DUF1489 - PFAM28P - GREMLIN Contacts

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DUF1489 - Protein of unknown function (DUF1489)

PFAM:	PF07370	Sequences: LIKLCVGCDSVEDLAAWQLAEARRRGEPGELRHVTRMTPKRADELLDGGSLYWVIKGQILARQRILGLEEVTDEDGIGRCAIVLDPELVPVEPRPRRAFQGWRYLEPEDAPPDLGAGAAGGLAALPPELRRELAELGLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (137)
Sequences:	4862 (2723)
Seq/√Len:	232.6
META:	0.893

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_R	85_D	3.266	1.00
8_C	13_D	3.082	1.00
5_C	8_C	3.044	1.00
8_C	17_W	2.772	1.00
61_A	88_L	2.754	1.00
68_L	82_I	2.739	1.00
41_R	44_E	2.636	1.00
65_I	82_I	2.636	1.00
13_D	17_W	2.359	1.00
5_C	51_L	2.347	1.00
34_V	81_A	2.339	1.00
1_L	45_L	2.337	1.00
2_I	59_I	2.326	1.00
45_L	65_I	2.302	1.00
67_G	83_V	2.162	1.00
73_D	79_R	2.106	1.00
32_R	81_A	2.100	1.00
15_A	90_P	2.088	1.00
91_V	94_R	2.087	1.00
92_E	112_P	2.010	1.00
54_V	99_F	1.976	1.00
58_Q	93_P	1.913	1.00
106_E	109_D	1.883	1.00
38_T	70_E	1.865	1.00
15_A	88_L	1.751	1.00
71_V	81_A	1.727	1.00
105_L	110_A	1.619	1.00
9_D	13_D	1.616	1.00
69_E	83_V	1.597	1.00
11_V	61_A	1.554	1.00
30_E	69_E	1.523	1.00
132_E	135_E	1.517	1.00
70_E	78_G	1.485	1.00
18_Q	31_L	1.483	1.00
71_V	79_R	1.466	1.00
11_V	90_P	1.459	1.00
41_R	106_E	1.386	1.00
38_T	42_A	1.317	1.00
4_L	99_F	1.279	1.00
12_E	16_A	1.269	1.00
10_S	13_D	1.266	1.00
21_E	25_R	1.261	1.00
127_P	131_R	1.256	1.00
42_A	67_G	1.249	1.00
60_L	93_P	1.211	1.00
96_R	109_D	1.190	1.00
30_E	83_V	1.158	1.00
12_E	15_A	1.156	1.00
4_L	54_V	1.152	1.00
22_A	27_E	1.152	1.00
115_G	118_A	1.109	1.00
125_L	129_L	1.108	1.00
9_D	56_K	1.097	1.00
107_P	110_A	1.097	1.00
45_L	68_L	1.095	1.00
5_C	17_W	1.093	1.00
72_T	78_G	1.093	1.00
73_D	77_I	1.082	1.00
5_C	13_D	1.080	1.00
42_A	68_L	1.070	1.00
59_I	94_R	1.057	1.00
42_A	46_L	1.039	1.00
69_E	81_A	1.019	1.00
15_A	18_Q	1.000	1.00
73_D	78_G	0.991	1.00
8_C	14_L	0.986	1.00
125_L	130_R	0.976	1.00
11_V	55_I	0.959	1.00
1_L	82_I	0.943	1.00
132_E	138_L	0.927	1.00
132_E	136_L	0.926	1.00
38_T	78_G	0.920	1.00
130_R	134_A	0.908	1.00
10_S	55_I	0.908	1.00
20_A	24_R	0.889	0.99
62_R	113_D	0.888	0.99
5_C	14_L	0.886	0.99
34_V	71_V	0.884	0.99
66_L	85_D	0.882	0.99
38_T	68_L	0.881	0.99
22_A	29_G	0.876	0.99
33_H	82_I	0.875	0.99
33_H	84_L	0.870	0.99
64_R	87_E	0.865	0.99
8_C	55_I	0.850	0.99
128_E	131_R	0.849	0.99
30_E	67_G	0.848	0.99
55_I	60_L	0.847	0.99
75_D	79_R	0.823	0.99
22_A	28_P	0.810	0.99
38_T	80_C	0.804	0.99
46_L	67_G	0.799	0.99
117_G	120_G	0.798	0.99
63_Q	88_L	0.795	0.99
127_P	130_R	0.791	0.99
95_P	98_A	0.789	0.99
2_I	96_R	0.786	0.99
5_C	10_S	0.786	0.99
26_G	29_G	0.775	0.98
34_V	79_R	0.770	0.98
32_R	83_V	0.769	0.98
63_Q	84_L	0.768	0.98
118_A	121_G	0.768	0.98
3_K	33_H	0.768	0.98
59_I	91_V	0.763	0.98
