DUF2859 - PFAM28P - GREMLIN Contacts

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DUF2859 - Protein of unknown function (DUF2859)

PFAM:	PF11072	Sequences: VEDSGGVSALPYYEALNLQPRASAPAQPPAPPPVPASPAAEAAMLPVRSPELTPGPVARRVLNAPGLRPFFLIGDDPLSRAWLRQRRDRLRELGAVGLVVNVETAEALAALRALAPGLPLLPASGDDLAQRLGLRHYPVLITATGI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (146)
Sequences:	725 (481)
Seq/√Len:	39.8
META:	0.597

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
71_F	97_G	7.174	1.00
49_S	52_L	4.780	1.00
51_E	126_D	4.071	1.00
111_L	120_L	3.205	1.00
80_R	114_L	3.129	1.00
50_P	126_D	3.071	1.00
9_A	13_Y	3.035	1.00
99_V	120_L	2.908	1.00
99_V	111_L	2.903	1.00
75_D	107_A	2.653	1.00
57_V	136_H	2.336	1.00
80_R	110_A	2.333	1.00
49_S	126_D	2.320	1.00
105_A	109_A	2.270	1.00
100_V	125_G	2.201	0.99
41_E	112_R	2.097	0.99
53_T	136_H	1.981	0.99
2_E	6_G	1.945	0.99
99_V	108_L	1.929	0.99
70_F	141_I	1.831	0.98
13_Y	16_L	1.688	0.97
54_P	78_L	1.670	0.96
36_A	40_A	1.614	0.96
45_L	108_L	1.609	0.95
75_D	111_L	1.552	0.94
75_D	80_R	1.523	0.94
45_L	104_T	1.488	0.93
78_L	81_A	1.477	0.93
134_L	139_V	1.474	0.93
115_A	120_L	1.461	0.92
49_S	127_D	1.442	0.92
143_A	146_I	1.419	0.91
52_L	129_A	1.413	0.91
118_L	124_S	1.413	0.91
37_S	40_A	1.347	0.89
115_A	118_L	1.319	0.88
108_L	112_R	1.314	0.88
41_E	45_L	1.306	0.87
92_E	106_E	1.289	0.87
72_L	100_V	1.272	0.86
70_F	96_V	1.270	0.86
75_D	102_V	1.260	0.85
1_V	12_Y	1.254	0.85
71_F	115_A	1.234	0.84
8_S	18_L	1.233	0.84
52_L	100_V	1.203	0.83
87_R	117_G	1.188	0.82
110_A	114_L	1.185	0.82
72_L	124_S	1.175	0.81
14_E	17_N	1.175	0.81
73_I	99_V	1.159	0.80
7_V	18_L	1.155	0.80
52_L	134_L	1.137	0.79
89_R	93_L	1.132	0.79
71_F	95_A	1.130	0.79
1_V	10_L	1.129	0.78
125_G	129_A	1.128	0.78
27_Q	31_P	1.067	0.74
47_V	102_V	1.066	0.74
111_L	128_L	1.066	0.74
48_R	103_E	1.062	0.74
1_V	39_A	1.052	0.73
57_V	60_R	1.050	0.73
75_D	101_N	1.046	0.73
57_V	134_L	1.029	0.72
57_V	139_V	1.028	0.72
7_V	125_G	1.027	0.72
97_G	115_A	1.020	0.71
87_R	91_R	0.987	0.68
4_S	8_S	0.976	0.68
91_R	117_G	0.963	0.67
9_A	16_L	0.961	0.66
121_L	128_L	0.958	0.66
88_D	91_R	0.955	0.66
47_V	101_N	0.952	0.66
93_L	118_L	0.949	0.65
2_E	9_A	0.943	0.65
53_T	57_V	0.938	0.64
13_Y	41_E	0.926	0.63
99_V	102_V	0.910	0.62
45_L	53_T	0.905	0.62
4_S	9_A	0.885	0.60
86_R	89_R	0.876	0.59
77_P	86_R	0.862	0.58
71_F	118_L	0.862	0.58
107_A	111_L	0.857	0.57
86_R	99_V	0.852	0.57
111_L	126_D	0.850	0.57
99_V	107_A	0.834	0.55
47_V	120_L	0.822	0.54
121_L	127_D	0.820	0.54
14_E	21_R	0.820	0.54
102_V	108_L	0.813	0.53
31_P	34_V	0.804	0.53
10_L	14_E	0.802	0.52
29_P	32_P	0.797	0.52
8_S	17_N	0.797	0.52
42_A	105_A	0.791	0.51
127_D	142_T	0.791	0.51
60_R	65_P	0.779	0.50
104_T	107_A	0.769	0.49
35_P	38_P	0.768	0.49
87_R	115_A	0.765	0.49
73_I	114_L	0.764	0.49
7_V	10_L	0.763	0.49
102_V	107_A	0.761	0.49
40_A	47_V	0.757	0.48
113_A	116_P	0.746	0.47
49_S	134_L	0.732	0.46
18_L	21_R	0.732	0.46
8_S	69_P	0.730	0.46
