=0.351 Sum_probs=32.0
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
..++.+...++..|+.+..-++.-.++++.|+..+..|+++++.
T Consensus 71 ~~L~~el~~l~~ry~t~LellGEK~E~veEL~~Dv~DlK~myr~ 114 (120)
T PF12325_consen 71 EELEQELEELQQRYQTLLELLGEKSEEVEELRADVQDLKEMYRE 114 (120)
T ss_pred HHHHHHHHHHHHHHHHHHHHhcchHHHHHHHHHHHHHHHHHHHH
Confidence 34556666666666666666666678888888888888888764
No 108
>PF03670 UPF0184: Uncharacterised protein family (UPF0184); InterPro: IPR022788 This family of proteins has no known function.
Probab=33.49 E-value=1.2e+02 Score=23.36 Aligned_cols=35 Identities=26% Similarity=0.447 Sum_probs=21.2
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKT 125 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l 125 (247)
..++..+....+.|....+.|++-++.|..+|+.|
T Consensus 25 ~~E~~~ins~LD~Lns~LD~LE~rnD~l~~~L~~L 59 (83)
T PF03670_consen 25 EEEYAAINSMLDQLNSCLDHLEQRNDHLHAQLQEL 59 (83)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHH
Confidence 34566666666666666666666666665555443
No 109
>PRK10884 SH3 domain-containing protein; Provisional
Probab=33.43 E-value=1.7e+02 Score=25.91 Aligned_cols=38 Identities=16% Similarity=0.109 Sum_probs=21.9
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
...........|..++..|+++.+.++.++..|+.++.
T Consensus 126 ~~~~~~~~~~~L~~~n~~L~~~l~~~~~~~~~l~~~~~ 163 (206)
T PRK10884 126 KVAQSDSVINGLKEENQKLKNQLIVAQKKVDAANLQLD 163 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555666666666666666666666555544
No 110
>PHA01750 hypothetical protein
Probab=32.44 E-value=2.1e+02 Score=21.28 Aligned_cols=39 Identities=23% Similarity=0.360 Sum_probs=30.3
Q ss_pred HHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 92 RDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 92 ~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
.-.+..+++.++|.-+.+.++...+.|..++.+++.++-
T Consensus 35 AvkeIV~~ELdNL~~ei~~~kikqDnl~~qv~eik~k~d 73 (75)
T PHA01750 35 AVKEIVNSELDNLKTEIEELKIKQDELSRQVEEIKRKLD 73 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHhhc
Confidence 335566788888888888888888888888888887764
No 111
>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=31.81 E-value=2.5e+02 Score=21.93 Aligned_cols=37 Identities=14% Similarity=0.341 Sum_probs=25.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccch
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNR 81 (247)
...+.|+..++..|.. ....+.+|++-..|+..+...
T Consensus 34 ~gyR~Y~~~~i~~l~~-------------I~~lr~~G~sl~eI~~~l~~~ 70 (123)
T cd04770 34 NGYRLYGEADLARLRF-------------IRRAQALGFSLAEIRELLSLR 70 (123)
T ss_pred CCCccCCHHHHHHHHH-------------HHHHHHCCCCHHHHHHHHHhh
Confidence 3467899999998843 334577788777777666543
No 112
>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=31.42 E-value=2.3e+02 Score=21.48 Aligned_cols=39 Identities=15% Similarity=0.181 Sum_probs=32.7
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHH
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTN 126 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~ 126 (247)
..+......|-..++.+..+++.|+.||+.|..-+..|-
T Consensus 26 ~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~nLm 64 (80)
T PF10224_consen 26 LELQDSLEALSDRVEEVKEENEKLESENEYLQQYIGNLM 64 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356667778888899999999999999999999887763
No 113
>PF12476 DUF3696: Protein of unknown function (DUF3696); InterPro: IPR022532 This domain is found in bacteria and archaea, and is approximately 50 amino acids in length.
Probab=31.22 E-value=25 Score=23.99 Aligned_cols=38 Identities=21% Similarity=0.519 Sum_probs=20.3
Q ss_pred cccccc--ccCCCccccccccccCCCCCCCcccccccCCCCCccCCC
Q 025886 193 IKTEYF--GLHEDEPNLMTMVEPAESSMTSPEDWGNFESDGLFDQSS 237 (247)
Q Consensus 193 ~~~~~~--~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 237 (247)
..+-|| ..++..+.+..+.=..+|.| .+| |.|||||.-
T Consensus 6 v~i~ff~~~~~~~~t~v~~i~id~~G~l---~~W----P~GFFDq~~ 45 (52)
T PF12476_consen 6 VSIYFFEREDEEGETEVRKIKIDEDGRL---SNW----PEGFFDQWD 45 (52)
T ss_pred EEEEEEEecCCCCCcEEEEeeECCCCCC---ccC----CCchhhHHH
Confidence 445566 33332232333332234445 688 899999863
No 114
>KOG1962 consensus B-cell receptor-associated protein and related proteins [Defense mechanisms]
Probab=30.97 E-value=1.8e+02 Score=26.19 Aligned_cols=36 Identities=22% Similarity=0.290 Sum_probs=20.5
Q ss_pred HHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 95 NILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 95 ~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
+..+...+.|.-..+.+..|-++|.++.++|++++.
T Consensus 175 e~~~~~~~al~Kq~e~~~~EydrLlee~~~Lq~~i~ 210 (216)
T KOG1962|consen 175 EKAQKKVDALKKQSEGLQDEYDRLLEEYSKLQEQIE 210 (216)
T ss_pred HHHHHHHHHHHHHHHHcccHHHHHHHHHHHHHHHHh
Confidence 333444444444445555566666777777777765
No 115
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=30.81 E-value=31 Score=22.73 Aligned_cols=39 Identities=21% Similarity=0.265 Sum_probs=18.1
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeee
Q 025886 34 KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIW 77 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiW 77 (247)
.+.||.++...++..+... ....+||+.||.++..|..+
T Consensus 2 ~~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~re 40 (44)
T PF13936_consen 2 YKHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSRE 40 (44)
T ss_dssp ----------HHHHHHCS--------HHHHHHHTT--HHHHHHH
T ss_pred ccchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHH
Confidence 3568888888888876533 34567999999988777544
No 116
>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=30.27 E-value=38 Score=24.35 Aligned_cols=44 Identities=18% Similarity=0.450 Sum_probs=21.8
Q ss_pred CCCCCHH-HHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 34 KRRFSDE-QIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 34 Rt~fT~~-Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
|..|+.. -+.+++.....+. --..+|. .|+++|+++++|+-|-+
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 3455553 3455554443322 2223333 49999999999999853
No 117
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=29.61 E-value=1.4e+02 Score=27.59 Aligned_cols=44 Identities=23% Similarity=0.246 Sum_probs=30.9
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
.+..+.+.|+...+.|...++.|..++..|..++..+++.|...
T Consensus 101 dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~ 144 (292)
T KOG4005|consen 101 DLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAEL 144 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Confidence 44667777777777777777777777777777776666655443
No 118
>PF13518 HTH_28: Helix-turn-helix domain
Probab=29.33 E-value=18 Score=23.68 Aligned_cols=22 Identities=23% Similarity=0.542 Sum_probs=18.4
Q ss_pred HHHHHHHHhCCCccceeeeccc
Q 025886 59 KKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQN 80 (247)
...++|.++|++..+|..|.+.