50_S	62_R	0.762	0.98
45_L	49_G	0.757	0.98
25_R	29_G	0.755	0.98
33_H	83_V	0.750	0.98
128_E	132_E	0.750	0.98
37_M	99_F	0.748	0.98
130_R	139_L	0.728	0.98
63_Q	86_P	0.725	0.98
119_A	123_A	0.722	0.98
129_L	132_E	0.722	0.98
128_E	135_E	0.721	0.98
23_R	27_E	0.710	0.97
45_L	107_P	0.705	0.97
40_K	106_E	0.702	0.97
5_C	55_I	0.700	0.97
32_R	71_V	0.698	0.97
23_R	29_G	0.697	0.97
20_A	23_R	0.696	0.97
43_D	47_D	0.690	0.97
60_L	94_R	0.689	0.97
131_R	135_E	0.688	0.97
68_L	80_C	0.684	0.97
134_A	138_L	0.682	0.97
13_D	16_A	0.680	0.97
31_L	86_P	0.678	0.96
2_I	99_F	0.676	0.96
33_H	53_W	0.675	0.96
4_L	9_D	0.674	0.96
21_E	29_G	0.671	0.96
55_I	61_A	0.671	0.96
22_A	26_G	0.669	0.96
20_A	27_E	0.668	0.96
50_S	113_D	0.666	0.96
21_E	24_R	0.658	0.96
92_E	118_A	0.658	0.96
18_Q	86_P	0.658	0.96
70_E	81_A	0.657	0.96
34_V	77_I	0.653	0.96
37_M	40_K	0.649	0.95
32_R	69_E	0.649	0.95
2_I	91_V	0.648	0.95
46_L	68_L	0.647	0.95
8_C	51_L	0.645	0.95
31_L	84_L	0.640	0.95
10_S	16_A	0.639	0.95
37_M	68_L	0.639	0.95
120_G	123_A	0.634	0.95
5_C	53_W	0.634	0.95
36_R	65_I	0.628	0.95
31_L	85_D	0.624	0.94
21_E	27_E	0.621	0.94
132_E	137_G	0.614	0.94
22_A	25_R	0.611	0.94
37_M	73_D	0.610	0.94
33_H	51_L	0.609	0.94
4_L	37_M	0.607	0.94
129_L	138_L	0.606	0.94
58_Q	131_R	0.606	0.94
93_P	114_L	0.604	0.93
66_L	84_L	0.602	0.93
59_I	96_R	0.601	0.93
4_L	7_G	0.597	0.93
59_I	105_L	0.597	0.93
46_L	65_I	0.592	0.93
45_L	48_G	0.589	0.93
24_R	29_G	0.589	0.93
58_Q	127_P	0.587	0.92
116_A	120_G	0.579	0.92
116_A	119_A	0.578	0.92
68_L	71_V	0.576	0.92
56_K	98_A	0.575	0.92
50_S	63_Q	0.573	0.92
1_L	65_I	0.569	0.91
53_W	61_A	0.566	0.91
73_D	81_A	0.564	0.91
18_Q	84_L	0.559	0.91
57_G	99_F	0.555	0.90
27_E	30_E	0.554	0.90
51_L	82_I	0.554	0.90
11_V	14_L	0.551	0.90
37_M	79_R	0.546	0.89
119_A	127_P	0.546	0.89
85_D	89_V	0.545	0.89
128_E	137_G	0.544	0.89
37_M	42_A	0.542	0.89
30_E	66_L	0.536	0.89
64_R	89_V	0.534	0.88
14_L	55_I	0.532	0.88
37_M	78_G	0.528	0.88
96_R	105_L	0.527	0.88
18_Q	63_Q	0.515	0.87
6_V	55_I	0.515	0.87
94_R	112_P	0.515	0.87
5_C	61_A	0.515	0.87
71_V	77_I	0.513	0.86
130_R	135_E	0.509	0.86
33_H	86_P	0.505	0.86
121_G	124_A	0.504	0.85
115_G	119_A	0.503	0.85
65_I	68_L	0.502	0.85
133_L	136_L	0.500	0.85

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
2mk9A	2	0.2302	10.6	0.954	Contact Map
2jd3A	2	0.2878	9.8	0.954	Contact Map
2rodB	1	0.1223	9.4	0.955	Contact Map
5af7A	4	0.3453	9.3	0.955	Contact Map
4xvxA	4	0.3237	8.4	0.956	Contact Map
1ivhA	4	0.3885	8.2	0.956	Contact Map
1vr3A	1	0.2662	7.7	0.957	Contact Map
1ukwA	4	0.3669	7.3	0.957	Contact Map
3m9vA	4	0.3885	7.1	0.957	Contact Map
4x28D	2	0.3813	6.8	0.958	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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