TF2B1 - SULSO - GREMLIN Contacts

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TF2B1 - Transcription initiation factor IIB 1

UniProt:	P58111	Sequences: MLYLSEENKSVSTPCPPDKIIFDAERGEYICSETGEVLEDKIIDQGPEWRAFTPEEKEKRSRVGGPLNNTIHDRGLSTLIDWKDKDAMGRTLDPKRRLEALRWRKWQIRARIQSSIDRNLAQAMNELERIGNLLNLPKSVKDEAALIYRKAVEKGLVRGRSIESVVAAAIYAACRRMKLARTLDEIAQYTKANRKEVARCYRLLLRELDVSVPVSDPKDYVTRIANLLGLSGAVMKTAAEIIDKAKGSGLTAGKDPAGLAAAAIYIASLLHDERRTQKEIAQVAGVTEVTVRNRYKELTQELKISIPTQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	309 (277)
Sequences:	1030 (673)
Seq/√Len:	40.4

HALSA - TF2B4 TF2B7 TF2B2 TF2B6 TF2B3 TF2B5 TF2B1
SULSO - TF2B1 TF2B2

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
225_A	264_I	6.441	1.00
31_C	34_T	3.927	1.00
131_G	170_I	3.685	1.00
294_R	297_E	3.618	1.00
123_A	148_Y	3.540	1.00
231_S	273_E	3.530	1.00
12_S	34_T	3.403	1.00
237_T	271_H	3.392	1.00
277_Q	292_R	3.305	1.00
23_D	26_R	2.857	1.00
126_E	129_R	2.783	1.00
278_K	288_E	2.703	1.00
124_M	145_A	2.625	1.00
131_G	141_K	2.588	1.00
130_I	170_I	2.571	1.00
59_K	64_G	2.468	1.00
51_A	54_P	2.416	1.00
170_I	186_I	2.415	1.00
20_I	29_Y	2.390	1.00
48_E	62_R	2.368	1.00
12_S	15_C	2.326	1.00
237_T	240_E	2.296	1.00
15_C	31_C	2.268	1.00
194_R	198_A	2.204	1.00
144_A	173_A	2.167	0.99
136_L	170_I	2.149	0.99
288_E	296_K	2.044	0.99
20_I	38_L	2.036	0.99
159_G	256_P	1.996	0.99
143_E	176_R	1.987	0.99
130_I	189_Y	1.965	0.99
12_S	31_C	1.951	0.99
238_A	267_A	1.886	0.98
238_A	260_A	1.885	0.98
72_H	75_G	1.885	0.98
12_S	16_P	1.860	0.98
140_V	173_A	1.854	0.98
19_K	33_E	1.750	0.97
224_I	228_L	1.746	0.97
278_K	291_V	1.716	0.97
15_C	34_T	1.716	0.97
181_R	185_E	1.653	0.96
241_I	267_A	1.624	0.96
224_I	264_I	1.621	0.96
123_A	199_R	1.610	0.96
186_I	189_Y	1.585	0.95
205_L	212_V	1.576	0.95
241_I	263_A	1.568	0.95
83_K	117_D	1.554	0.95
50_R	62_R	1.531	0.94
48_E	60_R	1.528	0.94
242_I	259_L	1.506	0.94
258_G	262_A	1.490	0.93
258_G	290_T	1.489	0.93
51_A	56_E	1.484	0.93
175_R	198_A	1.466	0.93
148_Y	157_V	1.455	0.93
261_A	284_A	1.439	0.92
146_L	149_R	1.420	0.92
218_K	243_D	1.420	0.92
46_G	49_W	1.408	0.91
150_K	154_K	1.395	0.91
100_A	103_W	1.377	0.90
268_S	283_V	1.370	0.90
216_D	219_D	1.368	0.90
276_T	279_E	1.367	0.90
242_I	263_A	1.364	0.90
72_H	292_R	1.362	0.90
230_L	275_R	1.357	0.90
279_E	283_V	1.354	0.90
274_R	279_E	1.342	0.89
234_V	271_H	1.327	0.89
183_L	194_R	1.301	0.88
185_E	223_R	1.300	0.88
234_V	273_E	1.295	0.87
220_Y	225_A	1.289	0.87
33_E	131_G	1.288	0.87
60_R	64_G	1.288	0.87
143_E	177_M	1.282	0.87
31_C	35_G	1.281	0.87
275_R	279_E	1.274	0.87
172_A	210_V	1.267	0.86
264_I	284_A	1.252	0.86
120_L	145_A	1.243	0.85
277_Q	289_V	1.240	0.85
29_Y	241_I	1.232	0.85
186_I	212_V	1.226	0.84
204_L	227_L	1.225	0.84
19_K	32_S	1.219	0.84
14_P	17_P	1.219	0.84
