Query 019570
Match_columns 339
No_of_seqs 282 out of 1589
Neff 4.7
Searched_HMMs 46136
Date Fri Mar 29 02:49:09 2013
Command hhsearch -i /work/01045/syshi/csienesis_hhblits_a3m/019570.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/019570hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0483 Transcription factor H 99.8 1.8E-21 3.9E-26 178.4 7.4 105 54-158 47-151 (198)
2 KOG0842 Transcription factor t 99.7 4.2E-17 9.2E-22 157.9 5.5 67 56-122 150-218 (307)
3 KOG0488 Transcription factor B 99.6 3.4E-16 7.5E-21 152.1 8.4 54 64-117 179-232 (309)
4 KOG0489 Transcription factor z 99.6 1.3E-16 2.8E-21 151.4 3.1 61 57-117 159-219 (261)
5 KOG0487 Transcription factor A 99.6 1.5E-15 3.3E-20 147.1 4.4 63 57-119 235-297 (308)
6 PF00046 Homeobox: Homeobox do 99.6 3.9E-15 8.5E-20 109.0 4.8 57 58-114 1-57 (57)
7 KOG0843 Transcription factor E 99.5 3.9E-15 8.5E-20 134.6 5.2 63 57-119 102-164 (197)
8 KOG0484 Transcription factor P 99.5 2.9E-15 6.3E-20 125.4 3.1 57 60-116 20-76 (125)
9 KOG0485 Transcription factor N 99.5 1.5E-14 3.2E-19 134.3 6.6 59 58-116 103-163 (268)
10 KOG0492 Transcription factor M 99.5 3.4E-14 7.3E-19 131.1 7.1 61 57-117 144-204 (246)
11 KOG0850 Transcription factor D 99.5 2.4E-14 5.3E-19 133.5 5.7 53 63-115 128-180 (245)
12 KOG0494 Transcription factor C 99.5 5.4E-14 1.2E-18 133.4 6.1 54 64-117 148-201 (332)
13 KOG2251 Homeobox transcription 99.4 6.1E-14 1.3E-18 130.2 4.8 62 56-117 36-97 (228)
14 KOG0493 Transcription factor E 99.4 1.6E-13 3.5E-18 130.2 7.0 94 26-119 212-308 (342)
15 cd00086 homeodomain Homeodomai 99.4 2.1E-13 4.7E-18 99.2 4.9 57 59-115 2-58 (59)
16 KOG0848 Transcription factor C 99.4 1.3E-13 2.8E-18 131.2 3.6 53 64-116 206-258 (317)
17 smart00389 HOX Homeodomain. DN 99.4 3.1E-13 6.8E-18 97.9 4.5 55 59-113 2-56 (56)
18 COG5576 Homeodomain-containing 99.4 7.6E-13 1.6E-17 117.7 5.3 66 53-118 47-112 (156)
19 KOG4577 Transcription factor L 99.3 4.9E-13 1.1E-17 128.5 3.5 91 53-144 163-253 (383)
20 TIGR01565 homeo_ZF_HD homeobox 99.3 4.3E-12 9.3E-17 96.0 5.0 52 58-109 2-57 (58)
21 KOG0486 Transcription factor P 99.3 4.4E-12 9.5E-17 123.0 5.0 54 64-117 119-172 (351)
22 KOG0844 Transcription factor E 99.2 3.3E-12 7.2E-17 123.6 3.4 62 57-118 181-242 (408)
23 KOG3802 Transcription factor O 99.2 7.1E-12 1.5E-16 124.6 4.4 61 56-116 293-353 (398)
24 KOG0491 Transcription factor B 99.2 2.5E-12 5.5E-17 115.3 0.7 56 62-117 105-160 (194)
25 KOG0847 Transcription factor, 99.2 7.9E-12 1.7E-16 116.5 2.4 62 55-116 165-226 (288)
26 KOG0490 Transcription factor, 99.0 1.4E-10 3.1E-15 105.0 3.6 60 57-116 60-119 (235)
27 KOG1168 Transcription factor A 98.8 3E-09 6.5E-14 102.7 3.2 65 52-116 304-368 (385)
28 KOG0849 Transcription factor P 98.8 4.8E-09 1E-13 104.0 4.5 59 58-116 177-235 (354)
29 KOG0775 Transcription factor S 98.6 3.4E-08 7.3E-13 94.8 4.1 51 64-114 183-233 (304)
30 KOG0774 Transcription factor P 98.1 1.2E-06 2.6E-11 84.1 2.5 59 57-115 188-249 (334)
31 PF05920 Homeobox_KN: Homeobox 98.1 1.6E-06 3.5E-11 61.0 1.5 34 78-111 7-40 (40)
32 PF02183 HALZ: Homeobox associ 97.9 1.9E-05 4.1E-10 57.1 4.8 44 115-158 1-44 (45)
33 KOG0490 Transcription factor, 97.7 4.2E-05 9.1E-10 69.3 4.1 59 59-117 155-213 (235)
34 KOG2252 CCAAT displacement pro 97.5 0.0001 2.2E-09 76.7 4.5 53 60-112 423-475 (558)
35 KOG1146 Homeobox protein [Gene 96.9 0.0011 2.4E-08 74.8 4.9 62 56-117 902-963 (1406)
36 KOG0773 Transcription factor M 96.2 0.005 1.1E-07 60.3 4.0 55 63-117 245-302 (342)
37 PF11569 Homez: Homeodomain le 95.8 0.0043 9.3E-08 47.0 1.5 41 69-109 10-50 (56)
38 PF02183 HALZ: Homeobox associ 92.3 0.3 6.4E-06 35.4 4.6 35 124-158 3-37 (45)
39 KOG3623 Homeobox transcription 92.0 0.13 2.9E-06 56.0 3.4 48 69-116 568-615 (1007)
40 PRK09413 IS2 repressor TnpA; R 90.8 0.9 1.9E-05 38.4 6.7 43 59-106 8-51 (121)
41 smart00340 HALZ homeobox assoc 87.9 0.9 1.9E-05 32.9 3.8 28 128-155 7-34 (44)
42 PF04218 CENP-B_N: CENP-B N-te 86.7 1.1 2.4E-05 33.0 3.9 46 59-109 2-47 (53)
43 PF06156 DUF972: Protein of un 79.3 8.6 0.00019 32.6 6.9 47 115-161 11-57 (107)
44 KOG4196 bZIP transcription fac 77.9 26 0.00056 31.1 9.6 81 62-157 22-112 (135)
45 PRK13169 DNA replication intia 71.4 15 0.00032 31.5 6.4 45 115-159 11-55 (110)
46 PF06005 DUF904: Protein of un 71.3 18 0.00039 28.6 6.4 35 120-154 19-53 (72)
47 PF00170 bZIP_1: bZIP transcri 70.3 28 0.00061 26.1 7.1 35 121-155 28-62 (64)
48 PF10224 DUF2205: Predicted co 69.7 22 0.00047 28.9 6.7 47 111-157 15-61 (80)
49 KOG4005 Transcription factor X 65.1 17 0.00038 35.3 6.1 54 106-159 82-137 (292)
50 COG4467 Regulator of replicati 62.7 18 0.0004 31.1 5.2 44 115-158 11-54 (114)
51 PF06005 DUF904: Protein of un 62.6 43 0.00093 26.5 7.0 44 113-156 19-62 (72)
52 KOG3119 Basic region leucine z 60.4 27 0.00058 33.9 6.6 48 109-159 208-255 (269)
53 PF01527 HTH_Tnp_1: Transposas 59.9 2.7 5.9E-05 31.7 -0.2 44 59-106 2-45 (76)
54 PF00170 bZIP_1: bZIP transcri 59.1 38 0.00082 25.4 6.0 34 116-149 30-63 (64)
55 PF04545 Sigma70_r4: Sigma-70, 58.1 14 0.00031 26.0 3.3 39 63-106 4-42 (50)
56 cd06171 Sigma70_r4 Sigma70, re 57.6 9.8 0.00021 25.4 2.3 43 64-111 11-53 (55)
57 PF13443 HTH_26: Cro/C1-type H 56.8 8 0.00017 28.2 1.9 41 86-126 12-52 (63)
58 PF04967 HTH_10: HTH DNA bindi 55.4 13 0.00028 27.8 2.8 38 64-101 1-40 (53)
59 smart00338 BRLZ basic region l 55.4 65 0.0014 24.1 6.7 34 123-156 30-63 (65)
60 PRK00888 ftsB cell division pr 54.6 23 0.0005 29.7 4.5 28 127-154 35-62 (105)
61 PF15058 Speriolin_N: Sperioli 53.1 26 0.00057 33.0 5.0 42 121-163 7-48 (200)
62 COG4026 Uncharacterized protei 52.2 33 0.00071 33.3 5.6 27 127-153 157-183 (290)
63 PF14775 NYD-SP28_assoc: Sperm 51.7 31 0.00067 26.3 4.4 31 128-158 28-58 (60)
64 PF07716 bZIP_2: Basic region 50.4 57 0.0012 23.8 5.5 27 128-154 27-53 (54)
65 KOG4571 Activating transcripti 48.1 61 0.0013 32.3 6.8 49 110-159 240-288 (294)
66 cd00569 HTH_Hin_like Helix-tur 46.1 30 0.00066 20.4 3.1 37 63-104 5-41 (42)
67 KOG0249 LAR-interacting protei 46.0 75 0.0016 35.5 7.7 52 109-160 213-264 (916)
68 PF07407 Seadorna_VP6: Seadorn 43.7 29 0.00063 35.3 4.0 32 127-158 33-64 (420)
69 KOG4403 Cell surface glycoprot 43.5 64 0.0014 34.1 6.5 61 102-162 229-324 (575)
70 PF06156 DUF972: Protein of un 42.8 58 0.0013 27.6 5.2 41 114-154 17-57 (107)
71 cd04766 HTH_HspR Helix-Turn-He 42.3 90 0.0019 24.8 6.0 70 87-157 4-89 (91)
72 COG3413 Predicted DNA binding 40.6 36 0.00078 31.3 3.9 48 63-112 155-204 (215)
73 PRK13922 rod shape-determining 39.9 55 0.0012 31.1 5.2 36 124-159 74-112 (276)
74 PRK13169 DNA replication intia 39.9 67 0.0014 27.5 5.1 40 115-154 18-57 (110)
75 TIGR02449 conserved hypothetic 38.9 1.1E+02 0.0024 23.9 5.8 35 122-156 10-44 (65)
76 PF00424 REV: REV protein (ant 38.3 46 0.001 27.8 3.7 33 69-117 14-48 (91)
77 smart00338 BRLZ basic region l 37.4 1E+02 0.0022 23.0 5.3 30 127-156 27-56 (65)
78 TIGR00219 mreC rod shape-deter 36.9 1.1E+02 0.0023 29.9 6.7 18 143-160 94-111 (283)
79 KOG0483 Transcription factor H 36.0 49 0.0011 31.0 4.0 36 125-160 111-146 (198)
80 KOG1146 Homeobox protein [Gene 35.4 12 0.00026 43.8 -0.2 58 61-118 448-505 (1406)
81 KOG3156 Uncharacterized membra 35.0 1E+02 0.0022 29.5 6.0 47 118-164 100-147 (220)
82 cd04779 HTH_MerR-like_sg4 Heli 34.6 2.4E+02 0.0053 24.5 7.9 37 60-109 34-70 (134)
83 PRK13729 conjugal transfer pil 34.6 96 0.0021 32.9 6.2 44 113-156 77-120 (475)
84 KOG4005 Transcription factor X 33.8 93 0.002 30.5 5.5 46 114-159 99-144 (292)
85 PRK03975 tfx putative transcri 33.6 59 0.0013 28.9 4.0 48 61-114 4-51 (141)
86 COG3074 Uncharacterized protei 33.5 2E+02 0.0044 23.2 6.5 36 119-154 25-60 (79)
87 PF05700 BCAS2: Breast carcino 32.2 1.7E+02 0.0038 27.3 7.1 40 120-159 176-215 (221)
88 PF15058 Speriolin_N: Sperioli 32.2 55 0.0012 30.9 3.6 35 125-159 4-38 (200)
89 cd01106 HTH_TipAL-Mta Helix-Tu 31.7 1.8E+02 0.004 23.5 6.3 35 61-108 36-70 (103)
90 KOG0709 CREB/ATF family transc 31.3 2.2E+02 0.0048 30.2 8.1 14 62-75 219-232 (472)
91 PF10668 Phage_terminase: Phag 31.1 19 0.00041 27.7 0.4 19 86-104 24-42 (60)
92 PF04899 MbeD_MobD: MbeD/MobD 30.9 1.5E+02 0.0033 23.5 5.4 39 119-157 21-59 (70)
93 PRK10884 SH3 domain-containing 29.9 1.7E+02 0.0036 27.5 6.5 28 128-155 134-161 (206)
94 PF08281 Sigma70_r4_2: Sigma-7 29.8 56 0.0012 23.0 2.6 41 64-109 11-51 (54)
95 PF07334 IFP_35_N: Interferon- 29.6 67 0.0015 26.0 3.3 24 137-160 4-27 (76)
96 PRK15422 septal ring assembly 29.5 1.5E+02 0.0033 24.2 5.3 9 145-153 51-59 (79)
97 PF12808 Mto2_bdg: Micro-tubul 29.3 1.6E+02 0.0035 22.1 5.1 38 121-158 10-47 (52)
98 TIGR01069 mutS2 MutS2 family p 29.3 1.3E+02 0.0029 33.4 6.6 21 82-102 480-500 (771)
99 PRK14127 cell division protein 29.0 94 0.002 26.6 4.3 31 129-159 33-63 (109)
100 PRK15422 septal ring assembly 28.6 2.4E+02 0.0051 23.1 6.2 36 120-155 33-68 (79)
101 PF04977 DivIC: Septum formati 28.1 1.2E+02 0.0025 22.9 4.4 22 131-152 29-50 (80)
102 KOG4571 Activating transcripti 27.5 1.3E+02 0.0029 30.0 5.6 31 130-160 245-275 (294)
103 KOG4343 bZIP transcription fac 27.3 1.2E+02 0.0025 33.0 5.4 23 136-158 312-334 (655)
104 PRK10884 SH3 domain-containing 26.9 2.4E+02 0.0052 26.5 7.0 31 124-154 137-167 (206)
105 PRK00409 recombination and DNA 26.0 1.6E+02 0.0034 32.9 6.5 19 84-102 487-505 (782)
106 PRK09642 RNA polymerase sigma 25.9 98 0.0021 26.2 3.9 47 64-115 107-153 (160)
107 TIGR02937 sigma70-ECF RNA poly 25.5 72 0.0016 25.5 2.9 45 64-113 111-155 (158)
108 KOG4343 bZIP transcription fac 25.2 1.5E+02 0.0032 32.3 5.7 34 121-154 304-337 (655)
109 PRK09652 RNA polymerase sigma 24.5 96 0.0021 26.3 3.6 45 64-113 129-173 (182)
110 PF00038 Filament: Intermediat 24.4 2.1E+02 0.0045 27.4 6.3 61 98-158 186-255 (312)
111 TIGR03752 conj_TIGR03752 integ 24.4 1.2E+02 0.0026 32.1 4.9 11 63-73 41-51 (472)
112 PF09607 BrkDBD: Brinker DNA-b 23.8 81 0.0018 24.3 2.6 43 62-106 4-47 (58)
113 PF08172 CASP_C: CASP C termin 23.8 2.3E+02 0.005 27.4 6.4 38 109-146 90-127 (248)
114 PRK09646 RNA polymerase sigma 23.6 1.1E+02 0.0024 27.1 4.0 46 64-114 143-188 (194)
115 PRK00888 ftsB cell division pr 23.6 2.4E+02 0.0052 23.6 5.7 48 100-148 16-63 (105)
116 cd04770 HTH_HMRTR Helix-Turn-H 23.6 3.5E+02 0.0077 22.4 6.8 36 61-109 36-71 (123)
117 cd01109 HTH_YyaN Helix-Turn-He 23.1 3.6E+02 0.0079 22.1 6.7 35 61-108 36-70 (113)
118 PF13518 HTH_28: Helix-turn-he 22.9 41 0.00089 23.2 0.9 21 86-106 14-34 (52)
119 KOG3119 Basic region leucine z 22.9 2.2E+02 0.0049 27.6 6.2 29 129-157 218-246 (269)
120 PF14197 Cep57_CLD_2: Centroso 22.9 3.7E+02 0.0081 21.0 7.0 15 141-155 48-62 (69)
121 PTZ00454 26S protease regulato 22.6 2.1E+02 0.0046 29.2 6.2 42 118-159 21-62 (398)
122 COG4026 Uncharacterized protei 22.6 2.6E+02 0.0057 27.3 6.4 46 109-154 118-163 (290)
123 PF04568 IATP: Mitochondrial A 22.5 3.3E+02 0.0072 23.0 6.3 29 128-156 71-99 (100)
124 PF00196 GerE: Bacterial regul 22.5 95 0.0021 22.4 2.8 45 63-113 3-47 (58)
125 PRK12514 RNA polymerase sigma 22.4 88 0.0019 27.1 3.0 46 64-114 130-175 (179)
126 PF08826 DMPK_coil: DMPK coile 22.4 3.7E+02 0.008 20.7 6.3 40 117-156 16-55 (61)
127 PRK06759 RNA polymerase factor 22.4 1E+02 0.0023 25.7 3.4 44 64-112 107-150 (154)
128 PF13936 HTH_38: Helix-turn-he 22.4 50 0.0011 23.2 1.2 39 62-105 3-41 (44)
129 TIGR02449 conserved hypothetic 22.2 3.9E+02 0.0084 21.0 6.2 36 120-155 15-50 (65)
130 COG4467 Regulator of replicati 21.7 1.6E+02 0.0035 25.5 4.3 37 115-151 18-54 (114)
131 TIGR03879 near_KaiC_dom probab 21.6 29 0.00063 27.7 -0.1 35 73-107 21-55 (73)
132 PF11932 DUF3450: Protein of u 21.5 3.3E+02 0.0072 25.6 6.9 31 123-153 60-90 (251)
133 PF07407 Seadorna_VP6: Seadorn 21.4 1.3E+02 0.0028 30.8 4.3 27 304-330 330-358 (420)
134 PF07888 CALCOCO1: Calcium bin 21.0 5.8E+02 0.013 27.7 9.2 42 118-159 416-457 (546)
135 PF11559 ADIP: Afadin- and alp 20.9 4.3E+02 0.0093 22.8 7.0 41 115-155 83-123 (151)
136 PF04880 NUDE_C: NUDE protein, 20.6 71 0.0015 29.3 2.1 23 134-156 25-47 (166)
137 PRK12526 RNA polymerase sigma 20.5 1.3E+02 0.0029 27.0 3.9 46 64-114 154-199 (206)
138 TIGR03752 conj_TIGR03752 integ 20.5 2.4E+02 0.0053 29.9 6.2 8 330-337 353-360 (472)
139 cd04761 HTH_MerR-SF Helix-Turn 20.5 43 0.00092 22.8 0.5 23 87-109 3-25 (49)
140 PRK11924 RNA polymerase sigma 20.4 1.1E+02 0.0024 25.8 3.2 46 64-114 126-171 (179)
141 PF07798 DUF1640: Protein of u 20.2 3.1E+02 0.0068 24.6 6.2 32 133-164 73-104 (177)
No 1
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=99.84 E-value=1.8e-21 Score=178.38 Aligned_cols=105 Identities=60% Similarity=0.913 Sum_probs=92.9
Q ss_pred CCCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHHHHHHHHhhhhHHHHh
Q 019570 54 GGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALKL 133 (339)
Q Consensus 54 ~~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~eke~~~LKa~~d~Lk~ 133 (339)
+.....|++|||.+|+..||..|....|+.+.+|..||+.|||.+|||+|||||||||||.++++.+++.||..++.|+.
