TF2B2 - HALSA - GREMLIN Contacts

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TF2B2 - Transcription initiation factor IIB 2

UniProt:	Q9HRE6	Sequences: MSDSTIRTYSSDQRQTDNDETVSTPDEDVLTCPECGGQVIDDEEHGESVCVDCGLVVEENGIDRGPEWRAFNSTEKDEKSRVGAPTTNMMHDKGLSTNIGWQDKDAYGNSLSSNQRQKMQRLRKWNERFRTRNSKERNLKQALGEIERMASALGLPKEVRETASVIYRRALSEDLLPGRSIEGVATAALYASARQLSTPRSIDEVANVSRIDEMEFKRTYRYIVRELSLEVAPADPAQYVPRFASDLDLPDEVERRSRELISNAQADGVTSGKSPVGLAAAAIYASSLLTNHKVTQSEVSEVTDVSEVTIRNRYQELLEATEAAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	325 (280)
Sequences:	1079 (685)
Seq/√Len:	40.9

HALSA - TF2B2 TF2B4 TF2B6 TF2B7 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
244_A	283_I	6.568	1.00
150_A	189_L	4.114	1.00
50_C	53_C	3.851	1.00
250_P	292_H	3.764	1.00
32_C	53_C	3.762	1.00
39_V	48_S	3.710	1.00
313_R	316_E	3.708	1.00
256_R	290_T	3.620	1.00
296_Q	311_R	3.395	1.00
39_V	57_V	3.308	1.00
149_M	189_L	2.899	1.00
142_A	167_Y	2.835	1.00
145_E	148_R	2.789	1.00
32_C	35_C	2.747	1.00
189_L	205_V	2.699	1.00
35_C	50_C	2.613	1.00
297_S	307_E	2.565	1.00
150_A	160_R	2.554	1.00
143_L	164_S	2.532	1.00
159_V	192_S	2.336	1.00
32_C	50_C	2.302	1.00
42_D	45_H	2.269	1.00
280_A	303_T	2.246	1.00
307_E	315_Q	2.186	0.99
35_C	53_C	2.139	0.99
163_A	192_S	2.135	0.99
256_R	259_E	2.121	0.99
167_Y	176_L	2.028	0.99
178_G	275_P	2.019	0.99
213_E	217_K	1.998	0.99
70_A	73_S	1.964	0.99
155_L	189_L	1.931	0.99
261_I	278_L	1.929	0.99
149_M	208_V	1.912	0.99
257_S	279_A	1.903	0.99
257_S	286_S	1.897	0.99
38_Q	52_D	1.878	0.98
49_V	302_V	1.834	0.98
260_L	286_S	1.814	0.98
200_R	204_E	1.759	0.98
162_T	195_Q	1.754	0.98
165_V	168_R	1.745	0.97
70_A	75_E	1.664	0.97
68_W	79_K	1.659	0.97
224_V	231_V	1.652	0.96
142_A	171_L	1.635	0.96
142_A	218_R	1.617	0.96
249_L	294_V	1.577	0.95
205_V	208_V	1.564	0.95
277_G	309_T	1.558	0.95
243_F	283_I	1.553	0.95
68_W	71_F	1.549	0.95
253_V	290_T	1.524	0.94
38_Q	51_V	1.520	0.94
91_H	94_G	1.520	0.94
162_T	196_L	1.519	0.94
194_R	217_K	1.516	0.94
67_E	81_R	1.515	0.94
260_L	282_A	1.505	0.94
298_E	302_V	1.502	0.94
102_Q	126_N	1.502	0.94
243_F	247_L	1.500	0.94
42_D	46_G	1.498	0.94
295_T	298_E	1.497	0.94
297_S	310_I	1.489	0.94
65_G	68_W	1.484	0.94
293_K	298_E	1.430	0.92
287_S	302_V	1.404	0.92
169_R	173_E	1.377	0.91
277_G	281_A	1.362	0.90
261_I	282_A	1.353	0.90
225_R	298_E	1.338	0.89
237_A	262_S	1.318	0.89
253_V	292_H	1.316	0.89
305_V	310_I	1.311	0.88
191_A	229_L	1.307	0.88
146_I	164_S	1.287	0.87
37_G	52_D	1.279	0.87
104_K	108_G	1.262	0.86
142_A	146_I	1.261	0.86
235_D	238_Q	1.256	0.86
32_C	36_G	1.255	0.86
48_S	260_L	1.249	0.86
280_A	285_A	1.249	0.86
235_D	261_I	1.247	0.86
204_E	242_R	1.245	0.86
296_Q	308_V	1.245	0.86
129_F	186_T	1.236	0.85
