Query psy3459
Match_columns 296
No_of_seqs 266 out of 892
Neff 5.0
Searched_HMMs 46136
Date Fri Aug 16 17:14:58 2013
Command hhsearch -i /work/01045/syshi/Psyhhblits/psy3459.a3m -d /work/01045/syshi/HHdatabase/Cdd.hhm -o /work/01045/syshi/hhsearch_cdd/3459hhsearch_cdd -cpu 12 -v 0
No Hit Prob E-value P-value Score SS Cols Query HMM Template HMM
1 KOG0869|consensus 100.0 1E-30 2.3E-35 224.9 9.2 100 3-102 26-125 (168)
2 KOG0871|consensus 100.0 7.6E-29 1.7E-33 211.6 9.9 119 4-122 7-133 (156)
3 KOG0869|consensus 100.0 6.2E-29 1.3E-33 214.0 7.6 87 118-204 37-123 (168)
4 KOG0871|consensus 99.9 3E-28 6.6E-33 207.9 7.6 121 115-239 13-134 (156)
5 COG5150 Class 2 transcription 99.9 7.3E-24 1.6E-28 177.3 9.5 120 4-124 6-134 (148)
6 COG5150 Class 2 transcription 99.9 3.2E-24 6.8E-29 179.5 7.2 121 115-241 12-135 (148)
7 KOG0870|consensus 99.9 7.3E-24 1.6E-28 184.0 8.3 102 1-102 2-104 (172)
8 KOG0870|consensus 99.8 1.4E-21 3E-26 169.8 7.6 87 120-206 17-104 (172)
9 PF00808 CBFD_NFYB_HMF: Histon 99.6 7.7E-16 1.7E-20 114.7 7.1 64 9-73 2-65 (65)
10 COG2036 HHT1 Histones H3 and H 99.6 5.8E-15 1.3E-19 118.2 6.0 78 3-82 13-90 (91)
11 PF00808 CBFD_NFYB_HMF: Histon 99.4 9.3E-13 2E-17 98.1 5.5 59 118-177 7-65 (65)
12 cd00076 H4 Histone H4, one of 99.1 4E-10 8.8E-15 89.4 7.8 72 8-81 12-83 (85)
13 PLN00035 histone H4; Provision 99.0 7.3E-10 1.6E-14 90.7 7.8 70 8-79 28-97 (103)
14 COG2036 HHT1 Histones H3 and H 99.0 7.7E-10 1.7E-14 88.8 5.3 67 118-186 24-90 (91)
15 PTZ00015 histone H4; Provision 99.0 2.6E-09 5.6E-14 87.4 7.9 73 7-81 28-100 (102)
16 smart00803 TAF TATA box bindin 98.8 1.1E-08 2.4E-13 77.2 6.9 64 9-74 2-65 (65)
17 smart00417 H4 Histone H4. 98.8 1.1E-08 2.4E-13 79.3 5.8 62 8-71 12-73 (74)
18 cd07981 TAF12 TATA Binding Pro 98.5 3.8E-07 8.2E-12 69.9 7.7 65 10-75 2-66 (72)
19 PF00125 Histone: Core histone 98.4 6E-07 1.3E-11 68.0 5.9 68 7-74 3-73 (75)
20 smart00428 H3 Histone H3. 98.4 1E-06 2.2E-11 72.6 6.4 71 4-74 24-99 (105)
21 COG5208 HAP5 CCAAT-binding fac 98.2 6.9E-07 1.5E-11 81.9 3.4 75 6-82 106-181 (286)
22 smart00576 BTP Bromodomain tra 98.1 1.1E-05 2.3E-10 62.4 7.5 66 12-79 9-74 (77)
23 cd07979 TAF9 TATA Binding Prot 97.9 5.5E-05 1.2E-09 63.2 8.4 77 14-92 6-83 (117)
24 cd00074 H2A Histone 2A; H2A is 97.9 4E-05 8.6E-10 64.1 6.5 67 7-74 18-84 (115)
25 cd00076 H4 Histone H4, one of 97.8 5E-05 1.1E-09 60.4 5.9 67 117-185 16-83 (85)
26 PLN00160 histone H3; Provision 97.7 9E-05 2E-09 60.4 6.2 70 4-73 16-89 (97)
27 PLN00161 histone H3; Provision 97.7 0.00015 3.2E-09 62.3 7.1 70 4-73 50-123 (135)
28 PLN00121 histone H3; Provision 97.6 8.9E-05 1.9E-09 63.7 5.5 70 4-73 57-129 (136)
29 cd07981 TAF12 TATA Binding Pro 97.6 0.00013 2.8E-09 55.9 5.5 55 125-179 12-66 (72)
30 PLN00035 histone H4; Provision 97.6 0.00014 3E-09 59.8 6.0 67 115-183 30-97 (103)
31 KOG1657|consensus 97.6 7.8E-05 1.7E-09 69.4 4.4 73 8-81 73-145 (236)
32 PTZ00018 histone H3; Provision 97.5 0.00019 4.2E-09 61.7 6.1 70 4-73 57-129 (136)
33 PTZ00015 histone H4; Provision 97.5 0.00023 4.9E-09 58.5 5.9 66 118-185 35-100 (102)
34 PF00125 Histone: Core histone 97.5 0.00025 5.3E-09 53.6 5.3 54 125-178 20-73 (75)
35 cd08050 TAF6 TATA Binding Prot 97.4 0.00039 8.5E-09 67.5 7.6 67 11-79 1-67 (343)
36 PF15630 CENP-S: Kinetochore c 97.4 0.00063 1.4E-08 53.1 6.4 61 14-74 10-71 (76)
37 smart00803 TAF TATA box bindin 97.3 0.00052 1.1E-08 51.8 5.2 57 120-178 9-65 (65)
38 PF07524 Bromo_TP: Bromodomain 97.2 0.0022 4.7E-08 49.2 7.7 65 13-79 10-74 (77)
39 PF15511 CENP-T: Centromere ki 97.1 0.00068 1.5E-08 67.6 5.6 62 7-68 349-414 (414)
40 smart00427 H2B Histone H2B. 97.1 0.002 4.4E-08 51.8 6.8 63 14-77 6-68 (89)
41 KOG3467|consensus 97.0 0.002 4.3E-08 51.7 6.4 68 10-79 30-97 (103)
42 smart00576 BTP Bromodomain tra 97.0 0.0015 3.2E-08 50.5 5.2 53 131-183 22-74 (77)
43 smart00417 H4 Histone H4. 96.9 0.0018 3.9E-08 50.4 4.9 57 118-176 18-74 (74)
44 PF09415 CENP-X: CENP-S associ 96.8 0.0016 3.4E-08 50.3 4.3 65 11-75 1-67 (72)
45 PF03847 TFIID_20kDa: Transcri 96.8 0.005 1.1E-07 47.0 6.6 63 12-75 2-64 (68)
46 cd08048 TAF11 TATA Binding Pro 96.8 0.0063 1.4E-07 48.4 7.4 66 9-76 16-84 (85)
47 PLN00158 histone H2B; Provisio 96.7 0.0055 1.2E-07 51.4 6.9 65 12-77 30-94 (116)
48 PTZ00463 histone H2B; Provisio 96.7 0.0065 1.4E-07 51.0 6.9 63 14-77 33-95 (117)
49 PF02969 TAF: TATA box binding 96.6 0.011 2.3E-07 45.1 7.0 64 9-74 3-66 (66)
50 COG5262 HTA1 Histone H2A [Chro 96.3 0.0083 1.8E-07 50.6 5.3 67 7-74 24-90 (132)
51 PF07524 Bromo_TP: Bromodomain 96.3 0.01 2.2E-07 45.5 5.3 52 132-183 23-74 (77)
52 PF04719 TAFII28: hTAFII28-lik 96.0 0.023 5E-07 45.7 6.3 67 9-76 23-90 (90)
53 PF15630 CENP-S: Kinetochore c 96.0 0.016 3.4E-07 45.3 5.2 64 115-178 7-71 (76)
54 KOG1745|consensus 95.8 0.0069 1.5E-07 52.2 2.7 73 4-76 58-133 (137)
55 PF03847 TFIID_20kDa: Transcri 95.7 0.025 5.4E-07 43.2 5.3 56 124-179 9-64 (68)
56 smart00428 H3 Histone H3. 95.5 0.029 6.2E-07 46.4 5.4 48 130-177 51-98 (105)
57 smart00414 H2A Histone 2A. 95.5 0.041 8.8E-07 45.5 6.1 67 7-74 7-73 (106)
58 KOG1659|consensus 95.4 0.033 7.1E-07 51.3 5.9 76 9-85 13-88 (224)
59 PLN00154 histone H2A; Provisio 95.3 0.048 1E-06 47.1 6.0 68 7-74 36-103 (136)
60 cd07979 TAF9 TATA Binding Prot 95.1 0.077 1.7E-06 44.4 6.6 77 120-198 8-85 (117)
61 smart00427 H2B Histone H2B. 95.0 0.05 1.1E-06 43.8 5.1 60 121-181 9-68 (89)
62 COG5247 BUR6 Class 2 transcrip 94.9 0.047 1E-06 45.1 4.8 78 9-87 23-100 (113)
63 cd08050 TAF6 TATA Binding Prot 94.9 0.044 9.4E-07 53.4 5.4 52 132-183 16-67 (343)
64 KOG1756|consensus 94.6 0.086 1.9E-06 45.0 5.8 67 7-74 25-91 (131)
65 PF02269 TFIID-18kDa: Transcri 94.5 0.048 1E-06 43.8 3.9 60 15-75 7-66 (93)
66 PTZ00017 histone H2A; Provisio 94.3 0.095 2.1E-06 45.2 5.4 67 7-74 25-91 (134)
67 KOG1744|consensus 94.2 0.15 3.2E-06 43.6 6.3 61 14-75 42-102 (127)
68 PF02291 TFIID-31kDa: Transcri 94.2 0.18 4E-06 43.1 6.9 84 6-91 7-93 (129)
69 PF15510 CENP-W: Centromere ki 93.9 0.089 1.9E-06 42.7 4.2 66 9-75 16-95 (102)
70 KOG3467|consensus 93.9 0.098 2.1E-06 42.2 4.3 52 132-183 46-97 (103)
71 PLN00156 histone H2AX; Provisi 93.6 0.17 3.8E-06 43.8 5.7 67 7-74 27-93 (139)
72 PLN00153 histone H2A; Provisio 93.5 0.17 3.6E-06 43.4 5.4 67 7-74 22-88 (129)
73 PLN00157 histone H2A; Provisio 93.5 0.15 3.3E-06 43.8 5.2 67 7-74 24-90 (132)
74 PTZ00463 histone H2B; Provisio 93.4 0.18 4E-06 42.4 5.5 60 121-181 36-95 (117)
75 PLN00158 histone H2B; Provisio 93.3 0.18 3.9E-06 42.5 5.3 61 120-181 34-94 (116)
76 PF02269 TFIID-18kDa: Transcri 93.3 0.12 2.7E-06 41.5 4.1 54 126-179 13-66 (93)
77 KOG1142|consensus 93.0 0.19 4.1E-06 47.5 5.5 66 9-75 154-219 (258)
78 KOG1657|consensus 92.3 0.18 3.9E-06 47.1 4.4 82 115-196 75-159 (236)
79 PLN00161 histone H3; Provision 92.2 0.36 7.8E-06 41.7 5.7 51 127-177 73-123 (135)
80 PLN00160 histone H3; Provision 92.1 0.38 8.2E-06 39.4 5.4 50 128-177 40-89 (97)
81 KOG1658|consensus 91.8 0.13 2.7E-06 45.4 2.6 67 8-76 58-125 (162)
82 PF15511 CENP-T: Centromere ki 91.8 0.21 4.5E-06 50.0 4.4 46 127-172 369-414 (414)
83 cd08048 TAF11 TATA Binding Pro 91.6 0.45 9.7E-06 37.9 5.3 60 119-180 22-84 (85)
84 KOG3219|consensus 91.6 0.21 4.4E-06 45.6 3.7 69 9-79 112-181 (195)
85 cd00074 H2A Histone 2A; H2A is 91.4 0.39 8.4E-06 40.3 5.0 63 116-179 21-85 (115)
86 KOG1658|consensus 91.4 0.6 1.3E-05 41.3 6.3 113 8-179 10-124 (162)
87 PTZ00018 histone H3; Provision 89.9 0.56 1.2E-05 40.6 4.8 51 127-177 79-129 (136)
88 PLN00121 histone H3; Provision 89.6 0.63 1.4E-05 40.3 4.8 51 127-177 79-129 (136)
89 cd07978 TAF13 The TATA Binding 89.5 1.7 3.7E-05 35.0 7.0 83 13-99 6-88 (92)
90 PF02969 TAF: TATA box binding 89.2 0.91 2E-05 34.6 4.9 47 132-178 20-66 (66)
91 TIGR02639 ClpA ATP-dependent C 89.1 1.4 3.1E-05 46.9 8.1 94 51-178 11-111 (731)
92 PTZ00252 histone H2A; Provisio 89.0 1.2 2.5E-05 38.5 6.0 67 7-74 23-91 (134)
93 KOG1744|consensus 88.3 1.1 2.4E-05 38.3 5.4 61 119-180 43-103 (127)
94 KOG3423|consensus 86.3 3.1 6.7E-05 37.3 7.2 70 8-79 85-168 (176)
95 KOG1142|consensus 86.0 1.2 2.7E-05 42.2 4.8 55 125-179 165-219 (258)
96 CHL00095 clpC Clp protease ATP 85.2 2.9 6.4E-05 45.2 7.9 96 51-178 15-113 (821)
97 COG5208 HAP5 CCAAT-binding fac 84.0 0.69 1.5E-05 43.1 2.1 66 120-186 116-181 (286)
98 KOG4336|consensus 82.7 5.7 0.00012 38.7 7.8 77 14-94 10-86 (323)
99 cd07978 TAF13 The TATA Binding 82.7 3.4 7.4E-05 33.3 5.4 65 127-194 15-79 (92)
100 PF04719 TAFII28: hTAFII28-lik 80.3 2.6 5.6E-05 34.0 3.9 66 115-180 24-90 (90)
101 PF09415 CENP-X: CENP-S associ 80.0 2 4.3E-05 33.2 3.1 59 120-178 6-66 (72)
102 PRK00411 cdc6 cell division co 79.9 18 0.00039 34.7 10.4 65 12-76 209-282 (394)
103 COG5262 HTA1 Histone H2A [Chro 79.1 3.2 6.9E-05 35.3 4.2 64 115-179 26-91 (132)
104 TIGR03346 chaperone_ClpB ATP-d 78.1 8.3 0.00018 42.0 8.2 95 51-177 11-110 (852)
105 KOG2549|consensus 78.0 7.3 0.00016 40.8 7.2 67 11-79 13-79 (576)
106 cd08045 TAF4 TATA Binding Prot 77.7 17 0.00037 33.0 8.9 70 8-77 43-120 (212)
107 TIGR03015 pepcterm_ATPase puta 76.4 3.7 8E-05 37.1 4.3 53 130-182 213-268 (269)
108 TIGR03015 pepcterm_ATPase puta 76.2 6.9 0.00015 35.3 6.0 69 10-78 192-268 (269)
109 PF15510 CENP-W: Centromere ki 76.1 2.7 5.9E-05 34.2 2.9 58 120-178 23-94 (102)
110 KOG1745|consensus 71.3 6.1 0.00013 34.3 4.0 54 125-178 78-131 (137)
111 PRK00411 cdc6 cell division co 70.2 8.2 0.00018 37.1 5.2 51 132-182 228-284 (394)
112 KOG4336|consensus 66.5 16 0.00034 35.8 6.1 80 116-198 7-86 (323)
113 COG1067 LonB Predicted ATP-dep 64.8 5.4 0.00012 42.5 3.0 33 42-75 366-398 (647)
114 KOG3334|consensus 64.6 41 0.00089 29.6 7.8 62 31-92 33-95 (148)
115 KOG2389|consensus 64.1 16 0.00036 36.1 5.9 81 9-91 29-112 (353)
116 PF02291 TFIID-31kDa: Transcri 60.1 17 0.00037 31.1 4.7 65 133-197 30-95 (129)
117 PRK10865 protein disaggregatio 59.2 36 0.00078 37.3 8.1 25 51-75 16-40 (857)
118 TIGR02928 orc1/cdc6 family rep 57.9 31 0.00068 32.7 6.6 64 14-77 203-275 (365)
119 TIGR02928 orc1/cdc6 family rep 57.8 19 0.00041 34.2 5.1 72 113-185 202-279 (365)
120 PF13654 AAA_32: AAA domain; P 55.4 38 0.00082 35.1 7.1 59 15-75 436-505 (509)
121 PF02861 Clp_N: Clp amino term 52.4 7.8 0.00017 26.5 1.1 26 156-181 1-26 (53)
122 KOG1659|consensus 51.6 27 0.00058 32.6 4.7 58 132-189 31-88 (224)
123 TIGR03345 VI_ClpV1 type VI sec 50.5 61 0.0013 35.6 8.1 96 51-178 11-110 (852)
124 PRK11034 clpA ATP-dependent Cl 50.1 61 0.0013 35.3 7.9 24 50-73 11-34 (758)
125 KOG3423|consensus 48.1 30 0.00064 31.2 4.3 47 137-183 108-168 (176)
126 PF13654 AAA_32: AAA domain; P 46.4 34 0.00074 35.4 5.1 48 132-179 447-505 (509)
127 KOG1756|consensus 46.3 34 0.00073 29.5 4.2 59 116-179 28-92 (131)
128 PF02861 Clp_N: Clp amino term 44.0 15 0.00032 25.0 1.5 24 52-75 1-24 (53)
129 PF13335 Mg_chelatase_2: Magne 43.0 48 0.001 26.5 4.5 48 131-178 41-94 (96)
130 smart00414 H2A Histone 2A. 42.9 40 0.00087 27.9 4.1 59 120-179 16-74 (106)
131 PLN00154 histone H2A; Provisio 42.6 49 0.0011 28.8 4.7 60 116-179 39-104 (136)
132 TIGR00764 lon_rel lon-related 42.3 70 0.0015 33.8 6.8 49 28-76 330-391 (608)
133 PF08369 PCP_red: Proto-chloro 41.0 31 0.00067 24.2 2.7 41 135-176 3-44 (45)
134 PF13335 Mg_chelatase_2: Magne 39.2 81 0.0018 25.2 5.3 48 27-74 41-94 (96)
135 KOG2389|consensus 37.2 44 0.00095 33.2 4.0 47 137-183 51-97 (353)
136 COG5162 Transcription initiati 34.3 2.3E+02 0.0049 25.7 7.6 69 9-79 88-189 (197)
137 PF09114 MotA_activ: Transcrip 33.5 67 0.0015 26.3 3.9 34 13-46 51-88 (96)
138 PF03540 TFIID_30kDa: Transcri 32.6 2E+02 0.0043 21.0 6.2 48 9-58 2-49 (51)
139 KOG1757|consensus 32.6 74 0.0016 27.0 4.1 64 7-74 28-95 (131)
140 COG5095 TAF6 Transcription ini 32.3 1.5E+02 0.0032 29.7 6.7 53 27-79 21-73 (450)
141 TIGR02902 spore_lonB ATP-depen 32.1 1E+02 0.0023 31.8 6.1 63 12-75 265-331 (531)
142 TIGR00764 lon_rel lon-related 31.0 90 0.002 33.0 5.5 50 132-181 330-392 (608)
143 KOG2549|consensus 30.4 84 0.0018 33.2 5.0 51 132-182 28-78 (576)
144 TIGR02902 spore_lonB ATP-depen 30.3 83 0.0018 32.5 5.0 54 130-187 280-336 (531)
145 KOG3219|consensus 29.9 35 0.00075 31.3 1.9 63 120-183 118-181 (195)
146 COG1067 LonB Predicted ATP-dep 26.3 36 0.00078 36.4 1.6 32 147-179 367-398 (647)
147 PTZ00017 histone H2A; Provisio 25.7 87 0.0019 27.2 3.5 59 120-179 34-92 (134)
148 PF00356 LacI: Bacterial regul 25.1 1.5E+02 0.0033 20.7 4.1 32 9-44 10-41 (46)
149 PRK00080 ruvB Holliday junctio 24.9 2.3E+02 0.0049 26.9 6.6 71 10-80 180-254 (328)
150 PF07647 SAM_2: SAM domain (St 24.2 57 0.0012 23.3 1.9 25 167-191 3-27 (66)
151 CHL00081 chlI Mg-protoporyphyr 23.9 1.5E+02 0.0034 29.2 5.4 52 21-73 261-319 (350)
152 PF06782 UPF0236: Uncharacteri 23.6 1.3E+02 0.0029 30.6 5.0 57 126-184 111-167 (470)
153 KOG3334|consensus 23.4 1.5E+02 0.0033 26.2 4.6 59 141-199 39-98 (148)
154 PRK09862 putative ATP-dependen 23.4 2E+02 0.0043 29.9 6.3 58 27-84 437-500 (506)
155 TIGR02030 BchI-ChlI magnesium 23.3 1.7E+02 0.0036 28.7 5.4 53 20-73 247-306 (337)
156 PLN00157 histone H2A; Provisio 22.9 1.2E+02 0.0025 26.3 3.8 59 120-179 33-91 (132)
157 TIGR02442 Cob-chelat-sub cobal 22.4 1.9E+02 0.004 30.7 5.9 50 26-75 247-303 (633)
158 PTZ00252 histone H2A; Provisio 22.4 71 0.0015 27.7 2.3 55 120-179 32-92 (134)
159 cd00166 SAM Sterile alpha moti 22.2 48 0.0011 22.9 1.1 24 169-192 3-26 (63)
160 PLN00156 histone H2AX; Provisi 22.0 1.3E+02 0.0029 26.2 4.0 55 120-179 36-94 (139)
161 TIGR00635 ruvB Holliday juncti 21.9 3.5E+02 0.0077 24.9 7.1 68 12-79 161-232 (305)
162 PHA02940 hypothetical protein; 21.8 2.3E+02 0.005 27.5 5.8 123 13-145 113-239 (315)
163 PF00536 SAM_1: SAM domain (St 21.4 65 0.0014 22.9 1.7 22 169-190 4-25 (64)
164 COG5247 BUR6 Class 2 transcrip 21.0 1.5E+02 0.0032 24.9 3.8 56 126-181 34-90 (113)
165 PF09371 Tex_N: Tex-like prote 21.0 39 0.00084 30.7 0.5 23 239-263 19-42 (193)
166 PLN00153 histone H2A; Provisio 21.0 1.4E+02 0.003 25.7 3.9 59 120-179 31-89 (129)
167 COG0542 clpA ATP-binding subun 20.7 2E+02 0.0044 31.7 5.9 98 51-181 12-110 (786)
168 cd04752 Commd4 COMM_Domain con 20.0 6E+02 0.013 22.3 8.3 50 40-96 43-93 (174)
No 1
>KOG0869|consensus
Probab=99.97 E-value=1e-30 Score=224.93 Aligned_cols=100 Identities=70% Similarity=1.110 Sum_probs=95.9
Q ss_pred CCccccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcch
Q psy3459 3 LREQDRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYV 82 (296)
Q Consensus 3 ~~~~d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv 82 (296)
++++|+.||+|+|.||||.+||.+++|||||++.+|+|+++||+|||++|++.|..++||||++|||||||..|||++|+
T Consensus 26 ~reqDr~LPIANV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~ 105 (168)
T KOG0869|consen 26 LREQDRFLPIANVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYA 105 (168)
T ss_pred cchhhhhccHHHHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHH
Confidence 68899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHHhcccccc
Q psy3459 83 EPLKIYLQKYREATKGEKSV 102 (296)
Q Consensus 83 ~~l~~~L~~~re~~k~kk~~ 102 (296)
++|+.+|.+||+....+...
T Consensus 106 eplkiyL~kYRe~e~e~~~~ 125 (168)
T KOG0869|consen 106 EPLKIYLQKYRELEGERGRS 125 (168)
T ss_pred HHHHHHHHHHHHHhhhcccc
Confidence 99999999999986655544
No 2
>KOG0871|consensus
Probab=99.96 E-value=7.6e-29 Score=211.58 Aligned_cols=119 Identities=31% Similarity=0.533 Sum_probs=105.4
Q ss_pred CccccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchH
Q psy3459 4 REQDRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE 83 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~ 83 (296)
..++++||+|+|++|||+.||.+++|++||+++|..||.+||++||++||++|..+.||||++|||++||+.|||.+|++
T Consensus 7 ~dde~sLPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYie 86 (156)
T KOG0871|consen 7 EDDELSLPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIE 86 (156)
T ss_pred ccccccCcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHH
Confidence 67899999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccccc-chhhhhhhhh-------hhhccchhhh
Q psy3459 84 PLKIYLQKYREATKGEKSV-NCEVYQEISV-------EDVFQSSGTI 122 (296)
Q Consensus 84 ~l~~~L~~~re~~k~kk~~-~~e~~~~~~~-------e~Lf~~s~ri 122 (296)
.+...|++|+..++.++++ .+..-.||++ ++||+.++.+
T Consensus 87 e~~~vl~~~K~~~~~~~~kssk~e~~Gi~eEEL~~qQqeLf~~ARar 133 (156)
T KOG0871|consen 87 EAEEVLENCKEEAKKRRRKSSKFEKSGIPEEELLRQQQELFAKARAR 133 (156)
T ss_pred HHHHHHHHHHHHHHHhhhhhhhHHhcCCCHHHHHHHHHHHHHHHHHH
Confidence 9999999999988877666 3333344444 4566666543
No 3
>KOG0869|consensus
Probab=99.95 E-value=6.2e-29 Score=213.99 Aligned_cols=87 Identities=60% Similarity=0.960 Sum_probs=83.9
Q ss_pred chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHHHHHH
Q psy3459 118 SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYR 197 (296)
Q Consensus 118 ~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L~~~r 197 (296)
++.||||+.||++++||||||+.+|+|+++||+|||++|++.|..++|||||+|||||||..|||++|++||+.||.+||
T Consensus 37 NV~RIMK~~lP~naKIsKDAKE~vQECVSEfISFvT~EAsekC~~EkRKTIngdDllwAm~tLGFe~Y~eplkiyL~kYR 116 (168)
T KOG0869|consen 37 NVSRIMKKALPANAKISKDAKETVQECVSEFISFVTGEASEKCQREKRKTINGDDLLWAMSTLGFENYAEPLKIYLQKYR 116 (168)
T ss_pred HHHHHHHhcCCcccccchHHHHHHHHHHHHHHHHHhhHHHHHHHHHhcCcccHHHHHHHHHHcCcHhHHHHHHHHHHHHH
Confidence 77999999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHhcccc
Q psy3459 198 EATKGEK 204 (296)
Q Consensus 198 e~~k~kk 204 (296)
+....+.
