TF2B1 - HALSA - GREMLIN Contacts

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TF2B1 - Transcription initiation factor IIB 1

UniProt:	Q9HNA2	Sequences: MQHPHRCPECDGTIRETDTEHVCADCGLVVTDAPIDHGPEWRTFSDDPDHAPERTGAPLTRSRHDRGLSTEIGYSARLTGRKRRKFARLRRQHKRATIPSKADYNRIYGFTEIRRLIGTFGIGTGLRDQACTLFASAQTAGLLHGRTIEGFAAAGVYATCRTNGVTRTLDEIAAAARATRPELTTAYDAMNRDLGLPTGPIDPREYLPRYADALSLPARIERQARELVAALETDGLVAGRNPSGVAAGCLYTAATETDHAVTQSAAAAVADVTPVTLRATYQNLTDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	287 (271)
Sequences:	1050 (688)
Seq/√Len:	41.8

HALSA - TF2B1 TF2B4 TF2B2 TF2B5 TF2B3 TF2B7 TF2B6
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
211_A	250_L	6.709	1.00
117_I	156_V	4.395	1.00
217_P	259_H	4.024	1.00
23_C	26_C	3.819	1.00
280_T	283_N	3.683	1.00
263_Q	278_R	3.621	1.00
223_Q	257_T	3.471	1.00
109_G	134_F	3.186	1.00
7_C	26_C	2.950	1.00
110_F	131_C	2.897	1.00
117_I	127_R	2.809	1.00
116_L	156_V	2.750	1.00
122_I	156_V	2.689	1.00
112_E	115_R	2.671	1.00
264_S	274_P	2.452	1.00
126_L	159_T	2.452	1.00
247_A	270_A	2.234	1.00
156_V	172_I	2.231	1.00
223_Q	226_E	2.229	1.00
130_A	159_T	2.193	1.00
180_R	184_T	2.183	1.00
10_C	23_C	2.089	0.99
43_T	46_D	2.083	0.99
51_A	56_G	2.054	0.99
145_G	242_P	2.001	0.99
274_P	282_Q	1.984	0.99
224_A	246_A	1.879	0.99
7_C	23_C	1.877	0.99
113_I	152_A	1.865	0.98
40_E	54_R	1.839	0.98
210_Y	214_L	1.808	0.98
224_A	253_A	1.788	0.98
264_S	277_L	1.782	0.98
167_R	171_E	1.775	0.98
7_C	10_C	1.774	0.98
134_F	143_L	1.732	0.97
244_G	276_T	1.719	0.97
53_E	56_G	1.689	0.97
227_L	253_A	1.682	0.97
116_L	175_A	1.666	0.97
161_R	184_T	1.634	0.96
228_V	249_C	1.620	0.96
202_D	205_E	1.610	0.96
43_T	48_P	1.580	0.96
129_Q	162_T	1.569	0.95
41_W	52_P	1.562	0.95
210_Y	250_L	1.550	0.95
23_C	27_G	1.474	0.94
216_L	261_V	1.469	0.94
109_G	138_Q	1.457	0.93
38_G	41_W	1.439	0.93
220_I	259_H	1.439	0.93
41_W	58_P	1.439	0.93
262_T	265_A	1.437	0.93
220_I	257_T	1.423	0.92
132_T	135_A	1.405	0.92
41_W	44_F	1.375	0.91
107_I	111_T	1.369	0.91
261_V	265_A	1.369	0.91
254_A	269_V	1.363	0.91
129_Q	163_N	1.362	0.91
227_L	249_C	1.355	0.90
158_A	196_L	1.354	0.90
228_V	245_V	1.352	0.90
248_G	276_T	1.350	0.90
204_R	229_A	1.340	0.90
9_E	28_L	1.334	0.90
169_L	184_T	1.332	0.90
64_H	67_G	1.316	0.89
42_R	54_R	1.303	0.89
113_I	131_C	1.297	0.88
86_F	89_L	1.294	0.88
230_A	234_D	1.292	0.88
236_L	254_A	1.287	0.88
263_Q	275_V	1.286	0.88
184_T	210_Y	1.267	0.87
54_R	72_I	1.262	0.87
244_G	248_G	1.240	0.86
73_G	198_T	1.235	0.86
65_D	68_L	1.228	0.85
172_I	175_A	1.226	0.85
171_E	209_R	1.224	0.85
8_P	30_V	1.223	0.85
15_R	19_T	1.223	0.85
109_G	113_I	1.219	0.85
