DUF432 - PFAM28P - GREMLIN Contacts

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DUF432 - Protein of unknown function (DUF432)

PFAM:	PF04254	Sequences: PVNLPKEITNYLLIEFEKPIVLEPGSSATIYLTFPIEIGVFLSSKKDYELLDIFSLVRPKYTLYGSPESGVICRYWKSEVYTEIPDVDPLREGVMELTIRNTSDEWVEVSKVVFPAYGMKIYY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	123 (123)
Sequences:	714 (549)
Seq/√Len:	49.5
META:	0.88

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
14_I	78_S	4.729	1.00
15_E	77_K	3.806	1.00
29_T	96_E	3.358	1.00
62_T	73_C	2.976	1.00
32_L	97_L	2.887	1.00
13_L	62_T	2.745	1.00
33_T	92_E	2.682	1.00
17_E	77_K	2.660	1.00
27_S	100_R	2.603	1.00
50_L	53_I	2.550	1.00
97_L	112_V	2.345	1.00
22_L	99_I	2.116	1.00
99_I	109_V	2.111	1.00
33_T	76_W	1.881	0.99
17_E	79_E	1.874	0.99
33_T	81_Y	1.860	0.99
20_I	80_V	1.710	0.98
34_F	93_G	1.617	0.98
3_N	37_E	1.584	0.97
5_P	9_T	1.579	0.97
3_N	9_T	1.535	0.97
11_Y	71_V	1.517	0.97
73_C	111_K	1.507	0.97
16_F	64_Y	1.490	0.96
51_L	113_V	1.481	0.96
38_I	110_S	1.442	0.96
33_T	79_E	1.367	0.94
40_V	54_F	1.348	0.94
107_V	110_S	1.346	0.94
16_F	112_V	1.342	0.93
39_G	50_L	1.337	0.93
20_I	86_D	1.333	0.93
9_T	115_P	1.313	0.93
61_Y	74_R	1.292	0.92
64_Y	113_V	1.285	0.92
1_P	5_P	1.279	0.92
63_L	72_I	1.269	0.91
6_K	9_T	1.239	0.90
25_G	75_Y	1.235	0.90
52_D	64_Y	1.227	0.90
23_E	106_W	1.209	0.89
51_L	84_I	1.178	0.88
63_L	74_R	1.158	0.87
29_T	123_Y	1.152	0.87
47_D	87_V	1.150	0.87
30_I	66_S	1.109	0.85
88_D	91_R	1.103	0.84
37_E	64_Y	1.100	0.84
66_S	69_S	1.089	0.84
82_T	92_E	1.085	0.83
29_T	67_P	1.082	0.83
55_S	73_C	1.067	0.82
2_V	5_P	1.067	0.82
45_K	123_Y	1.060	0.82
54_F	64_Y	1.052	0.81
95_M	112_V	1.044	0.81
109_V	121_I	1.044	0.81
19_P	66_S	1.041	0.81
73_C	116_A	1.026	0.80
3_N	10_N	1.021	0.79
29_T	100_R	1.005	0.78
38_I	90_L	0.985	0.77
37_E	66_S	0.977	0.76
52_D	113_V	0.967	0.76
61_Y	64_Y	0.958	0.75
59_P	103_S	0.951	0.74
102_T	112_V	0.947	0.74
34_F	85_P	0.937	0.73
57_V	91_R	0.932	0.73
114_F	119_M	0.928	0.72
7_E	10_N	0.911	0.71
54_F	101_N	0.904	0.71
10_N	66_S	0.900	0.70
67_P	122_Y	0.886	0.69
79_E	82_T	0.884	0.69
11_Y	31_Y	0.870	0.68
76_W	115_P	0.859	0.67
10_N	96_E	0.858	0.66
38_I	45_K	0.858	0.66
30_I	99_I	0.855	0.66
22_L	26_S	0.854	0.66
28_A	112_V	0.853	0.66
39_G	53_I	0.832	0.64
103_S	123_Y	0.831	0.64
17_E	80_V	0.817	0.63
13_L	73_C	0.804	0.61
75_Y	115_P	0.802	0.61
45_K	87_V	0.798	0.61
22_L	118_G	0.794	0.60
55_S	62_T	0.787	0.60
18_K	79_E	0.784	0.59
65_G	70_G	0.782	0.59
37_E	74_R	0.778	0.59
42_L	51_L	0.773	0.58