T Consensus 47 ~~~~~~kk~Rlt~eQ~~~LE~~F~~~~~L~p~~K~~LAk~LgL~pRQVavWFQNRRARwK~kqlE~d~~~Lk~~~~~l~~ 126 (198)
T KOG0483|consen 47 GSKGKGKKRRLTSEQVKFLEKSFESEKKLEPERKKKLAKELGLQPRQVAVWFQNRRARWKTKQLEKDYESLKRQLESLRS 126 (198)
T ss_pred ccccccccccccHHHHHHhHHhhccccccChHHHHHHHHhhCCChhHHHHHHhhccccccchhhhhhHHHHHHHHHHHhh
Confidence 34466788889999999999999999999999999999999999999999999999999999999999999998888888
Q ss_pred hhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 134 NYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 134 e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
+++.++.++..|++++..++..+..
T Consensus 127 ~~~~Lq~e~~eL~~~~~~~~~~~~~ 151 (198)
T KOG0483|consen 127 ENDRLQSEVQELVAELSSLKREMQK 151 (198)
T ss_pred hhhHHHHHHHHHHHHHhhhhhhhcc
Confidence 7777777777777777766666554
No 2
>KOG0842 consensus Transcription factor tinman/NKX2-3, contains HOX domain [Transcription]
Probab=99.67 E-value=4.2e-17 Score=157.87 Aligned_cols=67 Identities=37% Similarity=0.584 Sum_probs=59.7
Q ss_pred CcCCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHHHHHH
Q 019570 56 HVSEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYG 122 (339)
Q Consensus 56 ~~krKRrR--fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~eke~~ 122 (339)
.++|||+| ||..|+.+||+.|.+.+|++..+|+.||..|+|+++||||||||||-|.||++.++...
T Consensus 150 ~~~kRKrRVLFSqAQV~ELERRFrqQRYLSAPERE~LA~~LrLT~TQVKIWFQNrRYK~KR~~~dk~~~ 218 (307)
T KOG0842|consen 150 KRKKRKRRVLFSQAQVYELERRFRQQRYLSAPEREHLASSLRLTPTQVKIWFQNRRYKTKRQQKDKALE 218 (307)
T ss_pred cccccccccccchhHHHHHHHHHHhhhccccHhHHHHHHhcCCCchheeeeeecchhhhhhhhhhhhhh
Confidence 33444444 99999999999999999999999999999999999999999999999999998776533
No 3
>KOG0488 consensus Transcription factor BarH and related HOX domain proteins [General function prediction only]
Probab=99.64 E-value=3.4e-16 Score=152.05 Aligned_cols=54 Identities=43% Similarity=0.714 Sum_probs=52.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
||..|+..||+.|++.+|++..+|.+||+.|||+..||++||||||+||||+..
T Consensus 179 FT~~Ql~~LEkrF~~QKYLS~~DR~~LA~~LgLTdaQVKtWfQNRRtKWKrq~a 232 (309)
T KOG0488|consen 179 FSDHQLFELEKRFEKQKYLSVADRIELAASLGLTDAQVKTWFQNRRTKWKRQTA 232 (309)
T ss_pred hhHHHHHHHHHHHHHhhcccHHHHHHHHHHcCCchhhHHHHHhhhhHHHHHHHH
Confidence 999999999999999999999999999999999999999999999999999764
No 4
>KOG0489 consensus Transcription factor zerknullt and related HOX domain proteins [General function prediction only]
Probab=99.62 E-value=1.3e-16 Score=151.36 Aligned_cols=61 Identities=33% Similarity=0.671 Sum_probs=55.8
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
.||.|+-||..|+.+||+.|..++|+++.+|.+||..|.|+++||||||||||+||||...
T Consensus 159 ~kR~RtayT~~QllELEkEFhfN~YLtR~RRiEiA~~L~LtErQIKIWFQNRRMK~Kk~~k 219 (261)
T KOG0489|consen 159 SKRRRTAFTRYQLLELEKEFHFNKYLTRSRRIEIAHALNLTERQIKIWFQNRRMKWKKENK 219 (261)
T ss_pred CCCCCcccchhhhhhhhhhhccccccchHHHHHHHhhcchhHHHHHHHHHHHHHHHHHhhc
Confidence 4444455999999999999999999999999999999999999999999999999999653
No 5
>KOG0487 consensus Transcription factor Abd-B, contains HOX domain [Transcription]
Probab=99.56 E-value=1.5e-15 Score=147.14 Aligned_cols=63 Identities=33% Similarity=0.502 Sum_probs=57.2
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ek 119 (339)
.||||..+|..|+.+||+.|..+.|++.+.|.+|++.|+|++|||+|||||||+|.||..++.
T Consensus 235 ~RKKRcPYTK~QtlELEkEFlfN~YitkeKR~ElSr~lNLTeRQVKIWFQNRRMK~KK~~re~ 297 (308)
T KOG0487|consen 235 GRKKRCPYTKHQTLELEKEFLFNMYITKEKRLELSRTLNLTERQVKIWFQNRRMKEKKVNREN 297 (308)
T ss_pred cccccCCchHHHHHHHHHHHHHHHHHhHHHHHHHHHhcccchhheeeeehhhhhHHhhhhhhh
Confidence 445555699999999999999999999999999999999999999999999999999976533
No 6
>PF00046 Homeobox: Homeobox domain not present here.; InterPro: IPR001356 The homeobox domain was first identified in a number of drosophila homeotic and segmentation proteins, but is now known to be well-conserved in many other animals, including vertebrates [, , ]. Hox genes encode homeodomain-containing transcriptional regulators that operate differential genetic programs along the anterior-posterior axis of animal bodies []. The domain binds DNA through a helix-turn-helix (HTH) structure. The HTH motif is characterised by two alpha-helices, which make intimate contacts with the DNA and are joined by a short turn. The second helix binds to DNA via a number of hydrogen bonds and hydrophobic interactions, which occur between specific side chains and the exposed bases and thymine methyl groups within the major groove of the DNA []. The first helix helps to stabilise the structure. The motif is very similar in sequence and structure in a wide range of DNA-binding proteins (e.g., cro and repressor proteins, homeotic proteins, etc.). One of the principal differences between HTH motifs in these different proteins arises from the stereo-chemical requirement for glycine in the turn which is needed to avoid steric interference of the beta-carbon with the main chain: for cro and repressor proteins the glycine appears to be mandatory, while for many of the homeotic and other DNA-binding proteins the requirement is relaxed.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0043565 sequence-specific DNA binding, 0006355 regulation of transcription, DNA-dependent; PDB: 2DA3_A 1LFB_A 2LFB_A 2ECB_A 2DA5_A 3D1N_O 3A03_A 2XSD_C 3CMY_A 1AHD_P ....
Probab=99.55 E-value=3.9e-15 Score=109.03 Aligned_cols=57 Identities=42% Similarity=0.647 Sum_probs=54.1
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 58 krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
+++|++||.+|+..|+..|..++||+..++..||..+||+..+|++||+|||+++|+
T Consensus 1 kr~r~~~t~~q~~~L~~~f~~~~~p~~~~~~~la~~l~l~~~~V~~WF~nrR~k~kk 57 (57)
T PF00046_consen 1 KRKRTRFTKEQLKVLEEYFQENPYPSKEEREELAKELGLTERQVKNWFQNRRRKEKK 57 (57)
T ss_dssp SSSSSSSSHHHHHHHHHHHHHSSSCHHHHHHHHHHHHTSSHHHHHHHHHHHHHHHHH
T ss_pred CcCCCCCCHHHHHHHHHHHHHhccccccccccccccccccccccccCHHHhHHHhCc
Confidence 456777999999999999999999999999999999999999999999999999986
No 7
>KOG0843 consensus Transcription factor EMX1 and related HOX domain proteins [Transcription]
Probab=99.55 E-value=3.9e-15 Score=134.58 Aligned_cols=63 Identities=35% Similarity=0.491 Sum_probs=56.8
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLER 119 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ek 119 (339)
.+|.|+.||.+|+..||..|+.++|....+|++||+.|+|++.||+|||||||+|.||.+.+.
T Consensus 102 ~kr~RT~ft~~Ql~~LE~~F~~~~Yvvg~eR~~LA~~L~LsetQVkvWFQNRRtk~kr~~~e~ 164 (197)
T KOG0843|consen 102 PKRIRTAFTPEQLLKLEHAFEGNQYVVGAERKQLAQSLSLSETQVKVWFQNRRTKHKRMQQED 164 (197)
T ss_pred CCccccccCHHHHHHHHHHHhcCCeeechHHHHHHHHcCCChhHhhhhhhhhhHHHHHHHHHh
Confidence 344444599999999999999999999999999999999999999999999999999987543
No 8
>KOG0484 consensus Transcription factor PHOX2/ARIX, contains HOX domain [Transcription]
Probab=99.54 E-value=2.9e-15 Score=125.36 Aligned_cols=57 Identities=28% Similarity=0.525 Sum_probs=53.3
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 60 KRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
-|+.||..||..||+.|...+||++..|++||.++.|++.+|+|||||||||.|++.
T Consensus 20 IRTTFTS~QLkELErvF~ETHYPDIYTREEiA~kidLTEARVQVWFQNRRAKfRKQE 76 (125)
T KOG0484|consen 20 IRTTFTSAQLKELERVFAETHYPDIYTREEIALKIDLTEARVQVWFQNRRAKFRKQE 76 (125)
T ss_pred hhhhhhHHHHHHHHHHHHhhcCCcchhHHHHHHhhhhhHHHHHHHHHhhHHHHHHHH
Confidence 334499999999999999999999999999999999999999999999999999864
No 9
>KOG0485 consensus Transcription factor NKX-5.1/HMX1, contains HOX domain [Transcription]
Probab=99.52 E-value=1.5e-14 Score=134.30 Aligned_cols=59 Identities=42% Similarity=0.684 Sum_probs=54.7
Q ss_pred CCCCCc--CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 58 SEKKRR--LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 58 krKRrR--fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
+|||+| |+..|+..||..|+..+|++..+|..||++|.|++.||||||||||.||||+-
T Consensus 103 RKKktRTvFSraQV~qLEs~Fe~krYLSsaeRa~LA~sLqLTETQVKIWFQNRRnKwKRq~ 163 (268)
T KOG0485|consen 103 RKKKTRTVFSRAQVFQLESTFELKRYLSSAERAGLAASLQLTETQVKIWFQNRRNKWKRQY 163 (268)
T ss_pred ccccchhhhhHHHHHHHHHHHHHHhhhhHHHHhHHHHhhhhhhhhhhhhhhhhhHHHHHHH
Confidence 444444 99999999999999999999999999999999999999999999999999974
No 10
>KOG0492 consensus Transcription factor MSH, contains HOX domain [General function prediction only]
Probab=99.50 E-value=3.4e-14 Score=131.12 Aligned_cols=61 Identities=31% Similarity=0.491 Sum_probs=55.4
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
.|+-|+.||.+||..||+.|+..+|+++.+|.+++..|.|++.||+|||||||+|.||-+.
T Consensus 144 nRkPRtPFTtqQLlaLErkfrekqYLSiaEraefSsSL~LTeTqVKIWFQNRRAKaKRlQe 204 (246)
T KOG0492|consen 144 NRKPRTPFTTQQLLALERKFREKQYLSIAERAEFSSSLELTETQVKIWFQNRRAKAKRLQE 204 (246)
T ss_pred CCCCCCCCCHHHHHHHHHHHhHhhhhhHHHHHhhhhhhhhhhhheehhhhhhhHHHHHHHH
Confidence 3444445999999999999999999999999999999999999999999999999999653
No 11
>KOG0850 consensus Transcription factor DLX and related proteins with LIM Zn-binding and HOX domains [Transcription]
Probab=99.49 E-value=2.4e-14 Score=133.51 Aligned_cols=53 Identities=38% Similarity=0.614 Sum_probs=51.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHH
Q 019570 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krk 115 (339)
.++.-||..|.+.|+++.|+--.+|.+||..|||+..||||||||||.|.||.
T Consensus 128 IYSS~QLqaL~rRFQkTQYLALPERAeLAAsLGLTQTQVKIWFQNrRSK~KKl 180 (245)
T KOG0850|consen 128 IYSSLQLQALNRRFQQTQYLALPERAELAASLGLTQTQVKIWFQNRRSKFKKL 180 (245)
T ss_pred cccHHHHHHHHHHHhhcchhcCcHHHHHHHHhCCchhHhhhhhhhhHHHHHHH
Confidence 39999999999999999999999999999999999999999999999999984
No 12
>KOG0494 consensus Transcription factor CHX10 and related HOX domain proteins [General function prediction only]
Probab=99.47 E-value=5.4e-14 Score=133.36 Aligned_cols=54 Identities=31% Similarity=0.569 Sum_probs=52.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
||..|+..||+.|+..+||+...|+.||.++.|++.+|+|||||||+||||+..
T Consensus 148 FT~~Qle~LEkaFkeaHYPDv~Are~la~ktelpEDRIqVWfQNRRAKWRk~Ek 201 (332)
T KOG0494|consen 148 FTSYQLEELEKAFKEAHYPDVYAREMLADKTELPEDRIQVWFQNRRAKWRKTEK 201 (332)
T ss_pred hhHHHHHHHHHHHhhccCccHHHHHHHhhhccCchhhhhHHhhhhhHHhhhhhh
Confidence 999999999999999999999999999999999999999999999999998754
No 13
>KOG2251 consensus Homeobox transcription factor [Transcription]
Probab=99.45 E-value=6.1e-14 Score=130.17 Aligned_cols=62 Identities=27% Similarity=0.433 Sum_probs=56.8
Q ss_pred CcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 56 ~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
+.+|-|++|+..|+++||..|.+.+||+...|++||.+|+|.+.+|+|||+|||+|+|+++.
T Consensus 36 kqRRERTtFtr~QlevLe~LF~kTqYPDv~~rEelAlklnLpeSrVqVWFKNRRAK~r~qq~ 97 (228)
T KOG2251|consen 36 KQRRERTTFTRKQLEVLEALFAKTQYPDVFMREELALKLNLPESRVQVWFKNRRAKCRRQQQ 97 (228)
T ss_pred hcccccceecHHHHHHHHHHHHhhcCccHHHHHHHHHHhCCchhhhhhhhccccchhhHhhh
Confidence 34455566999999999999999999999999999999999999999999999999999764
No 14
>KOG0493 consensus Transcription factor Engrailed, contains HOX domain [General function prediction only]
Probab=99.44 E-value=1.6e-13 Score=130.24 Aligned_cols=94 Identities=26% Similarity=0.401 Sum_probs=67.9
Q ss_pred CCCCCCCCccccccccCCCCCCCc-c--ccCCCCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCcccee
Q 019570 26 SPRNNQVYSREFQTMLDGLDEEGC-L--EESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVA 102 (339)
Q Consensus 26 spr~~~~y~~~~~s~~~~~~~~~~-~--~~~~~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVk 102 (339)
...+.|+||..|......-..... . ......-||-|+-||.+||..|+..|+.++|++..+|.+||.+|||.+.||+
T Consensus 212 ~mwPAWVycTRYSDRPSsGPR~Rk~kkkk~~~~eeKRPRTAFtaeQL~RLK~EF~enRYlTEqRRQ~La~ELgLNEsQIK 291 (342)
T KOG0493|consen 212 SMWPAWVYCTRYSDRPSSGPRHRKPKKKKSSSKEEKRPRTAFTAEQLQRLKAEFQENRYLTEQRRQELAQELGLNESQIK 291 (342)
T ss_pred cccceeeeeecccCCCCCCcccccccccCCccchhcCccccccHHHHHHHHHHHhhhhhHHHHHHHHHHHHhCcCHHHhh
Confidence 455667888877665322111110 0 0011111222333999999999999999999999999999999999999999
Q ss_pred ehhhhhHHHhhHHHHHH
Q 019570 103 VWFQNRRARWKTKQLER 119 (339)
Q Consensus 103 VWFQNRRaK~Krkq~ek 119 (339)
|||||+|+|.|+..--+
T Consensus 292 IWFQNKRAKiKKsTgsk 308 (342)
T KOG0493|consen 292 IWFQNKRAKIKKSTGSK 308 (342)
T ss_pred HHhhhhhhhhhhccCCC
Confidence 99999999999876543
No 15
>cd00086 homeodomain Homeodomain; DNA binding domains involved in the transcriptional regulation of key eukaryotic developmental processes; may bind to DNA as monomers or as homo- and/or heterodimers, in a sequence-specific manner.
