TF2B6 - HALSA - GREMLIN Contacts

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TF2B6 - Transcription initiation factor IIB 6

UniProt:	Q9HSB3	Sequences: MTDARMRSREQERTDETESESTDGCPECGGLVVNDEEHGESVCADCGLVVEEDGIDRGPEWRAFDSKEKDEKSRVGAPTTNTMHDKGLSTNIDWRDKDAYGNSLSSNQRQKMQRLRKWNERFRTRDAKERNLKQALGEIDRMASALGLPDNVRETASVIYRRALEDDLLPGRSIEGVATSCVYAAARQAGVPRSLDEIADVSRVEKAEIARTYRYVVRELGLEVAPADPESYVPRFASDLGLSDEASHRARELLKTAKDKGVHSGKSPVGLAAAAVYAAALLTNEKTTQAKVSEVADISEVTIRNRYHELLEAEDTIPV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	319 (277)
Sequences:	1058 (664)
Seq/√Len:	39.9

HALSA - TF2B6 TF2B4 TF2B2 TF2B3 TF2B7 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
237_A	276_V	6.120	1.00
25_C	46_C	4.062	1.00
43_C	46_C	3.934	1.00
243_S	285_E	3.895	1.00
143_A	182_V	3.800	1.00
306_R	309_E	3.594	1.00
25_C	28_C	3.354	1.00
249_R	283_T	3.288	1.00
289_Q	304_R	3.147	1.00
135_A	160_Y	3.107	1.00
32_V	41_S	3.050	1.00
32_V	50_V	2.999	1.00
138_E	141_R	2.796	1.00
28_C	43_C	2.792	1.00
142_M	182_V	2.779	1.00
182_V	198_I	2.643	1.00
290_A	300_E	2.603	1.00
143_A	153_R	2.507	1.00
25_C	43_C	2.486	1.00
136_L	157_S	2.454	1.00
63_A	66_S	2.388	1.00
300_E	308_H	2.245	1.00
142_M	201_V	2.166	0.99
28_C	46_C	2.144	0.99
61_W	64_F	2.143	0.99
250_A	272_A	2.143	0.99
35_D	38_H	2.130	0.99
249_R	252_E	2.099	0.99
206_K	210_A	2.099	0.99
156_A	185_A	2.083	0.99
273_A	296_A	2.030	0.99
148_L	182_V	2.005	0.99
60_E	74_R	1.981	0.99
171_G	268_P	1.901	0.98
152_V	185_A	1.879	0.98
112_M	115_L	1.829	0.98
25_C	29_G	1.749	0.97
160_Y	169_L	1.748	0.97
253_L	279_A	1.738	0.97
112_M	116_R	1.727	0.97
250_A	279_A	1.711	0.97
155_T	188_Q	1.669	0.96
58_G	61_W	1.658	0.96
193_R	197_E	1.641	0.96
60_E	64_F	1.631	0.96
254_L	271_L	1.620	0.96
236_F	276_V	1.569	0.95
217_V	224_V	1.562	0.95
270_G	302_T	1.551	0.95
84_H	87_G	1.548	0.94
62_R	74_R	1.544	0.94
34_N	51_E	1.512	0.94
288_T	291_K	1.511	0.94
114_R	298_I	1.510	0.94
290_A	303_I	1.494	0.93
236_F	240_L	1.481	0.93
135_A	164_L	1.470	0.93
61_W	72_K	1.453	0.92
111_K	115_L	1.434	0.92
42_V	295_V	1.427	0.92
270_G	274_A	1.420	0.91
253_L	275_A	1.403	0.91
246_A	283_T	1.402	0.91
135_A	211_R	1.391	0.91
158_V	161_R	1.387	0.90
228_D	231_S	1.382	0.90
162_R	166_D	1.379	0.90
246_A	285_E	1.378	0.90
184_A	222_L	1.376	0.90
286_K	291_K	1.373	0.90
228_D	254_L	1.361	0.90
187_R	210_A	1.346	0.89
155_T	189_A	1.346	0.89
30_G	45_D	1.309	0.88
198_I	201_V	1.300	0.87
25_C	30_G	1.292	0.87
197_E	235_R	1.281	0.87
254_L	275_A	1.276	0.86
256_T	260_K	1.266	0.86
27_E	48_L	1.253	0.85
280_A	295_V	1.238	0.85
135_A	303_I	1.237	0.85
242_L	287_T	1.234	0.84
275_A	279_A	1.233	0.84
218_R	291_K	1.206	0.83
43_C	47_G	1.200	0.83
291_K	295_V	1.184	0.82
