TBP - SULSO - GREMLIN Contacts

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TBP - TATA-box-binding protein

UniProt:	P58178	Sequences: MSNSAVSYKPIVNIENIVATVTLEQSLDLYAMERSIPNIEYDPDQFPGLIFRLEQPKVTALIFKSGKMVVTGAKSTEELIKAVKRIIKTLKKYGIKIVGKPKIQIQNIVASANLHVNVNLDKAAFLLENNMYEPEQFPGLIFRMDDPRVVLLIFSSGKMVITGAKREDEVSKAVKRIFDKLAELDCVKPIEEEEELEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	198 (174)
Sequences:	544 (346)
Seq/√Len:	26.2

HALSA - TBPD TBPF TBPE TBPB
SULSO - TBP

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_L	32_M	5.298	1.00
58_V	73_A	4.110	1.00
144_M	147_P	3.245	1.00
63_F	71_T	2.990	1.00
137_F	154_F	2.931	1.00
46_F	63_F	2.731	0.99
19_A	79_L	2.467	0.99
58_V	82_A	2.432	0.99
39_I	49_L	2.412	0.99
152_L	160_V	2.310	0.98
71_T	162_T	2.238	0.98
46_F	61_L	2.230	0.98
40_E	52_R	2.194	0.97
48_G	156_S	2.190	0.97
16_N	107_N	2.181	0.97
88_K	91_K	2.138	0.97
149_V	173_A	2.094	0.97
17_I	75_S	2.052	0.96
50_I	63_F	1.983	0.95
37_P	44_D	1.978	0.95
144_M	177_I	1.928	0.95
58_V	86_I	1.913	0.94
84_K	88_K	1.898	0.94
17_I	79_L	1.862	0.93
22_T	102_K	1.858	0.93
23_L	90_L	1.836	0.93
144_M	176_R	1.804	0.92
109_V	160_V	1.783	0.92
161_I	170_V	1.768	0.92
51_F	62_I	1.681	0.89
30_Y	34_R	1.622	0.88
151_L	159_M	1.586	0.86
123_A	151_L	1.538	0.85
26_S	64_K	1.524	0.84
151_L	177_I	1.485	0.82
106_Q	109_V	1.476	0.82
50_I	61_L	1.448	0.81
46_F	107_N	1.432	0.80
138_P	154_F	1.382	0.77
137_F	152_L	1.374	0.77
61_L	69_V	1.362	0.76
134_P	157_G	1.331	0.75
114_L	161_I	1.330	0.75
21_V	68_M	1.312	0.74
19_A	70_V	1.295	0.73
124_A	140_L	1.293	0.73
58_V	79_L	1.278	0.72
129_N	142_F	1.276	0.72
156_S	181_L	1.274	0.71
25_Q	95_I	1.269	0.71
146_D	172_K	1.249	0.70
69_V	111_S	1.248	0.70
109_V	152_L	1.241	0.69
72_G	134_P	1.219	0.68
12_V	174_V	1.169	0.65
23_L	87_I	1.147	0.63
35_S	93_Y	1.146	0.63
127_L	142_F	1.146	0.63
55_Q	96_K	1.145	0.63
45_Q	49_L	1.139	0.63
63_F	69_V	1.126	0.62
31_A	182_A	1.120	0.61
15_E	111_S	1.116	0.61
65_S	133_E	1.114	0.61
75_S	82_A	1.108	0.60
88_K	98_V	1.101	0.60
51_F	89_T	1.098	0.60
107_N	162_T	1.094	0.59
119_N	155_S	1.094	0.59
60_A	86_I	1.086	0.59
139_G	156_S	1.086	0.59
65_S	78_E	1.084	0.59
54_E	180_K	1.076	0.58
86_I	111_S	1.072	0.58
97_I	153_I	1.068	0.57
24_E	75_S	1.066	0.57
49_L	170_V	1.064	0.57
33_E	39_I	1.056	0.57
16_N	162_T	1.044	0.56
