TF2B3 - HALSA - GREMLIN Contacts

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TF2B3 - Transcription initiation factor IIB 3

UniProt:	Q9HHK5	Sequences: MERATREREKEQREQAQTNDEAQQCPECNSANVITDQSERVCEDCGLVLEDDQIDHGPEWRAFNSSERDQKSRVGAPTTKTMHDKGLTTQIDWKDKDAYGRSLDAKKRNQMNRLRKWQERIRTKDAGERNLQFALSEIDRMASALGVPRSVREVASVIYRRALKEDLIRGRSIEGVATACLYAACRQEGIPRTLEEVTEVARIDQKEIGRTYRYVAQELSLEIQPTDPKEYLPRFASDLELSEEVIAKAREIIDTSAEQGLLSGKSPSGFAAAAIYAASLLCNEKKTQREVANVANVTEVTIRNRYQEQIEAMGFGV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	317 (280)
Sequences:	1053 (675)
Seq/√Len:	40.3

HALSA - TF2B3 TF2B6 TF2B4 TF2B7 TF2B2 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
236_A	275_I	6.379	1.00
25_C	45_C	4.001	1.00
242_S	284_E	3.936	1.00
142_A	181_L	3.889	1.00
42_C	45_C	3.806	1.00
305_R	308_E	3.704	1.00
248_K	282_C	3.548	1.00
134_A	159_Y	3.178	1.00
288_Q	303_R	3.175	1.00
25_C	28_C	3.033	1.00
33_V	40_R	2.927	1.00
142_A	152_R	2.851	1.00
141_M	181_L	2.762	1.00
137_E	140_R	2.736	1.00
28_C	42_C	2.708	1.00
33_V	49_L	2.685	1.00
135_L	156_S	2.472	1.00
289_R	299_E	2.468	1.00
25_C	42_C	2.422	1.00
181_L	197_V	2.409	1.00
299_E	307_Q	2.234	1.00
59_E	63_F	2.208	1.00
141_M	200_V	2.174	0.99
155_A	184_A	2.167	0.99
61_R	73_R	2.048	0.99
272_A	295_A	2.031	0.99
205_Q	209_G	2.001	0.99
249_A	271_A	1.956	0.99
59_E	73_R	1.920	0.99
32_N	44_D	1.870	0.98
248_K	251_E	1.864	0.98
170_G	267_P	1.848	0.98
249_A	278_A	1.834	0.98
28_C	45_C	1.812	0.98
216_A	223_I	1.796	0.98
83_H	86_G	1.792	0.98
147_V	181_L	1.782	0.98
252_I	278_A	1.763	0.97
192_R	196_E	1.744	0.97
25_C	29_N	1.736	0.97
62_A	65_S	1.699	0.97
60_W	63_F	1.688	0.97
151_V	184_A	1.676	0.97
197_V	200_V	1.662	0.96
235_F	239_L	1.662	0.96
245_V	284_E	1.661	0.96
159_Y	168_I	1.648	0.96
183_A	221_L	1.601	0.96
154_V	187_Q	1.578	0.95
289_R	302_I	1.520	0.94
235_F	275_I	1.518	0.94
57_G	60_W	1.492	0.93
36_D	179_A	1.489	0.93
32_N	43_E	1.489	0.93
186_R	209_G	1.486	0.93
134_A	210_R	1.479	0.93
60_W	73_R	1.447	0.92
35_T	40_R	1.432	0.92
111_M	114_L	1.421	0.92
269_G	301_T	1.410	0.91
273_A	301_T	1.407	0.91
253_I	270_F	1.406	0.91
161_R	165_E	1.401	0.91
157_V	160_R	1.393	0.91
252_I	274_A	1.392	0.91
134_A	163_L	1.380	0.90
288_Q	300_V	1.377	0.90
42_C	46_G	1.371	0.90
274_A	278_A	1.369	0.90
227_D	230_E	1.361	0.90
62_A	67_E	1.360	0.90
253_I	274_A	1.349	0.89
54_I	59_E	1.322	0.88
255_T	259_Q	1.300	0.88
110_Q	114_L	1.297	0.87
279_S	294_V	1.270	0.86
196_E	234_R	1.256	0.86
44_D	142_A	1.256	0.86
47_L	87_L	1.245	0.85
241_L	286_K	1.243	0.85
245_V	282_C	1.243	0.85
54_I	60_W	1.236	0.85
217_Q	290_E	1.232	0.85
27_E	30_S	1.228	0.84
229_K	254_D	1.227	0.84
30_S	44_D	1.223	0.84
27_E	47_L	1.219	0.84
132_Q	136_S	1.219	0.84
159_Y	173_I	1.199	0.83