191_N	198_T	1.218	0.85
129_Q	132_T	1.217	0.85
127_R	156_V	1.215	0.85
202_D	228_V	1.195	0.84
179_T	182_E	1.194	0.84
16_E	19_T	1.188	0.84
109_G	185_T	1.187	0.83
260_A	265_A	1.185	0.83
36_D	40_E	1.180	0.83
221_E	225_R	1.180	0.83
247_A	252_T	1.178	0.83
25_D	117_I	1.178	0.83
247_A	277_L	1.154	0.82
157_Y	201_I	1.151	0.82
54_R	70_T	1.151	0.82
94_K	178_A	1.138	0.81
60_T	244_G	1.131	0.80
192_R	265_A	1.127	0.80
249_C	253_A	1.122	0.80
272_V	277_L	1.119	0.80
12_G	25_D	1.117	0.80
22_V	269_V	1.109	0.79
11_D	14_I	1.106	0.79
105_N	158_A	1.102	0.79
219_R	257_T	1.097	0.78
169_L	180_R	1.092	0.78
167_R	209_R	1.091	0.78
22_V	282_Q	1.091	0.78
40_E	52_P	1.087	0.78
7_C	11_D	1.086	0.78
261_V	274_P	1.077	0.77
265_A	269_V	1.067	0.76
158_A	161_R	1.063	0.76
22_V	96_A	1.059	0.76
258_D	262_T	1.059	0.76
14_I	222_R	1.048	0.75
94_K	107_I	1.046	0.75
10_C	26_C	1.043	0.75
264_S	272_V	1.028	0.74
52_P	56_G	1.027	0.73
228_V	246_A	1.027	0.73
101_K	154_A	1.026	0.73
139_T	264_S	1.025	0.73
21_H	227_L	1.011	0.72
202_D	232_E	1.009	0.72
87_A	91_R	1.002	0.72
9_E	12_G	1.000	0.71
145_G	276_T	1.000	0.71
14_I	21_H	0.997	0.71
168_T	171_E	0.987	0.70
92_Q	134_F	0.987	0.70
267_A	270_A	0.986	0.70
178_A	213_A	0.983	0.70
151_F	186_A	0.977	0.70
275_V	278_R	0.974	0.69
126_L	165_V	0.970	0.69
173_A	178_A	0.969	0.69
134_F	148_I	0.966	0.69
6_R	24_A	0.958	0.68
209_R	241_N	0.955	0.68
151_F	190_M	0.953	0.68
147_T	188_D	0.953	0.68
135_A	159_T	0.952	0.68
131_C	138_Q	0.943	0.67
96_A	99_P	0.943	0.67
109_G	248_G	0.942	0.67
96_A	153_A	0.941	0.67
106_R	131_C	0.939	0.67
43_T	280_T	0.934	0.66
236_L	247_A	0.928	0.66
68_L	72_I	0.924	0.65
252_T	266_A	0.923	0.65
6_R	11_D	0.922	0.65
250_L	266_A	0.920	0.65
137_A	190_M	0.917	0.65
206_Y	211_A	0.907	0.64
166_T	205_E	0.906	0.64
32_D	37_H	0.904	0.64
131_C	135_A	0.901	0.63
184_T	187_Y	0.896	0.63
40_E	44_F	0.894	0.63
35_I	41_W	0.888	0.62
46_D	51_A	0.887	0.62
105_N	134_F	0.887	0.62
182_E	207_L	0.885	0.62
21_H	24_A	0.885	0.62
109_G	137_A	0.884	0.62
75_S	93_H	0.883	0.62
95_R	146_R	0.879	0.61
251_Y	255_T	0.865	0.60
168_T	172_I	0.862	0.60
109_G	117_I	0.856	0.59
227_L	239_G	0.854	0.59
246_A	270_A	0.850	0.59
218_A	222_R	0.838	0.58
133_L	155_G	0.837	0.58
45_S	52_P	0.837	0.58
65_D	72_I	0.836	0.58
254_A	260_A	0.835	0.57
106_R	166_T	0.834	0.57
120_F	231_L	0.828	0.57
113_I	134_F	0.826	0.57
144_H	196_L	0.822	0.56
117_I	245_V	0.819	0.56
44_F	210_Y	0.819	0.56
245_V	280_T	0.817	0.56
187_Y	244_G	0.815	0.56
247_A	267_A	0.814	0.55
130_A	155_G	0.813	0.55
160_C	228_V	0.812	0.55
181_P	282_Q	0.809	0.55
40_E	70_T	0.809	0.55
90_R	134_F	0.808	0.55
109_G	147_T	0.805	0.55
204_R	271_D	0.805	0.55