50_C	54_G	1.235	0.85
282_A	286_S	1.235	0.85
191_A	194_R	1.232	0.85
91_H	311_R	1.222	0.85
52_D	150_A	1.217	0.84
146_I	185_A	1.206	0.84
202_I	217_K	1.200	0.83
254_E	258_R	1.180	0.82
142_A	310_I	1.174	0.82
34_E	55_L	1.172	0.82
34_E	37_G	1.169	0.82
98_N	126_N	1.161	0.81
153_L	266_A	1.143	0.80
294_V	298_E	1.134	0.80
69_R	81_R	1.133	0.80
167_Y	181_I	1.118	0.79
78_E	83_G	1.114	0.79
63_D	67_E	1.104	0.78
217_K	243_F	1.102	0.78
164_S	171_L	1.100	0.78
140_K	144_G	1.098	0.78
205_V	268_G	1.077	0.76
261_I	279_A	1.076	0.76
268_G	273_K	1.070	0.76
247_L	283_I	1.063	0.75
280_A	310_I	1.058	0.75
83_G	168_R	1.056	0.75
81_R	97_T	1.055	0.75
139_L	164_S	1.053	0.75
184_V	223_I	1.048	0.74
235_D	265_Q	1.047	0.74
300_S	303_T	1.047	0.74
131_T	146_I	1.037	0.73
68_W	85_P	1.033	0.73
201_S	204_E	1.026	0.73
190_Y	234_A	1.024	0.72
252_E	290_T	1.022	0.72
150_A	278_L	1.017	0.72
263_N	267_D	1.015	0.72
294_V	307_E	1.011	0.71
281_A	309_T	1.009	0.71
162_T	165_V	1.003	0.71
48_S	51_V	1.001	0.71
256_R	289_L	1.001	0.71
202_I	213_E	0.975	0.69
87_T	102_Q	0.970	0.68
283_I	303_T	0.968	0.68
32_C	37_G	0.965	0.68
41_D	58_E	0.964	0.68
138_N	191_A	0.964	0.68
41_D	47_E	0.961	0.68
41_D	48_S	0.957	0.67
201_S	205_V	0.950	0.67
269_V	287_S	0.948	0.66
280_A	300_S	0.946	0.66
217_K	220_Y	0.941	0.66
146_I	152_A	0.941	0.66
71_F	243_F	0.931	0.65
33_P	57_V	0.928	0.65
31_T	51_V	0.927	0.65
92_D	296_Q	0.926	0.65
36_G	40_I	0.923	0.64
279_A	303_T	0.921	0.64
41_D	260_L	0.920	0.64
62_I	68_W	0.919	0.64
220_Y	223_I	0.916	0.64
40_I	51_V	0.907	0.63
291_N	295_T	0.901	0.62
186_T	193_A	0.894	0.62
49_V	315_Q	0.890	0.62
39_V	44_E	0.890	0.62
308_V	311_R	0.889	0.61
31_T	36_G	0.888	0.61
191_A	287_S	0.882	0.61
68_W	81_R	0.879	0.61
209_S	314_Y	0.878	0.60
239_Y	244_A	0.877	0.60
146_I	163_A	0.876	0.60
277_G	313_R	0.875	0.60
56_V	88_N	0.866	0.59
164_S	168_R	0.866	0.59
283_I	299_V	0.865	0.59
134_S	187_A	0.865	0.59
135_K	248_D	0.862	0.59
166_I	188_A	0.861	0.59
249_L	253_V	0.857	0.59
214_M	315_Q	0.856	0.59
100_G	148_R	0.855	0.58
173_E	298_E	0.848	0.58
145_E	218_R	0.844	0.57
55_L	95_L	0.843	0.57
142_A	281_A	0.841	0.57
155_L	319_E	0.835	0.57
87_T	91_H	0.827	0.56
217_K	274_S	0.823	0.56
184_V	219_T	0.823	0.56
200_R	242_R	0.821	0.55
284_Y	288_L	0.817	0.55
215_E	218_R	0.810	0.54
108_G	202_I	0.808	0.54
277_G	305_V	0.808	0.54
159_V	198_T	0.807	0.54
237_A	265_Q	0.805	0.54
67_E	79_K	0.803	0.54
136_E	173_E	0.803	0.54
67_E	71_F	0.796	0.53
57_V	274_S	0.796	0.53
242_R	274_S	0.789	0.52
155_L	193_A	0.787	0.52
36_G	53_C	0.785	0.52
36_G	232_A	0.784	0.52
212_D	215_E	0.784	0.52
92_D	95_L	0.783	0.52
172_S	297_S	0.779	0.51
177_P	229_L	0.778	0.51
41_D	49_V	0.777	0.51
274_S	310_I	0.777	0.51
249_L	292_H	0.771	0.51