154_V	188_E	1.186	0.82
40_R	252_I	1.183	0.82
131_L	156_S	1.183	0.82
112_N	116_K	1.178	0.82
287_T	290_E	1.170	0.81
209_G	235_F	1.166	0.81
183_A	279_S	1.155	0.81
286_K	290_E	1.153	0.80
297_V	302_I	1.147	0.80
269_G	273_A	1.144	0.80
64_N	67_E	1.142	0.80
41_V	294_V	1.128	0.79
229_K	257_A	1.127	0.79
227_D	253_I	1.117	0.78
88_T	179_A	1.112	0.78
272_A	302_I	1.108	0.78
154_V	157_V	1.097	0.77
286_K	299_E	1.092	0.77
183_A	186_R	1.092	0.77
26_P	49_L	1.091	0.77
25_C	30_S	1.090	0.77
197_V	260_G	1.081	0.76
178_T	185_C	1.076	0.76
194_L	209_G	1.075	0.75
194_L	205_Q	1.073	0.75
300_V	303_R	1.067	0.75
260_G	265_K	1.066	0.75
176_V	215_V	1.066	0.75
60_W	77_P	1.062	0.75
246_I	250_R	1.060	0.74
285_K	290_E	1.060	0.74
292_A	295_A	1.049	0.74
272_A	277_A	1.045	0.73
156_S	163_L	1.036	0.73
35_T	38_S	1.033	0.73
59_E	71_K	1.028	0.72
83_H	303_R	1.026	0.72
79_T	269_G	1.018	0.71
275_I	295_A	1.014	0.71
244_E	282_C	1.008	0.71
151_V	190_I	1.004	0.70
120_R	171_R	1.003	0.70
232_L	253_I	1.003	0.70
192_R	234_R	1.003	0.70
94_K	128_E	0.996	0.70
138_I	144_A	0.980	0.68
206_K	307_Q	0.977	0.68
227_D	257_A	0.976	0.68
151_V	257_A	0.976	0.68
239_L	275_I	0.972	0.68
48_V	180_C	0.972	0.68
145_L	258_E	0.972	0.68
182_Y	226_T	0.968	0.68
44_D	148_P	0.968	0.68
34_I	43_E	0.965	0.67
77_P	84_D	0.963	0.67
77_P	83_H	0.960	0.67
164_K	289_R	0.955	0.66
193_T	196_E	0.954	0.66
24_Q	43_E	0.954	0.66
117_W	159_Y	0.953	0.66
134_A	138_I	0.952	0.66
142_A	270_F	0.950	0.66
253_I	271_A	0.943	0.65
169_R	299_E	0.940	0.65
134_A	273_A	0.940	0.65
138_I	177_A	0.938	0.65
137_E	210_R	0.931	0.64
152_R	181_L	0.927	0.64
113_R	171_R	0.927	0.64
248_K	281_L	0.911	0.63
90_Q	118_Q	0.906	0.62
269_G	305_R	0.905	0.62
119_E	132_Q	0.905	0.62
254_D	258_E	0.900	0.62
138_I	156_S	0.897	0.62
231_Y	236_A	0.896	0.61
172_S	213_R	0.893	0.61
241_L	245_V	0.893	0.61
128_E	165_E	0.892	0.61
279_S	285_K	0.891	0.61
92_D	140_R	0.889	0.61
41_V	307_Q	0.888	0.61
234_R	266_S	0.888	0.61
176_V	211_T	0.885	0.60
162_A	221_L	0.884	0.60
41_V	59_E	0.882	0.60
84_D	87_L	0.882	0.60
170_G	301_T	0.878	0.60
191_P	230_E	0.877	0.60
193_T	197_V	0.874	0.60
134_A	302_I	0.872	0.59
160_R	184_A	0.870	0.59
49_L	266_S	0.867	0.59
197_V	223_I	0.866	0.59
290_E	294_V	0.865	0.59
34_I	272_A	0.864	0.59
289_R	297_V	0.862	0.58
35_T	39_E	0.860	0.58
147_V	185_C	0.853	0.58
145_L	256_S	0.852	0.58
130_N	183_A	0.852	0.58
35_T	50_E	0.847	0.57
159_Y	222_E	0.847	0.57
29_N	34_I	0.845	0.57
207_E	210_R	0.840	0.56
121_I	186_R	0.837	0.56
204_D	207_E	0.836	0.56
212_Y	269_G	0.834	0.56
156_S	160_R	0.834	0.56
182_Y	185_C	0.831	0.56
138_I	159_Y	0.826	0.55
209_G	266_S	0.823	0.55
26_P	45_C	0.821	0.55
279_S	284_E	0.819	0.55
58_P	62_A	0.818	0.54
155_A	180_C	0.817	0.54