T Consensus 14 s~~~~a~~~gis~~tv~~w~~~ 35 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIKR 35 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHHH
Confidence 3556999999999999999753
No 119
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.23 E-value=2.6e+02 Score=21.34 Aligned_cols=42 Identities=21% Similarity=0.218 Sum_probs=25.1
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHH-------HHHHHHHHHHHH
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQA-------LVIQLQKTNELL 129 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~-------L~~e~~~l~~~l 129 (247)
++.......|+-..+.|+..+..+..+++. |..++.+|+...
T Consensus 14 qqAvdtI~LLqmEieELKekn~~L~~e~~~~~~~r~~L~~en~qLk~E~ 62 (79)
T PRK15422 14 QQAIDTITLLQMEIEELKEKNNSLSQEVQNAQHQREELERENNHLKEQQ 62 (79)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHHHHHHHHHHHH
Confidence 344455556666666666666666666554 666666666544
No 120
>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=29.22 E-value=2.3e+02 Score=20.97 Aligned_cols=41 Identities=27% Similarity=0.343 Sum_probs=35.5
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
+..++.|+..+.....+...|...+..|-.+|..|.+.+..
T Consensus 27 q~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~~Ls~ql~r 67 (70)
T PF04899_consen 27 QSSYADLQHMFEQTSQENAALSEQVNNLSQQVQRLSEQLER 67 (70)
T ss_pred HHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 56788888888888888999999999999999999888764
No 121
>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=28.82 E-value=37 Score=23.62 Aligned_cols=32 Identities=28% Similarity=0.557 Sum_probs=24.1
Q ss_pred HHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcccee
Q 025886 40 EQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVA 75 (247)
Q Consensus 40 ~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVk 75 (247)
.|+..|+-.+. +...+.. +||..||++.+.|+
T Consensus 6 rq~~Ll~~L~~-~~~~~~~---ela~~l~~S~rti~ 37 (59)
T PF08280_consen 6 RQLKLLELLLK-NKWITLK---ELAKKLNISERTIK 37 (59)
T ss_dssp HHHHHHHHHHH-HTSBBHH---HHHHHCTS-HHHHH
T ss_pred HHHHHHHHHHc-CCCCcHH---HHHHHHCCCHHHHH
Confidence 57888888888 6666544 89999999987764
No 122
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=28.36 E-value=1.5e+02 Score=26.65 Aligned_cols=36 Identities=25% Similarity=0.266 Sum_probs=18.2
Q ss_pred HHHhhhhhHHHHHHHHHHHH---HHHHHHHHHHHHHhcC
Q 025886 97 LQANFNNLASRFEALKKEKQ---ALVIQLQKTNELLQNK 132 (247)
Q Consensus 97 lk~~~~~L~~~~~~l~~E~~---~L~~e~~~l~~~l~~~ 132 (247)
++++...|..++..++.++. .++.|+.+|+++|.-.
T Consensus 74 l~~en~~L~~e~~~l~~~~~~~~~l~~en~~L~~lL~~~ 112 (276)
T PRK13922 74 LREENEELKKELLELESRLQELEQLEAENARLRELLNLK 112 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCc
Confidence 33333444444444444433 5566666777766543
No 123
>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=27.87 E-value=18 Score=23.31 Aligned_cols=22 Identities=23% Similarity=0.229 Sum_probs=18.4
Q ss_pred HHHHHHHhCCCccceeeeccch
Q 025886 60 KLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 60 r~eLA~~LgLs~rQVkiWFQNR 81 (247)
..++|+.+|+++..|+.|.++-
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g 24 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIG 24 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCC
Confidence 4578999999999999997554
No 124
>PF08826 DMPK_coil: DMPK coiled coil domain like; InterPro: IPR014930 This domain is found in the myotonic dystrophy protein kinase (DMPK) and adopts a coiled coil structure. It plays a role in dimerisation []. ; GO: 0004674 protein serine/threonine kinase activity, 0005524 ATP binding, 0006468 protein phosphorylation; PDB: 1WT6_D.
Probab=27.73 E-value=2.4e+02 Score=20.36 Aligned_cols=42 Identities=7% Similarity=0.260 Sum_probs=31.0
Q ss_pred HHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 90 LERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 90 ~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
+..+....+..+-.+..........|..|..++..|+..|..
T Consensus 16 ~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ee 57 (61)
T PF08826_consen 16 IQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEMEE 57 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555666667777777777788888888888888888754
No 125
>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=27.67 E-value=70 Score=25.03 Aligned_cols=33 Identities=21% Similarity=0.716 Sum_probs=19.0
Q ss_pred HHHHHHHHhhcCCCCHH--HHHHHHHHhCCCccceeeeccchhhHHhhHHH
Q 025886 42 IRSLELMFENETRLEPR--KKLQLAKELGLQPRQVAIWFQNKRARWKSKQL 90 (247)
Q Consensus 42 l~~LE~~F~~~~~ps~~--~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~ 90 (247)
+.+..-.|+.++||.+. .... .|||.+|++.+.
T Consensus 14 vRiIk~LyqsnPyP~~~GTr~aR----------------RnRRRRWR~rq~ 48 (91)
T PF00424_consen 14 VRIIKILYQSNPYPSPEGTRQAR----------------RNRRRRWRARQR 48 (91)
T ss_dssp HHHHHHHHHTS-S--S-S-HHHH----------------HHHHHHHHHHHH
T ss_pred HHHHHHHHccccCCCCCCccccc----------------cchhhhHHHHHH
Confidence 34555668999998744 1121 589999998654
No 126
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=27.40 E-value=3.1e+02 Score=22.95 Aligned_cols=37 Identities=30% Similarity=0.435 Sum_probs=18.3
Q ss_pred HHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 94 YNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 94 ~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
...+......|..+..++..|+..|..+++++++++.
T Consensus 61 l~~lt~el~~L~~EL~~l~sEk~~L~k~lq~~q~kv~ 97 (140)
T PF10473_consen 61 LEELTSELNQLELELDTLRSEKENLDKELQKKQEKVS 97 (140)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333444444444445555555555555555555543
No 127
>KOG4286 consensus Dystrophin-like protein [Cell motility; Signal transduction mechanisms; Cytoskeleton]
Probab=26.87 E-value=2.4e+02 Score=30.26 Aligned_cols=45 Identities=20% Similarity=0.316 Sum_probs=38.3
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCC
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPRR 135 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~~ 135 (247)
-.+...++++-.+|......+.+.|+.|..||+.|+..+..|...
T Consensus 840 ~AEAkaLRqHK~RLE~R~rILEdhNKQLESQLqRLr~LLrQP~s~ 884 (966)
T KOG4286|consen 840 IAEAKALRQHKGRLEARMQILEDHNKQLESQLHRLRQLLRQPQAE 884 (966)
T ss_pred HHHHHHHHHhhhhHHHHHHHHHHHhHHHHHHHHHHHHHHhCCCCc
Confidence 345667788888999999999999999999999999999866553
No 128
>PF06056 Terminase_5: Putative ATPase subunit of terminase (gpP-like); InterPro: IPR010332 This family of proteins are annotated as ATPase subunits of phage terminase after []. Terminases are viral proteins that are involved in packaging viral DNA into the capsid.; GO: 0005524 ATP binding, 0019069 viral capsid assembly
Probab=26.85 E-value=23 Score=25.02 Aligned_cols=27 Identities=30% Similarity=0.618 Sum_probs=20.8
Q ss_pred HHHHHHHHhCCCccceeeeccchhhHHhh
Q 025886 59 KKLQLAKELGLQPRQVAIWFQNKRARWKS 87 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQNRRaK~Kr 87 (247)
...+||..||++.+.|..|-+ |-+|..