Probab=99.41 E-value=2.1e-13 Score=99.20 Aligned_cols=57 Identities=46% Similarity=0.738 Sum_probs=53.2
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHH
Q 019570 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 59 rKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krk 115 (339)
+++.+++..|+..||.+|..++||+..++..||..+||+..||++||+|||++.++.
T Consensus 2 ~~r~~~~~~~~~~Le~~f~~~~~P~~~~~~~la~~~~l~~~qV~~WF~nrR~~~~~~ 58 (59)
T cd00086 2 RKRTRFTPEQLEELEKEFEKNPYPSREEREELAKELGLTERQVKIWFQNRRAKLKRS 58 (59)
T ss_pred CCCCcCCHHHHHHHHHHHHhCCCCCHHHHHHHHHHHCcCHHHHHHHHHHHHHHHhcc
Confidence 345669999999999999999999999999999999999999999999999998864
No 16
>KOG0848 consensus Transcription factor Caudal, contains HOX domain [Transcription]
Probab=99.40 E-value=1.3e-13 Score=131.17 Aligned_cols=53 Identities=42% Similarity=0.626 Sum_probs=51.5
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
+|..|.-+||+.|...+|.++.++.+||..|||++|||||||||||||.||..
T Consensus 206 YTDhQRLELEKEfh~SryITirRKSELA~~LgLsERQVKIWFQNRRAKERK~n 258 (317)
T KOG0848|consen 206 YTDHQRLELEKEFHTSRYITIRRKSELAATLGLSERQVKIWFQNRRAKERKDN 258 (317)
T ss_pred ecchhhhhhhhhhccccceeeehhHHHHHhhCccHhhhhHhhhhhhHHHHHHH
Confidence 99999999999999999999999999999999999999999999999999864
No 17
>smart00389 HOX Homeodomain. DNA-binding factors that are involved in the transcriptional regulation of key developmental processes
Probab=99.39 E-value=3.1e-13 Score=97.91 Aligned_cols=55 Identities=45% Similarity=0.792 Sum_probs=51.1
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhh
Q 019570 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 59 rKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~K 113 (339)
+.|.+++.+|+..|+..|..++||+..++..||..+||+..||+.||+|||++.|
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 3455699999999999999999999999999999999999999999999999864
No 18
>COG5576 Homeodomain-containing transcription factor [Transcription]
Probab=99.35 E-value=7.6e-13 Score=117.69 Aligned_cols=66 Identities=32% Similarity=0.555 Sum_probs=60.3
Q ss_pred CCCCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHH
Q 019570 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (339)
Q Consensus 53 ~~~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~e 118 (339)
.....+++|+|.|..|+.+|+..|..++||+...|..|+..++|+++-|++||||||++.|+....
T Consensus 47 ~s~~~~~~r~R~t~~Q~~vL~~~F~i~p~Ps~~~r~~L~~~lnm~~ksVqIWFQNkR~~~k~~~~~ 112 (156)
T COG5576 47 GSSPPKSKRRRTTDEQLMVLEREFEINPYPSSITRIKLSLLLNMPPKSVQIWFQNKRAKEKKKRSG 112 (156)
T ss_pred CCCcCcccceechHHHHHHHHHHhccCCCCCHHHHHHHHHhcCCChhhhhhhhchHHHHHHHhccc
Confidence 335567788889999999999999999999999999999999999999999999999999987643
No 19
>KOG4577 consensus Transcription factor LIM3, contains LIM and HOX domains [Transcription]
Probab=99.34 E-value=4.9e-13 Score=128.51 Aligned_cols=91 Identities=22% Similarity=0.374 Sum_probs=76.8
Q ss_pred CCCCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHHHHHHHHhhhhHHHH
Q 019570 53 SGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKANYDALK 132 (339)
Q Consensus 53 ~~~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~eke~~~LKa~~d~Lk 132 (339)
.++..||.|+.+|+.||+.|+..|+..++|.+..|++|+.++||..|.|+|||||||||.||-+...-...|.+.+..++
T Consensus 163 gd~~nKRPRTTItAKqLETLK~AYn~SpKPARHVREQLsseTGLDMRVVQVWFQNRRAKEKRLKKDAGR~RWgqyfrsmK 242 (383)
T KOG4577|consen 163 GDASNKRPRTTITAKQLETLKQAYNTSPKPARHVREQLSSETGLDMRVVQVWFQNRRAKEKRLKKDAGRTRWGQYFRSMK 242 (383)
T ss_pred cccccCCCcceeeHHHHHHHHHHhcCCCchhHHHHHHhhhccCcceeehhhhhhhhhHHHHhhhhhcchhHHHHHHHHhh
Confidence 33445566666999999999999999999999999999999999999999999999999999766666667888888888
Q ss_pred hhhhhhHHhHHH
Q 019570 133 LNYDSLQHDNEA 144 (339)
Q Consensus 133 ~e~~sl~~ene~ 144 (339)
.. .+-+.|++.
T Consensus 243 ~s-gs~r~ekds 253 (383)
T KOG4577|consen 243 RS-GSSRAEKDS 253 (383)
T ss_pred cc-CCccccccc
Confidence 76 555555554
No 20
>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=99.28 E-value=4.3e-12 Score=96.01 Aligned_cols=52 Identities=15% Similarity=0.360 Sum_probs=48.7
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCC----CCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 58 SEKKRRLSVDQVKALEKNFEVENK----LEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 58 krKRrRfT~eQl~~LE~~F~~~~y----Ps~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
++.|+.||.+|+..||..|...+| |+...+.+||..+||++++|+|||||.+
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 556677999999999999999999 9999999999999999999999999964
No 21
>KOG0486 consensus Transcription factor PTX1, contains HOX domain [Transcription]
Probab=99.25 E-value=4.4e-12 Score=122.96 Aligned_cols=54 Identities=28% Similarity=0.570 Sum_probs=52.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
||.+|+..||..|++++||+...|++||..++|++.+|+|||.|||+|||++..
T Consensus 119 FtSqqlqele~tF~rNrypdMstrEEIavwtNlTE~rvrvwfknrrakwrkrEr 172 (351)
T KOG0486|consen 119 FTSQQLQELEATFQRNRYPDMSTREEIAVWTNLTEARVRVWFKNRRAKWRKRER 172 (351)
T ss_pred hHHHHHHHHHHHHhhccCCccchhhHHHhhccccchhhhhhcccchhhhhhhhh
Confidence 999999999999999999999999999999999999999999999999998653
No 22
>KOG0844 consensus Transcription factor EVX1, contains HOX domain [Transcription]
Probab=99.24 E-value=3.3e-12 Score=123.59 Aligned_cols=62 Identities=34% Similarity=0.553 Sum_probs=56.5
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~e 118 (339)
.+|-|+-||.+||..||+.|.+..|-++.+|.+||..|+|++..|||||||||+|+||+.+-
T Consensus 181 mRRYRTAFTReQIaRLEKEFyrENYVSRprRcELAAaLNLPEtTIKVWFQNRRMKDKRQRla 242 (408)
T KOG0844|consen 181 MRRYRTAFTREQIARLEKEFYRENYVSRPRRCELAAALNLPETTIKVWFQNRRMKDKRQRLA 242 (408)
T ss_pred HHHHHhhhhHHHHHHHHHHHHHhccccCchhhhHHHhhCCCcceeehhhhhchhhhhhhhhh
Confidence 44444559999999999999999999999999999999999999999999999999998753
No 23
>KOG3802 consensus Transcription factor OCT-1, contains POU and HOX domains [Transcription]
Probab=99.22 E-value=7.1e-12 Score=124.65 Aligned_cols=61 Identities=31% Similarity=0.436 Sum_probs=55.3
Q ss_pred CcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 56 ~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
++||||+.|.......||+.|..|++|+..++..||.+|+|...+|+|||||||.|.||-.
T Consensus 293 RkRKKRTSie~~vr~aLE~~F~~npKPt~qEIt~iA~~L~leKEVVRVWFCNRRQkeKR~~ 353 (398)
T KOG3802|consen 293 RKRKKRTSIEVNVRGALEKHFLKNPKPTSQEITHIAESLQLEKEVVRVWFCNRRQKEKRIT 353 (398)
T ss_pred cccccccceeHHHHHHHHHHHHhCCCCCHHHHHHHHHHhccccceEEEEeeccccccccCC
Confidence 3445555599999999999999999999999999999999999999999999999999853
No 24
>KOG0491 consensus Transcription factor BSH, contains HOX domain [General function prediction only]
Probab=99.21 E-value=2.5e-12 Score=115.26 Aligned_cols=56 Identities=39% Similarity=0.560 Sum_probs=53.2
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 62 rRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
+.|+..|+..||+.|+..+|++..+|.+||..|+|++.||+.||||||+|.||.+.
T Consensus 105 tvfs~~ql~~l~~rFe~QrYLS~~e~~ELan~L~LS~~QVKTWFQNrRMK~Kk~~r 160 (194)
T KOG0491|consen 105 TVFSDPQLSGLEKRFERQRYLSTPERQELANALSLSETQVKTWFQNRRMKHKKQQR 160 (194)
T ss_pred ccccCccccccHHHHhhhhhcccHHHHHHHHHhhhhHHHHHHHHHHHHHHHHHHHh
Confidence 34999999999999999999999999999999999999999999999999999764
No 25
>KOG0847 consensus Transcription factor, contains HOX domain [Transcription]
Probab=99.18 E-value=7.9e-12 Score=116.52 Aligned_cols=62 Identities=37% Similarity=0.692 Sum_probs=55.7
Q ss_pred CCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 55 GHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 55 ~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
++++..|..|+..|+..||..|...+||-...|.+||..+|+++.||+|||||||+|||++.
T Consensus 165 G~rk~srPTf~g~qi~~le~~feqtkylaG~~ra~lA~~lgmteSqvkVWFQNRRTKWRKkh 226 (288)
T KOG0847|consen 165 GQRKQSRPTFTGHQIYQLERKFEQTKYLAGADRAQLAQELNMTESQVKVWFQNRRTKWRKKH 226 (288)
T ss_pred ccccccCCCccchhhhhhhhhhhhhhcccchhHHHhhccccccHHHHHHHHhcchhhhhhhh
Confidence 43444444499999999999999999999999999999999999999999999999999975
No 26
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=99.03 E-value=1.4e-10 Score=104.95 Aligned_cols=60 Identities=28% Similarity=0.342 Sum_probs=55.2
Q ss_pred cCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
.++.|+.|+..|+++||+.|...+||+...|+.||..+++++..|+|||||||++|+++.
T Consensus 60 ~rr~rt~~~~~ql~~ler~f~~~h~Pd~~~r~~la~~~~~~e~rVqvwFqnrrak~r~~~ 119 (235)
T KOG0490|consen 60 KRCARCKFTISQLDELERAFEKVHLPCFACRECLALLLTGDEFRVQVWFQNRRAKDRKEE 119 (235)
T ss_pred ccccCCCCCcCHHHHHHHhhcCCCcCccchHHHHhhcCCCCeeeeehhhhhhcHhhhhhh
Confidence 444555599999999999999999999999999999999999999999999999999865
No 27
>KOG1168 consensus Transcription factor ACJ6/BRN-3, contains POU and HOX domains [Transcription]
Probab=98.78 E-value=3e-09 Score=102.75 Aligned_cols=65 Identities=28% Similarity=0.495 Sum_probs=58.6
Q ss_pred cCCCCcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 52 ESGGHVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 52 ~~~~~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
..++.+||||+.+.......||++|...+.|+.+.+..||.+|+|....|+|||||.|.|.||..
T Consensus 304 ~~~~ekKRKRTSIAAPEKRsLEayFavQPRPS~EkIAaIAekLDLKKNVVRVWFCNQRQKQKRm~ 368 (385)
T KOG1168|consen 304 LPGGEKKRKRTSIAAPEKRSLEAYFAVQPRPSGEKIAAIAEKLDLKKNVVRVWFCNQRQKQKRMK 368 (385)
T ss_pred cCccccccccccccCcccccHHHHhccCCCCchhHHHHHHHhhhhhhceEEEEeeccHHHHHHhh
Confidence 34556777777788889999999999999999999999999999999999999999999999854
No 28
>KOG0849 consensus Transcription factor PRD and related proteins, contain PAX and HOX domains [Transcription]
Probab=98.78 E-value=4.8e-09 Score=104.00 Aligned_cols=59 Identities=36% Similarity=0.620 Sum_probs=54.8
Q ss_pred CCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 58 SEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 58 krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
+++|+.|+..|+..||+.|+.++||+...|+.||.++++++.+|+|||+|||++|+|..
T Consensus 177 rr~rtsft~~Q~~~le~~f~rt~yP~i~~Re~La~~i~l~e~riqvwf~nrra~~rr~~ 235 (354)
T KOG0849|consen 177 RRNRTSFSPSQLEALEECFQRTPYPDIVGRETLAKETGLPEPRVQVWFQNRRAKWRRQH 235 (354)
T ss_pred cccccccccchHHHHHHHhcCCCCCchhhHHHHhhhccCCchHHHHHHhhhhhhhhhcc
Confidence 34445699999999999999999999999999999999999999999999999999975
No 29
>KOG0775 consensus Transcription factor SIX and related HOX domain proteins [Transcription]
Probab=98.59 E-value=3.4e-08 Score=94.81 Aligned_cols=51 Identities=29% Similarity=0.428 Sum_probs=47.7
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
|...-...|..+|..++||++.++.+||+.+||+..||-+||.|||+|+|.
T Consensus 183 FKekSR~~LrewY~~~~YPsp~eKReLA~aTgLt~tQVsNWFKNRRQRDRa 233 (304)
T KOG0775|consen 183 FKEKSRSLLREWYLQNPYPSPREKRELAEATGLTITQVSNWFKNRRQRDRA 233 (304)
T ss_pred hhHhhHHHHHHHHhcCCCCChHHHHHHHHHhCCchhhhhhhhhhhhhhhhh
Confidence 566677899999999999999999999999999999999999999999984
No 30
>KOG0774 consensus Transcription factor PBX and related HOX domain proteins [Transcription]
Probab=98.13 E-value=1.2e-06 Score=84.06 Aligned_cols=59 Identities=29% Similarity=0.461 Sum_probs=54.0
Q ss_pred cCCCCCcCCHHHHHHHHHhhh---hcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHH
Q 019570 57 VSEKKRRLSVDQVKALEKNFE---VENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 57 ~krKRrRfT~eQl~~LE~~F~---~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krk 115 (339)
.+||||.|+..-.++|..+|. .++||+.+.+++||++++++..||..||.|+|-++|+.
T Consensus 188 arRKRRNFsK~aTeiLneyF~~h~~nPYPSee~K~eLAkqCnItvsQvsnwfgnkrIrykK~ 249 (334)
T KOG0774|consen 188 ARRKRRNFSKQATEILNEYFYSHLSNPYPSEEAKEELAKQCNITVSQVSNWFGNKRIRYKKN 249 (334)
T ss_pred HHHhhcccchhHHHHHHHHHHHhcCCCCCcHHHHHHHHHHcCceehhhccccccceeehhhh
Confidence 456777799999999999996 57899999999999999999999999999999999884
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=98.06 E-value=1.6e-06 Score=60.99 Aligned_cols=34 Identities=35% Similarity=0.556 Sum_probs=28.9
Q ss_pred hcCCCCHHHHHHHHHHhCCCccceeehhhhhHHH
Q 019570 78 VENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 78 ~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK 111 (339)
.++||+.+++..||..+||+..||..||-|.|.|
T Consensus 7 ~nPYPs~~ek~~L~~~tgls~~Qi~~WF~NaRrR 40 (40)
T PF05920_consen 7 HNPYPSKEEKEELAKQTGLSRKQISNWFINARRR 40 (40)
T ss_dssp TSGS--HHHHHHHHHHHTS-HHHHHHHHHHHHHH
T ss_pred CCCCCCHHHHHHHHHHcCCCHHHHHHHHHHhHcc
Confidence 3689999999999999999999999999999975
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=97.91 E-value=1.9e-05 Score=57.09 Aligned_cols=44 Identities=61% Similarity=0.900 Sum_probs=41.4
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
+|++++|..||+.|+.|+.++++|+.||+.|++++..|+.++..
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 47899999999999999999999999999999999999998864
No 33
>KOG0490 consensus Transcription factor, contains HOX domain [General function prediction only]
Probab=97.66 E-value=4.2e-05 Score=69.31 Aligned_cols=59 Identities=32% Similarity=0.603 Sum_probs=53.5
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 59 rKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
+.+..++..|+..|+..|...++|+...+..|+..+|++++.|++||||+|++.++...
