DUF3180 - PFAM28P - GREMLIN Contacts

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DUF3180 - Protein of unknown function (DUF3180)

PFAM:	PF11377	Sequences: LVAAAVVAAVLGWLLVRLLAYGSLPPLPWTAPVTLLLLAVAEAVLARPVRRRIRGRPGRRPLDPLRAARTVVLAKASALVGALVAGWYAGVLLYLLGRLDLPAAREDAVAAGVAAVAALALVAAALWLERACRVPP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	136 (136)
Sequences:	2793 (1897)
Seq/√Len:	162.6
META:	0.702

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
112_G	116_V	2.967	1.00
108_A	112_G	2.927	1.00
119_L	123_A	2.875	1.00
123_A	127_W	2.784	1.00
109_V	113_V	2.678	1.00
39_A	124_A	2.488	1.00
46_A	128_L	2.418	1.00
81_G	122_V	2.307	1.00
50_R	54_R	2.229	1.00
42_E	125_A	2.047	1.00
36_L	117_A	2.047	1.00
80_V	84_V	2.026	1.00
65_L	68_A	2.024	1.00
49_V	62_L	2.017	1.00
65_L	69_R	1.875	1.00
85_A	115_A	1.797	1.00
46_A	131_A	1.792	1.00
127_W	131_A	1.781	1.00
77_S	121_L	1.763	1.00
124_A	128_L	1.763	1.00
49_V	70_T	1.744	1.00
47_R	51_R	1.713	1.00
128_L	131_A	1.688	1.00
105_R	109_V	1.687	1.00
16_V	90_G	1.685	1.00
43_A	47_R	1.633	1.00
74_A	125_A	1.629	1.00
85_A	119_L	1.579	1.00
99_L	108_A	1.578	1.00
131_A	134_V	1.521	1.00
8_A	83_L	1.507	1.00
75_K	79_L	1.503	1.00
42_E	77_S	1.465	1.00
75_K	129_E	1.448	1.00
4_A	8_A	1.436	1.00
11_L	15_L	1.429	1.00
55_G	58_G	1.410	1.00
47_R	131_A	1.355	1.00
1_L	78_A	1.332	1.00
5_A	85_A	1.307	1.00
77_S	125_A	1.302	1.00
41_A	45_L	1.292	1.00
12_G	87_W	1.271	1.00
35_L	118_A	1.267	1.00
53_I	131_A	1.260	1.00
8_A	12_G	1.260	1.00
40_V	44_V	1.249	1.00
87_W	91_V	1.232	1.00
42_E	121_L	1.217	1.00
89_A	115_A	1.216	1.00
92_L	112_G	1.199	1.00
44_V	47_R	1.158	1.00
55_G	61_P	1.151	1.00
71_V	79_L	1.137	1.00
14_L	17_R	1.127	1.00
45_L	70_T	1.125	1.00
78_A	126_L	1.121	1.00
85_A	118_A	1.119	1.00
109_V	112_G	1.109	1.00
92_L	111_A	1.104	1.00
12_G	16_V	1.095	1.00
17_R	20_A	1.085	1.00
97_G	100_D	1.083	0.99
101_L	104_A	1.075	0.99
32_P	117_A	1.074	0.99
70_T	74_A	1.069	0.99
62_L	67_A	1.066	0.99
88_Y	114_A	1.051	0.99
71_V	78_A	1.043	0.99
28_P	31_A	1.024	0.99
44_V	48_P	1.014	0.99
99_L	105_R	1.013	0.99
7_V	11_L	1.005	0.99
104_A	107_D	1.003	0.99
32_P	113_V	0.992	0.99
28_P	80_V	0.989	0.99
89_A	92_L	0.985	0.99
120_A	124_A	0.985	0.99
75_K	78_A	0.982	0.99
68_A	71_V	0.977	0.99
19_L	23_S	0.961	0.99
48_P	66_R	0.955	0.99
85_A	122_V	0.946	0.99
92_L	108_A	0.941	0.99
6_V	9_A	0.937	0.99
63_D	66_R	0.925	0.98
66_R	70_T	0.924	0.98
67_A	71_V	0.913	0.98
62_L	70_T	0.906	0.98
30_T	114_A	0.892	0.98
4_A	79_L	0.891	0.98
126_L	130_R	0.886	0.98
15_L	18_L	0.870	0.98
122_V	125_A	0.869	0.98
46_A	49_V	0.868	0.98
71_V	75_K	0.858	0.97
55_G	60_R	0.855	0.97
53_I	135_P	0.837	0.97
95_L	107_D	0.835	0.97
43_A	127_W	0.835	0.97
43_A	124_A	0.833	0.97
100_D	105_R	0.830	0.97