T Consensus 117 e~e~e~~ 123 (168)
T KOG0869|consen 117 ELEGERG 123 (168)
T ss_pred HHhhhcc
Confidence 9865553
No 4
>KOG0871|consensus
Probab=99.95 E-value=3e-28 Score=207.90 Aligned_cols=121 Identities=26% Similarity=0.449 Sum_probs=101.4
Q ss_pred hccch-hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHH
Q psy3459 115 VFQSS-GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYL 193 (296)
Q Consensus 115 Lf~~s-~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L 193 (296)
|++++ ..+|+..+|++++|++|||++|++||++||++|||+||++|.++.||||+|+||++||+.|||++|++.+.+.|
T Consensus 13 LPkAtv~KmIke~lP~d~rvakeareliincCvEFI~liSsEAneic~~e~KKTIa~EHV~KALe~LgF~eYiee~~~vl 92 (156)
T KOG0871|consen 13 LPKATVNKMIKEMLPKDVRVAKEARELIINCCVEFINLISSEANEICNKEAKKTIAPEHVIKALENLGFGEYIEEAEEVL 92 (156)
T ss_pred CcHHHHHHHHHHhCCcccccchHHHHHHHHHHHHHHHHHHHHHHHHHhHHhcccCCHHHHHHHHHHcchHHHHHHHHHHH
Confidence 56665 45556778889999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhcccccccccccchhhhhhHHHhhhhchhhHHHHhhhcCC
Q psy3459 194 QKYREATKGEKFISFITSEASDRCHLEKRKTINGEDILFAMSALGF 239 (296)
Q Consensus 194 ~~~re~~k~kk~~~~~~se~~~r~~~e~~~~~~~qe~lf~~a~~~f 239 (296)
++|+..++.+..+++.-.. .....++++++|++||+.||..|
T Consensus 93 ~~~K~~~~~~~~kssk~e~----~Gi~eEEL~~qQqeLf~~ARar~ 134 (156)
T KOG0871|consen 93 ENCKEEAKKRRRKSSKFEK----SGIPEEELLRQQQELFAKARARL 134 (156)
T ss_pred HHHHHHHHHhhhhhhhHHh----cCCCHHHHHHHHHHHHHHHHHHH
Confidence 9999887654322211111 22334899999999999999653
No 5
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.90 E-value=7.3e-24 Score=177.30 Aligned_cols=120 Identities=29% Similarity=0.460 Sum_probs=109.8
Q ss_pred CccccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchH
Q psy3459 4 REQDRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE 83 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~ 83 (296)
..++..||+|+|.+++.+.||.+..+++||++.++.||.+||+.|+++||++|....+|||.++||++||+.|||.+|++
T Consensus 6 ~dDe~sLPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~ 85 (148)
T COG5150 6 NDDENSLPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIE 85 (148)
T ss_pred ccccccCcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHH
Confidence 67889999999999999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHHHHHHHhcccccc---------chhhhhhhhhhhhccchhhhhh
Q psy3459 84 PLKIYLQKYREATKGEKSV---------NCEVYQEISVEDVFQSSGTILE 124 (296)
Q Consensus 84 ~l~~~L~~~re~~k~kk~~---------~~e~~~~~~~e~Lf~~s~rimk 124 (296)
.+.+.+.+|+..+|.|.++ +.|.+..+| |+||..++-++.
T Consensus 86 ~~~e~~~n~k~~qK~ke~k~sKFk~SGls~eELlrQQ-eeLf~~ar~rf~ 134 (148)
T COG5150 86 SCMEEHENYKSYQKQKESKISKFKDSGLSMEELLRQQ-EELFQNARLRFE 134 (148)
T ss_pred HHHHHHHHHHHHHhhchhhhhHHHhcCCCHHHHHHHH-HHHHHHHHHHhc
Confidence 9999999999999999888 444555555 677777766663
No 6
>COG5150 Class 2 transcription repressor NC2, beta subunit (Dr1) [Transcription]
Probab=99.90 E-value=3.2e-24 Score=179.47 Aligned_cols=121 Identities=25% Similarity=0.392 Sum_probs=106.0
Q ss_pred hccc-hhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHH
Q psy3459 115 VFQS-SGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYL 193 (296)
Q Consensus 115 Lf~~-s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L 193 (296)
|+.+ +...+...+|.+..++||||+++++||.+||+.||++||++|.++.+|||+++||++||+.|||.+|++.+.+.+
T Consensus 12 LPKATVqKMvS~iLp~dl~ftKearei~in~cieFi~~lsseAne~ce~EaKKTIa~EHviKALenLef~eyi~~~~e~~ 91 (148)
T COG5150 12 LPKATVQKMVSSILPKDLVFTKEAREIFINACIEFINMLSSEANEACEEEAKKTIAYEHVIKALENLEFEEYIESCMEEH 91 (148)
T ss_pred CcHHHHHHHHHHhccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhccccHHHHHHHHHhccHHHHHHHHHHHH
Confidence 4443 366667889999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred HHHHHHhccc--ccccccccchhhhhhHHHhhhhchhhHHHHhhhcCCCC
Q psy3459 194 QKYREATKGE--KFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDS 241 (296)
Q Consensus 194 ~~~re~~k~k--k~~~~~~se~~~r~~~e~~~~~~~qe~lf~~a~~~f~~ 241 (296)
.+|+..+|.| |...|..|.. .+++++++|++||.+||++|+-
T Consensus 92 ~n~k~~qK~ke~k~sKFk~SGl------s~eELlrQQeeLf~~ar~rf~h 135 (148)
T COG5150 92 ENYKSYQKQKESKISKFKDSGL------SMEELLRQQEELFQNARLRFEH 135 (148)
T ss_pred HHHHHHHhhchhhhhHHHhcCC------CHHHHHHHHHHHHHHHHHHhcc
Confidence 9999988765 3333444443 3489999999999999999964
No 7
>KOG0870|consensus
Probab=99.90 E-value=7.3e-24 Score=184.02 Aligned_cols=102 Identities=35% Similarity=0.548 Sum_probs=97.8
Q ss_pred CCCCccccCCchhHHHHHHHhhCCCC-CcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 1 MPLREQDRFLPIANVAKIMKKAIPES-GKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 1 m~~~~~d~~LP~A~I~RIiK~~LP~~-~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
|..+++|+.||+|+|+||+|++||.. +.|||||+.+|+++|++||+||++.|+++|+.++||||+++||+.||.++||.
T Consensus 2 e~eri~dl~lP~AiI~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs 81 (172)
T KOG0870|consen 2 EDERIEDLNLPNAIITRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFS 81 (172)
T ss_pred cchhHHHhhccHHHHHHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchH
Confidence 45688999999999999999999987 99999999999999999999999999999999999999999999999999999
Q ss_pred cchHHHHHHHHHHHHHhcccccc
Q psy3459 80 SYVEPLKIYLQKYREATKGEKSV 102 (296)
Q Consensus 80 ~yv~~l~~~L~~~re~~k~kk~~ 102 (296)
.|+++|+..|+.|+...++||..
T Consensus 82 ~f~~plk~~Le~yk~~~k~Kk~~ 104 (172)
T KOG0870|consen 82 SFVNPLKSALEAYKKAVKQKKLA 104 (172)
T ss_pred HHhhHHHHHHHHHHHHHHHHHHh
Confidence 99999999999999999888844
No 8
>KOG0870|consensus
Probab=99.85 E-value=1.4e-21 Score=169.81 Aligned_cols=87 Identities=31% Similarity=0.532 Sum_probs=83.4
Q ss_pred hhhhhhcCCCc-cccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHHHHHHH
Q psy3459 120 GTILEQQNGQN-ETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYRE 198 (296)
Q Consensus 120 ~rimk~~lp~~-~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L~~~re 198 (296)
+|++|+.+|.. +.|||||+.+|+++|++||+|||+.|+++|+..+||||+|+|||+||++|||.+|++||+..|+.|+.
T Consensus 17 ~rlvke~l~E~~vsisKeA~~Ai~raAtVFv~~Lts~s~e~A~~q~rKt~sadDVl~aL~Eiefs~f~~plk~~Le~yk~ 96 (172)
T KOG0870|consen 17 TRLVKEVLPESNVSISKEARLAIARAATVFVIFLTSVSNEIAKDQKRKTISADDVLKALDEIEFSSFVNPLKSALEAYKK 96 (172)
T ss_pred HHHHHHhCccccccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCcccHHHHHHHHHHhchHHHhhHHHHHHHHHHH
Confidence 88999999987 99999999999999999999999999999999999999999999999999999999999999999999
Q ss_pred Hhcccccc
Q psy3459 199 ATKGEKFI 206 (296)
Q Consensus 199 ~~k~kk~~ 206 (296)
..+.||..
T Consensus 97 ~~k~Kk~~ 104 (172)
T KOG0870|consen 97 AVKQKKLA 104 (172)
T ss_pred HHHHHHHh
Confidence 88877644
No 9
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.63 E-value=7.7e-16 Score=114.70 Aligned_cols=64 Identities=38% Similarity=0.610 Sum_probs=59.3
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
.||++.|.||||.. |+..+||+||..+|.+|+++||.||+.+|++.|..++||||+++||..||
T Consensus 2 ~lP~a~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 2 SLPLARVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp SS-HHHHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred CCChHHHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 69999999999999 99899999999999999999999999999999999999999999999986
No 10
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=99.55 E-value=5.8e-15 Score=118.20 Aligned_cols=78 Identities=36% Similarity=0.507 Sum_probs=73.6
Q ss_pred CCccccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcch
Q psy3459 3 LREQDRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYV 82 (296)
Q Consensus 3 ~~~~d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv 82 (296)
++..+..||+++|.||||++.++ +||.+|.+++++++++|+..|+..|++.|.|+|||||+++||..|++.+||..|.
T Consensus 13 ~~~~~~~Lp~apv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~~ 90 (91)
T COG2036 13 QRSTDLLLPKAPVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYG 90 (91)
T ss_pred hhhhhhhcCchHHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccccc
Confidence 45678899999999999999776 9999999999999999999999999999999999999999999999999998763
No 11
>PF00808 CBFD_NFYB_HMF: Histone-like transcription factor (CBF/NF-Y) and archaeal histone; InterPro: IPR003958 The CCAAT-binding factor (CBF) is a mammalian transcription factor that binds to a CCAAT motif in the promoters of a wide variety of genes, including type I collagen and albumin. The factor is a heteromeric complex of A and B subunits, both of which are required for DNA-binding [, ]. The subunits can interact in the absence of DNA-binding, conserved regions in each being important in mediating this interaction. The A subunit can be split into 3 domains on the basis of sequence similarity, a non-conserved N-terminal 'A domain'; a highly-conserved central 'B domain' involved in DNA-binding; and a C-terminal 'C domain', which contains a number of glutamine and acidic residues involved in protein-protein interactions []. The A subunit shows striking similarity to the HAP3 subunit of the yeast CCAAT-binding heterotrimeric transcription factor [, ]. The Kluyveromyces lactis HAP3 protein has been predicted to contain a 4-cysteine zinc finger, which is thought to be present in similar HAP3 and CBF subunit A proteins, in which the third cysteine is replaced by a serine []. This domain is found in the CCAAT transcription factor and archaeal histones.; GO: 0043565 sequence-specific DNA binding, 0005622 intracellular; PDB: 1F1E_A 2BYM_D 2BYK_D 1HTA_A 1B67_A 1JFI_B 1KU5_B 1N1J_A 1BFM_A 1B6W_A ....
Probab=99.36 E-value=9.3e-13 Score=98.08 Aligned_cols=59 Identities=29% Similarity=0.446 Sum_probs=53.1
Q ss_pred chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 118 SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 118 ~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
.+.++||.. |++.+||+||.++|.+|+.+||+||+.+|++.|..++||||+++||..||
T Consensus 7 ~vkri~k~~-~~~~~vs~ea~~~i~~a~e~Fi~~l~~~A~~~a~~~~rkti~~~Dv~~Av 65 (65)
T PF00808_consen 7 RVKRIMKSD-PDVMRVSKEAVEAIAKAAEEFIQYLAKEANEIAQRDKRKTITYEDVAKAV 65 (65)
T ss_dssp HHHHHHHHT-STTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTTSSEE-HHHHHHHH
T ss_pred HHHHHhccC-CCccchhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCccCHHHHHHHC
Confidence 447777777 99999999999999999999999999999999999999999999999986
No 12
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=99.08 E-value=4e-10 Score=89.36 Aligned_cols=72 Identities=15% Similarity=0.326 Sum_probs=67.3
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcc
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 81 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~y 81 (296)
-.||+++|.||++.. +..+||.|+.+.+.++..+|+..|...|..+|++++||||+++||..||+..|-.-|
T Consensus 12 ~gi~k~~I~RLarr~--GvkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 12 KGITKPAIRRLARRG--GVKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred ccCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 369999999999998 778999999999999999999999999999999999999999999999999985533
No 13
>PLN00035 histone H4; Provisional
Probab=99.04 E-value=7.3e-10 Score=90.72 Aligned_cols=70 Identities=14% Similarity=0.258 Sum_probs=66.3
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
..||+++|.||++.. +..+||.|+.+.+.+...+|+..|+..|..+|+|++||||+++||..||+..|-.
T Consensus 28 ~~ipk~~IrRLARr~--GvkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 28 QGITKPAIRRLARRG--GVKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred ccCCHHHHHHHHHHc--CcccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 359999999999998 7789999999999999999999999999999999999999999999999988764
No 14
>COG2036 HHT1 Histones H3 and H4 [Chromatin structure and dynamics]
Probab=98.97 E-value=7.7e-10 Score=88.80 Aligned_cols=67 Identities=30% Similarity=0.435 Sum_probs=63.6
Q ss_pred chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccch
Q psy3459 118 SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYV 186 (296)
Q Consensus 118 ~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv 186 (296)
+..|++++..++ +||.+|.+++++|..+|+..|+..|+++|...|||||+++||.-|+..+||..|.
T Consensus 24 pv~Ri~r~~~~~--Rvs~~A~~~l~~~~e~~~~~i~~~A~~~A~ha~RKTV~~~DI~la~~~~~~~~~~ 90 (91)
T COG2036 24 PVRRILRKAGAE--RVSSSAIEELQEALEEYLEEIAEDAVELAEHAKRKTVKAEDIKLALKRLGRRIYG 90 (91)
T ss_pred HHHHHHHHHhHH--HhhHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeecHHHHHHHHHHhcccccc
Confidence 669999988887 9999999999999999999999999999999999999999999999999998764
No 15
>PTZ00015 histone H4; Provisional
Probab=98.95 E-value=2.6e-09 Score=87.39 Aligned_cols=73 Identities=18% Similarity=0.355 Sum_probs=67.8
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcc
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 81 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~y 81 (296)
...||+++|.||++.. +..+||.|+.+.+.+...+|+..|..+|..+|++++||||+++||..||+..|-.-|
T Consensus 28 i~gI~k~~IrRLarr~--GvkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 28 IRGITKGAIRRLARRG--GVKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred ccCCCHHHHHHHHHHc--CCccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 3479999999999998 778999999999999999999999999999999999999999999999999886533
No 16
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=98.83 E-value=1.1e-08 Score=77.23 Aligned_cols=64 Identities=25% Similarity=0.292 Sum_probs=60.6
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.||.++|.||++.. |..+||.|+...|.+-.+.|+.-|..+|..++.|.+||||+++||-.||+
T Consensus 2 ~~p~~~i~ria~~~--Gi~ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 2 WLPKETIKDVAESL--GIGNLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred CCCHHHHHHHHHHC--CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 58999999999987 66789999999999999999999999999999999999999999999874
No 17
>smart00417 H4 Histone H4.
Probab=98.79 E-value=1.1e-08 Score=79.27 Aligned_cols=62 Identities=11% Similarity=0.280 Sum_probs=58.7
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHH
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILF 71 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~ 71 (296)
..||+++|.||++.+ +.-+||.++.+.+.+...+|+..|...|..+|++++||||+++||.-
T Consensus 12 ~gI~k~~IrRLaRr~--GvkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~ 73 (74)
T smart00417 12 QGITKPAIRRLARRG--GVKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVY 73 (74)
T ss_pred cCCCHHHHHHHHHHc--CcchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHhee
Confidence 469999999999998 77799999999999999999999999999999999999999999964
No 18
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=98.53 E-value=3.8e-07 Score=69.89 Aligned_cols=65 Identities=17% Similarity=0.327 Sum_probs=61.2
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 10 LPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 10 LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
||+..+..++++.-|+ .+++.||.++|++.+..|+.-++..|...|+|.||+||.++||.-+|+.
T Consensus 2 ~~k~~l~~lv~~id~~-~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 2 LTKRKLQELLKEIDPR-EQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred CcHHHHHHHHHhhCCC-CCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 6788899999988775 7999999999999999999999999999999999999999999999875
No 19
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=98.40 E-value=6e-07 Score=67.96 Aligned_cols=68 Identities=25% Similarity=0.346 Sum_probs=62.3
Q ss_pred ccCCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPE---SGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~---~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
+..+|+.+|.|+.|+..++ ..+||.+|...|+..++.|+.-|...|...|.+.+|+||++.||..|+.
T Consensus 3 ~~~~~~~~~~r~~r~i~~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 3 RRLIPKFPFSRLLREIGEEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp SHSSSHHHHHHHHHHHHHTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred ccccCceEEeeeeehhhcccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 4578999999999988765 2599999999999999999999999999999999999999999999875
No 20
>smart00428 H3 Histone H3.
Probab=98.35 E-value=1e-06 Score=72.60 Aligned_cols=71 Identities=17% Similarity=0.205 Sum_probs=64.8
Q ss_pred CccccCCchhHHHHHHHhhCCC-----CCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 4 REQDRFLPIANVAKIMKKAIPE-----SGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP~-----~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
+..++.+|+.+..|++++...+ +.+++.+|..+||++++.|+--+...|+..|.|++|+||++.|+..|..
T Consensus 24 kst~lLI~k~pF~RLVREI~~~~~~~~~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~r 99 (105)
T smart00428 24 KSTDLLIRKAPFQRLVREIAQKFTTGVDLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLARR 99 (105)
T ss_pred cCcccccccccHHHHHHHHHHHcCCCCCceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHHH
Confidence 4578899999999999988743 6799999999999999999999999999999999999999999987764
No 21
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=98.24 E-value=6.9e-07 Score=81.86 Aligned_cols=75 Identities=27% Similarity=0.321 Sum_probs=68.1
Q ss_pred cccCCchhHHHHHHHhhCCCCC-cccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcch
Q psy3459 6 QDRFLPIANVAKIMKKAIPESG-KIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYV 82 (296)
Q Consensus 6 ~d~~LP~A~I~RIiK~~LP~~~-rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv 82 (296)
.+.+||+|.|.|+||-- +++ .||.||..++.+.++.||..||-.|+-.++.++|+|+...||-.|++.-++-+|.
T Consensus 106 k~h~LPlARIkkvMKtd--edVkMisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFL 181 (286)
T COG5208 106 KDHNLPLARIKKVMKTD--EDVKMISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFL 181 (286)
T ss_pred HhccCcHHHHHHHHhcc--cchhheecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHH
Confidence 46789999999999965 444 5999999999999999999999999999999999999999999999988877764
No 22
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=98.13 E-value=1.1e-05 Score=62.41 Aligned_cols=66 Identities=23% Similarity=0.321 Sum_probs=60.5
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 12 IANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 12 ~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
+-.|.+|++.+ |--+++.+|.+.|.+....|+..|+..+..+|.+.||++.++.||..||+++|+.
T Consensus 9 ~~~Vaqil~~~--Gf~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 9 RIAVAQILESA--GFDSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred HHHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 44678888877 6569999999999999999999999999999999999999999999999999984
No 23
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=97.92 E-value=5.5e-05 Score=63.20 Aligned_cols=77 Identities=14% Similarity=0.182 Sum_probs=65.8
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHH-HHHHHHHH
Q psy3459 14 NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP-LKIYLQKY 92 (296)
Q Consensus 14 ~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~-l~~~L~~~ 92 (296)
.|.+|+|+. +..+++.+++..|.+.+..++.-|..+|..+|.|+||+||+++||..|++..+-..|..+ -++.|-..
T Consensus 6 ~v~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~ 83 (117)
T cd07979 6 VIAAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLEL 83 (117)
T ss_pred HHHHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHH
Confidence 688999987 667999999999999999999999999999999999999999999999997666555544 55554433
No 24
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=97.85 E-value=4e-05 Score=64.11 Aligned_cols=67 Identities=13% Similarity=0.220 Sum_probs=61.3
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||.+.|.|+||+.- ...|||.+|...|..+.+.+..-|...|...|.+.+|++|+++||..|+.
T Consensus 18 gL~fPV~ri~R~Lk~~~-~a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~ 84 (115)
T cd00074 18 GLQFPVGRIHRYLKKGR-YAERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVR 84 (115)
T ss_pred CccCcHHHHHHHHHcCc-cccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHh
Confidence 57899999999999843 33699999999999999999999999999999999999999999999975
No 25
>cd00076 H4 Histone H4, one of the four histones, along with H2A, H2B and H3, which forms the eukaryotic nucleosome core; along with H3, it plays a central role in nucleosome formation; histones bind to DNA and wrap the genetic material into "beads on a string" in which DNA (the string) is wrapped around small blobs of histones (the beads) at regular intervals; play a role in the inheritance of specialized chromosome structures and the control of gene activity; defects in the establishment of proper chromosome structure by histones may activate or silence genes aberrantly and thus lead to disease; the sequence of histone H4 has remained almost invariant in more than 2 billion years of evolution
Probab=97.80 E-value=5e-05 Score=60.41 Aligned_cols=67 Identities=16% Similarity=0.311 Sum_probs=58.0
Q ss_pred cch-hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccc
Q psy3459 117 QSS-GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 185 (296)
Q Consensus 117 ~~s-~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~y 185 (296)
.++ +|+++... --+||.|+.+.+.++..+|..-|...|..+|+-.+||||+++||.-||+..|-.-|
T Consensus 16 k~~I~RLarr~G--vkRIS~d~y~e~~~~l~~~l~~I~~dav~ya~Ha~RKTVt~~DV~~alkr~g~~~y 83 (85)
T cd00076 16 KPAIRRLARRGG--VKRISGGVYDEVRNVLKSYLEDVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRTLY 83 (85)
T ss_pred HHHHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHCCCCcc
Confidence 444 56655443 46999999999999999999999999999999999999999999999999985543
No 26
>PLN00160 histone H3; Provisional
Probab=97.71 E-value=9e-05 Score=60.35 Aligned_cols=70 Identities=17% Similarity=0.147 Sum_probs=63.5
Q ss_pred CccccCCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 4 REQDRFLPIANVAKIMKKAIP----ESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP----~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
+..++.+|+++..|++++... ++.++..+|..+||++++.|+--+-..|+-.|.|++|.||.+.|+..|.
T Consensus 16 kst~lLI~k~pF~RLVREI~~~~~~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 16 KSTDLLIRRLPFARLVREIQMEMSREAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred cchhhhhccccHHHHHHHHHHHcCCCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 456788999999999998863 4589999999999999999999999999999999999999999997775
No 27
>PLN00161 histone H3; Provisional
Probab=97.66 E-value=0.00015 Score=62.25 Aligned_cols=70 Identities=17% Similarity=0.227 Sum_probs=63.6
Q ss_pred CccccCCchhHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 4 REQDRFLPIANVAKIMKKAI----PESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~L----P~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
+..++.+|+++..|++++.. +.+.++..+|..+||++++.|+--+-..|+-.|.|++|.||.+.|+..|.
