VirE_N - PFAM28P - GREMLIN Contacts

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VirE_N - VirE N-terminal domain

PFAM:	PF08800	Sequences: QLKKKLPAVTFSGTFSGKRKDDNLIEHSGLICLDFDHLDNPEELEELKEKLKKDPYVYAAFISPSGNGLKVLVKIPAPDENKLPQDEEEIELFHKEAFRALEKYFEELYGIEIDKSCKDVSRLCFLSYDPDIYY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	134 (118)
Sequences:	6626 (5072)
Seq/√Len:	466.9
META:	0.952

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_A	123_L	3.630	1.00
11_F	72_L	2.386	1.00
119_D	122_R	2.265	1.00
117_C	122_R	2.075	1.00
21_D	121_S	2.032	1.00
20_K	23_N	2.020	1.00
30_L	72_L	2.015	1.00
48_K	62_I	2.006	1.00
59_A	72_L	1.971	1.00
48_K	52_K	1.969	1.00
70_K	124_C	1.902	1.00
30_L	58_Y	1.901	1.00
21_D	119_D	1.877	1.00
64_P	70_K	1.871	1.00
16_S	25_I	1.815	1.00
54_D	104_Y	1.790	1.00
18_K	23_N	1.738	1.00
27_H	94_H	1.732	1.00
57_V	105_F	1.708	1.00
102_E	115_K	1.703	1.00
14_T	26_E	1.624	1.00
32_C	70_K	1.595	1.00
37_H	67_N	1.579	1.00
95_K	118_K	1.550	1.00
57_V	71_V	1.524	1.00
52_K	60_A	1.495	1.00
99_R	102_E	1.469	1.00
43_E	46_E	1.445	1.00
32_C	117_C	1.405	1.00
99_R	118_K	1.393	1.00
47_L	50_K	1.385	1.00
57_V	60_A	1.366	1.00
60_A	69_L	1.351	1.00
35_F	71_V	1.347	1.00
44_L	69_L	1.344	1.00
44_L	62_I	1.334	1.00
13_G	24_L	1.327	1.00
49_E	52_K	1.319	1.00
48_K	69_L	1.262	1.00
6_L	64_P	1.260	1.00
60_A	71_V	1.257	1.00
103_K	107_E	1.247	1.00
59_A	132_I	1.203	1.00
61_F	124_C	1.185	1.00
58_Y	74_K	1.184	1.00
106_E	112_E	1.176	1.00
51_L	71_V	1.174	1.00
35_F	113_I	1.161	1.00
102_E	106_E	1.158	1.00
46_E	50_K	1.143	1.00
33_L	71_V	1.139	1.00
52_K	133_Y	1.132	1.00
38_L	47_L	1.128	1.00
61_F	70_K	1.127	1.00
98_F	102_E	1.121	1.00
54_D	109_Y	1.101	1.00
61_F	72_L	1.095	1.00
78_P	81_N	1.090	1.00
64_P	124_C	1.088	1.00
97_A	100_A	1.088	1.00
35_F	111_I	1.086	1.00
39_D	43_E	1.079	1.00
51_L	60_A	1.071	1.00
12_S	27_H	1.068	1.00
2_L	5_K	1.027	1.00
49_E	53_K	1.016	1.00
95_K	99_R	1.011	1.00
63_S	70_K	1.005	1.00
16_S	23_N	1.003	1.00
48_K	60_A	0.983	1.00
27_H	75_I	0.975	1.00
62_I	66_G	0.955	1.00
4_K	125_F	0.947	1.00
32_C	124_C	0.938	1.00
11_F	32_C	0.933	1.00
9_V	126_L	0.917	1.00
19_R	23_N	0.912	1.00
64_P	125_F	0.910	1.00
47_L	111_I	0.905	1.00
11_F	124_C	0.902	1.00
40_N	43_E	0.900	1.00
57_V	73_V	0.865	1.00
95_K	120_V	0.865	1.00
10_T	123_L	0.855	1.00
39_D	42_E	0.854	1.00
31_I	101_L	0.846	1.00
61_F	127_S	0.845	1.00
14_T	25_I	0.841	1.00
32_C	72_L	0.838	1.00
76_P	97_A	0.837	1.00
45_E	48_K	0.828	1.00
