TF2B4 - HALSA - GREMLIN Contacts

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TF2B4 - Transcription initiation factor IIB 4

UniProt:	Q9HR45	Sequences: MTNQRTTRDGSHGTESVPTQRSRESTDEDHGCPECNGDLVTDEDRGETTCGECGLVVEEDGIDHGPEWRAFNAQEQDEKSRVGAPTTNMMHDKGLSTNIGWQDKDAYGNTLSGRQRRKMQRLRKWNERFRTRNSKERNLKQALGEIERMASAFGLPDSVRETASVIYRRALGEDLLPGRSIEGVATSALYAAARQANTPRSLDEVASVSRVDRGEIARTYRYVARELSLEVAPTDPASYVPRFCSDLELSGDVERRARDLLAAAADAGITSGKSPVGLAAASVYAAALLTNERVTQNEVSTVANVSEVTIRNRYHEILDAGGEPGVEA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	328 (279)
Sequences:	1068 (671)
Seq/√Len:	40.2

HALSA - TF2B4 TF2B2 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_C	283_V	6.542	1.00
39_L	57_V	3.891	1.00
32_C	53_C	3.890	1.00
50_C	53_C	3.849	1.00
256_R	290_T	3.686	1.00
313_R	316_E	3.630	1.00
250_S	292_E	3.598	1.00
150_A	189_L	3.588	1.00
142_A	167_Y	3.286	1.00
296_Q	311_R	3.234	1.00
39_L	48_T	3.159	1.00
32_C	35_C	2.849	1.00
149_M	189_L	2.836	1.00
297_N	307_E	2.704	1.00
35_C	50_C	2.670	1.00
150_A	160_R	2.632	1.00
145_E	148_R	2.564	1.00
143_L	164_S	2.555	1.00
189_L	205_V	2.537	1.00
32_C	50_C	2.344	1.00
42_D	45_R	2.229	1.00
163_A	192_A	2.218	1.00
149_M	208_V	2.199	0.99
257_A	286_A	2.170	0.99
256_R	259_D	2.161	0.99
307_E	315_H	2.158	0.99
213_R	217_A	2.152	0.99
67_E	81_R	2.133	0.99
280_A	303_A	2.104	0.99
70_A	73_A	2.027	0.99
178_G	275_P	1.993	0.99
35_C	53_C	1.991	0.99
162_T	195_Q	1.982	0.99
167_Y	176_L	1.961	0.99
159_V	192_A	1.903	0.98
155_L	189_L	1.892	0.98
118_K	122_L	1.883	0.98
257_A	279_A	1.841	0.98
119_M	122_L	1.807	0.98
119_M	123_R	1.807	0.98
243_F	283_V	1.794	0.98
115_Q	118_K	1.769	0.98
32_C	36_N	1.750	0.97
42_D	46_G	1.729	0.97
297_N	310_I	1.647	0.96
260_L	286_A	1.640	0.96
200_R	204_E	1.599	0.95
38_D	52_E	1.586	0.95
277_G	309_T	1.573	0.95
224_A	231_V	1.569	0.95
165_V	168_R	1.566	0.95
194_R	217_A	1.550	0.95
261_L	278_L	1.547	0.95
142_A	171_L	1.542	0.94
205_V	208_V	1.524	0.94
249_L	294_V	1.513	0.94
162_T	196_A	1.508	0.94
68_W	79_K	1.505	0.94
142_A	218_R	1.463	0.93
253_V	290_T	1.449	0.92
70_A	75_E	1.432	0.92
260_L	282_S	1.429	0.92
295_T	298_E	1.415	0.91
277_G	281_A	1.413	0.91
305_V	310_I	1.399	0.91
91_H	94_G	1.399	0.91
225_R	298_E	1.396	0.91
287_A	302_V	1.388	0.91
65_G	68_W	1.383	0.90
91_H	311_R	1.380	0.90
243_F	247_L	1.355	0.90
38_D	51_G	1.327	0.89
300_S	303_A	1.317	0.88
191_A	229_L	1.311	0.88
36_N	40_V	1.309	0.88
204_E	242_R	1.292	0.87
261_L	282_S	1.288	0.87
202_L	217_A	1.267	0.86
281_A	309_T	1.262	0.86
298_E	302_V	1.256	0.86
67_E	79_K	1.252	0.85
69_R	81_R	1.250	0.85
253_V	292_E	1.249	0.85
283_V	303_A	1.246	0.85
50_C	54_G	1.232	0.84
169_R	173_E	1.228	0.84
296_Q	308_V	1.226	0.84
235_D	261_L	1.224	0.84