T Consensus 50 kst~lLIpklPF~RLVREI~~~~~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 50 KSTELLIRKLPFARLVREISNEMLREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred cccccccccccHHHHHHHHHHhcCCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 45678899999999999885 34689999999999999999999999999999999999999999997775
No 28
>PLN00121 histone H3; Provisional
Probab=97.64 E-value=8.9e-05 Score=63.72 Aligned_cols=70 Identities=14% Similarity=0.187 Sum_probs=64.2
Q ss_pred CccccCCchhHHHHHHHhhCCC---CCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 4 REQDRFLPIANVAKIMKKAIPE---SGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP~---~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
+..++.+|+++..|++++...+ +.++..+|..+||++++.|+--+-..++-.+.|++|.||.+.|+..+.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cccccccccccHHHHHHHHHHHhCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 4568899999999999998754 689999999999999999999999999999999999999999997775
No 29
>cd07981 TAF12 TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 12 (TAF12) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of the seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs function such as serving as activator-bind
Probab=97.61 E-value=0.00013 Score=55.86 Aligned_cols=55 Identities=16% Similarity=0.296 Sum_probs=50.8
Q ss_pred hcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 125 QQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 125 ~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
+...|+.+++.||.++|++.+-.|+.-++..|...|+..||+||.++||.-+|+.
T Consensus 12 ~~id~~~~~~~da~~~l~~~~e~fv~~v~~~a~~lAkHr~~~tv~~~Di~l~l~r 66 (72)
T cd07981 12 KEIDPREQLDPDVEELLLEIADDFVDDVVEDACRLAKHRKSDTLEVKDVQLHLER 66 (72)
T ss_pred HhhCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHH
Confidence 3445679999999999999999999999999999999999999999999998875
No 30
>PLN00035 histone H4; Provisional
Probab=97.60 E-value=0.00014 Score=59.83 Aligned_cols=67 Identities=15% Similarity=0.242 Sum_probs=57.5
Q ss_pred hccch-hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 115 VFQSS-GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 115 Lf~~s-~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
|..++ +|+++..- --+||.|+.+.+.+...+|+.-|...|..+|+-.+||||+++||.-||+..|=.
T Consensus 30 ipk~~IrRLARr~G--vkRIS~~ay~elr~vle~~l~~I~~dav~ya~HA~RKTV~~~DV~~Alkr~g~~ 97 (103)
T PLN00035 30 ITKPAIRRLARRGG--VKRISGLIYEETRGVLKIFLENVIRDAVTYTEHARRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred CCHHHHHHHHHHcC--cccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCcHHHHHHHHHHcCCc
Confidence 33444 66665543 469999999999999999999999999999999999999999999999988754
No 31
>KOG1657|consensus
Probab=97.56 E-value=7.8e-05 Score=69.36 Aligned_cols=73 Identities=25% Similarity=0.312 Sum_probs=64.7
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcc
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 81 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~y 81 (296)
..||++.|.+|||.- ++--+|+.||..++.++|+.||..|+..|+..+...+|+|+...|+-.|+..-.-.+|
T Consensus 73 ~~lPlaRiKkimK~d-edv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdF 145 (236)
T KOG1657|consen 73 HILPLARIKKIMKSD-EDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDF 145 (236)
T ss_pred ccCcHhhcccccccc-ccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccc
Confidence 469999999999965 3334799999999999999999999999999999999999999999999987554444
No 32
>PTZ00018 histone H3; Provisional
Probab=97.53 E-value=0.00019 Score=61.69 Aligned_cols=70 Identities=14% Similarity=0.174 Sum_probs=63.9
Q ss_pred CccccCCchhHHHHHHHhhCC---CCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 4 REQDRFLPIANVAKIMKKAIP---ESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~LP---~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
+..|+.+|+.+..|++++... .+.++..+|..+||++++.|+--+-..++-.|.|++|.||.+.|+..|.
T Consensus 57 kst~lLI~k~pF~RLVREI~~~~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 57 KSTELLIRKLPFQRLVREIAQDFKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred ccchhccccccHHHHHHHHHHHcCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 456889999999999999863 4689999999999999999999999999999999999999999997775
No 33
>PTZ00015 histone H4; Provisional
Probab=97.51 E-value=0.00023 Score=58.51 Aligned_cols=66 Identities=18% Similarity=0.342 Sum_probs=57.3
Q ss_pred chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccc
Q psy3459 118 SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 185 (296)
Q Consensus 118 ~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~y 185 (296)
+.+|+++..- --+||.|+.+.+.+...+|+.-|...|..+|+-.+||||+++||.-||+..|-.-|
T Consensus 35 ~IrRLarr~G--vkRIS~d~y~e~r~vle~~l~~I~rdav~~aeHA~RKTVt~~DV~~AlKr~g~~~y 100 (102)
T PTZ00015 35 AIRRLARRGG--VKRISGDIYEEVRGVLKAFLENVVRDSTAYTEYARRKTVTAMDVVYALKRQGRTLY 100 (102)
T ss_pred HHHHHHHHcC--CccchHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHHHHHHHhcCCCCC
Confidence 4466665543 36899999999999999999999999999999999999999999999998886543
No 34
>PF00125 Histone: Core histone H2A/H2B/H3/H4 histone h2a signature histone h2b signature histone h3 signature histone h4 signature; InterPro: IPR007125 The core histones together with some other DNA binding proteins appear to form a superfamily defined by a common fold and distant sequence similarities [, ]. Some proteins contain local homology domains related to the histone fold [].; GO: 0003677 DNA binding; PDB: 2YFW_D 2YFV_B 1U35_H 2F8N_D 2PYO_D 2NQB_D 3AN2_C 3AZJ_C 3AV1_G 3AZM_G ....
Probab=97.46 E-value=0.00025 Score=53.60 Aligned_cols=54 Identities=26% Similarity=0.268 Sum_probs=48.9
Q ss_pred hcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 125 QQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 125 ~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
.......+||++|..+|+..+-.|+.-|...|+..|...||+||++.||..|+.
T Consensus 20 ~~~~~~~ris~~a~~~L~~~~E~~~~~il~~A~~~a~~~kR~tI~~~DI~~A~r 73 (75)
T PF00125_consen 20 EEILSKYRISSEALVALQSVLEYLLVEILEEAGNLARHAKRKTITPRDIQLAVR 73 (75)
T ss_dssp HTTSSSSEECHHHHHHHHHHHHHHHHHHHHHHHHHHHHTTBSEEGHHHHHHHHH
T ss_pred cccccccccccccchhhhhhhhhhhhhhhhHHHHHHhhcCCcEecHHHHHHHHh
Confidence 333334899999999999999999999999999999999999999999999875
No 35
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=97.43 E-value=0.00039 Score=67.48 Aligned_cols=67 Identities=16% Similarity=0.211 Sum_probs=60.5
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 11 PIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 11 P~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
|..+|.-|++.. +..++|+||..++.+.++.++..|+.+|...+++.+|||++++||-.||+.++.+
T Consensus 1 ~~~~i~~ia~~~--Gi~~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 1 PQESIKLIAESL--GIDSLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred ChhHHHHHHHHc--CCCcCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 456777777766 5569999999999999999999999999999999999999999999999987765
No 36
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=97.35 E-value=0.00063 Score=53.07 Aligned_cols=61 Identities=16% Similarity=0.208 Sum_probs=51.7
Q ss_pred HHHHHHHhhC-CCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 14 NVAKIMKKAI-PESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 14 ~I~RIiK~~L-P~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
+|.||..+.. +.++.+|+.+..+|.+.+-.++.-++..---.|+|+||+||+++||+....
T Consensus 10 ~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 10 TVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 5788888874 667899999999999999999999999999999999999999999987654
No 37
>smart00803 TAF TATA box binding protein associated factor. TAFs (TATA box binding protein associated factors) are part of the transcription initiation factor TFIID multimeric protein complex. TFIID is composed of the TATA box binding protein (TBP) and a number of TAFs. The TAFs provide binding sites for many different transcriptional activators and co-activators that modulate transcription initiation by Pol II. TAF proteins adopt a histone-like fold.
Probab=97.29 E-value=0.00052 Score=51.84 Aligned_cols=57 Identities=26% Similarity=0.229 Sum_probs=49.3
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
+++.+. .+-. +||.|+...+.+-...|+.-|.-.|..+++..+|||++++||-.||+
T Consensus 9 ~ria~~-~Gi~-ris~~a~~~l~~~~e~rl~~i~~~A~k~~~hakRktlt~~DI~~Alk 65 (65)
T smart00803 9 KDVAES-LGIG-NLSDEAAKLLAEDVEYRIKEIVQEALKFMRHSKRTTLTTSDIDSALR 65 (65)
T ss_pred HHHHHH-CCCc-cccHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCeecHHHHHHHhC
Confidence 444443 3322 79999999999999999999999999999999999999999998874
No 38
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=97.18 E-value=0.0022 Score=49.18 Aligned_cols=65 Identities=18% Similarity=0.265 Sum_probs=57.3
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 13 ANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 13 A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
-.|.+|++.+ +=..++..|.+.|...+..|+..|+..+...|.+.||...++.||..||.++|+.
T Consensus 10 ~~va~il~~~--GF~~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 10 RSVAQILKHA--GFDSASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred HHHHHHHHHc--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 3456666654 3347999999999999999999999999999999999999999999999999984
No 39
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=97.12 E-value=0.00068 Score=67.55 Aligned_cols=62 Identities=26% Similarity=0.281 Sum_probs=47.2
Q ss_pred ccCCchhHHHHHHHhhCC----CCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCccc
Q psy3459 7 DRFLPIANVAKIMKKAIP----ESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGED 68 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP----~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eD 68 (296)
--.||.+.|.|++....- .+++|++||..+|.+|..-|-..|+..--.+|.|+|||||...|
T Consensus 349 ~P~lP~~~vK~la~~~ak~s~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 349 YPSLPPGVVKKLAQHFAKSSGGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ---S-HHHHHHHHHHHH-------S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred CCCCCccHHHHHHHHHHHhhcccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 346999999888877643 46899999999999999999999999999999999999998876
No 40
>smart00427 H2B Histone H2B.
Probab=97.08 E-value=0.002 Score=51.76 Aligned_cols=63 Identities=22% Similarity=0.338 Sum_probs=57.6
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcC
Q psy3459 14 NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 77 (296)
Q Consensus 14 ~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lg 77 (296)
-|+|++|+.-|+ ..||..|...|.-.+..+..-|+.+|...|...+|+||++.+|..|..-+-
T Consensus 6 Yi~kvLKqVhpd-~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 6 YIYKVLKQVHPD-TGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHHHHhCCC-ccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 589999999988 589999999999999999999999999999999999999999999986543
No 41
>KOG3467|consensus
Probab=97.04 E-value=0.002 Score=51.74 Aligned_cols=68 Identities=16% Similarity=0.290 Sum_probs=60.6
Q ss_pred CchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 10 LPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 10 LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
+.+-+|.||.+.. +--+|+--.-+.+...+.+|+.-+-+.|...+++++||||++-||+-+|+..|.-
T Consensus 30 itKpaIRRlARr~--GVkRi~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 30 ITKPAIRRLARRG--GVKRISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred cchHHHHHHHHhc--CcchhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 5567899999886 5557888888889999999999999999999999999999999999999998754
No 42
>smart00576 BTP Bromodomain transcription factors and PHD domain containing proteins. subdomain of archael histone-like transcription factors
Probab=97.00 E-value=0.0015 Score=50.45 Aligned_cols=53 Identities=21% Similarity=0.357 Sum_probs=50.4
Q ss_pred cccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 131 ETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 131 ~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
-+++..|.+.+.+-...|+.-|+..+..+|+..||+++++.||..||.++|..
T Consensus 22 ~~~~~sale~ltdi~~~yl~~l~~~~~~~a~~agR~~~~~~Dv~~Al~~~gi~ 74 (77)
T smart00576 22 DSFQESALETLTDILQSYIQELGRTAHSYAELAGRTEPNLGDVVLALENLGIS 74 (77)
T ss_pred cccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCcc
Confidence 47888999999999999999999999999999999999999999999999974
No 43
>smart00417 H4 Histone H4.
Probab=96.90 E-value=0.0018 Score=50.39 Aligned_cols=57 Identities=14% Similarity=0.258 Sum_probs=49.3
Q ss_pred chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhc
Q psy3459 118 SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFA 176 (296)
Q Consensus 118 ~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~A 176 (296)
+.+|+++... --+||.++.+.+.+...+|..-|...|..+|+-.+||||+++||..|
T Consensus 18 ~IrRLaRr~G--vkRIS~~~y~elr~vle~~l~~I~rdav~~a~ha~RKTV~~~DV~~a 74 (74)
T smart00417 18 AIRRLARRGG--VKRISGLIYDETRNVLKSFLENVVRDAVTYTEHARRKTVTAMDVVYA 74 (74)
T ss_pred HHHHHHHHcC--cchhhHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcccHHHheeC
Confidence 4466665542 35899999999999999999999999999999999999999999754
No 44
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=96.85 E-value=0.0016 Score=50.31 Aligned_cols=65 Identities=18% Similarity=0.286 Sum_probs=54.2
Q ss_pred chhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCc-cCcccHHHHhhh
Q psy3459 11 PIANVAKIMKKAIP-ESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKT-INGEDILFAMSA 75 (296)
Q Consensus 11 P~A~I~RIiK~~LP-~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKT-I~~eDVl~AL~~ 75 (296)
|..+|.||++.... +.++||+||..++.+....||..-...|.+.+...|..+ |..+|+-+.+-.
T Consensus 1 p~~li~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~pq 67 (72)
T PF09415_consen 1 PPELIARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILPQ 67 (72)
T ss_dssp -CHHHHHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCHC
T ss_pred ChHHHHHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHHH
Confidence 88999999997764 568999999999999999999999999999999999888 999999876544
No 45
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=96.80 E-value=0.005 Score=47.04 Aligned_cols=63 Identities=19% Similarity=0.294 Sum_probs=50.5
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 12 IANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 12 ~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
+..+.-++++.-|. ..+..|+.++|.+.|..||.-+++.|...|++-|-.|+...||.-.|+.
T Consensus 2 K~~l~~Lv~~iDp~-~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 2 KRKLQELVKQIDPN-EKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHHHHHHHHCC-SS-----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred hHHHHHHHHHcCCC-CCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 34677889987655 6999999999999999999999999999999999999999999888864
No 46
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=96.80 E-value=0.0063 Score=48.41 Aligned_cols=66 Identities=15% Similarity=0.168 Sum_probs=60.5
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCC---CccCcccHHHHhhhc
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKR---KTINGEDILFAMSAL 76 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~R---KTI~~eDVl~AL~~l 76 (296)
.||++.|.|||...++ ..++.+...+|.-.+.+||.-|..+|.++....+. .-|.|+||-.|...|
T Consensus 16 ~f~k~~iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 16 SFPKAAIKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred hccHHHHHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 5999999999999977 58999999999999999999999999999987655 889999999998765
No 47
>PLN00158 histone H2B; Provisional
Probab=96.73 E-value=0.0055 Score=51.42 Aligned_cols=65 Identities=18% Similarity=0.299 Sum_probs=58.5
Q ss_pred hhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcC
Q psy3459 12 IANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 77 (296)
Q Consensus 12 ~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lg 77 (296)
..-|+|++|+.-|+ ..||..|...|.-....+..-|+.+|...|.-.+|+||++.+|..|..-+-
T Consensus 30 ~~YI~kVLKQVhPd-~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 30 KIYIYKVLKQVHPD-TGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHHHHHHhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence 34699999999988 589999999999999999999999999999999999999999999976543
No 48
>PTZ00463 histone H2B; Provisional
Probab=96.67 E-value=0.0065 Score=51.04 Aligned_cols=63 Identities=21% Similarity=0.372 Sum_probs=57.2
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcC
Q psy3459 14 NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 77 (296)
Q Consensus 14 ~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lg 77 (296)
-|+|++|+.-|+ ..||..|...|.-.......-|+++|...|.-.+|+||++.+|..|..-+-
T Consensus 33 YI~KVLKqVhPd-~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL 95 (117)
T PTZ00463 33 YIFKVLKQVHPD-TGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL 95 (117)
T ss_pred HHHHHHHhhCCC-CCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence 489999999987 589999999999989998899999999999999999999999999976543
No 49
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=96.58 E-value=0.011 Score=45.11 Aligned_cols=64 Identities=20% Similarity=0.209 Sum_probs=49.9
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
-+|..+|.-+.... |-..+++|+...|..-++--|..|..+|.....+.+|++++++||-.||+
T Consensus 3 ~~~~esvk~iAes~--Gi~~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 3 VFSQESVKDIAESL--GISNLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp ---HHHHHHHHHHT--T---B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred cCCHHHHHHHHHHc--CCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 47888887777655 44579999999999999999999999999999999999999999999984
No 50
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=96.28 E-value=0.0083 Score=50.58 Aligned_cols=67 Identities=18% Similarity=0.242 Sum_probs=59.2
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.+|...|.|+||.. ...+||+.+|...+.-|.+-.+..|..-|-..|...++|-|+|.|+-.|+.
T Consensus 24 gl~fpvgrvkr~lk~~-~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIr 90 (132)
T COG5262 24 GLIFPVGRVKRLLKKG-NYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIR 90 (132)
T ss_pred CccccHHHHHHHHHcC-ccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhc
Confidence 4579999999999933 356899999999999998888888888889999999999999999999875
No 51
>PF07524 Bromo_TP: Bromodomain associated; InterPro: IPR006565 This bromodomain is found in eukaryotic transcription factors and PHD domain containing proteins (IPR001965 from INTERPRO). The tandem PHD finger-bromodomain is found in many chromatin-associated proteins. It is involved in gene silencing by the human co-repressor KRAB-associated protein 1 (KAP1). The tandem PHD finger-bromodomain of KAP1 has a distinct structure that joins the two protein modules. The first helix, alpha(Z), of an atypical bromodomain forms the central hydrophobic core that anchors the other three helices of the bromodomain on one side and the zinc binding PHD finger on the other []. The Rap1 GTPase-activating protein, Sipa1, is modulated by the cellular bromodomain protein, Brd4. Brd4 belongs to the BET family and is a multifunctional protein involved in transcription, replication, the signal transduction pathway, and cell cycle progression. All of these functions are linked to its association with acetylated chromatin. It has tandem bromodomains []. The dysregulation of the Brd4-associated pathways may play an important role in breast cancer progression []. Bovine papillomavirus type 1 E2 also binds to chromosomes in a complex with Brd4. Interaction with Brd4 is additionally important for E2-mediated transcriptional regulation [, ].
Probab=96.25 E-value=0.01 Score=45.49 Aligned_cols=52 Identities=13% Similarity=0.231 Sum_probs=49.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
.++..|.+.+..-+..||.-|...+..+|+..+|...++.||..||.++|+.
T Consensus 23 ~~~~~al~~Ltdi~~~yl~~l~~~~~~~ae~~gRt~~~~~Dv~~al~~~gi~ 74 (77)
T PF07524_consen 23 SASPSALDTLTDILQRYLQELGRTAKRYAEHAGRTEPNLQDVEQALEEMGIS 74 (77)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCC
Confidence 6888999999999999999999999999999999999999999999999984
No 52
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=95.98 E-value=0.023 Score=45.73 Aligned_cols=67 Identities=15% Similarity=0.159 Sum_probs=51.4
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcC-CCccCcccHHHHhhhc
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEK-RKTINGEDILFAMSAL 76 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~-RKTI~~eDVl~AL~~l 76 (296)
.||++.|.|||...++ +..||.....++.-.+..||-.|-.+|.+++...+ -..|.|.|+-.|...|
T Consensus 23 ~~~k~~ikkli~~~~~-~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 23 SFNKAAIKKLINQVLG-NQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp ---HHHHHHHHHHHHS--S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred cCCHHHHHHHHHHHcC-CCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 5999999999999985 36899999999999999999999999999998654 3489999999987654
No 53
>PF15630 CENP-S: Kinetochore component CENP-S; PDB: 4DRA_C 4DRB_H 3V9R_C.
Probab=95.96 E-value=0.016 Score=45.25 Aligned_cols=64 Identities=16% Similarity=0.249 Sum_probs=51.7
Q ss_pred hccchhhhhhhc-CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 115 VFQSSGTILEQQ-NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 115 Lf~~s~rimk~~-lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
|+-.++++..++ .+.++.+|+.+..+|.+.+-.++.-++..---.|+-.||+||+++||+=..+
T Consensus 7 l~~~v~ki~ee~~~~~~~~~s~~~i~al~ELv~~q~~~~a~DLe~FAkHA~R~tI~~dDV~Ll~R 71 (76)
T PF15630_consen 7 LWYTVGKIVEEEAKEKGVEVSPQFIAALTELVYKQLENLAKDLEAFAKHAGRSTINMDDVKLLAR 71 (76)
T ss_dssp HHHHHHHHHHHCCCCTTSEE-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHTT
T ss_pred HHHHHHHHHHHHHhccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHHHhh
Confidence 344567777666 4789999999999999999999999999999999999999999999985543
No 54
>KOG1745|consensus
Probab=95.78 E-value=0.0069 Score=52.22 Aligned_cols=73 Identities=15% Similarity=0.170 Sum_probs=62.7
Q ss_pred CccccCCchhHHHHHHHhhC---CCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhc
Q psy3459 4 REQDRFLPIANVAKIMKKAI---PESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSAL 76 (296)
Q Consensus 4 ~~~d~~LP~A~I~RIiK~~L---P~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~l 76 (296)
+..|+.+++.+-.|++++.- -.+.++...|..+||++++.|+--|--.+|-.|.|++|-||.+.|+--|..-.
T Consensus 58 kstdLlI~K~PFqRlvrei~q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArrir 133 (137)
T KOG1745|consen 58 KSTDLLIRKLPFQRLVREIAQDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARRIR 133 (137)
T ss_pred hhhHHHhhcCcHHHHhHHHHhcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhhcc
Confidence 35678888999999998443 34689999999999999999999999999999999999999999998876543
No 55
>PF03847 TFIID_20kDa: Transcription initiation factor TFIID subunit A; InterPro: IPR003228 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription [].; GO: 0006352 transcription initiation, DNA-dependent, 0005669 transcription factor TFIID complex; PDB: 1H3O_B.
Probab=95.74 E-value=0.025 Score=43.23 Aligned_cols=56 Identities=21% Similarity=0.274 Sum_probs=45.0
Q ss_pred hhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 124 EQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 124 k~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
-+++.|+.++..|+.+++.+.|-.||.-+++.|-..|+..+-.|+.+.||.-.|+.
T Consensus 9 v~~iDp~~~ld~~vee~Ll~laddFv~~v~~~ac~lAKhR~s~tle~~Dv~~~Ler 64 (68)
T PF03847_consen 9 VKQIDPNEKLDPDVEELLLELADDFVDDVVSFACRLAKHRKSSTLEVKDVQLHLER 64 (68)
T ss_dssp HHCC-SS----HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHHHHHHHHH
T ss_pred HHHcCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCCCHHHHHHHHHh
Confidence 35668999999999999999999999999999999999999999999999887764
No 56
>smart00428 H3 Histone H3.
Probab=95.54 E-value=0.029 Score=46.42 Aligned_cols=48 Identities=21% Similarity=0.174 Sum_probs=45.7
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 130 NETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 130 ~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
+.+++.+|..+||+++-.|+--+...||..+.-.||+||.+.|+--|.
T Consensus 51 ~~R~~~~Al~aLQeasE~ylv~lfeda~~~a~HAkRvTl~~kDi~La~ 98 (105)
T smart00428 51 DLRFQSSAIMALQEAAEAYLVGLFEDTNLLAIHAKRVTIMPKDIQLAR 98 (105)
T ss_pred CceeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCccCcHhhHHHHH
Confidence 799999999999999999999999999999999999999999996664
No 57
>smart00414 H2A Histone 2A.
Probab=95.49 E-value=0.041 Score=45.51 Aligned_cols=67 Identities=10% Similarity=0.237 Sum_probs=57.9
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||..-|.|+||+.-.. .||+..|...|..+.+-+...|-.-|...|...+++.|++.|+..|+.
T Consensus 7 gL~fPVgRi~r~Lk~~~~~-~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~ 73 (106)
T smart00414 7 GLQFPVGRIHRLLRKGTYA-KRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIR 73 (106)
T ss_pred CccCchHHHHHHHHcCccc-cccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhcc
Confidence 5789999999999986433 599999999999888888777777788889999999999999999975
No 58
>KOG1659|consensus
Probab=95.43 E-value=0.033 Score=51.29 Aligned_cols=76 Identities=16% Similarity=0.242 Sum_probs=66.1
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHH
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPL 85 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l 85 (296)
.+|.|.|.|||..- -+-.+|+.-....+.++.+.|+.-|-..+.+++...+-|||+++|+..|+..-.-.+|...+
T Consensus 13 rfp~aRiKKIMQ~d-EdIGKvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~ 88 (224)
T KOG1659|consen 13 RFPPARIKKIMQSD-EDIGKVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEV 88 (224)
T ss_pred cCCHHHHHHHHhhh-hhhhhhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHH
Confidence 58999999999854 23358999999999999999999999999999999999999999999999876666665553
No 59
>PLN00154 histone H2A; Provisional
Probab=95.27 E-value=0.048 Score=47.06 Aligned_cols=68 Identities=13% Similarity=0.217 Sum_probs=56.0
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||...|.|++|+...-..||+..|...|.-..+-+...|-.-|-..|...+++-|+|.||..|+.