T Consensus 155 ~~~~~~~~~~~~~~~~~~~~~~~P~~~~~~~l~~~~~~~~~~~q~~~~~~~~~~~~~~~ 213 (235)
T KOG0490|consen 155 RPRTTFTENQLEVLETVFRATPKPDADDREQLAEETGLSERVIQVWFQNRRAKLRKHKR 213 (235)
T ss_pred CCccccccchhHhhhhcccCCCCCchhhHHHHHHhcCCChhhhhhhcccHHHHHHhhcc
Confidence 33344899999999999999999999999999999999999999999999999998653
No 34
>KOG2252 consensus CCAAT displacement protein and related homeoproteins [Transcription]
Probab=97.48 E-value=0.0001 Score=76.69 Aligned_cols=53 Identities=23% Similarity=0.287 Sum_probs=49.4
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHh
Q 019570 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (339)
Q Consensus 60 KRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~ 112 (339)
-|..||..|...|.++|+.+++|+.+..+.|+.+|+|...-|.+||-|-|.|.
T Consensus 423 PRlVfTd~QkrTL~aiFke~~RPS~Emq~tIS~qL~L~~sTV~NfFmNaRRRs 475 (558)
T KOG2252|consen 423 PRLVFTDIQKRTLQAIFKENKRPSREMQETISQQLNLELSTVINFFMNARRRS 475 (558)
T ss_pred ceeeecHHHHHHHHHHHhcCCCCCHHHHHHHHHHhCCcHHHHHHHHHhhhhhc
Confidence 33349999999999999999999999999999999999999999999998876
No 35
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=96.86 E-value=0.0011 Score=74.81 Aligned_cols=62 Identities=27% Similarity=0.381 Sum_probs=57.0
Q ss_pred CcCCCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 56 HVSEKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 56 ~~krKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
.++.+|++++..||..|..+|....||...+.+.|...+++.++.|+|||||-|+|.|+..+
T Consensus 902 ~r~a~~~~~~d~qlk~i~~~~~~q~~~~~~~~E~l~~~~~~~~~~i~vw~qna~~~s~k~~~ 963 (1406)
T KOG1146|consen 902 GRRAYRTQESDLQLKIIKACYEAQRTPTMQECEVLEEPIGLPKRVIQVWFQNARAKSKKAKL 963 (1406)
T ss_pred hhhhhccchhHHHHHHHHHHHhhccCChHHHHHhhcccccCCcchhHHhhhhhhhhhhhhhh
Confidence 45667778999999999999999999999999999999999999999999999999998654
No 36
>KOG0773 consensus Transcription factor MEIS1 and related HOX domain proteins [Transcription]
Probab=96.16 E-value=0.005 Score=60.26 Aligned_cols=55 Identities=27% Similarity=0.342 Sum_probs=47.0
Q ss_pred cCCHHHHHHHHHhhhh---cCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 63 RLSVDQVKALEKNFEV---ENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~---~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
.+....+.+|+.+... .+||+...+..||+++||+..||.+||-|.|-|..+-..
T Consensus 245 ~lP~~a~~ilr~Wl~~h~~~PYPse~~K~~La~~TGLs~~Qv~NWFINaR~R~w~p~~ 302 (342)
T KOG0773|consen 245 GLPKEAVSILRAWLFEHLLHPYPSDDEKLMLAKQTGLSRPQVSNWFINARVRLWKPMI 302 (342)
T ss_pred CCCHHHHHHHHHHHHHhccCCCCcchhccccchhcCCCcccCCchhhhcccccCCchH
Confidence 4899999999988443 579999999999999999999999999999887665443
No 37
>PF11569 Homez: Homeodomain leucine-zipper encoding, Homez; PDB: 2YS9_A.
Probab=95.83 E-value=0.0043 Score=47.03 Aligned_cols=41 Identities=24% Similarity=0.424 Sum_probs=31.2
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 69 l~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
+..|+.+|...+++.......|..+.+|+..||+.||--|+
T Consensus 10 ~~pL~~Yy~~h~~L~E~DL~~L~~kS~ms~qqVr~WFa~~~ 50 (56)
T PF11569_consen 10 IQPLEDYYLKHKQLQEEDLDELCDKSRMSYQQVRDWFAERM 50 (56)
T ss_dssp -HHHHHHHHHT----TTHHHHHHHHTT--HHHHHHHHHHHS
T ss_pred hHHHHHHHHHcCCccHhhHHHHHHHHCCCHHHHHHHHHHhc
Confidence 56699999999999999999999999999999999997554
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=92.34 E-value=0.3 Score=35.41 Aligned_cols=35 Identities=43% Similarity=0.721 Sum_probs=31.1
Q ss_pred HhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 124 LKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 124 LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
+-..|+.|+.++++|..++++|..|+..|++.+..
T Consensus 3 lE~Dy~~LK~~yd~Lk~~~~~L~~E~~~L~aev~~ 37 (45)
T PF02183_consen 3 LERDYDALKASYDSLKAEYDSLKKENEKLRAEVQE 37 (45)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 45689999999999999999999999999988754
No 39
>KOG3623 consensus Homeobox transcription factor SIP1 [Transcription]
Probab=91.99 E-value=0.13 Score=55.98 Aligned_cols=48 Identities=23% Similarity=0.372 Sum_probs=44.9
Q ss_pred HHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHH
Q 019570 69 VKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQ 116 (339)
Q Consensus 69 l~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq 116 (339)
+..|..+|..+..|+.++...+|...||+.+.|+.||+++++....-.
T Consensus 568 ~sllkayyaln~~ps~eelskia~qvglp~~vvk~wfE~~~a~e~sv~ 615 (1007)
T KOG3623|consen 568 TSLLKAYYALNGLPSEEELSKIAQQVGLPFAVVKAWFEDEEAEEMSVE 615 (1007)
T ss_pred HHHHHHHHHhcCCCCHHHHHHHHHHhcccHHHHHHHHHhhhhhhhhhc
Confidence 789999999999999999999999999999999999999999877654
No 40
>PRK09413 IS2 repressor TnpA; Reviewed
Probab=90.80 E-value=0.9 Score=38.41 Aligned_cols=43 Identities=23% Similarity=0.439 Sum_probs=28.2
Q ss_pred CCCCcCCHHHHH-HHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhh
Q 019570 59 EKKRRLSVDQVK-ALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 59 rKRrRfT~eQl~-~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQ 106 (339)
++++++|.++.. ++...+. +.+ ...++|+++|+++.+|..|.+
T Consensus 8 ~~rr~ys~EfK~~aV~~~~~-~g~----sv~evA~e~gIs~~tl~~W~r 51 (121)
T PRK09413 8 EKRRRRTTQEKIAIVQQSFE-PGM----TVSLVARQHGVAASQLFLWRK 51 (121)
T ss_pred CCCCCCCHHHHHHHHHHHHc-CCC----CHHHHHHHHCcCHHHHHHHHH
Confidence 345667777643 4333333 222 356789999999999999953
No 41
>smart00340 HALZ homeobox associated leucin zipper.
Probab=87.93 E-value=0.9 Score=32.86 Aligned_cols=28 Identities=36% Similarity=0.506 Sum_probs=23.1
Q ss_pred hHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 128 YDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 128 ~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
.+.|+.+.++|..||.+|++|+.+|++-
T Consensus 7 Ce~LKrcce~LteeNrRL~ke~~eLral 34 (44)
T smart00340 7 CELLKRCCESLTEENRRLQKEVQELRAL 34 (44)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 3456668888999999999999999863
No 42
>PF04218 CENP-B_N: CENP-B N-terminal DNA-binding domain; InterPro: IPR006695 Centromere Protein B (CENP-B) is a DNA-binding protein localized to the centromere. Within the N-terminal 125 residues, there is a DNA-binding region, which binds to a corresponding 17bp CENP-B box sequence. CENP-B dimers either bind two separate DNA molecules or alternatively, they may bind two CENP-B boxes on one DNA molecule, with the intervening stretch of DNA forming a loop structure. The CENP-B DNA-binding domain consists of two repeating domains, RP1 and RP2. This family corresponds to RP1 has been shown to consist of four helices in a helix-turn-helix structure [].; GO: 0003677 DNA binding, 0000775 chromosome, centromeric region; PDB: 1BW6_A 1HLV_A 2ELH_A.
Probab=86.67 E-value=1.1 Score=33.02 Aligned_cols=46 Identities=22% Similarity=0.420 Sum_probs=31.5
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 59 rKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
++|+.+|.++-..+=..++... ....||+++|++..+|..|..|+.
T Consensus 2 rkR~~LTl~eK~~iI~~~e~g~-----s~~~ia~~fgv~~sTv~~I~K~k~ 47 (53)
T PF04218_consen 2 RKRKSLTLEEKLEIIKRLEEGE-----SKRDIAREFGVSRSTVSTILKNKD 47 (53)
T ss_dssp SSSSS--HHHHHHHHHHHHCTT------HHHHHHHHT--CCHHHHHHHCHH
T ss_pred CCCccCCHHHHHHHHHHHHcCC-----CHHHHHHHhCCCHHHHHHHHHhHH
Confidence 4566688887766666666555 477899999999999999998753
No 43
>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=79.34 E-value=8.6 Score=32.60 Aligned_cols=47 Identities=30% Similarity=0.405 Sum_probs=39.9
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhhhc
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENT 161 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~~ 161 (339)
.+.+++...+-+....|+..-..+..||..|+-||..|+..|.+..+
T Consensus 11 ~~le~~l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 11 DQLEQQLGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 45677777888888888889999999999999999999999987754
No 44
>KOG4196 consensus bZIP transcription factor MafK [Transcription]
Probab=77.89 E-value=26 Score=31.09 Aligned_cols=81 Identities=26% Similarity=0.306 Sum_probs=49.7
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHH----------hhHHHHHHHHHHHhhhhHHH
Q 019570 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR----------WKTKQLERDYGVLKANYDAL 131 (339)
Q Consensus 62 rRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK----------~Krkq~eke~~~LKa~~d~L 131 (339)
.+|+.++|-.+ ..|+.=-.--|++...|-.|=|-||+- .||-+.+.+ |.+....|
T Consensus 22 d~lsDd~Lvsm------------SVReLNr~LrG~~reEVvrlKQrRRTLKNRGYA~sCR~KRv~Qk~e---LE~~k~~L 86 (135)
T KOG4196|consen 22 DRLSDDELVSM------------SVRELNRHLRGLSREEVVRLKQRRRTLKNRGYAQSCRVKRVQQKHE---LEKEKAEL 86 (135)
T ss_pred CCcCHHHHHHh------------hHHHHHHHhcCCCHHHHHHHHHHHHHHhhhhHHHHHHHHHHHHHHH---HHHHHHHH
Confidence 56888888776 233222233488888899998888763 333333333 33444455
Q ss_pred HhhhhhhHHhHHHHHHHHHHHHHHhh
Q 019570 132 KLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 132 k~e~~sl~~ene~L~~E~~~Lk~~l~ 157 (339)
..+-+.|.+|+.+++.|+.-++.+..
T Consensus 87 ~qqv~~L~~e~s~~~~E~da~k~k~e 112 (135)
T KOG4196|consen 87 QQQVEKLKEENSRLRRELDAYKSKYE 112 (135)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 66666666677777777766666543
No 45
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=71.36 E-value=15 Score=31.48 Aligned_cols=45 Identities=36% Similarity=0.457 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
.++++....+-+....|+..-..+..||..|+-||..|+.+|.+.
T Consensus 11 ~~le~~l~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~ 55 (110)
T PRK13169 11 DDLEQNLGVLLKELGALKKQLAELLEENTALRLENDKLRERLEEL 55 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 456677777777888888888889999999999999999998764
No 46
>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=71.30 E-value=18 Score=28.64 Aligned_cols=35 Identities=29% Similarity=0.422 Sum_probs=18.4
Q ss_pred HHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 120 e~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
.+..|+-.++.|+..+..+..+++.|+.++.+|+.
T Consensus 19 ti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~ 53 (72)
T PF06005_consen 19 TIALLQMENEELKEKNNELKEENEELKEENEQLKQ 53 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHH
Confidence 34444445555555555555555555555555553
No 47
>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=70.32 E-value=28 Score=26.11 Aligned_cols=35 Identities=31% Similarity=0.419 Sum_probs=21.4
Q ss_pred HHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 121 ~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
...|......|..+++.|..++..|..++..|+..
T Consensus 28 ~~~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e 62 (64)
T PF00170_consen 28 IEELEEKVEELESENEELKKELEQLKKEIQSLKSE 62 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 34455556666666666666666666666666554
No 48
>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=69.67 E-value=22 Score=28.88 Aligned_cols=47 Identities=19% Similarity=0.246 Sum_probs=36.5
Q ss_pred HhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhh
Q 019570 111 RWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 111 K~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~ 157 (339)
+..+..+.++...|+...+.|....+.++.|++.|..||+-|...+.
T Consensus 15 ~e~k~~Li~ei~~LQ~sL~~L~~Rve~Vk~E~~kL~~EN~~Lq~YI~ 61 (80)
T PF10224_consen 15 KEEKEELIQEILELQDSLEALSDRVEEVKEENEKLESENEYLQQYIG 61 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33445566677778888888888888889999999999988887654
No 49
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=65.11 E-value=17 Score=35.35 Aligned_cols=54 Identities=33% Similarity=0.364 Sum_probs=37.1
Q ss_pred hhhHHHhhH--HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 106 QNRRARWKT--KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 106 QNRRaK~Kr--kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
|+-|.|.|- ..++.+...|-..++.|+.+++.|+..|+.|..++.+|...|...
T Consensus 82 QtaRDrKKaRm~eme~~i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~ 137 (292)
T KOG4005|consen 82 QTARDRKKARMEEMEYEIKDLTEENEILQNENDSLRAINESLLAKNHELDSELELL 137 (292)
T ss_pred hhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHH
Confidence 444444433 333445556677888888888888888888888888888777644
No 50
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=62.70 E-value=18 Score=31.14 Aligned_cols=44 Identities=39% Similarity=0.504 Sum_probs=37.5
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
...++....+-+....++..-.++..||..|+-||..|+.+|..
T Consensus 11 ~~le~~l~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 11 DNLEEQLGVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 35566777777788888888899999999999999999999976
No 51
>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=62.65 E-value=43 Score=26.51 Aligned_cols=44 Identities=25% Similarity=0.336 Sum_probs=29.1
Q ss_pred hHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 113 KTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 113 Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
....++.+...|+..+..|..++..|..+|+.|+.+....+.++
T Consensus 19 ti~~Lq~e~eeLke~n~~L~~e~~~L~~en~~L~~e~~~~~~rl 62 (72)
T PF06005_consen 19 TIALLQMENEELKEKNNELKEENEELKEENEQLKQERNAWQERL 62 (72)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455666667777777777777777777777777665555544
No 52
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=60.42 E-value=27 Score=33.89 Aligned_cols=48 Identities=25% Similarity=0.271 Sum_probs=28.2
Q ss_pred HHHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 109 RaK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
|.|.++++.+. .++.....|..+++.|+.+.+.|++|+..|+..+..-
T Consensus 208 kSR~~~k~~~~---e~~~r~~~leken~~lr~~v~~l~~el~~~~~~~~~~ 255 (269)
T KOG3119|consen 208 KSRDKRKQKED---EMAHRVAELEKENEALRTQVEQLKKELATLRRLFLQL 255 (269)
T ss_pred HhhhhHHHHHH---HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhh
Confidence 45555554442 2333445566666777777777777777777655543
No 53
>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=59.87 E-value=2.7 Score=31.70 Aligned_cols=44 Identities=23% Similarity=0.379 Sum_probs=26.7
Q ss_pred CCCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhh
Q 019570 59 EKKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 59 rKRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQ 106 (339)
+++++||+++...+=..+.. .......+|+++|+++.++..|-.
T Consensus 2 ~~r~~ys~e~K~~~v~~~~~----~g~sv~~va~~~gi~~~~l~~W~~ 45 (76)
T PF01527_consen 2 RKRRRYSPEFKLQAVREYLE----SGESVSEVAREYGISPSTLYNWRK 45 (76)
T ss_dssp -SS----HHHHHHHHHHHHH----HHCHHHHHHHHHTS-HHHHHHHHH
T ss_pred CCCCCCCHHHHHHHHHHHHH----CCCceEeeecccccccccccHHHH
Confidence 35566998876665444421 224577899999999999999953
No 54
>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=59.11 E-value=38 Score=25.39 Aligned_cols=34 Identities=24% Similarity=0.348 Sum_probs=15.7
Q ss_pred HHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHH
Q 019570 116 QLERDYGVLKANYDALKLNYDSLQHDNEALLKEI 149 (339)
Q Consensus 116 q~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~ 149 (339)
.++.....|...++.|......+..++..|..++
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~L~~~~~~L~~e~ 63 (64)
T PF00170_consen 30 ELEEKVEELESENEELKKELEQLKKEIQSLKSEN 63 (64)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 3344444444444444444444444444444443
No 55
>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=58.12 E-value=14 Score=25.97 Aligned_cols=39 Identities=15% Similarity=0.223 Sum_probs=29.1
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhh
Q 019570 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQ 106 (339)
.+++.+..+|...|. ....-.++|..+|++...|+.|..
T Consensus 4 ~L~~~er~vi~~~y~-----~~~t~~eIa~~lg~s~~~V~~~~~ 42 (50)
T PF04545_consen 4 QLPPREREVIRLRYF-----EGLTLEEIAERLGISRSTVRRILK 42 (50)
T ss_dssp TS-HHHHHHHHHHHT-----ST-SHHHHHHHHTSCHHHHHHHHH
T ss_pred hCCHHHHHHHHHHhc-----CCCCHHHHHHHHCCcHHHHHHHHH
Confidence 378888999988882 223467899999999999887754
No 56
>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=57.57 E-value=9.8 Score=25.41 Aligned_cols=43 Identities=14% Similarity=0.146 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRAR 111 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK 111 (339)
+++.+..++...|... ....++|..+|++...|..|....+.+
T Consensus 11 l~~~~~~~~~~~~~~~-----~~~~~ia~~~~~s~~~i~~~~~~~~~~ 53 (55)
T cd06171 11 LPEREREVILLRFGEG-----LSYEEIAEILGISRSTVRQRLHRALKK 53 (55)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCcCHHHHHHHHHHHHHH
Confidence 6777777777766422 235678999999999999997654443
No 57
>PF13443 HTH_26: Cro/C1-type HTH DNA-binding domain; PDB: 3TYR_A 3TYS_A 3B7H_A.
