DUF2785 - PFAM28P - GREMLIN Contacts

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DUF2785 - Protein of unknown function (DUF2785)

PFAM:	PF10978	Sequences: LFYGIGETGTDSVFRRSFSALVLAEIARRDRKAPFLSAEERRALLDAALAYLAAERDLRGFDPGKGWAHAVAHGADLLKQLARNPALDKADLARILDAIAAKLAPADHVYVHGEDERLARAVLSILRRGDLDEAELEAWLARLAAPLAWKAAPPDPAGLARRHNTKNFLRSLYF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	174 (171)
Sequences:	1989 (1523)
Seq/√Len:	116.4
META:	0.782

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_A	77_L	4.367	1.00
7_E	10_T	3.488	1.00
78_L	95_I	3.125	1.00
30_D	84_N	2.665	1.00
14_F	65_K	2.662	1.00
11_D	65_K	2.657	1.00
52_L	118_L	2.483	1.00
69_H	72_A	2.463	1.00
62_D	68_A	2.440	1.00
92_L	130_D	2.404	1.00
18_F	69_H	2.373	1.00
88_D	91_D	2.364	1.00
82_A	125_I	2.263	1.00
14_F	68_A	2.204	1.00
92_L	125_I	2.181	1.00
96_L	122_V	2.159	1.00
42_R	91_D	2.066	1.00
13_V	68_A	2.038	1.00
50_A	54_A	2.024	1.00
18_F	73_H	1.938	1.00
18_F	21_L	1.936	1.00
93_A	135_E	1.893	1.00
109_V	112_H	1.827	1.00
37_S	40_E	1.817	1.00
132_D	135_E	1.802	1.00
99_I	118_L	1.702	1.00
27_A	44_L	1.694	1.00
24_A	80_Q	1.638	1.00
122_V	168_F	1.625	1.00
79_K	124_S	1.615	1.00
72_A	76_D	1.610	1.00
52_L	74_G	1.575	1.00
140_L	172_L	1.573	1.00
115_D	167_N	1.564	1.00
46_D	94_R	1.546	1.00
116_E	166_K	1.543	1.00
30_D	86_A	1.510	1.00
14_F	62_D	1.481	1.00
20_A	77_L	1.463	1.00
29_R	35_F	1.461	1.00
112_H	156_P	1.458	1.00
93_A	131_L	1.434	1.00
62_D	65_K	1.432	1.00
65_K	68_A	1.432	1.00
76_D	117_R	1.400	1.00
40_E	43_A	1.399	1.00
6_G	12_S	1.360	1.00
149_W	152_A	1.350	1.00
51_Y	74_G	1.334	1.00
92_L	128_R	1.315	1.00
44_L	77_L	1.314	1.00
4_G	12_S	1.313	1.00
89_K	93_A	1.304	1.00
42_R	46_D	1.294	1.00
97_D	142_R	1.283	0.99
80_Q	83_R	1.257	0.99
45_L	95_I	1.249	0.99
25_E	28_R	1.230	0.99
31_R	85_P	1.228	0.99
38_A	86_A	1.214	0.99
159_L	163_H	1.212	0.99
25_E	80_Q	1.212	0.99
26_I	35_F	1.212	0.99
28_R	80_Q	1.185	0.99
45_L	49_L	1.179	0.99
17_S	20_A	1.174	0.99
15_R	19_S	1.139	0.99
69_H	73_H	1.122	0.99
166_K	170_R	1.119	0.99
75_A	118_L	1.116	0.99
79_K	120_R	1.106	0.98
31_R	84_N	1.105	0.98
29_R	32_K	1.099	0.98
116_E	170_R	1.095	0.98
21_L	73_H	1.092	0.98
58_L	70_A	1.092	0.98
161_R	165_T	1.091	0.98
55_E	74_G	1.086	0.98