T Consensus 36 gL~FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAVLEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIr 103 (136)
T PLN00154 36 GLQFPVGRIHRQLKQRVSAHGRVGATAAVYTAAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 103 (136)
T ss_pred CccCchHHHHHHHHhhhhhccccccchHHHHHHHHHHHHHHHHHHHHHHHHhhCCceecHHHhhhhcc
Confidence 57899999999999975445699999998888777665555555667778889999999999999974
No 60
>cd07979 TAF9 TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 9 (TAF9) is one of several TAFs that bind TBP and are involved in forming the TFIID complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. The TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Human TAF9 has a paralogue gene (TAF9L) whi
Probab=95.06 E-value=0.077 Score=44.40 Aligned_cols=77 Identities=13% Similarity=0.162 Sum_probs=62.8
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHH-HHHHHHHHHH
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP-LKIYLQKYRE 198 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~-l~~~L~~~re 198 (296)
.++++.+ +-..++.++...|.+-+-.++.-|...|..++.-.||+||+++||--|++..+-..|..+ -++.|-..-.
T Consensus 8 ~~iLk~~--Gv~~~~~~v~~~Lle~~~ry~~~il~dA~~~a~hA~r~tV~~eDV~lAi~~r~~~~f~~~p~~~~l~~~a~ 85 (117)
T cd07979 8 AAILKSM--GITEYEPRVINQLLEFAYRYTTDVLDDAKVYSEHAGKANIDADDVKLAIQSRVDYSFTSPPPRDFLLELAR 85 (117)
T ss_pred HHHHHHC--CCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHhccCCCCCCcHHHHHHHHH
Confidence 4555554 224799999999999999999999999999999999999999999999988776555554 6666655544
No 61
>smart00427 H2B Histone H2B.
Probab=95.03 E-value=0.05 Score=43.81 Aligned_cols=60 Identities=22% Similarity=0.312 Sum_probs=51.4
Q ss_pred hhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 121 TILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 121 rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
+.+|+.. |+..||+.|...+.--...+..-|+++|...|+..+|+||++.+|..|.+-+=
T Consensus 9 kvLKqVh-pd~giS~kam~imnSfvnDiferIa~EAs~L~~~nkr~TltsreIqtAvrl~L 68 (89)
T smart00427 9 KVLKQVH-PDTGISSKAMSIMNSFVNDIFERIAAEASKLARYNKKSTLSSREIQTAVRLIL 68 (89)
T ss_pred HHHHHhC-CCccccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHHc
Confidence 4445444 56699999999999888888889999999999999999999999999987653
No 62
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=94.94 E-value=0.047 Score=45.07 Aligned_cols=78 Identities=17% Similarity=0.224 Sum_probs=65.3
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHH
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKI 87 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~ 87 (296)
.+|.|.|.|||.-- -+-.+|+.-......++.+.|+..|-..+...++..+-|-|+.+++..|.+.-+=.+|...+..
T Consensus 23 rFP~ar~KkIMQ~d-eDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sdekFdFL~~~~~ 100 (113)
T COG5247 23 RFPIARLKKIMQLD-EDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDEKFDFLKNMEQ 100 (113)
T ss_pred cCCHHHHHHHHHhh-hhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhHHHHHHHHHHH
Confidence 58999999999743 2335899999999999999999999999999999999999999999999876555555544433
No 63
>cd08050 TAF6 TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 6 (TAF6) is one of several TAFs that bind TBP and are involved in forming Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTFs) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs are named after their electrophoretic mobility in polyacrylamide gels in different species. A new, unified nomenclature has been suggested for the pol II TAFs to show the relationship between TAF orthologs and paralogs. Several hypotheses are proposed for TAFs functions such as serving as
Probab=94.88 E-value=0.044 Score=53.37 Aligned_cols=52 Identities=17% Similarity=0.228 Sum_probs=50.0
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
++++||..++.+.+..++.-|..+|...++..+|||++++||-.||+.++.+
T Consensus 16 ~~~~~a~~~La~~~e~~~~~i~~~A~k~~~hskR~~l~~~Di~~Al~~~n~e 67 (343)
T cd08050 16 SLSDEVAQLLAEDVEYRLREIIQEAAKFMRHSKRRKLTTSDVNHALRLRNVE 67 (343)
T ss_pred cCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCcCCHHHHHHHHHHhCCC
Confidence 8999999999999999999999999999999999999999999999987764
No 64
>KOG1756|consensus
Probab=94.61 E-value=0.086 Score=45.04 Aligned_cols=67 Identities=12% Similarity=0.235 Sum_probs=54.0
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.+|...|.|++|+. --..+|+.+|...+.-+.+-....|..-|-..+..+++.-|+|.|+..|+.
T Consensus 25 gl~fPvgri~r~Lr~~-~~~~ri~~gapV~laavLeYL~Aeile~agnaardnkk~ri~PrH~~lAI~ 91 (131)
T KOG1756|consen 25 GLQFPVGRIHRLLRKG-RYAQRVGAGAPVYLAAVLEYLTAEILELAGNAARDNKKTRITPRHLQLAIR 91 (131)
T ss_pred ccccCHHHHHHHHHcc-chhhhccCCChHHHHHHHHHHHHHHHHHhHHHhhhcCccccChHHHHHHHh
Confidence 5679999999999983 234799999999998666555555556666667788999999999999985
No 65
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=94.52 E-value=0.048 Score=43.82 Aligned_cols=60 Identities=22% Similarity=0.335 Sum_probs=30.0
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 15 VAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 15 I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
|..||- +.++...-..|+..+|-+...+||..+...|..+|...|+++|+.+|++-+|..
T Consensus 7 I~~mMy-~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 7 IRQMMY-GFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CHHHHH-CTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HHHHHH-HcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 345555 345556788999999999999999999999999999999999999999999864
No 66
>PTZ00017 histone H2A; Provisional
Probab=94.29 E-value=0.095 Score=45.17 Aligned_cols=67 Identities=16% Similarity=0.223 Sum_probs=57.9
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||..-|.|+|++.--. .||+..|...|.-+.+-+...|-.-|...|...+++-|+|.||..|+.
T Consensus 25 gL~FPVgRi~R~Lk~g~~a-~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~ 91 (134)
T PTZ00017 25 GLQFPVGRVHRYLKKGRYA-KRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIR 91 (134)
T ss_pred CcccchHHHHHHHhccchh-ccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhcc
Confidence 5789999999999986433 599999999999888888777777788889999999999999999974
No 67
>KOG1744|consensus
Probab=94.21 E-value=0.15 Score=43.62 Aligned_cols=61 Identities=30% Similarity=0.381 Sum_probs=56.1
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 14 NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 14 ~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
.|.|++|++-|+ ..||..+...+.-....+..-|+++|+..+.-.+|.||+..++..|..-
T Consensus 42 yv~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rL 102 (127)
T KOG1744|consen 42 YVYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRL 102 (127)
T ss_pred ehhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHH
Confidence 478899999998 6799999999999999999999999999999999999999999888643
No 68
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=94.16 E-value=0.18 Score=43.06 Aligned_cols=84 Identities=19% Similarity=0.230 Sum_probs=49.3
Q ss_pred cccCCchh--HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh-hcCCCcch
Q psy3459 6 QDRFLPIA--NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS-ALGFDSYV 82 (296)
Q Consensus 6 ~d~~LP~A--~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~-~lgF~~yv 82 (296)
..-.+|+. .|.-|+|+. +-......+...|.+.+-.|+.-|-..|..++.++||++|+.+||..|++ .+++.-..
T Consensus 7 ~~~~~PrDa~~i~~iL~~~--Gv~~yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~ 84 (129)
T PF02291_consen 7 QSKSLPRDARVIHLILKSM--GVTEYEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQ 84 (129)
T ss_dssp ------HHHHHHHHHHHHT--T---B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT-------
T ss_pred CCccCChHHHHHHHHHHHc--CCcccCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccC
Confidence 34467775 667777766 44467778888899999999999999999999999999999999999998 56666555
Q ss_pred HHHHHHHHH
Q psy3459 83 EPLKIYLQK 91 (296)
Q Consensus 83 ~~l~~~L~~ 91 (296)
++-+++|..
T Consensus 85 pppre~lle 93 (129)
T PF02291_consen 85 PPPREFLLE 93 (129)
T ss_dssp ---------
T ss_pred CCChHHHHH
Confidence 555554443
No 69
>PF15510 CENP-W: Centromere kinetochore component W
Probab=93.90 E-value=0.089 Score=42.69 Aligned_cols=66 Identities=20% Similarity=0.212 Sum_probs=53.8
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHH--------------HHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDAREC--------------VQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~a--------------l~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.-|+..+.|++|..-|. .++....-.+ +.--|-.|++-|+-+|..-|-.++-.||.++||+.|.+
T Consensus 16 kaPrgfLkrv~Kr~Kph-lRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 16 KAPRGFLKRVFKRQKPH-LRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred hCchHHHHHHHHhcCCc-eeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 46999999999977665 4655544333 55668899999999999999999999999999999865
Q ss_pred h
Q psy3459 75 A 75 (296)
Q Consensus 75 ~ 75 (296)
.
T Consensus 95 v 95 (102)
T PF15510_consen 95 V 95 (102)
T ss_pred H
Confidence 3
No 70
>KOG3467|consensus
Probab=93.86 E-value=0.098 Score=42.17 Aligned_cols=52 Identities=21% Similarity=0.289 Sum_probs=45.7
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
+|+--.-+-+.+.+.+||.-+-+-|-.+++..+||||++-||+-+|+..|-.
T Consensus 46 Ri~G~~yeE~~~~~k~fl~n~i~~A~~yt~HAKRKTvT~~dvv~~LKR~G~~ 97 (103)
T KOG3467|consen 46 RISGLIYEETRGVLKVFLENVIRDAVTYTEHAKRKTVTAMDVVYALKRQGRT 97 (103)
T ss_pred hhchhhHHHHHHHHHHHHHHHHHHHHHHHhhhhhceeeHHHHHHHHHHcCce
Confidence 4555566677889999999999999999999999999999999999998753
No 71
>PLN00156 histone H2AX; Provisional
Probab=93.56 E-value=0.17 Score=43.81 Aligned_cols=67 Identities=13% Similarity=0.202 Sum_probs=55.8
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||...|.|++++.--. .||+..|...|.-+.+-....|-.-|-..|...+++-|+|.||..|+.
T Consensus 27 gL~FPVgRi~R~Lk~g~ya-~RVga~ApVYLAAVLEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIr 93 (139)
T PLN00156 27 GLQFPVGRIARFLKAGKYA-ERVGAGAPVYLSAVLEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVR 93 (139)
T ss_pred CcccchHHHHHHHhcCChh-hccCCccHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhcc
Confidence 5789999999999986433 599999999988887766666666677778889999999999999974
No 72
>PLN00153 histone H2A; Provisional
Probab=93.50 E-value=0.17 Score=43.40 Aligned_cols=67 Identities=16% Similarity=0.219 Sum_probs=57.2
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.+|..-|.|++++.-.. .||+..|...|.-+.+-....|-.-|...|...+++-|+|.||..|+.
T Consensus 22 gL~FpVgRi~R~Lr~g~~a-~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 88 (129)
T PLN00153 22 GLQFPVGRIARYLKKGKYA-ERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIR 88 (129)
T ss_pred CcccchHHHHHHHhcCchh-hccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhcc
Confidence 5789999999999986443 599999999998887777777777777888899999999999999974
No 73
>PLN00157 histone H2A; Provisional
Probab=93.47 E-value=0.15 Score=43.80 Aligned_cols=67 Identities=13% Similarity=0.186 Sum_probs=56.6
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
.+.||..-|.|++|+.--. .||+..|...|.-+.+-....|-.-|...|...+++-|++.||..|+.
T Consensus 24 gL~FPVgRi~R~Lk~g~~a-~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~ 90 (132)
T PLN00157 24 GLQFPVGRIARYLKAGKYA-TRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVR 90 (132)
T ss_pred CcccchHHHHHHHhcCchh-hhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhccc
Confidence 5789999999999986433 599999999998887777777767777788899999999999999974
No 74
>PTZ00463 histone H2B; Provisional
Probab=93.43 E-value=0.18 Score=42.43 Aligned_cols=60 Identities=20% Similarity=0.334 Sum_probs=50.8
Q ss_pred hhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 121 TILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 121 rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
+.+|+. -|+..||..|...|.--......-|+++|...|+-.+|+||++.+|..|.+-+=
T Consensus 36 KVLKqV-hPd~gIS~kaM~ImnSfvnDifErIA~EAs~La~~nkr~TltsrEIQtAvrLlL 95 (117)
T PTZ00463 36 KVLKQV-HPDTGISRKSMNIMNSFLVDTFEKIATEASRLCKYTRRDTLSSREIQTAIRLVL 95 (117)
T ss_pred HHHHhh-CCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCcCCHHHHHHHHhhcc
Confidence 444444 456789999999999888888889999999999999999999999999977553
No 75
>PLN00158 histone H2B; Provisional
Probab=93.33 E-value=0.18 Score=42.46 Aligned_cols=61 Identities=18% Similarity=0.253 Sum_probs=51.5
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
-+.+|+ .-|+..||..+...|.--...+..-|+++|...|+-.+|+||++.+|..|.+-+=
T Consensus 34 ~kVLKQ-VhPd~gIS~kaM~ImnSfvnDiferIA~EAs~La~~nkr~TltsrEIqtAvrLvL 94 (116)
T PLN00158 34 YKVLKQ-VHPDTGISSKAMSIMNSFINDIFEKIATEAGKLARYNKKPTVTSREIQTAVRLIL 94 (116)
T ss_pred HHHHHH-hCCCCCccHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCcCCHHHHHHHHHHhc
Confidence 344444 4456789999999999888888889999999999999999999999999977553
No 76
>PF02269 TFIID-18kDa: Transcription initiation factor IID, 18kD subunit; InterPro: IPR003195 This family includes the Spt3 yeast transcription factors and the 18 kDa subunit from human transcription initiation factor IID (TFIID-18). Determination of the crystal structure reveals an atypical histone fold [].; GO: 0006366 transcription from RNA polymerase II promoter; PDB: 1BH9_A 1BH8_A.
Probab=93.29 E-value=0.12 Score=41.47 Aligned_cols=54 Identities=26% Similarity=0.335 Sum_probs=27.4
Q ss_pred cCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 126 QNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 126 ~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
..++.-.-..|+..+|-+-..+||.-+...|..+|...|+++|+.+|++-+|+.
T Consensus 13 ~fGD~~~P~~eTv~lvE~iv~~~i~~l~~~A~~~a~~rg~~~i~~eDl~F~lR~ 66 (93)
T PF02269_consen 13 GFGDVEEPLPETVDLVEDIVREYIIELCQEAMEVAQRRGSKKIKVEDLLFLLRK 66 (93)
T ss_dssp CTTS-SS--HHHHHHHHHHHHHHHHHHHHHHHC---------------------
T ss_pred HcCCCCCCcHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCcCcHHHHHHHHhc
Confidence 456666788999999999999999999999999999999999999999999985
No 77
>KOG1142|consensus
Probab=92.97 E-value=0.19 Score=47.52 Aligned_cols=66 Identities=17% Similarity=0.287 Sum_probs=58.3
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
-|=+--+.-+++..- +...|.+|+.++|.+.|..||.-|+..|..+|+|-+..||-+-||...|+.
T Consensus 154 il~k~kl~dLvqqId-~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 154 ILSKRKLDDLVQQID-GTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred cccccchhHHHHhhc-CcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 344556778888774 447999999999999999999999999999999999999999999999984
No 78
>KOG1657|consensus
Probab=92.30 E-value=0.18 Score=47.14 Aligned_cols=82 Identities=21% Similarity=0.214 Sum_probs=61.6
Q ss_pred hccchhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhc---CCccchHHHHH
Q psy3459 115 VFQSSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSAL---GFDSYVEPLKI 191 (296)
Q Consensus 115 Lf~~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~L---gF~~yv~~l~~ 191 (296)
|+....+++.+.-++-=.|+.||--++.+||-.||..||..|...+.+.+|+|+...|+-.|+..- +|--.+-|-+.
T Consensus 75 lPlaRiKkimK~dedv~mI~~Eapvl~aka~E~Fi~elt~~sw~~Tee~~rrtl~~sdia~av~~s~~fdFL~DivP~~~ 154 (236)
T KOG1657|consen 75 LPLARIKKIMKSDEDVSMITAEAPVLFAKACELFITELTLRSWVHTEENKRRTLQKSDIAAAVTQSETFDFLRDIVPRKI 154 (236)
T ss_pred CcHhhccccccccccccccchhHHHHHHHHHHHHHHHHHHHhhhhhcccccccchHHHHHHHhccCCCccceeccccchh
Confidence 334444444444443339999999999999999999999999999999999999999999999873 34333344445
Q ss_pred HHHHH
Q psy3459 192 YLQKY 196 (296)
Q Consensus 192 ~L~~~ 196 (296)
....|
T Consensus 155 ~~~~~ 159 (236)
T KOG1657|consen 155 LAEKY 159 (236)
T ss_pred ccccc
Confidence 55555
No 79
>PLN00161 histone H3; Provisional
Probab=92.18 E-value=0.36 Score=41.68 Aligned_cols=51 Identities=20% Similarity=0.168 Sum_probs=46.8
Q ss_pred CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 127 NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 127 lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
.+.+.+++.+|..|||+++-.|+--+-..||-.|.-.+|-||.+.|+.-|.
T Consensus 73 ~~~~~Rfq~~Al~ALQEAsEayLV~lFeda~lcaiHAkRVTlm~kDm~La~ 123 (135)
T PLN00161 73 LREPFRWTAEALLALQEATEDFLVHLFEDCNLCAIHAKRVTIMPKDMQLAR 123 (135)
T ss_pred CCCCcEeeHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcCcccchhhHHHHH
Confidence 345799999999999999999999999999999999999999999996654
No 80
>PLN00160 histone H3; Provisional
Probab=92.07 E-value=0.38 Score=39.37 Aligned_cols=50 Identities=18% Similarity=0.078 Sum_probs=46.1
Q ss_pred CCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 128 GQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 128 p~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
+.+.+++.+|..|+|+++--|+--+-..||-.|.-.||-||.+.|+--|.
T Consensus 40 ~~~~Rfq~~Al~ALQeAsEayLv~lfed~~lca~HakRVTl~~kD~~L~~ 89 (97)
T PLN00160 40 REAYRWQGSAILALQEAAEAHLVGLFEDSNLCAIHGKRVTIMPKDMQLAR 89 (97)
T ss_pred CCCcEeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcccccchhhHHHHH
Confidence 46699999999999999999999999999999999999999999996554
No 81
>KOG1658|consensus
Probab=91.84 E-value=0.13 Score=45.40 Aligned_cols=67 Identities=24% Similarity=0.313 Sum_probs=56.8
Q ss_pred cCCchhHHHHHHHhhCCCCCc-ccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhc
Q psy3459 8 RFLPIANVAKIMKKAIPESGK-IAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSAL 76 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~r-ISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~l 76 (296)
..||++.|..++|- +++.+ ..+++..++.+++..||..|+..+...+...+|||+.--|+-.|++..
T Consensus 58 ~rLpL~rik~vvkl--~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~kt~qr~d~D~ai~~~ 125 (162)
T KOG1658|consen 58 SRLPLARIKQVVKL--DPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKRKTEQRRDYDTAIEAV 125 (162)
T ss_pred hhccHHHHHhhccC--CcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHhhhhhhhcccccccch
Confidence 57999999999973 45555 566788889999999999999999999999999999998887776543
No 82
>PF15511 CENP-T: Centromere kinetochore component CENP-T; PDB: 3B0D_T 3B0C_T 3VH5_T 3VH6_T.
Probab=91.76 E-value=0.21 Score=50.01 Aligned_cols=46 Identities=26% Similarity=0.367 Sum_probs=36.6
Q ss_pred CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchh
Q psy3459 127 NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGED 172 (296)
Q Consensus 127 lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eD 172 (296)
...+++|+|||.++|.+|.-.|-.-|..-=-.+|.-.|||||..+|
T Consensus 369 ~~sK~kiskdal~aleqasdwfFeQl~dDL~aYA~HAgRKTIdesD 414 (414)
T PF15511_consen 369 GGSKMKISKDALEALEQASDWFFEQLGDDLEAYAKHAGRKTIDESD 414 (414)
T ss_dssp ----S-B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SEE-HHH
T ss_pred cccCCccCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCcCCCCC
Confidence 4578999999999999999999999999999999999999998876
No 83
>cd08048 TAF11 TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 11 (TAF11) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypothes
Probab=91.60 E-value=0.45 Score=37.85 Aligned_cols=60 Identities=15% Similarity=0.168 Sum_probs=51.0
Q ss_pred hhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCC---CcccchhHhhchhhc
Q psy3459 119 SGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKR---KTINGEDILFAMSAL 180 (296)
Q Consensus 119 s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kR---KTI~~eDVl~AL~~L 180 (296)
+.+++...++ .+++.+...+|.-.+.+||.=|..+|.++..+.+. .-|.|+||-.|...|
T Consensus 22 iKr~~~~~~~--~~v~~~v~i~v~glaKvFVGeivE~A~~V~~~~~~~~~~Pl~P~HireA~rrl 84 (85)
T cd08048 22 IKRLIQSVTG--QSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGEANTGPLQPRHLREAYRRL 84 (85)
T ss_pred HHHHHHHHcC--CCCCchHHHHHHHHHHHHHHHHHHHHHHHHHHhccccCCCCCcHHHHHHHHHh
Confidence 3455443343 78999999999999999999999999999998776 889999999998876
No 84
>KOG3219|consensus
Probab=91.56 E-value=0.21 Score=45.56 Aligned_cols=69 Identities=16% Similarity=0.180 Sum_probs=60.7
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcC-CCccCcccHHHHhhhcCCC
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEK-RKTINGEDILFAMSALGFD 79 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~-RKTI~~eDVl~AL~~lgF~ 79 (296)
.||+|.|.|||....+. .|+.-+..+++-.+.+||--|--+|.++|..-+ ---|.|.||-.|...|+..
T Consensus 112 ~f~Ka~iKkL~~~itg~--~v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 112 AFPKAQIKKLMSSITGQ--SVSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred cCCHHHHHHHHHHHhCC--ccCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 69999999999998765 399999999999999999999999999998755 4569999999998877654
No 85
>cd00074 H2A Histone 2A; H2A is a subunit of the nucleosome. The nucleosome is an octamer containing two H2A, H2B, H3, and H4 subunits. The H2A subunit performs essential roles in maintaining structural integrity of the nucleosome, chromatin condensation, and binding of specific chromatin-associated proteins.
Probab=91.41 E-value=0.39 Score=40.31 Aligned_cols=63 Identities=14% Similarity=0.163 Sum_probs=51.1
Q ss_pred cc--chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 116 FQ--SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 116 f~--~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
|+ .+.|+|++... ..+|+.+|.-.+..+.-.+..=|...|...|+..+|++|+|+||-.|+..
T Consensus 21 fPV~ri~R~Lk~~~~-a~RVs~~A~VyLaAvLEYL~aEIlelA~n~ak~~k~krItp~hi~lAi~n 85 (115)
T cd00074 21 FPVGRIHRYLKKGRY-AERVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKKRITPRHLQLAVRN 85 (115)
T ss_pred CcHHHHHHHHHcCcc-ccccccchHHHHHHHHHHHHHHHHHHHHHHHHHcCCCeEcHHHHHHHHhc
Confidence 55 34677765332 37999999999998887777778888889999999999999999999765
No 86
>KOG1658|consensus
Probab=91.39 E-value=0.6 Score=41.27 Aligned_cols=113 Identities=23% Similarity=0.257 Sum_probs=82.5
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHH
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKI 87 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~ 87 (296)
.-||.+-+.||-|.. |.-+.=+.+|..+..-+...|+.-++.-+. .-
T Consensus 10 p~~p~ekvkkiak~d-Pey~~te~~a~~etafatE~fvq~lv~~p~-----------------a~--------------- 56 (162)
T KOG1658|consen 10 PKLPMEKVKKIAKND-PEYMDTEDDAFVETAFATEQFVQVLVHLPQ-----------------AS--------------- 56 (162)
T ss_pred ccccHHHHHHhhcCC-chhhhcccchHHHHHHHHHHHHhhhhhhhh-----------------hh---------------
Confidence 468999999998865 665667778877777888888777765110 00
Q ss_pred HHHHHHHHhccccccchhhhhhhhhhhhccch-hhhhhhcCCCccccchH-HHHHHHHHHHHHHHHHHHHhhHHhhhcCC
Q psy3459 88 YLQKYREATKGEKSVNCEVYQEISVEDVFQSS-GTILEQQNGQNETIAKD-ARECVQECVSEFISFITSEASDRCHLEKR 165 (296)
Q Consensus 88 ~L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s-~rimk~~lp~~~~iskd-Akeai~~caseFI~~lts~An~~c~~~kR 165 (296)
++ .|..++ ..++ -++|++.++.| +..++.+++--||..|+..|...+...+|
T Consensus 57 ----------------------l~--rLpL~rik~vv--kl~pdl~l~~dea~~l~a~aaelfi~~Ln~~~~~~~q~~k~ 110 (162)
T KOG1658|consen 57 ----------------------LS--RLPLARIKQVV--KLDPDLTLLNDEASQLIAKAAELFIQELNDVAYTTAQLRKR 110 (162)
T ss_pred ----------------------hh--hccHHHHHhhc--cCCcchhhhhhHHHHHHHHHHHHHHHHHHhccchhHHHHHh
Confidence 11 222322 3333 46788888765 88899999999999999999999999999
Q ss_pred CcccchhHhhchhh
Q psy3459 166 KTINGEDILFAMSA 179 (296)
Q Consensus 166 KTI~~eDVl~AL~~ 179 (296)
||+.--|+=.|.+.