237_A	262_A	1.204	0.83
282_S	286_A	1.185	0.82
48_T	260_L	1.183	0.82
159_V	198_T	1.180	0.82
235_D	238_S	1.174	0.81
81_R	97_T	1.160	0.81
162_T	165_V	1.159	0.81
217_A	243_F	1.155	0.80
205_V	231_V	1.144	0.80
294_V	298_E	1.144	0.80
140_K	144_G	1.142	0.80
280_A	310_I	1.138	0.79
280_A	285_A	1.127	0.79
142_A	180_S	1.123	0.78
291_N	295_T	1.121	0.78
263_A	267_A	1.113	0.78
52_E	150_A	1.110	0.78
190_Y	234_T	1.102	0.77
191_A	194_R	1.102	0.77
63_D	67_E	1.102	0.77
202_L	213_R	1.093	0.77
142_A	146_I	1.089	0.76
294_V	307_E	1.088	0.76
41_T	58_E	1.081	0.76
146_I	164_S	1.077	0.75
34_E	55_L	1.074	0.75
164_S	171_L	1.068	0.75
261_L	279_A	1.067	0.75
254_E	258_R	1.066	0.75
146_I	185_A	1.064	0.75
131_T	146_I	1.056	0.74
235_D	265_A	1.056	0.74
68_W	71_F	1.052	0.74
70_A	78_E	1.046	0.73
33_P	57_V	1.040	0.73
153_F	266_D	1.033	0.72
68_W	85_P	1.032	0.72
33_P	283_V	1.031	0.72
49_T	302_V	1.029	0.72
56_V	188_A	1.017	0.71
40_V	51_G	1.015	0.71
308_V	311_R	1.015	0.71
214_G	315_H	1.003	0.70
41_T	47_E	0.996	0.70
31_G	36_N	0.990	0.69
172_G	297_N	0.986	0.69
39_L	44_D	0.984	0.69
41_T	48_T	0.984	0.69
293_R	298_E	0.981	0.68
128_R	272_G	0.970	0.68
155_L	319_D	0.966	0.67
139_L	164_S	0.955	0.66
95_L	98_N	0.954	0.66
177_P	307_E	0.952	0.66
52_E	156_P	0.950	0.66
115_Q	119_M	0.949	0.66
199_P	238_S	0.949	0.66
167_Y	181_I	0.943	0.65
150_A	278_L	0.940	0.65
256_R	289_L	0.936	0.65
86_T	133_N	0.933	0.64
163_A	188_A	0.930	0.64
217_A	220_Y	0.922	0.64
39_L	46_G	0.920	0.63
249_L	253_V	0.920	0.63
184_V	223_V	0.919	0.63
168_R	192_A	0.916	0.63
185_A	230_E	0.914	0.63
102_Q	136_E	0.913	0.63
274_S	310_I	0.900	0.62
186_T	193_A	0.899	0.62
87_T	91_H	0.893	0.61
67_E	71_F	0.891	0.61
31_G	51_G	0.886	0.60
200_R	242_R	0.886	0.60
212_D	215_E	0.884	0.60
215_E	218_R	0.882	0.60
177_P	229_L	0.880	0.60
273_K	286_A	0.878	0.60
201_S	204_E	0.875	0.59
155_L	193_A	0.870	0.59
280_A	300_S	0.863	0.58
153_F	179_R	0.861	0.58
90_M	102_Q	0.859	0.58
247_L	283_V	0.856	0.58
164_S	168_R	0.855	0.58
277_G	305_V	0.854	0.58
40_V	280_A	0.847	0.57
100_G	231_V	0.845	0.57
277_G	313_R	0.844	0.57
159_V	265_A	0.840	0.56
179_R	227_L	0.833	0.56
146_I	152_A	0.831	0.55
71_F	243_F	0.830	0.55
160_R	189_L	0.825	0.55
59_E	64_H	0.821	0.55
180_S	221_R	0.815	0.54
68_W	81_R	0.815	0.54
40_V	48_T	0.812	0.54
48_T	51_G	0.810	0.54
145_E	218_R	0.806	0.53
37_G	223_V	0.805	0.53
295_T	307_E	0.803	0.53
115_Q	212_D	0.799	0.53
138_N	191_A	0.798	0.52
264_A	270_T	0.795	0.52
217_A	291_N	0.794	0.52
206_A	211_V	0.793	0.52
201_S	205_V	0.789	0.52
217_A	274_S	0.788	0.52
41_T	260_L	0.785	0.51
36_N	53_C	0.783	0.51
56_V	88_N	0.783	0.51
240_V	261_L	0.779	0.51
244_C	247_L	0.768	0.50
237_A	304_N	0.767	0.50
239_Y	244_C	0.766	0.50
212_D	216_I	0.765	0.49
