DUF1854 - PFAM28P - GREMLIN Contacts

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DUF1854 - Domain of unknown function (DUF1854)

PFAM:	PF08909	Sequences: HEGVVPVRAFPISAPDEYISLRDADGKELGWIEDLADLPPESRALLEEELARRYFVPEITRILSVSEEFGPSTWEVETDRGPTRFVLRGLEEDIRRLGDGRLLITDVDGNRYLIPDLRALDRKSRRLLERF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	131 (129)
Sequences:	3832 (2806)
Seq/√Len:	247.1
META:	0.936

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_R	47_E	3.481	1.00
63_L	77_E	3.253	1.00
14_A	17_E	2.982	1.00
121_D	124_S	2.960	1.00
39_P	42_S	2.918	1.00
61_R	77_E	2.741	1.00
75_E	82_P	2.669	1.00
76_V	85_F	2.554	1.00
63_L	82_P	2.546	1.00
17_E	34_D	2.545	1.00
6_P	21_L	2.543	1.00
34_D	37_D	2.543	1.00
75_E	84_R	2.523	1.00
116_D	119_A	2.488	1.00
58_E	115_P	2.378	1.00
16_D	47_E	2.373	1.00
77_E	82_P	2.352	1.00
60_T	77_E	2.288	1.00
100_G	116_D	2.186	1.00
44_A	48_E	2.049	1.00
63_L	75_E	1.962	1.00
16_D	36_A	1.902	1.00
40_P	44_A	1.902	1.00
23_D	27_K	1.824	1.00
73_T	86_V	1.811	1.00
64_S	75_E	1.807	1.00
101_R	113_L	1.770	1.00
100_G	118_R	1.748	1.00
20_S	28_E	1.734	1.00
38_L	46_L	1.551	1.00
78_T	81_G	1.499	1.00
61_R	121_D	1.445	1.00
18_Y	31_W	1.433	1.00
6_P	46_L	1.428	1.00
33_E	37_D	1.427	1.00
67_E	72_S	1.416	1.00
42_S	45_L	1.416	1.00
59_I	76_V	1.401	1.00
21_L	32_I	1.391	1.00
41_E	44_A	1.375	1.00
6_P	19_I	1.365	1.00
49_E	52_R	1.355	1.00
9_A	31_W	1.308	1.00
73_T	84_R	1.306	1.00
44_A	47_E	1.265	1.00
123_K	127_L	1.229	1.00
58_E	113_L	1.212	1.00
88_R	93_D	1.163	1.00
17_E	33_E	1.149	1.00
89_G	92_E	1.147	1.00
3_G	24_A	1.125	1.00
105_T	111_R	1.084	1.00
32_I	37_D	1.070	1.00
60_T	79_D	1.057	1.00
35_L	46_L	1.029	1.00
87_L	104_I	1.027	1.00
61_R	124_S	0.983	1.00
58_E	79_D	0.977	1.00
125_R	129_E	0.971	1.00
62_I	127_L	0.967	1.00
64_S	127_L	0.962	1.00
83_T	108_D	0.944	1.00
68_E	73_T	0.940	1.00
7_V	22_R	0.939	1.00
74_W	85_F	0.935	1.00
8_R	50_L	0.913	1.00
45_L	48_E	0.907	1.00
71_P	86_V	0.902	1.00
98_G	101_R	0.894	1.00
97_L	103_L	0.885	1.00
23_D	29_L	0.881	1.00
32_I	38_L	0.879	1.00
57_P	79_D	0.873	0.99
40_P	43_R	0.856	0.99
40_P	47_E	0.836	0.99
76_V	83_T	0.834	0.99
5_V	26_G	0.830	0.99
45_L	49_E	0.827	0.99
74_W	87_L	0.808	0.99
60_T	63_L	0.806	0.99
106_D	110_N	0.792	0.99
56_V	113_L	0.787	0.99
65_V	127_L	0.783	0.99
100_G	117_L	0.774	0.99
106_D	113_L	0.772	0.99
56_V	106_D	0.771	0.99
72_S	91_E	0.768	0.99
49_E	53_R	0.768	0.99
2_E	5_V	0.758	0.99
62_I	128_L	0.758	0.99
57_P	80_R	0.749	0.98
70_G	86_V	0.746	0.98
104_I	114_I	0.728	0.98
62_I	124_S	0.726	0.98
38_L	42_S	0.719	0.98
19_I	50_L	0.716	0.98
117_L	125_R	0.714	0.98
106_D	129_E	0.704	0.98
54_Y	110_N	0.702	0.98