141_I	152_L	1.039	0.55
125_F	128_E	1.032	0.55
121_D	125_F	1.032	0.55
159_M	179_D	1.023	0.54
172_K	175_K	1.019	0.54
48_G	63_F	1.015	0.54
127_L	136_Q	1.014	0.54
61_L	152_L	1.010	0.53
79_L	82_A	1.007	0.53
48_G	61_L	1.007	0.53
70_V	177_I	1.006	0.53
70_V	79_L	1.005	0.53
113_N	158_K	1.004	0.53
78_E	166_R	0.999	0.52
14_I	24_E	0.996	0.52
28_D	31_A	0.989	0.52
85_R	89_T	0.981	0.51
118_V	153_I	0.978	0.51
53_L	111_S	0.970	0.50
133_E	163_G	0.965	0.50
46_F	50_I	0.962	0.50
150_V	162_T	0.959	0.49
128_E	145_D	0.957	0.49
123_A	140_L	0.944	0.48
72_G	163_G	0.937	0.48
59_T	83_V	0.932	0.47
49_L	128_E	0.931	0.47
62_I	138_P	0.921	0.47
100_K	103_I	0.904	0.45
12_V	112_A	0.902	0.45
47_P	114_L	0.897	0.45
14_I	53_L	0.892	0.45
112_A	170_V	0.883	0.44
50_I	59_T	0.870	0.43
20_T	50_I	0.867	0.43
67_K	107_N	0.863	0.42
25_Q	93_Y	0.850	0.41
19_A	47_P	0.850	0.41
146_D	176_R	0.844	0.41
57_K	148_R	0.842	0.41
21_V	100_K	0.839	0.41
13_N	142_F	0.837	0.41
17_I	105_I	0.835	0.40
161_I	174_V	0.831	0.40
14_I	111_S	0.818	0.39
17_I	146_D	0.815	0.39
32_M	40_E	0.815	0.39
52_R	106_Q	0.813	0.39
42_D	117_N	0.810	0.39
164_A	173_A	0.809	0.39
13_N	74_K	0.809	0.39
52_R	56_P	0.803	0.38
27_L	93_Y	0.803	0.38
56_P	147_P	0.799	0.38
59_T	63_F	0.793	0.37
15_E	123_A	0.786	0.37
158_K	165_K	0.785	0.37
108_I	163_G	0.785	0.37
49_L	110_A	0.784	0.37
33_E	90_L	0.781	0.37
35_S	42_D	0.779	0.36
69_V	82_A	0.778	0.36
57_K	156_S	0.770	0.36
143_R	156_S	0.770	0.36
60_A	178_F	0.769	0.36
139_G	164_A	0.762	0.35
65_S	149_V	0.760	0.35
45_Q	148_R	0.755	0.35
25_Q	32_M	0.752	0.35
44_D	119_N	0.741	0.34
143_R	150_V	0.736	0.34
17_I	159_M	0.731	0.33
53_L	82_A	0.730	0.33
61_L	137_F	0.725	0.33
43_P	123_A	0.724	0.33
75_S	115_H	0.723	0.33
139_G	154_F	0.722	0.33
44_D	161_I	0.720	0.32
21_V	115_H	0.710	0.32
27_L	41_Y	0.709	0.32
31_A	35_S	0.703	0.31
159_M	178_F	0.702	0.31
149_V	164_A	0.700	0.31
122_K	125_F	0.699	0.31
133_E	143_R	0.698	0.31
126_L	170_V	0.698	0.31
36_I	122_K	0.696	0.31
74_K	165_K	0.695	0.31
78_E	175_K	0.694	0.31
81_K	100_K	0.691	0.31
62_I	110_A	0.690	0.31
25_Q	98_V	0.689	0.30
108_I	166_R	0.687	0.30
77_E	176_R	0.684	0.30
85_R	179_D	0.682	0.30
70_V	73_A	0.678	0.30
105_I	153_I	0.678	0.30
127_L	131_M	0.677	0.30
46_F	74_K	0.674	0.30
11_I	171_S	0.673	0.29
133_E	139_G	0.664	0.29
83_V	112_A	0.661	0.29
23_L	178_F	0.659	0.29
