Pox_VLTF3 - PFAM28P - GREMLIN Contacts

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Pox_VLTF3 - Poxvirus Late Transcription Factor VLTF3 like

PFAM:	PF04947	Sequences: NKSSKYAYKRINHFNEWLAQFQAKETTDIPDEVIEKIKNEIKKERITLSKITKKKIREILKKLGLNKYYEHIPYIINKLTGIPPPIISPELEEKLRNMFKEIQEPFEKLHCPKDRKNFLSYSYVLYKLCELLGEDEYLPYFPLLKSREKLIEQDEIWKKICEELGWEF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	168 (164)
Sequences:	1941 (1333)
Seq/√Len:	104.1
META:	0.969

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_K	65_L	4.441	1.00
15_N	96_R	3.536	1.00
108_K	163_E	3.317	1.00
127_K	130_E	3.244	1.00
32_E	36_K	3.055	1.00
31_D	35_E	2.969	1.00
37_I	59_I	2.692	1.00
157_W	161_C	2.654	1.00
40_E	43_K	2.644	1.00
88_S	91_L	2.539	1.00
17_W	122_S	2.516	1.00
102_I	160_I	2.478	1.00
14_F	95_L	2.392	1.00
110_H	163_E	2.312	1.00
30_P	68_Y	2.259	1.00
91_L	134_E	2.197	1.00
123_Y	154_D	2.194	1.00
87_I	137_Y	2.132	1.00
25_E	71_H	2.114	1.00
95_L	128_L	2.088	1.00
34_I	78_K	2.030	1.00
109_L	163_E	1.996	1.00
37_I	41_I	1.949	1.00
158_K	162_E	1.931	1.00
98_M	128_L	1.868	1.00
87_I	91_L	1.803	1.00
36_K	63_L	1.797	1.00
118_F	124_V	1.736	1.00
44_E	59_I	1.703	1.00
11_I	100_K	1.648	1.00
135_D	167_E	1.647	1.00
56_I	76_I	1.609	1.00
147_R	151_I	1.559	1.00
91_L	94_K	1.540	1.00
102_I	118_F	1.507	1.00
24_K	92_E	1.446	1.00
126_Y	138_L	1.430	1.00
22_Q	92_E	1.427	1.00
30_P	33_V	1.424	1.00
99_F	121_Y	1.404	1.00
159_K	162_E	1.397	1.00
33_V	65_L	1.395	1.00
109_L	112_P	1.364	1.00
44_E	55_K	1.343	0.99
34_I	74_Y	1.327	0.99
20_Q	70_E	1.326	0.99
41_I	59_I	1.323	0.99
76_I	80_T	1.321	0.99
87_I	129_C	1.308	0.99
123_Y	127_K	1.304	0.99
157_W	168_F	1.284	0.99
82_I	85_P	1.277	0.99
127_K	157_W	1.272	0.99
25_E	74_Y	1.269	0.99
53_K	72_I	1.252	0.99
23_A	84_P	1.248	0.99
41_I	56_I	1.246	0.99
102_I	128_L	1.220	0.99
126_Y	130_E	1.220	0.99
35_E	39_N	1.219	0.99
155_E	159_K	1.207	0.99
115_R	119_L	1.171	0.98
22_Q	91_L	1.156	0.98
131_L	157_W	1.132	0.98
41_I	46_I	1.119	0.98
146_S	149_K	1.113	0.98
77_N	84_P	1.101	0.98
98_M	132_L	1.080	0.97
124_V	128_L	1.066	0.97
21_F	134_E	1.061	0.97
23_A	73_P	1.052	0.97
131_L	135_D	1.039	0.97
77_N	83_P	1.030	0.97
159_K	163_E	1.017	0.96
94_K	97_N	1.016	0.96
81_G	85_P	1.006	0.96
16_E	70_E	1.006	0.96
123_Y	168_F	0.998	0.96
12_N	16_E	0.996	0.96
33_V	36_K	0.996	0.96
37_I	79_L	0.995	0.96
40_E	62_K	0.985	0.96
95_L	129_C	0.973	0.95
18_L	96_R	0.969	0.95
91_L	129_C	0.961	0.95
127_K	154_D	0.947	0.95
10_R	103_Q	0.927	0.94
129_C	134_E	0.927	0.94
31_D	38_K	0.925	0.94
20_Q	71_H	0.922	0.94
151_I	155_E	0.922	0.94
34_I	38_K	0.918	0.94
93_E	96_R	0.905	0.93
17_W	125_L	0.904	0.93
56_I	59_I	0.901	0.93
94_K	98_M	0.894	0.93
74_Y	78_K	0.894	0.93
17_W	120_S	0.891	0.93
6_Y	106_F	0.878	0.92
14_F	128_L	0.877	0.92
129_C	138_L	0.871	0.92
13_H	117_N	0.863	0.91
90_E	94_K	0.856	0.91
128_L	132_L	0.856	0.91
119_L	124_V	0.855	0.91
54_K	58_E	0.853	0.91
53_K	141_F	0.831	0.90
11_I	15_N	0.830	0.90
129_C	137_Y	0.826	0.89
56_I	80_T	0.821	0.89
47_T	50_K	0.817	0.89
53_K	73_P	0.816	0.89
10_R	107_E	0.813	0.89
143_L	150_L	0.812	0.89
102_I	105_P	0.801	0.88
55_K	58_E	0.795	0.88
125_L	129_C	0.793	0.87
48_L	51_I	0.789	0.87
17_W	20_Q	0.774	0.86
22_Q	25_E	0.772	0.86
51_I	76_I	0.764	0.85
46_I	55_K	0.755	0.85
5_K	15_N	0.747	0.84
