DUF2958 - PFAM28P - GREMLIN Contacts

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DUF2958 - Protein of unknown function (DUF2958)

PFAM:	PF11171	Sequences: LLTKEIRKKLLANGSQSAEGPEKDPVPVVKLFTPDGAATWLLTELDPEDGDIAFGLCDLGFGEPELGYVSLSELESVRGPLGLPIERDLYFKPTKPLSEYAEAARRAGRIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (101)
Sequences:	4026 (2658)
Seq/√Len:	264.5
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_T	36_G	2.963	1.00
42_L	69_V	2.960	1.00
35_D	79_G	2.849	1.00
51_D	72_S	2.535	1.00
35_D	84_P	2.240	1.00
33_T	79_G	2.089	1.00
22_E	25_P	2.051	1.00
33_T	38_A	2.043	1.00
33_T	85_I	1.993	1.00
95_K	99_E	1.940	1.00
58_D	62_G	1.898	1.00
58_D	64_P	1.883	1.00
42_L	53_A	1.877	1.00
30_K	39_T	1.875	1.00
57_C	69_V	1.860	1.00
35_D	81_L	1.807	1.00
17_S	25_P	1.762	1.00
45_L	53_A	1.745	1.00
3_T	6_I	1.723	1.00
93_P	100_Y	1.718	1.00
4_K	7_R	1.665	1.00
56_L	64_P	1.596	1.00
38_A	59_L	1.566	1.00
52_I	68_Y	1.540	1.00
53_A	71_L	1.472	1.00
66_L	97_L	1.436	1.00
4_K	8_K	1.397	1.00
31_L	85_I	1.367	1.00
43_T	66_L	1.307	1.00
78_R	84_P	1.306	1.00
7_R	45_L	1.296	1.00
27_P	43_T	1.274	1.00
96_P	99_E	1.273	1.00
7_R	11_L	1.257	1.00
11_L	14_G	1.222	1.00
14_G	17_S	1.174	1.00
31_L	42_L	1.169	1.00
51_D	70_S	1.166	1.00
16_Q	19_E	1.162	1.00
53_A	69_V	1.152	1.00
47_P	50_G	1.135	1.00
33_T	37_A	1.132	1.00
54_F	68_Y	1.130	1.00
59_L	62_G	1.128	1.00
11_L	15_S	1.121	1.00
46_D	50_G	1.116	1.00
26_V	93_P	1.067	1.00
31_L	53_A	1.054	1.00
2_L	7_R	1.038	1.00
20_G	25_P	1.023	1.00
50_G	72_S	1.021	1.00
35_D	83_L	1.013	1.00
72_S	76_S	1.002	1.00
44_E	54_F	0.970	1.00
9_K	28_V	0.968	1.00
2_L	71_L	0.963	1.00
5_E	9_K	0.954	1.00
6_I	9_K	0.948	1.00
33_T	80_P	0.939	1.00
26_V	96_P	0.939	1.00
8_K	12_A	0.939	1.00
45_L	50_G	0.936	1.00
52_I	70_S	0.927	1.00
79_G	84_P	0.923	1.00
2_L	31_L	0.914	1.00
19_E	22_E	0.910	1.00
49_D	52_I	0.904	1.00
17_S	20_G	0.903	1.00
20_G	23_K	0.898	1.00
70_S	73_E	0.898	1.00
71_L	75_E	0.881	1.00
25_P	43_T	0.856	1.00
38_A	61_F	0.851	1.00
54_F	66_L	0.848	1.00
46_D	68_Y	0.832	0.99
47_P	52_I	0.822	0.99
46_D	52_I	0.820	0.99
11_L	45_L	0.812	0.99
6_I	29_V	0.810	0.99
12_A	15_S	0.806	0.99
21_P	25_P	0.792	0.99
10_L	13_N	0.790	0.99
27_P	41_L	0.787	0.99
45_L	52_I	0.779	0.99
28_V	93_P	0.768	0.99
16_Q	25_P	0.766	0.99
55_G	58_D	0.759	0.99
33_T	84_P	0.757	0.99
81_L	84_P	0.755	0.99
37_A	59_L	0.744	0.99
95_K	100_Y	0.731	0.99
17_S	22_E	0.731	0.99
34_P	83_L	0.723	0.98
56_L	66_L	0.712	0.98
79_G	83_L	0.709	0.98
55_G	69_V	0.709	0.98
34_P	79_G	0.691	0.98
33_T	77_V	0.690	0.98
18_A	21_P	0.689	0.98
73_E	76_S	0.685	0.98
25_P	98_S	0.678	0.98
35_D	80_P	0.676	0.98
40_W	69_V	0.673	0.98
4_K	9_K	0.673	0.98
30_K	88_D	0.671	0.97
58_D	61_F	0.667	0.97
31_L	74_L	0.666	0.97
57_C	64_P	0.658	0.97
6_I	10_L	0.653	0.97
91_F	94_T	0.648	0.97
77_V	80_P	0.648	0.97
43_T	97_L	0.644	0.97
32_F	86_E	0.635	0.96
37_A	62_G	0.633	0.96
9_K	13_N	0.631	0.96
72_S	75_E	0.624	0.96
74_L	85_I	0.617	0.96
29_V	42_L	0.609	0.96
26_V	94_T	0.607	0.95
33_T	81_L	0.604	0.95
41_L	64_P	0.596	0.95
12_A	16_Q	0.594	0.95
41_L	58_D	0.589	0.95
13_N	16_Q	0.585	0.94
53_A	57_C	0.580	0.94
19_E	25_P	0.576	0.94
35_D	78_R	0.576	0.94
33_T	83_L	0.574	0.94
35_D	77_V	0.571	0.94
58_D	63_E	0.569	0.94
6_I	87_R	0.569	0.94
27_P	64_P	0.567	0.94
32_F	39_T	0.565	0.93
69_V	74_L	0.561	0.93
17_S	23_K	0.559	0.93
42_L	45_L	0.557	0.93
17_S	44_E	0.550	0.92
27_P	56_L	0.549	0.92
24_D	98_S	0.547	0.92
98_S	101_A	0.546	0.92
65_E	73_E	0.541	0.92
10_L	14_G	0.538	0.92
25_P	96_P	0.528	0.91
83_L	86_E	0.526	0.91
8_K	11_L	0.515	0.90
10_L	42_L	0.513	0.90
2_L	6_I	0.510	0.89
92_K	95_K	0.504	0.89
43_T	56_L	0.504	0.89
16_Q	23_K	0.502	0.89
25_P	66_L	0.501	0.89
93_P	96_P	0.500	0.88

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
2pd0A	2	0.8919	11.1	0.922	Contact Map
1sraA	1	0.9099	8.2	0.927	Contact Map
4r8aA	1	0.964	8	0.927	Contact Map
2pgsA	4	0.7928	5.9	0.932	Contact Map
2wyaA	2	0.4414	5.3	0.933	Contact Map
2f82A	2	0.4865	5	0.934	Contact Map
2p8uA	2	0.4865	4.3	0.936	Contact Map
3mlnA	2	0.7658	4.2	0.936	Contact Map
3sqzA	2	0.4324	4.1	0.936	Contact Map
1y6zA	2	0.9369	3.8	0.937	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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