DM4_12 - PFAM28P - GREMLIN Contacts

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DM4_12 - DM4/DM12 family

PFAM:	PF07841	Sequences: RRDLYRKLEDLLERYGFDGRACLLRAICEAAQRPLHHHNGLLGELLHIIFTPSSSEDEEYDEAERAGRSGGDCARLYPEC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (80)
Sequences:	744 (550)
Seq/√Len:	61.5
META:	0.083

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
53_S	64_E	4.254	1.00
63_A	67_G	3.401	1.00
18_D	21_A	2.629	1.00
39_N	43_G	2.447	1.00
40_G	43_G	2.419	1.00
20_R	59_E	2.231	1.00
1_R	5_Y	2.204	1.00
62_E	66_A	2.183	1.00
25_R	74_A	1.676	0.99
15_Y	42_L	1.634	0.99
20_R	37_H	1.600	0.99
73_C	80_C	1.596	0.99
72_D	75_R	1.566	0.99
37_H	43_G	1.442	0.98
9_E	20_R	1.418	0.97
68_R	77_Y	1.396	0.97
22_C	28_C	1.385	0.97
25_R	29_E	1.366	0.97
30_A	47_H	1.358	0.97
32_Q	42_L	1.353	0.97
16_G	19_G	1.328	0.96
63_A	77_Y	1.328	0.96
52_P	60_Y	1.324	0.96
10_D	15_Y	1.297	0.96
25_R	65_R	1.287	0.95
31_A	34_P	1.273	0.95
19_G	44_E	1.265	0.95
69_S	72_D	1.265	0.95
12_L	49_I	1.239	0.94
29_E	52_P	1.239	0.94
28_C	73_C	1.231	0.94
24_L	59_E	1.218	0.94
47_H	66_A	1.214	0.94
31_A	51_T	1.166	0.92
44_E	47_H	1.159	0.92
31_A	44_E	1.117	0.91
23_L	30_A	1.106	0.90
22_C	73_C	1.099	0.90
7_K	10_D	1.058	0.88
10_D	14_R	1.044	0.88
27_I	53_S	1.024	0.86
23_L	44_E	1.015	0.86
2_R	62_E	1.001	0.85
21_A	32_Q	0.973	0.84
54_S	57_D	0.971	0.83
9_E	60_Y	0.965	0.83
49_I	75_R	0.961	0.83
24_L	60_Y	0.949	0.82
19_G	23_L	0.938	0.81
3_D	10_D	0.930	0.81
50_F	70_G	0.928	0.81
21_A	79_E	0.908	0.79
3_D	77_Y	0.889	0.78
41_L	47_H	0.883	0.77
3_D	11_L	0.880	0.77
19_G	24_L	0.818	0.72
56_E	68_R	0.810	0.71
32_Q	49_I	0.807	0.70
51_T	67_G	0.807	0.70
45_L	49_I	0.805	0.70
17_F	29_E	0.799	0.70
13_E	36_H	0.799	0.70
12_L	33_R	0.791	0.69
65_R	69_S	0.787	0.69
56_E	71_G	0.772	0.67
48_I	56_E	0.763	0.66
4_L	78_P	0.762	0.66
3_D	68_R	0.755	0.65
44_E	60_Y	0.753	0.65
34_P	52_P	0.743	0.64
42_L	49_I	0.740	0.64
21_A	69_S	0.730	0.63
71_G	74_A	0.726	0.62
6_R	9_E	0.715	0.61
1_R	11_L	0.714	0.61
27_I	56_E	0.705	0.60
4_L	11_L	0.674	0.57
46_L	79_E	0.668	0.56
28_C	80_C	0.663	0.55
42_L	79_E	0.660	0.55
8_L	24_L	0.659	0.55
10_D	13_E	0.658	0.55
23_L	58_E	0.658	0.55
36_H	46_L	0.637	0.52
40_G	48_I	0.636	0.52
15_Y	59_E	0.634	0.52
3_D	62_E	0.633	0.52
53_S	71_G	0.627	0.51
7_K	18_D	0.626	0.51
35_L	39_N	0.622	0.51
62_E	72_D	0.622	0.51
17_F	21_A	0.620	0.51
18_D	78_P	0.617	0.50
19_G	64_E	0.617	0.50
65_R	77_Y	0.615	0.50
17_F	74_A	0.614	0.50
29_E	47_H	0.613	0.50
8_L	74_A	0.604	0.49
39_N	44_E	0.592	0.47
31_A	47_H	0.586	0.47
6_R	14_R	0.577	0.46
13_E	56_E	0.571	0.45
31_A	64_E	0.570	0.45
13_E	55_S	0.565	0.44
5_Y	9_E	0.558	0.43
43_G	77_Y	0.558	0.43
26_A	71_G	0.553	0.43
19_G	30_A	0.547	0.42
55_S	76_L	0.546	0.42
2_R	65_R	0.539	0.41
46_L	50_F	0.524	0.40
55_S	58_E	0.521	0.39
5_Y	64_E	0.520	0.39
19_G	27_I	0.518	0.39
3_D	54_S	0.518	0.39
38_H	78_P	0.516	0.39
27_I	48_I	0.506	0.38
2_R	61_D	0.505	0.38
46_L	71_G	0.505	0.38
25_R	52_P	0.500	0.37

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
2knjA	1	0.775	8.9	0.882	Contact Map
4e8uA	4	0.7875	4.1	0.9	Contact Map
3ec8A	2	0.8375	3.6	0.902	Contact Map
1yqfA	3	0.6	3.3	0.904	Contact Map
2vmlB	3	0.7625	2.8	0.907	Contact Map
1p32A	3	0.625	2.7	0.909	Contact Map
3l0fB	3	0.7625	2.7	0.909	Contact Map
3qv0A	3	0.6	2.6	0.909	Contact Map
3jv1A	3	0.6	2.6	0.909	Contact Map
2c7lB	3	0.7625	2.5	0.91	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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