DUF1642 - PFAM28P - GREMLIN Contacts

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DUF1642 - Protein of unknown function (DUF1642)

PFAM:	PF07852	Sequences: PQKVVVPQFVADWIEECKDNGETNLFDALTAINYAEDNEDDEVKEWLNEEDNQETFARAWLDGYEVEKEKRYLVKLKGVNGYYNSLLLLVLKNGNGNIYLFYNNFDGKWFYSNKETKHTRKELEEIAGFGWVFDIEVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	138 (131)
Sequences:	1685 (1502)
Seq/√Len:	131.2
META:	0.665

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_W	135_I	5.807	1.00
58_R	62_D	4.849	1.00
58_R	61_L	4.164	1.00
131_W	134_D	3.933	1.00
8_Q	12_D	2.386	1.00
99_Y	103_N	2.094	1.00
5_V	65_E	2.089	1.00
79_V	82_Y	2.052	1.00
103_N	106_D	2.016	1.00
96_G	100_L	1.782	1.00
52_N	56_F	1.774	1.00
102_Y	105_F	1.733	1.00
73_L	76_L	1.711	1.00
54_E	60_W	1.672	1.00
102_Y	106_D	1.620	1.00
11_A	15_E	1.606	1.00
120_R	124_E	1.591	1.00
13_W	17_C	1.590	1.00
78_G	118_H	1.580	1.00
78_G	81_G	1.561	1.00
28_A	31_A	1.542	1.00
50_E	53_Q	1.525	1.00
79_V	118_H	1.490	1.00
81_G	116_T	1.486	1.00
97_N	100_L	1.470	1.00
88_L	91_L	1.444	1.00
102_Y	107_G	1.442	1.00
101_F	104_N	1.376	1.00
26_F	30_T	1.349	1.00
95_N	99_Y	1.344	1.00
98_I	103_N	1.332	1.00
97_N	101_F	1.301	1.00
57_A	60_W	1.284	1.00
76_L	79_V	1.284	1.00
121_K	125_E	1.271	1.00
28_A	32_I	1.233	1.00
131_W	137_V	1.215	1.00
44_K	50_E	1.207	0.99
7_P	10_V	1.207	0.99
30_T	35_A	1.200	0.99
93_N	96_G	1.196	0.99
14_I	59_A	1.175	0.99
99_Y	107_G	1.156	0.99
129_F	132_V	1.156	0.99
99_Y	102_Y	1.153	0.99
54_E	61_L	1.153	0.99
104_N	107_G	1.130	0.99
76_L	113_N	1.122	0.99
26_F	29_L	1.122	0.99
80_N	116_T	1.110	0.99
33_N	37_D	1.091	0.99
94_G	97_N	1.089	0.99
33_N	36_E	1.087	0.99
25_L	28_A	1.078	0.99
96_G	101_F	1.054	0.99
100_L	103_N	1.044	0.99
99_Y	106_D	1.043	0.99
81_G	115_E	1.039	0.98
94_G	99_Y	1.038	0.98
89_L	92_K	1.038	0.98
104_N	108_K	1.010	0.98
98_I	104_N	1.006	0.98
31_A	36_E	1.003	0.98
98_I	102_Y	0.993	0.98
26_F	32_I	0.985	0.98
70_K	73_L	0.981	0.98
105_F	108_K	0.967	0.98
98_I	101_F	0.948	0.97
78_G	82_Y	0.948	0.97
112_S	115_E	0.947	0.97
21_G	25_L	0.947	0.97
101_F	106_D	0.947	0.97
98_I	106_D	0.936	0.97
65_E	68_K	0.933	0.97
30_T	44_K	0.917	0.97
88_L	92_K	0.912	0.97
44_K	49_E	0.911	0.97
96_G	99_Y	0.904	0.96
54_E	58_R	0.893	0.96
99_Y	108_K	0.891	0.96
97_N	102_Y	0.883	0.96
76_L	82_Y	0.879	0.96
98_I	107_G	0.873	0.96
117_K	120_R	0.870	0.95
103_N	108_K	0.867	0.95
30_T	33_N	0.863	0.95
52_N	59_A	0.862	0.95
95_N	98_I	0.861	0.95
81_G	106_D	0.860	0.95
14_I	60_W	0.850	0.95
27_D	33_N	0.846	0.95
106_D	110_F	0.844	0.95
92_K	95_N	0.842	0.95
92_K	96_G	0.841	0.95
107_G	110_F	0.836	0.94
130_G	134_D	0.831	0.94
34_Y	37_D	0.826	0.94
30_T	49_E	0.817	0.94
31_A	45_E	0.815	0.94