91_V	111_A	0.819	0.97
81_G	125_A	0.811	0.96
52_R	128_L	0.803	0.96
31_A	88_Y	0.801	0.96
21_Y	107_D	0.799	0.96
131_A	135_P	0.797	0.96
67_A	70_T	0.796	0.96
85_A	89_A	0.793	0.96
50_R	131_A	0.790	0.96
78_A	129_E	0.788	0.96
92_L	115_A	0.777	0.95
84_V	118_A	0.771	0.95
33_V	37_L	0.761	0.95
4_A	83_L	0.749	0.94
9_A	12_G	0.747	0.94
9_A	89_A	0.740	0.94
32_P	114_A	0.739	0.94
4_A	68_A	0.738	0.94
95_L	103_A	0.728	0.94
59_R	87_W	0.728	0.94
87_W	90_G	0.728	0.94
9_A	16_V	0.726	0.93
73_L	78_A	0.708	0.93
116_V	120_A	0.706	0.92
122_V	126_L	0.702	0.92
7_V	10_V	0.701	0.92
4_A	90_G	0.699	0.92
79_L	83_L	0.697	0.92
87_W	129_E	0.683	0.91
51_R	55_G	0.682	0.91
27_L	110_A	0.682	0.91
82_A	86_G	0.679	0.91
36_L	40_V	0.679	0.91
36_L	120_A	0.672	0.90
70_T	132_C	0.670	0.90
98_R	105_R	0.670	0.90
47_R	50_R	0.668	0.90
32_P	39_A	0.666	0.90
89_A	93_L	0.662	0.90
74_A	81_G	0.662	0.90
56_R	59_R	0.657	0.89
41_A	66_R	0.654	0.89
3_A	7_V	0.647	0.89
96_L	108_A	0.627	0.87
46_A	127_W	0.625	0.87
39_A	117_A	0.624	0.87
54_R	131_A	0.624	0.87
21_Y	25_P	0.624	0.87
16_V	94_Y	0.623	0.87
68_A	72_V	0.623	0.87
2_V	5_A	0.622	0.87
113_V	117_A	0.621	0.87
8_A	16_V	0.620	0.87
9_A	93_L	0.618	0.86
26_P	106_E	0.616	0.86
95_L	108_A	0.616	0.86
115_A	118_A	0.616	0.86
32_P	110_A	0.606	0.85
5_A	9_A	0.600	0.85
14_L	118_A	0.598	0.85
78_A	87_W	0.595	0.84
76_A	120_A	0.592	0.84
69_R	73_L	0.591	0.84
22_G	103_A	0.582	0.83
125_A	136_P	0.580	0.83
13_W	90_G	0.575	0.82
93_L	112_G	0.572	0.82
27_L	36_L	0.572	0.82
33_V	36_L	0.569	0.82
15_L	19_L	0.568	0.82
10_V	14_L	0.567	0.81
56_R	60_R	0.563	0.81
48_P	101_L	0.563	0.81
32_P	90_G	0.563	0.81
74_A	77_S	0.560	0.81
52_R	60_R	0.560	0.81
126_L	129_E	0.558	0.80
16_V	91_V	0.555	0.80
20_A	24_L	0.551	0.80
32_P	46_A	0.549	0.79
1_L	5_A	0.548	0.79
45_L	66_R	0.547	0.79
29_W	33_V	0.545	0.79
48_P	51_R	0.543	0.79
49_V	67_A	0.542	0.78
131_A	136_P	0.535	0.78
35_L	84_V	0.534	0.77
118_A	121_L	0.533	0.77
11_L	14_L	0.533	0.77
104_A	111_A	0.531	0.77
93_L	113_V	0.530	0.77
98_R	102_P	0.528	0.77
20_A	23_S	0.525	0.76
2_V	14_L	0.525	0.76
37_L	40_V	0.525	0.76
29_W	32_P	0.522	0.76
71_V	135_P	0.518	0.75
49_V	53_I	0.512	0.74
43_A	131_A	0.512	0.74
74_A	78_A	0.503	0.73
31_A	69_R	0.501	0.73
94_Y	97_G	0.500	0.73

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
4mt1A	3	0.9118	13.7	0.916	Contact Map
4xnjA	1	0.9853	11.4	0.92	Contact Map
4k0jA	3	0.9118	8.4	0.924	Contact Map
2l2tA	2	0.3015	8	0.925	Contact Map
1pw4A	1	0.9338	7.6	0.926	Contact Map
2drnC	1	0.0882	7.1	0.927	Contact Map
3wdoA	1	0.9706	6.3	0.928	Contact Map
2gfpA	2	0.9706	6	0.929	Contact Map
2cfqA	1	0.9706	5.9	0.929	Contact Map
3ne5A	3	0.9044	5.6	0.93	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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