Probab=56.81 E-value=8 Score=28.17 Aligned_cols=41 Identities=15% Similarity=0.203 Sum_probs=24.8
Q ss_pred HHHHHHHHhCCCccceeehhhhhHHHhhHHHHHHHHHHHhh
Q 019570 86 RKVKLAQELGLQPRQVAVWFQNRRARWKTKQLERDYGVLKA 126 (339)
Q Consensus 86 ~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~eke~~~LKa 126 (339)
....||+.+|++...|..|+.++...+....+.+-...|.-
T Consensus 12 t~~~La~~~gis~~tl~~~~~~~~~~~~~~~l~~ia~~l~~ 52 (63)
T PF13443_consen 12 TQKDLARKTGISRSTLSRILNGKPSNPSLDTLEKIAKALNC 52 (63)
T ss_dssp -HHHHHHHHT--HHHHHHHHTTT-----HHHHHHHHHHHT-
T ss_pred CHHHHHHHHCcCHHHHHHHHhcccccccHHHHHHHHHHcCC
Confidence 45689999999999999999988667766666555444443
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=55.37 E-value=13 Score=27.79 Aligned_cols=38 Identities=26% Similarity=0.285 Sum_probs=31.1
Q ss_pred CCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccce
Q 019570 64 LSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQV 101 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~y--Ps~~~ReeLA~~LgLs~rQV 101 (339)
+|+.|.++|...|...-| |-...-.+||.++|+++.-|
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 588999999999997765 55556678999999998664
No 59
>smart00338 BRLZ basic region leucin zipper.
Probab=55.36 E-value=65 Score=24.14 Aligned_cols=34 Identities=29% Similarity=0.462 Sum_probs=19.2
Q ss_pred HHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 123 VLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 123 ~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
.|......|..++..|..+...|..++..|+..+
T Consensus 30 ~Le~~~~~L~~en~~L~~~~~~l~~e~~~lk~~~ 63 (65)
T smart00338 30 ELERKVEQLEAENERLKKEIERLRRELEKLKSEL 63 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3444455555555556666666666666665544
No 60
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=54.55 E-value=23 Score=29.68 Aligned_cols=28 Identities=29% Similarity=0.392 Sum_probs=18.6
Q ss_pred hhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 127 NYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 127 ~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
....++.++..++++|+.|+.++..|+.
T Consensus 35 q~~~~~~e~~~l~~~n~~L~~eI~~L~~ 62 (105)
T PRK00888 35 QVAAQQQTNAKLKARNDQLFAEIDDLKG 62 (105)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhhC
Confidence 3444555666667777777777777765
No 61
>PF15058 Speriolin_N: Speriolin N terminus
Probab=53.14 E-value=26 Score=32.96 Aligned_cols=42 Identities=31% Similarity=0.391 Sum_probs=25.9
Q ss_pred HHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhhhccC
Q 019570 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEENTES 163 (339)
Q Consensus 121 ~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~~~~ 163 (339)
|+.++..+++|-.+|..||. .-+|.+||.+||.+|.+.+.+.
T Consensus 7 yeGlrhqierLv~ENeeLKK-lVrLirEN~eLksaL~ea~~~~ 48 (200)
T PF15058_consen 7 YEGLRHQIERLVRENEELKK-LVRLIRENHELKSALGEACAEP 48 (200)
T ss_pred hHHHHHHHHHHHhhhHHHHH-HHHHHHHHHHHHHHHHHhhccc
Confidence 44455555555556666554 3456667778888877776544
No 62
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=52.21 E-value=33 Score=33.30 Aligned_cols=27 Identities=22% Similarity=0.336 Sum_probs=10.5
Q ss_pred hhHHHHhhhhhhHHhHHHHHHHHHHHH
Q 019570 127 NYDALKLNYDSLQHDNEALLKEIRELK 153 (339)
Q Consensus 127 ~~d~Lk~e~~sl~~ene~L~~E~~~Lk 153 (339)
.+..+..++..++...++|..|+.+|.
T Consensus 157 eleele~e~ee~~erlk~le~E~s~Le 183 (290)
T COG4026 157 ELEELEAEYEEVQERLKRLEVENSRLE 183 (290)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333333333333333344444443333
No 63
>PF14775 NYD-SP28_assoc: Sperm tail C-terminal domain
Probab=51.74 E-value=31 Score=26.34 Aligned_cols=31 Identities=29% Similarity=0.484 Sum_probs=24.5
Q ss_pred hHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 128 YDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 128 ~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
|..+-.+..++..|+++|+++|.+|+.-|.+
T Consensus 28 Y~~vL~~R~~l~~e~~~L~~qN~eLr~lLkq 58 (60)
T PF14775_consen 28 YNKVLLDRAALIQEKESLEQQNEELRSLLKQ 58 (60)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 3445567778888999999999999987753
No 64
>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=50.38 E-value=57 Score=23.78 Aligned_cols=27 Identities=30% Similarity=0.464 Sum_probs=16.2
Q ss_pred hHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 128 YDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 128 ~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
...+......|..+|..|..++..|+.
T Consensus 27 ~~~le~~~~~L~~en~~L~~~i~~L~~ 53 (54)
T PF07716_consen 27 EEELEQEVQELEEENEQLRQEIAQLER 53 (54)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 334445555566677777777766653
No 65
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=48.08 E-value=61 Score=32.30 Aligned_cols=49 Identities=24% Similarity=0.361 Sum_probs=31.0
Q ss_pred HHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 110 ARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 110 aK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
+|+|.+++. +.+.+--....|-..|+.|+.+-..|.+|++.||..+.+.
T Consensus 240 tRYRqKkRa-e~E~l~ge~~~Le~rN~~LK~qa~~lerEI~ylKqli~e~ 288 (294)
T KOG4571|consen 240 TRYRQKKRA-EKEALLGELEGLEKRNEELKDQASELEREIRYLKQLILEV 288 (294)
T ss_pred HHHHHHHHH-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344443332 3333344566677777778888888888888888777654
No 66
>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=46.13 E-value=30 Score=20.35 Aligned_cols=37 Identities=14% Similarity=0.337 Sum_probs=25.2
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeeh
Q 019570 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVW 104 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVW 104 (339)
.++..+...+...|... + ....+|..+|++...|..|
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 36666666666666532 2 4567899999998887776
No 67
>KOG0249 consensus LAR-interacting protein and related proteins [General function prediction only]
Probab=46.03 E-value=75 Score=35.52 Aligned_cols=52 Identities=23% Similarity=0.327 Sum_probs=43.4
Q ss_pred HHHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhhh
Q 019570 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 109 RaK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~ 160 (339)
-|..++..+.++...+|..++.+.+..+.+..+++.|+.++..|+.......
T Consensus 213 aAle~kn~L~~e~~s~kk~l~~~~~~k~rl~~d~E~Lr~e~~qL~~~~~~~~ 264 (916)
T KOG0249|consen 213 AALEDKNRLEQELESVKKQLEEMRHDKDKLRTDIEDLRGELDQLRRSSLEKE 264 (916)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHhhh
Confidence 3566777788888899999999999999999999999999999996544443
No 68
>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=43.67 E-value=29 Score=35.30 Aligned_cols=32 Identities=25% Similarity=0.387 Sum_probs=22.5
Q ss_pred hhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 127 NYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 127 ~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
+.-+|+.++.+|++||+.|+.|+.+|++.+..
T Consensus 33 e~~aLr~EN~~LKkEN~~Lk~eVerLE~e~l~ 64 (420)
T PF07407_consen 33 ENFALRMENHSLKKENNDLKIEVERLENEMLR 64 (420)
T ss_pred hhhhHHHHhHHHHHHHHHHHHHHHHHHHHhhh
Confidence 34456777777777777777777777766654
No 69
>KOG4403 consensus Cell surface glycoprotein STIM, contains SAM domain [General function prediction only]
Probab=43.51 E-value=64 Score=34.07 Aligned_cols=61 Identities=25% Similarity=0.452 Sum_probs=37.3
Q ss_pred eehh---hhhHHHhhHHHHHHHHHHHhh----------hhHHHHhhhhh-----------h-----------HHhHHHHH
Q 019570 102 AVWF---QNRRARWKTKQLERDYGVLKA----------NYDALKLNYDS-----------L-----------QHDNEALL 146 (339)
Q Consensus 102 kVWF---QNRRaK~Krkq~eke~~~LKa----------~~d~Lk~e~~s-----------l-----------~~ene~L~ 146 (339)
-+|| ||+.+|.+-...-++.+.|+. ..+..+.++.. + -.+|+..+
T Consensus 229 gcw~ay~Qnk~akehv~km~kdle~Lq~aEqsl~dlQk~Lekar~e~rnvavek~~lerkl~ea~rl~elreg~e~e~~r 308 (575)
T KOG4403|consen 229 GCWFAYRQNKKAKEHVNKMMKDLEGLQRAEQSLEDLQKRLEKAREEQRNVAVEKLDLERKLDEAPRLSELREGVENETSR 308 (575)
T ss_pred hhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhchhhhhhhHHHHHhhhhhhhhhhcchhHHHHH
Confidence 4688 899888887666666555543 22222222110 1 12667778
Q ss_pred HHHHHHHHHhhhhhcc
Q 019570 147 KEIRELKSKLNEENTE 162 (339)
Q Consensus 147 ~E~~~Lk~~l~~~~~~ 162 (339)
+|++.|+.+|.+.+.+
T Consensus 309 kelE~lR~~L~kAEke 324 (575)
T KOG4403|consen 309 KELEQLRVALEKAEKE 324 (575)
T ss_pred HHHHHHHHHHHHHHHH
Confidence 8888899888877653
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=42.81 E-value=58 Score=27.59 Aligned_cols=41 Identities=27% Similarity=0.299 Sum_probs=32.5
Q ss_pred HHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 114 rkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
-..+-.+...||.....|-.++..|+.||+.|+..+.++..
T Consensus 17 l~~l~~~~~~LK~~~~~l~EEN~~L~~EN~~Lr~~l~~~~~ 57 (107)
T PF06156_consen 17 LGQLLEELEELKKQLQELLEENARLRIENEHLRERLEELEQ 57 (107)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 34556677788888888888888888888888888887766
No 71
>cd04766 HTH_HspR Helix-Turn-Helix DNA binding domain of the HspR transcription regulator. Helix-turn-helix (HTH) transcription regulator HspR, N-terminal domain. Heat shock protein regulators (HspR) have been shown to regulate expression of specific regulons in response to high temperature or high osmolarity in Streptomyces and Helicobacter, respectively. These proteins share the N-terminal DNA binding domain with other transcription regulators of the MerR superfamily that promote transcription by reconfiguring the spacer between the -35 and -10 promoter elements. A typical MerR regulator is comprised of distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their conserved N-terminal domains contain predicted winged HTH motifs that mediate DNA binding, while the dissimilar C-terminal domains bind specific coactivator molecules.
Probab=42.28 E-value=90 Score=24.79 Aligned_cols=70 Identities=21% Similarity=0.244 Sum_probs=38.5
Q ss_pred HHHHHHHhCCCccceeehhhhhHHHhhHH------HHHHHHHHHhh----------hhHHHHhhhhhhHHhHHHHHHHHH
Q 019570 87 KVKLAQELGLQPRQVAVWFQNRRARWKTK------QLERDYGVLKA----------NYDALKLNYDSLQHDNEALLKEIR 150 (339)
Q Consensus 87 ReeLA~~LgLs~rQVkVWFQNRRaK~Krk------q~eke~~~LKa----------~~d~Lk~e~~sl~~ene~L~~E~~ 150 (339)
..++|..+|++++.|+.|-+...-+-.+. =...+...++. ....++. .-.+..+.+.|++++.
T Consensus 4 i~e~A~~~gvs~~tLr~ye~~Gli~p~r~~~g~R~y~~~dv~~l~~i~~L~~d~g~~l~~i~~-~l~l~~~~~~l~~~l~ 82 (91)
T cd04766 4 ISVAAELSGMHPQTLRLYERLGLLSPSRTDGGTRRYSERDIERLRRIQRLTQELGVNLAGVKR-ILELEEELAELRAELD 82 (91)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCCcCCCcCCCCCeeECHHHHHHHHHHHHHHHHcCCCHHHHHH-HHHHHHHHHHHHHHHH
Confidence 45789999999999999976442221110 01112222211 1111111 1126667788888888
Q ss_pred HHHHHhh
Q 019570 151 ELKSKLN 157 (339)
Q Consensus 151 ~Lk~~l~ 157 (339)
+|+.++.
T Consensus 83 ~l~~~~~ 89 (91)
T cd04766 83 ELRARLR 89 (91)
T ss_pred HHHHHhc
Confidence 8887775
No 72
>COG3413 Predicted DNA binding protein [General function prediction only]
Probab=40.58 E-value=36 Score=31.26 Aligned_cols=48 Identities=23% Similarity=0.222 Sum_probs=36.0
Q ss_pred cCCHHHHHHHHHhhhhcCC--CCHHHHHHHHHHhCCCccceeehhhhhHHHh
Q 019570 63 RLSVDQVKALEKNFEVENK--LEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~~~y--Ps~~~ReeLA~~LgLs~rQVkVWFQNRRaK~ 112 (339)
.+|..|+++|...|...-| |-...-.+||+++|+++.- +|.-=|||..
T Consensus 155 ~LTdrQ~~vL~~A~~~GYFd~PR~~~l~dLA~~lGISkst--~~ehLRrAe~ 204 (215)
T COG3413 155 DLTDRQLEVLRLAYKMGYFDYPRRVSLKDLAKELGISKST--LSEHLRRAER 204 (215)
T ss_pred cCCHHHHHHHHHHHHcCCCCCCccCCHHHHHHHhCCCHHH--HHHHHHHHHH
Confidence 4999999999999997764 5555667899999999865 3444444443
No 73
>PRK13922 rod shape-determining protein MreC; Provisional
Probab=39.93 E-value=55 Score=31.09 Aligned_cols=36 Identities=25% Similarity=0.254 Sum_probs=18.8
Q ss_pred HhhhhHHHHhhhhhhHHhHH---HHHHHHHHHHHHhhhh
Q 019570 124 LKANYDALKLNYDSLQHDNE---ALLKEIRELKSKLNEE 159 (339)
Q Consensus 124 LKa~~d~Lk~e~~sl~~ene---~L~~E~~~Lk~~l~~~ 159 (339)
+++.++.|+.+...++.+.. .+++|+.+|+..|.-.
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 33344444444444444333 6677777777766433
No 74
>PRK13169 DNA replication intiation control protein YabA; Reviewed
Probab=39.93 E-value=67 Score=27.51 Aligned_cols=40 Identities=25% Similarity=0.389 Sum_probs=34.0
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
..+-++.+.||+....+-.++..|+.||+.|+..+.++..
T Consensus 18 ~~l~~el~~LK~~~~el~EEN~~L~iEN~~Lr~~l~~~~~ 57 (110)
T PRK13169 18 GVLLKELGALKKQLAELLEENTALRLENDKLRERLEELEA 57 (110)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhc
Confidence 4566778888999999999999999999999999998744
No 75
>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=38.89 E-value=1.1e+02 Score=23.92 Aligned_cols=35 Identities=20% Similarity=0.128 Sum_probs=15.4
Q ss_pred HHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 122 GVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 122 ~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
+.|-..+..|+.+|..+.++...+..|...|.++.
T Consensus 10 e~Li~~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekn 44 (65)
T TIGR02449 10 EHLLEYLERLKSENRLLRAQEKTWREERAQLLEKN 44 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333444444444444444444444444444433
No 76
>PF00424 REV: REV protein (anti-repression trans-activator protein); InterPro: IPR000625 REV is a viral anti-repression trans-activator protein, which appears to act post-transcriptionally [] to relieve negative repression of GAG and ENV production. It is a phosphoprotein [, ] whose state of phosphorylation is mediated by a specific serine kinase activity present in the nucleus []. REV accumulates in the nucleoli [].; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0042025 host cell nucleus; PDB: 1ETF_B 1ETG_B 1ULL_B 3LPH_B 2X7L_R.
Probab=38.27 E-value=46 Score=27.77 Aligned_cols=33 Identities=27% Similarity=0.605 Sum_probs=19.4
Q ss_pred HHHHHHhhhhcCCCCHHH--HHHHHHHhCCCccceeehhhhhHHHhhHHHH
Q 019570 69 VKALEKNFEVENKLEPER--KVKLAQELGLQPRQVAVWFQNRRARWKTKQL 117 (339)
Q Consensus 69 l~~LE~~F~~~~yPs~~~--ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~ 117 (339)
+....-.|+.++||...- +.. .|||.+|++.+.
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 344555688899997542 222 689999998764
No 77
>smart00338 BRLZ basic region leucin zipper.
Probab=37.35 E-value=1e+02 Score=23.01 Aligned_cols=30 Identities=33% Similarity=0.535 Sum_probs=16.7
Q ss_pred hhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 127 NYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 127 ~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
....|......|..+|..|..++..|+..+
T Consensus 27 ~~~~Le~~~~~L~~en~~L~~~~~~l~~e~ 56 (65)
T smart00338 27 EIEELERKVEQLEAENERLKKEIERLRREL 56 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 445555555555556666665555555443
No 78
>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=36.94 E-value=1.1e+02 Score=29.93 Aligned_cols=18 Identities=28% Similarity=0.248 Sum_probs=12.9
Q ss_pred HHHHHHHHHHHHHhhhhh
Q 019570 143 EALLKEIRELKSKLNEEN 160 (339)
Q Consensus 143 e~L~~E~~~Lk~~l~~~~ 160 (339)
+.|++||++||..|.-..