41_D	50_E	0.813	0.93
104_N	110_F	0.811	0.93
89_L	96_G	0.808	0.93
81_G	117_K	0.808	0.93
76_L	80_N	0.805	0.93
101_F	105_F	0.801	0.93
31_A	35_A	0.798	0.93
27_D	32_I	0.795	0.93
42_E	50_E	0.788	0.92
101_F	108_K	0.788	0.92
79_V	116_T	0.785	0.92
108_K	112_S	0.784	0.92
105_F	109_W	0.778	0.92
97_N	104_N	0.775	0.92
128_G	134_D	0.772	0.92
97_N	106_D	0.769	0.91
56_F	60_W	0.768	0.91
27_D	34_Y	0.762	0.91
32_I	36_E	0.760	0.91
22_E	50_E	0.760	0.91
80_N	99_Y	0.756	0.91
91_L	100_L	0.754	0.91
90_V	95_N	0.750	0.90
110_F	113_N	0.747	0.90
13_W	43_V	0.746	0.90
22_E	52_N	0.741	0.90
31_A	34_Y	0.741	0.90
100_L	106_D	0.739	0.90
82_Y	106_D	0.733	0.89
23_T	27_D	0.733	0.89
88_L	96_G	0.729	0.89
16_E	30_T	0.726	0.89
11_A	64_Y	0.721	0.89
14_I	56_F	0.718	0.88
49_E	53_Q	0.717	0.88
36_E	44_K	0.717	0.88
19_D	43_V	0.716	0.88
135_I	138_E	0.711	0.88
13_W	53_Q	0.706	0.88
31_A	37_D	0.699	0.87
88_L	93_N	0.698	0.87
27_D	31_A	0.695	0.87
27_D	30_T	0.695	0.87
97_N	103_N	0.691	0.86
37_D	41_D	0.684	0.86
89_L	93_N	0.683	0.86
75_K	78_G	0.671	0.85
29_L	35_A	0.670	0.85
82_Y	116_T	0.668	0.85
103_N	107_G	0.666	0.84
75_K	116_T	0.662	0.84
94_G	98_I	0.659	0.84
17_C	53_Q	0.657	0.84
128_G	131_W	0.650	0.83
124_E	130_G	0.649	0.83
23_T	26_F	0.647	0.83
29_L	32_I	0.646	0.83
75_K	118_H	0.642	0.82
90_V	93_N	0.641	0.82
45_E	49_E	0.640	0.82
73_L	78_G	0.636	0.82
92_K	98_I	0.632	0.81
27_D	44_K	0.629	0.81
109_W	112_S	0.624	0.80
99_Y	104_N	0.623	0.80
100_L	116_T	0.605	0.78
23_T	47_L	0.594	0.77
101_F	107_G	0.594	0.77
16_E	20_N	0.582	0.76
30_T	34_Y	0.579	0.75
106_D	112_S	0.579	0.75
90_V	96_G	0.576	0.75
6_V	9_F	0.572	0.74
128_G	132_V	0.570	0.74
44_K	53_Q	0.563	0.73
41_D	44_K	0.563	0.73
25_L	50_E	0.556	0.72
29_L	33_N	0.544	0.71
91_L	97_N	0.541	0.70
103_N	113_N	0.539	0.70
105_F	110_F	0.537	0.70
107_G	115_E	0.536	0.70
91_L	99_Y	0.533	0.69
5_V	67_E	0.528	0.68
33_N	42_E	0.527	0.68
91_L	94_G	0.526	0.68
94_G	100_L	0.524	0.68
82_Y	117_K	0.522	0.68
95_N	105_F	0.519	0.67
104_N	109_W	0.519	0.67
99_Y	105_F	0.517	0.67
101_F	116_T	0.514	0.66
37_D	50_E	0.508	0.65
82_Y	108_K	0.505	0.65
127_A	131_W	0.505	0.65
36_E	49_E	0.503	0.65
82_Y	97_N	0.500	0.64

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
1yb3A	2	0.6087	2.2	0.945	Contact Map
3p0cA	2	0.3768	2.1	0.945	Contact Map
3cnqP	1	0.4565	2.1	0.945	Contact Map
4fxsA	3	0.4058	2	0.946	Contact Map
1kmdA	1	0.3623	1.8	0.947	Contact Map
3ostA	1	0.5797	1.7	0.948	Contact Map
2mhdA	1	0.6594	1.5	0.95	Contact Map
2vdwB	1	0.3986	1.5	0.95	Contact Map
2l14B	1	0.1522	1.4	0.951	Contact Map
2p22D	1	0.3188	1.4	0.951	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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