T Consensus 111 kt~qr~d~D~ai~~ 124 (162)
T KOG1658|consen 111 KTEQRRDYDTAIEA 124 (162)
T ss_pred hhhhhhcccccccc
Confidence 99988777666544
No 87
>PTZ00018 histone H3; Provisional
Probab=89.92 E-value=0.56 Score=40.55 Aligned_cols=51 Identities=20% Similarity=0.134 Sum_probs=47.0
Q ss_pred CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 127 NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 127 lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
...+.+++.+|..+||+++-.|+--+-..+|-.+.-.+|-||.+.|+.-|.
T Consensus 79 ~~~~~rf~~~al~aLQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PTZ00018 79 FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred cCCcceeeHHHHHHHHHHHHHHHHHHhhhhHHHHHhhcceecchhhHHHHH
Confidence 456899999999999999999999999999999999999999999996554
No 88
>PLN00121 histone H3; Provisional
Probab=89.59 E-value=0.63 Score=40.25 Aligned_cols=51 Identities=20% Similarity=0.134 Sum_probs=46.9
Q ss_pred CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 127 NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 127 lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
...+.+++.+|..+||+++-.|+--+-..+|-.+.-.+|-||.+.|+.-++
T Consensus 79 ~~~~~Rf~~~Al~ALQeaaE~yLv~lfed~~lca~HakRVTl~~kD~~L~~ 129 (136)
T PLN00121 79 FKTDLRFQSSAVLALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLAR 129 (136)
T ss_pred hCccceeeHHHHHHHHHHHHHHHHHHHhhhHHHHHHhcceecchhhHHHHH
Confidence 346899999999999999999999999999999999999999999996554
No 89
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=89.50 E-value=1.7 Score=35.01 Aligned_cols=83 Identities=16% Similarity=0.264 Sum_probs=57.1
Q ss_pred hHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHH
Q psy3459 13 ANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKY 92 (296)
Q Consensus 13 A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~ 92 (296)
.-|..||-. .++...-..|+..+|-+...+||.-+..+|.++|. .++.-++.||++-+|..= ...+.-++.+|.--
T Consensus 6 ~ei~~mmy~-~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~~k 81 (92)
T cd07978 6 KEIRQMMYG-FGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLSMK 81 (92)
T ss_pred HHHHHHHHH-cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHHHH
Confidence 346666763 34545678899999999999999999999999999 444445999999998531 12333444544433
Q ss_pred HHHhccc
Q psy3459 93 REATKGE 99 (296)
Q Consensus 93 re~~k~k 99 (296)
....+.+
T Consensus 82 ~~~k~ar 88 (92)
T cd07978 82 DELKKAR 88 (92)
T ss_pred HHHHHHH
Confidence 3333333
No 90
>PF02969 TAF: TATA box binding protein associated factor (TAF); InterPro: IPR004823 The TATA box binding protein associated factor (TAF) is part of the transcription initiation factor TFIID multimeric protein complex. TFIID plays a central role in mediating promoter responses to various activators and repressors. It binds tightly to TAFII-250 and directly interacts with TAFII-40. TFIID is composed of TATA binding protein (TBP)and a number of TBP-associated factors (TAFS). TAF proteins adopt a histone-like fold.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus; PDB: 1TAF_B.
Probab=89.18 E-value=0.91 Score=34.58 Aligned_cols=47 Identities=23% Similarity=0.237 Sum_probs=40.9
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
.++.|+..+|.+=+.--|..|-.+|..+.+..+|++++++||=.||+
T Consensus 20 ~l~de~a~~La~dveyrlreiiq~a~kfm~hskR~~Lt~~Di~~ALr 66 (66)
T PF02969_consen 20 NLSDEAAKALAEDVEYRLREIIQEALKFMRHSKRTKLTTDDINSALR 66 (66)
T ss_dssp -B-HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHH-
T ss_pred CCCHHHHHHHHHHHHHHHHHHHHHHHHHHHHhCCCCCCHHHHHHHhC
Confidence 69999999999999999999999999999999999999999998874
No 91
>TIGR02639 ClpA ATP-dependent Clp protease ATP-binding subunit clpA.
Probab=89.07 E-value=1.4 Score=46.91 Aligned_cols=94 Identities=19% Similarity=0.139 Sum_probs=56.9
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHHHHhccccccchhhhhhhhhhhhccchhhhhhhcC---
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQQN--- 127 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~~l--- 127 (296)
.|...|..-+...|+++|++.|| |.-++ ....|.. .+++.+.|-....+.+...+
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaL--L~~~~----~~~iL~~----------------~gid~~~l~~~l~~~l~~~~p~~ 68 (731)
T TIGR02639 11 AALEEAKKRRHEFVTLEHILLAL--LFDSD----AIEILEE----------------CGGDVEALRKDLEDYLENNLPSI 68 (731)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHH--HcCch----HHHHHHH----------------cCCCHHHHHHHHHHHHhhcCCCC
Confidence 47778999999999999999997 32222 1122221 12222233222222221111
Q ss_pred ----CCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 128 ----GQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 128 ----p~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
+.....|..++.++..+ ...+...+...|+++|+|-||-
T Consensus 69 ~~~~~~~~~~S~~lk~vL~~A------------~~~A~~~g~~~I~teHLLLALl 111 (731)
T TIGR02639 69 TEENEADPEQTVGVQRVLQRA------------LLHVKSAGKKEIGIGDILVALF 111 (731)
T ss_pred CCCCCCCCCcCHHHHHHHHHH------------HHHHHHcCCCccCHHHHHHHHh
Confidence 12356788888888774 3445666899999999998864
No 92
>PTZ00252 histone H2A; Provisional
Probab=89.01 E-value=1.2 Score=38.54 Aligned_cols=67 Identities=9% Similarity=0.197 Sum_probs=48.3
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHh--cCCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHL--EKRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~--~~RKTI~~eDVl~AL~ 74 (296)
.+.||...|.|++++.--. .||+.-|...|.-+.+-....|-.-|...|.. .+++-|+|.||..|+.
T Consensus 23 GL~FPVgRi~R~Lr~g~ya-~RIga~ApVYLAAVLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIr 91 (134)
T PTZ00252 23 GLIFPVGRVGSLLRRGQYA-RRIGASGAVYMAAVLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVR 91 (134)
T ss_pred CccCchHHHHHHHHcCCcc-cccCCccHHHHHHHHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhcc
Confidence 5789999999999987543 59999998887765443333333334444433 5678899999999974
No 93
>KOG1744|consensus
Probab=88.32 E-value=1.1 Score=38.32 Aligned_cols=61 Identities=28% Similarity=0.320 Sum_probs=52.9
Q ss_pred hhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhc
Q psy3459 119 SGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSAL 180 (296)
Q Consensus 119 s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~L 180 (296)
+.+.+++..|+ .-|+..+..++.--..++.--|+++|+..++-.+|.||+..++..|..-|
T Consensus 43 v~kvlk~Vhpd-~gis~~a~~vmnsf~ndife~iA~ea~rla~y~krstisSreiqta~rLl 103 (127)
T KOG1744|consen 43 VYKVLKQVHPD-LGISSKAMGVMNSFVNDIFERIASEAGRLAHYNKRSTISSREIQTAVRLL 103 (127)
T ss_pred hhhhhhcccCC-CCcCHHHHHHHHHHHHHHHHHHHHHHhhhhhhcCCCcccHHHHHHHHHHh
Confidence 34566666666 77999999999999999999999999999999999999999999886543
No 94
>KOG3423|consensus
Probab=86.35 E-value=3.1 Score=37.30 Aligned_cols=70 Identities=21% Similarity=0.277 Sum_probs=56.7
Q ss_pred cCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcC--------------CCccCcccHHHHh
Q psy3459 8 RFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEK--------------RKTINGEDILFAM 73 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~--------------RKTI~~eDVl~AL 73 (296)
..||-+.+.-.++.+ +-.....-.+.++.-++-.||+-|+..|.+.|+-.+ |-|++-+|+-.||
T Consensus 85 P~IPDavt~~yL~~a--Gf~~~D~rv~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL 162 (176)
T KOG3423|consen 85 PTIPDAVTDHYLKKA--GFQTSDPRVKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPAL 162 (176)
T ss_pred CCCcHHHHHHHHHhc--CCCcCcHHHHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHH
Confidence 369999999999876 422344455668999999999999999999997543 5689999999999
Q ss_pred hhcCCC
Q psy3459 74 SALGFD 79 (296)
Q Consensus 74 ~~lgF~ 79 (296)
.+.|+.
T Consensus 163 ~EyGin 168 (176)
T KOG3423|consen 163 AEYGIN 168 (176)
T ss_pred HHhCcc
Confidence 999985
No 95
>KOG1142|consensus
Probab=86.00 E-value=1.2 Score=42.18 Aligned_cols=55 Identities=20% Similarity=0.290 Sum_probs=51.5
Q ss_pred hcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 125 QQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 125 ~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
+.+..+.+|-.|+.++|.+-|-.||.-|+..|-..|+..+..||-+-||.-.|+.
T Consensus 165 qqId~~~~LD~dVedlLleiADdFV~sii~~sC~LAKHRKsdtlEvrDIqLhLEr 219 (258)
T KOG1142|consen 165 QQIDGTTKLDDDVEDLLLEIADDFVSSIIHRSCKLAKHRKSDTVEVRDIQLHLER 219 (258)
T ss_pred HhhcCcccccHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCccchhheeeeeec
Confidence 4557889999999999999999999999999999999999999999999998875
No 96
>CHL00095 clpC Clp protease ATP binding subunit
Probab=85.19 E-value=2.9 Score=45.18 Aligned_cols=96 Identities=13% Similarity=0.139 Sum_probs=56.2
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHHHHhccccccchhhhhhhhhhhhccchhhhhhh--c-C
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQ--Q-N 127 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~--~-l 127 (296)
.|.+.|..-+...|+++|++.||=.-+-+ .....|.. .+++.+.|.....+.+.. . .
T Consensus 15 ~A~~~A~~~~h~~V~~EHLLLaLL~~~~~----~a~~iL~~----------------~gid~~~l~~~l~~~l~~~~~~~ 74 (821)
T CHL00095 15 LSQEEARRLGHNFVGTEQILLGLIGEGTG----IAARALKS----------------MGVTLKDARIEVEKIIGRGTGFV 74 (821)
T ss_pred HHHHHHHHhCCCcCcHHHHHHHHHhCCCc----hHHHHHHH----------------cCCCHHHHHHHHHHHHhcCCCCC
Confidence 47788999999999999999998322211 11222222 112222222211111110 0 1
Q ss_pred CCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 128 GQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 128 p~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
+....+|..+..++..| ...|...+...|+++|+|.||=
T Consensus 75 ~~~~~~S~~~~~vL~~A------------~~~A~~~~~~~I~~eHLLlALL 113 (821)
T CHL00095 75 AVEIPFTPRAKRVLEMS------------LEEARDLGHNYIGTEHLLLALL 113 (821)
T ss_pred ccccccCHHHHHHHHHH------------HHHHHHhCCCcccHHHHHHHHH
Confidence 12356788888888764 4556666888999999999873
No 97
>COG5208 HAP5 CCAAT-binding factor, subunit C [Transcription]
Probab=84.02 E-value=0.69 Score=43.10 Aligned_cols=66 Identities=18% Similarity=0.214 Sum_probs=54.9
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccch
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYV 186 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv 186 (296)
++.||..-.-. -||.||--++.+.|-.||.-||-.|--.+++.+|+|+.-.||-.|++.-+.-+|.
T Consensus 116 kkvMKtdedVk-MisaEaPvlFak~~EiFI~ELTmRAW~~ae~NkRRtLQksDia~Av~kSeMfDFL 181 (286)
T COG5208 116 KKVMKTDEDVK-MISAEAPVLFAKITEIFIEELTMRAWINAEENKRRTLQKSDIAAAVKKSEMFDFL 181 (286)
T ss_pred HHHHhcccchh-heecccchHHHHHHHHHHHHHHHHHHHHHhHhhhhHHHHHHHHHHHHHHHHHhHH
Confidence 55555432222 4899999999999999999999999999999999999999999999987765543
No 98
>KOG4336|consensus
Probab=82.73 E-value=5.7 Score=38.70 Aligned_cols=77 Identities=22% Similarity=0.325 Sum_probs=63.2
Q ss_pred HHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHH
Q psy3459 14 NVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYR 93 (296)
Q Consensus 14 ~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~r 93 (296)
+|.-|.+.. +--.|++-|.+.|.+....+|.-+..++..+|.++||.-.|.-||-.+|-.+|+. ++.|..+++.+-
T Consensus 10 VV~~Ll~~~--gfd~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~~~ 85 (323)
T KOG4336|consen 10 VVSNLLKTK--GFDSISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQKQE 85 (323)
T ss_pred HHHHHHHHh--CchHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHhcc
Confidence 445555554 2236999999999999999999999999999999999999999999999999998 456666665544
Q ss_pred H
Q psy3459 94 E 94 (296)
Q Consensus 94 e 94 (296)
.
T Consensus 86 ~ 86 (323)
T KOG4336|consen 86 F 86 (323)
T ss_pred c
Confidence 3
No 99
>cd07978 TAF13 The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 13 (TAF13) is one of several TAFs that bind TBP and is involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryotes. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAFs orthologs and paralogs. Several hy
Probab=82.72 E-value=3.4 Score=33.25 Aligned_cols=65 Identities=17% Similarity=0.298 Sum_probs=48.6
Q ss_pred CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHHH
Q psy3459 127 NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQ 194 (296)
Q Consensus 127 lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L~ 194 (296)
.++.-.-..|+..+|-+...+||.-+..+|.++|. .++.-|+++|++-+|..= .-.+.-++.+|.
T Consensus 15 ~GD~~~P~~eTv~llE~iv~~~i~~l~~~a~~~A~-~r~~k~~~eD~~FliR~D--~~Kl~Rl~~lL~ 79 (92)
T cd07978 15 FGDVQNPLPETVDLLEDIVVEYIIELCHKAAEVAQ-RRRGKVKVEDLIFLLRKD--PKKLARLRELLS 79 (92)
T ss_pred cCCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHH-cCCCCCCHHHHHHHHhcC--HHHHHHHHHHHH
Confidence 44555667899999999999999999999999999 444445999999998641 223334444444
No 100
>PF04719 TAFII28: hTAFII28-like protein conserved region; InterPro: IPR006809 The general transcription factor, TFIID, consists of the TATA-binding protein (TBP) associated with a series of TBP-associated factors (TAFs) that together participate in the assembly of the transcription preinitiation complex. The conserved region is found at the C terminus of most member proteins. The crystal structure of hTAFII28 with hTAFII18 shows that this region is involved in the binding of these two subunits. The conserved region contains four alpha helices and three loops arranged as in histone H3 [, ].; GO: 0006367 transcription initiation from RNA polymerase II promoter, 0005634 nucleus; PDB: 1BH9_B 1BH8_B.
Probab=80.34 E-value=2.6 Score=34.01 Aligned_cols=66 Identities=17% Similarity=0.096 Sum_probs=46.2
Q ss_pred hccchhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCC-cccchhHhhchhhc
Q psy3459 115 VFQSSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRK-TINGEDILFAMSAL 180 (296)
Q Consensus 115 Lf~~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRK-TI~~eDVl~AL~~L 180 (296)
|-++..+++.++...|..++.-...+|.-.|.+||.=|-.+|.+++.+.+.. .|.|.|+-.|...|
T Consensus 24 ~~k~~ikkli~~~~~~qsv~~~v~i~v~g~aKvFVGEiVE~A~~Vq~~~~~~~pl~P~hlreA~rrL 90 (90)
T PF04719_consen 24 FNKAAIKKLINQVLGNQSVSQNVVIAVAGIAKVFVGEIVEEARDVQEEWGETGPLQPDHLREAYRRL 90 (90)
T ss_dssp --HHHHHHHHHHHHS-S---HHHHHHHHHHHHHHHHHHHHHHHHHHHHTT--SS--HHHHHHHHHHH
T ss_pred CCHHHHHHHHHHHcCCCCCChhHHHHHHHHHHHHHHHHHHHHHHHHHHhcCCCCCCcHHHHHHHHhC
Confidence 3345555555555567899999999999999999999999999999865544 79999998887654
No 101
>PF09415 CENP-X: CENP-S associating Centromere protein X; InterPro: IPR018552 Centromere protein X (CENP-X) is a component of the CENP-S complex. The CENP-S complex is composed of at least of CENP-S and CENP-X and is essential for the stable assembly of the outer kinetchore []. CENP-X is also a DNA-binding component of the Fanconi anemia (FA) core complex involved in DNA damage repair and genome maintenance. The FA complex is composed of CENPS, FANCA, FANCB, FANCC, FANCE, FANCF, FANCG, FANCL/PHF9, FANCM, FAAP24 and CENPX. Interacts with CENPS, FANCM and FAAP24 [, ].; PDB: 4DRB_L 4DRA_H 3V9R_D.
Probab=79.97 E-value=2 Score=33.17 Aligned_cols=59 Identities=17% Similarity=0.265 Sum_probs=46.1
Q ss_pred hhhhhhc-CCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCc-ccchhHhhchh
Q psy3459 120 GTILEQQ-NGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKT-INGEDILFAMS 178 (296)
Q Consensus 120 ~rimk~~-lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKT-I~~eDVl~AL~ 178 (296)
.++++.. -.++.+|++||..++.+-...||.=-...|.+.+..++..+ |..+|+-+-+-
T Consensus 6 ~rll~~~f~~~~tkIs~dal~l~~eyl~iFV~EAv~Ra~~~a~~e~~~~~le~e~LEki~p 66 (72)
T PF09415_consen 6 ARLLHEHFKDDKTKISKDALKLSAEYLRIFVREAVARAAEQAEAEGDEGFLEVEHLEKILP 66 (72)
T ss_dssp HHHHCTTSSSTT-EE-CCCHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSEE-HHHHHHHCH
T ss_pred HHHHHHHhcCCCCCcCHHHHHHHHHHHHHHHHHHHHHHHHHHHHcCCCCCCCHHHHHHHHH
Confidence 4555433 24889999999999999999999999999999999999998 99999876543
No 102
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=79.92 E-value=18 Score=34.75 Aligned_cols=65 Identities=14% Similarity=0.190 Sum_probs=45.9
Q ss_pred hhHHHHHHHhhCCC---CCcccHHHHHHHHHHH------HHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhc
Q psy3459 12 IANVAKIMKKAIPE---SGKIAKDARECVQECV------SEFISFITSEASDRCHLEKRKTINGEDILFAMSAL 76 (296)
Q Consensus 12 ~A~I~RIiK~~LP~---~~rISkDA~~al~~~a------~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~l 76 (296)
...+..|++..+.. ...++.++.+.+.+.+ -..+..+...|...|...++.+|+.+||..|+..+
T Consensus 209 ~~e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~ 282 (394)
T PRK00411 209 ADEIFDILKDRVEEGFYPGVVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKS 282 (394)
T ss_pred HHHHHHHHHHHHHhhcccCCCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHH
Confidence 34455555544321 1258888888887766 33445556778888888999999999999998876
No 103
>COG5262 HTA1 Histone H2A [Chromatin structure and dynamics]
Probab=79.15 E-value=3.2 Score=35.33 Aligned_cols=64 Identities=16% Similarity=0.190 Sum_probs=52.4
Q ss_pred hcc--chhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 115 VFQ--SSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 115 Lf~--~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|+ .+.|+|| .-.-.++|+++|--.+.-|..-.+.-|+.-|-..|...++|.|+|-|+-.|+..
T Consensus 26 ~fpvgrvkr~lk-~~~~~~Rig~~A~Vyl~AvleYL~aEilelAgNaA~d~kkkri~PrHlqlAIrn 91 (132)
T COG5262 26 IFPVGRVKRLLK-KGNYRMRIGAGAPVYLAAVLEYLAAEILELAGNAARDNKKKRIIPRHLQLAIRN 91 (132)
T ss_pred cccHHHHHHHHH-cCccceeecCCcHHHHHHHHHHHHHHHHHHhhhhhhhcCcceechHHHHHHhcC
Confidence 355 4477777 445679999999999988877777777778888899999999999999999764
No 104
>TIGR03346 chaperone_ClpB ATP-dependent chaperone ClpB. Members of this protein family are the bacterial ATP-dependent chaperone ClpB. This protein belongs to the AAA family, ATPases associated with various cellular activities (pfam00004). This molecular chaperone does not act as a protease, but rather serves to disaggregate misfolded and aggregated proteins.
Probab=78.10 E-value=8.3 Score=42.00 Aligned_cols=95 Identities=18% Similarity=0.165 Sum_probs=56.1
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHHHHhccccccchhhhhhhhhhhhccchhhhhhh-----
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQ----- 125 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~----- 125 (296)
.|...|...+...|+++|++.||=.-+=+ .....|.. .+++.+.|-....+.+..
T Consensus 11 ~A~~~A~~~~h~~V~~EHLLlaLl~~~~g----~a~~iL~~----------------~Gvd~~~l~~~l~~~l~~~~~~~ 70 (852)
T TIGR03346 11 AAQSLALGRDHQQIEPEHLLKALLDQEGG----LARRLLQK----------------AGVNVGALRQALEKELEKLPKVS 70 (852)
T ss_pred HHHHHHHHcCCCcccHHHHHHHHHhCCcc----HHHHHHHH----------------cCCCHHHHHHHHHHHhcccccCC
Confidence 57789999999999999999998433221 11222222 122222221111111110
Q ss_pred cCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhch
Q psy3459 126 QNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAM 177 (296)
Q Consensus 126 ~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL 177 (296)
..+....+|..++.++..| ...+...++..|.++|+|-||
T Consensus 71 ~~~~~~~~S~~~~~vLe~A------------~~~A~~~g~~~I~teHLLlAL 110 (852)
T TIGR03346 71 GPGGQVYLSPELNRLLNLA------------EKLAQKRGDEFISSEHLLLAL 110 (852)
T ss_pred CCCCCCCcCHHHHHHHHHH------------HHHHHHcCCCcccHHHHHHHH
Confidence 0012456788888888885 334555678899999999887
No 105
>KOG2549|consensus
Probab=77.96 E-value=7.3 Score=40.79 Aligned_cols=67 Identities=19% Similarity=0.233 Sum_probs=56.8
Q ss_pred chhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 11 PIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 11 P~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
|...+.-+++.. +-..|++|+..+|..=.+.=|.-|+-+|.+.-.+.+|.+++.+||..||.-+.-+
T Consensus 13 ~~Es~k~vAEsl--Gi~nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nVe 79 (576)
T KOG2549|consen 13 PKESVKVVAESL--GITNLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNVE 79 (576)
T ss_pred cHHHHHHHHHHh--CccccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhcccc
Confidence 355666666544 4457999999999999999999999999999999999999999999999976544
No 106
>cd08045 TAF4 TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and is involved in forming Transcription Factor IID (TFIID) complex. The TATA Binding Protein (TBP) Associated Factor 4 (TAF4) is one of several TAFs that bind TBP and are involved in forming the Transcription Factor IID (TFIID) complex. TFIID is one of seven General Transcription Factors (GTF) (TFIIA, TFIIB, TFIID, TFIIE, TFIIF, and TFIID) that are involved in accurate initiation of transcription by RNA polymerase II in eukaryote. TFIID plays an important role in the recognition of promoter DNA and assembly of the pre-initiation complex. TFIID complex is composed of the TBP and at least 13 TAFs. TAFs from various species were originally named by their predicted molecular weight or their electrophoretic mobility in polyacrylamide gels. A new, unified nomenclature for the pol II TAFs has been suggested to show the relationship between TAF orthologs and paralogs. Several hypotheses are
Probab=77.71 E-value=17 Score=32.98 Aligned_cols=70 Identities=13% Similarity=0.151 Sum_probs=50.2
Q ss_pred cCCchhHHHHHHHhhCCCC--CcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhc------CCCccCcccHHHHhhhcC
Q psy3459 8 RFLPIANVAKIMKKAIPES--GKIAKDARECVQECVSEFISFITSEASDRCHLE------KRKTINGEDILFAMSALG 77 (296)
Q Consensus 8 ~~LP~A~I~RIiK~~LP~~--~rISkDA~~al~~~a~eFI~~las~An~~a~~~------~RKTI~~eDVl~AL~~lg 77 (296)
..|....+.+.|....... ..|+.|...+|.-||..++..|-......|++- ..++..-.||-..|..|+
T Consensus 43 ~fl~~~~l~~~~~~i~~~~g~~~~~~d~~~lis~a~e~rlr~li~k~~~~s~hR~~~~~~~~r~~~~sdvr~qL~~l~ 120 (212)
T cd08045 43 SFLNPSPLAKKIRKIAKKHGLKEVDEDVLDLISLALEERLRNLLEKLIEVSEHRVDSEKEDERYEITSDVRKQLRFLE 120 (212)
T ss_pred hccCHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHHHHHHHHHHHHHhhhhhcCCCCceeecchHHHHHHHHH
Confidence 3555666665555554322 279999999999999999999999988888763 346666677766665444
No 107
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=76.39 E-value=3.7 Score=37.10 Aligned_cols=53 Identities=15% Similarity=0.334 Sum_probs=47.0
Q ss_pred ccccchHHHHHHHHHHHH---HHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCC
Q psy3459 130 NETIAKDARECVQECVSE---FISFITSEASDRCHLEKRKTINGEDILFAMSALGF 182 (296)
Q Consensus 130 ~~~iskdAkeai~~case---FI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF 182 (296)
+..++.++.+.|.+.+.= .|+.+...|-..+-..+.++|+++||-.++.++.|
T Consensus 213 ~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 213 APVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 456899999999887765 79999999999988899999999999999999875
No 108
>TIGR03015 pepcterm_ATPase putative secretion ATPase, PEP-CTERM locus subfamily. Members of this protein are marked as probable ATPases by the nucleotide binding P-loop motif GXXGXGKTT, a motif DEAQ similar to the DEAD/H box of helicases, and extensive homology to ATPases of MSHA-type pilus systems and to GspA proteins associated with type II protein secretion systems.