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 356899999999999999953 455443
No 129
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=26.84 E-value=3.8e+02 Score=22.43 Aligned_cols=42 Identities=19% Similarity=0.226 Sum_probs=37.0
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
.++.+...|.+..+.|..++..+..|.+.++.....|..-..
T Consensus 78 eLE~~k~~L~qqv~~L~~e~s~~~~E~da~k~k~e~l~~~~~ 119 (135)
T KOG4196|consen 78 ELEKEKAELQQQVEKLKEENSRLRRELDAYKSKYEALQNSAV 119 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 567788889999999999999999999999999888887665
No 130
>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=26.72 E-value=42 Score=22.88 Aligned_cols=44 Identities=16% Similarity=0.325 Sum_probs=30.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHH
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARW 85 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~ 85 (247)
.||+.++.+|.....- ....++|..+++++..|.....+=+.|.
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl 46 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKL 46 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHH
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHh
Confidence 5788888888766542 3367899999999999987665544443
No 131
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=26.45 E-value=1.9e+02 Score=29.77 Aligned_cols=51 Identities=18% Similarity=0.163 Sum_probs=35.3
Q ss_pred HHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC--CCCCCCCCCccccc
Q 025886 96 ILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK--PRREDQSPSERQCC 146 (247)
Q Consensus 96 ~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~--~~~~~~sp~~~~~~ 146 (247)
.-|.....|.....++.+|++.|+.|+..|+.+|... .......|+....|
T Consensus 299 KKKEy~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~En~~~kvpsp~~~~ 351 (655)
T KOG4343|consen 299 KKKEYMLGLEARLQALLSENEQLKKENATLKRQLDELVSENQRLKVPSPKGRN 351 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhhcCcccccCCCcccc
Confidence 3444555788888999999999999999999987643 23333444444333
No 132
>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=26.39 E-value=2.3e+02 Score=25.77 Aligned_cols=30 Identities=17% Similarity=0.204 Sum_probs=21.8
Q ss_pred hhhHHHHHHHHHHHHHHHHHHHHHHHHHhc
Q 025886 102 NNLASRFEALKKEKQALVIQLQKTNELLQN 131 (247)
Q Consensus 102 ~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~ 131 (247)
..+......|+.|.++|++.+.+|-++++=
T Consensus 103 r~~~~~~~~L~~Ev~~L~~DN~kLYEKiRy 132 (248)
T PF08172_consen 103 RKQQQTISSLRREVESLRADNVKLYEKIRY 132 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334456677778888888888888888763
No 133
>KOG0150 consensus Spliceosomal protein FBP21 [RNA processing and modification]
Probab=26.31 E-value=1.7e+02 Score=27.94 Aligned_cols=54 Identities=15% Similarity=0.249 Sum_probs=28.6
Q ss_pred eeeeccchhhHHhhH-HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 74 VAIWFQNKRARWKSK-QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 74 VkiWFQNRRaK~Krk-q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
.+|||+|.|+-.+-- +-.++.+.+...+.........-.++-+.|..+++++..
T Consensus 16 CKiWi~dN~~Sv~~He~GkrHke~V~Kritdi~rks~~kekeekKls~~la~mEa 70 (336)
T KOG0150|consen 16 CKIWIKDNPASVRFHERGKRHKENVAKRITDIHRKSLKKEKEEKKLSKELAAMEA 70 (336)
T ss_pred hhhhhcCChHHHHhHhhhhHHHHHHHHHHHHHHHhhHHHHHHHHhhhhHHHHHHH
Confidence 579999988876533 223444444444444444443334444445445544443
No 134
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=26.28 E-value=2.2e+02 Score=27.49 Aligned_cols=46 Identities=20% Similarity=0.229 Sum_probs=30.7
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
........++.....|..+...+..+...++.++.++++++.+...
T Consensus 19 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 64 (398)
T PTZ00454 19 DLYEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRIQS 64 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhC
Confidence 3444444455566677777777777777777777777777766554
No 135
>COG4367 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=26.06 E-value=78 Score=24.83 Aligned_cols=37 Identities=16% Similarity=0.170 Sum_probs=29.6
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCcc
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPR 72 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~r 72 (247)
.+.++|...-...|+.+--+++-...++|..|++++-
T Consensus 2 SLn~eq~~~Tk~elqan~el~~LS~~~iA~~Ln~t~~ 38 (97)
T COG4367 2 SLNPEQKQRTKQELQANFELCPLSDEEIATALNWTEV 38 (97)
T ss_pred CCCHHHHHHHHHHHHHhhhhccccHHHHHHHhCCCHH
Confidence 3567888877777777777777888999999998874
No 136
>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=25.91 E-value=3e+02 Score=24.47 Aligned_cols=22 Identities=18% Similarity=0.383 Sum_probs=13.1
Q ss_pred cccccccccCCCCCcccccccc
Q 025886 179 AELRLGVLSDDDSSIKTEYFGL 200 (247)
Q Consensus 179 ~~~~~~~~~~~~~~~~~~~~~~ 200 (247)
++-+.|.+..+|..+.|+++..
T Consensus 168 i~~~~~~i~~dG~~~~V~~Lrl 189 (251)
T PF11932_consen 168 IEVYQGTITLDGEERQVDFLRL 189 (251)
T ss_pred eeEEEEEEeECCeEEEEEEEee
Confidence 3335666666777777766544
No 137
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=25.88 E-value=64 Score=25.61 Aligned_cols=39 Identities=13% Similarity=0.060 Sum_probs=25.0
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccc
Q 025886 37 FSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 37 fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
+++.+..++...|- ......+||..||+++..|+.+...
T Consensus 107 L~~~~r~ii~l~~~-----~~~s~~EIA~~l~is~~tV~~~~~r 145 (154)
T PRK06759 107 LDEKEKYIIFERFF-----VGKTMGEIALETEMTYYQVRWIYRQ 145 (154)
T ss_pred CCHHHHHHHHHHHh-----cCCCHHHHHHHHCCCHHHHHHHHHH
Confidence 44444444444332 2233578999999999999887653
No 138
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=25.75 E-value=34 Score=27.53 Aligned_cols=28 Identities=18% Similarity=0.215 Sum_probs=20.7
Q ss_pred HHHHHHHHhCCCccceeeeccchhhHHh
Q 025886 59 KKLQLAKELGLQPRQVAIWFQNKRARWK 86 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQNRRaK~K 86 (247)
...+||..+|+++..|..|...-|.+.|
T Consensus 143 ~~~eIA~~lgis~~tv~~~~~ra~~~lr 170 (179)
T PRK11924 143 SYREIAEILGVPVGTVKSRLRRARQLLR 170 (179)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 3478999999999999887654444443
No 139
>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=25.53 E-value=3.2e+02 Score=23.21 Aligned_cols=15 Identities=13% Similarity=0.124 Sum_probs=8.7
Q ss_pred HHHHHHHHHhhcCCC
Q 025886 41 QIRSLELMFENETRL 55 (247)
Q Consensus 41 Ql~~LE~~F~~~~~p 55 (247)
-+..|+..+..+.-.