41_S	253_L	1.179	0.82
195_L	206_K	1.179	0.82
133_K	137_G	1.173	0.81
230_E	255_K	1.169	0.81
160_Y	174_I	1.164	0.81
210_A	236_F	1.142	0.79
184_A	187_R	1.138	0.79
287_T	300_E	1.130	0.79
273_A	278_A	1.129	0.79
273_A	303_I	1.127	0.78
48_L	88_L	1.125	0.78
198_I	261_G	1.123	0.78
31_L	216_V	1.098	0.77
27_E	30_G	1.095	0.76
33_V	273_A	1.095	0.76
183_Y	227_A	1.093	0.76
152_V	191_V	1.088	0.76
32_V	39_G	1.086	0.76
247_S	251_R	1.084	0.76
139_I	178_A	1.083	0.76
56_D	60_E	1.080	0.75
254_L	272_A	1.075	0.75
287_T	291_K	1.065	0.74
244_D	248_H	1.065	0.74
155_T	158_V	1.059	0.74
195_L	210_A	1.056	0.74
177_V	216_V	1.055	0.74
143_A	271_L	1.052	0.73
289_Q	301_V	1.050	0.73
274_A	302_T	1.049	0.73
132_L	157_S	1.038	0.72
32_V	37_E	1.029	0.72
93_D	141_R	1.021	0.71
31_L	232_Y	1.019	0.71
193_R	235_R	1.017	0.71
293_S	296_A	1.016	0.71
139_I	157_S	0.996	0.69
170_P	271_L	0.994	0.69
135_A	274_A	0.991	0.69
60_E	72_K	0.990	0.69
139_I	145_A	0.989	0.69
26_P	50_V	0.986	0.69
146_L	259_D	0.982	0.68
230_E	258_K	0.982	0.68
35_D	39_G	0.975	0.68
198_I	224_V	0.963	0.67
273_A	293_S	0.958	0.66
45_D	143_A	0.957	0.66
199_A	204_V	0.957	0.66
242_L	246_A	0.953	0.66
45_D	149_P	0.951	0.66
131_N	184_A	0.949	0.66
61_W	74_R	0.948	0.65
63_A	71_E	0.947	0.65
148_L	186_A	0.946	0.65
165_E	290_A	0.936	0.64
63_A	69_K	0.933	0.64
24_G	44_A	0.930	0.64
194_S	198_I	0.929	0.64
79_T	126_D	0.925	0.64
280_A	286_K	0.922	0.63
29_G	33_V	0.918	0.63
205_E	208_E	0.917	0.63
152_V	258_K	0.917	0.63
56_D	61_W	0.911	0.62
135_A	173_S	0.906	0.62
146_L	172_R	0.904	0.62
240_L	276_V	0.903	0.62
171_G	302_T	0.903	0.62
69_K	77_A	0.900	0.61
148_L	312_E	0.898	0.61
135_A	139_I	0.897	0.61
66_S	71_E	0.897	0.61
55_I	61_W	0.896	0.61
84_H	304_R	0.896	0.61
80_T	84_H	0.893	0.61
276_V	296_A	0.892	0.61
41_S	44_A	0.889	0.60
179_T	186_A	0.889	0.60
301_V	304_R	0.888	0.60
34_N	37_E	0.886	0.60
153_R	182_V	0.884	0.60
207_A	308_H	0.882	0.60
154_E	167_D	0.873	0.59
34_N	253_L	0.872	0.59
64_F	71_E	0.872	0.59
69_K	72_K	0.869	0.59
65_D	271_L	0.867	0.58
177_V	212_T	0.855	0.57
157_S	164_L	0.855	0.57
194_S	197_E	0.855	0.57
261_G	266_K	0.855	0.57
210_A	267_S	0.854	0.57
89_S	180_S	0.854	0.57
298_I	303_I	0.853	0.57
183_Y	186_A	0.852	0.57
226_P	288_T	0.846	0.57
50_V	267_S	0.844	0.56
96_D	110_Q	0.840	0.56
29_G	46_C	0.839	0.56
97_K	139_I	0.837	0.56
284_N	288_T	0.837	0.56
290_A	298_I	0.832	0.55
186_A	254_L	0.829	0.55
228_D	258_K	0.826	0.55
161_R	185_A	0.819	0.54
192_P	231_S	0.818	0.54
173_S	214_R	0.817	0.54
232_Y	237_A	0.816	0.54
139_I	160_Y	0.814	0.54
61_W	78_P	0.813	0.54
235_R	267_S	0.807	0.53
120_E	205_E	0.807	0.53
60_E	92_I	0.805	0.53
262_V	280_A	0.804	0.53
33_V	149_P	0.795	0.52
63_A	306_R	0.793	0.52
49_V	181_C	0.793	0.52
