GRP - PFAM28P - GREMLIN Contacts

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GRP - Glycine rich protein family

PFAM:	PF07172	Sequences: MASKALLLLGLLLAAVLLISSEVAARELAETEKSESENTVQDAKYGGGGGGGGGGYGGGGGGGGGGGGYGGGGGGYGGGGGGGGGGYGGGYGGGG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	95 (92)
Sequences:	559 (505)
Seq/√Len:	52.6
META:	0.274

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_G	65_G	2.482	1.00
6_L	11_L	2.209	1.00
89_G	92_G	2.208	1.00
15_A	20_S	2.180	1.00
31_T	36_S	2.061	1.00
73_G	81_G	2.040	1.00
56_Y	91_Y	1.961	1.00
2_A	15_A	1.885	0.99
41_Q	44_K	1.878	0.99
59_G	73_G	1.816	0.99
84_G	87_Y	1.810	0.99
85_G	89_G	1.765	0.99
57_G	70_G	1.744	0.99
69_Y	76_Y	1.662	0.98
81_G	86_G	1.660	0.98
66_G	73_G	1.653	0.98
67_G	89_G	1.641	0.98
76_Y	83_G	1.608	0.98
84_G	92_G	1.605	0.98
82_G	86_G	1.513	0.97
8_L	15_A	1.466	0.97
81_G	87_Y	1.442	0.96
83_G	91_Y	1.433	0.96
63_G	77_G	1.384	0.95
85_G	92_G	1.381	0.95
3_S	7_L	1.337	0.94
57_G	77_G	1.331	0.94
30_E	33_K	1.311	0.94
64_G	71_G	1.297	0.93
34_S	39_T	1.259	0.92
45_Y	48_G	1.239	0.92
12_L	42_D	1.233	0.91
81_G	84_G	1.224	0.91
65_G	72_G	1.213	0.91
2_A	8_L	1.204	0.90
70_G	77_G	1.190	0.90
70_G	84_G	1.179	0.90
15_A	28_L	1.154	0.89
69_Y	78_G	1.148	0.88
22_E	26_R	1.148	0.88
10_G	41_Q	1.126	0.87
62_G	76_Y	1.121	0.87
71_G	78_G	1.098	0.86
17_L	23_V	1.082	0.85
11_L	23_V	1.068	0.84
56_Y	63_G	1.060	0.84
70_G	75_G	1.048	0.83
5_A	11_L	1.038	0.83
6_L	17_L	1.029	0.82
21_S	27_E	1.025	0.82
6_L	10_G	1.020	0.81
82_G	85_G	1.005	0.80
18_L	24_A	1.000	0.80
23_V	26_R	0.995	0.80
62_G	69_Y	0.991	0.80
6_L	15_A	0.982	0.79
3_S	6_L	0.980	0.79
54_G	61_G	0.976	0.78
72_G	79_G	0.970	0.78
14_A	20_S	0.959	0.77
56_Y	76_Y	0.949	0.77
38_N	42_D	0.941	0.76
34_S	37_E	0.940	0.76
14_A	28_L	0.909	0.73
38_N	45_Y	0.908	0.73
10_G	18_L	0.907	0.73
29_A	41_Q	0.880	0.71
23_V	27_E	0.877	0.71
78_G	84_G	0.876	0.71
65_G	83_G	0.865	0.70
11_L	17_L	0.852	0.68
16_V	27_E	0.845	0.68
12_L	24_A	0.839	0.67
67_G	74_G	0.834	0.67
46_G	49_G	0.832	0.67
75_G	91_Y	0.832	0.67
11_L	21_S	0.822	0.66
39_T	42_D	0.810	0.64
9_L	19_I	0.802	0.64
56_Y	64_G	0.798	0.63
83_G	86_G	0.796	0.63
69_Y	83_G	0.785	0.62
82_G	87_Y	0.776	0.61
22_E	25_A	0.771	0.61
83_G	87_Y	0.769	0.60
63_G	70_G	0.764	0.60
12_L	32_E	0.762	0.60
25_A	28_L	0.757	0.59
71_G	77_G	0.748	0.58
29_A	33_K	0.739	0.57
56_Y	59_G	0.733	0.57
76_Y	87_Y	0.727	0.56
87_Y	90_G	0.718	0.55
4_K	37_E	0.713	0.55
5_A	10_G	0.710	0.54
4_K	86_G	0.707	0.54
61_G	69_Y	0.703	0.54
58_G	64_G	0.701	0.53
30_E	44_K	0.698	0.53
73_G	89_G	0.695	0.53
8_L	26_R	0.690	0.52
9_L	22_E	0.689	0.52
29_A	32_E	0.684	0.52
57_G	64_G	0.677	0.51
31_T	34_S	0.674	0.51
32_E	44_K	0.672	0.50
8_L	14_A	0.671	0.50
37_E	43_A	0.669	0.50
18_L	42_D	0.667	0.50
18_L	59_G	0.665	0.50
16_V	22_E	0.653	0.48
45_Y	51_G	0.612	0.44
69_Y	91_Y	0.606	0.43
32_E	39_T	0.602	0.43
58_G	72_G	0.598	0.43
1_M	4_K	0.580	0.41
82_G	89_G	0.580	0.41
67_G	73_G	0.578	0.41
78_G	85_G	0.578	0.41
19_I	37_E	0.571	0.40
3_S	18_L	0.564	0.39
29_A	36_S	0.559	0.39
79_G	86_G	0.559	0.39
29_A	34_S	0.558	0.39
10_G	20_S	0.556	0.38
60_G	78_G	0.554	0.38
65_G	79_G	0.553	0.38
47_G	50_G	0.543	0.37
11_L	26_R	0.542	0.37
12_L	19_I	0.542	0.37
35_E	39_T	0.538	0.37
52_G	58_G	0.537	0.37
59_G	66_G	0.532	0.36
70_G	92_G	0.516	0.34
41_Q	45_Y	0.504	0.33
86_G	89_G	0.503	0.33
65_G	77_G	0.503	0.33
2_A	6_L	0.500	0.33

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
2pk2A	3	0.3895	77.8	0.758	Contact Map
4kblA	2	0	59.9	0.787	Contact Map
1zrtD	1	0.3895	36.3	0.815	Contact Map
3cx5D	2	0.4316	31.2	0.821	Contact Map
4d6uD	1	0.4	31.1	0.821	Contact Map
1pp9D	2	0.4	30.4	0.822	Contact Map
2yiuB	1	0.2947	29.4	0.823	Contact Map
3dl8E	1	0.2316	24.4	0.83	Contact Map
2dckA	1	0.6	24	0.83	Contact Map
4p02B	1	0.3158	20.8	0.835	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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