T Consensus 34 vLE~Le~~~~~n~~~ 48 (158)
T PF09744_consen 34 VLELLESLASRNQEH 48 (158)
T ss_pred HHHHHHHHHHhhhhh
Confidence 345666667666633
No 140
>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=25.51 E-value=55 Score=24.90 Aligned_cols=40 Identities=18% Similarity=0.212 Sum_probs=24.4
Q ss_pred CCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccch
Q 025886 37 FSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 37 fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNR 81 (247)
+++.+..++...|- ......+||..+|+++..|..+...-
T Consensus 111 L~~~~~~ii~~~~~-----~g~s~~eIA~~l~~s~~~v~~~~~~~ 150 (158)
T TIGR02937 111 LPEREREVLVLRYL-----EGLSYKEIAEILGISVGTVKRRLKRA 150 (158)
T ss_pred CCHHHHHHHhhHHh-----cCCCHHHHHHHHCCCHHHHHHHHHHH
Confidence 44445445443332 22345688999999999888765443
No 141
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=25.37 E-value=2.2e+02 Score=30.13 Aligned_cols=21 Identities=24% Similarity=0.388 Sum_probs=14.4
Q ss_pred CCHHHHHHHHHHhCCCcccee
Q 025886 55 LEPRKKLQLAKELGLQPRQVA 75 (247)
Q Consensus 55 ps~~~r~eLA~~LgLs~rQVk 75 (247)
|....-..+|+.+|+++.-|.
T Consensus 485 ~g~S~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 485 PGKSNAFEIAKRLGLPENIIE 505 (782)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 344455678888888877664
No 142
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=25.31 E-value=1.2e+02 Score=27.18 Aligned_cols=27 Identities=37% Similarity=0.342 Sum_probs=17.1
Q ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 025886 99 ANFNNLASRFEALKKEKQALVIQLQKT 125 (247)
Q Consensus 99 ~~~~~L~~~~~~l~~E~~~L~~e~~~l 125 (247)
..+..+..+++.|++|+..|+.++.++
T Consensus 69 ~~~~~l~~en~~L~~e~~~l~~~~~~~ 95 (276)
T PRK13922 69 ASLFDLREENEELKKELLELESRLQEL 95 (276)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 345566666777777776666666644
No 143
>COG3416 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=25.24 E-value=2.7e+02 Score=25.17 Aligned_cols=35 Identities=11% Similarity=-0.002 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHhcCCCCCCCCCCccccc
Q 025886 112 KKEKQALVIQLQKTNELLQNKPRREDQSPSERQCC 146 (247)
Q Consensus 112 ~~E~~~L~~e~~~l~~~l~~~~~~~~~sp~~~~~~ 146 (247)
++-.+++..|+.+|+.+++........++++.+..
T Consensus 54 E~ALk~a~~~i~eLe~ri~~lq~~~~~sgsFLs~~ 88 (233)
T COG3416 54 EQALKKASTQIKELEKRIAILQAGEAGSGSFLSNA 88 (233)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhcccCCCcchhhhh
Confidence 34456667777777777776666556666665554
No 144
>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=25.10 E-value=3.2e+02 Score=24.04 Aligned_cols=42 Identities=10% Similarity=0.164 Sum_probs=28.5
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
......|......+...+-.+..+...|..|+..|+......
T Consensus 174 ~~~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~ 215 (221)
T PF05700_consen 174 GEELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAEL 215 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334445666666667777777777788888888887766544
No 145
>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=25.09 E-value=2.3e+02 Score=25.80 Aligned_cols=49 Identities=18% Similarity=0.273 Sum_probs=40.0
Q ss_pred hhHHhhHHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 82 RARWKSKQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 82 RaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
|-|.|-..++.+...+++....|..+.+.|+.+|-+|=..+.=|+..-.
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLYEKiRylqSY~~ 138 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLYEKIRYLQSYNN 138 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCcc
Confidence 5556666788888888899999999999999999999888877766543
No 146
>PF15058 Speriolin_N: Speriolin N terminus
Probab=25.07 E-value=1.6e+02 Score=26.25 Aligned_cols=39 Identities=21% Similarity=0.245 Sum_probs=29.4
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcC
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNK 132 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~ 132 (247)
.|+.++..++.|..+++.||+.++-| .|++.|+..|-+.
T Consensus 6 ~yeGlrhqierLv~ENeeLKKlVrLi-rEN~eLksaL~ea 44 (200)
T PF15058_consen 6 NYEGLRHQIERLVRENEELKKLVRLI-RENHELKSALGEA 44 (200)
T ss_pred chHHHHHHHHHHHhhhHHHHHHHHHH-HHHHHHHHHHHHh
Confidence 46677778888889999999887655 4777888876443
No 147
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=24.93 E-value=2.8e+02 Score=20.28 Aligned_cols=40 Identities=13% Similarity=0.110 Sum_probs=20.7
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHh
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQ 130 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~ 130 (247)
+.....|....+....+....-.++..|+.++..|+..+.
T Consensus 25 ~~~~k~L~~ERd~~~~~l~~a~~e~~~Lk~E~e~L~~el~ 64 (69)
T PF14197_consen 25 EIENKRLRRERDSAERQLGDAYEENNKLKEENEALRKELE 64 (69)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444445555556666655555544
No 148
>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=24.88 E-value=3.3e+02 Score=21.04 Aligned_cols=75 Identities=16% Similarity=0.259 Sum_probs=41.6
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchhhHHhhHHHHHHHHHHHHhhhhhHHHHHHHH
Q 025886 33 NKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKRARWKSKQLERDYNILQANFNNLASRFEALK 112 (247)
Q Consensus 33 ~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRRaK~Krkq~e~e~~~lk~~~~~L~~~~~~l~ 112 (247)
..+.|+..++..|.. ....+.+|++-.+|+..+........ ........|......+.
T Consensus 35 gyR~Y~~~~l~~l~~-------------I~~lr~~G~sL~eI~~~l~~~~~~~~---------~~~~~~~~l~~~~~~l~ 92 (113)
T cd01109 35 GIRDFTEEDLEWLEF-------------IKCLRNTGMSIKDIKEYAELRREGDS---------TIPERLELLEEHREELE 92 (113)
T ss_pred CCccCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHHHHccCCc---------cHHHHHHHHHHHHHHHH
Confidence 355799999888853 33456778887777766654321110 01112233444555555
Q ss_pred HHHHHHHHHHHHHHHHH
Q 025886 113 KEKQALVIQLQKTNELL 129 (247)
Q Consensus 113 ~E~~~L~~e~~~l~~~l 129 (247)
.+...|...+..|..++
T Consensus 93 ~~i~~l~~~~~~l~~~~ 109 (113)
T cd01109 93 EQIAELQETLAYLDYKI 109 (113)
T ss_pred HHHHHHHHHHHHHHHHH
Confidence 66666665555555554
No 149
>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=24.85 E-value=1.8e+02 Score=20.61 Aligned_cols=30 Identities=33% Similarity=0.420 Sum_probs=19.6
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQAL 118 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L 118 (247)
+...+...++...+.+..+++.++.+.+.|
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 344556666666666777777777776666
No 150
>PF07716 bZIP_2: Basic region leucine zipper; InterPro: IPR011700 The basic-leucine zipper (bZIP) transcription factors [, ] of eukaryotes are proteins that contain a basic region mediating sequence-specific DNA-binding, followed by a leucine zipper region (see IPR002158 from INTERPRO), which is required for dimerization.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0046983 protein dimerization activity, 0006355 regulation of transcription, DNA-dependent; PDB: 1NWQ_A 1H89_B 1H88_A 1GTW_B 2E43_A 1IO4_A 1GU4_B 2E42_A 1H8A_B 1GU5_B ....