69_H	117_R	1.081	0.98
163_H	167_N	1.070	0.98
55_E	70_A	1.063	0.98
4_G	7_E	1.061	0.98
133_E	137_E	1.039	0.98
78_L	99_I	1.038	0.98
100_A	139_W	1.030	0.98
31_R	80_Q	1.012	0.97
158_G	161_R	1.004	0.97
120_R	124_S	1.001	0.97
45_L	91_D	0.999	0.97
11_D	14_F	0.987	0.97
38_A	88_D	0.978	0.97
60_G	69_H	0.977	0.97
29_R	33_A	0.976	0.97
149_W	158_G	0.972	0.97
143_L	165_T	0.959	0.96
87_L	91_D	0.957	0.96
96_L	125_I	0.950	0.96
82_A	95_I	0.939	0.96
162_R	166_K	0.936	0.96
82_A	121_A	0.933	0.96
149_W	153_P	0.930	0.96
45_L	81_L	0.927	0.96
109_V	156_P	0.925	0.95
58_L	102_K	0.919	0.95
102_K	105_P	0.917	0.95
11_D	16_R	0.912	0.95
38_A	42_R	0.908	0.95
51_Y	70_A	0.907	0.95
63_P	156_P	0.894	0.95
10_T	13_V	0.893	0.94
72_A	117_R	0.878	0.94
41_R	86_A	0.874	0.94
18_F	60_G	0.869	0.94
49_L	94_R	0.869	0.94
18_F	117_R	0.858	0.93
89_K	135_E	0.856	0.93
70_A	102_K	0.850	0.93
52_L	78_L	0.847	0.93
81_L	84_N	0.840	0.92
134_A	138_A	0.837	0.92
41_R	92_L	0.833	0.92
24_A	28_R	0.831	0.92
49_L	53_A	0.829	0.92
96_L	135_E	0.829	0.92
155_D	158_G	0.824	0.92
103_L	168_F	0.817	0.91
79_K	83_R	0.810	0.91
52_L	102_K	0.803	0.91
14_F	17_S	0.801	0.91
156_P	160_A	0.789	0.90
16_R	55_E	0.787	0.90
21_L	67_W	0.786	0.90
49_L	98_A	0.785	0.90
21_L	76_D	0.780	0.89
96_L	131_L	0.779	0.89
73_H	117_R	0.775	0.89
67_W	117_R	0.772	0.89
3_Y	15_R	0.765	0.89
153_P	158_G	0.763	0.88
23_L	27_A	0.762	0.88
23_L	77_L	0.761	0.88
43_A	47_A	0.748	0.87
91_D	94_R	0.739	0.87
69_H	76_D	0.736	0.87
71_V	118_L	0.723	0.86
52_L	71_V	0.721	0.85
58_L	71_V	0.711	0.85
151_A	155_D	0.709	0.84
18_F	72_A	0.708	0.84
70_A	74_G	0.706	0.84
20_A	74_G	0.703	0.84
105_P	110_Y	0.701	0.84
156_P	159_L	0.698	0.84
28_R	83_R	0.697	0.83
25_E	79_K	0.696	0.83
6_G	9_G	0.690	0.83
99_I	122_V	0.689	0.83
99_I	103_L	0.686	0.82
21_L	72_A	0.682	0.82
102_K	110_Y	0.677	0.82
39_E	157_A	0.671	0.81
6_G	13_V	0.668	0.81
60_G	67_W	0.667	0.81
30_D	85_P	0.659	0.80
45_L	94_R	0.658	0.80
21_L	117_R	0.657	0.80
21_L	69_H	0.655	0.79
87_L	92_L	0.654	0.79
72_A	114_E	0.654	0.79
18_F	76_D	0.653	0.79
166_K	171_S	0.653	0.79
71_V	121_A	0.653	0.79
17_S	70_A	0.650	0.79
95_I	99_I	0.648	0.79
13_V	16_R	0.646	0.79
42_R	45_L	0.639	0.78
52_L	99_I	0.637	0.78
154_P	159_L	0.636	0.77
100_A	143_L	0.635	0.77