T Consensus 94 ~~l~~EN~rLr~LL~~~~ 111 (283)
T TIGR00219 94 QNLKQENVRLRELLNSPL 111 (283)
T ss_pred HHHHHHHHHHHHHhcCcc
Confidence 348888888888776543
No 79
>KOG0483 consensus Transcription factor HEX, contains HOX and HALZ domains [Transcription]
Probab=36.00 E-value=49 Score=31.04 Aligned_cols=36 Identities=31% Similarity=0.566 Sum_probs=31.3
Q ss_pred hhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhhh
Q 019570 125 KANYDALKLNYDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 125 Ka~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~ 160 (339)
-..++.|+.+++++..++++|+.++.+|+..+....
T Consensus 111 E~d~~~Lk~~~~~l~~~~~~Lq~e~~eL~~~~~~~~ 146 (198)
T KOG0483|consen 111 EKDYESLKRQLESLRSENDRLQSEVQELVAELSSLK 146 (198)
T ss_pred hhhHHHHHHHHHHHhhhhhHHHHHHHHHHHHHhhhh
Confidence 347899999999999999999999999998876543
No 80
>KOG1146 consensus Homeobox protein [General function prediction only]
Probab=35.44 E-value=12 Score=43.79 Aligned_cols=58 Identities=21% Similarity=0.110 Sum_probs=50.6
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHHHHH
Q 019570 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTKQLE 118 (339)
Q Consensus 61 RrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krkq~e 118 (339)
++|++.-|..+|-.+|+...+|.-.++..++..|++..|.+-.||++++.+|.....+
T Consensus 448 s~r~~~~~t~~L~S~~kt~~cpkc~~~yk~a~~L~vhmRskhp~~~~~~c~~gq~~~~ 505 (1406)
T KOG1146|consen 448 SKRSLEGQTVVLHSFFKTLKCPKCNWHYKLAQTLGVHMRSKHPESQSAYCKAGQNHPR 505 (1406)
T ss_pred hhcccccceeeeecccccccCCccchhhhhHHHhhhcccccccccchhHhHhcccccc
Confidence 3457888899999999999999999999999999999999999999988888765443
No 81
>KOG3156 consensus Uncharacterized membrane protein [Function unknown]
Probab=35.04 E-value=1e+02 Score=29.50 Aligned_cols=47 Identities=21% Similarity=0.426 Sum_probs=32.9
Q ss_pred HHHHHHHhhhhH-HHHhhhhhhHHhHHHHHHHHHHHHHHhhhhhccCC
Q 019570 118 ERDYGVLKANYD-ALKLNYDSLQHDNEALLKEIRELKSKLNEENTESN 164 (339)
Q Consensus 118 eke~~~LKa~~d-~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~~~~~ 164 (339)
+.++..++.+.. ..+.++..++.||++|..+++++|..|..+.....
T Consensus 100 ~~~f~kiRsel~S~e~sEF~~lr~e~EklkndlEk~ks~lr~ei~~~~ 147 (220)
T KOG3156|consen 100 KVDFAKIRSELVSIERSEFANLRAENEKLKNDLEKLKSSLRHEISKTT 147 (220)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcc
Confidence 334444444332 23467788899999999999999999987765433
No 82
>cd04779 HTH_MerR-like_sg4 Helix-Turn-Helix DNA binding domain of putative transcription regulators from the MerR superfamily. Putative helix-turn-helix (HTH) MerR-like transcription regulators (subgroup 4). Based on sequence similarity, these proteins are predicted to function as transcription regulators that mediate responses to stress in eubacteria. They belong to the MerR superfamily of transcription regulators that promote transcription of various stress regulons by reconfiguring the operator sequence located between the -35 and -10 promoter elements. A typical MerR regulator is comprised of two distinct domains that harbor the regulatory (effector-binding) site and the active (DNA-binding) site. Their N-terminal domains are homologous and contain a DNA-binding winged HTH motif, while the C-terminal domains are often dissimilar and bind specific coactivator molecules such as metal ions, drugs, and organic substrates.
Probab=34.63 E-value=2.4e+02 Score=24.52 Aligned_cols=37 Identities=8% Similarity=0.029 Sum_probs=24.4
Q ss_pred CCCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 60 KKRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 60 KRrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
..|.|+..++..|... ...+.+|++-..|+-++.+..
T Consensus 34 g~R~Y~~~~l~~l~~I-------------~~lr~~G~sL~eI~~~l~~~~ 70 (134)
T cd04779 34 NYRYYDETALDRLQLI-------------EHLKGQRLSLAEIKDQLEEVQ 70 (134)
T ss_pred CCeeECHHHHHHHHHH-------------HHHHHCCCCHHHHHHHHHhhc
Confidence 3455999999998532 224667777777777775543
No 83
>PRK13729 conjugal transfer pilus assembly protein TraB; Provisional
Probab=34.57 E-value=96 Score=32.89 Aligned_cols=44 Identities=18% Similarity=0.274 Sum_probs=29.9
Q ss_pred hHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 113 KTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 113 Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
|...++++++.++++.+.+......++...+.|..|+.+|+.++
T Consensus 77 kasELEKqLaaLrqElq~~saq~~dle~KIkeLEaE~~~Lk~Ql 120 (475)
T PRK13729 77 TAAQMQKQYEEIRRELDVLNKQRGDDQRRIEKLGQDNAALAEQV 120 (475)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhhhhHHHHHHHHHHHHHHHHHHH
Confidence 44555666666666666555566666777777888888888877
No 84
>KOG4005 consensus Transcription factor XBP-1 [Transcription]
Probab=33.79 E-value=93 Score=30.47 Aligned_cols=46 Identities=28% Similarity=0.372 Sum_probs=36.5
Q ss_pred HHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 114 TKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 114 rkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
-+.+.++...|+..++.|+..+..|..+|..|..++..|+..|.+-
T Consensus 99 i~dL~een~~L~~en~~Lr~~n~~L~~~n~el~~~le~~~~~l~~~ 144 (292)
T KOG4005|consen 99 IKDLTEENEILQNENDSLRAINESLLAKNHELDSELELLRQELAEL 144 (292)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHHHHHHhh
Confidence 3456777888888888888888888888888888888888777544
No 85
>PRK03975 tfx putative transcriptional regulator; Provisional
Probab=33.64 E-value=59 Score=28.90 Aligned_cols=48 Identities=19% Similarity=0.189 Sum_probs=35.1
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 61 RrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
...+|+.|..+|... . . .....++|..+|++...|+.|-+..+.+.|+
T Consensus 4 ~~~Lt~rqreVL~lr-~-~----GlTq~EIAe~LGiS~~tVs~ie~ra~kkLr~ 51 (141)
T PRK03975 4 ESFLTERQIEVLRLR-E-R----GLTQQEIADILGTSRANVSSIEKRARENIEK 51 (141)
T ss_pred ccCCCHHHHHHHHHH-H-c----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 345899999999773 2 1 2235689999999999999998755554443
No 86
>COG3074 Uncharacterized protein conserved in bacteria [Function unknown]
Probab=33.50 E-value=2e+02 Score=23.19 Aligned_cols=36 Identities=31% Similarity=0.376 Sum_probs=16.6
Q ss_pred HHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 119 RDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 119 ke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
-+.+.||..+..|..+....+...+.|..++..||.
T Consensus 25 mEieELKEknn~l~~e~q~~q~~reaL~~eneqlk~ 60 (79)
T COG3074 25 MEIEELKEKNNSLSQEVQNAQHQREALERENEQLKE 60 (79)
T ss_pred HHHHHHHHHhhHhHHHHHHHHHHHHHHHHHHHHHHH
Confidence 344444444444444444444444455555554444
No 87
>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=32.24 E-value=1.7e+02 Score=27.29 Aligned_cols=40 Identities=25% Similarity=0.270 Sum_probs=25.9
Q ss_pred HHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 120 e~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
+...|......+...+-.+......|+.|+.+||.+..+.
T Consensus 176 ~L~~Le~~W~~~v~kn~eie~a~~~Le~ei~~l~~~~~~~ 215 (221)
T PF05700_consen 176 ELRYLEQRWKELVSKNLEIEVACEELEQEIEQLKRKAAEL 215 (221)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344555555556666667777778888888877766544
No 88
>PF15058 Speriolin_N: Speriolin N terminus
Probab=32.21 E-value=55 Score=30.87 Aligned_cols=35 Identities=26% Similarity=0.430 Sum_probs=26.4
Q ss_pred hhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 125 KANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 125 Ka~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
-.+|+-+.+..+.+-.||+.|++.++-+|+.+.-+
T Consensus 4 l~~yeGlrhqierLv~ENeeLKKlVrLirEN~eLk 38 (200)
T PF15058_consen 4 LTNYEGLRHQIERLVRENEELKKLVRLIRENHELK 38 (200)
T ss_pred ccchHHHHHHHHHHHhhhHHHHHHHHHHHHHHHHH
Confidence 35678888888888888888888888888765544
No 89
>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=31.71 E-value=1.8e+02 Score=23.49 Aligned_cols=35 Identities=14% Similarity=0.364 Sum_probs=24.7
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhh
Q 019570 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (339)
Q Consensus 61 RrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNR 108 (339)
++.|+..++..|.... ..+.+|++..+++-++...
T Consensus 36 ~R~y~~~di~~l~~i~-------------~lr~~g~~l~~i~~~~~~~ 70 (103)
T cd01106 36 YRLYTEEDLERLQQIL-------------FLKELGFSLKEIKELLKDP 70 (103)
T ss_pred ceeeCHHHHHHHHHHH-------------HHHHcCCCHHHHHHHHHcC
Confidence 4459999999986432 2456788888888777654
No 90
>KOG0709 consensus CREB/ATF family transcription factor [Transcription]
Probab=31.25 E-value=2.2e+02 Score=30.23 Aligned_cols=14 Identities=21% Similarity=0.278 Sum_probs=9.7
Q ss_pred CcCCHHHHHHHHHh
Q 019570 62 RRLSVDQVKALEKN 75 (339)
Q Consensus 62 rRfT~eQl~~LE~~ 75 (339)
-++|.+....|.+.
T Consensus 219 L~LteeEkrLL~kE 232 (472)
T KOG0709|consen 219 LVLTEEEKRLLTKE 232 (472)
T ss_pred eeccHHHHHHHHhc
Confidence 34788877777654
No 91
>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=31.06 E-value=19 Score=27.74 Aligned_cols=19 Identities=21% Similarity=0.604 Sum_probs=16.8
Q ss_pred HHHHHHHHhCCCccceeeh
Q 019570 86 RKVKLAQELGLQPRQVAVW 104 (339)
Q Consensus 86 ~ReeLA~~LgLs~rQVkVW 104 (339)
.-.+||.+||+++.+|+.|
T Consensus 24 ~lkdIA~~Lgvs~~tIr~W 42 (60)
T PF10668_consen 24 KLKDIAEKLGVSESTIRKW 42 (60)
T ss_pred cHHHHHHHHCCCHHHHHHH
Confidence 3457899999999999999
No 92
>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=30.89 E-value=1.5e+02 Score=23.46 Aligned_cols=39 Identities=15% Similarity=0.384 Sum_probs=28.5
Q ss_pred HHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhh
Q 019570 119 RDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 119 ke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~ 157 (339)
+....|+..|..|+.....-.+++..|.+.+..|-.++.
T Consensus 21 ~q~~~Wq~sy~~Lq~~~~~t~~~~a~L~~qv~~Ls~qv~ 59 (70)
T PF04899_consen 21 KQQQEWQSSYADLQHMFEQTSQENAALSEQVNNLSQQVQ 59 (70)
T ss_pred HHHHHHHHHHHHHHHHHHHhHHHHHHHHHHHHHHHHHHH
Confidence 344567777888888888888888888888777766554
No 93
>PRK10884 SH3 domain-containing protein; Provisional
Probab=29.92 E-value=1.7e+02 Score=27.54 Aligned_cols=28 Identities=14% Similarity=0.149 Sum_probs=12.1
Q ss_pred hHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 128 YDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 128 ~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
...|+.++..++.+.+.++.+++.|+.+
T Consensus 134 ~~~L~~~n~~L~~~l~~~~~~~~~l~~~ 161 (206)
T PRK10884 134 INGLKEENQKLKNQLIVAQKKVDAANLQ 161 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3334444444444444444444444433
No 94
>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=29.75 E-value=56 Score=23.05 Aligned_cols=41 Identities=17% Similarity=0.192 Sum_probs=25.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
+++.+..++.-.|- ....-.++|..+|+++..|+.|.+.-|
T Consensus 11 L~~~~r~i~~l~~~-----~g~s~~eIa~~l~~s~~~v~~~l~ra~ 51 (54)
T PF08281_consen 11 LPERQREIFLLRYF-----QGMSYAEIAEILGISESTVKRRLRRAR 51 (54)
T ss_dssp S-HHHHHHHHHHHT-----S---HHHHHHHCTS-HHHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHH-----HCcCHHHHHHHHCcCHHHHHHHHHHHH
Confidence 45555555554443 233467899999999999999986433
No 95
>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=29.55 E-value=67 Score=25.97 Aligned_cols=24 Identities=29% Similarity=0.570 Sum_probs=17.6
Q ss_pred hhHHhHHHHHHHHHHHHHHhhhhh
Q 019570 137 SLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 137 sl~~ene~L~~E~~~Lk~~l~~~~ 160 (339)
+++.+|..|+.++.+|++.|++..
T Consensus 4 ei~eEn~~Lk~eiqkle~ELq~~~ 27 (76)
T PF07334_consen 4 EIQEENARLKEEIQKLEAELQQNK 27 (76)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHH
Confidence 566788888888888877776643
No 96
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=29.46 E-value=1.5e+02 Score=24.18 Aligned_cols=9 Identities=44% Similarity=0.468 Sum_probs=3.6
Q ss_pred HHHHHHHHH
Q 019570 145 LLKEIRELK 153 (339)
Q Consensus 145 L~~E~~~Lk 153 (339)
|..++..||
T Consensus 51 L~~en~qLk 59 (79)
T PRK15422 51 LERENNHLK 59 (79)
T ss_pred HHHHHHHHH
Confidence 334444443
No 97
>PF12808 Mto2_bdg: Micro-tubular organiser Mto1 C-term Mto2-binding region; InterPro: IPR024545 This domain occurs at the C terminus of microtubule organising proteins in both budding and fission fungi. In Schizosaccharomyces pombe it has been shown to interact with the Mto2p protein, an interaction which is critical for anchoring the cytokinetic actin ring to the medial region of the cell and for proper coordination of mitosis with cytokinesis [, ].
Probab=29.27 E-value=1.6e+02 Score=22.10 Aligned_cols=38 Identities=26% Similarity=0.237 Sum_probs=27.0
Q ss_pred HHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 121 ~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
...|++.-+.-..+..+.......|..||..|+++|..
T Consensus 10 e~klkaerE~R~~d~~~a~~rl~~l~~EN~~Lr~eL~~ 47 (52)
T PF12808_consen 10 ERKLKAEREARSLDRSAARKRLSKLEGENRLLRAELER 47 (52)
T ss_pred HHHHHHhHHhccCCchhHHHHHHHHHHHHHHHHHHHHH
Confidence 34566666666666777777788888888888887754
No 98
>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=29.26 E-value=1.3e+02 Score=33.41 Aligned_cols=21 Identities=14% Similarity=0.162 Sum_probs=14.6
Q ss_pred CCHHHHHHHHHHhCCCcccee
Q 019570 82 LEPERKVKLAQELGLQPRQVA 102 (339)
Q Consensus 82 Ps~~~ReeLA~~LgLs~rQVk 102 (339)
|....=..+|+.+|+++..|.
