TF2B5 - HALSA - GREMLIN Contacts

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TF2B5 - Transcription initiation factor IIB 5

UniProt:	Q9HHH8	Sequences: MTTSEPYERAFDEDIQRGTTEPCPECGGPVRTNSAETVCADCGLIIDEQSIDRGPEWHRDDADTAKRTGAPLTPARHDRGLSTVIGSGQDARGTALSSEKRRRLARMRREQSRGRWRSTKERNLGHGLTEIRRIASALGLADSVRDQACQLFRTAQNERLLKGRSIEAMAAASVFGACRCNGESWLIDDVAPMAQVGQNRVENAYTVLNEELGLPTPPVSLDQFVPRLASDLGCTDVVRRRAEELVVQAVDAGITTGVHPSGFAAACLYMAACVHDAPLTQADAAAAAGVTVETIRSHRDRLLSIVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	307 (275)
Sequences:	1037 (664)
Seq/√Len:	40.0

HALSA - TF2B5 TF2B3 TF2B2 TF2B6 TF2B4 TF2B7 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
229_A	268_L	6.595	1.00
135_A	174_V	4.103	1.00
23_C	42_C	3.953	1.00
39_C	42_C	3.909	1.00
235_T	277_A	3.906	1.00
57_W	60_D	3.397	1.00
298_H	301_R	3.392	1.00
31_R	34_S	3.375	1.00
241_R	275_H	3.358	1.00
281_Q	296_R	3.333	1.00
127_G	152_F	2.993	1.00
134_I	174_V	2.840	1.00
26_C	39_C	2.812	1.00
282_A	292_V	2.760	1.00
130_E	133_R	2.721	1.00
90_D	93_G	2.654	1.00
23_C	39_C	2.540	1.00
135_A	145_R	2.532	1.00
30_V	37_T	2.496	1.00
128_L	149_C	2.491	1.00
23_C	26_C	2.483	1.00
148_A	177_A	2.416	1.00
174_V	190_V	2.339	1.00
140_L	174_V	2.302	1.00
59_R	62_A	2.273	1.00
56_E	67_R	2.164	0.99
198_Q	202_E	2.161	0.99
134_I	193_M	2.109	0.99
242_A	264_A	2.086	0.99
265_A	288_A	2.072	0.99
245_L	271_A	2.036	0.99
26_C	42_C	1.985	0.99
292_V	300_D	1.983	0.99
163_G	260_P	1.983	0.99
241_R	244_E	1.946	0.99
31_R	35_A	1.876	0.98
58_H	67_R	1.845	0.98
23_C	27_G	1.812	0.98
144_V	177_A	1.792	0.98
228_L	268_L	1.674	0.96
228_L	232_L	1.657	0.96
242_A	271_A	1.626	0.96
38_V	287_A	1.613	0.96
147_Q	180_C	1.612	0.96
104_L	107_M	1.605	0.96
152_F	161_L	1.597	0.95
185_W	189_D	1.588	0.95
60_D	67_R	1.585	0.95
246_V	267_C	1.584	0.95
150_Q	153_R	1.550	0.95
262_G	294_T	1.545	0.94
29_P	208_L	1.543	0.94
190_V	193_M	1.523	0.94
127_G	203_N	1.520	0.94
245_L	267_C	1.499	0.94
222_D	247_V	1.491	0.93
282_A	295_I	1.490	0.93
280_T	283_D	1.484	0.93
56_E	65_A	1.471	0.93
209_N	216_T	1.442	0.92
54_G	57_W	1.442	0.92
210_E	283_D	1.421	0.92
238_V	277_A	1.399	0.91
88_G	92_R	1.396	0.91
220_S	223_Q	1.394	0.91
246_V	263_F	1.379	0.90
190_V	253_G	1.362	0.90
279_L	283_D	1.356	0.89
179_R	202_E	1.340	0.89
39_C	43_G	1.339	0.89
55_P	59_R	1.329	0.89
189_D	227_R	1.328	0.88
278_P	283_D	1.314	0.88
127_G	156_Q	1.312	0.88
262_G	266_A	1.309	0.88
116_W	131_I	1.306	0.88
25_E	44_L	1.285	0.87
52_D	56_E	1.284	0.87
267_C	271_A	1.277	0.86
37_T	245_L	1.275	0.86
238_V	275_H	1.272	0.86
272_A	287_A	1.270	0.86
281_Q	293_E	1.266	0.86
202_E	228_L	1.265	0.86
52_D	57_W	1.265	0.86
234_C	279_L	1.262	0.86
147_Q	181_N	1.232	0.84
