TBPB - HALSA - GREMLIN Contacts

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TBPB - TATA-box-binding protein B

UniProt:	Q48325	Sequences: MSTLADTIHIENVVASSDLGQELALDQLSTDLPGAEYNPEDFPGVVYRLQEPKSATLIFRSGKVVCTGAKSVDDVHEALGIVFGDIRELGIDVTSNPPIEVQNIVSSASLEQSLNLNAIAIGLGLEQIEYEPEQFPGLVYRLDDPDVVVLLFGSGKLVITGGQNPDEAEQALAHVQDRLTELGLLD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	186 (174)
Sequences:	532 (341)
Seq/√Len:	25.8

HALSA - TBPB TBPD TBPF TBPE
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
23_L	28_L	5.306	1.00
54_S	69_A	4.263	1.00
35_A	45_V	2.982	1.00
142_L	145_P	2.913	1.00
59_F	67_T	2.822	1.00
42_F	57_L	2.787	1.00
135_F	152_F	2.556	0.99
15_A	75_V	2.506	0.99
80_G	84_G	2.430	0.99
42_F	59_F	2.401	0.99
84_G	87_R	2.365	0.98
54_S	78_A	2.327	0.98
44_G	154_S	2.291	0.98
150_L	158_V	2.240	0.98
67_T	160_T	2.235	0.98
12_N	103_N	2.119	0.97
147_V	171_A	2.046	0.96
105_V	158_V	1.933	0.94
46_V	59_F	1.914	0.94
36_E	48_R	1.897	0.94
26_D	30_T	1.878	0.93
54_S	82_V	1.854	0.93
46_V	57_L	1.845	0.93
13_V	71_S	1.820	0.92
124_G	127_Q	1.819	0.92
18_D	98_P	1.817	0.92
149_V	175_V	1.768	0.91
142_L	175_V	1.745	0.91
13_V	75_V	1.744	0.91
149_V	157_L	1.672	0.89
159_I	168_A	1.664	0.88
132_P	155_G	1.617	0.87
135_F	150_L	1.604	0.86
19_L	86_I	1.596	0.86
33_P	40_E	1.579	0.86
22_E	60_R	1.555	0.85
142_L	174_H	1.545	0.84
102_Q	105_V	1.507	0.83
136_P	152_F	1.446	0.80
119_I	149_V	1.384	0.77
57_L	65_V	1.368	0.76
47_Y	58_I	1.319	0.73
17_S	64_V	1.303	0.72
154_S	179_L	1.280	0.71
8_I	172_L	1.280	0.71
56_T	82_V	1.277	0.71
144_D	170_Q	1.263	0.70
47_Y	85_D	1.262	0.70
44_G	57_L	1.241	0.69
124_G	129_E	1.238	0.68
91_I	95_S	1.234	0.68
110_L	159_I	1.192	0.65
13_V	144_D	1.187	0.65
54_S	75_V	1.184	0.65
103_N	160_T	1.181	0.65
65_V	107_S	1.179	0.65
42_F	103_N	1.164	0.64
45_V	168_A	1.148	0.63
21_Q	91_I	1.129	0.61
124_G	128_I	1.119	0.60
19_L	83_F	1.114	0.60
10_I	20_G	1.110	0.60
120_A	138_L	1.107	0.60
49_L	107_S	1.105	0.59
139_V	150_L	1.103	0.59
124_G	140_Y	1.085	0.58
71_S	78_A	1.084	0.58
61_S	131_E	1.083	0.58
12_N	160_T	1.081	0.58
15_A	66_C	1.068	0.57
50_Q	178_R	1.065	0.57
31_D	89_L	1.061	0.56
44_G	59_F	1.058	0.56
20_G	71_S	1.052	0.56
173_A	181_E	1.042	0.55
42_F	46_V	1.041	0.55
52_P	145_P	1.035	0.54
162_G	171_A	1.030	0.54
101_V	151_L	1.029	0.54
