DUF1835 - PFAM28P - GREMLIN Contacts

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DUF1835 - Domain of unknown function (DUF1835)

PFAM:	PF08874	Sequences: LHIVFGDSAAGTLRQALELGGLLGEVLVWRDDLSVGPLPDLDTEEGREARAEWLAEVLGGDYEGEEDIEETLAELDELLDALPEGEEVVLWFEHDLHDQLGLYWLLSQLKDFQGRIFILNT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (115)
Sequences:	4317 (3211)
Seq/√Len:	299.4
META:	0.84

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_D	30_R	3.389	1.00
6_G	9_A	3.081	1.00
72_L	75_L	2.708	1.00
77_E	81_A	2.415	1.00
52_E	56_E	2.343	1.00
5_F	101_G	2.274	1.00
71_T	75_L	2.232	1.00
8_S	11_G	2.220	1.00
69_E	73_A	2.108	1.00
8_S	12_T	2.099	1.00
39_P	49_A	1.989	1.00
7_D	28_V	1.956	1.00
10_A	28_V	1.941	1.00
25_E	78_L	1.926	1.00
99_Q	103_Y	1.889	1.00
65_E	68_I	1.826	1.00
15_Q	18_E	1.773	1.00
38_L	46_G	1.659	1.00
17_L	20_G	1.642	1.00
107_S	110_K	1.557	1.00
72_L	76_D	1.556	1.00
4_V	13_L	1.503	1.00
11_G	15_Q	1.482	1.00
75_L	78_L	1.417	1.00
50_R	54_L	1.408	1.00
77_E	80_D	1.403	1.00
104_W	107_S	1.400	1.00
11_G	14_R	1.394	1.00
104_W	108_Q	1.389	1.00
71_T	74_E	1.387	1.00
70_E	74_E	1.378	1.00
34_S	97_H	1.374	1.00
74_E	78_L	1.316	1.00
21_G	24_G	1.315	1.00
10_A	26_V	1.275	1.00
37_P	53_W	1.272	1.00
61_D	66_E	1.265	1.00
76_D	80_D	1.248	1.00
70_E	73_A	1.237	1.00
41_L	49_A	1.210	1.00
99_Q	102_L	1.203	1.00
12_T	16_A	1.203	1.00
61_D	64_G	1.190	1.00
64_G	68_I	1.182	1.00
43_T	47_R	1.178	1.00
13_L	26_V	1.169	1.00
71_T	78_L	1.153	1.00
79_L	82_L	1.130	1.00
48_E	52_E	1.109	1.00
31_D	37_P	1.097	1.00
63_E	68_I	1.095	1.00
13_L	16_A	1.087	1.00
12_T	17_L	1.073	1.00
105_L	108_Q	1.067	1.00
43_T	46_G	1.033	1.00
12_T	15_Q	1.022	1.00
2_H	89_V	1.021	1.00
95_D	98_D	1.014	1.00
48_E	51_A	1.012	1.00
53_W	57_V	1.011	1.00
80_D	112_F	1.009	1.00
9_A	13_L	1.003	1.00
78_L	81_A	0.997	1.00
75_L	79_L	0.988	1.00
49_A	52_E	0.985	1.00
46_G	50_R	0.980	1.00
82_L	85_G	0.973	1.00
73_A	77_E	0.973	1.00
29_W	104_W	0.961	1.00
101_G	104_W	0.960	1.00
52_E	55_A	0.957	1.00
25_E	85_G	0.955	1.00
15_Q	19_L	0.953	1.00
80_D	83_P	0.947	1.00
41_L	46_G	0.926	1.00
4_V	28_V	0.913	1.00
72_L	78_L	0.910	1.00
10_A	14_R	0.900	1.00
2_H	37_P	0.897	1.00
17_L	26_V	0.884	1.00
74_E	77_E	0.879	1.00
45_E	49_A	0.876	1.00
31_D	50_R	0.875	1.00
64_G	67_D	0.868	1.00
71_T	76_D	0.858	1.00
31_D	100_L	0.840	1.00
54_L	57_V	0.834	1.00
93_E	98_D	0.832	1.00