163_A	188_A	0.770	0.51
168_R	192_S	0.769	0.51
52_D	156_P	0.762	0.50
125_W	167_Y	0.761	0.50
264_A	320_A	0.761	0.50
121_R	125_W	0.758	0.49
40_I	280_A	0.757	0.49
264_A	270_T	0.755	0.49
76_K	84_A	0.753	0.49
234_A	276_V	0.752	0.49
206_A	211_I	0.751	0.49
289_L	314_Y	0.744	0.48
137_R	145_E	0.744	0.48
128_R	272_G	0.739	0.48
193_A	261_I	0.736	0.47
46_G	61_G	0.735	0.47
72_N	278_L	0.735	0.47
190_Y	193_A	0.733	0.47
297_S	312_N	0.733	0.47
180_S	221_R	0.733	0.47
274_S	284_Y	0.725	0.46
134_S	316_E	0.722	0.46
212_D	216_F	0.721	0.46
216_F	262_S	0.721	0.46
287_S	293_K	0.720	0.46
260_L	272_G	0.719	0.46
160_R	189_L	0.716	0.46
210_R	280_A	0.715	0.46
85_P	295_T	0.710	0.45
139_L	199_P	0.710	0.45
170_A	229_L	0.709	0.45
136_E	160_R	0.706	0.45
77_D	86_T	0.700	0.44
142_A	180_S	0.699	0.44
240_V	261_I	0.699	0.44
178_G	309_T	0.699	0.44
41_D	108_G	0.698	0.44
59_E	64_R	0.697	0.44
232_A	244_A	0.696	0.44
205_V	231_V	0.695	0.44
134_S	222_Y	0.693	0.44
270_T	280_A	0.693	0.44
138_N	167_Y	0.693	0.44
237_A	304_D	0.685	0.43
67_E	83_G	0.685	0.43
142_A	170_A	0.685	0.43
166_I	192_S	0.682	0.43
244_A	247_L	0.681	0.42
146_I	167_Y	0.680	0.42
189_L	268_G	0.680	0.42
40_I	156_P	0.675	0.42
159_V	265_Q	0.675	0.42
73_S	78_E	0.674	0.42
220_Y	277_G	0.674	0.42
145_E	149_M	0.672	0.42
273_K	278_L	0.672	0.42
55_L	245_S	0.671	0.42
125_W	128_R	0.670	0.41
199_P	238_Q	0.667	0.41
293_K	302_V	0.667	0.41
102_Q	136_E	0.666	0.41
297_S	305_V	0.661	0.41
32_C	39_V	0.661	0.41
273_K	286_S	0.657	0.40
185_A	230_E	0.657	0.40
167_Y	313_R	0.651	0.40
158_E	245_S	0.649	0.40
141_Q	265_Q	0.648	0.39
305_V	309_T	0.647	0.39
139_L	143_L	0.647	0.39
280_A	284_Y	0.646	0.39
180_S	275_P	0.643	0.39
269_V	316_E	0.643	0.39
186_T	209_S	0.642	0.39
70_A	78_E	0.641	0.39
127_E	140_K	0.641	0.39
56_V	188_A	0.641	0.39
93_K	175_L	0.641	0.39
168_R	255_R	0.639	0.39
177_P	278_L	0.637	0.38
67_E	70_A	0.635	0.38
285_A	299_V	0.634	0.38
177_P	307_E	0.633	0.38
72_N	75_E	0.630	0.38
207_N	304_D	0.630	0.38
190_Y	231_V	0.630	0.38
91_H	161_E	0.629	0.38
216_F	234_A	0.628	0.38
129_F	239_Y	0.627	0.38
278_L	313_R	0.627	0.38
162_T	197_S	0.627	0.38
153_L	264_A	0.626	0.38
287_S	292_H	0.623	0.37
65_G	70_A	0.623	0.37
70_A	313_R	0.620	0.37
96_S	187_A	0.617	0.37
285_A	315_Q	0.617	0.37
170_A	303_T	0.616	0.37
225_R	245_S	0.615	0.37
298_E	301_E	0.613	0.36
100_G	283_I	0.612	0.36
205_V	299_V	0.611	0.36
269_V	280_A	0.610	0.36
58_E	302_V	0.610	0.36
153_L	208_V	0.610	0.36
219_T	310_I	0.607	0.36
95_L	99_I	0.606	0.36
74_T	319_E	0.602	0.35
161_E	164_S	0.601	0.35
138_N	148_R	0.601	0.35
63_D	69_R	0.600	0.35
173_E	176_L	0.600	0.35
63_D	97_T	0.599	0.35
193_A	234_A	0.599	0.35
143_L	161_E	0.599	0.35
199_P	282_A	0.598	0.35
74_T	284_Y	0.598	0.35
251_D	255_R	0.596	0.35