57_W	65_A	1.231	0.84
56_E	60_D	1.224	0.84
220_S	246_V	1.224	0.84
248_Q	252_A	1.213	0.83
28_G	41_D	1.194	0.82
38_V	300_D	1.194	0.82
25_E	28_G	1.187	0.82
114_G	179_R	1.175	0.81
82_S	269_Y	1.169	0.81
131_I	170_A	1.167	0.81
89_Q	93_G	1.159	0.81
124_L	149_C	1.158	0.80
144_V	250_V	1.154	0.80
131_I	149_C	1.137	0.79
176_G	214_L	1.123	0.78
41_D	135_A	1.112	0.78
125_G	129_T	1.103	0.77
61_D	279_L	1.101	0.77
153_R	177_A	1.100	0.77
239_R	243_E	1.099	0.77
61_D	263_F	1.098	0.77
27_G	30_V	1.089	0.76
232_L	268_L	1.071	0.75
187_I	198_Q	1.068	0.75
283_D	287_A	1.067	0.75
290_V	295_I	1.064	0.74
60_D	63_D	1.062	0.74
176_G	179_R	1.058	0.74
162_K	263_F	1.045	0.73
135_A	263_F	1.045	0.73
187_I	202_E	1.044	0.73
282_A	290_V	1.041	0.73
56_E	68_T	1.037	0.73
279_L	292_V	1.032	0.72
265_A	270_M	1.029	0.72
41_D	141_A	1.026	0.72
154_T	158_E	1.024	0.72
268_L	288_A	1.021	0.71
138_L	251_D	1.017	0.71
171_A	178_C	1.011	0.71
149_C	156_Q	1.006	0.70
258_V	263_F	1.004	0.70
236_D	240_R	0.996	0.69
190_V	216_T	0.993	0.69
147_Q	150_Q	0.975	0.68
285_A	288_A	0.972	0.68
45_I	74_P	0.965	0.67
144_V	183_E	0.958	0.66
234_C	238_V	0.957	0.66
185_W	227_R	0.954	0.66
197_G	201_V	0.952	0.66
163_G	294_T	0.948	0.66
59_R	64_T	0.941	0.65
73_T	76_R	0.938	0.65
152_F	166_I	0.933	0.64
57_W	67_R	0.928	0.64
37_T	40_A	0.924	0.64
175_F	178_C	0.923	0.63
23_C	28_G	0.919	0.63
131_I	137_A	0.919	0.63
199_N	300_D	0.918	0.63
127_G	266_A	0.914	0.63
224_F	229_A	0.912	0.63
46_I	259_H	0.908	0.62
22_P	40_A	0.905	0.62
82_S	134_I	0.903	0.62
169_M	208_L	0.902	0.62
176_G	272_A	0.897	0.61
169_M	204_A	0.896	0.61
112_S	125_G	0.892	0.61
220_S	250_V	0.892	0.61
191_A	196_V	0.891	0.61
202_E	259_H	0.891	0.61
253_G	258_V	0.890	0.61
127_G	295_I	0.888	0.60
265_A	295_I	0.887	0.60
266_A	294_T	0.880	0.60
30_V	292_V	0.869	0.59
48_E	53_R	0.868	0.59
259_H	295_I	0.868	0.59
24_P	46_I	0.863	0.58
110_E	152_F	0.861	0.58
184_S	223_Q	0.858	0.58
262_G	290_V	0.849	0.57
175_F	219_V	0.846	0.57
246_V	264_A	0.845	0.57
196_V	231_D	0.842	0.56
157_N	282_A	0.841	0.56
127_G	131_I	0.834	0.56
114_G	171_A	0.830	0.55
123_N	176_G	0.830	0.55
148_A	173_S	0.829	0.55
45_I	173_S	0.824	0.55
124_L	184_S	0.824	0.55
88_G	121_E	0.819	0.54
258_V	278_P	0.817	0.54
120_K	233_G	0.814	0.54
262_G	298_H	0.811	0.54
86_G	216_T	0.811	0.54
145_R	174_V	0.808	0.53
58_H	64_T	0.807	0.53
205_Y	262_G	0.806	0.53
105_A	109_R	0.805	0.53
184_S	267_C	0.804	0.53
195_Q	265_A	0.802	0.53
77_H	296_R	0.800	0.53
254_I	272_A	0.799	0.52
57_W	71_P	0.797	0.52
167_E	170_A	0.797	0.52
27_G	42_C	0.790	0.52
186_L	189_D	0.790	0.52
113_R	257_G	0.785	0.51
83_T	185_W	0.784	0.51
197_G	200_R	0.782	0.51
138_L	164_R	0.774	0.50