290_A	305_N	0.791	0.52
32_V	143_A	0.789	0.51
132_L	192_P	0.785	0.51
127_A	180_S	0.781	0.51
33_V	44_A	0.778	0.50
263_H	273_A	0.775	0.50
62_R	72_K	0.774	0.50
257_A	263_H	0.773	0.50
120_E	133_K	0.771	0.50
208_E	233_V	0.771	0.50
61_W	90_T	0.769	0.50
63_A	73_S	0.768	0.49
203_R	273_A	0.763	0.49
230_E	297_D	0.760	0.49
160_Y	163_A	0.759	0.49
29_G	225_A	0.759	0.49
138_E	142_M	0.758	0.49
80_T	270_G	0.757	0.48
134_Q	258_K	0.757	0.48
276_V	292_V	0.757	0.48
221_G	273_A	0.755	0.48
138_E	211_R	0.754	0.48
270_G	306_R	0.751	0.48
90_T	193_R	0.746	0.47
159_I	181_C	0.744	0.47
161_R	248_H	0.738	0.47
186_A	227_A	0.729	0.46
249_R	282_L	0.726	0.46
131_N	160_Y	0.725	0.46
209_I	255_K	0.725	0.46
267_S	303_I	0.723	0.45
42_V	308_H	0.723	0.45
255_K	259_D	0.723	0.45
184_A	280_A	0.723	0.45
291_K	294_E	0.723	0.45
208_E	211_R	0.722	0.45
74_R	90_T	0.721	0.45
152_V	189_A	0.720	0.45
271_L	296_A	0.719	0.45
84_H	275_A	0.717	0.45
253_L	265_G	0.716	0.45
157_S	161_R	0.714	0.45
93_D	96_D	0.710	0.44
262_V	273_A	0.709	0.44
272_A	296_A	0.709	0.44
80_T	95_R	0.707	0.44
166_D	169_L	0.706	0.44
162_R	222_L	0.705	0.44
205_E	209_I	0.694	0.43
280_A	285_E	0.693	0.43
186_A	189_A	0.693	0.43
84_H	89_S	0.692	0.43
192_P	275_A	0.692	0.43
298_I	302_T	0.690	0.42
116_R	175_E	0.689	0.42
156_A	181_C	0.687	0.42
179_T	202_S	0.686	0.42
213_Y	216_V	0.684	0.42
139_I	218_R	0.684	0.42
213_Y	270_G	0.684	0.42
82_T	157_S	0.682	0.42
129_E	153_R	0.680	0.42
199_A	287_T	0.679	0.41
282_L	307_Y	0.677	0.41
266_K	271_L	0.672	0.41
216_V	239_D	0.670	0.41
124_T	139_I	0.670	0.41
49_V	81_N	0.666	0.40
262_V	309_E	0.663	0.40
65_D	72_K	0.662	0.40
83_M	95_R	0.660	0.40
42_V	60_E	0.660	0.40
85_D	88_L	0.658	0.40
93_D	114_R	0.656	0.39
121_R	265_G	0.655	0.39
202_S	307_Y	0.654	0.39
170_P	300_E	0.654	0.39
196_D	206_K	0.653	0.39
270_G	298_I	0.652	0.39
233_V	305_N	0.651	0.39
135_A	143_A	0.651	0.39
238_S	273_A	0.651	0.39
74_R	92_I	0.650	0.39
289_Q	293_S	0.649	0.39
26_P	276_V	0.649	0.39
135_A	299_S	0.647	0.39
35_D	243_S	0.647	0.39
253_L	308_H	0.644	0.38
132_L	136_L	0.643	0.38
198_I	208_E	0.640	0.38
295_V	303_I	0.640	0.38
69_K	230_E	0.638	0.38
59_P	63_A	0.637	0.38
151_N	238_S	0.632	0.37
64_F	72_K	0.631	0.37
288_T	304_R	0.630	0.37
210_A	213_Y	0.630	0.37
30_G	46_C	0.629	0.37
38_H	296_A	0.626	0.37
24_G	29_G	0.626	0.37
160_Y	306_R	0.625	0.37
127_A	309_E	0.621	0.36
95_R	129_E	0.620	0.36
77_A	273_A	0.618	0.36
129_E	166_D	0.618	0.36
163_A	222_L	0.613	0.36
250_A	254_L	0.612	0.36
160_Y	213_Y	0.610	0.35
53_D	59_P	0.610	0.35
286_K	295_V	0.608	0.35
50_V	204_V	0.606	0.35
178_A	223_E	0.606	0.35
278_A	292_V	0.605	0.35
220_L	302_T	0.605	0.35
77_A	271_L	0.604	0.35
307_Y	311_L	0.602	0.35