Probab=24.65 E-value=2.3e+02 Score=19.20 Aligned_cols=29 Identities=21% Similarity=0.219 Sum_probs=18.0
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHH
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQ 121 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e 121 (247)
....+......|..++..|..++..|..|
T Consensus 26 ~~~~le~~~~~L~~en~~L~~~i~~L~~E 54 (54)
T PF07716_consen 26 REEELEQEVQELEEENEQLRQEIAQLERE 54 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 34455556666667777777776666543
No 151
>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=24.26 E-value=25 Score=31.82 Aligned_cols=33 Identities=18% Similarity=0.166 Sum_probs=0.0
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHH
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALVIQLQKT 125 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l 125 (247)
.+.-|+...+.|..+++.|++||+.|.+++..|
T Consensus 130 ~I~dLrrlVe~L~aeNErLr~EnkqL~ae~arL 162 (243)
T PF08961_consen 130 KIADLRRLVEFLLAENERLRRENKQLKAENARL 162 (243)
T ss_dssp ---------------------------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 356778888889999999999999999988887
No 152
>PF10473 CENP-F_leu_zip: Leucine-rich repeats of kinetochore protein Cenp-F/LEK1; InterPro: IPR019513 Cenp-F, a centromeric kinetochore, microtubule-binding protein consisting of two 1,600-amino acid-long coils, is essential for the full functioning of the mitotic checkpoint pathway [, ]. There are several leucine-rich repeats along the sequence of LEK1 that are considered to be zippers, though they do not appear to be binding DNA directly in this instance []. ; GO: 0008134 transcription factor binding, 0042803 protein homodimerization activity, 0045502 dynein binding
Probab=24.13 E-value=4e+02 Score=22.26 Aligned_cols=8 Identities=13% Similarity=0.044 Sum_probs=2.8
Q ss_pred HHHHHHHH
Q 025886 118 LVIQLQKT 125 (247)
Q Consensus 118 L~~e~~~l 125 (247)
+..+...|
T Consensus 78 l~sEk~~L 85 (140)
T PF10473_consen 78 LRSEKENL 85 (140)
T ss_pred HHHHHHHH
Confidence 33333333
No 153
>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=23.94 E-value=2.7e+02 Score=29.46 Aligned_cols=21 Identities=10% Similarity=0.170 Sum_probs=14.2
Q ss_pred CCHHHHHHHHHHhCCCcccee
Q 025886 55 LEPRKKLQLAKELGLQPRQVA 75 (247)
Q Consensus 55 ps~~~r~eLA~~LgLs~rQVk 75 (247)
|....-..+|+.+|+++.-|.
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 444455678888888876654
No 154
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=23.82 E-value=2.6e+02 Score=25.21 Aligned_cols=29 Identities=28% Similarity=0.379 Sum_probs=20.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 025886 105 ASRFEALKKEKQALVIQLQKTNELLQNKP 133 (247)
Q Consensus 105 ~~~~~~l~~E~~~L~~e~~~l~~~l~~~~ 133 (247)
.+++..++.|+++|+.++.+++..+.+..
T Consensus 115 ~sEF~~lr~e~EklkndlEk~ks~lr~ei 143 (220)
T KOG3156|consen 115 RSEFANLRAENEKLKNDLEKLKSSLRHEI 143 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45666777788888888888877776443
No 155
>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=23.71 E-value=2.4e+02 Score=21.90 Aligned_cols=33 Identities=24% Similarity=0.323 Sum_probs=20.2
Q ss_pred HHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 97 LQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 97 lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
+....+.|..+...+..|++.|+.++...+...
T Consensus 47 wek~v~~L~~e~~~l~~E~e~L~~~l~~e~~Ek 79 (87)
T PF12709_consen 47 WEKKVDELENENKALKRENEQLKKKLDTEREEK 79 (87)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 334455666666777777777776666555543
No 156
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=23.68 E-value=44 Score=27.44 Aligned_cols=26 Identities=12% Similarity=0.263 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCccceeeeccchhhHH
Q 025886 60 KLQLAKELGLQPRQVAIWFQNKRARW 85 (247)
Q Consensus 60 r~eLA~~LgLs~rQVkiWFQNRRaK~ 85 (247)
..+||..||+++..|+++...-|.+.
T Consensus 148 ~~eIA~~lgis~~tV~~~l~Rar~~L 173 (179)
T PRK12514 148 YKELAERHDVPLNTMRTWLRRSLLKL 173 (179)
T ss_pred HHHHHHHHCCChHHHHHHHHHHHHHH
Confidence 56899999999999987665444333
No 157
>PRK14872 rod shape-determining protein MreC; Provisional
Probab=23.66 E-value=1.3e+02 Score=28.72 Aligned_cols=26 Identities=19% Similarity=0.057 Sum_probs=13.4
Q ss_pred HhhhhhHHHHHHHHHHHHHHHHHHHH
Q 025886 99 ANFNNLASRFEALKKEKQALVIQLQK 124 (247)
Q Consensus 99 ~~~~~L~~~~~~l~~E~~~L~~e~~~ 124 (247)
..|-.|..+++.|++|+..|..++..
T Consensus 57 ~~y~~L~~EN~~Lk~Ena~L~~~l~~ 82 (337)
T PRK14872 57 SHALVLETENFLLKERIALLEERLKS 82 (337)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33444555555555555555444444
No 158
>cd04785 HTH_CadR-PbrR-like Helix-Turn-Helix DNA binding domain of the CadR- and PbrR-like transcription regulators. Helix-turn-helix (HTH) CadR- and PbrR-like transcription regulators. CadR and PbrR regulate expression of the cadmium and lead resistance operons, respectively. These proteins are comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the C-terminal domains have three conserved cysteines which comprise a putative metal binding site. Some members in this group have a histidine-rich C-terminal extension. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements.
Probab=23.51 E-value=3.8e+02 Score=21.26 Aligned_cols=35 Identities=14% Similarity=0.390 Sum_probs=23.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
...+.|+..++..|... ..++.+|++-.+|+..+.
T Consensus 34 ~g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~ 68 (126)
T cd04785 34 GGYRLYGAAHVERLRFI-------------RRARDLGFSLEEIRALLA 68 (126)
T ss_pred CCccccCHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHh
Confidence 34567999999888643 335677777777666654
No 159
>PF05377 FlaC_arch: Flagella accessory protein C (FlaC); InterPro: IPR008039 Although archaeal flagella appear superficially similar to those of bacteria, they are quite distinct []. In several archaea, the flagellin genes are followed immediately by the flagellar accessory genes flaCDEFGHIJ. The gene products may have a role in translocation, secretion, or assembly of the flagellum. FlaC is a protein whose exact role is unknown but it has been shown to be membrane-associated (by immuno-blotting fractionated cells) [].