72_L	83_L	0.724	0.45
2_E	16_L	0.723	0.45
120_L	126_D	0.720	0.45
78_L	110_A	0.718	0.45
51_E	130_Q	0.714	0.44
26_A	29_P	0.712	0.44
117_G	132_L	0.710	0.44
74_G	102_V	0.709	0.44
135_R	146_I	0.692	0.42
49_S	131_R	0.688	0.42
102_V	117_G	0.681	0.41
3_D	6_G	0.679	0.41
45_L	66_G	0.675	0.41
41_E	44_M	0.670	0.40
79_S	82_W	0.669	0.40
60_R	100_V	0.667	0.40
10_L	18_L	0.663	0.40
122_P	136_H	0.662	0.40
100_V	129_A	0.661	0.40
50_P	141_I	0.656	0.39
73_I	87_R	0.655	0.39
7_V	67_L	0.654	0.39
138_P	141_I	0.640	0.38
60_R	122_P	0.640	0.38
76_D	90_L	0.639	0.38
9_A	12_Y	0.637	0.38
73_I	113_A	0.635	0.37
46_P	74_G	0.631	0.37
85_Q	121_L	0.629	0.37
111_L	121_L	0.626	0.37
9_A	94_G	0.622	0.36
54_P	125_G	0.618	0.36
43_A	111_L	0.616	0.36
108_L	127_D	0.614	0.36
68_R	133_G	0.614	0.36
54_P	74_G	0.610	0.35
57_V	108_L	0.609	0.35
53_T	56_P	0.607	0.35
53_T	125_G	0.607	0.35
53_T	134_L	0.607	0.35
72_L	119_P	0.602	0.35
1_V	5_G	0.601	0.35
118_L	121_L	0.599	0.34
72_L	104_T	0.599	0.34
78_L	106_E	0.599	0.34
45_L	124_S	0.598	0.34
31_P	40_A	0.596	0.34
10_L	13_Y	0.596	0.34
7_V	87_R	0.596	0.34
54_P	127_D	0.595	0.34
54_P	115_A	0.591	0.34
97_G	120_L	0.590	0.34
49_S	118_L	0.589	0.34
47_V	111_L	0.586	0.33
1_V	6_G	0.586	0.33
33_P	36_A	0.583	0.33
11_P	20_P	0.582	0.33
54_P	102_V	0.577	0.33
5_G	8_S	0.577	0.33
80_R	143_A	0.575	0.32
129_A	132_L	0.574	0.32
13_Y	126_D	0.573	0.32
17_N	23_S	0.571	0.32
7_V	12_Y	0.571	0.32
68_R	78_L	0.568	0.32
58_A	100_V	0.566	0.32
104_T	114_L	0.565	0.32
83_L	98_L	0.564	0.32
74_G	125_G	0.563	0.32
28_P	32_P	0.563	0.32
23_S	115_A	0.562	0.31
117_G	145_G	0.557	0.31
33_P	77_P	0.556	0.31
1_V	9_A	0.554	0.31
80_R	123_A	0.552	0.31
107_A	131_R	0.552	0.31
55_G	122_P	0.551	0.31
3_D	8_S	0.545	0.30
11_P	16_L	0.544	0.30
41_E	108_L	0.542	0.30
40_A	94_G	0.542	0.30
7_V	16_L	0.537	0.30
50_P	130_Q	0.536	0.29
62_L	103_E	0.528	0.29
103_E	106_E	0.527	0.29
25_P	139_V	0.527	0.29
70_F	103_E	0.522	0.28
109_A	113_A	0.520	0.28
106_E	110_A	0.519	0.28
74_G	129_A	0.518	0.28
60_R	136_H	0.517	0.28
8_S	14_E	0.517	0.28
19_Q	141_I	0.516	0.28
22_A	26_A	0.516	0.28
1_V	17_N	0.515	0.28
112_R	122_P	0.514	0.28
76_D	79_S	0.513	0.28
55_G	71_F	0.512	0.28
31_P	73_I	0.511	0.28
134_L	140_L	0.511	0.28
6_G	131_R	0.510	0.27
83_L	97_G	0.505	0.27
65_P	144_T	0.504	0.27
113_A	135_R	0.502	0.27
94_G	119_P	0.501	0.27
52_L	98_L	0.501	0.27
45_L	68_R	0.500	0.27
57_V	123_A	0.500	0.27

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
3lorA	3	0.7534	57	0.911	Contact Map
4ma9A	5	0.7466	53.1	0.913	Contact Map
3razA	1	0.6849	52.7	0.913	Contact Map
4gqcA	4	0.7466	51.3	0.914	Contact Map
1we0A	3	0.7466	50.9	0.914	Contact Map
3fw2A	2	0.726	48.1	0.915	Contact Map
3drnA	1	0.726	47.2	0.916	Contact Map
3zl5A	3	0.7534	47	0.916	Contact Map
2bmxA	3	0.7603	44.4	0.917	Contact Map
3eytA	4	0.7603	43.8	0.918	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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