34_N	40_E	0.602	0.35
157_S	162_R	0.602	0.35
78_P	240_L	0.601	0.35
288_T	300_E	0.599	0.35
59_P	277_Y	0.599	0.35
155_T	226_P	0.598	0.34
128_K	241_G	0.592	0.34
34_N	230_E	0.591	0.34
52_E	57_R	0.590	0.34
80_T	157_S	0.590	0.34
150_D	223_E	0.585	0.33
75_V	82_T	0.583	0.33
206_K	290_A	0.580	0.33
236_F	295_V	0.580	0.33
197_E	208_E	0.579	0.33
246_A	275_A	0.579	0.33
271_L	293_S	0.577	0.33
90_T	236_F	0.577	0.33
24_G	31_L	0.577	0.33
147_G	184_A	0.575	0.33
267_S	277_Y	0.574	0.32
127_A	215_Y	0.571	0.32
255_K	297_D	0.571	0.32
38_H	304_R	0.570	0.32
28_C	44_A	0.569	0.32
273_A	277_Y	0.567	0.32
133_K	254_L	0.565	0.32
146_L	257_A	0.564	0.32
72_K	76_G	0.562	0.32
198_I	234_P	0.560	0.31
160_Y	223_E	0.559	0.31
183_Y	224_V	0.558	0.31
98_D	140_D	0.556	0.31
41_S	50_V	0.556	0.31
172_R	195_L	0.555	0.31
66_S	269_V	0.553	0.31
216_V	269_V	0.552	0.31
98_D	254_L	0.551	0.31
153_R	292_V	0.551	0.31
145_A	201_V	0.550	0.31
233_V	254_L	0.549	0.31
270_G	299_S	0.549	0.31
34_N	41_S	0.548	0.30
110_Q	113_Q	0.548	0.30
260_K	297_D	0.547	0.30
178_A	250_A	0.546	0.30
156_A	262_V	0.545	0.30
210_A	284_N	0.545	0.30
139_I	156_A	0.545	0.30
130_R	138_E	0.544	0.30
51_E	57_R	0.544	0.30
29_G	67_K	0.543	0.30
200_D	297_D	0.543	0.30
42_V	221_G	0.539	0.30
209_I	273_A	0.536	0.30
163_A	229_P	0.536	0.30
154_E	157_S	0.536	0.30
98_D	112_M	0.536	0.30
240_L	292_V	0.535	0.29
221_G	241_G	0.532	0.29
176_G	180_S	0.532	0.29
213_Y	265_G	0.531	0.29
220_L	281_L	0.531	0.29
32_V	140_D	0.531	0.29
253_L	282_L	0.531	0.29
33_V	39_G	0.530	0.29
98_D	113_Q	0.527	0.29
52_E	278_A	0.526	0.29
215_Y	253_L	0.526	0.29
173_S	268_P	0.524	0.29
211_R	215_Y	0.524	0.29
24_G	32_V	0.522	0.28
212_T	303_I	0.520	0.28
64_F	76_G	0.520	0.28
132_L	302_T	0.519	0.28
177_V	203_R	0.519	0.28
180_S	233_V	0.518	0.28
157_S	211_R	0.516	0.28
172_R	220_L	0.516	0.28
97_K	209_I	0.516	0.28
131_N	141_R	0.515	0.28
63_A	72_K	0.515	0.28
146_L	201_V	0.514	0.28
77_A	86_K	0.511	0.28
148_L	180_S	0.511	0.28
132_L	161_R	0.509	0.27
246_A	250_A	0.508	0.27
31_L	178_A	0.507	0.27
36_E	140_D	0.507	0.27
67_K	74_R	0.506	0.27
276_V	297_D	0.505	0.27
166_D	216_V	0.504	0.27
109_R	143_A	0.504	0.27
39_G	148_L	0.501	0.27
162_R	208_E	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	0.5893	100	0.263	Contact Map
1aisB	1	0.5925	100	0.596	Contact Map
1c9bA	1	0.6019	100	0.604	Contact Map
2pk2A	3	0.6803	99.9	0.719	Contact Map
2w96A	1	0.7147	99.9	0.725	Contact Map
4f6uB	1	0.7147	99.9	0.726	Contact Map
3g33B	2	0.6771	99.9	0.731	Contact Map
2b9rA	1	0.6865	99.9	0.732	Contact Map
3k1fM	1	0.1661	99.9	0.736	Contact Map
4eojB	1	0.6991	99.9	0.736	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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