TBPF - HALSA - GREMLIN Contacts

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TBPF - TATA-box-binding protein F

UniProt:	Q9HHE9	Sequences: MSSLADTIHIENVVASSDLGQELALDQLATDLDGAEYNPEDFPGVVYRLQEPKSATLIFRSGKVVCTGAKSVDAVHDALEIVFDDLRELGIDVDSTPPVKVQNIVSSASLEQSLNLNAIAIGLGLEQIEYEPEQFPGLVYRLDDPDVVVLLFGSGKLVITGAAESADAQHALAHVNDRLTELGLLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	186 (173)
Sequences:	536 (343)
Seq/√Len:	26.1

HALSA - TBPF TBPD TBPB TBPE TBPC
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	5.133	1.00
54_S	69_A	3.991	1.00
142_L	145_P	3.036	1.00
59_F	67_T	3.027	1.00
42_F	57_L	2.871	1.00
35_A	45_V	2.772	1.00
135_F	152_F	2.638	0.99
54_S	78_A	2.480	0.99
15_A	75_V	2.395	0.99
42_F	59_F	2.390	0.99
84_D	87_R	2.361	0.98
150_L	158_V	2.217	0.98
80_E	84_D	2.187	0.97
147_V	171_A	2.175	0.97
67_T	160_T	2.094	0.97
44_G	154_S	2.075	0.96
18_D	98_P	1.987	0.95
12_N	103_N	1.970	0.95
36_E	48_R	1.933	0.95
105_V	158_V	1.912	0.94
33_D	40_E	1.904	0.94
46_V	59_F	1.885	0.94
159_I	168_A	1.814	0.92
54_S	82_V	1.809	0.92
13_V	71_S	1.808	0.92
26_D	30_T	1.784	0.92
13_V	75_V	1.773	0.92
46_V	57_L	1.752	0.91
142_L	175_V	1.749	0.91
149_V	175_V	1.694	0.90
124_G	127_Q	1.633	0.88
19_L	86_L	1.611	0.87
149_V	157_L	1.594	0.86
142_L	174_H	1.572	0.86
22_E	60_R	1.570	0.86
102_Q	105_V	1.560	0.85
136_P	152_F	1.491	0.82
135_F	150_L	1.441	0.80
119_I	149_V	1.398	0.78
47_Y	85_D	1.379	0.77
8_I	172_L	1.357	0.76
57_L	65_V	1.355	0.76
17_S	64_V	1.332	0.75
47_Y	58_I	1.331	0.74
93_V	151_L	1.331	0.74
144_D	170_H	1.304	0.73
44_G	57_L	1.300	0.73
110_L	159_I	1.282	0.72
154_S	179_L	1.266	0.71
42_F	103_N	1.251	0.70
56_T	82_V	1.242	0.69
132_P	155_G	1.229	0.68
21_Q	91_I	1.228	0.68
15_A	66_C	1.228	0.68
124_G	129_E	1.221	0.68
109_S	156_K	1.209	0.67
59_F	65_V	1.209	0.67
162_A	171_A	1.203	0.67
68_G	132_P	1.195	0.66
50_Q	178_R	1.190	0.66
120_A	138_L	1.179	0.65
124_G	140_Y	1.175	0.65
11_E	107_S	1.162	0.64
13_V	144_D	1.158	0.64
19_L	83_F	1.137	0.62
101_V	151_L	1.133	0.62
52_P	145_P	1.129	0.62
124_G	128_I	1.123	0.61
55_A	59_F	1.120	0.61
127_Q	140_Y	1.116	0.61
103_N	160_T	1.106	0.60
117_N	121_I	1.073	0.58
77_D	81_I	1.060	0.57
65_V	107_S	1.059	0.57
139_V	150_L	1.054	0.56
28_L	36_E	1.040	0.55
42_F	46_V	1.039	0.55
40_E	159_I	1.034	0.55
44_G	59_F	1.034	0.55
