TF2B2 - SULSO - GREMLIN Contacts

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TF2B2 - Transcription initiation factor IIB 2

UniProt:	P58110	Sequences: MKCPYCKTDNAITYDVEKGMYVCTNCASVIEDSAVDPGPDWRAYNAKDRNEKERVGSPSTPKVHDWGFHTIIGYGRAKDRLKTLKMQRMQNKIRVSPKDKKLVTLLSILNDESSKLELPEHVKETASLIIRKMVETGLTKRIDQYTLIVAALYYSCQVNNIPRHLQEFKVRYSISSSEFWSALKRVQYVANSIPGFRPKIKPAEYIPKILYKLNLPPIIGTKASELVDLMHKQGLTSGKGYLSLSAASVYLISALMDIKKTQKEVADSLDITEVTIRNRYKDIVDNFDIVVTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	293 (276)
Sequences:	1059 (709)
Seq/√Len:	42.7

HALSA - TF2B4 TF2B7 TF2B2 TF2B6 TF2B3 TF2B5 TF2B1
SULSO - TF2B2 TF2B1

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
210_L	249_V	6.487	1.00
113_S	152_L	4.746	1.00
23_C	26_C	3.974	1.00
262_Q	277_R	3.520	1.00
279_R	282_D	3.442	1.00
222_K	256_M	3.386	1.00
216_P	258_I	3.338	1.00
15_D	18_K	3.130	1.00
105_L	130_I	3.115	1.00
112_E	152_L	2.874	1.00
3_C	26_C	2.768	1.00
106_L	127_S	2.603	1.00
113_S	123_K	2.541	1.00
3_C	6_C	2.530	1.00
108_I	111_D	2.500	1.00
246_A	269_L	2.497	1.00
152_L	168_F	2.418	1.00
12_I	30_I	2.409	1.00
263_K	273_E	2.402	1.00
118_L	152_L	2.389	1.00
141_R	241_Y	2.379	1.00
126_A	155_S	2.267	1.00
176_S	180_W	2.212	1.00
43_A	46_A	2.211	1.00
122_V	155_S	2.178	1.00
6_C	23_C	2.114	0.99
40_D	54_R	2.096	0.99
273_E	281_K	2.001	0.99
222_K	225_E	1.873	0.99
130_I	139_T	1.870	0.99
12_I	21_Y	1.807	0.98
263_K	276_I	1.792	0.98
3_C	7_K	1.791	0.98
22_V	268_S	1.778	0.98
226_L	252_I	1.771	0.98
223_A	252_I	1.764	0.98
209_I	213_L	1.749	0.98
223_A	245_S	1.744	0.98
15_D	19_G	1.738	0.98
23_C	27_A	1.721	0.98
227_V	248_S	1.708	0.97
128_L	131_R	1.705	0.97
209_I	249_V	1.701	0.97
227_V	244_L	1.694	0.97
3_C	23_C	1.688	0.97
112_E	171_R	1.686	0.97
125_T	159_N	1.665	0.97
43_A	48_D	1.622	0.97
163_R	167_E	1.595	0.96
261_T	264_E	1.550	0.95
243_S	275_T	1.531	0.95
105_L	109_L	1.501	0.95
226_L	248_S	1.496	0.94
215_L	260_K	1.489	0.94
125_T	158_V	1.489	0.94
40_D	52_K	1.483	0.94
54_R	70_T	1.459	0.94
109_L	148_I	1.445	0.93
41_W	52_K	1.443	0.93
141_R	275_T	1.439	0.93
6_C	26_C	1.428	0.93
203_A	228_D	1.427	0.93
38_G	41_W	1.427	0.93
253_S	268_S	1.412	0.93
262_Q	274_V	1.405	0.92
190_A	193_I	1.385	0.92
116_L	232_K	1.371	0.91
83_T	86_M	1.367	0.91
5_Y	28_S	1.367	0.91
219_I	256_M	1.367	0.91
109_L	127_S	1.356	0.91
105_L	134_V	1.343	0.91
260_K	264_E	1.342	0.91
157_Q	180_W	1.336	0.90
3_C	8_T	1.326	0.90
154_Y	157_Q	1.315	0.90
180_W	209_I	1.310	0.89
105_L	181_S	1.304	0.89
245_S	269_L	1.304	0.89
201_K	204_E	1.298	0.89
41_W	44_Y	1.298	0.89
220_G	224_S	1.289	0.89
168_F	171_R	1.276	0.88
154_Y	195_G	1.257	0.87
248_S	252_I	1.251	0.87
249_V	265_V	1.250	0.87
60_T	64_H	1.245	0.87
