DUF3750 - PFAM28P - GREMLIN Contacts

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DUF3750 - Protein of unknown function (DUF3750)

PFAM:	PF12570	Sequences: EAVVQVYAARTGGWRGIFAVHTWIAVKPAGAARYTRYEVVGWRGPPVRINGRAPDGRWFGNRPELLADVRGAGAEALIPRIEAAVASYPYANDYRAWPGPNSNTFVAWVLRAVPELGLDLPPTAIGKDY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	129 (128)
Sequences:	3775 (1976)
Seq/√Len:	174.7
META:	0.922

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_A	75_E	4.000	1.00
110_L	118_L	3.843	1.00
80_R	115_E	3.663	1.00
57_R	62_R	3.439	1.00
69_V	77_L	3.438	1.00
8_A	20_V	3.314	1.00
28_P	82_E	2.757	1.00
4_V	81_I	2.712	1.00
28_P	79_P	2.460	1.00
28_P	31_A	2.288	1.00
89_P	108_W	2.050	1.00
82_E	86_A	1.999	1.00
43_R	48_R	1.883	1.00
83_A	87_S	1.882	1.00
53_A	56_G	1.867	1.00
52_R	56_G	1.846	1.00
8_A	66_L	1.826	1.00
87_S	108_W	1.723	1.00
8_A	22_T	1.714	1.00
37_Y	49_I	1.690	1.00
19_A	96_A	1.589	1.00
38_E	48_R	1.498	1.00
81_I	109_V	1.498	1.00
74_A	79_P	1.480	1.00
5_Q	68_D	1.477	1.00
108_W	112_A	1.474	1.00
37_Y	82_E	1.463	1.00
35_T	49_I	1.418	1.00
113_V	116_L	1.416	1.00
11_T	15_R	1.401	1.00
35_T	82_E	1.385	1.00
45_P	91_A	1.385	1.00
85_V	105_F	1.377	1.00
29_A	74_A	1.376	1.00
26_V	37_Y	1.353	1.00
106_V	109_V	1.349	1.00
72_A	75_E	1.332	1.00
82_E	85_V	1.323	1.00
73_G	76_A	1.315	1.00
22_T	106_V	1.297	1.00
122_P	128_D	1.284	1.00
33_R	51_G	1.271	1.00
49_I	85_V	1.228	1.00
119_D	122_P	1.223	1.00
24_I	109_V	1.196	1.00
39_V	47_V	1.190	1.00
47_V	91_A	1.183	1.00
4_V	77_L	1.171	1.00
11_T	96_A	1.169	1.00
36_R	50_N	1.165	1.00
37_Y	85_V	1.136	1.00
55_D	63_P	1.111	1.00
36_R	56_G	1.080	1.00
36_R	52_R	1.079	1.00
38_E	52_R	1.074	1.00
69_V	73_G	1.073	1.00
25_A	36_R	1.069	1.00
123_T	128_D	1.067	1.00
38_E	50_N	1.057	1.00
67_A	110_L	1.042	0.99
20_V	123_T	1.031	0.99
75_E	79_P	1.028	0.99
12_G	15_R	1.015	0.99
123_T	127_K	1.015	0.99
87_S	112_A	1.015	0.99
107_A	111_R	1.012	0.99
121_P	124_A	0.999	0.99
33_R	50_N	0.989	0.99
72_A	76_A	0.959	0.99
104_T	108_W	0.956	0.99
76_A	80_R	0.947	0.99
67_A	118_L	0.936	0.99
3_V	68_D	0.924	0.99
12_G	61_N	0.904	0.99
7_Y	10_R	0.900	0.99
14_W	18_F	0.896	0.98
40_V	43_R	0.887	0.98
77_L	113_V	0.879	0.98
86_A	91_A	0.870	0.98
40_V	48_R	0.860	0.98
84_A	113_V	0.857	0.98
26_V	85_V	0.850	0.98
5_Q	70_R	0.847	0.98
36_R	39_V	0.832	0.98
45_P	89_P	0.830	0.97
59_F	62_R	0.830	0.97
28_P	35_T	0.825	0.97
45_P	48_R	0.778	0.96
76_A	79_P	0.777	0.96
100_P	103_N	0.773	0.96
44_G	92_N	0.769	0.96
74_A	77_L	0.766	0.96
62_R	65_L	0.763	0.96
26_V	81_I	0.763	0.96
13_G	17_I	0.759	0.96
77_L	80_R	0.759	0.96
3_V	7_Y	0.755	0.96