46_V	55_A	1.024	0.54
11_E	107_S	1.023	0.54
59_F	65_V	1.022	0.53
41_D	146_D	1.018	0.53
55_A	59_F	1.016	0.53
137_G	154_S	1.013	0.53
27_Q	180_T	1.005	0.52
117_N	121_I	1.004	0.52
137_G	162_G	0.996	0.52
109_S	156_K	0.993	0.51
67_T	102_Q	0.992	0.51
66_C	75_V	0.990	0.51
40_E	159_I	0.988	0.51
124_G	178_R	0.986	0.51
148_V	160_T	0.972	0.50
93_V	151_L	0.969	0.50
10_I	49_L	0.968	0.50
63_K	103_N	0.965	0.49
77_E	81_I	0.959	0.49
115_N	153_G	0.956	0.49
104_I	161_G	0.955	0.49
131_E	137_G	0.955	0.49
45_V	126_E	0.954	0.48
105_V	150_L	0.935	0.47
66_C	175_V	0.934	0.47
170_Q	173_A	0.926	0.46
24_A	27_Q	0.925	0.46
68_G	132_P	0.917	0.46
114_L	151_L	0.914	0.46
35_A	181_E	0.908	0.45
21_Q	95_S	0.906	0.45
49_L	59_F	0.898	0.44
15_A	43_P	0.893	0.44
59_F	135_F	0.893	0.44
23_L	37_Y	0.885	0.43
58_I	136_P	0.880	0.43
41_D	45_V	0.880	0.43
24_A	114_L	0.879	0.43
57_L	150_L	0.873	0.43
16_S	46_V	0.869	0.42
27_Q	31_D	0.862	0.42
20_G	179_L	0.856	0.41
55_A	79_L	0.850	0.41
121_I	126_E	0.847	0.41
84_G	178_R	0.840	0.40
150_L	156_K	0.837	0.40
17_S	111_E	0.824	0.39
74_D	164_N	0.818	0.39
75_V	78_A	0.817	0.39
53_K	154_S	0.811	0.38
119_I	138_L	0.809	0.38
24_A	113_S	0.807	0.38
81_I	177_D	0.806	0.38
49_L	78_A	0.806	0.38
66_C	69_A	0.797	0.37
10_I	107_S	0.796	0.37
51_E	92_D	0.795	0.37
22_E	118_A	0.795	0.37
65_V	78_A	0.790	0.37
106_S	110_L	0.789	0.37
29_S	86_I	0.788	0.37
28_L	36_E	0.784	0.36
40_E	115_N	0.782	0.36
144_D	174_H	0.780	0.36
9_H	70_K	0.771	0.35
127_Q	140_Y	0.769	0.35
45_V	106_S	0.768	0.35
120_A	126_E	0.767	0.35
62_G	68_G	0.767	0.35
21_Q	28_L	0.759	0.35
29_S	35_A	0.756	0.34
10_I	147_V	0.754	0.34
59_F	64_V	0.751	0.34
31_D	38_N	0.748	0.34
120_A	171_A	0.747	0.34
8_I	108_A	0.740	0.33
68_G	161_G	0.734	0.33
108_A	168_A	0.733	0.33
13_V	101_V	0.732	0.33
9_H	21_Q	0.730	0.33
162_G	165_P	0.728	0.33
53_K	146_D	0.727	0.33
169_E	173_A	0.726	0.32
71_S	111_E	0.723	0.32
48_R	52_P	0.722	0.32
48_R	90_G	0.721	0.32
9_H	140_Y	0.714	0.32
17_S	128_I	0.709	0.31
38_N	107_S	0.705	0.31
59_F	63_K	0.704	0.31
15_A	116_L	0.698	0.31
14_V	42_F	0.696	0.31
141_R	154_S	0.681	0.30
125_L	129_E	0.671	0.29
47_Y	55_A	0.671	0.29
57_L	135_F	0.668	0.29
157_L	177_D	0.663	0.29
29_S	60_R	0.657	0.28
28_L	107_S	0.657	0.28
102_Q	136_P	0.656	0.28
102_Q	163_Q	0.655	0.28
105_V	160_T	0.653	0.28
82_V	107_S	0.651	0.28
