DUF2939 - PFAM28P - GREMLIN Contacts

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DUF2939 - Protein of unknown function (DUF2939)

PFAM:	PF11159	Sequences: LLLLLAAYAASPYYALYRLRSAARAGDAAALERYVDFPALRESLKAQLVAALDLRRAGKDPSDNPLAALGAALAPALADPAVDALVTPEGLAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	94 (91)
Sequences:	4247 (3190)
Seq/√Len:	334.4
META:	0.917

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_L	31_L	3.605	1.00
43_S	47_Q	2.791	1.00
8_Y	11_S	2.546	1.00
20_R	24_R	2.139	1.00
32_E	37_F	2.085	1.00
18_R	34_Y	2.065	1.00
76_A	80_P	2.032	1.00
45_K	82_V	1.912	1.00
18_R	30_A	1.907	1.00
87_T	90_G	1.809	1.00
11_S	15_A	1.769	1.00
39_A	43_S	1.766	1.00
28_A	32_E	1.747	1.00
51_A	56_R	1.734	1.00
14_Y	18_R	1.679	1.00
19_L	34_Y	1.677	1.00
27_D	30_A	1.664	1.00
7_A	11_S	1.641	1.00
30_A	34_Y	1.512	1.00
56_R	59_K	1.510	1.00
21_S	25_A	1.468	1.00
37_F	47_Q	1.438	1.00
76_A	79_D	1.431	1.00
15_A	18_R	1.407	1.00
5_L	9_A	1.405	1.00
42_E	46_A	1.392	1.00
6_A	10_A	1.365	1.00
90_G	93_A	1.338	1.00
17_Y	21_S	1.336	1.00
10_A	14_Y	1.328	1.00
22_A	30_A	1.316	1.00
70_G	73_L	1.298	1.00
39_A	42_E	1.243	1.00
29_A	32_E	1.228	1.00
14_Y	17_Y	1.224	1.00
15_A	34_Y	1.215	1.00
45_K	79_D	1.188	1.00
10_A	13_Y	1.174	1.00
54_L	58_G	1.160	1.00
40_L	43_S	1.155	1.00
36_D	39_A	1.133	1.00
42_E	45_K	1.123	1.00
21_S	24_R	1.117	1.00
11_S	14_Y	1.074	1.00
31_L	92_A	1.065	1.00
9_A	13_Y	1.033	1.00
25_A	30_A	1.017	1.00
63_D	66_L	1.009	1.00
78_A	82_V	0.996	1.00
79_D	83_D	0.987	1.00
41_R	83_D	0.968	1.00
38_P	42_E	0.959	1.00
4_L	8_Y	0.953	1.00
37_F	41_R	0.945	1.00
31_L	35_V	0.939	1.00
75_P	79_D	0.930	1.00
72_A	76_A	0.928	1.00
4_L	7_A	0.922	1.00
70_G	75_P	0.908	1.00
45_K	83_D	0.904	1.00
22_A	31_L	0.887	1.00
31_L	37_F	0.885	1.00
49_V	52_L	0.882	1.00
51_A	55_R	0.881	1.00
28_A	89_E	0.867	1.00
13_Y	17_Y	0.853	1.00
49_V	79_D	0.846	1.00
57_A	60_D	0.843	1.00
72_A	75_P	0.843	1.00
44_L	82_V	0.823	1.00
54_L	60_D	0.818	1.00
74_A	77_L	0.817	1.00
41_R	45_K	0.804	1.00
72_A	89_E	0.803	1.00
7_A	14_Y	0.799	1.00
54_L	57_A	0.796	1.00
56_R	60_D	0.789	1.00
38_P	41_R	0.782	1.00
9_A	14_Y	0.769	1.00
74_A	78_A	0.765	1.00
26_G	92_A	0.756	1.00
59_K	71_A	0.748	0.99
44_L	47_Q	0.736	0.99
41_R	47_Q	0.731	0.99
17_Y	20_R	0.728	0.99
70_G	74_A	0.721	0.99
49_V	78_A	0.716	0.99
81_A	86_V	0.709	0.99
45_K	52_L	0.705	0.99
12_P	15_A	0.692	0.99
46_A	50_A	0.680	0.99
40_L	47_Q	0.677	0.99
59_K	63_D	0.671	0.99
71_A	75_P	0.657	0.99
85_L	90_G	0.651	0.99
26_G	89_E	0.645	0.98
79_D	82_V	0.633	0.98
23_A	37_F	0.628	0.98
63_D	67_A	0.627	0.98
80_P	84_A	0.624	0.98
55_R	58_G	0.624	0.98
58_G	61_P	0.618	0.98
8_Y	13_Y	0.615	0.98
26_G	34_Y	0.611	0.98
5_L	8_Y	0.607	0.98
70_G	78_A	0.606	0.98
47_Q	51_A	0.599	0.98
78_A	81_A	0.598	0.98
55_R	59_K	0.586	0.97
41_R	79_D	0.583	0.97
65_P	69_L	0.569	0.97
22_A	27_D	0.569	0.97
13_Y	19_L	0.566	0.97
31_L	87_T	0.563	0.96
18_R	21_S	0.563	0.96
86_V	90_G	0.561	0.96
17_Y	91_L	0.557	0.96
15_A	19_L	0.557	0.96
50_A	63_D	0.556	0.96
87_T	91_L	0.552	0.96
69_L	72_A	0.551	0.96
84_A	88_P	0.550	0.96
37_F	43_S	0.541	0.96
35_V	40_L	0.540	0.96
65_P	68_A	0.539	0.96
4_L	10_A	0.539	0.96
45_K	48_L	0.539	0.96
75_P	91_L	0.530	0.95
57_A	61_P	0.529	0.95
6_A	17_Y	0.527	0.95
64_N	68_A	0.520	0.95
18_R	22_A	0.515	0.94
16_L	20_R	0.514	0.94
52_L	84_A	0.510	0.94
36_D	71_A	0.504	0.94
20_R	23_A	0.500	0.93

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
1ofdA	1	0.9468	6.6	0.877	Contact Map
3k7cA	2	0.8723	4.5	0.886	Contact Map
3qnqA	2	0.3511	3.9	0.89	Contact Map
1dm5A	4	0.7872	3.8	0.891	Contact Map
1ea0A	1	0.9043	3	0.896	Contact Map
4pwuA	4	0.7979	2.8	0.898	Contact Map
2jy0A	1	0.1596	2.8	0.898	Contact Map
4bxhA	3	0.9043	2.7	0.899	Contact Map
1yiiA	1	0.7766	2.6	0.899	Contact Map
1n00A	1	0.8191	2.6	0.899	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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