172_A	175_R	1.204	0.83
250_L	268_S	1.188	0.82
61_S	64_G	1.180	0.82
198_A	224_I	1.174	0.82
52_F	224_I	1.173	0.82
263_A	267_A	1.166	0.81
14_P	36_E	1.165	0.81
121_A	125_N	1.152	0.80
123_A	152_V	1.137	0.80
106_W	148_Y	1.137	0.80
123_A	127_L	1.126	0.79
183_L	198_A	1.125	0.79
262_A	290_T	1.125	0.79
272_D	276_T	1.125	0.79
68_N	83_K	1.114	0.78
11_V	32_S	1.111	0.78
131_G	259_L	1.109	0.78
171_Y	215_S	1.098	0.77
21_I	261_A	1.094	0.77
64_G	80_I	1.093	0.77
167_A	174_C	1.093	0.77
242_I	260_A	1.086	0.76
49_W	60_R	1.081	0.76
232_G	236_K	1.080	0.76
110_A	167_A	1.071	0.75
235_M	239_A	1.070	0.75
149_R	173_A	1.066	0.75
216_D	246_K	1.063	0.75
51_A	59_K	1.060	0.75
216_D	242_I	1.059	0.74
49_W	52_F	1.059	0.74
140_V	179_L	1.058	0.74
158_R	288_E	1.058	0.74
30_I	296_K	1.051	0.74
206_R	279_E	1.051	0.74
20_I	25_E	1.048	0.74
286_V	291_V	1.047	0.74
143_E	146_L	1.036	0.73
148_Y	162_I	1.028	0.72
66_P	72_H	1.027	0.72
22_F	39_E	1.025	0.72
186_I	249_G	1.023	0.72
33_E	137_P	1.023	0.72
165_V	200_C	1.014	0.71
140_V	246_K	1.011	0.71
76_L	80_I	1.002	0.70
181_R	223_R	0.998	0.70
30_I	283_V	0.998	0.70
261_A	291_V	0.995	0.70
115_S	168_A	0.993	0.70
119_N	172_A	0.989	0.69
49_W	66_P	0.987	0.69
102_R	106_W	0.987	0.69
136_L	300_Q	0.976	0.68
16_P	213_P	0.973	0.68
66_P	73_D	0.973	0.68
165_V	204_L	0.973	0.68
264_I	280_I	0.969	0.68
254_K	259_L	0.968	0.68
79_L	107_Q	0.963	0.67
258_G	286_V	0.956	0.67
268_S	274_R	0.954	0.66
237_T	270_L	0.945	0.66
68_N	258_G	0.934	0.65
193_N	197_V	0.933	0.65
145_A	149_R	0.932	0.65
195_K	296_K	0.932	0.65
23_D	27_G	0.930	0.64
244_K	248_S	0.925	0.64
136_L	174_C	0.924	0.64
117_D	154_K	0.921	0.64
78_T	107_Q	0.921	0.64
158_R	259_L	0.919	0.64
37_V	169_A	0.910	0.63
13_T	264_I	0.902	0.62
153_E	278_K	0.900	0.62
44_D	48_E	0.899	0.62
145_A	152_V	0.893	0.61
171_Y	174_C	0.891	0.61
26_R	284_A	0.884	0.60
218_K	285_G	0.883	0.60
151_A	210_V	0.881	0.60
221_V	242_I	0.880	0.60
172_A	268_S	0.878	0.60
231_S	234_V	0.876	0.60
180_A	219_D	0.876	0.60
36_E	76_L	0.876	0.60
48_E	52_F	0.871	0.59
22_F	28_E	0.867	0.59
141_K	170_I	0.867	0.59
193_N	196_E	0.864	0.59
144_A	169_A	0.863	0.59
275_R	288_E	0.861	0.58
109_R	253_G	0.861	0.58
243_D	247_G	0.860	0.58
127_L	166_V	0.855	0.58
63_V	79_L	0.854	0.58
281_A	284_A	0.851	0.58
214_V	276_T	0.849	0.57
123_A	262_A	0.846	0.57
127_L	148_Y	0.843	0.57
150_K	210_V	0.842	0.57
54_P	59_K	0.839	0.56
53_T	56_E	0.836	0.56
100_A	125_N	0.834	0.56
198_A	255_D	0.834	0.56
182_T	185_E	0.824	0.55
12_S	17_P	0.821	0.55
20_I	27_G	0.818	0.55
110_A	142_D	0.812	0.54
37_V	69_N	0.811	0.54
19_K	77_S	0.811	0.54
258_G	294_R	0.803	0.53
123_A	162_I	0.800	0.53
11_V	20_I	0.798	0.53
29_Y	32_S	0.792	0.52
218_K	246_K	0.791	0.52
210_V	242_I	0.789	0.52
223_R	255_D	0.783	0.51
123_A	151_A	0.783	0.51
37_V	179_L	0.783	0.51
119_N	148_Y	0.781	0.51
