DUF3054 - PFAM28P - GREMLIN Contacts

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DUF3054 - Protein of unknown function (DUF3054)

PFAM:	PF11255	Sequences: AAGDVLAVLVFVAIGRASHGEGLSLAGVLRTAWPFLAGLAVGWLLVAPLYRPARAWRRPPALWRTGVVVWLVTVPVGMLLRALFGQGTAPSFVVVALVFLALFLLGWRALA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (105)
Sequences:	3838 (2749)
Seq/√Len:	268.3
META:	0.823

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
99_F	103_F	3.091	1.00
94_V	98_V	2.861	1.00
70_W	101_A	2.833	1.00
74_V	97_L	2.562	1.00
7_A	103_F	2.549	1.00
90_P	94_V	2.354	1.00
78_M	93_V	2.229	1.00
82_A	85_G	2.191	1.00
38_G	72_V	2.187	1.00
3_G	107_W	2.132	1.00
33_W	84_F	2.049	1.00
38_G	76_V	2.009	1.00
5_V	36_L	1.979	1.00
8_V	100_L	1.959	1.00
72_V	75_P	1.939	1.00
32_A	36_L	1.924	1.00
8_V	39_L	1.916	1.00
41_V	76_V	1.847	1.00
16_R	21_E	1.772	1.00
27_G	31_T	1.688	1.00
99_F	102_L	1.648	1.00
16_R	31_T	1.511	1.00
42_G	46_V	1.492	1.00
88_T	93_V	1.461	1.00
91_S	95_V	1.461	1.00
98_V	102_L	1.441	1.00
59_P	62_L	1.415	1.00
82_A	86_Q	1.364	1.00
101_A	105_L	1.359	1.00
16_R	27_G	1.354	1.00
86_Q	89_A	1.282	1.00
9_L	32_A	1.252	1.00
18_S	21_E	1.241	1.00
33_W	37_A	1.225	1.00
53_A	68_V	1.201	1.00
82_A	88_T	1.193	1.00
78_M	96_A	1.183	1.00
62_L	65_T	1.149	1.00
54_R	57_R	1.115	1.00
64_R	68_V	1.089	1.00
13_A	28_V	1.072	1.00
61_A	64_R	1.040	1.00
23_L	28_V	1.037	1.00
97_L	101_A	1.013	1.00
89_A	93_V	1.009	1.00
42_G	72_V	1.008	1.00
39_L	43_W	0.978	1.00
59_P	64_R	0.969	1.00
42_G	73_T	0.965	1.00
11_F	96_A	0.954	1.00
91_S	94_V	0.945	1.00
74_V	78_M	0.943	1.00
20_G	24_S	0.942	1.00
69_V	72_V	0.941	1.00
77_G	96_A	0.940	1.00
60_P	64_R	0.936	1.00
66_G	69_V	0.928	1.00
53_A	56_W	0.924	1.00
12_V	32_A	0.922	1.00
95_V	99_F	0.922	1.00
70_W	100_L	0.917	1.00
70_W	104_L	0.904	1.00
65_T	69_V	0.902	1.00
62_L	105_L	0.902	1.00
80_L	84_F	0.901	1.00
13_A	17_A	0.892	1.00
69_V	73_T	0.889	1.00
10_V	14_I	0.877	1.00
17_A	28_V	0.868	1.00
20_G	23_L	0.847	1.00
39_L	73_T	0.846	1.00
97_L	100_L	0.843	1.00
26_A	29_L	0.843	1.00
74_V	96_A	0.840	1.00
67_V	71_L	0.835	0.99
63_W	67_V	0.833	0.99
100_L	104_L	0.832	0.99
90_P	93_V	0.828	0.99
31_T	86_Q	0.824	0.99
15_G	81_R	0.820	0.99
55_A	65_T	0.819	0.99
80_L	83_L	0.816	0.99
11_F	103_F	0.814	0.99
85_G	88_T	0.812	0.99
37_A	84_F	0.810	0.99
17_A	21_E	0.795	0.99
37_A	80_L	0.786	0.99
11_F	16_R	0.778	0.99
22_G	28_V	0.777	0.99
84_F	88_T	0.775	0.99
7_A	104_L	0.768	0.99
25_L	28_V	0.755	0.99
7_A	10_V	0.754	0.99
2_A	6_L	0.752	0.99
19_H	92_F	0.741	0.99
14_I	18_S	0.740	0.99
29_L	33_W	0.739	0.99
7_A	107_W	0.736	0.99
74_V	100_L	0.730	0.99
65_T	68_V	0.726	0.99
82_A	87_G	0.723	0.99
67_V	70_W	0.718	0.98
5_V	44_L	0.717	0.98
37_A	40_A	0.709	0.98
35_F	77_G	0.702	0.98
15_G	19_H	0.690	0.98
46_V	49_L	0.688	0.98
17_A	24_S	0.688	0.98
12_V	74_V	0.682	0.98
62_L	66_G	0.679	0.98
63_W	105_L	0.675	0.98
12_V	28_V	0.674	0.98
79_L	82_A	0.666	0.97
75_P	79_L	0.661	0.97
46_V	72_V	0.659	0.97
27_G	30_R	0.659	0.97
11_F	19_H	0.658	0.97
64_R	67_V	0.658	0.97
100_L	103_F	0.656	0.97
78_M	88_T	0.648	0.97
53_A	57_R	0.648	0.97
8_V	36_L	0.644	0.97
85_G	89_A	0.642	0.97
3_G	60_P	0.639	0.97
43_W	55_A	0.638	0.97
71_L	97_L	0.637	0.97
45_L	49_L	0.619	0.96
6_L	10_V	0.618	0.96
23_L	26_A	0.615	0.96
91_S	99_F	0.611	0.96
30_R	33_W	0.609	0.96
33_W	42_G	0.606	0.96
16_R	28_V	0.605	0.96
71_L	75_P	0.603	0.95
9_L	28_V	0.595	0.95
72_V	76_V	0.589	0.95
14_I	99_F	0.586	0.95
68_V	72_V	0.581	0.94
91_S	97_L	0.575	0.94
68_V	71_L	0.562	0.93
12_V	17_A	0.562	0.93
104_L	107_W	0.562	0.93
17_A	20_G	0.561	0.93
11_F	14_I	0.560	0.93
96_A	99_F	0.555	0.93
57_R	60_P	0.543	0.92
12_V	77_G	0.541	0.92
46_V	54_R	0.540	0.92
44_L	48_P	0.533	0.92
66_G	105_L	0.531	0.91
33_W	106_G	0.527	0.91
92_F	95_V	0.527	0.91
64_R	105_L	0.520	0.91
36_L	44_L	0.516	0.90
5_V	39_L	0.510	0.90
56_W	65_T	0.507	0.89
31_T	34_P	0.504	0.89
10_V	13_A	0.500	0.89

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
4r0cA	3	0.5225	1.2	0.932	Contact Map
1fl2A	2	0.3333	1	0.936	Contact Map
1hr0W	1	0.2162	1	0.936	Contact Map
1hyuA	2	0.3333	1	0.936	Contact Map
2lotA	1	0.1982	0.9	0.937	Contact Map
4uc1A	3	0.5225	0.9	0.937	Contact Map
4ql5A	4	0.2252	0.9	0.938	Contact Map
4p02A	1	0.6757	0.9	0.938	Contact Map
2ksfA	1	0.4865	0.8	0.939	Contact Map
1xioA	2	0.2162	0.8	0.939	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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