Probab=76.22 E-value=6.9 Score=35.32 Aligned_cols=69 Identities=13% Similarity=0.301 Sum_probs=53.2
Q ss_pred CchhHHHHHHHhhCC-----CCCcccHHHHHHHHHHHHH---HHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCC
Q psy3459 10 LPIANVAKIMKKAIP-----ESGKIAKDARECVQECVSE---FISFITSEASDRCHLEKRKTINGEDILFAMSALGF 78 (296)
Q Consensus 10 LP~A~I~RIiK~~LP-----~~~rISkDA~~al~~~a~e---FI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF 78 (296)
|....+..++...+. ....++.++.+.|.+.+.= .|+.+...|...+-..+.++|++++|-.++.++.|
T Consensus 192 l~~~e~~~~l~~~l~~~g~~~~~~~~~~~~~~i~~~s~G~p~~i~~l~~~~~~~a~~~~~~~i~~~~v~~~~~~~~~ 268 (269)
T TIGR03015 192 LDREETREYIEHRLERAGNRDAPVFSEGAFDAIHRFSRGIPRLINILCDRLLLSAFLEEKREIGGEEVREVIAEIDF 268 (269)
T ss_pred CCHHHHHHHHHHHHHHcCCCCCCCcCHHHHHHHHHHcCCcccHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhhc
Confidence 344455555554431 2346999999999888764 79999999999988899999999999999988764
No 109
>PF15510 CENP-W: Centromere kinetochore component W
Probab=76.14 E-value=2.7 Score=34.25 Aligned_cols=58 Identities=19% Similarity=0.180 Sum_probs=44.4
Q ss_pred hhhhhhcCCCccccchHHHHH--------------HHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 120 GTILEQQNGQNETIAKDAREC--------------VQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkea--------------i~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
++++|++ .|..++...+-.+ +.-.|-.|+|-|+-+|..-+=+++-.||.++||+.|-+
T Consensus 23 krv~Kr~-KphlRl~~~~Dllv~~~~f~~~~~~~~vhLncLLFvhrLAEEaRtnA~EnK~~~Ik~~Hv~AaaK 94 (102)
T PF15510_consen 23 KRVFKRQ-KPHLRLETSGDLLVRFCPFSGWQWGGEVHLNCLLFVHRLAEEARTNACENKCGTIKKEHVLAAAK 94 (102)
T ss_pred HHHHHhc-CCceeecccccHHHhhcccccccccceeehhHHHHHHHHHHHHHHHHHHHhhccccHHHHHHHHH
Confidence 3444433 3456665555444 66778999999999999999999999999999998854
No 110
>KOG1745|consensus
Probab=71.28 E-value=6.1 Score=34.32 Aligned_cols=54 Identities=20% Similarity=0.163 Sum_probs=48.6
Q ss_pred hcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 125 QQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 125 ~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
+..-+++++.+.|..++|+++--|+--|--.+|-.+...+|-||.|.|+--|..
T Consensus 78 q~f~~dLrfqs~Ai~ALQeA~EayLv~LfEdtnlcAihAkRVTimpkdiQlArr 131 (137)
T KOG1745|consen 78 QDFKTDLRFQSSAIAALQEAAEAYLVGLFEDTNLCAIHAKRVTIMPKDIQLARR 131 (137)
T ss_pred hcccccceehHHHHHHHHHHHHHHHHHhccccchhhhccceeEecccceehhhh
Confidence 445579999999999999999999999999999999999999999999877654
No 111
>PRK00411 cdc6 cell division control protein 6; Reviewed
Probab=70.18 E-value=8.2 Score=37.10 Aligned_cols=51 Identities=10% Similarity=0.096 Sum_probs=40.6
Q ss_pred ccchHHHHHHHHHH------HHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCC
Q psy3459 132 TIAKDARECVQECV------SEFISFITSEASDRCHLEKRKTINGEDILFAMSALGF 182 (296)
Q Consensus 132 ~iskdAkeai~~ca------seFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF 182 (296)
.++.++.+.+.+.+ ...+..+...|-..|...++.+|+.+||-.|++.+..
T Consensus 228 ~~~~~~l~~i~~~~~~~~Gd~r~a~~ll~~a~~~a~~~~~~~I~~~~v~~a~~~~~~ 284 (394)
T PRK00411 228 VVDDEVLDLIADLTAREHGDARVAIDLLRRAGLIAEREGSRKVTEEDVRKAYEKSEI 284 (394)
T ss_pred CCCHhHHHHHHHHHHHhcCcHHHHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHHHH
Confidence 57888888887766 3344555678888888899999999999999998843
No 112
>KOG4336|consensus
Probab=66.51 E-value=16 Score=35.79 Aligned_cols=80 Identities=21% Similarity=0.311 Sum_probs=64.1
Q ss_pred ccchhhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHHHHHHHH
Q psy3459 116 FQSSGTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQK 195 (296)
Q Consensus 116 f~~s~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l~~~L~~ 195 (296)
+..+...|....+=+ .|++-|.+.+.+.....|.=+.-++..+|.-.||...|.-||--+|-++|+. +..|..+++.
T Consensus 7 l~~VV~~Ll~~~gfd-~is~~aletlvell~~yi~eigrq~~n~celagRT~pT~~Dv~l~Li~mnI~--v~sL~~~~q~ 83 (323)
T KOG4336|consen 7 LAPVVSNLLKTKGFD-SISNAALETLVELLQSYIREIGRQLHNYCELAGRTIPTQGDVKLTLIEMNIK--VSSLYAYFQK 83 (323)
T ss_pred HHHHHHHHHHHhCch-HHHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccCCcHHHHHHHHHHhCCC--hhhhHHHHHh
Confidence 344433333333322 3899999999999999999999999999999999999999999999999997 5777777765
Q ss_pred HHH
Q psy3459 196 YRE 198 (296)
Q Consensus 196 ~re 198 (296)
+-.
T Consensus 84 ~~~ 86 (323)
T KOG4336|consen 84 QEF 86 (323)
T ss_pred ccc
Confidence 544
No 113
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=64.79 E-value=5.4 Score=42.48 Aligned_cols=33 Identities=30% Similarity=0.352 Sum_probs=28.2
Q ss_pred HHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 42 SEFISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 42 ~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
......|. +|+++|..++++-|+++||.+|++.
T Consensus 366 rdl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 366 RDLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 44555555 8999999999999999999999976
No 114
>KOG3334|consensus
Probab=64.61 E-value=41 Score=29.58 Aligned_cols=62 Identities=18% Similarity=0.233 Sum_probs=46.2
Q ss_pred HHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchH-HHHHHHHHH
Q psy3459 31 KDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE-PLKIYLQKY 92 (296)
Q Consensus 31 kDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~-~l~~~L~~~ 92 (296)
.-..-.|.+.+--++.-|-..|.-++.|+++.||.++||-.|++..+=.+|.+ +=+++|-.+
T Consensus 33 prVi~qlLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~l 95 (148)
T KOG3334|consen 33 PRVINQLLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLEL 95 (148)
T ss_pred hHHHHHHHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHH
Confidence 33444566666667777778899999999999999999999999877666666 444444444
No 115
>KOG2389|consensus
Probab=64.06 E-value=16 Score=36.15 Aligned_cols=81 Identities=21% Similarity=0.203 Sum_probs=62.6
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC---cchHHH
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD---SYVEPL 85 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~---~yv~~l 85 (296)
.|-+..|..|.. +|+-+ ....-|.+.|...+..||.-++..|..++...||--.+..||..||+.|+.. .++...
T Consensus 29 sla~~avaQIcq-slg~~-~~~~sale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s~~~~~~~~~ 106 (353)
T KOG2389|consen 29 SLARVAVAQICQ-SLGYS-STQNSALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSASLGASGSSGE 106 (353)
T ss_pred HHHHHHHHHHHH-hcCCc-ccccHHHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhhcccccccch
Confidence 345567777776 45543 4445588999999999999999999999999999999999999999998775 234334
Q ss_pred HHHHHH
Q psy3459 86 KIYLQK 91 (296)
Q Consensus 86 ~~~L~~ 91 (296)
...|..
T Consensus 107 s~~L~d 112 (353)
T KOG2389|consen 107 SHCLLD 112 (353)
T ss_pred hHHHhh
Confidence 444443
No 116
>PF02291 TFIID-31kDa: Transcription initiation factor IID, 31kD subunit; InterPro: IPR003162 Human transcription initiation factor TFIID is composed of the TATA-binding polypeptide (TBP) and at least 13 TBP-associated factors (TAFs) that collectively or individually are involved in activator-dependent transcription []. TAFII-31 protein is a transcriptional coactivator of the p53 protein [].; GO: 0006352 transcription initiation, DNA-dependent; PDB: 1TAF_A.
Probab=60.06 E-value=17 Score=31.07 Aligned_cols=65 Identities=17% Similarity=0.203 Sum_probs=39.7
Q ss_pred cchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchh-hcCCccchHHHHHHHHHHH
Q psy3459 133 IAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMS-ALGFDSYVEPLKIYLQKYR 197 (296)
Q Consensus 133 iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~-~LgF~~yv~~l~~~L~~~r 197 (296)
....+...+.+-+-.|+.-|-..|..++.-.+|++|+.+||--|++ .+++.-.-++-++.|-+.-
T Consensus 30 yeprVv~qLLEfayRYt~~vL~DA~~ya~hA~~~~i~~~DVrLAi~~r~~~~f~~pppre~llelA 95 (129)
T PF02291_consen 30 YEPRVVNQLLEFAYRYTSDVLEDAQVYADHAGRSTIDADDVRLAIQSRLDHSFTQPPPREFLLELA 95 (129)
T ss_dssp B-THHHHHHHHHHHHHHHHHHHHHHHHHHHTT-SSB-HHHHHHHHHHT------------------
T ss_pred cCHHHHHHHHHHHHHHHHHHHHHHHHHHHhcccccCChHHHHHHHHHHHhhhccCCCChHHHHHHH
Confidence 4556777888899999999999999999999999999999999999 5677766677777766553
No 117
>PRK10865 protein disaggregation chaperone; Provisional
Probab=59.25 E-value=36 Score=37.33 Aligned_cols=25 Identities=12% Similarity=0.066 Sum_probs=21.6
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
.|...|..-+...|+++|++.||=.
T Consensus 16 ~a~~~a~~~~~~~~~~~hll~~l~~ 40 (857)
T PRK10865 16 DAQSLALGHDNQFIEPLHLMSALLN 40 (857)
T ss_pred HHHHHHHHcCCCcccHHHHHHHHHh
Confidence 4777899999999999999999844
No 118
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=57.94 E-value=31 Score=32.68 Aligned_cols=64 Identities=8% Similarity=0.058 Sum_probs=42.7
Q ss_pred HHHHHHHhhCC---CCCcccHHHHHHHHHHHH------HHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcC
Q psy3459 14 NVAKIMKKAIP---ESGKIAKDARECVQECVS------EFISFITSEASDRCHLEKRKTINGEDILFAMSALG 77 (296)
Q Consensus 14 ~I~RIiK~~LP---~~~rISkDA~~al~~~a~------eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lg 77 (296)
.+..|++..+. ....+++++...+.+.+. -.+..+-..|...|...++.+|+.+||..|+..+.
T Consensus 203 e~~~il~~r~~~~~~~~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~ 275 (365)
T TIGR02928 203 ELRDILENRAEKAFYDGVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIE 275 (365)
T ss_pred HHHHHHHHHHHhhccCCCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHH
Confidence 45556654442 123588888777655442 23344555677788888899999999999998773
No 119
>TIGR02928 orc1/cdc6 family replication initiation protein. Members of this protein family are found exclusively in the archaea. This set of DNA binding proteins shows homology to the origin recognition complex subunit 1/cell division control protein 6 family in eukaryotes. Several members may be found in genome and interact with each other.
Probab=57.84 E-value=19 Score=34.19 Aligned_cols=72 Identities=8% Similarity=-0.018 Sum_probs=44.7
Q ss_pred hhhccchhhhhhhcCCCccccchHHHHHHHHHHH------HHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccc
Q psy3459 113 EDVFQSSGTILEQQNGQNETIAKDARECVQECVS------EFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSY 185 (296)
Q Consensus 113 e~Lf~~s~rimk~~lp~~~~iskdAkeai~~cas------eFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~y 185 (296)
+++..-..++++....+ ..++.++.+.+.+-+. ..+.-+-..|-+.|..+++.+|+.+||-.|++.+....+
T Consensus 202 ~e~~~il~~r~~~~~~~-~~~~~~~l~~i~~~~~~~~Gd~R~al~~l~~a~~~a~~~~~~~it~~~v~~a~~~~~~~~~ 279 (365)
T TIGR02928 202 EELRDILENRAEKAFYD-GVLDDGVIPLCAALAAQEHGDARKAIDLLRVAGEIAEREGAERVTEDHVEKAQEKIEKDRL 279 (365)
T ss_pred HHHHHHHHHHHHhhccC-CCCChhHHHHHHHHHHHhcCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHHHHHHH
Confidence 44444344444333332 3477777776654331 233334456778888889999999999999998853333
No 120
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=55.39 E-value=38 Score=35.10 Aligned_cols=59 Identities=20% Similarity=0.209 Sum_probs=40.5
Q ss_pred HHHHHHhhCCCCCcccHHHHHHHHHHHHH-----------HHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 15 VAKIMKKAIPESGKIAKDARECVQECVSE-----------FISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 15 I~RIiK~~LP~~~rISkDA~~al~~~a~e-----------FI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
|.+++++. +--.++.+|...|.+.+.. -|.-|-.+|+.+|...++++|+++||..|++.
T Consensus 436 i~~~~~~~--~L~~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 436 IASICQKE--GLPPFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp HHHHHHHH--SS--BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred HHHHHHhC--CCCCCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 44444443 2225777777777666532 45566789999999999999999999999875
No 121
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=52.39 E-value=7.8 Score=26.48 Aligned_cols=26 Identities=19% Similarity=0.188 Sum_probs=21.0
Q ss_pred hhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 156 ASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 156 An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
|.+.|...+...|+++|+|.||=+-+
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~~~ 26 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLEDP 26 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHHHT
T ss_pred CHHHHHHcCCCcccHHHHHHHHHhhh
Confidence 56789999999999999999965543
No 122
>KOG1659|consensus
Probab=51.58 E-value=27 Score=32.60 Aligned_cols=58 Identities=9% Similarity=0.132 Sum_probs=48.5
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchHHH
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEPL 189 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~~l 189 (296)
+|+--+--.+.++---|+.-|-..+-+++...+-||||++|+..|...-.-=+|...+
T Consensus 31 KvaqavPViisralElFl~~l~~~t~~~t~~~~aKt~s~~hlkq~v~~~~~FdFLk~~ 88 (224)
T KOG1659|consen 31 KVAQAVPVIISRALELFLESLLQKTLEITRSRGAKTVSSSHLKQAVESDPKFDFLKEV 88 (224)
T ss_pred hhhhhhhhHHHHHHHHHHHHHHHHHHHHHHhcCccccCHHHHHHHHhccchhHHHHHH
Confidence 5666666788899999999999999999999999999999999998876555555443
No 123
>TIGR03345 VI_ClpV1 type VI secretion ATPase, ClpV1 family. Members of this protein family are homologs of ClpB, an ATPase associated with chaperone-related functions. These ClpB homologs, designated ClpV1, are a key component of the bacterial pathogenicity-associated type VI secretion system.
Probab=50.50 E-value=61 Score=35.62 Aligned_cols=96 Identities=16% Similarity=0.153 Sum_probs=53.6
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHHHHhccccccchhhhhhhhhhhhccchhhhhhh---cC
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQ---QN 127 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~---~l 127 (296)
.|...|..-+...|+++|++.||=.- ++ ..+...|.. .++++++|.....+.+.. ..
T Consensus 11 ~A~~~A~~~~h~~I~~eHLLlaLL~~--~~--~~~~~iL~~----------------~Gvd~~~Lr~~le~~l~~~p~~~ 70 (852)
T TIGR03345 11 QAAALCVARGHPEVELEHWLLALLDQ--PD--SDLAAILRH----------------FGVDLGRLKADLARALDKLPRGN 70 (852)
T ss_pred HHHHHHHHhCCCcccHHHHHHHHHhc--cC--cHHHHHHHH----------------cCCCHHHHHHHHHHHhccCCCCC
Confidence 57788999999999999999998222 11 111222221 122222222222111111 00
Q ss_pred CCccccchHHHHHHHHHHHHHHHHHHHHhhH-HhhhcCCCcccchhHhhchh
Q psy3459 128 GQNETIAKDARECVQECVSEFISFITSEASD-RCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 128 p~~~~iskdAkeai~~caseFI~~lts~An~-~c~~~kRKTI~~eDVl~AL~ 178 (296)
+....+|..+..++..+. . .+...+..-|+++|+|-||=
T Consensus 71 ~~~~~~S~~l~~vL~~A~------------~~~a~~~g~~~I~teHLLlALl 110 (852)
T TIGR03345 71 TRTPVFSPHLVELLQEAW------------LLASLELGDGRIRSGHLLLALL 110 (852)
T ss_pred CCCCCcCHHHHHHHHHHH------------HHHHHHcCCCcccHHHHHHHHH
Confidence 113457888888887752 2 23334667899999998873
No 124
>PRK11034 clpA ATP-dependent Clp protease ATP-binding subunit; Provisional
Probab=50.06 E-value=61 Score=35.26 Aligned_cols=24 Identities=21% Similarity=0.302 Sum_probs=21.5
Q ss_pred HHhhHHHHhcCCCccCcccHHHHh
Q psy3459 50 SEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 50 s~An~~a~~~~RKTI~~eDVl~AL 73 (296)
..|...|..-+...|+++|++.||
T Consensus 11 ~~a~~~a~~~~~~~~~~~h~l~~l 34 (758)
T PRK11034 11 NMAFARAREHRHEFMTVEHLLLAL 34 (758)
T ss_pred HHHHHHHHHcCCCcchHHHHHHHH
Confidence 357889999999999999999998
No 125
>KOG3423|consensus
Probab=48.09 E-value=30 Score=31.19 Aligned_cols=47 Identities=21% Similarity=0.359 Sum_probs=39.9
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHhhhcC--------------CCcccchhHhhchhhcCCc
Q psy3459 137 ARECVQECVSEFISFITSEASDRCHLEK--------------RKTINGEDILFAMSALGFD 183 (296)
Q Consensus 137 Akeai~~caseFI~~lts~An~~c~~~k--------------RKTI~~eDVl~AL~~LgF~ 183 (296)
.+-+|.-+|-.||+=|+.-|-+.|+-.. |-|++-+|+-.||.+.|..
T Consensus 108 v~RLvsLaAQKfvSDIa~DA~Q~~k~r~~~~~~~~k~~~kdkK~tLtmeDL~~AL~EyGin 168 (176)
T KOG3423|consen 108 VKRLVSLAAQKFVSDIANDALQHSKIRTKTAIGKDKKQAKDKKYTLTMEDLSPALAEYGIN 168 (176)
T ss_pred HHHHHHHHHHHHHHHHHHHHHHHhhhccccccccccccccccceeeeHHHHHHHHHHhCcc
Confidence 4568888999999999999999996443 5689999999999999874
No 126
>PF13654 AAA_32: AAA domain; PDB: 3K1J_B.
Probab=46.38 E-value=34 Score=35.40 Aligned_cols=48 Identities=19% Similarity=0.199 Sum_probs=37.2
Q ss_pred ccchHHHHHHHHHHHH-----------HHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 132 TIAKDARECVQECVSE-----------FISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 132 ~iskdAkeai~~case-----------FI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
-++.+|...|.+-++. -|.-|-.+|+.+|...++++|+++||..|++.
T Consensus 447 ~~~~~Av~~li~~~~R~~q~kLsl~~~~l~~ll~EA~~~A~~~~~~~I~~~~V~~Ai~~ 505 (509)
T PF13654_consen 447 PFDRSAVARLIEYSARLDQDKLSLRFSWLADLLREANYWARKEGAKVITAEHVEQAIEE 505 (509)
T ss_dssp -BBHHHHHHHHHHHHHCC-SEEE--HHHHHHHHHHHHHHHHHCT-SSB-HHHHHHHHHH
T ss_pred CCCHHHHHHHHHHHHHHhCCEeCCCHHHHHHHHHHHHHHHHHhCCCccCHHHHHHHHHc
Confidence 4677777777776543 56667789999999999999999999999975
No 127
>KOG1756|consensus
Probab=46.27 E-value=34 Score=29.52 Aligned_cols=59 Identities=14% Similarity=0.273 Sum_probs=41.4
Q ss_pred ccch--hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhh----HHhhhcCCCcccchhHhhchhh
Q psy3459 116 FQSS--GTILEQQNGQNETIAKDARECVQECVSEFISFITSEAS----DRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 116 f~~s--~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An----~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
|+.+ .|+|++ .---.+|+.+|--.+.-| +.||+++.. ..+...++.-|+|.||..|+..
T Consensus 28 fPvgri~r~Lr~-~~~~~ri~~gapV~laav----LeYL~Aeile~agnaardnkk~ri~PrH~~lAI~N 92 (131)
T KOG1756|consen 28 FPVGRIHRLLRK-GRYAQRVGAGAPVYLAAV----LEYLTAEILELAGNAARDNKKTRITPRHLQLAIRN 92 (131)
T ss_pred cCHHHHHHHHHc-cchhhhccCCChHHHHHH----HHHHHHHHHHHhHHHhhhcCccccChHHHHHHHhC
Confidence 6633 566655 334578899988888743 345555554 4567788999999999999873
No 128
>PF02861 Clp_N: Clp amino terminal domain; InterPro: IPR004176 This short domain is found in one or two copies at the amino terminus of ClpA and ClpB proteins from bacteria and eukaryotes. The function of these domains is uncertain but they may form a protein binding site []. The proteins are thought to be subunits of ATP-dependent proteases which act as chaperones to target the proteases to substrates.; GO: 0019538 protein metabolic process; PDB: 3FH2_A 3ZRJ_A 3ZRI_A 1QVR_C 3FES_C 2Y1R_F 3PXG_D 2Y1Q_A 3PXI_C 2K77_A ....
Probab=44.02 E-value=15 Score=25.04 Aligned_cols=24 Identities=21% Similarity=0.281 Sum_probs=19.7
Q ss_pred hhHHHHhcCCCccCcccHHHHhhh
Q psy3459 52 ASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 52 An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
|.+.|...+...|+++|++.||=.
T Consensus 1 A~~~A~~~~~~~i~~eHlL~all~ 24 (53)
T PF02861_consen 1 AQELARERGHQYISPEHLLLALLE 24 (53)
T ss_dssp HHHHHHHTTBSSE-HHHHHHHHHH
T ss_pred CHHHHHHcCCCcccHHHHHHHHHh
Confidence 567899999999999999999644
No 129
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=42.98 E-value=48 Score=26.54 Aligned_cols=48 Identities=21% Similarity=0.252 Sum_probs=37.4
Q ss_pred cccchHHHHHHHHHHHHH------HHHHHHHhhHHhhhcCCCcccchhHhhchh
Q psy3459 131 ETIAKDARECVQECVSEF------ISFITSEASDRCHLEKRKTINGEDILFAMS 178 (296)
Q Consensus 131 ~~iskdAkeai~~caseF------I~~lts~An~~c~~~kRKTI~~eDVl~AL~ 178 (296)
..+++++..++..++.-| ++=|---|-.+|.-++...|+.+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 456777777777766654 344555789999999999999999999974
No 130
>smart00414 H2A Histone 2A.
Probab=42.91 E-value=40 Score=27.86 Aligned_cols=59 Identities=10% Similarity=0.165 Sum_probs=38.4
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|.|++.. -..+|+..|--.+.-+---+..-|-.-|-..|...+++.|+|.|+..|+..
T Consensus 16 ~r~Lk~~~-~~~Rv~~~A~VyLaAvLEYLtaEILeLagn~a~~~k~~rItp~hi~lAi~n 74 (106)
T smart00414 16 HRLLRKGT-YAKRVGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKRRITPRHLQLAIRN 74 (106)
T ss_pred HHHHHcCc-cccccccccHHHHHHHHHHHHHHHHHHHHHHHHhcCCCccchHHHhhhccC
Confidence 45554432 234787777666655433333334444666788889999999999999875
No 131
>PLN00154 histone H2A; Provisional
Probab=42.58 E-value=49 Score=28.78 Aligned_cols=60 Identities=18% Similarity=0.248 Sum_probs=40.0
Q ss_pred ccch--hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHH----hhHHhhhcCCCcccchhHhhchhh
Q psy3459 116 FQSS--GTILEQQNGQNETIAKDARECVQECVSEFISFITSE----ASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 116 f~~s--~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~----An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
|+.+ .+.+++-..-..+|+..|--.+.-. +.|||++ |-..|+..+++-|+|.||..|+..