265_K	285_K	0.816	0.54
79_T	94_K	0.806	0.53
113_R	117_W	0.806	0.53
26_P	275_I	0.802	0.53
201_A	306_Y	0.800	0.53
89_T	192_R	0.799	0.53
55_D	60_W	0.798	0.53
283_N	287_T	0.798	0.53
73_R	77_P	0.795	0.52
40_R	43_E	0.792	0.52
97_D	139_D	0.790	0.52
55_D	59_E	0.779	0.51
134_A	172_S	0.775	0.51
97_D	111_M	0.771	0.50
265_K	270_F	0.770	0.50
182_Y	223_I	0.768	0.50
75_G	160_R	0.759	0.49
181_L	260_G	0.759	0.49
297_V	301_T	0.750	0.48
261_L	272_A	0.749	0.48
249_A	253_I	0.749	0.48
86_G	92_D	0.745	0.48
134_A	171_R	0.744	0.48
252_I	264_G	0.744	0.48
59_E	239_L	0.742	0.47
29_N	45_C	0.742	0.47
281_L	306_Y	0.738	0.47
126_A	308_E	0.737	0.47
97_D	117_W	0.735	0.47
241_L	264_G	0.733	0.47
133_F	257_A	0.728	0.46
147_V	179_A	0.726	0.46
37_Q	295_A	0.724	0.46
198_T	203_I	0.723	0.46
29_N	224_Q	0.723	0.46
28_C	31_A	0.723	0.46
79_T	83_H	0.718	0.45
149_R	153_E	0.717	0.45
212_Y	215_V	0.714	0.45
215_V	238_D	0.714	0.45
123_T	138_I	0.714	0.45
161_R	187_Q	0.713	0.45
243_E	247_A	0.712	0.45
119_E	204_D	0.711	0.45
137_E	141_M	0.706	0.44
128_E	152_R	0.704	0.44
201_A	226_T	0.704	0.44
60_W	71_K	0.704	0.44
165_E	290_E	0.703	0.44
73_R	89_T	0.702	0.44
129_R	137_E	0.702	0.44
146_G	183_A	0.702	0.44
119_E	173_I	0.699	0.44
269_G	297_V	0.698	0.43
156_S	210_R	0.695	0.43
229_K	296_N	0.690	0.43
34_I	252_I	0.689	0.43
266_S	302_I	0.688	0.43
120_R	264_G	0.688	0.43
24_Q	29_N	0.684	0.42
155_A	261_L	0.684	0.42
134_A	162_A	0.683	0.42
138_I	155_A	0.682	0.42
252_I	281_L	0.681	0.42
68_R	76_A	0.681	0.42
159_Y	305_R	0.679	0.42
155_A	183_A	0.678	0.42
179_A	232_L	0.671	0.41
158_I	180_C	0.670	0.41
134_A	173_I	0.669	0.41
208_I	254_D	0.666	0.41
86_G	156_S	0.665	0.40
271_A	295_A	0.664	0.40
272_A	276_Y	0.664	0.40
149_R	222_E	0.661	0.40
159_Y	212_Y	0.661	0.40
185_C	253_I	0.654	0.40
38_S	53_Q	0.654	0.40
49_L	203_I	0.654	0.40
126_A	214_Y	0.654	0.40
220_S	272_A	0.653	0.39
51_D	220_S	0.652	0.39
169_R	270_F	0.650	0.39
289_R	304_N	0.648	0.39
65_S	70_Q	0.645	0.39
275_I	296_N	0.645	0.39
270_F	295_A	0.644	0.39
50_E	56_H	0.639	0.38
209_G	212_Y	0.636	0.38
84_D	88_T	0.636	0.38
287_T	299_E	0.635	0.38
95_D	245_V	0.635	0.38
81_T	138_I	0.632	0.38
153_E	166_D	0.632	0.38
60_W	89_T	0.630	0.37
162_A	215_V	0.628	0.37
147_V	311_E	0.621	0.37
177_A	181_L	0.620	0.37
127_G	240_E	0.617	0.36
62_A	68_R	0.617	0.36
147_V	158_I	0.617	0.36
130_N	159_Y	0.617	0.36
24_Q	258_E	0.616	0.36
35_T	138_I	0.615	0.36
256_S	262_L	0.615	0.36
85_K	167_L	0.615	0.36
175_G	179_A	0.613	0.36
77_P	270_F	0.613	0.36
62_A	70_Q	0.612	0.36
232_L	304_N	0.612	0.36
224_Q	236_A	0.608	0.36
150_S	237_S	0.608	0.36
151_V	188_E	0.607	0.35
33_V	38_S	0.607	0.35
126_A	179_A	0.606	0.35
63_F	235_F	0.604	0.35
56_H	206_K	0.600	0.35
261_L	308_E	0.600	0.35