62_Y	66_E	0.817	1.00
56_E	59_G	0.815	1.00
16_A	19_L	0.812	1.00
82_L	109_L	0.812	1.00
69_E	75_L	0.802	1.00
5_F	98_D	0.787	0.99
46_G	49_A	0.785	0.99
90_L	93_E	0.779	0.99
44_E	73_A	0.774	0.99
68_I	72_L	0.763	0.99
63_E	67_D	0.756	0.99
34_S	101_G	0.754	0.99
9_A	12_T	0.753	0.99
62_Y	65_E	0.752	0.99
105_L	109_L	0.741	0.99
7_D	10_A	0.734	0.99
100_L	103_Y	0.733	0.99
29_W	105_L	0.731	0.99
68_I	76_D	0.730	0.99
48_E	69_E	0.729	0.99
63_E	66_E	0.718	0.99
50_R	56_E	0.709	0.99
39_P	45_E	0.706	0.99
98_D	101_G	0.705	0.99
94_H	99_Q	0.698	0.99
73_A	76_D	0.692	0.99
47_R	51_A	0.676	0.98
93_E	97_H	0.672	0.98
51_A	69_E	0.670	0.98
69_E	72_L	0.662	0.98
88_V	94_H	0.660	0.98
41_L	104_W	0.659	0.98
9_A	26_V	0.653	0.98
90_L	101_G	0.652	0.98
5_F	9_A	0.651	0.98
2_H	31_D	0.648	0.98
4_V	26_V	0.648	0.98
32_D	95_D	0.647	0.98
33_L	97_H	0.646	0.98
46_G	53_W	0.643	0.98
4_V	9_A	0.641	0.98
7_D	11_G	0.640	0.98
65_E	69_E	0.631	0.98
37_P	50_R	0.630	0.97
27_L	78_L	0.629	0.97
27_L	35_V	0.628	0.97
55_A	58_L	0.615	0.97
32_D	97_H	0.615	0.97
4_V	8_S	0.615	0.97
97_H	101_G	0.612	0.97
96_L	100_L	0.611	0.97
27_L	75_L	0.610	0.97
40_D	45_E	0.603	0.97
78_L	82_L	0.601	0.97
30_R	97_H	0.601	0.97
40_D	46_G	0.599	0.97
43_T	104_W	0.592	0.96
6_G	33_L	0.591	0.96
112_F	115_R	0.582	0.96
45_E	48_E	0.581	0.96
33_L	104_W	0.577	0.96
61_D	67_D	0.576	0.96
72_L	81_A	0.572	0.96
50_R	58_L	0.561	0.95
42_D	46_G	0.559	0.95
40_D	43_T	0.559	0.95
42_D	45_E	0.556	0.95
52_E	65_E	0.535	0.94
76_D	79_L	0.532	0.94
101_G	105_L	0.529	0.93
31_D	98_D	0.528	0.93
92_F	96_L	0.526	0.93
5_F	93_E	0.524	0.93
62_Y	68_I	0.522	0.93
68_I	71_T	0.519	0.93
30_R	71_T	0.518	0.93
44_E	49_A	0.517	0.93
35_V	54_L	0.515	0.92
30_R	92_F	0.512	0.92
1_L	86_E	0.510	0.92
47_R	69_E	0.509	0.92
6_G	12_T	0.504	0.92
7_D	12_T	0.504	0.92
5_F	8_S	0.500	0.91

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
1mw9X	1	0.8595	15.5	0.897	Contact Map
4dduA	1	0.9587	9	0.907	Contact Map
1wy5A	4	0.4959	8.7	0.908	Contact Map
3qyfA	2	0.9504	6.9	0.912	Contact Map
3a2kA	1	0.4463	6.7	0.913	Contact Map
1k7cA	1	0.8017	6.5	0.913	Contact Map
4blpA	3	0.5372	5.6	0.916	Contact Map
1mgpA	1	0.9339	4.8	0.919	Contact Map
2gaiA	1	0.8512	4.7	0.919	Contact Map
1i7dA	1	0.9752	4.7	0.919	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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