102_L	114_I	0.699	0.98
23_D	26_G	0.696	0.97
101_R	115_P	0.688	0.97
21_L	29_L	0.687	0.97
7_V	53_R	0.686	0.97
88_R	107_V	0.685	0.97
12_I	111_R	0.675	0.97
106_D	112_Y	0.666	0.97
60_T	82_P	0.663	0.97
35_L	43_R	0.663	0.97
2_E	24_A	0.654	0.96
88_R	91_E	0.653	0.96
59_I	112_Y	0.650	0.96
67_E	93_D	0.648	0.96
114_I	117_L	0.644	0.96
26_G	80_R	0.640	0.96
9_A	15_P	0.639	0.96
8_R	16_D	0.638	0.96
48_E	52_R	0.627	0.95
47_E	51_A	0.623	0.95
85_F	107_V	0.617	0.95
18_Y	33_E	0.610	0.95
69_F	107_V	0.606	0.94
9_A	18_Y	0.604	0.94
125_R	128_L	0.604	0.94
56_V	129_E	0.603	0.94
16_D	34_D	0.603	0.94
73_T	99_D	0.601	0.94
123_K	126_R	0.599	0.94
126_R	129_E	0.599	0.94
122_R	125_R	0.597	0.94
95_R	128_L	0.594	0.94
56_V	103_L	0.592	0.94
122_R	127_L	0.589	0.94
18_Y	22_R	0.588	0.94
94_I	128_L	0.586	0.93
68_E	89_G	0.586	0.93
75_E	85_F	0.585	0.93
35_L	38_L	0.582	0.93
44_A	119_A	0.579	0.93
31_W	54_Y	0.578	0.93
87_L	96_R	0.577	0.93
72_S	89_G	0.575	0.93
87_L	94_I	0.570	0.93
51_A	79_D	0.568	0.92
8_R	19_I	0.566	0.92
96_R	102_L	0.565	0.92
83_T	87_L	0.563	0.92
68_E	127_L	0.563	0.92
56_V	69_F	0.563	0.92
84_R	107_V	0.562	0.92
101_R	117_L	0.562	0.92
88_R	101_R	0.561	0.92
53_R	109_G	0.561	0.92
4_V	85_F	0.561	0.92
65_V	70_G	0.559	0.92
10_F	13_S	0.559	0.92
87_L	109_G	0.556	0.92
53_R	86_V	0.555	0.91
56_V	68_E	0.554	0.91
31_W	66_S	0.549	0.91
93_D	129_E	0.549	0.91
66_S	73_T	0.548	0.91
55_F	113_L	0.547	0.91
91_E	108_D	0.542	0.91
74_W	104_I	0.539	0.90
41_E	47_E	0.535	0.90
67_E	89_G	0.533	0.90
39_P	43_R	0.531	0.90
49_E	56_V	0.530	0.90
6_P	49_E	0.529	0.89
87_L	91_E	0.526	0.89
87_L	102_L	0.524	0.89
12_I	22_R	0.524	0.89
69_F	110_N	0.523	0.89
46_L	89_G	0.523	0.89
59_I	85_F	0.522	0.89
52_R	110_N	0.522	0.89
99_D	117_L	0.520	0.89
86_V	107_V	0.518	0.88
101_R	111_R	0.518	0.88
1_H	29_L	0.518	0.88
35_L	47_E	0.515	0.88
65_V	74_W	0.513	0.88
58_E	122_R	0.513	0.88
24_A	33_E	0.512	0.88
74_W	81_G	0.512	0.88
34_D	42_S	0.510	0.88
54_Y	91_E	0.510	0.88
87_L	95_R	0.510	0.88
99_D	111_R	0.506	0.87
2_E	6_P	0.506	0.87
117_L	120_L	0.503	0.87
54_Y	70_G	0.503	0.87
14_A	18_Y	0.500	0.87

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
3pgvA	3	0.2366	27.1	0.923	Contact Map
3pcoA	2	0.6489	17.3	0.93	Contact Map
3daoA	1	0.313	16.3	0.931	Contact Map
4p72C	2	0.6489	10.9	0.936	Contact Map
3u1wA	3	0.8626	10.1	0.937	Contact Map
1b7yA	2	0.7099	8.5	0.939	Contact Map
1xy7A	2	0.2519	8.2	0.94	Contact Map
3itwA	4	0.313	6.1	0.943	Contact Map
2qvwA	3	0.5038	5.6	0.944	Contact Map
1xmkA	1	0.5344	4.5	0.946	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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