125_T	128_L	1.243	0.87
40_D	44_Y	1.238	0.87
165_L	180_W	1.237	0.87
127_S	131_R	1.227	0.86
64_H	67_G	1.217	0.86
8_T	25_N	1.205	0.85
56_G	60_T	1.197	0.85
271_I	276_I	1.192	0.84
153_Y	200_I	1.190	0.84
127_S	134_V	1.183	0.84
135_E	263_K	1.171	0.83
167_E	208_K	1.169	0.83
247_A	275_T	1.165	0.83
246_A	251_L	1.161	0.83
5_Y	8_T	1.113	0.80
69_H	112_E	1.111	0.80
102_L	127_S	1.110	0.80
130_I	144_Q	1.105	0.80
174_I	212_K	1.104	0.79
217_P	221_T	1.089	0.79
227_V	245_S	1.086	0.78
219_I	258_I	1.085	0.78
132_K	136_T	1.084	0.78
12_I	19_G	1.082	0.78
21_Y	24_T	1.077	0.78
246_A	276_I	1.076	0.78
25_N	113_S	1.072	0.77
264_E	268_S	1.071	0.77
165_L	176_S	1.069	0.77
243_S	247_A	1.055	0.76
169_K	174_I	1.050	0.76
101_K	154_Y	1.048	0.76
43_A	51_E	1.040	0.75
54_R	72_I	1.037	0.75
250_Y	254_A	1.029	0.74
89_M	130_I	1.020	0.74
122_V	161_I	1.020	0.74
95_V	109_L	1.018	0.74
41_W	58_P	1.016	0.74
259_K	264_E	1.013	0.73
147_L	182_A	1.006	0.73
136_T	264_E	1.000	0.72
13_T	21_Y	0.998	0.72
154_Y	253_S	0.997	0.72
21_Y	226_L	0.991	0.72
22_V	281_K	0.986	0.71
31_E	37_P	0.979	0.71
12_I	17_E	0.973	0.70
105_L	113_S	0.972	0.70
192_S	227_V	0.969	0.70
177_S	281_K	0.967	0.70
22_V	194_P	0.966	0.70
266_A	269_L	0.966	0.70
149_V	156_C	0.964	0.70
103_V	107_S	0.964	0.70
126_A	151_A	0.962	0.69
175_S	178_E	0.961	0.69
90_Q	113_S	0.954	0.69
164_H	168_F	0.953	0.69
251_L	265_V	0.949	0.68
235_L	253_S	0.946	0.68
60_T	63_V	0.938	0.67
229_L	233_Q	0.934	0.67
61_P	64_H	0.919	0.66
42_R	54_R	0.919	0.66
257_D	261_T	0.913	0.65
178_E	206_I	0.911	0.65
201_K	227_V	0.906	0.65
59_S	62_K	0.906	0.65
105_L	133_M	0.902	0.64
203_A	270_D	0.901	0.64
116_L	230_M	0.900	0.64
102_L	162_P	0.898	0.64
235_L	246_A	0.897	0.64
274_V	277_R	0.890	0.63
13_T	24_T	0.881	0.62
243_S	279_R	0.872	0.62
109_L	130_I	0.870	0.61
253_S	258_I	0.870	0.61
80_R	84_L	0.867	0.61
168_F	234_G	0.861	0.61
246_A	266_A	0.861	0.61
140_K	244_L	0.850	0.60
76_R	132_K	0.849	0.60
249_V	269_L	0.849	0.60
85_K	89_M	0.848	0.59
9_D	189_V	0.845	0.59
100_K	108_I	0.844	0.59
260_K	273_E	0.841	0.59
94_R	244_L	0.840	0.59
261_T	273_E	0.840	0.59
162_P	248_S	0.839	0.59
146_T	150_A	0.838	0.59
72_I	86_M	0.838	0.59
14_Y	21_Y	0.837	0.58
44_Y	209_I	0.836	0.58
36_D	39_P	0.835	0.58
45_N	164_H	0.833	0.58
189_V	193_I	0.831	0.58
89_M	92_K	0.829	0.58
226_L	238_G	0.828	0.58
83_T	107_S	0.823	0.57
180_W	183_L	0.820	0.57
14_Y	17_E	0.818	0.57
27_A	238_G	0.811	0.56
172_Y	280_Y	0.811	0.56
153_Y	197_R	0.810	0.56
175_S	179_F	0.808	0.56
32_D	37_P	0.807	0.56
81_L	84_L	0.805	0.56
108_I	181_S	0.803	0.55
218_I	256_M	0.803	0.55
153_Y	156_C	0.802	0.55
71_I	90_Q	0.802	0.55
47_K	54_R	0.801	0.55
181_S	188_Y	0.796	0.55