22_T	26_V	0.755	0.96
34_Y	68_D	0.753	0.96
118_L	121_P	0.747	0.95
110_L	116_L	0.745	0.95
81_I	113_V	0.731	0.95
13_G	18_F	0.721	0.94
7_Y	65_L	0.713	0.94
35_T	85_V	0.712	0.94
6_V	110_L	0.710	0.94
122_P	127_K	0.709	0.94
45_P	92_N	0.706	0.94
36_R	48_R	0.705	0.94
14_W	17_I	0.705	0.94
26_V	49_I	0.703	0.94
19_A	123_T	0.701	0.93
79_P	83_A	0.696	0.93
80_R	83_A	0.695	0.93
125_I	128_D	0.687	0.93
12_G	17_I	0.685	0.93
104_T	129_Y	0.677	0.92
51_G	56_G	0.674	0.92
38_E	53_A	0.672	0.92
5_Q	65_L	0.666	0.92
26_V	35_T	0.662	0.91
3_V	70_R	0.658	0.91
16_G	42_W	0.655	0.91
73_G	79_P	0.655	0.91
90_Y	108_W	0.650	0.91
126_G	129_Y	0.649	0.91
40_V	59_F	0.646	0.90
73_G	77_L	0.641	0.90
49_I	82_E	0.640	0.90
94_Y	99_G	0.639	0.90
84_A	105_F	0.639	0.90
50_N	53_A	0.638	0.90
24_I	106_V	0.636	0.90
64_E	67_A	0.635	0.90
4_V	9_A	0.635	0.90
110_L	119_D	0.627	0.89
12_G	40_V	0.623	0.89
111_R	128_D	0.619	0.88
102_S	105_F	0.618	0.88
12_G	59_F	0.618	0.88
97_W	127_K	0.612	0.88
43_R	46_P	0.610	0.88
10_R	123_T	0.609	0.88
59_F	63_P	0.605	0.87
104_T	127_K	0.604	0.87
70_R	73_G	0.604	0.87
79_P	82_E	0.604	0.87
6_V	118_L	0.600	0.87
61_N	64_E	0.596	0.86
32_A	73_G	0.595	0.86
28_P	74_A	0.593	0.86
120_L	123_T	0.592	0.86
17_I	36_R	0.591	0.86
22_T	124_A	0.588	0.86
46_P	93_D	0.587	0.86
36_R	43_R	0.585	0.85
124_A	127_K	0.580	0.85
10_R	61_N	0.580	0.85
78_I	85_V	0.575	0.84
67_A	116_L	0.573	0.84
97_W	128_D	0.571	0.84
84_A	112_A	0.570	0.84
93_D	108_W	0.568	0.84
43_R	57_R	0.566	0.84
96_A	104_T	0.562	0.83
17_I	97_W	0.556	0.82
5_Q	9_A	0.555	0.82
29_A	73_G	0.552	0.82
27_K	55_D	0.545	0.81
5_Q	34_Y	0.543	0.81
12_G	43_R	0.541	0.81
14_W	60_G	0.540	0.81
44_G	48_R	0.539	0.81
107_A	129_Y	0.535	0.80
44_G	50_N	0.534	0.80
68_D	111_R	0.533	0.80
5_Q	111_R	0.528	0.79
46_P	91_A	0.528	0.79
39_V	93_D	0.524	0.79
27_K	31_A	0.524	0.79
33_R	87_S	0.522	0.78
20_V	64_E	0.522	0.78
58_W	63_P	0.522	0.78
25_A	56_G	0.514	0.77
99_G	103_N	0.513	0.77
80_R	112_A	0.510	0.77
90_Y	128_D	0.510	0.77
5_Q	11_T	0.508	0.77
25_A	46_P	0.507	0.76
15_R	125_I	0.505	0.76
15_R	18_F	0.505	0.76
4_V	69_V	0.500	0.75

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
1lehA	5	0.9457	10.4	0.946	Contact Map
4ekxC	2	0.4419	4.1	0.955	Contact Map
4f0wA	1	0.3721	3.9	0.956	Contact Map
1c1dA	1	0.9457	3.9	0.956	Contact Map
1jogA	2	0.4496	3.9	0.956	Contact Map
3vpiA	1	0.3798	3.3	0.957	Contact Map
4lj1A	1	0.4341	3	0.958	Contact Map
2uw1A	2	0.8605	3	0.958	Contact Map
1wwpA	2	0.3411	3	0.958	Contact Map
4i6pA	2	0.3411	2.5	0.96	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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