T Consensus 480 ~g~S~a~~iA~~~Glp~~ii~ 500 (771)
T TIGR01069 480 PGESYAFEIAQRYGIPHFIIE 500 (771)
T ss_pred CCCcHHHHHHHHhCcCHHHHH
Confidence 333444568999999988764
No 99
>PRK14127 cell division protein GpsB; Provisional
Probab=29.03 E-value=94 Score=26.60 Aligned_cols=31 Identities=29% Similarity=0.471 Sum_probs=17.2
Q ss_pred HHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 129 DALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 129 d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
+.+-.+++.+..++..|+.++.+|+.++.+-
T Consensus 33 d~V~~dye~l~~e~~~Lk~e~~~l~~~l~e~ 63 (109)
T PRK14127 33 DDVIKDYEAFQKEIEELQQENARLKAQVDEL 63 (109)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3344445555556666666666666655433
No 100
>PRK15422 septal ring assembly protein ZapB; Provisional
Probab=28.57 E-value=2.4e+02 Score=23.10 Aligned_cols=36 Identities=11% Similarity=0.206 Sum_probs=18.3
Q ss_pred HHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 120 e~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
+...|....+.++..+..|.++|+.|+.|...-.++
T Consensus 33 kn~~L~~e~~~~~~~r~~L~~en~qLk~E~~~Wqer 68 (79)
T PRK15422 33 KNNSLSQEVQNAQHQREELERENNHLKEQQNGWQER 68 (79)
T ss_pred HHHHHHHHHHHHHhhHHHHHHHHHHHHHHHHHHHHH
Confidence 333344444444444555666666666665444433
No 101
>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=28.13 E-value=1.2e+02 Score=22.87 Aligned_cols=22 Identities=36% Similarity=0.579 Sum_probs=10.6
Q ss_pred HHhhhhhhHHhHHHHHHHHHHH
Q 019570 131 LKLNYDSLQHDNEALLKEIREL 152 (339)
Q Consensus 131 Lk~e~~sl~~ene~L~~E~~~L 152 (339)
++.....++.+++.|..++..|
T Consensus 29 l~~~i~~l~~e~~~L~~ei~~l 50 (80)
T PF04977_consen 29 LQKEIEELKKENEELKEEIERL 50 (80)
T ss_pred HHHHHHHHHHHHHHHHHHHHHh
Confidence 3334444444555555555555
No 102
>KOG4571 consensus Activating transcription factor 4 [Transcription]
Probab=27.48 E-value=1.3e+02 Score=29.98 Aligned_cols=31 Identities=26% Similarity=0.249 Sum_probs=20.2
Q ss_pred HHHhhhhhhHHhHHHHHHHHHHHHHHhhhhh
Q 019570 130 ALKLNYDSLQHDNEALLKEIRELKSKLNEEN 160 (339)
Q Consensus 130 ~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~~ 160 (339)
.-+.+.+++.-|.+.|.++|++||.+...-+
T Consensus 245 KkRae~E~l~ge~~~Le~rN~~LK~qa~~le 275 (294)
T KOG4571|consen 245 KKRAEKEALLGELEGLEKRNEELKDQASELE 275 (294)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3445566666677777777777777665544
No 103
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=27.34 E-value=1.2e+02 Score=33.00 Aligned_cols=23 Identities=43% Similarity=0.546 Sum_probs=12.1
Q ss_pred hhhHHhHHHHHHHHHHHHHHhhh
Q 019570 136 DSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 136 ~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
.++..||+.|++||..||.+|..
T Consensus 312 q~ll~Ene~Lk~ENatLk~qL~~ 334 (655)
T KOG4343|consen 312 QALLSENEQLKKENATLKRQLDE 334 (655)
T ss_pred HHHHHHHHHHHhhhHHHHHHHHH
Confidence 34445555555555555555443
No 104
>PRK10884 SH3 domain-containing protein; Provisional
Probab=26.94 E-value=2.4e+02 Score=26.49 Aligned_cols=31 Identities=19% Similarity=0.138 Sum_probs=15.4
Q ss_pred HhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 124 LKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 124 LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
|++.+..|+.+...++.+++.|..++..++.
T Consensus 137 L~~~n~~L~~~l~~~~~~~~~l~~~~~~~~~ 167 (206)
T PRK10884 137 LKEENQKLKNQLIVAQKKVDAANLQLDDKQR 167 (206)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444555555555555555555555554443
No 105
>PRK00409 recombination and DNA strand exchange inhibitor protein; Reviewed
Probab=26.02 E-value=1.6e+02 Score=32.90 Aligned_cols=19 Identities=21% Similarity=0.410 Sum_probs=13.9
Q ss_pred HHHHHHHHHHhCCCcccee
Q 019570 84 PERKVKLAQELGLQPRQVA 102 (339)
Q Consensus 84 ~~~ReeLA~~LgLs~rQVk 102 (339)
...=..+|+.+|+++..|.
T Consensus 487 ~S~a~~iA~~~Glp~~ii~ 505 (782)
T PRK00409 487 KSNAFEIAKRLGLPENIIE 505 (782)
T ss_pred CcHHHHHHHHhCcCHHHHH
Confidence 3344578999999988764
No 106
>PRK09642 RNA polymerase sigma factor SigW; Reviewed
Probab=25.94 E-value=98 Score=26.19 Aligned_cols=47 Identities=13% Similarity=0.124 Sum_probs=29.6
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhHH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKTK 115 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Krk 115 (339)
+++.+..++.-.|-.. ..-.++|..+|+++..|+++...-|.+.|..
T Consensus 107 Lp~~~r~v~~l~~~~g-----~s~~EIA~~lgis~~tV~~~l~Rar~~Lr~~ 153 (160)
T PRK09642 107 LPENYRDVVLAHYLEE-----KSYQEIALQEKIEVKTVEMKLYRARKWIKKH 153 (160)
T ss_pred CCHHHHHHHHHHHHhC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHHHHH
Confidence 4555555554433222 1245889999999999999887555554443
No 107
>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=25.49 E-value=72 Score=25.48 Aligned_cols=45 Identities=16% Similarity=0.175 Sum_probs=29.3
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhh
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~K 113 (339)
+++.+..++...|-. .....++|..+|+++..|..|...-+.+.|
T Consensus 111 L~~~~~~ii~~~~~~-----g~s~~eIA~~l~~s~~~v~~~~~~~~~kl~ 155 (158)
T TIGR02937 111 LPEREREVLVLRYLE-----GLSYKEIAEILGISVGTVKRRLKRARKKLR 155 (158)
T ss_pred CCHHHHHHHhhHHhc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 556666665544332 224568999999999999888764444433
No 108
>KOG4343 consensus bZIP transcription factor ATF6 [Transcription]
Probab=25.22 E-value=1.5e+02 Score=32.28 Aligned_cols=34 Identities=29% Similarity=0.350 Sum_probs=28.4
Q ss_pred HHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 121 YGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 121 ~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
...|++...+|..+++.|+.||..|+.++..|-.
T Consensus 304 ~~~Le~rLq~ll~Ene~Lk~ENatLk~qL~~l~~ 337 (655)
T KOG4343|consen 304 MLGLEARLQALLSENEQLKKENATLKRQLDELVS 337 (655)
T ss_pred HHHHHHHHHHHHHHHHHHHhhhHHHHHHHHHHhh
Confidence 3467888888999999999999999998888776
No 109
>PRK09652 RNA polymerase sigma factor RpoE; Provisional
Probab=24.49 E-value=96 Score=26.27 Aligned_cols=45 Identities=13% Similarity=0.016 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhh
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~K 113 (339)
+++.+..+|...|-. ...-.++|..+|+++..|+.|...-|.+.|
T Consensus 129 L~~~~r~vl~l~~~~-----~~s~~eIA~~lgis~~tV~~~l~ra~~~Lr 173 (182)
T PRK09652 129 LPEELRTAITLREIE-----GLSYEEIAEIMGCPIGTVRSRIFRAREALR 173 (182)
T ss_pred CCHHHHHHHHHHHHc-----CCCHHHHHHHHCCCHHHHHHHHHHHHHHHH
Confidence 777777777665432 223457899999999999998764333333
No 110
>PF00038 Filament: Intermediate filament protein; InterPro: IPR016044 Intermediate filaments (IF) [, , ] are proteins which are primordial components of the cytoskeleton and the nuclear envelope. They generally form filamentous structures 8 to 14 nm wide. IF proteins are members of a very large multigene family of proteins which has been subdivided in five major subgroups: Type I: Acidic cytokeratins. Type II: Basic cytokeratins. Type III: Vimentin, desmin, glial fibrillary acidic protein (GFAP), peripherin, and plasticin. Type IV: Neurofilaments L, H and M, alpha-internexin and nestin. Type V: Nuclear lamins A, B1, B2 and C. All IF proteins are structurally similar in that they consist of: a central rod domain comprising some 300 to 350 residues which is arranged in coiled-coiled alpha-helices, with at least two short characteristic interruptions; a N-terminal non-helical domain (head) of variable length; and a C-terminal domain (tail) which is also non-helical, and which shows extreme length variation between different IF proteins. While IF proteins are evolutionary and structurally related, they have limited sequence homologies except in several regions of the rod domain. This entry represents the central rod domain found in IF proteins.; PDB: 3TNU_B 3KLT_D 1GK4_F 3TRT_A 3G1E_A 3UF1_C 1GK6_B 1GK7_A 3TYY_B 3V4W_A ....
Probab=24.41 E-value=2.1e+02 Score=27.38 Aligned_cols=61 Identities=21% Similarity=0.500 Sum_probs=33.3
Q ss_pred ccceeehhhhhHHHhhH---------HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhh
Q 019570 98 PRQVAVWFQNRRARWKT---------KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNE 158 (339)
Q Consensus 98 ~rQVkVWFQNRRaK~Kr---------kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~ 158 (339)
...+..||+.+-...+. .....+...++.....|..+-.+++..|..|...+..|...+..
T Consensus 186 ~~e~e~~y~~k~~~l~~~~~~~~~~~~~~~~E~~~~r~~~~~l~~el~~l~~~~~~Le~~l~~le~~~~~ 255 (312)
T PF00038_consen 186 REELEEWYQSKLEELRQQSEKSSEELESAKEELKELRRQIQSLQAELESLRAKNASLERQLRELEQRLDE 255 (312)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred hhhhhhhcccccccccccccccccccchhHhHHHHHHhhhhHhhhhhhccccchhhhhhhHHHHHHHHHH
Confidence 45678899887443332 22233444455555555555555555566666666555554443
No 111
>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=24.36 E-value=1.2e+02 Score=32.11 Aligned_cols=11 Identities=45% Similarity=0.601 Sum_probs=6.4
Q ss_pred cCCHHHHHHHH
Q 019570 63 RLSVDQVKALE 73 (339)
Q Consensus 63 RfT~eQl~~LE 73 (339)
.++++++..|.
T Consensus 41 ~ltpee~kalG 51 (472)
T TIGR03752 41 ELSPEELKALG 51 (472)
T ss_pred cCCcchhHhcC
Confidence 36666665553
No 112
>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=23.78 E-value=81 Score=24.28 Aligned_cols=43 Identities=21% Similarity=0.425 Sum_probs=22.3
Q ss_pred CcCCHH-HHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhh
Q 019570 62 RRLSVD-QVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 62 rRfT~e-Ql~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQ 106 (339)
+.|+.. -|.+++.++. ...--...|. -|+++|++.++|+-|-+
T Consensus 4 rsy~~~FKL~Vv~~a~~-~~nc~~~~RA-aarkf~V~r~~Vr~W~k 47 (58)
T PF09607_consen 4 RSYTAEFKLKVVEYAEK-DNNCKGNQRA-AARKFNVSRRQVRKWRK 47 (58)
T ss_dssp ----HHHHHHHHHHHHH--TTTTT-HHH-HHHHTTS-HHHHHHHHT
T ss_pred cccChHHHHHHHHHHHH-ccchhhhHHH-HHHHhCccHHHHHHHHH
Confidence 335543 3555555443 3222223343 49999999999999953
No 113
>PF08172 CASP_C: CASP C terminal; InterPro: IPR012955 This domain is the C-terminal region of the CASP family of proteins. These are Golgi membrane proteins which are thought to have a role in vesicle transport [].; GO: 0006891 intra-Golgi vesicle-mediated transport, 0030173 integral to Golgi membrane
Probab=23.77 E-value=2.3e+02 Score=27.37 Aligned_cols=38 Identities=26% Similarity=0.371 Sum_probs=18.6
Q ss_pred HHHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHH
Q 019570 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALL 146 (339)
Q Consensus 109 RaK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~ 146 (339)
|=|.|...+|++...++.....|+.+-++|+.||..|=
T Consensus 90 RFR~Rn~ELE~elr~~~~~~~~L~~Ev~~L~~DN~kLY 127 (248)
T PF08172_consen 90 RFRQRNAELEEELRKQQQTISSLRREVESLRADNVKLY 127 (248)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44444555566655555544444444444444444443
No 114
>PRK09646 RNA polymerase sigma factor SigK; Reviewed
Probab=23.62 E-value=1.1e+02 Score=27.07 Aligned_cols=46 Identities=13% Similarity=0.117 Sum_probs=30.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
+++.+..+|...|-.. ..-.++|..||++...|++|...-|.+.|.
T Consensus 143 L~~~~r~vl~l~~~~~-----~s~~EIA~~Lgis~~tVk~~l~ra~~~Lr~ 188 (194)
T PRK09646 143 LTDTQRESVTLAYYGG-----LTYREVAERLAVPLGTVKTRMRDGLIRLRD 188 (194)
T ss_pred CCHHHHHHHHHHHHcC-----CCHHHHHHHhCCChHhHHHHHHHHHHHHHH
Confidence 6666666665544322 235688999999999999887544444433
No 115
>PRK00888 ftsB cell division protein FtsB; Reviewed
Probab=23.59 E-value=2.4e+02 Score=23.61 Aligned_cols=48 Identities=17% Similarity=0.223 Sum_probs=29.0
Q ss_pred ceeehhhhhHHHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHH
Q 019570 100 QVAVWFQNRRARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKE 148 (339)
Q Consensus 100 QVkVWFQNRRaK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E 148 (339)
+...||...- -.+-.+.+++...+++.++.++..+..|+.+.+.|+..
T Consensus 16 ~y~l~~g~~G-~~~~~~l~~q~~~~~~e~~~l~~~n~~L~~eI~~L~~~ 63 (105)
T PRK00888 16 QYSLWFGKNG-ILDYWRVNDQVAAQQQTNAKLKARNDQLFAEIDDLKGG 63 (105)
T ss_pred HHHHhccCCc-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhCc
Confidence 4457775431 11223345556666777777777777777777777653
No 116
>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=23.55 E-value=3.5e+02 Score=22.37 Aligned_cols=36 Identities=19% Similarity=0.235 Sum_probs=26.8
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhH
Q 019570 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 61 RrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
.|.|+..++..|. .....+.+|++-..|+..+....
T Consensus 36 yR~Y~~~~i~~l~-------------~I~~lr~~G~sl~eI~~~l~~~~ 71 (123)
T cd04770 36 YRLYGEADLARLR-------------FIRRAQALGFSLAEIRELLSLRD 71 (123)
T ss_pred CccCCHHHHHHHH-------------HHHHHHHCCCCHHHHHHHHHhhh
Confidence 4559999999984 33446888888888888876544
No 117
>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=23.09 E-value=3.6e+02 Score=22.11 Aligned_cols=35 Identities=17% Similarity=0.311 Sum_probs=26.1
Q ss_pred CCcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhh
Q 019570 61 KRRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNR 108 (339)
Q Consensus 61 RrRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNR 108 (339)
.|.|+..++..|. .....+.+|++-.+|+.++...
T Consensus 36 yR~Y~~~~l~~l~-------------~I~~lr~~G~sL~eI~~~l~~~ 70 (113)
T cd01109 36 IRDFTEEDLEWLE-------------FIKCLRNTGMSIKDIKEYAELR 70 (113)
T ss_pred CccCCHHHHHHHH-------------HHHHHHHcCCCHHHHHHHHHHH
Confidence 3459999999984 3344678889888888887654
No 118
>PF13518 HTH_28: Helix-turn-helix domain
Probab=22.95 E-value=41 Score=23.22 Aligned_cols=21 Identities=24% Similarity=0.540 Sum_probs=18.1
Q ss_pred HHHHHHHHhCCCccceeehhh
Q 019570 86 RKVKLAQELGLQPRQVAVWFQ 106 (339)
Q Consensus 86 ~ReeLA~~LgLs~rQVkVWFQ 106 (339)
...++|.++|++..+|..|.+
T Consensus 14 s~~~~a~~~gis~~tv~~w~~ 34 (52)
T PF13518_consen 14 SVREIAREFGISRSTVYRWIK 34 (52)
T ss_pred CHHHHHHHHCCCHhHHHHHHH
Confidence 355689999999999999975
No 119
>KOG3119 consensus Basic region leucine zipper transcription factor [Transcription]
Probab=22.91 E-value=2.2e+02 Score=27.56 Aligned_cols=29 Identities=31% Similarity=0.508 Sum_probs=18.1
Q ss_pred HHHHhhhhhhHHhHHHHHHHHHHHHHHhh
Q 019570 129 DALKLNYDSLQHDNEALLKEIRELKSKLN 157 (339)
Q Consensus 129 d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~ 157 (339)
+.+.+.-..|..||+.|+.++.+|+..+.
T Consensus 218 ~e~~~r~~~leken~~lr~~v~~l~~el~ 246 (269)
T KOG3119|consen 218 DEMAHRVAELEKENEALRTQVEQLKKELA 246 (269)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 44455555566677777777777766554
No 120
>PF14197 Cep57_CLD_2: Centrosome localisation domain of PPC89
Probab=22.90 E-value=3.7e+02 Score=20.99 Aligned_cols=15 Identities=27% Similarity=0.430 Sum_probs=6.8
Q ss_pred hHHHHHHHHHHHHHH
Q 019570 141 DNEALLKEIRELKSK 155 (339)
Q Consensus 141 ene~L~~E~~~Lk~~ 155 (339)
++..|+.|+..|+..
T Consensus 48 e~~~Lk~E~e~L~~e 62 (69)
T PF14197_consen 48 ENNKLKEENEALRKE 62 (69)
T ss_pred HHHHHHHHHHHHHHH
Confidence 444444444444444
No 121
>PTZ00454 26S protease regulatory subunit 6B-like protein; Provisional
Probab=22.65 E-value=2.1e+02 Score=29.21 Aligned_cols=42 Identities=12% Similarity=0.233 Sum_probs=23.6
Q ss_pred HHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 118 eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
+.....++..++.+......+..+...+++++.++++++..-
T Consensus 21 ~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~~ 62 (398)
T PTZ00454 21 YEKLKELEKELEFLDIQEEYIKEEQKNLKRELIRAKEEVKRI 62 (398)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333334444555555566666666666666666666665544
No 122
>COG4026 Uncharacterized protein containing TOPRIM domain, potential nuclease [General function prediction only]
Probab=22.57 E-value=2.6e+02 Score=27.33 Aligned_cols=46 Identities=43% Similarity=0.588 Sum_probs=21.6
Q ss_pred HHHhhHHHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHH
Q 019570 109 RARWKTKQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKS 154 (339)
Q Consensus 109 RaK~Krkq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~ 154 (339)
||-.|.-+.-.++..+|..+..++...+.++.+|+.|++++.+|..