275_I	291_V	0.599	0.35
215_V	268_S	0.598	0.35
64_N	193_T	0.597	0.35
153_E	156_S	0.596	0.35
270_F	292_A	0.596	0.35
225_P	287_T	0.595	0.34
261_L	279_S	0.595	0.34
92_D	95_D	0.593	0.34
202_R	272_A	0.593	0.34
35_T	41_V	0.591	0.34
51_D	56_H	0.588	0.34
240_E	294_V	0.588	0.34
235_F	265_K	0.585	0.34
135_L	206_K	0.583	0.33
191_P	274_A	0.583	0.33
141_M	157_V	0.581	0.33
178_T	201_A	0.579	0.33
174_E	306_Y	0.578	0.33
79_T	156_S	0.577	0.33
49_L	207_E	0.576	0.33
172_S	267_P	0.573	0.33
75_G	89_T	0.571	0.32
74_V	81_T	0.571	0.32
212_Y	264_G	0.570	0.32
272_A	292_A	0.570	0.32
46_G	264_G	0.569	0.32
159_Y	162_A	0.567	0.32
287_T	292_A	0.566	0.32
141_M	187_Q	0.566	0.32
118_Q	142_A	0.565	0.32
86_G	113_R	0.565	0.32
52_D	201_A	0.565	0.32
165_E	225_P	0.561	0.32
265_K	278_A	0.561	0.32
83_H	88_T	0.561	0.32
181_L	246_I	0.561	0.32
70_Q	73_R	0.559	0.32
180_C	283_N	0.558	0.31
252_I	307_Q	0.557	0.31
163_L	197_V	0.556	0.31
138_I	217_Q	0.556	0.31
70_Q	262_L	0.555	0.31
185_C	226_T	0.554	0.31
57_G	76_A	0.553	0.31
214_Y	252_I	0.553	0.31
162_A	167_L	0.553	0.31
27_E	44_D	0.552	0.31
94_K	118_Q	0.552	0.31
128_E	169_R	0.552	0.31
165_E	168_I	0.552	0.31
277_A	291_V	0.551	0.31
236_A	239_L	0.551	0.31
115_R	137_E	0.549	0.31
162_A	228_P	0.549	0.31
74_V	83_H	0.549	0.31
117_W	158_I	0.547	0.31
160_R	300_V	0.547	0.31
31_A	215_V	0.545	0.30
37_Q	253_I	0.544	0.30
245_V	249_A	0.542	0.30
134_A	142_A	0.542	0.30
294_V	302_I	0.541	0.30
219_L	301_T	0.536	0.30
131_L	191_P	0.534	0.30
204_D	208_I	0.531	0.29
78_T	125_D	0.531	0.29
48_V	190_I	0.529	0.29
76_A	85_K	0.529	0.29
261_L	310_I	0.528	0.29
207_E	232_L	0.525	0.29
48_V	174_E	0.525	0.29
276_Y	280_L	0.525	0.29
182_Y	212_Y	0.525	0.29
25_C	33_V	0.524	0.29
199_E	296_N	0.523	0.29
78_T	302_I	0.519	0.28
110_Q	135_L	0.518	0.28
145_L	200_V	0.515	0.28
211_T	302_I	0.514	0.28
245_V	274_A	0.514	0.28
24_Q	49_L	0.513	0.28
64_N	205_Q	0.513	0.28
235_F	294_V	0.511	0.28
215_V	285_K	0.510	0.28
81_T	160_R	0.509	0.28
72_S	180_C	0.508	0.28
191_P	253_I	0.508	0.28
109_N	112_N	0.508	0.28
81_T	156_S	0.507	0.28
52_D	58_P	0.506	0.27
203_I	238_D	0.506	0.27
173_I	177_A	0.505	0.27
70_Q	143_S	0.502	0.27
245_V	264_G	0.500	0.27
161_R	221_L	0.500	0.27
61_R	71_K	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	0.5899	100	0.265	Contact Map
1aisB	1	0.5931	100	0.584	Contact Map
1c9bA	1	0.6025	100	0.608	Contact Map
2pk2A	3	0.6814	99.9	0.708	Contact Map
2w96A	1	0.7161	99.9	0.718	Contact Map
4f6uB	1	0.7161	99.9	0.719	Contact Map
3g33B	2	0.6814	99.9	0.728	Contact Map
2i53A	1	0.7035	99.9	0.73	Contact Map
2b9rA	1	0.6877	99.9	0.73	Contact Map
4eojB	1	0.7003	99.9	0.732	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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