61_S	131_E	1.030	0.54
24_A	27_Q	1.027	0.54
45_V	126_E	1.020	0.54
45_V	168_A	1.008	0.53
29_A	86_L	1.005	0.53
58_I	136_P	1.003	0.52
105_V	150_L	0.999	0.52
137_G	162_A	0.998	0.52
66_C	75_V	0.985	0.51
104_I	161_G	0.984	0.51
10_I	20_G	0.979	0.51
66_C	175_V	0.973	0.50
27_Q	180_T	0.969	0.50
54_S	75_V	0.957	0.49
10_I	49_L	0.952	0.49
53_K	146_D	0.949	0.48
20_G	71_S	0.949	0.48
159_I	172_L	0.940	0.48
41_D	45_V	0.938	0.48
120_A	126_E	0.937	0.48
115_N	153_G	0.933	0.47
46_V	55_A	0.927	0.47
114_L	151_L	0.922	0.46
173_A	181_E	0.919	0.46
13_V	101_V	0.906	0.45
8_I	108_A	0.904	0.45
124_G	178_R	0.902	0.45
41_D	146_D	0.890	0.44
75_V	78_A	0.889	0.44
71_S	78_A	0.870	0.43
16_S	46_V	0.861	0.42
68_G	161_G	0.851	0.41
51_E	92_D	0.848	0.41
12_N	160_T	0.847	0.41
121_I	126_E	0.846	0.41
55_A	79_L	0.843	0.41
49_L	107_S	0.842	0.41
48_R	52_P	0.841	0.41
38_N	113_S	0.840	0.41
137_G	154_S	0.832	0.40
45_V	106_S	0.832	0.40
53_K	154_S	0.829	0.40
49_L	59_F	0.827	0.40
63_K	103_N	0.825	0.39
59_F	64_V	0.823	0.39
82_V	107_S	0.813	0.39
67_T	102_Q	0.811	0.38
84_D	94_D	0.811	0.38
148_V	160_T	0.811	0.38
10_I	147_V	0.809	0.38
157_L	177_D	0.809	0.38
74_A	164_E	0.808	0.38
47_Y	55_A	0.802	0.38
61_S	74_A	0.801	0.38
59_F	63_K	0.796	0.37
102_Q	163_A	0.795	0.37
57_L	150_L	0.794	0.37
23_L	37_Y	0.791	0.37
15_A	43_P	0.789	0.37
141_R	154_S	0.789	0.37
170_H	173_A	0.787	0.37
106_S	110_L	0.786	0.37
147_V	162_A	0.781	0.36
125_L	129_E	0.780	0.36
71_S	111_E	0.780	0.36
136_P	140_Y	0.764	0.35
109_S	141_R	0.762	0.35
27_Q	31_D	0.760	0.35
20_G	179_L	0.760	0.35
89_L	165_S	0.756	0.35
29_A	35_A	0.750	0.34
150_L	156_K	0.748	0.34
43_P	115_N	0.745	0.34
35_A	175_V	0.743	0.34
13_V	157_L	0.740	0.34
24_A	113_S	0.735	0.33
108_A	168_A	0.735	0.33
169_Q	173_A	0.730	0.33
59_F	135_F	0.728	0.33
9_H	21_Q	0.725	0.33
13_V	91_I	0.722	0.32
17_S	111_E	0.722	0.32
9_H	70_K	0.721	0.32
131_E	161_G	0.721	0.32
53_K	70_K	0.713	0.32
126_E	143_D	0.708	0.32
23_L	119_I	0.707	0.31
42_F	55_A	0.706	0.31
21_Q	28_L	0.706	0.31
162_A	165_S	0.699	0.31
22_E	118_A	0.697	0.31
21_Q	93_V	0.694	0.31
24_A	114_L	0.694	0.31
81_I	177_D	0.685	0.30
10_I	107_S	0.684	0.30
103_N	158_V	0.684	0.30
21_Q	95_S	0.682	0.30
34_G	48_R	0.675	0.29
49_L	78_A	0.668	0.29
105_V	160_T	0.668	0.29
156_K	161_G	0.664	0.29