Probab=23.51 E-value=2.8e+02 Score=19.73 Aligned_cols=39 Identities=10% Similarity=0.222 Sum_probs=29.3
Q ss_pred HHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 89 QLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 89 q~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
.++.+...+....+.+..+++.+.++.+.+..-+++|=.
T Consensus 4 elEn~~~~~~~~i~tvk~en~~i~~~ve~i~envk~ll~ 42 (55)
T PF05377_consen 4 ELENELPRIESSINTVKKENEEISESVEKIEENVKDLLS 42 (55)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 456667777778888888999999888888776655433
No 160
>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=23.20 E-value=96 Score=26.73 Aligned_cols=41 Identities=22% Similarity=0.220 Sum_probs=0.0
Q ss_pred HHHHHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 88 KQLERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELL 129 (247)
Q Consensus 88 kq~e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l 129 (247)
.+..+.++. .+-.+.-..+.+.|+.++|+|+.|+..|+..+
T Consensus 7 sklN~AIER-nalLE~ELdEKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 7 SKLNQAIER-NALLESELDEKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHHH-HHHHHHHHHHHHHHHHCH--------------
T ss_pred HHHHHHHHH-hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
No 161
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=23.17 E-value=47 Score=27.90 Aligned_cols=22 Identities=14% Similarity=0.187 Sum_probs=17.0
Q ss_pred HHHHHHHHhCCCccceeeeccc
Q 025886 59 KKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQN 80 (247)
...+||..||++...|+.+...
T Consensus 160 s~~EIA~~Lgis~~tVk~~l~r 181 (194)
T PRK09646 160 TYREVAERLAVPLGTVKTRMRD 181 (194)
T ss_pred CHHHHHHHhCCChHhHHHHHHH
Confidence 3467899999999999776543
No 162
>PHA02955 hypothetical protein; Provisional
Probab=22.94 E-value=1.1e+02 Score=27.50 Aligned_cols=42 Identities=7% Similarity=0.160 Sum_probs=33.6
Q ss_pred HHHHHHHHHHHhhc-CCCCHHHHHHHHHHhCCCccceeeeccc
Q 025886 39 DEQIRSLELMFENE-TRLEPRKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 39 ~~Ql~~LE~~F~~~-~~ps~~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
..++..|-..|... ..+++++|.++|++||+....|..||.+
T Consensus 60 ~~sf~lli~a~~Et~~~Lp~~qk~~ia~~lgI~~~~~~~d~~t 102 (213)
T PHA02955 60 EKNFQLLIEALIETIENFPEKEQKEIAADIGINIDDYKAGKKT 102 (213)
T ss_pred HHHHHHHHHHHHHHHHhCCHHHHHHHHHHhCCChhhccCcccc
Confidence 45666666666654 5788999999999999999878888876
No 163
>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=22.89 E-value=16 Score=27.37 Aligned_cols=35 Identities=17% Similarity=0.161 Sum_probs=25.3
Q ss_pred HHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccc
Q 025886 46 ELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 46 E~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
+..|....+.......+||..||+++..|+.|+.+
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 33444444444455788999999999999998764
No 164
>TIGR02047 CadR-PbrR Cd(II)/Pb(II)-responsive transcriptional regulator. This model represents the cadmium(II) and/or lead(II) responsive transcriptional activator of the proteobacterial metal efflux system. This protein is a member of the MerR family of transcriptional activators (pfam00376) and contains a distinctive pattern of cysteine residues in its metal binding loop, Cys-X(6-9)-Cys, as well as a conserved and critical cysteine at the N-terminal end of the dimerization helix.
Probab=22.76 E-value=4e+02 Score=21.24 Aligned_cols=35 Identities=11% Similarity=0.309 Sum_probs=24.8
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
...+.|+..++..|.. ...++.+|++-.+|+-.+.
T Consensus 34 ~gyR~Y~~~~l~~l~~-------------I~~lr~lG~sL~eI~~~l~ 68 (127)
T TIGR02047 34 NNYRVYTVGHVERLAF-------------IRNCRTLDMSLAEIRQLLR 68 (127)
T ss_pred CCCCcCCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHH
Confidence 4567899999888853 3346778888877776664
No 165
>smart00421 HTH_LUXR helix_turn_helix, Lux Regulon. lux regulon (activates the bioluminescence operon
Probab=22.57 E-value=72 Score=20.36 Aligned_cols=38 Identities=18% Similarity=0.336 Sum_probs=27.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
.+++.+..++...+. . ....++|..+|+++..|..+..
T Consensus 3 ~l~~~e~~i~~~~~~-g-----~s~~eia~~l~is~~tv~~~~~ 40 (58)
T smart00421 3 SLTPREREVLRLLAE-G-----LTNKEIAERLGISEKTVKTHLS 40 (58)
T ss_pred CCCHHHHHHHHHHHc-C-----CCHHHHHHHHCCCHHHHHHHHH
Confidence 467778887765432 1 2457899999999999977654
No 166
>PHA00728 hypothetical protein
Probab=22.54 E-value=1.5e+02 Score=24.59 Aligned_cols=28 Identities=32% Similarity=0.490 Sum_probs=23.6
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHHhcCC
Q 025886 106 SRFEALKKEKQALVIQLQKTNELLQNKP 133 (247)
Q Consensus 106 ~~~~~l~~E~~~L~~e~~~l~~~l~~~~ 133 (247)
.+.+.|++||+.|+..+++|...|.+..
T Consensus 5 teveql~keneelkkkla~leal~nn~~ 32 (151)
T PHA00728 5 TEVEQLKKENEELKKKLAELEALMNNES 32 (151)
T ss_pred hHHHHHHHhHHHHHHHHHHHHHHHcCCC
Confidence 3667899999999999999999987543
No 167
>PF13411 MerR_1: MerR HTH family regulatory protein; PDB: 2JML_A 3GP4_A 3GPV_B.
Probab=22.53 E-value=28 Score=24.24 Aligned_cols=20 Identities=25% Similarity=0.406 Sum_probs=17.1
Q ss_pred HHHHHHHhCCCccceeeecc
Q 025886 60 KLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 60 r~eLA~~LgLs~rQVkiWFQ 79 (247)
..++|+.+|+++..|+.|=+
T Consensus 3 i~eva~~~gvs~~tlr~y~~ 22 (69)
T PF13411_consen 3 IKEVAKLLGVSPSTLRYYER 22 (69)
T ss_dssp HHHHHHHTTTTHHHHHHHHH
T ss_pred HHHHHHHHCcCHHHHHHHHH
Confidence 45789999999999999954
No 168
>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=22.49 E-value=3.4e+02 Score=21.16 Aligned_cols=37 Identities=19% Similarity=0.445 Sum_probs=25.2
Q ss_pred CCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccchh
Q 025886 33 NKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNKR 82 (247)
Q Consensus 33 ~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNRR 82 (247)
..+.|+..++..|.. ....+.+|++-.+|+..+....