135_E	138_A	0.630	0.77
84_N	87_L	0.630	0.77
137_E	141_A	0.627	0.76
43_A	46_D	0.627	0.76
119_A	172_L	0.625	0.76
108_H	111_V	0.625	0.76
103_L	110_Y	0.620	0.76
71_V	80_Q	0.619	0.76
14_F	59_R	0.617	0.75
19_S	31_R	0.615	0.75
24_A	120_R	0.613	0.75
113_G	170_R	0.610	0.74
121_A	139_W	0.609	0.74
148_A	154_P	0.607	0.74
44_L	81_L	0.607	0.74
151_A	154_P	0.605	0.74
67_W	72_A	0.603	0.74
28_R	79_K	0.601	0.73
12_S	90_A	0.599	0.73
83_R	124_S	0.597	0.73
78_L	121_A	0.597	0.73
48_A	74_G	0.593	0.72
73_H	76_D	0.593	0.72
28_R	32_K	0.589	0.72
20_A	48_A	0.582	0.71
49_L	95_I	0.580	0.71
155_D	160_A	0.580	0.71
48_A	78_L	0.580	0.71
60_G	73_H	0.580	0.71
27_A	77_L	0.579	0.71
28_R	124_S	0.575	0.70
114_E	117_R	0.572	0.70
52_L	98_A	0.571	0.70
44_L	52_L	0.567	0.69
136_L	140_L	0.565	0.69
46_D	97_D	0.563	0.69
146_P	153_P	0.562	0.68
74_G	98_A	0.561	0.68
89_K	138_A	0.560	0.68
169_L	172_L	0.558	0.68
20_A	24_A	0.558	0.68
53_A	101_A	0.557	0.68
148_A	152_A	0.557	0.68
90_A	138_A	0.556	0.68
53_A	94_R	0.555	0.67
17_S	68_A	0.554	0.67
152_A	156_P	0.553	0.67
82_A	92_L	0.552	0.67
158_G	162_R	0.551	0.67
146_P	158_G	0.548	0.66
71_V	105_P	0.546	0.66
5_I	51_Y	0.544	0.66
92_L	131_L	0.544	0.66
87_L	121_A	0.543	0.66
104_A	161_R	0.542	0.66
100_A	142_R	0.540	0.65
29_R	62_D	0.538	0.65
126_L	136_L	0.537	0.65
160_A	163_H	0.536	0.65
90_A	93_A	0.535	0.65
11_D	15_R	0.534	0.64
27_A	84_N	0.529	0.64
17_S	21_L	0.529	0.64
6_G	11_D	0.526	0.63
9_G	13_V	0.525	0.63
155_D	165_T	0.523	0.63
17_S	73_H	0.520	0.62
61_F	65_K	0.519	0.62
31_R	63_P	0.519	0.62
103_L	136_L	0.518	0.62
149_W	155_D	0.515	0.62
39_E	43_A	0.514	0.62
159_L	170_R	0.514	0.62
46_D	50_A	0.511	0.61
93_A	97_D	0.510	0.61
87_L	95_I	0.509	0.61
45_L	77_L	0.500	0.59

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
1qgrA	1	0.8851	40.3	0.931	Contact Map
1ddgA	1	0.6782	36.4	0.933	Contact Map
3qfsA	1	0.6897	33	0.935	Contact Map
1ibrB	1	0.8851	24.1	0.939	Contact Map
3qe2A	1	0.7011	23.7	0.939	Contact Map
2bpoA	1	0.7011	13.3	0.946	Contact Map
4uqfA	5	0.7931	12.4	0.946	Contact Map
4jbsA	1	0.8678	11.7	0.947	Contact Map
4kx7A	1	0.8793	11.3	0.947	Contact Map
2yd0A	1	0.9253	10.6	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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