DUF3754 - PFAM28P - GREMLIN Contacts

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DUF3754 - Protein of unknown function (DUF3754)

PFAM:	PF12576	Sequences: YDRVVLLVRFKPEAYFAEKKRKRLRRPGSVYLKLFKNIPKADLEMLFPNTRVRMRLFDKLKLGVPALGGGGPVLLKLLSGEVVALDAASLLALLGGLAALGGYGFRQWLGYQNTKLRYQKQLTQNLYFKNLDNNAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (136)
Sequences:	1898 (1285)
Seq/√Len:	110.2
META:	0.862

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
130_N	133_N	4.553	1.00
120_K	124_Q	3.065	1.00
105_F	109_L	3.034	1.00
7_L	10_F	2.856	1.00
3_R	9_R	2.521	1.00
33_K	133_N	2.341	1.00
61_K	114_T	2.319	1.00
13_E	16_F	2.258	1.00
71_G	75_L	2.201	1.00
58_D	118_Y	2.167	1.00
132_D	136_G	2.104	1.00
55_R	58_D	2.092	1.00
3_R	11_K	2.035	1.00
106_R	110_G	1.914	1.00
21_R	25_R	1.869	1.00
108_W	112_Q	1.845	1.00
3_R	10_F	1.840	1.00
110_G	113_N	1.834	1.00
3_R	8_V	1.828	1.00
14_A	17_A	1.762	1.00
45_M	50_T	1.695	1.00
46_L	122_L	1.587	1.00
2_D	9_R	1.582	1.00
39_P	42_D	1.576	1.00
2_D	10_F	1.564	1.00
19_K	22_K	1.548	1.00
54_M	133_N	1.544	1.00
18_E	21_R	1.543	1.00
56_L	60_L	1.531	1.00
132_D	135_A	1.528	1.00
46_L	134_N	1.508	1.00
6_L	12_P	1.464	1.00
92_A	95_G	1.456	1.00
17_A	22_K	1.453	1.00
16_F	20_K	1.445	1.00
21_R	24_L	1.444	1.00
5_V	34_L	1.444	1.00
15_Y	19_K	1.424	1.00
35_F	127_Y	1.389	1.00
33_K	127_Y	1.374	1.00
5_V	10_F	1.355	1.00
16_F	21_R	1.335	1.00
13_E	17_A	1.334	1.00
13_E	18_E	1.323	1.00
3_R	131_L	1.316	0.99
15_Y	20_K	1.302	0.99
5_V	8_V	1.229	0.99
18_E	24_L	1.212	0.99
5_V	11_K	1.175	0.99
17_A	20_K	1.162	0.99
47_F	60_L	1.151	0.99
90_L	94_L	1.141	0.99
2_D	7_L	1.129	0.98
14_A	18_E	1.127	0.98
49_N	59_K	1.125	0.98
83_V	88_A	1.107	0.98
79_S	83_V	1.102	0.98
12_P	15_Y	1.094	0.98
15_Y	18_E	1.080	0.98
14_A	19_K	1.080	0.98
20_K	24_L	1.064	0.98
7_L	11_K	1.061	0.98
86_D	90_L	1.037	0.97
30_V	122_L	1.003	0.97
15_Y	21_R	1.003	0.97
13_E	20_K	0.999	0.97
127_Y	133_N	0.991	0.96
60_L	64_V	0.983	0.96
42_D	100_L	0.980	0.96
62_L	65_P	0.973	0.96
69_G	99_A	0.969	0.96
52_V	58_D	0.969	0.96
85_L	88_A	0.968	0.96
65_P	107_Q	0.962	0.96
8_V	12_P	0.958	0.96
81_E	84_A	0.955	0.96
8_V	11_K	0.953	0.95
17_A	21_R	0.951	0.95
66_A	107_Q	0.950	0.95
84_A	87_A	0.949	0.95
2_D	5_V	0.945	0.95
9_R	12_P	0.939	0.95
103_Y	106_R	0.937	0.95
13_E	19_K	0.922	0.95
62_L	107_Q	0.911	0.94
17_A	25_R	0.910	0.94
67_L	70_G	0.903	0.94
56_L	76_K	0.894	0.94
6_L	10_F	0.891	0.94
65_P	114_T	0.890	0.94
26_R	29_S	0.889	0.93
33_K	130_N	0.883	0.93
99_A	121_Q	0.874	0.93
12_P	17_A	0.871	0.93
11_K	14_A	0.865	0.93
38_I	55_R	0.860	0.92
91_L	95_G	0.858	0.92
16_F	25_R	0.854	0.92
111_Y	118_Y	0.852	0.92
45_M	122_L	0.847	0.92
3_R	36_K	0.846	0.92
86_D	89_S	0.843	0.92
62_L	96_G	0.819	0.90
20_K	80_G	0.816	0.90