197_V	243_D	0.780	0.51
159_G	290_T	0.779	0.51
278_K	286_V	0.777	0.51
105_K	185_E	0.777	0.51
201_Y	253_G	0.776	0.51
134_L	247_G	0.773	0.50
40_D	45_Q	0.772	0.50
230_L	273_E	0.769	0.50
16_P	34_T	0.767	0.50
182_T	186_I	0.766	0.50
140_V	177_M	0.765	0.50
126_E	199_R	0.763	0.49
289_V	292_R	0.763	0.49
76_L	79_L	0.757	0.49
78_T	181_R	0.757	0.49
30_I	110_A	0.752	0.48
101_L	105_K	0.750	0.48
142_D	145_A	0.747	0.48
126_E	130_I	0.742	0.48
259_L	294_R	0.739	0.47
38_L	192_A	0.737	0.47
187_A	192_A	0.730	0.46
238_A	242_I	0.730	0.46
75_G	80_I	0.727	0.46
250_L	297_E	0.723	0.46
283_V	291_V	0.716	0.45
21_I	137_P	0.714	0.45
56_E	279_E	0.710	0.45
107_Q	131_G	0.708	0.44
228_L	264_I	0.708	0.44
127_L	145_A	0.705	0.44
138_K	211_S	0.705	0.44
16_P	21_I	0.704	0.44
165_V	191_K	0.701	0.44
86_D	100_A	0.699	0.44
127_L	133_L	0.699	0.44
108_I	121_A	0.698	0.44
123_A	160_R	0.698	0.44
108_I	162_I	0.692	0.43
255_D	291_V	0.691	0.43
46_G	65_G	0.686	0.42
86_D	106_W	0.686	0.42
120_L	124_M	0.686	0.42
241_I	253_G	0.686	0.42
38_L	255_D	0.683	0.42
63_V	72_H	0.683	0.42
187_A	199_R	0.680	0.42
110_A	113_Q	0.679	0.42
62_R	78_T	0.679	0.42
72_H	77_S	0.679	0.42
201_Y	258_G	0.678	0.42
268_S	273_E	0.678	0.42
85_K	197_V	0.678	0.42
274_R	283_V	0.677	0.42
197_V	261_A	0.677	0.42
17_P	33_E	0.675	0.41
123_A	161_S	0.674	0.41
136_L	168_A	0.674	0.41
123_A	291_V	0.673	0.41
198_A	201_Y	0.670	0.41
133_L	189_Y	0.670	0.41
190_T	295_Y	0.667	0.41
230_L	264_I	0.667	0.41
53_T	182_T	0.666	0.41
27_G	42_I	0.665	0.41
148_Y	294_R	0.664	0.40
41_K	47_P	0.661	0.40
168_A	221_V	0.660	0.40
270_L	295_Y	0.659	0.40
53_T	259_L	0.659	0.40
190_T	215_S	0.657	0.40
41_K	190_T	0.657	0.40
150_K	176_R	0.656	0.40
164_S	168_A	0.656	0.40
228_L	280_I	0.656	0.40
266_I	280_I	0.655	0.40
192_A	227_L	0.650	0.39
148_Y	211_S	0.649	0.39
130_I	153_E	0.646	0.39
81_D	212_V	0.643	0.39
201_Y	204_L	0.642	0.39
62_R	80_I	0.642	0.39
106_W	109_R	0.639	0.38
144_A	172_A	0.638	0.38
129_R	235_M	0.633	0.38
134_L	160_R	0.631	0.38
115_S	203_L	0.629	0.37
40_D	266_I	0.625	0.37
266_I	296_K	0.625	0.37
118_R	126_E	0.625	0.37
225_A	234_V	0.621	0.37
151_A	284_A	0.620	0.37
147_I	169_A	0.619	0.37
261_A	266_I	0.618	0.36
166_V	211_S	0.618	0.36
163_E	166_V	0.618	0.36
166_V	170_I	0.616	0.36
17_P	41_K	0.614	0.36
186_I	222_T	0.609	0.36
259_L	284_A	0.607	0.36
136_L	147_I	0.606	0.35
106_W	207_E	0.603	0.35
123_A	287_T	0.602	0.35
49_W	62_R	0.601	0.35
103_W	107_Q	0.601	0.35
73_D	277_Q	0.599	0.35
134_L	245_A	0.598	0.35
121_A	242_I	0.596	0.35
145_A	199_R	0.594	0.34
67_L	114_S	0.593	0.34
75_G	145_A	0.589	0.34
113_Q	241_I	0.588	0.34
196_E	199_R	0.588	0.34
241_I	296_K	0.588	0.34
124_M	195_K	0.586	0.34
115_S	297_E	0.586	0.34
116_I	229_G	0.585	0.34
13_T	38_L	0.583	0.34
43_I	49_W	0.582	0.33
249_G	254_K	0.577	0.33
65_G	72_H	0.577	0.33