T Consensus 118 RAGLktL~~v~~~~d~ke~~ee~kekl~E~~~EkeeL~~eleele~ 163 (290)
T COG4026 118 RAGLKTLQRVPEYMDLKEDYEELKEKLEELQKEKEELLKELEELEA 163 (290)
T ss_pred HHHHHHHhccchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 4444444433444444444444444444444444444444444443
No 123
>PF04568 IATP: Mitochondrial ATPase inhibitor, IATP; InterPro: IPR007648 ATP synthase inhibitor prevents the enzyme from switching to ATP hydrolysis during collapse of the electrochemical gradient, for example during oxygen deprivation [] ATP synthase inhibitor forms a one to one complex with the F1 ATPase, possibly by binding at the alpha-beta interface. It is thought to inhibit ATP synthesis by preventing the release of ATP []. The minimum inhibitory region for bovine inhibitor (P01096 from SWISSPROT) is from residues 39 to 72 []. The inhibitor has two oligomeric states, dimer (the active state) and tetramer. At low pH , the inhibitor forms a dimer via antiparallel coiled coil interactions between the C-terminal regions of two monomers. At high pH, the inhibitor forms tetramers and higher oligomers by coiled coil interactions involving the N terminus and inhibitory region, thus preventing the inhibitory activity []. ; GO: 0004857 enzyme inhibitor activity, 0045980 negative regulation of nucleotide metabolic process, 0005739 mitochondrion; PDB: 1GMJ_B 1OHH_H 1HF9_B 2V7Q_J.
Probab=22.50 E-value=3.3e+02 Score=22.97 Aligned_cols=29 Identities=31% Similarity=0.352 Sum_probs=15.6
Q ss_pred hHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 128 YDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 128 ~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
.+.|+.-...+..+....++++++|...+
T Consensus 71 kEqL~~Lk~kl~~e~~~~~k~i~~le~~I 99 (100)
T PF04568_consen 71 KEQLKKLKEKLKEEIEHHRKEIDELEKHI 99 (100)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHhc
Confidence 33333333445555566666666666554
No 124
>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=22.47 E-value=95 Score=22.40 Aligned_cols=45 Identities=16% Similarity=0.179 Sum_probs=31.8
Q ss_pred cCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhh
Q 019570 63 RLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWK 113 (339)
Q Consensus 63 RfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~K 113 (339)
+||+.++.+|.....- ....++|..+++++..|..+..+=+.|..
T Consensus 3 ~LT~~E~~vl~~l~~G------~~~~eIA~~l~is~~tV~~~~~~i~~Kl~ 47 (58)
T PF00196_consen 3 SLTERELEVLRLLAQG------MSNKEIAEELGISEKTVKSHRRRIMKKLG 47 (58)
T ss_dssp SS-HHHHHHHHHHHTT------S-HHHHHHHHTSHHHHHHHHHHHHHHHHT
T ss_pred ccCHHHHHHHHHHHhc------CCcchhHHhcCcchhhHHHHHHHHHHHhC
Confidence 4788888888655442 23568999999999999988766555544
No 125
>PRK12514 RNA polymerase sigma factor; Provisional
Probab=22.40 E-value=88 Score=27.06 Aligned_cols=46 Identities=15% Similarity=0.294 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
+++.+..++.-.|- ......++|..+|+++..|+++...-|.+.|.
T Consensus 130 L~~~~r~i~~l~~~-----~g~s~~eIA~~lgis~~tV~~~l~Rar~~Lr~ 175 (179)
T PRK12514 130 LEKDRAAAVRRAYL-----EGLSYKELAERHDVPLNTMRTWLRRSLLKLRE 175 (179)
T ss_pred CCHHHHHHHHHHHH-----cCCCHHHHHHHHCCChHHHHHHHHHHHHHHHH
Confidence 55555555554442 22235689999999999999988755554443
No 126
>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=22.40 E-value=3.7e+02 Score=20.74 Aligned_cols=40 Identities=20% Similarity=0.318 Sum_probs=20.8
Q ss_pred HHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHh
Q 019570 117 LERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 117 ~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
+..+....++.+-.+...-......|..|..++..|+..+
T Consensus 16 ~~eEL~kvk~~n~~~e~kLqeaE~rn~eL~~ei~~L~~e~ 55 (61)
T PF08826_consen 16 IQEELTKVKSANLAFESKLQEAEKRNRELEQEIERLKKEM 55 (61)
T ss_dssp HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3444444555444444444444445666666666666555
No 127
>PRK06759 RNA polymerase factor sigma-70; Validated
Probab=22.39 E-value=1e+02 Score=25.69 Aligned_cols=44 Identities=16% Similarity=0.109 Sum_probs=29.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHh
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARW 112 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~ 112 (339)
+++.+..++...|-.. ....+||..+|++...|+.|...-|.+.
T Consensus 107 L~~~~r~ii~l~~~~~-----~s~~EIA~~l~is~~tV~~~~~ra~~~L 150 (154)
T PRK06759 107 LDEKEKYIIFERFFVG-----KTMGEIALETEMTYYQVRWIYRQALEKM 150 (154)
T ss_pred CCHHHHHHHHHHHhcC-----CCHHHHHHHHCCCHHHHHHHHHHHHHHH
Confidence 5666666665544322 3366899999999999999876444333
No 128
>PF13936 HTH_38: Helix-turn-helix domain; PDB: 2W48_A.
Probab=22.36 E-value=50 Score=23.16 Aligned_cols=39 Identities=18% Similarity=0.224 Sum_probs=19.5
Q ss_pred CcCCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehh
Q 019570 62 RRLSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWF 105 (339)
Q Consensus 62 rRfT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWF 105 (339)
+.+|.++...++..+... ....+||+.+|.++.-|..|.
T Consensus 3 ~~Lt~~eR~~I~~l~~~G-----~s~~~IA~~lg~s~sTV~rel 41 (44)
T PF13936_consen 3 KHLTPEERNQIEALLEQG-----MSIREIAKRLGRSRSTVSREL 41 (44)
T ss_dssp ---------HHHHHHCS--------HHHHHHHTT--HHHHHHHH
T ss_pred cchhhhHHHHHHHHHHcC-----CCHHHHHHHHCcCcHHHHHHH
Confidence 458888888888876533 335579999999988887665
No 129
>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=22.18 E-value=3.9e+02 Score=20.96 Aligned_cols=36 Identities=17% Similarity=0.231 Sum_probs=16.0
Q ss_pred HHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 120 DYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 120 e~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
-+..|+..+..|+.....+..|...|...+...+.+
T Consensus 15 ~~~~L~~EN~~Lr~q~~~~~~ER~~L~ekne~Ar~r 50 (65)
T TIGR02449 15 YLERLKSENRLLRAQEKTWREERAQLLEKNEQARQK 50 (65)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 333444444444444444444444444444444433
No 130
>COG4467 Regulator of replication initiation timing [Replication, recombination, and repair]
Probab=21.69 E-value=1.6e+02 Score=25.51 Aligned_cols=37 Identities=27% Similarity=0.322 Sum_probs=30.8
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHH
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRE 151 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~ 151 (339)
..+-++.+.+|++...+-.++..|+.||+.|++.+..
T Consensus 18 ~~l~~el~~lK~~l~~lvEEN~~L~lENe~LR~RL~~ 54 (114)
T COG4467 18 GVLLAELGGLKQHLGSLVEENTALRLENEKLRERLGE 54 (114)
T ss_pred HHHHHHHHHHHHHHHHHHHhhHHHHhhHHHHHHHhCC
Confidence 3456677888888888999999999999999988777
No 131
>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=21.60 E-value=29 Score=27.67 Aligned_cols=35 Identities=17% Similarity=0.229 Sum_probs=26.2
Q ss_pred HHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhh
Q 019570 73 EKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQN 107 (339)
Q Consensus 73 E~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQN 107 (339)
+..|...+|.......+||..+|+++..|+.|+.+
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 34455555545556788999999999999999753
No 132
>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=21.46 E-value=3.3e+02 Score=25.63 Aligned_cols=31 Identities=16% Similarity=0.294 Sum_probs=11.4
Q ss_pred HHhhhhHHHHhhhhhhHHhHHHHHHHHHHHH
Q 019570 123 VLKANYDALKLNYDSLQHDNEALLKEIRELK 153 (339)
Q Consensus 123 ~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk 153 (339)
.++...+.|...+..+......+++++.+|+
T Consensus 60 ~l~~e~e~L~~~~~~l~~~v~~q~~el~~L~ 90 (251)
T PF11932_consen 60 QLEREIENLEVYNEQLERQVASQEQELASLE 90 (251)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 3333333333333333333333333333333
No 133
>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=21.40 E-value=1.3e+02 Score=30.82 Aligned_cols=27 Identities=22% Similarity=0.481 Sum_probs=11.8
Q ss_pred hhhccccccccch--HhHHHHHHHHHHHh
Q 019570 304 FVKMEDTISLVMR--PAISSLMSSLLLFH 330 (339)
Q Consensus 304 ~~~~e~~~~~~~~--e~~~~~~~~~~~~~ 330 (339)
|+++|+..|.+|- .+.+-||-...|.|
T Consensus 330 y~~i~~~~~isg~v~~sit~l~~~~~l~~ 358 (420)
T PF07407_consen 330 YHEIEEDYFISGPVGPSITCLMKTYALYS 358 (420)
T ss_pred eeecccCceEeccccchHHHHHHHhhhhe
Confidence 3444555555443 23334444444444
No 134
>PF07888 CALCOCO1: Calcium binding and coiled-coil domain (CALCOCO1) like; InterPro: IPR012852 Proteins found in this family are similar to the coiled-coil transcriptional coactivator protein expressed by Mus musculus (CoCoA, Q8CGU1 from SWISSPROT). This protein binds to a highly conserved N-terminal domain of p160 coactivators, such as GRIP1 (Q61026 from SWISSPROT), and thus enhances transcriptional activation by a number of nuclear receptors. CoCoA has a central coiled-coil region with three leucine zipper motifs, which is required for its interaction with GRIP1 and may regulate the autonomous transcriptional activation activity of the C-terminal region [].
Probab=20.96 E-value=5.8e+02 Score=27.71 Aligned_cols=42 Identities=24% Similarity=0.406 Sum_probs=34.1
Q ss_pred HHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHHhhhh
Q 019570 118 ERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSKLNEE 159 (339)
Q Consensus 118 eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~l~~~ 159 (339)
.++...|++....++.+.+.+..+++-|+..+.+|..+|..-
T Consensus 416 ~rel~Elks~lrv~qkEKEql~~EkQeL~~yi~~Le~r~~~~ 457 (546)
T PF07888_consen 416 RRELQELKSSLRVAQKEKEQLQEEKQELLEYIERLEQRLDKV 457 (546)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 445556888888888888888889999999999998888755
No 135
>PF11559 ADIP: Afadin- and alpha -actinin-Binding; InterPro: IPR021622 This family is found in mammals where it is localised at cell-cell adherens junctions [], and in Sch. pombe and other fungi where it anchors spindle-pole bodies to spindle microtubules []. It is a coiled-coil structure, and in pombe, it is required for anchoring the minus end of spindle microtubules to the centrosome equivalent, the spindle-pole body. The name ADIP derives from the family being composed of Afadin- and alpha -Actinin-Binding Proteins Localised at Cell-Cell Adherens Junctions.
Probab=20.88 E-value=4.3e+02 Score=22.79 Aligned_cols=41 Identities=22% Similarity=0.328 Sum_probs=16.1
Q ss_pred HHHHHHHHHHhhhhHHHHhhhhhhHHhHHHHHHHHHHHHHH
Q 019570 115 KQLERDYGVLKANYDALKLNYDSLQHDNEALLKEIRELKSK 155 (339)
Q Consensus 115 kq~eke~~~LKa~~d~Lk~e~~sl~~ene~L~~E~~~Lk~~ 155 (339)
...+++...++.....+......+...+...++++.+++..
T Consensus 83 ~~~ere~~~~~~~~~~l~~~~~~~~~~~k~~kee~~klk~~ 123 (151)
T PF11559_consen 83 EELERELASAEEKERQLQKQLKSLEAKLKQEKEELQKLKNQ 123 (151)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 33333333333333333333333333344444444444433
No 136
>PF04880 NUDE_C: NUDE protein, C-terminal conserved region; InterPro: IPR006964 This domain represents the C-terminal conserved region of NUDE proteins. Emericella nidulans (Aspergillus nidulans) NUDE, acts in the cytoplasmic dynein/dynactin pathway and is required for distribution of nuclei []. It is a homologue of the nuclear distribution protein RO11 of Neurospora crassa. NUDE interacts with the NUDF via an N-terminal coiled coil domain; this is the only domain which is absolutely required for NUDE function.; PDB: 2V66_B 2V71_B.
Probab=20.58 E-value=71 Score=29.27 Aligned_cols=23 Identities=30% Similarity=0.562 Sum_probs=6.0
Q ss_pred hhhhhHHhHHHHHHHHHHHHHHh
Q 019570 134 NYDSLQHDNEALLKEIRELKSKL 156 (339)
Q Consensus 134 e~~sl~~ene~L~~E~~~Lk~~l 156 (339)
+.+.|+.++++|++|++.||..+
T Consensus 25 EKE~L~~~~QRLkDE~RDLKqEl 47 (166)
T PF04880_consen 25 EKENLREEVQRLKDELRDLKQEL 47 (166)
T ss_dssp HHHHHHHCH--------------
T ss_pred HHHHHHHHHHHHHHHHHHHHHHH
Confidence 45667777777777777777766
No 137
>PRK12526 RNA polymerase sigma factor; Provisional
Probab=20.49 E-value=1.3e+02 Score=27.00 Aligned_cols=46 Identities=20% Similarity=0.211 Sum_probs=28.9
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
+++.+..+|...| .......++|..+|+++..|+++...-|.+.++
T Consensus 154 L~~~~r~vl~l~~-----~~g~s~~EIA~~lgis~~tV~~~l~Ra~~~Lr~ 199 (206)
T PRK12526 154 LPEAQQTVVKGVY-----FQELSQEQLAQQLNVPLGTVKSRLRLALAKLKV 199 (206)
T ss_pred CCHHHHHHHHHHH-----HcCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 4555555554332 222345689999999999998887654444443
No 138
>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=20.48 E-value=2.4e+02 Score=29.94 Aligned_cols=8 Identities=63% Similarity=0.746 Sum_probs=3.3
Q ss_pred hheeeecC
Q 019570 330 HGIVLISG 337 (339)
Q Consensus 330 ~~~~~~~~ 337 (339)
|||=.|+|
T Consensus 353 ~GiPCIsG 360 (472)
T TIGR03752 353 YGIPCISG 360 (472)
T ss_pred CCCCCCCC
Confidence 44444443
No 139
>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=20.47 E-value=43 Score=22.84 Aligned_cols=23 Identities=17% Similarity=0.167 Sum_probs=18.9
Q ss_pred HHHHHHHhCCCccceeehhhhhH
Q 019570 87 KVKLAQELGLQPRQVAVWFQNRR 109 (339)
Q Consensus 87 ReeLA~~LgLs~rQVkVWFQNRR 109 (339)
..++|+.+|+++..|+.|.+...
T Consensus 3 ~~e~a~~~gv~~~tlr~~~~~g~ 25 (49)
T cd04761 3 IGELAKLTGVSPSTLRYYERIGL 25 (49)
T ss_pred HHHHHHHHCcCHHHHHHHHHCCC
Confidence 35789999999999999976543
No 140
>PRK11924 RNA polymerase sigma factor; Provisional
Probab=20.44 E-value=1.1e+02 Score=25.83 Aligned_cols=46 Identities=20% Similarity=0.208 Sum_probs=29.8
Q ss_pred CCHHHHHHHHHhhhhcCCCCHHHHHHHHHHhCCCccceeehhhhhHHHhhH
Q 019570 64 LSVDQVKALEKNFEVENKLEPERKVKLAQELGLQPRQVAVWFQNRRARWKT 114 (339)
Q Consensus 64 fT~eQl~~LE~~F~~~~yPs~~~ReeLA~~LgLs~rQVkVWFQNRRaK~Kr 114 (339)
+++.+..++...|- ....-.+||..+|+++..|..|..--|.+.|+
T Consensus 126 L~~~~r~i~~l~~~-----~~~~~~eIA~~lgis~~tv~~~~~ra~~~lr~ 171 (179)
T PRK11924 126 LPVKQREVFLLRYV-----EGLSYREIAEILGVPVGTVKSRLRRARQLLRE 171 (179)
T ss_pred CCHHHHHHhhHHHH-----cCCCHHHHHHHHCCCHHHHHHHHHHHHHHHHH
Confidence 45555555544432 22334689999999999999998654444443
No 141
>PF07798 DUF1640: Protein of unknown function (DUF1640); InterPro: IPR024461 This family consists of uncharacterised proteins.
Probab=20.16 E-value=3.1e+02 Score=24.60 Aligned_cols=32 Identities=31% Similarity=0.520 Sum_probs=21.1
Q ss_pred hhhhhhHHhHHHHHHHHHHHHHHhhhhhccCC
Q 019570 133 LNYDSLQHDNEALLKEIRELKSKLNEENTESN 164 (339)
Q Consensus 133 ~e~~sl~~ene~L~~E~~~Lk~~l~~~~~~~~ 164 (339)
.+...++.+++.|+.++..|+.+|.++...-.
T Consensus 73 ~~~~~lr~~~e~L~~eie~l~~~L~~ei~~l~ 104 (177)
T PF07798_consen 73 SEFAELRSENEKLQREIEKLRQELREEINKLR 104 (177)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHH
Confidence 34455667777777777777777776654333
Done!