268_G	273_K	0.764	0.49
145_E	149_M	0.762	0.49
166_I	188_A	0.761	0.49
297_N	305_V	0.760	0.49
220_Y	277_G	0.758	0.49
177_P	278_L	0.756	0.49
138_N	167_Y	0.756	0.49
220_Y	223_V	0.755	0.49
134_S	187_S	0.754	0.48
242_R	274_S	0.754	0.48
279_A	303_A	0.753	0.48
82_V	205_V	0.752	0.48
191_A	287_A	0.749	0.48
210_R	280_A	0.748	0.48
193_A	261_L	0.742	0.47
99_I	137_R	0.740	0.47
219_T	310_I	0.739	0.47
32_C	55_L	0.738	0.47
65_G	310_I	0.737	0.47
72_N	278_L	0.736	0.47
170_A	229_L	0.735	0.47
190_Y	193_A	0.732	0.46
123_R	255_R	0.726	0.46
57_V	274_S	0.726	0.46
47_E	121_R	0.725	0.46
56_V	198_T	0.724	0.46
295_T	311_R	0.724	0.46
203_D	213_R	0.724	0.46
205_V	268_G	0.718	0.45
216_I	262_A	0.716	0.45
237_A	265_A	0.715	0.45
297_N	312_N	0.710	0.44
142_A	181_I	0.709	0.44
209_S	234_T	0.704	0.44
225_R	245_S	0.702	0.44
65_G	70_A	0.702	0.44
247_L	299_V	0.702	0.44
178_G	309_T	0.699	0.43
281_A	286_A	0.698	0.43
142_A	306_S	0.697	0.43
142_A	281_A	0.696	0.43
211_V	246_D	0.693	0.43
228_S	248_E	0.689	0.43
73_A	78_E	0.689	0.43
167_Y	313_R	0.688	0.42
46_G	61_G	0.687	0.42
87_T	102_Q	0.685	0.42
249_L	292_E	0.681	0.42
141_Q	265_A	0.679	0.42
269_I	280_A	0.678	0.42
185_A	257_A	0.676	0.41
74_Q	319_D	0.675	0.41
72_N	75_E	0.674	0.41
209_S	314_Y	0.674	0.41
193_A	196_A	0.672	0.41
62_I	68_W	0.669	0.41
287_A	293_R	0.669	0.41
184_V	219_T	0.668	0.41
178_G	305_V	0.667	0.41
229_L	261_L	0.666	0.40
260_L	272_G	0.661	0.40
199_P	282_S	0.656	0.40
82_V	211_V	0.656	0.40
36_N	232_A	0.654	0.39
142_A	150_A	0.654	0.39
34_E	52_E	0.653	0.39
139_L	143_L	0.652	0.39
273_K	278_L	0.652	0.39
83_G	99_I	0.651	0.39
240_V	312_N	0.651	0.39
60_D	66_P	0.650	0.39
96_S	149_M	0.649	0.39
77_D	86_T	0.649	0.39
49_T	315_H	0.646	0.39
179_R	286_A	0.646	0.39
287_A	292_E	0.646	0.39
232_A	244_C	0.646	0.39
167_Y	170_A	0.644	0.39
163_A	269_I	0.636	0.38
87_T	277_G	0.635	0.38
139_L	168_R	0.630	0.37
269_I	287_A	0.630	0.37
305_V	309_T	0.629	0.37
157_D	161_E	0.628	0.37
36_N	137_R	0.628	0.37
146_I	225_R	0.628	0.37
92_D	296_Q	0.628	0.37
155_L	187_S	0.627	0.37
96_S	187_S	0.622	0.37
58_E	64_H	0.622	0.37
251_G	255_R	0.621	0.37
146_I	163_A	0.620	0.36
187_S	258_R	0.619	0.36
92_D	95_L	0.619	0.36
117_R	120_Q	0.618	0.36
278_L	303_A	0.617	0.36
167_Y	220_Y	0.617	0.36
104_K	291_N	0.614	0.36
137_R	145_E	0.612	0.36
72_N	201_S	0.611	0.36
140_K	261_L	0.611	0.36
183_G	187_S	0.610	0.36
182_E	185_A	0.610	0.36
49_T	198_T	0.609	0.36
193_A	234_T	0.608	0.35
89_M	92_D	0.605	0.35
285_A	299_V	0.604	0.35
97_T	137_R	0.603	0.35
70_A	76_Q	0.600	0.35
136_E	160_R	0.597	0.35
135_K	248_E	0.597	0.35
269_I	318_L	0.597	0.35
223_V	276_V	0.597	0.35
159_V	196_A	0.595	0.34
269_I	316_E	0.592	0.34
121_R	305_V	0.592	0.34
51_G	262_A	0.591	0.34