81_D	129_R	0.576	0.33
80_I	132_N	0.576	0.33
22_F	127_L	0.575	0.33
154_K	204_L	0.575	0.33
75_G	292_R	0.573	0.33
127_L	206_R	0.573	0.33
46_G	51_A	0.573	0.33
200_C	291_V	0.571	0.33
168_A	239_A	0.571	0.33
44_D	47_P	0.570	0.32
52_F	228_L	0.568	0.32
250_L	261_A	0.566	0.32
234_V	238_A	0.565	0.32
122_Q	246_K	0.565	0.32
278_K	293_N	0.564	0.32
254_K	274_R	0.564	0.32
286_V	290_T	0.561	0.32
234_V	263_A	0.559	0.32
276_T	292_R	0.558	0.32
28_E	292_R	0.557	0.31
161_S	202_R	0.557	0.31
204_L	274_R	0.556	0.31
44_D	54_P	0.555	0.31
295_Y	299_T	0.554	0.31
77_S	130_I	0.554	0.31
23_D	36_E	0.553	0.31
161_S	256_P	0.553	0.31
174_C	215_S	0.553	0.31
184_D	194_R	0.552	0.31
236_K	272_D	0.552	0.31
188_Q	301_E	0.551	0.31
47_P	51_A	0.549	0.31
279_E	282_Q	0.548	0.31
21_I	32_S	0.546	0.31
35_G	253_G	0.544	0.30
209_D	261_A	0.544	0.30
130_I	146_L	0.543	0.30
185_E	196_E	0.543	0.30
148_Y	151_A	0.541	0.30
117_D	141_K	0.541	0.30
196_E	221_V	0.541	0.30
35_G	171_Y	0.539	0.30
26_R	42_I	0.538	0.30
259_L	281_A	0.537	0.30
260_A	284_A	0.536	0.30
102_R	107_Q	0.536	0.30
234_V	267_A	0.534	0.30
14_P	20_I	0.534	0.30
129_R	207_E	0.534	0.30
105_K	191_K	0.532	0.29
198_A	272_D	0.532	0.29
143_E	214_V	0.529	0.29
170_I	249_G	0.526	0.29
73_D	76_L	0.526	0.29
192_A	255_D	0.526	0.29
39_E	45_Q	0.525	0.29
254_K	267_A	0.524	0.29
46_G	291_V	0.521	0.29
151_A	204_L	0.520	0.29
203_L	241_I	0.519	0.28
222_T	235_M	0.519	0.28
32_S	135_N	0.519	0.28
120_L	149_R	0.517	0.28
167_A	190_T	0.517	0.28
73_D	80_I	0.517	0.28
151_A	217_P	0.515	0.28
263_A	282_Q	0.513	0.28
80_I	118_R	0.511	0.28
155_G	233_A	0.510	0.28
127_L	144_A	0.510	0.28
11_V	19_K	0.509	0.28
60_R	65_G	0.509	0.28
245_A	251_T	0.508	0.28
84_D	234_V	0.508	0.28
191_K	261_A	0.505	0.27
152_V	263_A	0.505	0.27
163_E	295_Y	0.504	0.27
148_Y	201_Y	0.502	0.27
83_K	191_K	0.501	0.27
80_I	85_K	0.501	0.27
22_F	218_K	0.501	0.27
78_T	109_R	0.501	0.27
18_D	204_L	0.500	0.27

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) HHsearch results which uses the overall probability and per-site alignment prob. Inter oligomeric contacts in the pdb are in shades of red.

PDB	Chains	Cov	%	HHΔ
4bbrM	1	0.6117	100	0.245	Contact Map
1aisB	1	0.6181	100	0.581	Contact Map
1c9bA	1	0.6278	100	0.587	Contact Map
2pk2A	3	0.7055	99.9	0.702	Contact Map
4f6uB	1	0.7443	99.9	0.707	Contact Map
2w96A	1	0.7443	99.9	0.71	Contact Map
2b9rA	1	0.6926	99.9	0.719	Contact Map
4eojB	1	0.7023	99.9	0.721	Contact Map
3g33B	2	0.7023	99.9	0.722	Contact Map
2i53A	1	0.7282	99.9	0.726	Contact Map

Sequence Conservation (Image Generated using WebLogo v3)

Legend: Color is used to show Hydrophobicity (Blue: Hydrophilic, Green: Neutral and Black: Hydrophobic). Amount of gaps is represented by width.

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