49_Q	194_A	0.768	0.50
254_I	265_A	0.766	0.49
276_D	280_T	0.764	0.49
222_D	250_V	0.752	0.48
49_Q	55_P	0.751	0.48
290_V	294_T	0.750	0.48
126_H	250_V	0.749	0.48
77_H	80_G	0.748	0.48
293_E	296_R	0.748	0.48
119_T	301_R	0.747	0.48
283_D	286_A	0.746	0.48
127_G	165_S	0.745	0.47
200_R	203_N	0.743	0.47
113_R	164_R	0.742	0.47
280_T	292_V	0.741	0.47
165_S	206_T	0.741	0.47
58_H	65_A	0.739	0.47
272_A	277_A	0.738	0.47
268_L	284_A	0.737	0.47
61_D	186_L	0.736	0.47
162_K	292_V	0.735	0.47
222_D	289_G	0.732	0.46
272_A	278_P	0.730	0.46
119_T	172_A	0.730	0.46
130_E	134_I	0.728	0.46
24_P	268_L	0.728	0.46
131_I	152_F	0.727	0.46
130_E	203_N	0.725	0.46
265_A	285_A	0.725	0.46
70_A	269_Y	0.719	0.45
162_K	214_L	0.719	0.45
202_E	205_Y	0.717	0.45
282_A	297_S	0.711	0.44
30_V	240_R	0.706	0.44
140_L	172_A	0.703	0.44
227_R	259_H	0.703	0.44
59_R	298_H	0.702	0.44
228_L	258_V	0.700	0.43
121_E	158_E	0.697	0.43
241_R	274_V	0.695	0.43
41_D	70_A	0.692	0.43
86_G	142_D	0.686	0.42
89_Q	187_I	0.686	0.42
140_L	178_C	0.682	0.42
131_I	148_A	0.678	0.41
88_G	93_G	0.677	0.41
168_A	172_A	0.673	0.41
200_R	225_V	0.673	0.41
196_V	259_H	0.671	0.41
38_V	114_G	0.670	0.41
204_A	295_I	0.669	0.41
274_V	299_R	0.668	0.41
152_F	298_H	0.666	0.40
45_I	183_E	0.663	0.40
85_I	90_D	0.663	0.40
201_V	247_V	0.662	0.40
146_D	149_C	0.659	0.40
207_V	245_L	0.659	0.40
194_A	299_R	0.659	0.40
30_V	45_I	0.657	0.40
149_C	153_R	0.655	0.39
123_N	152_F	0.655	0.39
127_G	291_T	0.655	0.39
152_F	205_Y	0.653	0.39
31_R	162_K	0.653	0.39
110_E	113_R	0.652	0.39
208_L	231_D	0.648	0.39
217_P	229_A	0.643	0.38
70_A	263_F	0.641	0.38
137_A	193_M	0.640	0.38
249_A	255_T	0.640	0.38
254_I	301_R	0.639	0.38
68_T	196_V	0.639	0.38
55_P	67_R	0.639	0.38
88_G	111_Q	0.638	0.38
268_L	289_G	0.637	0.38
78_D	281_Q	0.636	0.38
242_A	246_V	0.635	0.38
155_A	214_L	0.635	0.38
61_D	65_A	0.633	0.37
104_L	108_R	0.633	0.37
71_P	77_H	0.632	0.37
119_T	207_V	0.624	0.37
56_E	66_K	0.621	0.36
144_V	181_N	0.621	0.36
171_A	257_G	0.621	0.36
278_P	287_A	0.621	0.36
41_D	87_S	0.620	0.36
264_A	288_A	0.619	0.36
127_G	155_A	0.618	0.36
172_A	225_V	0.617	0.36
210_E	230_S	0.617	0.36
103_R	107_M	0.613	0.36
156_Q	267_C	0.612	0.36
53_R	199_N	0.610	0.36
205_Y	208_L	0.608	0.35
171_A	190_V	0.604	0.35
47_D	287_A	0.604	0.35
191_A	279_L	0.603	0.35
75_A	262_G	0.603	0.35
169_M	195_Q	0.603	0.35
238_V	271_A	0.602	0.35
151_L	173_S	0.598	0.35
177_A	291_T	0.597	0.34
27_G	217_P	0.596	0.34
263_F	288_A	0.594	0.34
158_E	208_L	0.594	0.34
138_L	249_A	0.593	0.34
33_N	36_E	0.593	0.34
29_P	167_E	0.591	0.34
238_V	267_C	0.588	0.34
22_P	46_I	0.587	0.34
280_T	285_A	0.586	0.34
204_A	218_P	0.585	0.33
251_D	283_D	0.585	0.33
69_G	178_C	0.585	0.33