60_K	74_R	0.773	0.58
16_F	63_L	0.770	0.58
75_Y	105_E	0.769	0.58
114_F	117_Y	0.761	0.57
34_F	119_M	0.761	0.57
13_L	16_F	0.757	0.57
12_L	35_P	0.745	0.56
23_E	26_S	0.742	0.55
76_W	116_A	0.733	0.54
69_S	104_D	0.723	0.53
64_Y	101_N	0.722	0.53
77_K	95_M	0.704	0.51
51_L	72_I	0.696	0.51
37_E	61_Y	0.695	0.50
88_D	119_M	0.694	0.50
94_V	106_W	0.694	0.50
43_S	47_D	0.689	0.50
42_L	105_E	0.689	0.50
37_E	55_S	0.687	0.50
30_I	59_P	0.680	0.49
15_E	75_Y	0.676	0.49
81_Y	99_I	0.674	0.48
67_P	79_E	0.672	0.48
4_L	7_E	0.671	0.48
30_I	114_F	0.668	0.48
17_E	26_S	0.662	0.47
34_F	41_F	0.660	0.47
16_F	60_K	0.652	0.46
6_K	14_I	0.649	0.46
38_I	113_V	0.649	0.46
78_S	81_Y	0.647	0.46
18_K	93_G	0.646	0.45
102_T	110_S	0.645	0.45
6_K	59_P	0.644	0.45
32_L	78_S	0.636	0.44
26_S	102_T	0.634	0.44
44_S	109_V	0.630	0.44
37_E	54_F	0.627	0.44
106_W	113_V	0.626	0.43
57_V	111_K	0.625	0.43
43_S	111_K	0.622	0.43
117_Y	120_K	0.621	0.43
50_L	71_V	0.621	0.43
23_E	47_D	0.617	0.43
20_I	48_Y	0.616	0.42
66_S	115_P	0.614	0.42
25_G	39_G	0.612	0.42
16_F	42_L	0.610	0.42
9_T	116_A	0.605	0.41
8_I	23_E	0.604	0.41
91_R	116_A	0.603	0.41
89_P	122_Y	0.593	0.40
104_D	122_Y	0.589	0.40
20_I	82_T	0.588	0.40
42_L	45_K	0.587	0.40
49_E	67_P	0.586	0.40
22_L	120_K	0.584	0.39
17_E	103_S	0.580	0.39
88_D	93_G	0.580	0.39
22_L	28_A	0.579	0.39
25_G	86_D	0.577	0.39
18_K	109_V	0.574	0.38
25_G	104_D	0.574	0.38
37_E	60_K	0.567	0.38
12_L	47_D	0.564	0.37
91_R	110_S	0.562	0.37
93_G	121_I	0.560	0.37
68_E	91_R	0.558	0.37
93_G	99_I	0.551	0.36
4_L	86_D	0.548	0.36
31_Y	122_Y	0.548	0.36
27_S	45_K	0.545	0.36
34_F	37_E	0.544	0.35
28_A	51_L	0.542	0.35
112_V	120_K	0.540	0.35
84_I	99_I	0.539	0.35
98_T	107_V	0.539	0.35
31_Y	101_N	0.536	0.35
9_T	12_L	0.536	0.35
16_F	79_E	0.535	0.35
57_V	66_S	0.532	0.34
105_E	108_E	0.527	0.34
27_S	95_M	0.523	0.34
14_I	49_E	0.522	0.33
52_D	101_N	0.504	0.32
84_I	94_V	0.504	0.32
20_I	30_I	0.503	0.32
2_V	9_T	0.502	0.32
67_P	113_V	0.502	0.32
64_Y	74_R	0.500	0.31

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
3nrfA	3	0.4634	13.9	0.921	Contact Map
4b9pA	1	0.3902	12.7	0.922	Contact Map
4q6kA	4	0.374	7.3	0.931	Contact Map
4b9cA	1	0.374	5.8	0.934	Contact Map
2xbtA	1	0.3902	5.5	0.935	Contact Map
1g43A	1	0.3821	5	0.936	Contact Map
3zqxA	1	0.3496	4.3	0.938	Contact Map
3zucA	1	0.3821	4.2	0.938	Contact Map
3pcoB	2	0.935	4.2	0.938	Contact Map
4p72A	2	0.935	4	0.939	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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