T Consensus 39 FPVgRi~r~Lk~g~~~~~RVga~ApVYLAAV----LEYLtAEVLELAGNaA~d~kk~RItPrHi~lAIrn 104 (136)
T PLN00154 39 FPVGRIHRQLKQRVSAHGRVGATAAVYTAAI----LEYLTAEVLELAGNASKDLKVKRITPRHLQLAIRG 104 (136)
T ss_pred CchHHHHHHHHhhhhhccccccchHHHHHHH----HHHHHHHHHHHHHHHHHhhCCceecHHHhhhhccC
Confidence 5533 5566654434458887776555443 3556655 455678889999999999999854
No 132
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=42.29 E-value=70 Score=33.79 Aligned_cols=49 Identities=16% Similarity=0.137 Sum_probs=38.2
Q ss_pred cccHHHHHHHHHHHH-------------HHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhc
Q psy3459 28 KIAKDARECVQECVS-------------EFISFITSEASDRCHLEKRKTINGEDILFAMSAL 76 (296)
Q Consensus 28 rISkDA~~al~~~a~-------------eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~l 76 (296)
.++.+|...|.+.++ .=+.-|-.+|+.+|..+++.+|+++||..|++.-
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~ 391 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLA 391 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHH
Confidence 689999988876544 2344455678888988999999999999998754
No 133
>PF08369 PCP_red: Proto-chlorophyllide reductase 57 kD subunit; InterPro: IPR013580 This domain is found in bacteria and plant chloroplast proteins. It often appears at the C-terminal of nitrogenase component 1 type oxidoreductases (IPR000510 from INTERPRO) and sometimes independently in bacterial proteins such as the proto-chlorophyllide reductase subunit B of the cyanobacterium Synechocystis. This domain is also associated with chlorophyllide reductase subunit Z, converts chlorophylls (Chl) into bacteriochlorophylls (BChl) by reducing ring B of the tetrapyrrole.; GO: 0016491 oxidoreductase activity, 0015979 photosynthesis, 0015995 chlorophyll biosynthetic process, 0055114 oxidation-reduction process; PDB: 2KRU_A 2L09_A.
Probab=41.04 E-value=31 Score=24.16 Aligned_cols=41 Identities=15% Similarity=0.091 Sum_probs=26.5
Q ss_pred hHHHHHHHHHHHHHH-HHHHHHhhHHhhhcCCCcccchhHhhc
Q psy3459 135 KDARECVQECVSEFI-SFITSEASDRCHLEKRKTINGEDILFA 176 (296)
Q Consensus 135 kdAkeai~~caseFI-~~lts~An~~c~~~kRKTI~~eDVl~A 176 (296)
.||...|.+. -.|+ .-+-..+-.+|...|...||.++|..|
T Consensus 3 ~eA~~~L~~i-P~fvR~~~r~~~E~~Ar~~G~~~IT~e~v~~A 44 (45)
T PF08369_consen 3 DEAEARLDRI-PFFVRKKLRDAAEKYARERGYDEITVEVVDAA 44 (45)
T ss_dssp HHHHHHHCTS--HHHHHHHHHHHHHHHHHCT-SEE-HHHHHHH
T ss_pred HHHHHHHHHC-CHHHHHHHHHHHHHHHHHcCCCeECHHHHHhh
Confidence 4555555553 4455 345556677889999999999998765
No 134
>PF13335 Mg_chelatase_2: Magnesium chelatase, subunit ChlI
Probab=39.18 E-value=81 Score=25.22 Aligned_cols=48 Identities=21% Similarity=0.254 Sum_probs=38.7
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHhhHHHHhcCCCccCcccHHHHhh
Q psy3459 27 GKIAKDARECVQECVSEF------ISFITSEASDRCHLEKRKTINGEDILFAMS 74 (296)
Q Consensus 27 ~rISkDA~~al~~~a~eF------I~~las~An~~a~~~~RKTI~~eDVl~AL~ 74 (296)
..+++++...|..++..+ ++-|-.-|..+|--++...|+.+||..||.
T Consensus 41 ~~l~~~~~~~l~~~~~~~~lS~R~~~rilrvARTIADL~~~~~I~~~hi~EAl~ 94 (96)
T PF13335_consen 41 CPLSSEAKKLLEQAAEKLNLSARGYHRILRVARTIADLEGSERITREHIAEALS 94 (96)
T ss_pred cCCCHHHHHHHHHHHHHcCcCHHHHHHHHHHHHHHHhHcCCCCCCHHHHHHHHh
Confidence 367788888888877665 344556788899999999999999999974
No 135
>KOG2389|consensus
Probab=37.23 E-value=44 Score=33.24 Aligned_cols=47 Identities=21% Similarity=0.303 Sum_probs=45.1
Q ss_pred HHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCc
Q psy3459 137 ARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 183 (296)
Q Consensus 137 Akeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~ 183 (296)
|.+.|..-+..||.-|+-.|+.++.-.||--.|..||+.||++|+-.
T Consensus 51 ale~Ltd~~~qyvQ~lgk~a~~~~n~anR~epnl~Div~Al~dls~s 97 (353)
T KOG2389|consen 51 ALETLTDVLQQYVQNLGKTAHRYSNLANRTEPNLFDIVLALQDLSAS 97 (353)
T ss_pred HHHHHHHHHHHHHHHHHhhhhhhhhhcCCCCccHHHHHHHHHHhhhh
Confidence 99999999999999999999999999999999999999999999874
No 136
>COG5162 Transcription initiation factor TFIID, subunit TAF10 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=34.31 E-value=2.3e+02 Score=25.74 Aligned_cols=69 Identities=16% Similarity=0.225 Sum_probs=47.9
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHh------------------------------
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHL------------------------------ 58 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~------------------------------ 58 (296)
.||-+.+.=.+..+ +-.....-.+.++.-.+-.||+-|+..|-++.+-
T Consensus 88 liPd~v~DYyl~k~--Gf~~~D~rvKkLl~L~aqKFvsDiA~dayqYsrIr~~~sna~~t~~~a~~f~~gg~~~i~~~~~ 165 (197)
T COG5162 88 LIPDSVTDYYLEKA--GFVTSDQRVKKLLSLLAQKFVSDIAVDAYQYSRIRQGSSNAKATAQKAKRFAKGGASGIGSSGR 165 (197)
T ss_pred CccHHHHHHHHHhc--CceeccHHHHHHHHHHHHHHHHHHHHHHHHHHHHHhhcccchhhHHHHHHHHhccccccccccc
Confidence 46666666666543 3223444566788889999999998766555320
Q ss_pred ---cCCCccCcccHHHHhhhcCCC
Q psy3459 59 ---EKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 59 ---~~RKTI~~eDVl~AL~~lgF~ 79 (296)
.++-+++..|+-.||++.|+.
T Consensus 166 ~~dr~K~vltv~DLs~Al~EyGin 189 (197)
T COG5162 166 RGDRKKPVLTVVDLSKALEEYGIN 189 (197)
T ss_pred ccccCCceeeehHHHHHHHHhccc
Confidence 156678999999999998875
No 137
>PF09114 MotA_activ: Transcription factor MotA, activation domain; InterPro: IPR015198 Transcription factor MotA is required for the activation of middle promoters in Bacteriophage T4, in addition to phage T4 co-activator AsiA, and sigma-70-containing Escherichia coli RNA polymerase. Phage T4 middle promoters have the sigma70 -10 DNA element, but not the -35 element; instead, they have a MotA box at -30 to which the transcription factor MotA binds []. MotA and AsiA interact with the C-terminal of sigma70 (region 4), which normally binds the -35 element and the beta-flap, thereby diverting sigma70 away from host promoters that require -35 element-binding to phage T4 middle promoters. Transcription factor MotA has two domains: an N-terminal domain required for binding to sigma70, and a C-terminal domain required for binding to the -30 MotA box element in the phage T4 middle promoter. This entry represents the N-terminal (activation) domain of MotA factors that binds sigma70. The N-terminal domain adopts an almost completely alpha-helical topology, with five alpha-helices and a short, two-stranded, beta-ribbon. Four alpha helices (alpha1, alpha3, alpha4 and alpha5) are amphipathic and pack their hydrophobic surfaces around the central helix alpha2 [].; PDB: 1BJA_B 1I1S_A.
Probab=33.46 E-value=67 Score=26.28 Aligned_cols=34 Identities=12% Similarity=0.296 Sum_probs=28.0
Q ss_pred hHHHHHHHhhC----CCCCcccHHHHHHHHHHHHHHHH
Q psy3459 13 ANVAKIMKKAI----PESGKIAKDARECVQECVSEFIS 46 (296)
Q Consensus 13 A~I~RIiK~~L----P~~~rISkDA~~al~~~a~eFI~ 46 (296)
++|.++||..| +++..++.++.+.+++++..|..
T Consensus 51 SNIGvLIKkglIEKSGDGlv~T~~g~~Ii~~AA~l~a~ 88 (96)
T PF09114_consen 51 SNIGVLIKKGLIEKSGDGLVITEEGMDIIIQAAELWAQ 88 (96)
T ss_dssp HHHHHHHHTTSEEEETTEEEE-HHHHHHHHHHHHHHHH
T ss_pred HhHHHHHHcCcccccCCceEEechHHHHHHHHHHHHHh
Confidence 46788999888 56788999999999999999843
No 138
>PF03540 TFIID_30kDa: Transcription initiation factor TFIID 23-30kDa subunit; InterPro: IPR003923 Transcription initiation factor TFIID is a multimeric protein complex that plays a central role in mediating promoter responses to various activators and repressors. The complex includes TATA binding protein (TBP) and various TBP-associated factors (TAFS). TFIID a bona fide RNA polymerase II-specific TATA-binding protein-associated factor (TAF) and is essential for viability []. TFIID acts to nucleate the transcription complex, recruiting the rest of the factors through a direct interaction with TFIIB. The TBP subunit of TFIID is sufficient for TATA-element binding and TFIIB interaction, and can support basal transcription. The protein belongs to the TAF2H family.; GO: 0006352 transcription initiation, DNA-dependent, 0005634 nucleus
Probab=32.59 E-value=2e+02 Score=20.99 Aligned_cols=48 Identities=17% Similarity=0.250 Sum_probs=35.8
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHh
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHL 58 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~ 58 (296)
.+|-+.+.-+++.+ |--.-..-...++.-++-.||+-++..|.+.|+.
T Consensus 2 ~IPD~v~~~yL~~~--G~~~~D~rv~RLvSLaaQKFisdI~~dA~q~~k~ 49 (51)
T PF03540_consen 2 TIPDEVTDYYLERS--GFQTSDPRVKRLVSLAAQKFISDIANDAMQYCKI 49 (51)
T ss_pred CCCHHHHHHHHHHC--CCCCCCHhHHHHHHHHHHHHHHHHHHHHHHHHHh
Confidence 57888898888876 3112222334478889999999999999999874
No 139
>KOG1757|consensus
Probab=32.56 E-value=74 Score=27.04 Aligned_cols=64 Identities=16% Similarity=0.304 Sum_probs=48.5
Q ss_pred ccCCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhc----CCCccCcccHHHHhh
Q psy3459 7 DRFLPIANVAKIMKKAIPESGKIAKDARECVQECVSEFISFITSEASDRCHLE----KRKTINGEDILFAMS 74 (296)
Q Consensus 7 d~~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eFI~~las~An~~a~~~----~RKTI~~eDVl~AL~ 74 (296)
.+.+|...|.|.+|.-.....+|..-+..-. .-.+.||+.+-.+.|.++ +-|-|+|.|+-.|+.
T Consensus 28 GlqFpVgRihr~LK~r~t~h~rVGataavy~----aaileYLTaEVLeLAgNasKdLKvKRitprHlqLAiR 95 (131)
T KOG1757|consen 28 GLQFPVGRIHRHLKTRTTSHGRVGATAAVYS----AAILEYLTAEVLELAGNASKDLKVKRITPRHLQLAIR 95 (131)
T ss_pred ccccchHHHHHHHHHhcccccccchHHHHHH----HHHHHHHHHHHHHHcccccccceeeeccchhheeeec
Confidence 4679999999999999888888876553322 335678999988887654 457799999877764
No 140
>COG5095 TAF6 Transcription initiation factor TFIID, subunit TAF6 (also component of histone acetyltransferase SAGA) [Transcription]
Probab=32.28 E-value=1.5e+02 Score=29.75 Aligned_cols=53 Identities=25% Similarity=0.266 Sum_probs=48.8
Q ss_pred CcccHHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 27 GKIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 27 ~rISkDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
..|.+|+..++.--.+-=|+.+-.+|...-.+.+|..++.+||-.||..++.+
T Consensus 21 ~Ni~Dd~l~alamDlEYRI~ev~qea~KFmvhSKRtvLt~dDis~ALr~lNVe 73 (450)
T COG5095 21 SNIDDDALRALAMDLEYRIKEVCQEASKFMVHSKRTVLTIDDISYALRSLNVE 73 (450)
T ss_pred cccccHHHHHHHHhHHHHHHHHHHHHHHHhhcccceeeeHHhHHHHHHhcCCC
Confidence 47999999999988888899999999999999999999999999999998765
No 141
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=32.14 E-value=1e+02 Score=31.81 Aligned_cols=63 Identities=24% Similarity=0.215 Sum_probs=42.5
Q ss_pred hhHHHHHHHhhCC-CCCcccHHHHHHHHHHHHH---HHHHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 12 IANVAKIMKKAIP-ESGKIAKDARECVQECVSE---FISFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 12 ~A~I~RIiK~~LP-~~~rISkDA~~al~~~a~e---FI~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
...+..|++..+. .+..+++++.+.|.+.+.. .++.+ ..|..+|...+|++|+.+||.+++..
T Consensus 265 ~eei~~Il~~~a~k~~i~is~~al~~I~~y~~n~Rel~nll-~~Aa~~A~~~~~~~It~~dI~~vl~~ 331 (531)
T TIGR02902 265 DEEIKEIAKNAAEKIGINLEKHALELIVKYASNGREAVNIV-QLAAGIALGEGRKRILAEDIEWVAEN 331 (531)
T ss_pred HHHHHHHHHHHHHHcCCCcCHHHHHHHHHhhhhHHHHHHHH-HHHHHHHhhCCCcEEcHHHHHHHhCC
Confidence 3445566666553 2467899998887776652 23333 34455677788999999999999654
No 142
>TIGR00764 lon_rel lon-related putative ATP-dependent protease. Members of this family from Pyrococcus horikoshii and Pyrococcus abyssi each contain a predicted intein.
Probab=31.00 E-value=90 Score=32.96 Aligned_cols=50 Identities=16% Similarity=0.121 Sum_probs=38.6
Q ss_pred ccchHHHHHHHHHHH-------------HHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 132 TIAKDARECVQECVS-------------EFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 132 ~iskdAkeai~~cas-------------eFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
.++.+|.+.|.+-++ .=|.-|--+|+.+|..+++.+|+++||.+|++.-.
T Consensus 330 ~~s~~Av~~Li~~~~R~ag~r~~lsl~~R~L~~llR~A~~iA~~~~~~~I~~ehV~~Ai~~~~ 392 (608)
T TIGR00764 330 HFTRDAVEEIVREAQRRAGRKDHLTLRLRELGGLVRAAGDIAKSSGKVYVTAEHVLKAKKLAK 392 (608)
T ss_pred cCCHHHHHHHHHHHHHHHhcccccCCCHHHHHHHHHHHHHHHHhcCCceecHHHHHHHHHHHH
Confidence 688888888875444 23444556788899999999999999999987653
No 143
>KOG2549|consensus
Probab=30.37 E-value=84 Score=33.22 Aligned_cols=51 Identities=22% Similarity=0.244 Sum_probs=46.8
Q ss_pred ccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCC
Q psy3459 132 TIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGF 182 (296)
Q Consensus 132 ~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF 182 (296)
.++.|+..+|..=...=|.=|.-.|..+-...+|.++|.+||-.||.-+.-
T Consensus 28 nl~deaa~~La~dv~yrikEI~Q~aaKfm~hskR~kLtv~DV~~ALr~~nV 78 (576)
T KOG2549|consen 28 NLNDEAALLLAEDVEYRIKEIVQDAAKFMVHSKRTKLTVDDVDYALRSLNV 78 (576)
T ss_pred ccCHHHHHHHHHHHHHHHHHHHHHHHHHhhcCCCCcCcHHHHHHHHhhccc
Confidence 589999999999888889999999999999999999999999999997654
No 144
>TIGR02902 spore_lonB ATP-dependent protease LonB. Members of this protein are LonB, a paralog of the ATP-dependent protease La (LonA, TIGR00763). LonB proteins are found strictly, and almost universally, in endospore-forming bacteria. This protease was shown, in Bacillus subtilis, to be expressed specifically in the forespore, during sporulation, under control of sigma(F). The lonB gene, despite location immediately upstream of lonA, was shown to be monocistronic. LonB appears able to act on sigma(H) for post-translation control, but lonB mutation did not produce an obvious sporulation defect under the conditions tested. Note that additional paralogs of LonA and LonB occur in the Clostridium lineage and this model selects only one per species as the protein that corresponds to LonB in B. subtilis.
Probab=30.30 E-value=83 Score=32.55 Aligned_cols=54 Identities=26% Similarity=0.255 Sum_probs=39.0
Q ss_pred ccccchHHHHHHHHHHH---HHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchH
Q psy3459 130 NETIAKDARECVQECVS---EFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE 187 (296)
Q Consensus 130 ~~~iskdAkeai~~cas---eFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~ 187 (296)
++.+++++.+.|.+.+. +.++.+. .|..+|..++|++|+.+||.|++. .+.|.+
T Consensus 280 ~i~is~~al~~I~~y~~n~Rel~nll~-~Aa~~A~~~~~~~It~~dI~~vl~---~~~~~~ 336 (531)
T TIGR02902 280 GINLEKHALELIVKYASNGREAVNIVQ-LAAGIALGEGRKRILAEDIEWVAE---NGNYHP 336 (531)
T ss_pred CCCcCHHHHHHHHHhhhhHHHHHHHHH-HHHHHHhhCCCcEEcHHHHHHHhC---Cccccc
Confidence 46789999888766554 4444444 455677888999999999999965 445544
No 145
>KOG3219|consensus
Probab=29.93 E-value=35 Score=31.35 Aligned_cols=63 Identities=13% Similarity=0.051 Sum_probs=46.9
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCC-CcccchhHhhchhhcCCc
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKR-KTINGEDILFAMSALGFD 183 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kR-KTI~~eDVl~AL~~LgF~ 183 (296)
.+++....-... |+.-+.-++.--|.+||.=|--+|.++|..-+. --+.|.||=.|...|+..
T Consensus 118 iKkL~~~itg~~-v~~nv~Ia~~GiaKvFVGEvVEeAl~V~~~~~e~~PLqP~HIREA~rrL~~q 181 (195)
T KOG3219|consen 118 IKKLMSSITGQS-VSENVAIAMAGIAKVFVGEVVEEALDVREEWGESGPLQPKHIREAYRRLKLQ 181 (195)
T ss_pred HHHHHHHHhCCc-cCcceeeeecchhhHhHHHHHHHHHHHHHHhccCCCCCcHHHHHHHHHHHhc
Confidence 444433333333 777777788889999999999999999986654 348899998888777654
No 146
>COG1067 LonB Predicted ATP-dependent protease [Posttranslational modification, protein turnover, chaperones]
Probab=26.27 E-value=36 Score=36.42 Aligned_cols=32 Identities=31% Similarity=0.365 Sum_probs=27.8
Q ss_pred HHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 147 EFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 147 eFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.-.+.|. +|+++|..++++-|+++||.+|++.
T Consensus 367 dl~~lv~-~A~~ia~~~~~~~I~ae~Ve~a~~~ 398 (647)
T COG1067 367 DLGNLVR-EAGDIAVSEGRKLITAEDVEEALQK 398 (647)
T ss_pred HHHHHHH-HhhHHHhcCCcccCcHHHHHHHHHh
Confidence 3445555 9999999999999999999999987
No 147
>PTZ00017 histone H2A; Provisional
Probab=25.71 E-value=87 Score=27.16 Aligned_cols=59 Identities=14% Similarity=0.145 Sum_probs=37.0
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|.|++... ..+|+..|--.+.-+---+..=|-.-|-..|...+++-|+|.||..|+..
T Consensus 34 ~R~Lk~g~~-a~RV~a~A~VYLAAVLEYLtaEILELAgNaa~d~kk~RItPrHi~lAI~n 92 (134)
T PTZ00017 34 HRYLKKGRY-AKRVGAGAPVYLAAVLEYLTAEVLELAGNAAKDNKKKRITPRHIQLAIRN 92 (134)
T ss_pred HHHHhccch-hccccccchhhhHHHHHHHHHHHHHHHHHHHHhcCCCeecHHHHHhhccC
Confidence 455544322 23777776665554433333333334566778889999999999999853
No 148
>PF00356 LacI: Bacterial regulatory proteins, lacI family; InterPro: IPR000843 Numerous bacterial transcription regulatory proteins bind DNA via a helix-turn-helix (HTH) motif. These proteins are very diverse, but for convenience may be grouped into subfamilies on the basis of sequence similarity. One such family groups together a range of proteins, including ascG, ccpA, cytR, ebgR, fruR, galR, galS, lacI, malI, opnR, purF, rafR, rbtR and scrR [, ]. Within this family, the HTH motif is situated towards the N terminus.; GO: 0003700 sequence-specific DNA binding transcription factor activity, 0006355 regulation of transcription, DNA-dependent, 0005622 intracellular; PDB: 3KJX_C 1ZAY_A 1VPW_A 2PUA_A 1QQA_A 1PNR_A 1JFT_A 1QP4_A 2PUD_A 1JH9_A ....
Probab=25.14 E-value=1.5e+02 Score=20.70 Aligned_cols=32 Identities=16% Similarity=0.387 Sum_probs=26.4
Q ss_pred CCchhHHHHHHHhhCCCCCcccHHHHHHHHHHHHHH
Q psy3459 9 FLPIANVAKIMKKAIPESGKIAKDARECVQECVSEF 44 (296)
Q Consensus 9 ~LP~A~I~RIiK~~LP~~~rISkDA~~al~~~a~eF 44 (296)
.+..++|.|++... .+||.+.++-+.+++.+.
T Consensus 10 gvS~~TVSr~ln~~----~~vs~~tr~rI~~~a~~l 41 (46)
T PF00356_consen 10 GVSKSTVSRVLNGP----PRVSEETRERILEAAEEL 41 (46)
T ss_dssp TSSHHHHHHHHTTC----SSSTHHHHHHHHHHHHHH
T ss_pred CcCHHHHHHHHhCC----CCCCHHHHHHHHHHHHHH
Confidence 57789999999865 489999999998887653
No 149
>PRK00080 ruvB Holliday junction DNA helicase RuvB; Reviewed
Probab=24.92 E-value=2.3e+02 Score=26.93 Aligned_cols=71 Identities=15% Similarity=0.173 Sum_probs=46.8
Q ss_pred CchhHHHHHHHhhCC-CCCcccHHHHHHHHHHHH---HHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCc
Q psy3459 10 LPIANVAKIMKKAIP-ESGKIAKDARECVQECVS---EFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDS 80 (296)
Q Consensus 10 LP~A~I~RIiK~~LP-~~~rISkDA~~al~~~a~---eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~ 80 (296)
++...+..|++.... .+..++.|+...|.+.|. -.+..+-..+.+.+...+.+.|+.++|..++..++.+.
T Consensus 180 ~~~~e~~~il~~~~~~~~~~~~~~~~~~ia~~~~G~pR~a~~~l~~~~~~a~~~~~~~I~~~~v~~~l~~~~~~~ 254 (328)
T PRK00080 180 YTVEELEKIVKRSARILGVEIDEEGALEIARRSRGTPRIANRLLRRVRDFAQVKGDGVITKEIADKALDMLGVDE 254 (328)
T ss_pred CCHHHHHHHHHHHHHHcCCCcCHHHHHHHHHHcCCCchHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHHhCCCc
Confidence 334445555554432 346789998888777662 33444445566667666777999999999998876653
No 150
>PF07647 SAM_2: SAM domain (Sterile alpha motif); InterPro: IPR011510 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents a second domain related to the SAM domain. ; GO: 0005515 protein binding; PDB: 1B0X_A 1X9X_B 1OW5_A 1V38_A 3BS7_A 3BS5_A 3TAD_A 3TAC_B 2K60_A 2DL0_A ....
Probab=24.24 E-value=57 Score=23.30 Aligned_cols=25 Identities=24% Similarity=0.453 Sum_probs=21.1
Q ss_pred cccchhHhhchhhcCCccchHHHHH
Q psy3459 167 TINGEDILFAMSALGFDSYVEPLKI 191 (296)
Q Consensus 167 TI~~eDVl~AL~~LgF~~yv~~l~~ 191 (296)
+=++++|..-|..+||+.|.+....