177_R	247_A	0.799	0.54
253_A	258_D	0.794	0.54
158_A	254_A	0.793	0.54
120_F	233_T	0.792	0.53
254_A	259_H	0.792	0.53
102_A	215_S	0.790	0.53
113_I	119_T	0.789	0.53
126_L	232_E	0.788	0.53
64_H	68_L	0.787	0.53
223_Q	256_E	0.786	0.53
30_V	241_N	0.783	0.53
236_L	283_N	0.783	0.53
88_R	142_L	0.779	0.52
88_R	92_Q	0.779	0.52
108_Y	232_E	0.776	0.52
263_Q	267_A	0.771	0.51
47_D	54_R	0.770	0.51
15_R	24_A	0.770	0.51
92_Q	95_R	0.769	0.51
15_R	21_H	0.764	0.51
136_S	140_A	0.763	0.51
200_P	207_L	0.761	0.51
55_T	278_R	0.757	0.50
104_Y	112_E	0.756	0.50
15_R	31_T	0.756	0.50
75_S	103_D	0.753	0.50
31_T	37_H	0.751	0.50
29_V	155_G	0.751	0.50
183_L	229_A	0.749	0.49
196_L	228_V	0.748	0.49
204_R	232_E	0.747	0.49
58_P	65_D	0.746	0.49
176_A	281_Y	0.746	0.49
216_L	220_I	0.745	0.49
64_H	128_D	0.744	0.49
33_A	39_P	0.737	0.48
122_I	160_C	0.733	0.48
27_G	157_Y	0.729	0.48
157_Y	160_C	0.729	0.48
153_A	160_C	0.727	0.47
172_I	235_G	0.727	0.47
43_T	51_A	0.721	0.47
63_R	69_S	0.720	0.47
45_S	48_P	0.718	0.47
240_R	253_A	0.716	0.46
200_P	210_Y	0.713	0.46
40_E	56_G	0.706	0.45
116_L	162_T	0.705	0.45
195_G	247_A	0.705	0.45
244_G	280_T	0.704	0.45
120_F	146_R	0.704	0.45
128_D	141_G	0.702	0.45
171_E	182_E	0.701	0.45
91_R	171_E	0.700	0.45
172_I	198_T	0.699	0.45
240_R	245_V	0.698	0.45
62_S	65_D	0.697	0.45
32_D	35_I	0.695	0.44
250_L	270_A	0.693	0.44
229_A	271_D	0.692	0.44
160_C	201_I	0.692	0.44
241_N	277_L	0.691	0.44
160_C	163_N	0.688	0.44
64_H	278_R	0.688	0.44
59_L	100_S	0.687	0.44
56_G	160_C	0.687	0.44
30_V	178_A	0.686	0.44
29_V	61_R	0.685	0.43
106_R	135_A	0.685	0.43
67_G	131_C	0.684	0.43
122_I	133_L	0.673	0.42
121_G	158_A	0.671	0.42
207_L	225_R	0.670	0.42
207_L	228_V	0.668	0.42
134_F	197_P	0.667	0.42
28_L	212_D	0.666	0.42
214_L	250_L	0.664	0.42
249_C	268_A	0.661	0.41
244_G	272_V	0.660	0.41
256_E	281_Y	0.659	0.41
58_P	64_H	0.656	0.41
14_I	274_P	0.656	0.41
99_P	103_D	0.655	0.41
173_A	261_V	0.655	0.41
36_D	39_P	0.655	0.41
240_R	260_A	0.654	0.41
192_R	212_D	0.654	0.41
60_T	85_K	0.652	0.40
112_E	185_T	0.652	0.40
43_T	53_E	0.651	0.40
29_V	56_G	0.646	0.40
11_D	199_G	0.644	0.40
103_D	127_R	0.643	0.40
86_F	111_T	0.641	0.39
156_V	198_T	0.640	0.39
8_P	250_L	0.639	0.39
101_K	189_A	0.638	0.39
184_T	241_N	0.635	0.39
101_K	283_N	0.633	0.39
47_D	106_R	0.631	0.39
137_A	270_A	0.625	0.38
109_G	277_L	0.621	0.38
115_R	221_E	0.621	0.38
63_R	75_S	0.621	0.38
179_T	183_L	0.620	0.38
127_R	233_T	0.618	0.37
74_Y	277_L	0.616	0.37
260_A	269_V	0.614	0.37
220_I	224_A	0.613	0.37
114_R	131_C	0.611	0.37
159_T	163_N	0.610	0.37
109_G	152_A	0.608	0.37
144_H	245_V	0.607	0.36
174_A	209_R	0.606	0.36
