Usg - PFAM28P - GREMLIN Contacts

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Usg - Usg-like family

PFAM:	PF06233	Sequences: QLKGYGLTTAEILYRMPDHPSLLQSFVWQDYDLAPDFPELRKFLDFWQRELEGPLHSVRVAHARLIKPAEWRAVDGEFRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (79)
Sequences:	4522 (2057)
Seq/√Len:	231.4
META:	0.935

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_E	59_R	3.493	1.00
11_E	25_S	3.354	1.00
63_A	67_K	3.072	1.00
45_D	49_R	2.543	1.00
39_E	42_K	2.539	1.00
26_F	30_D	2.422	1.00
13_L	25_S	2.313	1.00
16_M	21_S	2.258	1.00
15_R	56_H	2.134	1.00
6_G	62_H	2.060	1.00
30_D	39_E	1.984	1.00
20_P	54_P	1.963	1.00
5_Y	33_L	1.922	1.00
45_D	48_Q	1.894	1.00
48_Q	54_P	1.813	1.00
40_L	60_V	1.601	1.00
74_V	77_E	1.572	1.00
30_D	40_L	1.567	1.00
12_I	44_L	1.563	1.00
67_K	70_E	1.537	1.00
48_Q	55_L	1.519	1.00
15_R	21_S	1.422	1.00
36_D	41_R	1.365	1.00
26_F	51_L	1.290	1.00
37_F	62_H	1.275	1.00
73_A	76_G	1.222	1.00
30_D	55_L	1.210	1.00
23_L	56_H	1.193	1.00
64_R	67_K	1.186	1.00
44_L	58_V	1.178	1.00
42_K	45_D	1.160	1.00
46_F	50_E	1.108	1.00
41_R	45_D	1.105	1.00
5_Y	39_E	1.097	1.00
16_M	22_L	1.071	1.00
10_A	40_L	1.050	1.00
15_R	53_G	1.050	1.00
6_G	11_E	1.030	1.00
9_T	27_V	0.998	1.00
15_R	54_P	0.983	1.00
15_R	23_L	0.959	1.00
65_L	68_P	0.945	1.00
70_E	73_A	0.942	1.00
8_T	62_H	0.900	0.99
2_L	63_A	0.878	0.99
30_D	62_H	0.868	0.99
65_L	70_E	0.839	0.99
13_L	23_L	0.835	0.99
72_R	76_G	0.833	0.99
41_R	48_Q	0.815	0.99
73_A	77_E	0.812	0.99
16_M	20_P	0.788	0.99
75_D	79_R	0.785	0.99
10_A	28_W	0.779	0.98
33_L	39_E	0.762	0.98
70_E	77_E	0.743	0.98
71_W	76_G	0.740	0.98
34_A	37_F	0.728	0.98
4_G	62_H	0.718	0.97
66_I	70_E	0.716	0.97
1_Q	66_I	0.711	0.97
24_Q	37_F	0.703	0.97
33_L	36_D	0.694	0.97
5_Y	8_T	0.692	0.97
44_L	47_W	0.691	0.97
14_Y	17_P	0.680	0.96
41_R	60_V	0.678	0.96
63_A	73_A	0.677	0.96
26_F	46_F	0.676	0.96
8_T	40_L	0.676	0.96
64_R	70_E	0.662	0.96
15_R	20_P	0.649	0.95
15_R	57_S	0.647	0.95
6_G	34_A	0.643	0.95
43_F	47_W	0.639	0.95
19_H	22_L	0.636	0.95
3_K	11_E	0.632	0.95
67_K	71_W	0.632	0.95
28_W	53_G	0.628	0.95
8_T	37_F	0.621	0.94
33_L	42_K	0.621	0.94
13_L	19_H	0.620	0.94
62_H	65_L	0.615	0.94
13_L	57_S	0.614	0.94
34_A	64_R	0.610	0.94
46_F	53_G	0.604	0.93
32_D	35_P	0.597	0.93
13_L	59_R	0.595	0.93
73_A	78_F	0.594	0.93
12_I	55_L	0.591	0.93
41_R	71_W	0.582	0.92
37_F	60_V	0.582	0.92
61_A	76_G	0.580	0.92
14_Y	18_D	0.579	0.92
12_I	27_V	0.576	0.92
10_A	58_V	0.571	0.91
72_R	75_D	0.563	0.91
1_Q	12_I	0.563	0.91
40_L	53_G	0.558	0.90
12_I	28_W	0.558	0.90
9_T	13_L	0.552	0.90
1_Q	75_D	0.551	0.90
12_I	24_Q	0.547	0.89
59_R	63_A	0.542	0.89
69_A	73_A	0.539	0.89
43_F	46_F	0.535	0.88
28_W	43_F	0.530	0.88
8_T	30_D	0.528	0.88
36_D	39_E	0.524	0.87
10_A	53_G	0.520	0.87
74_V	78_F	0.519	0.87
31_Y	46_F	0.516	0.87
48_Q	53_G	0.515	0.86
71_W	78_F	0.513	0.86
21_S	73_A	0.511	0.86
1_Q	4_G	0.509	0.86
53_G	58_V	0.504	0.85
64_R	69_A	0.500	0.85

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
3u6pA	1	0.575	19.7	0.913	Contact Map
4pd2A	1	0.5625	17.8	0.914	Contact Map
1ee8A	2	0.55	16	0.916	Contact Map
1k82A	1	0.575	13.2	0.919	Contact Map
3vk8A	1	0.5625	11.7	0.921	Contact Map
1k3xA	1	0.5375	10.2	0.923	Contact Map
2je8A	1	0.925	7.7	0.927	Contact Map
4mb1A	1	0.9875	7.1	0.929	Contact Map
1tdhA	1	0.575	6.7	0.929	Contact Map
2ze0A	2	0.9375	6.5	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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