T Consensus 34 ~yR~Y~~~d~~~l~~-------------I~~lr~~G~sl~eI~~~l~~~~ 70 (116)
T cd04769 34 NYRVYDAQHVECLRF-------------IKEARQLGFTLAELKAIFAGHE 70 (116)
T ss_pred CceeeCHHHHHHHHH-------------HHHHHHcCCCHHHHHHHHhccc
Confidence 456788888888753 3335777777777777665544
No 169
>PF07989 Microtub_assoc: Microtubule associated; InterPro: IPR012943 Proteins with this domain associate with the spindle body during cell division [].
Probab=22.42 E-value=1.5e+02 Score=22.12 Aligned_cols=24 Identities=29% Similarity=0.332 Sum_probs=11.0
Q ss_pred hHHHHHHHHHHHHHHHHHHHHHHH
Q 025886 104 LASRFEALKKEKQALVIQLQKTNE 127 (247)
Q Consensus 104 L~~~~~~l~~E~~~L~~e~~~l~~ 127 (247)
|..+...+++|.+.+...+.++..
T Consensus 48 LKve~~~L~~el~~~~~~l~~a~~ 71 (75)
T PF07989_consen 48 LKVEVESLKRELQEKKKLLKEAEK 71 (75)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444444444444444444444443
No 170
>PF13384 HTH_23: Homeodomain-like domain; PDB: 2X48_C.
Probab=22.29 E-value=25 Score=22.98 Aligned_cols=23 Identities=26% Similarity=0.465 Sum_probs=17.0
Q ss_pred HHHHHHHHHhCCCccceeeeccc
Q 025886 58 RKKLQLAKELGLQPRQVAIWFQN 80 (247)
Q Consensus 58 ~~r~eLA~~LgLs~rQVkiWFQN 80 (247)
....++|..||+++..|..|.+.
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 44678999999999999999653
No 171
>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=22.27 E-value=1.4e+02 Score=21.50 Aligned_cols=27 Identities=22% Similarity=0.394 Sum_probs=12.4
Q ss_pred HHHHHHHhhhhhHHHHHHHHHHHHHHH
Q 025886 93 DYNILQANFNNLASRFEALKKEKQALV 119 (247)
Q Consensus 93 e~~~lk~~~~~L~~~~~~l~~E~~~L~ 119 (247)
+.+.||..+..|...+..|+.||..|+
T Consensus 15 EVevLK~~I~eL~~~n~~Le~EN~~Lk 41 (59)
T PF01166_consen 15 EVEVLKEQIAELEERNSQLEEENNLLK 41 (59)
T ss_dssp SHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 444555544444444444444444433
No 172
>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=22.09 E-value=46 Score=26.54 Aligned_cols=21 Identities=24% Similarity=0.164 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCccceeeecc
Q 025886 59 KKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQ 79 (247)
...+||..+|+++..|+++..
T Consensus 129 ~~~eIA~~l~is~~tv~~~l~ 149 (159)
T TIGR02989 129 SLTALAEQLGRTVNAVYKALS 149 (159)
T ss_pred CHHHHHHHhCCCHHHHHHHHH
Confidence 456889999999999987543
No 173
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=21.99 E-value=45 Score=26.90 Aligned_cols=39 Identities=15% Similarity=0.055 Sum_probs=25.2
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
.+++.+..+|...|- ......++|..||+++..|+.+..
T Consensus 128 ~L~~~~r~vl~l~~~-----~~~s~~eIA~~lgis~~tV~~~l~ 166 (182)
T PRK09652 128 SLPEELRTAITLREI-----EGLSYEEIAEIMGCPIGTVRSRIF 166 (182)
T ss_pred hCCHHHHHHHHHHHH-----cCCCHHHHHHHHCCCHHHHHHHHH
Confidence 355555555554432 122346789999999999987765
No 174
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=21.93 E-value=51 Score=26.47 Aligned_cols=27 Identities=15% Similarity=0.138 Sum_probs=19.5
Q ss_pred HHHHHHHhCCCccceeeeccchhhHHh
Q 025886 60 KLQLAKELGLQPRQVAIWFQNKRARWK 86 (247)
Q Consensus 60 r~eLA~~LgLs~rQVkiWFQNRRaK~K 86 (247)
..+||..||+++..|+.....-|.+.|
T Consensus 125 ~~EIA~~lgis~~tV~~~l~Rar~~Lr 151 (160)
T PRK09642 125 YQEIALQEKIEVKTVEMKLYRARKWIK 151 (160)
T ss_pred HHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 358899999999999876654444333
No 175
>PRK04217 hypothetical protein; Provisional
Probab=21.81 E-value=77 Score=25.38 Aligned_cols=41 Identities=15% Similarity=0.101 Sum_probs=29.8
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeecc
Q 025886 34 KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQ 79 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQ 79 (247)
-..++.++..++...|...- ...+||+.+|++...|...+.
T Consensus 40 ~~~Lt~eereai~l~~~eGl-----S~~EIAk~LGIS~sTV~r~L~ 80 (110)
T PRK04217 40 PIFMTYEEFEALRLVDYEGL-----TQEEAGKRMGVSRGTVWRALT 80 (110)
T ss_pred cccCCHHHHHHHHHHHHcCC-----CHHHHHHHHCcCHHHHHHHHH
Confidence 34688889888877664333 467799999999988765443
No 176
>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=21.57 E-value=52 Score=21.56 Aligned_cols=38 Identities=21% Similarity=0.429 Sum_probs=23.9
Q ss_pred CCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeec
Q 025886 36 RFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWF 78 (247)
Q Consensus 36 ~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWF 78 (247)
.++.+++..+...+... ....+||+.+|++...|..++
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 35565566666666544 337789999999988776443
No 177
>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=21.42 E-value=3.4e+02 Score=24.09 Aligned_cols=13 Identities=31% Similarity=1.063 Sum_probs=7.4
Q ss_pred CCccCCCCccccc
Q 025886 231 GLFDQSSSEYQWW 243 (247)
Q Consensus 231 ~~~~~~~~~~~~~ 243 (247)
|++|+.....+|+
T Consensus 205 g~~~~~~~~W~~l 217 (251)
T PF11932_consen 205 GVWDPATGQWQWL 217 (251)
T ss_pred eeecCCCCCCeEC
Confidence 4666666554444
No 178
>COG2963 Transposase and inactivated derivatives [DNA replication, recombination, and repair]
Probab=21.23 E-value=1.1e+02 Score=23.69 Aligned_cols=42 Identities=17% Similarity=0.319 Sum_probs=31.6
Q ss_pred CCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCC-Cccceeeecc
Q 025886 34 KRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGL-QPRQVAIWFQ 79 (247)
Q Consensus 34 Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgL-s~rQVkiWFQ 79 (247)
+.+|+.+....+-..+....+ ....+|+++|+ .+.++..|-+
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 678999877666665554443 57789999996 9999888854
No 179
>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=21.22 E-value=2.4e+02 Score=25.94 Aligned_cols=17 Identities=24% Similarity=0.184 Sum_probs=12.0
Q ss_pred HHHHHHHHHHHHHhcCC
Q 025886 117 ALVIQLQKTNELLQNKP 133 (247)
Q Consensus 117 ~L~~e~~~l~~~l~~~~ 133 (247)
.|+.|+.+|+++|.-..