33_P	127_Q	0.650	0.28
27_Q	122_G	0.645	0.27
159_I	172_L	0.643	0.27
89_L	165_P	0.640	0.27
51_E	101_V	0.639	0.27
53_K	145_P	0.635	0.27
104_I	164_N	0.634	0.27
48_R	102_Q	0.633	0.27
11_E	119_I	0.627	0.26
85_D	88_E	0.625	0.26
128_I	182_L	0.617	0.26
61_S	146_D	0.616	0.26
58_I	106_S	0.614	0.26
129_E	134_Q	0.614	0.26
16_S	19_L	0.611	0.26
42_F	55_A	0.611	0.26
133_E	155_G	0.608	0.25
118_A	121_I	0.607	0.25
19_L	176_Q	0.604	0.25
103_N	158_V	0.604	0.25
147_V	162_G	0.602	0.25
43_P	110_L	0.602	0.25
35_A	175_V	0.602	0.25
38_N	113_S	0.597	0.25
21_Q	89_L	0.597	0.25
64_V	114_L	0.595	0.25
32_L	118_A	0.594	0.25
13_V	157_L	0.590	0.24
61_S	74_D	0.590	0.24
79_L	108_A	0.589	0.24
47_Y	65_V	0.588	0.24
39_P	119_I	0.587	0.24
99_I	113_S	0.581	0.24
8_I	101_V	0.581	0.24
16_S	55_A	0.574	0.23
61_S	147_V	0.573	0.23
137_G	160_T	0.573	0.23
126_E	143_D	0.571	0.23
7_T	169_E	0.570	0.23
156_K	161_G	0.569	0.23
95_S	104_I	0.569	0.23
27_Q	181_E	0.567	0.23
43_P	115_N	0.566	0.23
83_F	88_E	0.565	0.23
70_K	159_I	0.564	0.23
156_K	163_Q	0.563	0.23
111_E	151_L	0.559	0.23
35_A	172_L	0.558	0.23
136_P	140_Y	0.552	0.22
79_L	97_P	0.544	0.22
25_L	151_L	0.544	0.22
127_Q	153_G	0.541	0.22
102_Q	158_V	0.541	0.22
137_G	155_G	0.538	0.22
28_L	61_S	0.538	0.22
8_I	75_V	0.533	0.21
131_E	141_R	0.530	0.21
34_G	48_R	0.530	0.21
148_V	153_G	0.529	0.21
28_L	47_Y	0.526	0.21
135_F	158_V	0.525	0.21
150_L	160_T	0.524	0.21
26_D	104_I	0.523	0.21
12_N	130_Y	0.522	0.21
122_G	168_A	0.522	0.21
35_A	47_Y	0.522	0.21
13_V	106_S	0.521	0.21
38_N	56_T	0.518	0.21
157_L	176_Q	0.515	0.21
111_E	177_D	0.511	0.20
16_S	102_Q	0.510	0.20
83_F	87_R	0.508	0.20
8_I	48_R	0.506	0.20
122_G	182_L	0.504	0.20
164_N	168_A	0.504	0.20
73_D	174_H	0.504	0.20
14_V	133_E	0.503	0.20
152_F	158_V	0.501	0.20
178_R	182_L	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
1rm1A	1	0.9677	100	0.065	Contact Map
4b0aA	1	0.9624	100	0.069	Contact Map
1ytbA	1	0.9677	100	0.074	Contact Map
3eikA	2	0.957	100	0.078	Contact Map
1mp9A	2	0.9892	100	0.114	Contact Map
1aisA	1	0.9677	100	0.115	Contact Map
2z8uA	2	0.9462	100	0.117	Contact Map
2d0bA	1	0.4247	87.1	0.921	Contact Map
3vn5A	1	0.3871	74.4	0.931	Contact Map
4py5A	1	0.3817	69.1	0.934	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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