DUF4240 - PFAM28P - GREMLIN Contacts

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DUF4240 - Protein of unknown function (DUF4240)

PFAM:	PF14024	Sequences: MDEDEFWELIERARAAAGGDPDEQAEALVERLAKLSPEEIVAFDRIFDELLARAYTWDLWAAAYIINGGCSDDGFLYFRCWLIAQGREVYEAALADPDSLADLPDVEDDDEDLEFEELLYVASEAYER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	128 (124)
Sequences:	3903 (3073)
Seq/√Len:	276.0
META:	0.831

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
87_R	91_E	3.684	1.00
56_T	59_L	2.640	1.00
13_A	24_Q	2.449	1.00
50_L	53_R	2.343	1.00
81_W	85_Q	2.312	1.00
12_R	31_R	2.257	1.00
44_D	48_D	2.240	1.00
116_E	120_Y	2.149	1.00
46_I	50_L	2.059	1.00
73_D	77_Y	2.028	1.00
84_A	118_L	2.013	1.00
3_E	50_L	1.956	1.00
40_I	125_A	1.948	1.00
63_A	70_C	1.878	1.00
54_A	82_L	1.808	1.00
80_C	119_L	1.761	1.00
4_D	87_R	1.710	1.00
55_Y	79_R	1.700	1.00
42_A	46_I	1.676	1.00
51_L	80_C	1.642	1.00
47_F	80_C	1.636	1.00
93_A	99_S	1.621	1.00
57_W	61_A	1.613	1.00
35_L	39_E	1.612	1.00
36_S	39_E	1.586	1.00
31_R	34_K	1.571	1.00
60_W	70_C	1.543	1.00
29_V	33_A	1.537	1.00
46_I	49_E	1.526	1.00
50_L	90_Y	1.516	1.00
29_V	125_A	1.477	1.00
75_F	79_R	1.405	1.00
51_L	76_L	1.384	1.00
3_E	53_R	1.379	1.00
64_Y	69_G	1.374	1.00
54_A	59_L	1.364	1.00
54_A	90_Y	1.350	1.00
2_D	5_E	1.345	1.00
49_E	53_R	1.344	1.00
29_V	124_E	1.334	1.00
14_R	24_Q	1.269	1.00
27_A	31_R	1.248	1.00
50_L	91_E	1.233	1.00
5_E	35_L	1.210	1.00
121_V	125_A	1.198	1.00
21_P	115_F	1.194	1.00
11_E	14_R	1.186	1.00
88_E	92_A	1.174	1.00
3_E	46_I	1.166	1.00
77_Y	114_E	1.136	1.00
62_A	98_D	1.127	1.00
89_V	100_L	1.111	1.00
9_L	28_L	1.106	1.00
53_R	90_Y	1.085	1.00
54_A	94_L	1.080	1.00
32_L	40_I	1.068	1.00
51_L	83_I	1.062	1.00
77_Y	116_E	1.060	1.00
8_E	12_R	1.057	1.00
44_D	122_A	1.057	1.00
98_D	101_A	1.036	1.00
39_E	42_A	1.031	1.00
67_N	74_G	1.013	1.00
92_A	99_S	1.011	1.00
84_A	115_F	1.000	1.00
96_D	99_S	0.993	1.00
25_A	115_F	0.988	1.00
33_A	125_A	0.984	1.00
37_P	40_I	0.981	1.00
28_L	121_V	0.977	1.00
28_L	43_F	0.976	1.00
55_Y	60_W	0.974	1.00
85_Q	89_V	0.965	1.00
20_D	23_E	0.963	1.00
62_A	100_L	0.953	1.00
5_E	8_E	0.950	1.00
10_I	118_L	0.933	1.00
59_L	82_L	0.926	1.00
89_V	103_L	0.925	1.00
51_L	79_R	0.920	1.00
47_F	83_I	0.914	1.00
9_L	31_R	0.894	1.00
16_A	27_A	0.889	1.00
72_D	77_Y	0.884	1.00
5_E	39_E	0.884	1.00
54_A	79_R	0.881	1.00
67_N	113_L	0.875	1.00
74_G	114_E	0.865	1.00
76_L	80_C	0.864	1.00
80_C	118_L	0.859	1.00
64_Y	67_N	0.849	1.00
67_N	114_E	0.849	1.00
60_W	75_F	0.839	1.00
6_F	47_F	0.838	1.00