219_T	233_P	0.589	0.34
170_A	175_L	0.585	0.34
97_T	200_R	0.584	0.33
82_V	88_N	0.583	0.33
205_V	320_A	0.583	0.33
48_T	57_V	0.582	0.33
35_C	51_G	0.580	0.33
293_R	302_V	0.579	0.33
153_F	264_A	0.578	0.33
190_Y	220_Y	0.576	0.33
40_V	156_P	0.576	0.33
220_Y	272_G	0.576	0.33
40_V	46_G	0.576	0.33
139_L	199_P	0.575	0.33
253_V	257_A	0.574	0.33
216_I	280_A	0.574	0.33
138_N	180_S	0.573	0.33
87_T	90_M	0.573	0.33
82_V	89_M	0.573	0.33
207_S	320_A	0.573	0.33
49_T	228_S	0.572	0.32
74_Q	284_Y	0.571	0.32
134_S	316_E	0.571	0.32
164_S	169_R	0.570	0.32
186_T	209_S	0.570	0.32
187_S	280_A	0.567	0.32
152_A	208_V	0.567	0.32
189_L	268_G	0.566	0.32
91_H	95_L	0.566	0.32
60_D	209_S	0.565	0.32
161_E	164_S	0.564	0.32
283_V	299_V	0.563	0.32
154_G	191_A	0.562	0.32
57_V	211_V	0.560	0.32
52_E	84_A	0.559	0.31
75_E	298_E	0.558	0.31
216_I	234_T	0.558	0.31
146_I	167_Y	0.555	0.31
88_N	161_E	0.553	0.31
243_F	273_K	0.553	0.31
70_A	79_K	0.552	0.31
270_T	280_A	0.548	0.31
207_S	304_N	0.548	0.31
314_Y	318_L	0.547	0.31
63_D	69_R	0.546	0.30
180_S	275_P	0.545	0.30
142_A	310_I	0.545	0.30
283_V	304_N	0.544	0.30
253_V	272_G	0.544	0.30
142_A	170_A	0.540	0.30
298_E	301_T	0.540	0.30
257_A	261_L	0.539	0.30
38_D	61_G	0.536	0.30
153_F	208_V	0.531	0.29
264_A	320_A	0.531	0.29
188_A	268_G	0.531	0.29
92_D	96_S	0.531	0.29
41_T	146_I	0.530	0.29
161_E	174_D	0.530	0.29
192_A	196_A	0.530	0.29
44_D	47_E	0.529	0.29
85_P	295_T	0.529	0.29
91_H	161_E	0.529	0.29
262_A	266_D	0.528	0.29
103_D	253_V	0.524	0.29
308_V	312_N	0.524	0.29
153_F	226_E	0.524	0.29
32_C	39_L	0.521	0.29
133_N	181_I	0.520	0.28
280_A	284_Y	0.519	0.28
76_Q	84_A	0.519	0.28
79_K	186_T	0.518	0.28
71_F	247_L	0.517	0.28
173_E	298_E	0.517	0.28
41_T	237_A	0.516	0.28
254_E	298_E	0.515	0.28
139_L	309_T	0.514	0.28
198_T	225_R	0.513	0.28
234_T	276_V	0.513	0.28
175_L	223_V	0.513	0.28
100_G	148_R	0.513	0.28
289_L	314_Y	0.513	0.28
143_L	214_G	0.513	0.28
46_G	155_L	0.512	0.28
54_G	272_G	0.511	0.28
55_L	144_G	0.511	0.28
199_P	261_L	0.511	0.28
63_D	66_P	0.510	0.28
186_T	205_V	0.505	0.27
163_A	191_A	0.504	0.27
41_T	49_T	0.504	0.27
144_G	299_V	0.504	0.27
186_T	199_P	0.503	0.27
68_W	247_L	0.501	0.27
199_P	297_N	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	0.5732	100	0.28	Contact Map
1aisB	1	0.5823	100	0.603	Contact Map
1c9bA	1	0.5915	100	0.616	Contact Map
2pk2A	3	0.6677	99.9	0.721	Contact Map
4f6uB	1	0.7012	99.9	0.726	Contact Map
2w96A	1	0.7012	99.9	0.728	Contact Map
3g33B	2	0.6585	99.9	0.737	Contact Map
2b9rA	1	0.6738	99.9	0.74	Contact Map
4eojB	1	0.686	99.9	0.743	Contact Map
2i53A	1	0.6799	99.9	0.743	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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