106_R	110_E	0.584	0.33
73_T	229_A	0.583	0.33
54_G	59_R	0.579	0.33
114_G	219_V	0.578	0.33
109_R	189_D	0.577	0.33
32_T	153_R	0.575	0.33
106_R	109_R	0.575	0.33
52_D	55_P	0.574	0.33
266_A	275_H	0.574	0.33
138_L	193_M	0.573	0.32
60_D	66_K	0.570	0.32
76_R	272_A	0.569	0.32
40_A	139_G	0.566	0.32
170_A	174_V	0.566	0.32
121_E	145_R	0.566	0.32
265_A	269_Y	0.565	0.32
131_I	210_E	0.565	0.32
142_D	146_D	0.564	0.32
64_T	83_T	0.564	0.32
208_L	261_S	0.564	0.32
30_V	35_A	0.563	0.32
31_R	44_L	0.562	0.32
130_E	165_S	0.562	0.32
165_S	260_P	0.562	0.32
192_P	221_L	0.561	0.32
106_R	160_L	0.560	0.31
225_V	297_S	0.560	0.31
155_A	160_L	0.559	0.31
148_A	176_G	0.558	0.31
55_P	65_A	0.557	0.31
225_V	243_E	0.554	0.31
245_L	300_D	0.554	0.31
147_Q	182_G	0.553	0.31
186_L	190_V	0.553	0.31
190_V	226_P	0.552	0.31
22_P	27_G	0.552	0.31
84_V	107_M	0.550	0.31
28_G	42_C	0.550	0.31
266_A	271_A	0.549	0.31
171_A	194_A	0.546	0.30
194_A	219_V	0.545	0.30
214_L	246_V	0.544	0.30
63_D	119_T	0.543	0.30
282_A	286_A	0.541	0.30
106_R	164_R	0.541	0.30
147_Q	218_P	0.540	0.30
226_P	239_R	0.539	0.30
72_L	76_R	0.537	0.30
117_R	263_F	0.534	0.29
90_D	201_V	0.533	0.29
87_S	287_A	0.533	0.29
26_C	40_A	0.533	0.29
54_G	295_I	0.533	0.29
78_D	82_S	0.533	0.29
35_A	50_S	0.532	0.29
155_A	208_L	0.531	0.29
29_P	170_A	0.531	0.29
218_P	225_V	0.530	0.29
151_L	192_P	0.530	0.29
178_C	246_V	0.528	0.29
149_C	154_T	0.527	0.29
287_A	295_I	0.526	0.29
142_D	215_P	0.525	0.29
152_F	155_A	0.524	0.29
270_M	300_D	0.523	0.29
60_D	65_A	0.523	0.29
154_T	214_L	0.523	0.29
164_R	175_F	0.523	0.29
64_T	67_R	0.521	0.28
127_G	135_A	0.519	0.28
83_T	153_R	0.518	0.28
64_T	291_T	0.518	0.28
155_A	205_Y	0.515	0.28
73_T	262_G	0.515	0.28
84_V	111_Q	0.515	0.28
45_I	178_C	0.514	0.28
182_G	218_P	0.514	0.28
174_V	181_N	0.513	0.28
110_E	151_L	0.513	0.28
229_A	238_V	0.513	0.28
47_D	53_R	0.512	0.28
175_F	216_T	0.512	0.28
72_L	79_R	0.511	0.28
76_R	87_S	0.508	0.27
24_P	42_C	0.507	0.27
124_L	153_R	0.507	0.27
145_R	284_A	0.505	0.27
32_T	47_D	0.505	0.27
25_E	296_R	0.502	0.27
140_L	151_L	0.501	0.27
27_G	38_V	0.501	0.27
45_I	144_V	0.500	0.27
153_R	240_R	0.500	0.27
73_T	77_H	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	0.5961	100	0.262	Contact Map
1aisB	1	0.6026	100	0.577	Contact Map
1c9bA	1	0.6124	100	0.594	Contact Map
2pk2A	3	0.6938	99.9	0.699	Contact Map
2w96A	1	0.7296	99.9	0.71	Contact Map
4f6uB	1	0.7296	99.9	0.711	Contact Map
2b9rA	1	0.7003	99.9	0.719	Contact Map
4eojB	1	0.7134	99.9	0.721	Contact Map
3g33B	2	0.7003	99.9	0.722	Contact Map
2i53A	1	0.7166	99.9	0.723	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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