PGDYG - PFAM28P - GREMLIN Contacts

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PGDYG - PGDYG protein

PFAM:	PF14083	Sequences: GPNRYRAGDAILTGPTGERWPVSRERFDAKYEPVPPGTAAGEDGAYRKRPIPVLAKQMDEPFSVALSDGGDLLHGKAGDWLVQYGPGDYGVVAAAIFAQTYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (99)
Sequences:	1024 (710)
Seq/√Len:	71.3
META:	0.939

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
58_M	62_F	4.290	1.00
94_A	98_A	4.103	1.00
15_P	18_E	3.030	1.00
84_Y	90_G	2.794	1.00
75_G	78_G	2.572	1.00
66_L	71_D	2.563	1.00
24_R	28_D	2.416	1.00
96_I	100_T	2.414	1.00
12_L	22_V	2.398	1.00
3_N	21_P	2.190	1.00
39_A	42_E	2.123	1.00
32_E	49_R	2.007	1.00
64_V	81_L	1.945	1.00
5_Y	11_I	1.850	1.00
53_V	82_V	1.756	1.00
82_V	92_V	1.728	1.00
66_L	70_G	1.657	1.00
81_L	91_V	1.605	0.99
58_M	75_G	1.596	0.99
64_V	92_V	1.515	0.99
30_K	48_K	1.490	0.99
57_Q	94_A	1.483	0.99
21_P	48_K	1.434	0.99
16_T	96_I	1.425	0.99
18_E	21_P	1.359	0.98
20_W	73_L	1.337	0.98
62_F	75_G	1.333	0.98
28_D	40_A	1.248	0.97
97_F	101_Y	1.244	0.96
26_R	29_A	1.221	0.96
32_E	47_R	1.162	0.95
66_L	69_G	1.153	0.95
75_G	91_V	1.150	0.95
21_P	96_I	1.124	0.94
62_F	81_L	1.123	0.94
57_Q	80_W	1.116	0.94
14_G	18_E	1.093	0.93
35_P	38_T	1.089	0.93
3_N	66_L	1.073	0.92
73_L	78_G	1.060	0.92
83_Q	89_Y	1.060	0.92
20_W	75_G	1.059	0.92
21_P	52_P	1.037	0.91
6_R	25_E	1.034	0.91
33_P	46_Y	1.029	0.90
83_Q	86_P	1.006	0.89
22_V	46_Y	0.995	0.89
63_S	74_H	0.984	0.88
51_I	76_K	0.974	0.88
44_G	80_W	0.960	0.87
45_A	59_D	0.952	0.87
2_P	18_E	0.951	0.87
90_G	96_I	0.944	0.86
22_V	30_K	0.936	0.86
39_A	45_A	0.923	0.85
10_A	44_G	0.919	0.85
85_G	90_G	0.905	0.84
10_A	22_V	0.903	0.84
87_G	91_V	0.896	0.83
93_A	96_I	0.891	0.83
33_P	44_G	0.888	0.83
20_W	30_K	0.888	0.83
76_K	93_A	0.887	0.83
52_P	60_E	0.886	0.83
21_P	64_V	0.882	0.82
33_P	38_T	0.868	0.81
65_A	72_L	0.859	0.81
10_A	24_R	0.843	0.79
23_S	26_R	0.804	0.76
85_G	89_Y	0.803	0.76
10_A	46_Y	0.801	0.76
73_L	96_I	0.795	0.75
92_V	100_T	0.793	0.75
95_A	99_Q	0.783	0.74
16_T	49_R	0.779	0.74
3_N	48_K	0.768	0.73
16_T	93_A	0.768	0.73
29_A	54_L	0.743	0.70
58_M	81_L	0.738	0.70
79_D	91_V	0.734	0.69
11_I	62_F	0.734	0.69
26_R	30_K	0.728	0.69
78_G	94_A	0.721	0.68
69_G	72_L	0.719	0.68
94_A	99_Q	0.717	0.67
3_N	96_I	0.717	0.67
75_G	81_L	0.716	0.67
93_A	99_Q	0.695	0.65
34_V	45_A	0.690	0.64
14_G	20_W	0.688	0.64
10_A	84_Y	0.687	0.64
58_M	91_V	0.687	0.64
40_A	82_V	0.679	0.63
57_Q	78_G	0.677	0.63
32_E	40_A	0.675	0.63
16_T	99_Q	0.674	0.63
33_P	40_A	0.672	0.62
68_D	71_D	0.672	0.62
27_F	90_G	0.664	0.61
61_P	74_H	0.662	0.61
83_Q	88_D	0.653	0.60
16_T	69_G	0.651	0.60
36_P	81_L	0.638	0.58
75_G	80_W	0.638	0.58
35_P	60_E	0.634	0.58
4_R	49_R	0.627	0.57
11_I	35_P	0.620	0.56
22_V	27_F	0.602	0.54
46_Y	55_A	0.601	0.54
2_P	60_E	0.598	0.54
10_A	13_T	0.598	0.54
39_A	43_D	0.591	0.53
39_A	59_D	0.589	0.52
32_E	35_P	0.587	0.52
53_V	58_M	0.583	0.52
35_P	39_A	0.583	0.52
10_A	28_D	0.583	0.52
76_K	94_A	0.582	0.52
12_L	19_R	0.582	0.52
25_E	28_D	0.575	0.51
6_R	36_P	0.571	0.50
42_E	76_K	0.570	0.50
59_D	72_L	0.569	0.50
20_W	84_Y	0.566	0.50
48_K	91_V	0.566	0.50
57_Q	93_A	0.565	0.50
73_L	91_V	0.561	0.49
7_A	45_A	0.554	0.48
13_T	17_G	0.548	0.47
38_T	46_Y	0.546	0.47
82_V	100_T	0.545	0.47
30_K	51_I	0.544	0.47
2_P	82_V	0.543	0.47
18_E	64_V	0.541	0.47
13_T	18_E	0.538	0.46
77_A	80_W	0.532	0.45
50_P	59_D	0.532	0.45
4_R	7_A	0.532	0.45
50_P	80_W	0.529	0.45
44_G	47_R	0.526	0.45
48_K	71_D	0.523	0.44
28_D	47_R	0.519	0.44
2_P	12_L	0.519	0.44
54_L	57_Q	0.515	0.43
9_D	23_S	0.509	0.43
49_R	77_A	0.508	0.43
15_P	51_I	0.505	0.42
84_Y	88_D	0.500	0.42

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
1eybA	5	0.8039	9.2	0.922	Contact Map
3es4A	2	0.3431	6.3	0.928	Contact Map
4maqA	2	0.4412	5.7	0.93	Contact Map
2a6hD	1	0.902	5	0.932	Contact Map
2riqA	2	0.4118	4.4	0.933	Contact Map
3c9iA	5	0.402	4.3	0.934	Contact Map
2eb4A	5	0.4118	4.1	0.934	Contact Map
1hqmD	1	0.8725	3.9	0.935	Contact Map
2a7yA	1	0.2941	3.7	0.935	Contact Map
2ecdA	1	0.5882	3.7	0.936	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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