144_D	174_H	0.664	0.29
119_I	138_L	0.663	0.29
131_E	137_G	0.661	0.29
12_N	130_Y	0.657	0.28
102_Q	136_P	0.656	0.28
156_K	163_A	0.656	0.28
31_D	38_N	0.655	0.28
38_N	107_S	0.655	0.28
9_H	140_Y	0.647	0.28
47_Y	65_V	0.646	0.28
28_L	107_S	0.644	0.28
84_D	178_R	0.643	0.28
7_T	169_Q	0.636	0.27
83_F	87_R	0.630	0.27
132_P	161_G	0.622	0.26
35_A	172_L	0.619	0.26
14_V	42_F	0.619	0.26
27_Q	122_G	0.617	0.26
61_S	147_V	0.616	0.26
65_V	78_A	0.615	0.26
26_D	104_I	0.614	0.26
120_A	171_A	0.612	0.26
92_D	165_S	0.612	0.26
61_S	146_D	0.611	0.26
56_T	176_N	0.610	0.26
129_E	134_Q	0.608	0.26
41_D	56_T	0.606	0.25
38_N	56_T	0.602	0.25
152_F	158_V	0.601	0.25
136_P	158_V	0.599	0.25
70_K	159_I	0.595	0.25
38_N	140_Y	0.593	0.25
92_D	106_S	0.589	0.24
8_I	75_V	0.588	0.24
104_I	164_E	0.587	0.24
40_E	115_N	0.586	0.24
16_S	19_L	0.583	0.24
157_L	176_N	0.583	0.24
41_D	57_L	0.582	0.24
66_C	69_A	0.572	0.24
100_K	148_V	0.563	0.23
120_A	181_E	0.559	0.23
57_L	135_F	0.556	0.23
27_Q	170_H	0.555	0.23
16_S	55_A	0.554	0.23
118_A	121_I	0.551	0.22
73_D	174_H	0.549	0.22
62_G	68_G	0.549	0.22
71_S	181_E	0.548	0.22
11_E	119_I	0.546	0.22
19_L	169_Q	0.546	0.22
15_A	116_L	0.545	0.22
39_P	119_I	0.542	0.22
64_V	114_L	0.541	0.22
136_P	150_L	0.541	0.22
78_A	158_V	0.541	0.22
19_L	176_N	0.539	0.22
28_L	47_Y	0.534	0.22
48_R	102_Q	0.533	0.22
111_E	177_D	0.531	0.21
79_L	108_A	0.530	0.21
63_K	81_I	0.530	0.21
137_G	160_T	0.525	0.21
25_L	151_L	0.525	0.21
68_G	130_Y	0.520	0.21
42_F	65_V	0.519	0.21
14_V	133_E	0.519	0.21
95_S	177_D	0.517	0.21
32_L	82_V	0.517	0.21
13_V	54_S	0.516	0.21
72_V	146_D	0.512	0.20
148_V	153_G	0.509	0.20
29_A	60_R	0.507	0.20
30_T	88_E	0.506	0.20
137_G	152_F	0.505	0.20
102_Q	158_V	0.505	0.20
53_K	145_P	0.501	0.20
169_Q	180_T	0.501	0.20
99_V	113_S	0.500	0.20
120_A	125_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	0.064	Contact Map
4b0aA	1	0.9624	100	0.069	Contact Map
3eikA	2	0.957	100	0.071	Contact Map
1ytbA	1	0.9677	100	0.072	Contact Map
1mp9A	2	0.9892	100	0.113	Contact Map
1aisA	1	0.9677	100	0.117	Contact Map
2z8uA	2	0.9462	100	0.12	Contact Map
2d0bA	1	0.4247	90	0.918	Contact Map
3vn5A	1	0.3925	72.2	0.933	Contact Map
4py5A	1	0.3925	70.4	0.933	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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