DUF2721 - PFAM28P - GREMLIN Contacts

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DUF2721 - Protein of unknown function (DUF2721)

PFAM:	PF11026	Sequences: AVAPAFLLSAIGLLLLVLTNRLARIVDRIRALEAELEALPEDEERRERLLAQLRNLRRRARLIRRAITLGVLSALLFVLTILLLFLGALLGLDLAWLAAVLFILALLLLIASLVLFLREIRLATRALRI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (127)
Sequences:	12532 (8230)
Seq/√Len:	730.3
META:	0.935

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
70_G	112_S	4.297	1.00
69_L	111_A	3.422	1.00
24_R	27_D	3.023	1.00
9_S	13_L	2.926	1.00
16_L	20_N	2.771	1.00
68_T	117_L	2.743	1.00
34_A	38_A	2.490	1.00
75_L	110_I	2.306	1.00
65_R	115_L	2.295	1.00
25_I	63_I	2.252	1.00
31_A	34_A	2.185	1.00
78_V	110_I	2.176	1.00
72_L	108_L	2.104	1.00
31_A	35_E	2.081	1.00
62_L	115_L	2.034	1.00
9_S	16_L	1.782	1.00
18_L	66_A	1.780	1.00
13_L	16_L	1.770	1.00
118_R	121_R	1.713	1.00
83_L	101_L	1.687	1.00
114_V	118_R	1.626	1.00
73_S	109_L	1.618	1.00
77_F	105_A	1.617	1.00
98_A	102_F	1.588	1.00
11_I	73_S	1.566	1.00
58_R	122_L	1.551	1.00
61_R	65_R	1.462	1.00
36_L	50_L	1.454	1.00
76_L	108_L	1.448	1.00
25_I	56_L	1.388	1.00
111_A	115_L	1.354	1.00
11_I	74_A	1.334	1.00
68_T	120_I	1.332	1.00
28_R	31_A	1.309	1.00
23_A	27_D	1.304	1.00
32_L	49_L	1.288	1.00
62_L	118_R	1.280	1.00
57_R	128_R	1.280	1.00
26_V	30_R	1.249	1.00
71_V	117_L	1.242	1.00
75_L	114_V	1.196	1.00
71_V	113_L	1.188	1.00
68_T	121_R	1.173	1.00
50_L	54_R	1.157	1.00
100_V	104_L	1.153	1.00
71_V	116_F	1.143	1.00
115_L	118_R	1.139	1.00
18_L	112_S	1.114	1.00
125_R	128_R	1.105	1.00
25_I	60_A	1.104	1.00
40_P	43_E	1.099	1.00
65_R	68_T	1.098	1.00
29_I	53_L	1.087	1.00
87_G	94_L	1.066	1.00
80_T	98_A	1.059	1.00
76_L	101_L	1.059	1.00
35_E	38_A	1.049	1.00
18_L	70_G	1.037	1.00
99_A	102_F	1.034	1.00
39_L	49_L	1.018	1.00
83_L	97_L	1.016	1.00
80_T	101_L	1.012	1.00
57_R	60_A	1.012	1.00
96_W	100_V	0.993	1.00
107_L	111_A	0.972	1.00
123_A	126_A	0.972	1.00
61_R	128_R	0.970	1.00
93_D	96_W	0.959	1.00
55_N	126_A	0.956	1.00
41_E	45_R	0.929	1.00
103_I	106_L	0.926	1.00
33_E	37_E	0.904	1.00
58_R	62_L	0.899	1.00
41_E	46_R	0.896	1.00
74_A	113_L	0.887	1.00
34_A	37_E	0.884	1.00
17_V	71_V	0.880	1.00
69_L	108_L	0.877	1.00
85_F	103_I	0.876	1.00
19_T	23_A	0.863	1.00
118_R	122_L	0.861	1.00
48_R	52_Q	0.859	1.00
6_F	11_I	0.851	1.00
121_R	125_R	0.846	1.00
13_L	17_V	0.845	1.00
14_L	18_L	0.844	1.00
5_A	10_A	0.842	1.00
2_V	5_A	0.835	1.00
26_V	29_I	0.830	1.00
78_V	109_L	0.830	1.00
51_A	54_R	0.829	1.00
58_R	61_R	0.822	1.00
12_G	16_L	0.805	1.00
58_R	118_R	0.804	1.00
80_T	84_L	0.804	1.00