129_I	155_S	0.793	0.54
49_R	52_K	0.793	0.54
183_L	243_S	0.789	0.54
180_W	240_G	0.787	0.54
208_K	240_G	0.785	0.54
109_L	115_K	0.784	0.54
104_T	231_H	0.783	0.53
123_K	152_L	0.783	0.53
168_F	207_P	0.783	0.53
112_E	158_V	0.780	0.53
222_K	255_L	0.780	0.53
235_L	282_D	0.777	0.53
255_L	280_Y	0.775	0.53
7_K	13_T	0.762	0.51
239_K	252_I	0.760	0.51
92_K	238_G	0.760	0.51
129_I	151_A	0.757	0.51
35_V	41_W	0.756	0.51
210_L	213_L	0.754	0.51
166_Q	176_S	0.752	0.51
30_I	174_I	0.752	0.51
203_A	231_H	0.751	0.50
163_R	208_K	0.751	0.50
122_V	163_R	0.749	0.50
198_P	201_K	0.749	0.50
182_A	195_G	0.742	0.50
29_V	61_P	0.741	0.49
36_D	40_D	0.740	0.49
98_K	214_N	0.740	0.49
105_L	247_A	0.737	0.49
183_L	271_I	0.735	0.49
164_H	167_E	0.734	0.49
108_I	112_E	0.733	0.49
140_K	273_E	0.732	0.49
143_D	192_S	0.730	0.48
32_D	251_L	0.727	0.48
42_R	52_K	0.725	0.48
240_G	250_Y	0.724	0.48
85_K	90_Q	0.724	0.48
105_L	272_T	0.723	0.48
131_R	155_S	0.723	0.48
263_K	278_N	0.722	0.48
124_E	137_G	0.720	0.47
268_S	276_I	0.719	0.47
162_P	204_E	0.718	0.47
30_I	178_E	0.714	0.47
167_E	275_T	0.714	0.47
60_T	66_W	0.714	0.47
133_M	183_L	0.712	0.47
62_K	66_W	0.711	0.47
280_Y	284_V	0.711	0.47
99_D	136_T	0.711	0.47
122_V	140_K	0.710	0.47
101_K	143_D	0.709	0.46
132_K	178_E	0.708	0.46
170_V	286_N	0.708	0.46
263_K	271_I	0.707	0.46
68_F	71_I	0.699	0.46
60_T	65_D	0.698	0.45
7_K	26_C	0.696	0.45
117_E	154_Y	0.695	0.45
19_G	118_L	0.694	0.45
234_G	239_K	0.693	0.45
27_A	153_Y	0.693	0.45
4_P	30_I	0.690	0.45
127_S	181_S	0.689	0.45
87_Q	131_R	0.688	0.44
211_Y	246_A	0.688	0.44
59_S	66_W	0.683	0.44
271_I	275_T	0.682	0.44
205_Y	210_L	0.681	0.44
9_D	148_I	0.680	0.44
201_K	231_H	0.680	0.44
213_L	249_V	0.676	0.43
248_S	267_D	0.676	0.43
46_A	51_E	0.667	0.43
131_R	221_T	0.665	0.42
168_F	197_R	0.660	0.42
122_V	159_N	0.659	0.42
149_V	168_F	0.658	0.42
69_H	81_L	0.658	0.42
152_L	234_G	0.656	0.42
4_P	249_V	0.653	0.41
239_K	244_L	0.650	0.41
150_A	206_I	0.649	0.41
30_I	240_G	0.642	0.40
228_D	232_K	0.641	0.40
113_S	244_L	0.639	0.40
171_R	246_A	0.639	0.40
240_G	276_I	0.637	0.40
101_K	130_I	0.637	0.40
215_L	238_G	0.637	0.40
183_L	238_G	0.634	0.39
56_G	70_T	0.634	0.39
58_P	64_H	0.633	0.39
97_P	282_D	0.632	0.39
55_V	206_I	0.632	0.39
133_M	269_L	0.632	0.39
215_L	219_I	0.629	0.39
44_Y	56_G	0.626	0.39
31_E	268_S	0.624	0.39
49_R	203_A	0.620	0.38
13_T	17_E	0.619	0.38
99_D	123_K	0.618	0.38
106_L	124_E	0.618	0.38
162_P	191_N	0.615	0.38
173_S	246_A	0.614	0.38
172_Y	200_I	0.613	0.38
190_A	197_R	0.613	0.38
151_A	257_D	0.613	0.38
59_S	63_V	0.612	0.38
59_S	96_S	0.610	0.37
38_G	276_I	0.610	0.37
130_I	279_R	0.609	0.37
239_K	259_K	0.609	0.37
118_L	156_C	0.608	0.37
12_I	15_D	0.608	0.37