46_E	49_E	0.819	1.00
19_R	123_L	0.814	1.00
39_D	67_N	0.807	1.00
96_E	99_R	0.806	1.00
15_F	24_L	0.805	1.00
33_L	113_I	0.804	1.00
34_D	114_D	0.804	1.00
50_K	53_K	0.801	1.00
54_D	105_F	0.799	1.00
97_A	101_L	0.797	1.00
51_L	57_V	0.794	1.00
75_I	97_A	0.793	1.00
54_D	108_L	0.788	1.00
102_E	113_I	0.785	1.00
101_L	105_F	0.784	1.00
45_E	62_I	0.778	1.00
48_K	129_D	0.775	1.00
27_H	77_A	0.775	1.00
98_F	113_I	0.774	1.00
15_F	121_S	0.774	1.00
12_S	94_H	0.765	1.00
45_E	49_E	0.762	1.00
56_Y	73_V	0.751	1.00
36_D	114_D	0.746	1.00
100_A	104_Y	0.737	1.00
44_L	60_A	0.736	1.00
113_I	117_C	0.735	1.00
102_E	112_E	0.725	1.00
73_V	101_L	0.725	1.00
36_D	63_S	0.722	1.00
19_R	24_L	0.706	1.00
115_K	118_K	0.699	1.00
71_V	105_F	0.692	1.00
31_I	75_I	0.689	1.00
24_L	27_H	0.676	1.00
73_V	105_F	0.673	1.00
30_L	74_K	0.671	1.00
45_E	131_D	0.662	1.00
19_R	121_S	0.658	1.00
26_E	77_A	0.655	1.00
61_F	126_L	0.654	1.00
77_A	81_N	0.651	1.00
94_H	98_F	0.649	1.00
34_D	68_G	0.649	1.00
102_E	118_K	0.644	1.00
100_A	105_F	0.638	1.00
35_F	47_L	0.630	0.99
98_F	117_C	0.628	0.99
116_S	122_R	0.623	0.99
33_L	101_L	0.619	0.99
116_S	119_D	0.614	0.99
112_E	115_K	0.609	0.99
81_N	96_E	0.600	0.99
24_L	120_V	0.594	0.99
105_F	109_Y	0.592	0.99
62_I	69_L	0.590	0.99
36_D	68_G	0.580	0.99
77_A	80_E	0.578	0.99
56_Y	104_Y	0.572	0.99
99_R	103_K	0.559	0.99
44_L	48_K	0.558	0.99
38_L	44_L	0.557	0.99
13_G	28_S	0.557	0.99
98_F	101_L	0.551	0.99
99_R	115_K	0.551	0.99
12_S	32_C	0.549	0.99
106_E	113_I	0.547	0.99
63_S	124_C	0.545	0.99
10_T	19_R	0.544	0.98
75_I	78_P	0.541	0.98
43_E	47_L	0.541	0.98
31_I	98_F	0.538	0.98
61_F	71_V	0.538	0.98
63_S	68_G	0.536	0.98
40_N	46_E	0.534	0.98
21_D	120_V	0.527	0.98
29_G	74_K	0.526	0.98
95_K	98_F	0.526	0.98
27_H	120_V	0.524	0.98
48_K	131_D	0.522	0.98
32_C	122_R	0.521	0.98
35_F	106_E	0.515	0.98
127_S	132_I	0.513	0.98
105_F	113_I	0.508	0.98
78_P	97_A	0.504	0.98
65_S	125_F	0.500	0.97

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
3h20A	2	0.8134	21	0.908	Contact Map
3m1mA	1	0.8209	10.6	0.92	Contact Map
1zt2A	3	0.8881	7.7	0.924	Contact Map
3cueA	1	0.7537	7.1	0.926	Contact Map
1ro2A	1	0.8209	6.6	0.927	Contact Map
2j3tD	1	0.8433	6.5	0.927	Contact Map
2iruA	1	0.903	6.4	0.927	Contact Map
1v33A	1	0.8582	6.3	0.928	Contact Map
3wtsB	1	0.3358	5.3	0.93	Contact Map
2faoA	1	0.8806	5.1	0.93	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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