DUF4209 - PFAM28P - GREMLIN Contacts

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DUF4209 - Domain of unknown function (DUF4209)

PFAM:	PF13910	Sequences: IENALRDLLKLAGVPTTKLDRDQEKGLNDLLDDPELKEIFGEDLVFELRALLTDPRGLNLRNEVAHGLLDDDEFNSAYAIYLWWLLLRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	89 (87)
Sequences:	2144 (1766)
Seq/√Len:	189.3
META:	0.877

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_L	14_V	2.861	1.00
59_N	62_N	2.828	1.00
25_K	33_D	2.775	1.00
23_Q	55_P	2.758	1.00
52_L	85_L	2.312	1.00
63_E	73_E	2.227	1.00
37_K	42_E	2.046	1.00
41_G	45_V	2.042	1.00
35_E	38_E	1.980	1.00
25_K	29_D	1.883	1.00
69_L	73_E	1.772	1.00
3_N	7_D	1.737	1.00
5_L	30_L	1.711	1.00
14_V	35_E	1.683	1.00
81_Y	84_W	1.664	1.00
16_T	24_E	1.662	1.00
52_L	82_L	1.661	1.00
51_L	85_L	1.609	1.00
34_P	38_E	1.557	1.00
37_K	45_V	1.545	1.00
32_D	49_R	1.475	1.00
70_D	73_E	1.437	1.00
47_E	84_W	1.432	1.00
36_L	45_V	1.354	1.00
49_R	54_D	1.303	1.00
64_V	69_L	1.290	1.00
23_Q	26_G	1.281	1.00
24_E	68_L	1.262	1.00
36_L	40_F	1.237	1.00
8_L	12_A	1.234	1.00
47_E	81_Y	1.221	1.00
27_L	52_L	1.195	1.00
3_N	67_G	1.177	1.00
31_L	53_T	1.173	1.00
59_N	68_L	1.163	1.00
18_K	23_Q	1.145	1.00
31_L	48_L	1.140	1.00
14_V	33_D	1.137	1.00
31_L	45_V	1.114	1.00
75_N	78_Y	1.094	1.00
80_I	84_W	1.044	1.00
63_E	69_L	1.039	1.00
69_L	74_F	1.024	1.00
37_K	49_R	1.001	0.99
12_A	39_I	0.998	0.99
24_E	28_N	0.991	0.99
45_V	49_R	0.986	0.99
58_L	81_Y	0.975	0.99
28_N	32_D	0.972	0.99
20_D	23_Q	0.948	0.99
31_L	36_L	0.946	0.99
26_G	29_D	0.945	0.99
23_Q	28_N	0.928	0.99
76_S	80_I	0.917	0.99
50_A	58_L	0.915	0.99
12_A	15_P	0.901	0.99
24_E	27_L	0.892	0.99
23_Q	29_D	0.889	0.99
18_K	21_R	0.882	0.99
60_L	82_L	0.881	0.99
26_G	32_D	0.874	0.99
7_D	11_L	0.869	0.99
4_A	7_D	0.865	0.99
19_L	22_D	0.862	0.98
80_I	83_W	0.856	0.98
7_D	10_K	0.835	0.98
18_K	22_D	0.827	0.98
18_K	29_D	0.825	0.98
81_Y	85_L	0.817	0.98
76_S	83_W	0.813	0.98
49_R	53_T	0.792	0.97
29_D	32_D	0.792	0.97
43_D	46_F	0.785	0.97
2_E	5_L	0.776	0.97
57_G	65_A	0.768	0.97
27_L	30_L	0.760	0.97
28_N	53_T	0.756	0.97
10_K	16_T	0.735	0.96
16_T	19_L	0.724	0.96
70_D	74_F	0.717	0.95
64_V	74_F	0.709	0.95
51_L	58_L	0.709	0.95
9_L	12_A	0.700	0.95
49_R	56_R	0.690	0.94
42_E	46_F	0.687	0.94
8_L	40_F	0.672	0.93
51_L	81_Y	0.668	0.93
38_E	60_L	0.662	0.93
33_D	36_L	0.654	0.93
79_A	82_L	0.653	0.92
71_D	75_N	0.649	0.92
53_T	65_A	0.647	0.92
48_L	84_W	0.640	0.92
41_G	44_L	0.636	0.91
46_F	50_A	0.636	0.91
58_L	78_Y	0.626	0.91
40_F	44_L	0.624	0.91
32_D	37_K	0.624	0.91
47_E	65_A	0.622	0.91
17_T	21_R	0.621	0.90
36_L	48_L	0.612	0.90
44_L	50_A	0.611	0.90
30_L	39_I	0.608	0.90
52_L	65_A	0.601	0.89
76_S	79_A	0.599	0.89
51_L	60_L	0.597	0.89
13_G	16_T	0.595	0.89
7_D	12_A	0.593	0.88
55_P	59_N	0.593	0.88
53_T	68_L	0.591	0.88
5_L	40_F	0.580	0.87
47_E	58_L	0.577	0.87
8_L	15_P	0.577	0.87
68_L	81_Y	0.575	0.87
44_L	69_L	0.560	0.85
9_L	33_D	0.554	0.85
36_L	41_G	0.527	0.82
50_A	81_Y	0.526	0.82
6_R	13_G	0.525	0.82
52_L	86_L	0.522	0.81
2_E	6_R	0.519	0.81
58_L	62_N	0.509	0.80
27_L	62_N	0.507	0.79
34_P	37_K	0.506	0.79
21_R	41_G	0.505	0.79
5_L	35_E	0.503	0.79
36_L	63_E	0.502	0.79
59_N	63_E	0.501	0.78
76_S	84_W	0.500	0.78
24_E	65_A	0.500	0.78

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
4rgpA	2	1	56.3	0.826	Contact Map
3ohwB	1	0.5506	19.6	0.864	Contact Map
3osjA	1	0.5506	14.7	0.871	Contact Map
3nphB	1	0.5506	8.7	0.884	Contact Map
3pruC	1	0.6854	7.8	0.887	Contact Map
2ky4A	1	0.6742	6.7	0.89	Contact Map
1js1X	3	0.9775	5.3	0.895	Contact Map
3oq4A	1	0.3483	4.4	0.899	Contact Map
3oq0A	1	0.1685	4.4	0.899	Contact Map
2w37A	5	0.9326	3.7	0.903	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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