115_F	119_L	0.835	1.00
2_D	46_I	0.834	1.00
89_V	93_A	0.829	1.00
14_R	85_Q	0.827	0.99
76_L	119_L	0.825	0.99
66_I	93_A	0.822	0.99
100_L	103_L	0.819	0.99
71_S	77_Y	0.819	0.99
30_E	34_K	0.817	0.99
81_W	113_L	0.809	0.99
76_L	79_R	0.794	0.99
60_W	63_A	0.791	0.99
65_I	98_D	0.790	0.99
53_R	91_E	0.783	0.99
104_P	107_E	0.770	0.99
13_A	28_L	0.767	0.99
37_P	41_V	0.766	0.99
66_I	113_L	0.755	0.99
60_W	69_G	0.752	0.99
24_Q	84_A	0.747	0.99
13_A	27_A	0.746	0.99
77_Y	80_C	0.740	0.99
83_I	90_Y	0.733	0.99
115_F	118_L	0.727	0.99
55_Y	76_L	0.722	0.99
31_R	35_L	0.719	0.99
25_A	29_V	0.707	0.98
92_A	102_D	0.705	0.98
37_P	126_Y	0.696	0.98
3_E	49_E	0.681	0.98
26_E	29_V	0.679	0.98
117_E	120_Y	0.674	0.98
78_F	81_W	0.674	0.98
21_P	25_A	0.673	0.98
40_I	122_A	0.673	0.98
53_R	94_L	0.672	0.98
25_A	121_V	0.670	0.98
82_L	93_A	0.669	0.98
71_S	74_G	0.667	0.98
29_V	121_V	0.664	0.98
60_W	64_Y	0.660	0.98
44_D	47_F	0.658	0.98
59_L	62_A	0.656	0.97
124_E	127_E	0.654	0.97
16_A	31_R	0.634	0.97
6_F	46_I	0.634	0.97
73_D	116_E	0.628	0.97
14_R	17_A	0.620	0.96
77_Y	120_Y	0.618	0.96
1_M	32_L	0.612	0.96
24_Q	85_Q	0.612	0.96
3_E	91_E	0.611	0.96
92_A	103_L	0.611	0.96
61_A	65_I	0.609	0.96
82_L	100_L	0.604	0.96
11_E	87_R	0.602	0.96
78_F	100_L	0.601	0.96
18_G	23_E	0.597	0.96
63_A	69_G	0.596	0.96
36_S	40_I	0.594	0.95
61_A	68_G	0.592	0.95
120_Y	124_E	0.587	0.95
21_P	24_Q	0.587	0.95
4_D	8_E	0.586	0.95
17_A	27_A	0.585	0.95
45_R	49_E	0.584	0.95
117_E	124_E	0.583	0.95
42_A	45_R	0.579	0.95
51_L	54_A	0.573	0.95
104_P	113_L	0.566	0.94
63_A	74_G	0.563	0.94
106_V	112_D	0.562	0.94
52_A	55_Y	0.561	0.94
56_T	94_L	0.561	0.94
47_F	119_L	0.561	0.94
59_L	93_A	0.558	0.94
38_E	42_A	0.552	0.93
77_Y	119_L	0.538	0.92
91_E	95_A	0.537	0.92
5_E	9_L	0.535	0.92
24_Q	81_W	0.523	0.91
59_L	97_P	0.520	0.91
64_Y	70_C	0.518	0.91
11_E	15_A	0.513	0.91
92_A	95_A	0.510	0.90
85_Q	103_L	0.509	0.90
15_A	95_A	0.506	0.90
62_A	97_P	0.505	0.90
54_A	76_L	0.504	0.90
69_G	72_D	0.501	0.90
78_F	98_D	0.500	0.89
120_Y	123_S	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
1pueE	1	0.5391	17.2	0.896	Contact Map
3m8jA	2	0.5547	11.5	0.904	Contact Map
1awcA	1	0.5078	10	0.907	Contact Map
4co8A	2	0.5391	8.3	0.91	Contact Map
3nehA	1	0.9297	8	0.911	Contact Map
2i5gA	2	0.9531	6.3	0.915	Contact Map
1hbxG	1	0.5312	5.7	0.917	Contact Map
2l08A	1	0.5312	5	0.919	Contact Map
1yo5C	1	0.5234	4.8	0.919	Contact Map
1bc8C	1	0.5391	4.8	0.92	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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