229_A	233_T	0.606	0.36
60_T	63_R	0.605	0.36
60_T	64_H	0.604	0.36
190_M	213_A	0.603	0.36
95_R	239_G	0.602	0.36
27_G	239_G	0.601	0.36
39_P	43_T	0.600	0.36
137_A	203_P	0.600	0.36
55_T	71_E	0.598	0.36
239_G	248_G	0.598	0.36
105_N	147_T	0.597	0.36
18_D	34_P	0.597	0.36
136_S	182_E	0.595	0.35
16_E	22_V	0.593	0.35
76_A	136_S	0.592	0.35
75_S	139_T	0.592	0.35
220_I	239_G	0.589	0.35
171_E	226_E	0.588	0.35
52_P	57_A	0.587	0.35
182_E	185_T	0.582	0.34
187_Y	239_G	0.582	0.34
7_C	12_G	0.582	0.34
60_T	145_G	0.581	0.34
190_M	243_S	0.580	0.34
113_I	192_R	0.580	0.34
210_Y	240_R	0.578	0.34
210_Y	269_V	0.577	0.34
169_L	173_A	0.576	0.34
140_A	190_M	0.576	0.34
109_G	273_T	0.575	0.34
248_G	253_A	0.575	0.34
134_F	280_T	0.572	0.33
224_A	252_T	0.572	0.33
158_A	185_T	0.570	0.33
17_T	20_E	0.567	0.33
21_H	34_P	0.565	0.33
137_A	187_Y	0.565	0.33
186_A	277_L	0.563	0.33
6_R	233_T	0.561	0.33
39_P	150_G	0.559	0.32
130_A	158_A	0.558	0.32
250_L	271_D	0.558	0.32
214_L	247_A	0.557	0.32
44_F	240_R	0.555	0.32
175_A	247_A	0.554	0.32
230_A	255_T	0.554	0.32
217_P	220_I	0.553	0.32
220_I	249_C	0.553	0.32
176_A	232_E	0.548	0.32
13_T	190_M	0.548	0.32
39_P	251_Y	0.548	0.32
25_D	123_G	0.547	0.31
14_I	17_T	0.546	0.31
55_T	62_S	0.545	0.31
128_D	131_C	0.545	0.31
180_R	264_S	0.544	0.31
264_S	279_A	0.544	0.31
235_G	240_R	0.544	0.31
45_S	245_V	0.541	0.31
199_G	205_E	0.540	0.31
153_A	176_A	0.537	0.31
29_V	165_V	0.537	0.31
11_D	26_C	0.536	0.31
57_A	64_H	0.534	0.30
158_A	231_L	0.532	0.30
137_A	196_L	0.529	0.30
135_A	222_R	0.529	0.30
44_F	52_P	0.529	0.30
131_C	185_T	0.529	0.30
134_F	137_A	0.526	0.30
73_G	115_R	0.523	0.30
252_T	282_Q	0.523	0.30
45_S	168_T	0.523	0.30
179_T	264_S	0.519	0.29
30_V	235_G	0.517	0.29
231_L	237_V	0.517	0.29
172_I	208_P	0.517	0.29
211_A	214_L	0.514	0.29
65_D	278_R	0.514	0.29
10_C	13_T	0.513	0.29
85_K	179_T	0.512	0.29
187_Y	190_M	0.511	0.29
43_T	52_P	0.510	0.29
67_G	122_I	0.510	0.29
225_R	229_A	0.507	0.28
44_F	47_D	0.507	0.28
47_D	260_A	0.506	0.28
140_A	265_A	0.504	0.28
144_H	274_P	0.502	0.28
147_T	242_P	0.501	0.28
178_A	241_N	0.501	0.28
134_F	138_Q	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	0.6481	100	0.218	Contact Map
1aisB	1	0.6376	100	0.558	Contact Map
1c9bA	1	0.6481	100	0.573	Contact Map
2pk2A	3	0.7352	99.9	0.685	Contact Map
4f6uB	1	0.7735	99.9	0.693	Contact Map
2w96A	1	0.7735	99.9	0.695	Contact Map
2b9rA	1	0.7422	99.9	0.704	Contact Map
4eojB	1	0.7561	99.9	0.706	Contact Map
3g33B	2	0.7422	99.9	0.707	Contact Map
2i53A	1	0.7561	99.9	0.709	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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