155_L	166_I	0.596	0.35
253_V	257_S	0.595	0.35
71_F	247_L	0.595	0.35
39_V	46_G	0.594	0.35
159_V	196_L	0.593	0.35
120_Q	124_K	0.591	0.35
60_N	66_P	0.591	0.35
39_V	150_A	0.591	0.35
45_H	311_R	0.591	0.35
82_V	211_I	0.590	0.34
66_P	284_Y	0.590	0.34
198_T	225_R	0.589	0.34
78_E	270_T	0.588	0.34
253_V	282_A	0.588	0.34
223_I	276_V	0.588	0.34
175_L	223_I	0.588	0.34
54_G	272_G	0.586	0.34
223_I	246_D	0.583	0.34
240_V	312_N	0.580	0.34
160_R	266_A	0.578	0.33
161_E	174_D	0.577	0.33
100_G	103_D	0.577	0.33
209_S	234_A	0.576	0.33
48_S	61_G	0.575	0.33
37_G	53_C	0.573	0.33
97_T	200_R	0.571	0.33
167_Y	170_A	0.566	0.32
40_I	48_S	0.566	0.32
82_V	205_V	0.564	0.32
95_L	98_N	0.563	0.32
92_D	311_R	0.563	0.32
57_V	215_E	0.562	0.32
30_L	262_S	0.561	0.32
295_T	311_R	0.559	0.32
170_A	175_L	0.559	0.32
99_I	137_R	0.558	0.32
295_T	307_E	0.558	0.32
71_F	83_G	0.557	0.32
32_C	55_L	0.557	0.32
108_G	278_L	0.552	0.31
205_V	215_E	0.551	0.31
128_R	179_R	0.551	0.31
211_I	246_D	0.551	0.31
205_V	241_P	0.548	0.31
56_V	126_N	0.547	0.31
49_V	67_E	0.547	0.31
143_L	185_A	0.546	0.31
69_R	79_K	0.546	0.31
38_Q	58_E	0.546	0.31
34_E	52_D	0.546	0.31
257_S	261_I	0.545	0.31
146_I	225_R	0.545	0.31
140_K	261_I	0.543	0.31
46_G	155_L	0.541	0.30
80_S	83_G	0.541	0.30
89_M	92_D	0.539	0.30
217_K	291_N	0.539	0.30
55_L	63_D	0.538	0.30
34_E	311_R	0.537	0.30
142_A	179_R	0.535	0.30
87_T	90_M	0.534	0.30
163_A	269_V	0.534	0.30
133_N	181_I	0.534	0.30
182_E	314_Y	0.534	0.30
274_S	277_G	0.533	0.30
182_E	185_A	0.533	0.30
142_A	306_S	0.532	0.30
97_T	254_E	0.531	0.30
121_R	124_K	0.530	0.30
197_S	233_P	0.530	0.30
45_H	61_G	0.528	0.29
314_Y	318_L	0.528	0.29
302_V	310_I	0.528	0.29
86_T	110_S	0.526	0.29
170_A	236_P	0.523	0.29
70_A	79_K	0.523	0.29
220_Y	272_G	0.521	0.29
167_Y	230_E	0.520	0.29
207_N	259_E	0.520	0.29
51_V	262_S	0.520	0.29
73_S	306_S	0.517	0.29
180_S	311_R	0.515	0.28
31_T	37_G	0.513	0.28
221_R	238_Q	0.512	0.28
252_E	318_L	0.507	0.28
91_H	164_S	0.506	0.28
164_S	218_R	0.506	0.28
58_E	64_R	0.505	0.28
100_G	231_V	0.505	0.28
146_I	161_E	0.504	0.28
253_V	272_G	0.504	0.28
160_R	299_V	0.502	0.27
204_E	215_E	0.502	0.27
87_T	178_G	0.501	0.27
60_N	299_V	0.500	0.27
154_G	229_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	0.5785	100	0.265	Contact Map
1aisB	1	0.5785	100	0.599	Contact Map
1c9bA	1	0.5877	100	0.607	Contact Map
2pk2A	3	0.6646	99.9	0.714	Contact Map
4f6uB	1	0.6985	99.9	0.72	Contact Map
2w96A	1	0.6985	99.9	0.728	Contact Map
2b9rA	1	0.6492	99.9	0.732	Contact Map
4eojB	1	0.6585	99.9	0.736	Contact Map
3g33B	2	0.6646	99.9	0.737	Contact Map
2ivxA	1	0.6615	99.9	0.74	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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