14_L	109_L	0.797	1.00
96_W	99_A	0.795	1.00
35_E	49_L	0.793	1.00
55_N	58_R	0.791	1.00
99_A	103_I	0.783	1.00
124_T	128_R	0.782	1.00
14_L	74_A	0.778	1.00
42_D	46_R	0.775	1.00
109_L	113_L	0.772	1.00
27_D	31_A	0.771	1.00
48_R	51_A	0.766	1.00
2_V	6_F	0.763	1.00
29_I	33_E	0.760	1.00
57_R	61_R	0.745	1.00
93_D	99_A	0.741	1.00
124_T	127_L	0.740	1.00
47_E	51_A	0.737	1.00
54_R	58_R	0.733	1.00
41_E	44_E	0.730	1.00
82_L	103_I	0.729	1.00
82_L	110_I	0.723	1.00
44_E	47_E	0.712	1.00
42_D	45_R	0.710	1.00
39_L	47_E	0.708	1.00
47_E	50_L	0.708	1.00
46_R	50_L	0.696	1.00
5_A	9_S	0.692	1.00
37_E	43_E	0.690	1.00
46_R	52_Q	0.690	1.00
40_P	45_R	0.689	1.00
76_L	104_L	0.687	1.00
21_R	119_E	0.687	1.00
81_I	106_L	0.686	1.00
118_R	125_R	0.682	1.00
15_L	67_I	0.667	1.00
8_L	74_A	0.666	1.00
8_L	12_G	0.665	1.00
75_L	113_L	0.663	1.00
77_F	80_T	0.662	1.00
10_A	74_A	0.661	1.00
97_L	100_V	0.657	1.00
39_L	44_E	0.648	1.00
5_A	81_I	0.644	1.00
3_A	6_F	0.640	1.00
3_A	77_F	0.639	1.00
73_S	77_F	0.638	1.00
113_L	116_F	0.634	1.00
32_L	56_L	0.629	1.00
14_L	70_G	0.629	1.00
6_F	13_L	0.627	1.00
69_L	115_L	0.625	1.00
15_L	70_G	0.621	1.00
59_R	119_E	0.614	1.00
33_E	53_L	0.612	1.00
23_A	26_V	0.609	1.00
38_A	43_E	0.604	1.00
84_L	88_A	0.599	1.00
37_E	40_P	0.598	1.00
83_L	98_A	0.597	1.00
2_V	9_S	0.595	1.00
39_L	42_D	0.595	1.00
17_V	116_F	0.591	1.00
44_E	50_L	0.588	1.00
110_I	114_V	0.588	1.00
16_L	19_T	0.579	1.00
95_A	99_A	0.578	1.00
94_L	97_L	0.578	1.00
2_V	15_L	0.574	1.00
6_F	81_I	0.570	1.00
64_R	68_T	0.570	1.00
97_L	101_L	0.568	1.00
76_L	105_A	0.566	1.00
20_N	23_A	0.564	1.00
9_S	12_G	0.554	1.00
87_G	91_G	0.554	1.00
64_R	124_T	0.549	1.00
41_E	47_E	0.542	1.00
39_L	43_E	0.538	1.00
62_L	122_L	0.537	1.00
77_F	81_I	0.536	1.00
49_L	52_Q	0.535	1.00
79_L	101_L	0.532	1.00
69_L	112_S	0.532	1.00
18_L	67_I	0.530	1.00
72_L	117_L	0.528	1.00
84_L	98_A	0.524	1.00
33_E	36_L	0.523	1.00
3_A	9_S	0.521	1.00
46_R	49_L	0.516	1.00
42_D	47_E	0.515	1.00
45_R	50_L	0.513	1.00
22_L	123_A	0.512	1.00
88_A	91_G	0.512	1.00
64_R	74_A	0.500	0.99
65_R	121_R	0.500	0.99

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
3pjsK	4	0.5039	28.6	0.876	Contact Map
3effK	4	0.5039	19.9	0.884	Contact Map
3rvyA	3	0.1705	9.5	0.9	Contact Map
3vouA	4	0.4419	7.2	0.905	Contact Map
4h33A	3	0.2093	7	0.906	Contact Map
3d9sA	3	0.2946	6.3	0.908	Contact Map
3b5xA	2	0.9845	6.1	0.909	Contact Map
4ry2A	2	0.9845	5.7	0.91	Contact Map
4bgnA	3	0.2713	5.5	0.91	Contact Map
3b60A	2	0.9922	5.2	0.912	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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