19_K	23_R	0.810	0.90
55_R	69_G	0.806	0.90
86_D	92_A	0.803	0.89
85_L	89_S	0.794	0.89
7_L	12_P	0.794	0.89
69_G	122_L	0.781	0.88
3_R	7_L	0.771	0.87
66_A	111_Y	0.770	0.87
83_V	87_A	0.768	0.87
83_V	86_D	0.766	0.87
101_G	104_G	0.762	0.87
7_L	62_L	0.761	0.87
45_M	125_N	0.757	0.87
44_E	47_F	0.756	0.86
123_T	129_K	0.754	0.86
70_G	104_G	0.744	0.86
16_F	19_K	0.738	0.85
49_N	128_F	0.727	0.84
57_F	61_K	0.719	0.84
22_K	25_R	0.711	0.83
15_Y	22_K	0.710	0.83
44_E	76_K	0.703	0.82
32_L	98_A	0.698	0.82
18_E	23_R	0.691	0.81
1_Y	20_K	0.682	0.80
1_Y	8_V	0.680	0.80
36_K	134_N	0.679	0.80
16_F	24_L	0.676	0.80
110_G	114_T	0.674	0.79
85_L	95_G	0.670	0.79
5_V	26_R	0.668	0.79
47_F	59_K	0.666	0.79
27_P	71_G	0.656	0.78
31_Y	127_Y	0.647	0.77
113_N	119_Q	0.643	0.76
14_A	22_K	0.635	0.75
44_E	49_N	0.632	0.75
34_L	43_L	0.632	0.75
124_Q	129_K	0.626	0.74
39_P	50_T	0.625	0.74
111_Y	114_T	0.623	0.74
89_S	93_L	0.623	0.74
2_D	8_V	0.621	0.74
56_L	101_G	0.619	0.73
9_R	30_V	0.617	0.73
119_Q	133_N	0.617	0.73
37_N	102_G	0.616	0.73
104_G	108_W	0.614	0.73
14_A	25_R	0.613	0.73
35_F	45_M	0.612	0.73
14_A	21_R	0.611	0.73
16_F	22_K	0.608	0.72
61_K	109_L	0.608	0.72
2_D	13_E	0.608	0.72
112_Q	119_Q	0.607	0.72
81_E	85_L	0.601	0.71
116_L	120_K	0.601	0.71
46_L	70_G	0.600	0.71
39_P	44_E	0.600	0.71
55_R	63_G	0.597	0.71
109_L	113_N	0.597	0.71
89_S	98_A	0.591	0.70
41_A	50_T	0.588	0.70
125_N	135_A	0.588	0.70
36_K	68_G	0.587	0.70
38_I	46_L	0.587	0.70
123_T	132_D	0.582	0.69
105_F	113_N	0.582	0.69
88_A	91_L	0.581	0.69
14_A	20_K	0.579	0.68
47_F	55_R	0.573	0.68
107_Q	128_F	0.573	0.68
37_N	131_L	0.569	0.67
42_D	123_T	0.564	0.66
20_K	25_R	0.561	0.66
64_V	95_G	0.560	0.66
61_K	103_Y	0.559	0.66
119_Q	130_N	0.559	0.66
1_Y	11_K	0.559	0.66
53_R	60_L	0.556	0.65
121_Q	129_K	0.549	0.64
58_D	65_P	0.545	0.64
98_A	106_R	0.545	0.64
54_M	106_R	0.539	0.63
18_E	22_K	0.535	0.62
72_P	96_G	0.531	0.62
87_A	93_L	0.531	0.62
17_A	23_R	0.529	0.62
13_E	21_R	0.528	0.61
56_L	59_K	0.525	0.61
55_R	77_L	0.523	0.61
95_G	98_A	0.522	0.61
128_F	134_N	0.522	0.61
107_Q	124_Q	0.521	0.60
9_R	23_R	0.518	0.60
130_N	135_A	0.513	0.59
115_K	126_L	0.509	0.59
18_E	25_R	0.504	0.58
25_R	32_L	0.502	0.58
127_Y	136_G	0.500	0.57

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
3uauA	1	0.4926	9.6	0.925	Contact Map
2rngA	1	0.3676	3.3	0.94	Contact Map
2e6xA	2	0.3529	3.1	0.941	Contact Map
4ovdA	2	0.0735	2.6	0.943	Contact Map
2mmuA	1	0.3603	2.5	0.943	Contact Map
1njrA	2	0.3676	2.1	0.946	Contact Map
4c2wC	1	0.3235	2.1	0.946	Contact Map
4il3A	1	0.3824	2.1	0.946	Contact Map
1t6t1	2	0.3456	1.9	0.947	Contact Map
3h7hA	1	0.4485	1.8	0.948	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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