18_K	34_A	0.607	0.37
105_L	276_I	0.607	0.37
14_Y	109_L	0.605	0.37
263_K	267_D	0.604	0.37
38_G	43_A	0.603	0.37
209_I	239_K	0.598	0.36
178_E	181_S	0.598	0.36
39_P	250_Y	0.595	0.36
175_S	263_K	0.595	0.36
170_V	270_D	0.595	0.36
90_Q	94_R	0.593	0.36
105_L	142_I	0.590	0.36
110_N	127_S	0.589	0.35
76_R	219_I	0.589	0.35
253_S	259_K	0.588	0.35
190_A	195_G	0.585	0.35
225_E	237_S	0.584	0.35
83_T	232_K	0.582	0.35
90_Q	199_K	0.582	0.35
7_K	198_P	0.582	0.35
108_I	118_L	0.580	0.35
209_I	268_S	0.580	0.35
97_P	190_A	0.576	0.34
13_T	246_A	0.571	0.34
215_L	258_I	0.571	0.34
244_L	279_R	0.570	0.34
122_V	231_H	0.568	0.34
109_L	126_A	0.568	0.34
194_P	214_N	0.567	0.34
33_S	39_P	0.565	0.33
58_P	65_D	0.562	0.33
46_A	254_A	0.562	0.33
219_I	248_S	0.561	0.33
16_V	31_E	0.559	0.33
120_E	124_E	0.558	0.33
87_Q	130_I	0.557	0.33
168_F	265_V	0.556	0.33
246_A	250_Y	0.556	0.33
19_G	34_A	0.555	0.33
67_G	116_L	0.554	0.33
130_I	134_V	0.553	0.32
61_P	118_L	0.553	0.32
156_C	159_N	0.550	0.32
170_V	225_E	0.548	0.32
43_A	52_K	0.547	0.32
148_I	196_F	0.545	0.32
22_V	120_E	0.544	0.32
25_N	112_E	0.543	0.32
93_I	107_S	0.543	0.32
45_N	244_L	0.543	0.32
29_V	221_T	0.542	0.32
25_N	119_P	0.542	0.32
147_L	173_S	0.541	0.31
17_E	20_M	0.540	0.31
240_G	243_S	0.540	0.31
97_P	104_T	0.538	0.31
156_C	200_I	0.537	0.31
106_L	250_Y	0.537	0.31
143_D	241_Y	0.535	0.31
67_G	277_R	0.531	0.31
167_E	246_A	0.529	0.30
15_D	28_S	0.528	0.30
115_K	198_P	0.528	0.30
41_W	202_P	0.527	0.30
124_E	127_S	0.526	0.30
8_T	33_S	0.525	0.30
91_N	94_R	0.524	0.30
118_L	285_D	0.523	0.30
7_K	47_K	0.523	0.30
220_G	264_E	0.522	0.30
69_H	260_K	0.522	0.30
147_L	213_L	0.521	0.30
139_T	279_R	0.521	0.30
20_M	277_R	0.521	0.30
111_D	220_G	0.518	0.30
167_E	178_E	0.516	0.29
6_C	24_T	0.516	0.29
14_Y	20_M	0.516	0.29
49_R	57_S	0.515	0.29
156_C	227_V	0.515	0.29
182_A	199_K	0.515	0.29
69_H	72_I	0.514	0.29
180_W	268_S	0.514	0.29
55_V	70_T	0.514	0.29
29_V	151_A	0.512	0.29
121_H	160_N	0.510	0.29
230_M	233_Q	0.507	0.29
243_S	271_I	0.507	0.29
199_K	206_I	0.507	0.29
125_T	199_K	0.504	0.29
29_V	161_I	0.503	0.28
176_S	263_K	0.502	0.28
151_A	234_G	0.500	0.28
179_F	228_D	0.500	0.28

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	0.6485	100	0.208	Contact Map
1aisB	1	0.6485	100	0.569	Contact Map
1c9bA	1	0.6587	100	0.58	Contact Map
2pk2A	3	0.744	99.9	0.694	Contact Map
2w96A	1	0.7816	99.9	0.695	Contact Map
4f6uB	1	0.7816	99.9	0.705	Contact Map
3g33B	2	0.7372	99.9	0.711	Contact Map
2i53A	1	0.7645	99.9	0.717	Contact Map
2b9rA	1	0.7509	99.9	0.718	Contact Map
4eojB	1	0.7645	99.9	0.72	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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