HCNGP - PFAM28P - GREMLIN Contacts

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HCNGP - HCNGP-like protein

PFAM:	PF07818	Sequences: IPPSPPGSCDPALQAKFARFLELKKQGVHFNEKLQSSKAFRNPSLLEKLVEFVGIDEYGTNLPKDVWDPHGFPEEAYYEELAKAQKREMEKREK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (92)
Sequences:	539 (409)
Seq/√Len:	42.7
META:	0.382

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_F	34_L	2.800	1.00
86_K	90_E	2.795	1.00
80_E	83_K	2.597	1.00
82_A	85_Q	2.536	1.00
74_E	80_E	2.373	1.00
35_Q	76_A	2.314	1.00
56_D	70_H	2.228	1.00
22_E	26_Q	2.224	1.00
64_K	68_D	2.114	0.99
48_K	52_F	1.957	0.99
17_F	21_L	1.884	0.99
63_P	66_V	1.817	0.98
5_P	9_C	1.814	0.98
24_K	29_H	1.769	0.98
47_E	51_E	1.624	0.97
73_P	76_A	1.615	0.96
39_A	48_K	1.606	0.96
19_R	22_E	1.548	0.95
33_K	40_F	1.545	0.95
4_S	9_C	1.544	0.95
50_V	57_E	1.489	0.94
29_H	35_Q	1.486	0.94
40_F	61_N	1.436	0.93
84_A	87_R	1.401	0.92
42_N	45_L	1.363	0.91
78_Y	82_A	1.306	0.89
14_Q	59_G	1.292	0.89
20_F	30_F	1.292	0.89
45_L	61_N	1.266	0.88
9_C	14_Q	1.264	0.88
49_L	53_V	1.255	0.87
72_F	76_A	1.251	0.87
20_F	29_H	1.237	0.86
69_P	72_F	1.224	0.86
7_G	81_L	1.223	0.86
45_L	49_L	1.221	0.86
71_G	74_E	1.221	0.86
46_L	61_N	1.220	0.86
31_N	49_L	1.169	0.83
39_A	52_F	1.103	0.79
44_S	49_L	1.071	0.77
18_A	84_A	1.069	0.77
46_L	50_V	1.069	0.77
19_R	52_F	1.033	0.75
32_E	71_G	1.029	0.74
86_K	89_M	1.020	0.74
24_K	30_F	1.019	0.74
5_P	66_V	1.019	0.74
17_F	30_F	1.016	0.73
29_H	53_V	1.011	0.73
33_K	37_S	0.988	0.71
20_F	60_T	0.982	0.71
27_G	91_K	0.979	0.71
83_K	87_R	0.956	0.69
4_S	17_F	0.947	0.68
15_A	90_E	0.944	0.68
3_P	79_E	0.940	0.68
49_L	52_F	0.931	0.67
41_R	45_L	0.919	0.66
29_H	34_L	0.917	0.66
18_A	22_E	0.892	0.63
23_L	29_H	0.879	0.62
23_L	58_Y	0.871	0.62
47_E	82_A	0.856	0.60
13_L	59_G	0.854	0.60
20_F	23_L	0.852	0.60
67_W	71_G	0.839	0.59
47_E	80_E	0.833	0.58
16_K	49_L	0.830	0.58
15_A	47_E	0.822	0.57
47_E	61_N	0.820	0.57
58_Y	62_L	0.808	0.56
10_D	36_S	0.803	0.55
53_V	91_K	0.775	0.53
24_K	60_T	0.773	0.52
4_S	8_S	0.773	0.52
58_Y	77_Y	0.767	0.52
41_R	49_L	0.755	0.51
55_I	59_G	0.744	0.50
82_A	86_K	0.743	0.50
6_P	25_K	0.740	0.49
13_L	16_K	0.729	0.48
60_T	69_P	0.729	0.48
30_F	53_V	0.729	0.48
29_H	49_L	0.728	0.48
49_L	76_A	0.725	0.48
4_S	64_K	0.712	0.47
39_A	45_L	0.708	0.46
38_K	59_G	0.707	0.46
56_D	59_G	0.691	0.45
2_P	13_L	0.679	0.44
7_G	51_E	0.677	0.43
89_M	92_R	0.674	0.43
45_L	50_V	0.670	0.43
1_I	18_A	0.668	0.43
19_R	51_E	0.664	0.42
30_F	33_K	0.663	0.42
40_F	85_Q	0.656	0.41
28_V	87_R	0.644	0.40
50_V	53_V	0.642	0.40
60_T	67_W	0.641	0.40
80_E	84_A	0.638	0.40
87_R	90_E	0.636	0.40
64_K	70_H	0.633	0.39
37_S	59_G	0.630	0.39
32_E	57_E	0.625	0.39
12_A	58_Y	0.623	0.38
8_S	13_L	0.618	0.38
34_L	53_V	0.607	0.37
87_R	91_K	0.605	0.37
46_L	60_T	0.605	0.37
27_G	38_K	0.599	0.36
1_I	37_S	0.596	0.36
15_A	82_A	0.594	0.36
20_F	34_L	0.590	0.36
16_K	52_F	0.580	0.35
31_N	34_L	0.573	0.34
16_K	21_L	0.569	0.34
84_A	88_E	0.568	0.34
50_V	67_W	0.562	0.33
57_E	78_Y	0.558	0.33
36_S	74_E	0.547	0.32
59_G	66_V	0.544	0.32
51_E	64_K	0.543	0.32
1_I	71_G	0.542	0.32
46_L	57_E	0.536	0.31
39_A	49_L	0.533	0.31
18_A	91_K	0.533	0.31
83_K	86_K	0.530	0.31
66_V	69_P	0.529	0.30
28_V	33_K	0.525	0.30
30_F	77_Y	0.524	0.30
7_G	60_T	0.520	0.30
64_K	92_R	0.516	0.29
11_P	45_L	0.515	0.29
41_R	46_L	0.505	0.29
67_W	92_R	0.502	0.28
38_K	50_V	0.500	0.28

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
1ux5A	2	0.9043	23.4	0.899	Contact Map
1v9dA	3	0.883	10.6	0.914	Contact Map
3obvE	2	0.9255	8.8	0.917	Contact Map
3p1aA	1	0.4574	7.5	0.919	Contact Map
4u4cA	1	0.383	6.9	0.921	Contact Map
4yodA	1	0.8723	5.7	0.924	Contact Map
4qu4A	1	0.3191	5.6	0.924	Contact Map
4a4zA	1	0.383	5.5	0.924	Contact Map
2j1dG	2	0.9255	5.3	0.925	Contact Map
1ry2A	1	0.3511	5.2	0.925	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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