T Consensus 95 ~l~~EN~rLr~LL~~~~ 111 (283)
T TIGR00219 95 NLKQENVRLRELLNSPL 111 (283)
T ss_pred HHHHHHHHHHHHhcCcc
Confidence 37778888888776543
No 180
>PF13565 HTH_32: Homeodomain-like domain
Probab=21.16 E-value=2.6e+02 Score=19.54 Aligned_cols=32 Identities=28% Similarity=0.497 Sum_probs=24.4
Q ss_pred CHHHHHHHHHHHhhcCCCCHHHHHH-HHHHhCC
Q 025886 38 SDEQIRSLELMFENETRLEPRKKLQ-LAKELGL 69 (247)
Q Consensus 38 T~~Ql~~LE~~F~~~~~ps~~~r~e-LA~~LgL 69 (247)
++++...|...+..++..+..+... |+.++|+
T Consensus 32 ~~e~~~~i~~~~~~~p~wt~~~i~~~L~~~~g~ 64 (77)
T PF13565_consen 32 DPEQRERIIALIEEHPRWTPREIAEYLEEEFGI 64 (77)
T ss_pred cHHHHHHHHHHHHhCCCCCHHHHHHHHHHHhCC
Confidence 6777788888888888777776655 6777774
No 181
>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=21.15 E-value=47 Score=26.15 Aligned_cols=23 Identities=22% Similarity=0.372 Sum_probs=17.4
Q ss_pred HHHHHHHHhCCCccceeeeccch
Q 025886 59 KKLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 59 ~r~eLA~~LgLs~rQVkiWFQNR 81 (247)
...+||..+|+++..|+.+...-
T Consensus 131 ~~~eIA~~lgis~~tv~~~~~ra 153 (161)
T TIGR02985 131 SYKEIAEELGISVKTVEYHISKA 153 (161)
T ss_pred CHHHHHHHHCCCHHHHHHHHHHH
Confidence 34678999999999988765433
No 182
>PF06216 RTBV_P46: Rice tungro bacilliform virus P46 protein; InterPro: IPR009347 This family consists of several Rice tungro bacilliform virus P46 proteins. The function of this family is unknown.
Probab=20.96 E-value=2.5e+02 Score=26.31 Aligned_cols=44 Identities=11% Similarity=0.212 Sum_probs=32.9
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
+-+.+.-+.+...|..+...|++.++.+++++..+++.+.-.++
T Consensus 70 e~e~~sy~~e~~~l~~qvs~l~~~~~~~r~~~~~~~~~~eglre 113 (389)
T PF06216_consen 70 EFERQSYSNEWISLNDQVSHLQHQNSEQRQQIREMREIIEGLRE 113 (389)
T ss_pred HHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhh
Confidence 34455566677778888888888888888888888887665444
No 183
>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=20.76 E-value=1.9e+02 Score=23.25 Aligned_cols=14 Identities=36% Similarity=0.553 Sum_probs=10.7
Q ss_pred cceeeeccchhhHH
Q 025886 72 RQVAIWFQNKRARW 85 (247)
Q Consensus 72 rQVkiWFQNRRaK~ 85 (247)
||...||-.+|.-.
T Consensus 18 Rq~e~~FlqKr~~L 31 (106)
T PF11594_consen 18 RQMEAFFLQKRFEL 31 (106)
T ss_pred HHHHHHHHHHHHHH
Confidence 45579998888766
No 184
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=20.59 E-value=3.2e+02 Score=19.97 Aligned_cols=26 Identities=23% Similarity=0.304 Sum_probs=15.3
Q ss_pred hhhhHHHHHHHHHHHHHHHHHHHHHH
Q 025886 101 FNNLASRFEALKKEKQALVIQLQKTN 126 (247)
Q Consensus 101 ~~~L~~~~~~l~~E~~~L~~e~~~l~ 126 (247)
......+...|+.|++.|+.++...+
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 33444566666667777766665443
No 185
>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=20.30 E-value=4.4e+02 Score=20.79 Aligned_cols=37 Identities=24% Similarity=0.423 Sum_probs=27.5
Q ss_pred CCCCCCCHHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccceeeeccch
Q 025886 32 KNKRRFSDEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQVAIWFQNK 81 (247)
Q Consensus 32 r~Rt~fT~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQVkiWFQNR 81 (247)
...+.|+..++..|. .....+.+|++-..|+-.+...
T Consensus 34 ~gyR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 70 (126)
T cd04783 34 GGYRRYPEETVTRLR-------------FIKRAQELGFTLDEIAELLELD 70 (126)
T ss_pred CCCeecCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHhcc
Confidence 356789999998885 4445688888888888777554
No 186
>PF05812 Herpes_BLRF2: Herpesvirus BLRF2 protein; InterPro: IPR008642 This family consists of several herpes virus BLRF2 tegument proteins.; PDB: 2OA5_B 2H3R_D.
Probab=20.28 E-value=1.9e+02 Score=23.68 Aligned_cols=28 Identities=21% Similarity=0.227 Sum_probs=22.7
Q ss_pred HHHHHHHHHHHHHHHHHHHHHHHhcCCC
Q 025886 107 RFEALKKEKQALVIQLQKTNELLQNKPR 134 (247)
Q Consensus 107 ~~~~l~~E~~~L~~e~~~l~~~l~~~~~ 134 (247)
.++.|..|.+.|+.|+..|+.+|.....
T Consensus 4 t~EeLaaeL~kLqmENk~LKkkl~~~~~ 31 (118)
T PF05812_consen 4 TMEELAAELQKLQMENKALKKKLRQSVG 31 (118)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHTT-
T ss_pred CHHHHHHHHHHHHHHHHHHHHHHHccCC
Confidence 4677888999999999999999986644
No 187
>COG1905 NuoE NADH:ubiquinone oxidoreductase 24 kD subunit [Energy production and conversion]
Probab=20.21 E-value=1.3e+02 Score=25.83 Aligned_cols=36 Identities=25% Similarity=0.277 Sum_probs=31.3
Q ss_pred HHHHHHHHHHHhhcCCCCHHHHHHHHHHhCCCccce
Q 025886 39 DEQIRSLELMFENETRLEPRKKLQLAKELGLQPRQV 74 (247)
Q Consensus 39 ~~Ql~~LE~~F~~~~~ps~~~r~eLA~~LgLs~rQV 74 (247)
..-+..|...+....|........+|..||++...|
T Consensus 25 sAlip~L~~aQ~~~G~l~~~ai~~iA~~L~i~~~~v 60 (160)
T COG1905 25 SALIPLLHIAQEQFGWLPPEAIEEIADMLGIPRARV 60 (160)
T ss_pred hHHHHHHHHHHHHhCCCCHHHHHHHHHHhCCCHHHh
Confidence 455788888898888999999999999999998664
No 188
>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=20.14 E-value=3.3e+02 Score=19.70 Aligned_cols=28 Identities=21% Similarity=0.358 Sum_probs=12.1
Q ss_pred HHHHHHHHHhhhhhHHHHHHHHHHHHHH
Q 025886 91 ERDYNILQANFNNLASRFEALKKEKQAL 118 (247)
Q Consensus 91 e~e~~~lk~~~~~L~~~~~~l~~E~~~L 118 (247)
..+...+++..+.+..+++.|+.|...|
T Consensus 30 ~~~~~~~~~~~~~l~~en~~L~~ei~~l 57 (85)
T TIGR02209 30 NNELQKLQLEIDKLQKEWRDLQLEVAEL 57 (85)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444444444444444444444433
Done!