119_L	153_Q	0.746	0.84
56_I	82_I	0.742	0.84
160_I	163_E	0.728	0.83
6_Y	10_R	0.726	0.82
95_L	117_N	0.723	0.82
27_T	71_H	0.721	0.82
34_I	37_I	0.721	0.82
48_L	79_L	0.717	0.82
10_R	95_L	0.716	0.81
120_S	153_Q	0.715	0.81
10_R	73_P	0.715	0.81
33_V	37_I	0.710	0.81
38_K	79_L	0.706	0.81
115_R	118_F	0.706	0.81
21_F	87_I	0.703	0.80
20_Q	118_F	0.701	0.80
28_D	104_E	0.700	0.80
165_G	168_F	0.699	0.80
53_K	76_I	0.697	0.80
137_Y	141_F	0.697	0.80
120_S	128_L	0.695	0.80
88_S	94_K	0.692	0.79
73_P	77_N	0.682	0.78
99_F	118_F	0.682	0.78
36_K	79_L	0.681	0.78
89_P	100_K	0.675	0.78
135_D	138_L	0.675	0.78
130_E	154_D	0.675	0.78
110_H	159_K	0.673	0.77
152_E	155_E	0.666	0.77
149_K	153_Q	0.662	0.76
48_L	82_I	0.661	0.76
98_M	131_L	0.659	0.76
22_Q	71_H	0.653	0.75
126_Y	129_C	0.653	0.75
98_M	134_E	0.651	0.75
90_E	93_E	0.651	0.75
56_I	75_I	0.650	0.75
77_N	87_I	0.644	0.74
134_E	137_Y	0.642	0.74
6_Y	15_N	0.642	0.74
15_N	19_A	0.639	0.74
13_H	99_F	0.633	0.73
74_Y	106_F	0.632	0.73
122_S	125_L	0.632	0.73
120_S	143_L	0.632	0.73
83_P	104_E	0.622	0.72
23_A	77_N	0.617	0.71
58_E	86_I	0.617	0.71
66_N	126_Y	0.616	0.71
8_Y	16_E	0.616	0.71
41_I	51_I	0.614	0.71
75_I	114_D	0.613	0.71
37_I	44_E	0.610	0.70
24_K	86_I	0.608	0.70
106_F	118_F	0.608	0.70
16_E	20_Q	0.607	0.70
145_K	149_K	0.602	0.69
51_I	79_L	0.601	0.69
72_I	76_I	0.596	0.68
87_I	90_E	0.594	0.68
144_L	149_K	0.593	0.68
70_E	125_L	0.584	0.67
158_K	161_C	0.583	0.67
84_P	111_C	0.582	0.67
41_I	80_T	0.582	0.67
77_N	80_T	0.581	0.66
106_F	115_R	0.577	0.66
41_I	47_T	0.575	0.66
120_S	155_E	0.575	0.66
130_E	157_W	0.573	0.65
135_D	165_G	0.572	0.65
96_R	100_K	0.570	0.65
102_I	156_I	0.570	0.65
39_N	47_T	0.568	0.65
5_K	11_I	0.563	0.64
104_E	165_G	0.563	0.64
6_Y	89_P	0.562	0.64
34_I	79_L	0.562	0.64
9_K	121_Y	0.561	0.64
55_K	80_T	0.561	0.64
31_D	36_K	0.560	0.64
97_N	104_E	0.558	0.63
23_A	74_Y	0.557	0.63
126_Y	151_I	0.555	0.63
133_G	167_E	0.554	0.63
6_Y	11_I	0.553	0.63
144_L	153_Q	0.551	0.62
46_I	58_E	0.549	0.62
161_C	168_F	0.548	0.62
36_K	39_N	0.545	0.62
40_E	59_I	0.544	0.61
31_D	78_K	0.544	0.61
10_R	118_F	0.542	0.61
57_R	72_I	0.541	0.61
93_E	100_K	0.540	0.61
85_P	88_S	0.540	0.61
52_T	55_K	0.539	0.61
10_R	14_F	0.537	0.60
122_S	141_F	0.537	0.60
77_N	125_L	0.536	0.60
52_T	76_I	0.534	0.60
164_L	167_E	0.532	0.60
106_F	156_I	0.530	0.59
14_F	115_R	0.527	0.59
57_R	122_S	0.520	0.58
55_K	79_L	0.520	0.58
88_S	165_G	0.519	0.58
20_Q	25_E	0.519	0.58
104_E	107_E	0.518	0.58
51_I	82_I	0.518	0.58
151_I	168_F	0.516	0.57
103_Q	118_F	0.514	0.57
9_K	12_N	0.513	0.57
106_F	152_E	0.511	0.57
85_P	134_E	0.509	0.56
18_L	93_E	0.508	0.56
79_L	151_I	0.508	0.56
55_K	76_I	0.506	0.56
118_F	121_Y	0.505	0.56
57_R	96_R	0.502	0.55
21_F	85_P	0.501	0.55
38_K	48_L	0.500	0.55

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
4nl9C	1	0.3393	22.6	0.921	Contact Map
2f3nA	1	0.3631	18.4	0.924	Contact Map
2gleA	1	0.4405	17.6	0.925	Contact Map
2bsqE	2	0.4048	17.2	0.925	Contact Map
2cpgA	2	0.2679	16.3	0.926	Contact Map
3h87C	3	0.4286	14.8	0.927	Contact Map
2ovrB	1	0.4167	13.2	0.929	Contact Map
1p94A	2	0.381	13.2	0.929	Contact Map
3bq7A	3	0.3929	11.3	0.931	Contact Map
1pulA	1	0.4643	11	0.931	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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