17_I	95_I	0.653	0.28
81_K	85_R	0.647	0.28
106_Q	165_K	0.645	0.28
109_V	137_F	0.644	0.28
47_P	119_N	0.644	0.28
87_I	91_K	0.644	0.28
75_S	161_I	0.638	0.27
71_T	106_Q	0.634	0.27
148_R	153_I	0.632	0.27
106_Q	138_P	0.629	0.27
65_S	107_N	0.628	0.27
53_L	63_F	0.625	0.27
33_E	64_K	0.624	0.27
170_V	182_A	0.621	0.26
131_M	136_Q	0.620	0.26
75_S	122_K	0.612	0.26
158_K	163_G	0.607	0.26
164_A	167_E	0.607	0.26
16_N	132_Y	0.606	0.26
146_D	180_K	0.604	0.25
107_N	160_V	0.603	0.25
110_A	170_V	0.601	0.25
124_A	128_E	0.599	0.25
138_P	142_F	0.596	0.25
26_S	122_K	0.595	0.25
12_V	79_L	0.594	0.25
152_L	158_K	0.590	0.25
30_Y	108_I	0.590	0.25
88_K	180_K	0.587	0.24
28_D	117_N	0.586	0.24
115_H	179_D	0.585	0.24
26_S	35_S	0.585	0.24
39_I	174_V	0.583	0.24
62_I	76_T	0.582	0.24
137_F	158_K	0.581	0.24
20_T	59_T	0.581	0.24
51_F	83_V	0.577	0.24
87_I	166_R	0.573	0.24
13_N	88_K	0.572	0.24
87_I	92_K	0.572	0.24
18_V	135_E	0.570	0.24
130_N	141_I	0.568	0.23
13_N	25_Q	0.565	0.23
129_N	155_S	0.565	0.23
37_P	129_N	0.561	0.23
42_D	111_S	0.561	0.23
171_S	183_E	0.559	0.23
124_A	173_A	0.558	0.23
66_G	72_G	0.554	0.23
38_N	52_R	0.553	0.23
73_A	118_V	0.549	0.22
68_M	76_T	0.549	0.22
21_V	130_N	0.547	0.22
39_I	126_L	0.547	0.22
63_F	107_N	0.547	0.22
42_D	60_A	0.547	0.22
171_S	175_K	0.545	0.22
144_M	153_I	0.545	0.22
70_V	94_G	0.543	0.22
149_V	176_R	0.537	0.22
91_K	166_R	0.534	0.22
29_L	153_I	0.533	0.22
134_P	163_G	0.528	0.21
95_I	138_P	0.526	0.21
147_P	169_E	0.525	0.21
18_V	46_F	0.522	0.21
22_T	25_Q	0.520	0.21
103_I	117_N	0.518	0.21
82_A	160_V	0.516	0.21
63_F	67_K	0.514	0.21
104_Q	150_V	0.514	0.21
93_Y	97_I	0.514	0.21
36_I	51_F	0.510	0.20
150_V	155_S	0.507	0.20
132_Y	143_R	0.506	0.20
42_D	142_F	0.504	0.20
12_V	122_K	0.504	0.20
32_M	86_I	0.502	0.20
51_F	69_V	0.500	0.20

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
4b0aA	1	0.899	100	0.095	Contact Map
1rm1A	1	0.904	100	0.101	Contact Map
3eikA	2	0.8939	100	0.101	Contact Map
1ytbA	1	0.904	100	0.113	Contact Map
1mp9A	2	0.9848	100	0.137	Contact Map
1aisA	1	0.9141	100	0.145	Contact Map
2z8uA	2	0.8889	100	0.147	Contact Map
2d0bA	1	0.4495	85.3	0.925	Contact Map
3vn5A	1	0.399	75.5	0.932	Contact Map
4py5A	1	0.3788	68.3	0.936	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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