T Consensus 3 ~w~~~~v~~WL~~~gl~~y~~~f~~ 27 (66)
T PF07647_consen 3 TWSPEDVAEWLKSLGLEQYADNFRE 27 (66)
T ss_dssp GHCHHHHHHHHHHTTCGGGHHHHHH
T ss_pred CCCHHHHHHHHHHCCcHHHHHHHHH
Confidence 4478999999999999999987664
No 151
>CHL00081 chlI Mg-protoporyphyrin IX chelatase
Probab=23.94 E-value=1.5e+02 Score=29.23 Aligned_cols=52 Identities=21% Similarity=0.272 Sum_probs=40.1
Q ss_pred hhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 21 KAIPESGKIAKDARECVQECVSEFI-------SFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 21 ~~LP~~~rISkDA~~al~~~a~eFI-------~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
+.+|. +.||++....+.+.|..+= .++...|.-.|--+||..|+++||..+.
T Consensus 261 ~~~~~-V~v~~~~~~yi~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~pdDv~~~a 319 (350)
T CHL00081 261 NLLPK-VEIDYDLRVKISQICSELDVDGLRGDIVTNRAAKALAAFEGRTEVTPKDIFKVI 319 (350)
T ss_pred HhcCC-CccCHHHHHHHHHHHHHHCCCCChHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 34444 7899999988888887753 3455667778888999999999998775
No 152
>PF06782 UPF0236: Uncharacterised protein family (UPF0236); InterPro: IPR009620 This is a group of proteins of unknown function.
Probab=23.59 E-value=1.3e+02 Score=30.64 Aligned_cols=57 Identities=18% Similarity=0.222 Sum_probs=43.9
Q ss_pred cCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCcc
Q psy3459 126 QNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDS 184 (296)
Q Consensus 126 ~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~ 184 (296)
.+++.-++|.+++..+.+.|+. .+|=. .|..+-...+.-+||.+-|.+++..+|+..
T Consensus 111 Gl~~~~R~S~~~~~~i~~~a~~-~sYr~-aa~~l~~~~~~~~iS~~tV~~~v~~~g~~~ 167 (470)
T PF06782_consen 111 GLKKYQRISPELKEKIVELATE-MSYRK-AAEILEELLGNVSISKQTVWNIVKEAGFEE 167 (470)
T ss_pred CCCcccchhHHHHHHHHHHHhh-cCHHH-HHHHHhhccCCCccCHHHHHHHHHhccchh
Confidence 3567789999999999999888 66642 233333455779999999999999999543
No 153
>KOG3334|consensus
Probab=23.44 E-value=1.5e+02 Score=26.15 Aligned_cols=59 Identities=19% Similarity=0.268 Sum_probs=42.5
Q ss_pred HHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcCCccchH-HHHHHHHHHHHH
Q psy3459 141 VQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVE-PLKIYLQKYREA 199 (296)
Q Consensus 141 i~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~LgF~~yv~-~l~~~L~~~re~ 199 (296)
|.+-+--++.-|-..|.-++.-.+|.||.++||--|++-.+=-+|.. |=+++|-++-..
T Consensus 39 lLefa~rYtt~vL~DA~vys~HA~ka~i~~eDVrlA~~~~~~~sf~~pPpRe~lL~lA~~ 98 (148)
T KOG3334|consen 39 LLEFAYRYTTTVLDDAKVYSSHAKKATIDAEDVRLAIQMRVDHSFTPPPPREFLLELAAE 98 (148)
T ss_pred HHHHHHHHHHHHHHHHHHHHHhccCCCCcHHHHHHHHHHHhccccCCCCchHHHHHHHHh
Confidence 34444455555666788888888999999999999999988878877 444555544433
No 154
>PRK09862 putative ATP-dependent protease; Provisional
Probab=23.44 E-value=2e+02 Score=29.94 Aligned_cols=58 Identities=12% Similarity=0.147 Sum_probs=42.0
Q ss_pred CcccHHHHHHHHHHHHHH------HHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHH
Q psy3459 27 GKIAKDARECVQECVSEF------ISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP 84 (296)
Q Consensus 27 ~rISkDA~~al~~~a~eF------I~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~ 84 (296)
..++.++...+..+...+ .+.|-.-|..+|--+++..|+++||..|+.=-+++.....
T Consensus 437 ~~l~~~~~~~l~~~~~~~~lS~Ra~~rlLrvARTiADL~g~~~V~~~hv~eAl~yR~~~~~~~~ 500 (506)
T PRK09862 437 CKLESEDARWLEETLIHLGLSIRAWQRLLKVARTIADIDQSDIITRQHLQEAVSYRAIDRLLIH 500 (506)
T ss_pred hCCCHHHHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHcCCCCCCHHHHHHHHHhhcccHHHHH
Confidence 356777777776655433 4556677888999999999999999999975555544333
No 155
>TIGR02030 BchI-ChlI magnesium chelatase ATPase subunit I. This model represents one of two ATPase subunits of the trimeric magnesium chelatase responsible for insertion of magnesium ion into protoporphyrin IX. This is an essential step in the biosynthesis of both chlorophyll and bacteriochlorophyll. This subunit is found in green plants, photosynthetic algae, cyanobacteria and other photosynthetic bacteria.
Probab=23.27 E-value=1.7e+02 Score=28.70 Aligned_cols=53 Identities=21% Similarity=0.201 Sum_probs=38.9
Q ss_pred HhhCCCCCcccHHHHHHHHHHHHHHH-------HHHHHHhhHHHHhcCCCccCcccHHHHh
Q psy3459 20 KKAIPESGKIAKDARECVQECVSEFI-------SFITSEASDRCHLEKRKTINGEDILFAM 73 (296)
Q Consensus 20 K~~LP~~~rISkDA~~al~~~a~eFI-------~~las~An~~a~~~~RKTI~~eDVl~AL 73 (296)
++.+|. +.|+++....+.+.+..+= .++...|...|.-+||..|+++||..+.
T Consensus 247 ~~~~~~-V~v~d~~~~~i~~l~~~~~~~s~Ra~i~l~raArA~Aal~GR~~V~~dDv~~~a 306 (337)
T TIGR02030 247 QNLLPQ-VTIPYDVLVKVAELCAELDVDGLRGELTLNRAAKALAAFEGRTEVTVDDIRRVA 306 (337)
T ss_pred HHHhcc-CcCCHHHHHHHHHHHHHHCCCCCcHHHHHHHHHHHHHHHcCCCCCCHHHHHHHH
Confidence 334444 6899998888888776543 2344566777888999999999998764
No 156
>PLN00157 histone H2A; Provisional
Probab=22.90 E-value=1.2e+02 Score=26.33 Aligned_cols=59 Identities=12% Similarity=0.116 Sum_probs=35.4
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|.+++.. -..+|+..|--.+.-+---.+.=|-.-|-..|...+++-|+|.||..|+..
T Consensus 33 ~R~Lk~g~-~a~RIg~~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 91 (132)
T PLN00157 33 ARYLKAGK-YATRVGAGAPVYLAAVLEYLAAEVLELAGNAARDNKKSRIVPRHIQLAVRN 91 (132)
T ss_pred HHHHhcCc-hhhhcCCCcHhHHHHHHHHHHHHHHHHHHHHHHhcCCccccHHHHhhcccC
Confidence 45554432 235777776655544322222222223555678889999999999999854
No 157
>TIGR02442 Cob-chelat-sub cobaltochelatase subunit. A number of genomes (actinobacteria, cyanobacteria, betaproteobacteria and pseudomonads) which apparently biosynthesize B12, encode a cobN gene but are demonstrably lacking cobS and cobT. These genomes do, however contain a homolog (modelled here) of the magnesium chelatase subunits BchI/BchD family. Aside from the cyanobacteria (which have a separate magnesium chelatase trimer), these species do not make chlorins, so do not have any use for a magnesium chelatase. Furthermore, in nearly all cases the members of this family are proximal to either CobN itself or other genes involved in cobalt transport or B12 biosynthesis.
Probab=22.39 E-value=1.9e+02 Score=30.67 Aligned_cols=50 Identities=22% Similarity=0.248 Sum_probs=40.3
Q ss_pred CCcccHHHHHHHHHHHHHHH-------HHHHHHhhHHHHhcCCCccCcccHHHHhhh
Q psy3459 26 SGKIAKDARECVQECVSEFI-------SFITSEASDRCHLEKRKTINGEDILFAMSA 75 (296)
Q Consensus 26 ~~rISkDA~~al~~~a~eFI-------~~las~An~~a~~~~RKTI~~eDVl~AL~~ 75 (296)
.+.|+.+....+...+..+- .++..-|..+|.-++|.+|+.+||..|+.-
T Consensus 247 ~V~is~~~~~~l~~~~~~~~i~s~Ra~i~~~r~Ara~AaL~gr~~V~~~Dv~~A~~l 303 (633)
T TIGR02442 247 SVRISDSLIRFISELCIEFGVDGHRADIVMARAARALAALDGRRRVTAEDVREAAEL 303 (633)
T ss_pred CCCCCHHHHHHHHHHHHHhCCCCccHHHHHHHHHHHHHHHcCCCcCCHHHHHHHHHH
Confidence 47899999999988886652 345566777888999999999999888754
No 158
>PTZ00252 histone H2A; Provisional
Probab=22.38 E-value=71 Score=27.75 Aligned_cols=55 Identities=15% Similarity=0.260 Sum_probs=32.8
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhh------cCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHL------EKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~------~kRKTI~~eDVl~AL~~ 179 (296)
.|.+++..- .-+|+.-|--.+.- -+.||+++-.+.+-+ .+++-|+|.||..|+..
T Consensus 32 ~R~Lr~g~y-a~RIga~ApVYLAA----VLEYLtaEVLELAgnaa~d~~~kk~RItPrHi~lAIrN 92 (134)
T PTZ00252 32 GSLLRRGQY-ARRIGASGAVYMAA----VLEYLTAELLELSVKAAAQQAKKPKRLTPRTVTLAVRH 92 (134)
T ss_pred HHHHHcCCc-ccccCCccHHHHHH----HHHHHHHHHHHHHHHHHHhccCCcccccHHHHHhhccC
Confidence 444443322 23666555433332 246777776665532 46788999999999854
No 159
>cd00166 SAM Sterile alpha motif.; Widespread domain in signalling and nuclear proteins. In EPH-related tyrosine kinases, appears to mediate cell-cell initiated signal transduction via the binding of SH2-containing proteins to a conserved tyrosine that is phosphorylated. In many cases mediates homodimerization.
Probab=22.24 E-value=48 Score=22.87 Aligned_cols=24 Identities=21% Similarity=0.408 Sum_probs=19.8
Q ss_pred cchhHhhchhhcCCccchHHHHHH
Q psy3459 169 NGEDILFAMSALGFDSYVEPLKIY 192 (296)
Q Consensus 169 ~~eDVl~AL~~LgF~~yv~~l~~~ 192 (296)
++++|..-|+.+|+++|++.+...
T Consensus 3 ~~~~V~~wL~~~~~~~y~~~f~~~ 26 (63)
T cd00166 3 SPEDVAEWLESLGLGQYADNFREN 26 (63)
T ss_pred CHHHHHHHHHHcChHHHHHHHHHc
Confidence 678999999999998888877643
No 160
>PLN00156 histone H2AX; Provisional
Probab=22.02 E-value=1.3e+02 Score=26.19 Aligned_cols=55 Identities=16% Similarity=0.280 Sum_probs=34.7
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHH----hhHHhhhcCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSE----ASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~----An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|.|++.. -..+|+..|--.+.-+ +.||+++ |-..|...+++-|+|.|+..|+..
T Consensus 36 ~R~Lk~g~-ya~RVga~ApVYLAAV----LEYLtaEVLELAgNaa~d~kk~RItPrHi~lAIrn 94 (139)
T PLN00156 36 ARFLKAGK-YAERVGAGAPVYLSAV----LEYLAAEVLELAGNAARDNKKNRIVPRHIQLAVRN 94 (139)
T ss_pred HHHHhcCC-hhhccCCccHHHHHHH----HHHHHHHHHHHHHHHHHHcCCCcCcHHHHHhhccC
Confidence 45554432 2347777766555443 2344443 445678889999999999999854
No 161
>TIGR00635 ruvB Holliday junction DNA helicase, RuvB subunit. RuvA specifically binds Holliday junctions as a sandwich of two tetramers and maintains the configuration of the junction. It forms a complex with two hexameric rings of RuvB, the subunit that contains helicase activity. The complex drives ATP-dependent branch migration of the Holliday junction recombination intermediate. The endonuclease RuvC resolves junctions.
Probab=21.89 E-value=3.5e+02 Score=24.89 Aligned_cols=68 Identities=18% Similarity=0.195 Sum_probs=43.7
Q ss_pred hhHHHHHHHhhCC-CCCcccHHHHHHHHHHHH---HHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC
Q psy3459 12 IANVAKIMKKAIP-ESGKIAKDARECVQECVS---EFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD 79 (296)
Q Consensus 12 ~A~I~RIiK~~LP-~~~rISkDA~~al~~~a~---eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~ 79 (296)
...+..+++.... .+..++.++...|.+.+. -++.-+...+...+...+...|+.++|..++..++++
T Consensus 161 ~~e~~~il~~~~~~~~~~~~~~al~~ia~~~~G~pR~~~~ll~~~~~~a~~~~~~~it~~~v~~~l~~l~~~ 232 (305)
T TIGR00635 161 VEELAEIVSRSAGLLNVEIEPEAALEIARRSRGTPRIANRLLRRVRDFAQVRGQKIINRDIALKALEMLMID 232 (305)
T ss_pred HHHHHHHHHHHHHHhCCCcCHHHHHHHHHHhCCCcchHHHHHHHHHHHHHHcCCCCcCHHHHHHHHHHhCCC
Confidence 3344455544332 245788888877777653 2334444456667766666789999999999886554
No 162
>PHA02940 hypothetical protein; Provisional
Probab=21.77 E-value=2.3e+02 Score=27.46 Aligned_cols=123 Identities=11% Similarity=0.201 Sum_probs=62.0
Q ss_pred hHHHHHHHhhCCCCCccc-HHHHHHHHHHHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCCcchHH---HHHH
Q psy3459 13 ANVAKIMKKAIPESGKIA-KDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFDSYVEP---LKIY 88 (296)
Q Consensus 13 A~I~RIiK~~LP~~~rIS-kDA~~al~~~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~---l~~~ 88 (296)
.++.|+|++-+..+..++ .+..+.-|+ +.--|..|+..=.+..+.+.|+||. +++-+-|. =|-+|.+- |+..
T Consensus 113 nal~~~i~~~ik~~~~~t~~~~i~Ftqk-A~dtv~~la~~yvq~vk~d~r~~~a-~~l~keLs--~~~d~~enepdle~d 188 (315)
T PHA02940 113 NALLRLIRSFIKPEPTLTTPLFIDFTQK-AKDTVILLAGRYVQDVKKDDRRTIA-NKLSKELS--WTIDYQENEPDLESD 188 (315)
T ss_pred HHHHHHHHHhCCCCCCcCchHHHHHHHH-hhhHHHHHHHHHHHHccccHHHHHH-HHHHhhhh--HHHHHHhcCcchhhh
Confidence 467788888775433332 222222222 2222222222222233345555552 23322221 11233333 5555
Q ss_pred HHHHHHHhccccccchhhhhhhhhhhhccchhhhhhhcCCCccccchHHHHHHHHHH
Q psy3459 89 LQKYREATKGEKSVNCEVYQEISVEDVFQSSGTILEQQNGQNETIAKDARECVQECV 145 (296)
Q Consensus 89 L~~~re~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~~lp~~~~iskdAkeai~~ca 145 (296)
+.++.+.-..+-......| ..+..+..+|+..--.+++..++|+.+|-+=+
T Consensus 189 ~keie~~lE~~~dl~rGtY------~vL~~ald~m~ehy~kGi~~an~a~~~~~~da 239 (315)
T PHA02940 189 FKEIEEELEEKDDLSRGTY------KVLKRALDLMKEHYWKGIRLANEAKAMIKRDA 239 (315)
T ss_pred HHHHHHHHhccchhhhhHH------HHHHHHHHHHHHHHhhccccchhHHHHHHhhc
Confidence 5555554444433232333 23457788898888899999999999995543
No 163
>PF00536 SAM_1: SAM domain (Sterile alpha motif); InterPro: IPR021129 The sterile alpha motif (SAM) domain is a putative protein interaction module present in a wide variety of proteins [] involved in many biological processes. The SAM domain that spreads over around 70 residues is found in diverse eukaryotic organisms []. SAM domains have been shown to homo- and hetero-oligomerise, forming multiple self-association architectures and also binding to various non-SAM domain-containing proteins [], nevertheless with a low affinity constant []. SAM domains also appear to possess the ability to bind RNA []. Smaug, a protein that helps to establish a morphogen gradient in Drosophila embryos by repressing the translation of nanos (nos) mRNA, binds to the 3' untranslated region (UTR) of nos mRNA via two similar hairpin structures. The 3D crystal structure of the Smaug RNA-binding region shows a cluster of positively charged residues on the Smaug-SAM domain, which could be the RNA-binding surface. This electropositive potential is unique among all previously determined SAM-domain structures and is conserved among Smaug-SAM homologs. These results suggest that the SAM domain might have a primary role in RNA binding. Structural analyses show that the SAM domain is arranged in a small five-helix bundle with two large interfaces []. In the case of the SAM domain of EphB2, each of these interfaces is able to form dimers. The presence of these two distinct intermonomers binding surface suggest that SAM could form extended polymeric structures []. This entry represents type 1 SAM domains. ; PDB: 2KIV_A 3HIL_B 3KKA_A 3K1R_B 3SEN_B 3SEI_B 1V85_A 2KE7_A 2EAM_A 1WWV_A ....
Probab=21.39 E-value=65 Score=22.89 Aligned_cols=22 Identities=27% Similarity=0.496 Sum_probs=19.3
Q ss_pred cchhHhhchhhcCCccchHHHH
Q psy3459 169 NGEDILFAMSALGFDSYVEPLK 190 (296)
Q Consensus 169 ~~eDVl~AL~~LgF~~yv~~l~ 190 (296)
++++|..-|+.+|++.|++...
T Consensus 4 ~~~~V~~WL~~~~l~~y~~~F~ 25 (64)
T PF00536_consen 4 SVEDVSEWLKSLGLEQYAENFE 25 (64)
T ss_dssp SHHHHHHHHHHTTGGGGHHHHH
T ss_pred CHHHHHHHHHHCCCHHHHHHHH
Confidence 6789999999999999998763
No 164
>COG5247 BUR6 Class 2 transcription repressor NC2, alpha subunit (DRAP1 homolog) [Transcription]
Probab=21.01 E-value=1.5e+02 Score=24.88 Aligned_cols=56 Identities=11% Similarity=0.107 Sum_probs=45.7
Q ss_pred cCCCc-cccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 126 QNGQN-ETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 126 ~lp~~-~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
++..+ -+|+.-+--...++---|+..|-..+-..++..+-|-|+++++..|.+.-+
T Consensus 34 Q~deDiGKV~q~tPVIaskalE~Fl~~iv~~s~k~aR~~~skR~t~e~lk~a~~sde 90 (113)
T COG5247 34 QLDEDIGKVGQSTPVIASKALEMFLTEIVGLSLKEARKKSSKRMTSEFLKRATESDE 90 (113)
T ss_pred HhhhhhhhhhhcchHHHHHHHHHHHHHHHHHHHHHHHhccchhhHHHHHHHHHhhhH
Confidence 44433 366666667778889999999999999999999999999999999977543
No 165
>PF09371 Tex_N: Tex-like protein N-terminal domain; InterPro: IPR018974 This presumed domain is found at the N terminus of Q45388 from SWISSPROT. This protein defines a novel family of prokaryotic transcriptional accessory factors []. ; PDB: 2OCE_A 3BZK_A 3BZC_A.
Probab=20.98 E-value=39 Score=30.70 Aligned_cols=23 Identities=35% Similarity=0.355 Sum_probs=12.1
Q ss_pred CCCCCchhHHHHHHHH-HhhcCcccc
Q psy3459 239 FDSYVEPLKIYLQKYR-EATKGEKSV 263 (296)
Q Consensus 239 f~~~~~~~~~~~~~~~-~~~~~~~~~ 263 (296)
|+.+-++||| +||| |++||--.+
T Consensus 19 l~eG~TvPFI--ARYRKe~TG~Lde~ 42 (193)
T PF09371_consen 19 LDEGNTVPFI--ARYRKEMTGGLDEV 42 (193)
T ss_dssp HHTT--HHHH--HHH-HHHHTS--HH
T ss_pred HhCCCCcchh--hhhhhhhhCCCCHH
Confidence 3455677775 8998 678875433
No 166
>PLN00153 histone H2A; Provisional
Probab=20.98 E-value=1.4e+02 Score=25.74 Aligned_cols=59 Identities=15% Similarity=0.148 Sum_probs=35.4
Q ss_pred hhhhhhcCCCccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhh
Q psy3459 120 GTILEQQNGQNETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSA 179 (296)
Q Consensus 120 ~rimk~~lp~~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~ 179 (296)
.|.+++... ..+|+..|--.+.-+---.+.=|-.-|-..|...+++-|+|.|+..|+..
T Consensus 31 ~R~Lr~g~~-a~Rvga~A~VYLAAVLEYLtaEVLELAgnaa~d~kk~RItPrHi~lAI~n 89 (129)
T PLN00153 31 ARYLKKGKY-AERIGAGAPVYLAAVLEYLTAEVLELAGNAARDNKKNRIVPRHIQLAIRN 89 (129)
T ss_pred HHHHhcCch-hhccCCCchHHHHHHHHHHHHHHHHHHHHHHHhcCCCccChHHHHhhccC
Confidence 455544322 34777776655544322222222333455678889999999999999854
No 167
>COG0542 clpA ATP-binding subunits of Clp protease and DnaK/DnaJ chaperones [Posttranslational modification, protein turnover, chaperones]
Probab=20.69 E-value=2e+02 Score=31.68 Aligned_cols=98 Identities=15% Similarity=0.131 Sum_probs=53.5
Q ss_pred HhhHHHHhcCCCccCcccHHHHhhhcCCCcchHHHHHHHHHHH-HHhccccccchhhhhhhhhhhhccchhhhhhhcCCC
Q psy3459 51 EASDRCHLEKRKTINGEDILFAMSALGFDSYVEPLKIYLQKYR-EATKGEKSVNCEVYQEISVEDVFQSSGTILEQQNGQ 129 (296)
Q Consensus 51 ~An~~a~~~~RKTI~~eDVl~AL~~lgF~~yv~~l~~~L~~~r-e~~k~kk~~~~e~~~~~~~e~Lf~~s~rimk~~lp~ 129 (296)
.|.+.|...+...++++|++.||-..+=+. .. +..+- .....+ .+....++ ......+.
T Consensus 12 ~a~~~a~~~~h~~~~~eHll~~ll~~~~~~--~~----l~~~~~~~~~l~----~~~~~~~~----------~~~~~~~~ 71 (786)
T COG0542 12 LAQELARMRRHEYVTPEHLLLALLDQPKGD--EL----LNLCGIDLDKLR----QELEEFID----------KLPKVLGS 71 (786)
T ss_pred HHHHHHHHhCCCcccHHHHHHHHHcCCchH--HH----HHHcCCCHHHHH----HHHHHHHh----------ccCCCCCC
Confidence 467778888999999999999985544332 11 11110 000000 00111110 00000000
Q ss_pred ccccchHHHHHHHHHHHHHHHHHHHHhhHHhhhcCCCcccchhHhhchhhcC
Q psy3459 130 NETIAKDARECVQECVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALG 181 (296)
Q Consensus 130 ~~~iskdAkeai~~caseFI~~lts~An~~c~~~kRKTI~~eDVl~AL~~Lg 181 (296)
..+|......+++ |...+...++..|+.+|+|-|+-.-+
T Consensus 72 -~~~s~~~~~~~~~------------a~~~a~~~~~~~v~~~~llla~~~~~ 110 (786)
T COG0542 72 -PYLSPRLKRVLER------------AWLLAQSLGDEYVSTEHLLLALLNEP 110 (786)
T ss_pred -CCCCHHHHHHHHH------------HHHHHHhccCccccHHHHHHHHhccc
Confidence 2345555555544 66777777899999999999886655
No 168
>cd04752 Commd4 COMM_Domain containing protein 4. The COMM Domain is found at the C-terminus of a variety of proteins; presumably all COMM_Domain containing proteins are located in the nucleus and the COMM domain plays a role in protein-protein interactions. Several family members have been shown to bind and inhibit NF-kappaB.
Probab=20.01 E-value=6e+02 Score=22.27 Aligned_cols=50 Identities=20% Similarity=0.286 Sum_probs=34.3
Q ss_pred HHHHHHHHHHHHhhHHHHhcCCCccCcccHHHHhhhcCCC-cchHHHHHHHHHHHHHh
Q psy3459 40 CVSEFISFITSEASDRCHLEKRKTINGEDILFAMSALGFD-SYVEPLKIYLQKYREAT 96 (296)
Q Consensus 40 ~a~eFI~~las~An~~a~~~~RKTI~~eDVl~AL~~lgF~-~yv~~l~~~L~~~re~~ 96 (296)
.+...++||-..| -|..++++++..-|+.|||+ +.++.+...+..+++..
T Consensus 43 ~~va~l~fiL~~A-------~k~n~~~~~l~~eL~~lglp~e~~~~l~~~~~~~~~~l 93 (174)
T cd04752 43 ASIAVLSFILSSA-------AKYNVDGESLSSELQQLGLPKEHATSLCRSYEEKQSKL 93 (174)
T ss_pred HHHHHHHHHHHHH-------HHcCCCHHHHHHHHHHcCCCHHHHHHHHHHHHHHHHHH
Confidence 3444555554443 35559999999999999998 56677777666666543
Done!