DUF4476 - PFAM28P - GREMLIN Contacts

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DUF4476 - Domain of unknown function (DUF4476)

PFAM:	PF14771	Sequences: VMSDADFNQLLQSIKNESFDDDKLSVAKQAFKNNCFTTAQVKQLLQLFSFESNRLELAKLAYPRVVDPENYYQLYDAFTFSSSKDELNEYL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	91 (89)
Sequences:	6013 (4910)
Seq/√Len:	520.4
META:	0.96

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_V	65_V	3.001	1.00
51_E	83_S	2.999	1.00
20_D	53_N	2.528	1.00
28_K	60_L	2.176	1.00
67_D	70_N	2.150	1.00
10_L	30_A	1.926	1.00
42_K	77_A	1.856	1.00
3_S	6_D	1.765	1.00
27_A	57_L	1.723	1.00
41_V	61_A	1.702	1.00
11_L	43_Q	1.664	1.00
45_L	58_A	1.660	1.00
75_Y	88_N	1.628	1.00
7_F	43_Q	1.623	1.00
81_S	85_D	1.581	1.00
65_V	71_Y	1.574	1.00
31_F	57_L	1.520	1.00
50_F	80_F	1.516	1.00
46_Q	77_A	1.477	1.00
42_K	46_Q	1.439	1.00
45_L	77_A	1.428	1.00
38_T	73_Q	1.360	1.00
45_L	57_L	1.310	1.00
9_Q	73_Q	1.298	1.00
42_K	76_D	1.291	1.00
31_F	34_N	1.287	1.00
20_D	23_K	1.287	1.00
35_C	66_V	1.264	1.00
28_K	56_E	1.259	1.00
2_M	10_L	1.249	1.00
11_L	47_L	1.243	1.00
62_Y	71_Y	1.237	1.00
49_S	79_T	1.234	1.00
11_L	15_K	1.210	1.00
31_F	36_F	1.210	1.00
17_E	26_V	1.198	1.00
4_D	8_N	1.193	1.00
18_S	49_S	1.189	1.00
59_K	86_E	1.163	1.00
21_D	52_S	1.155	1.00
15_K	47_L	1.154	1.00
57_L	61_A	1.137	1.00
39_A	73_Q	1.137	1.00
48_F	57_L	1.136	1.00
55_L	59_K	1.126	1.00
17_E	22_D	1.123	1.00
27_A	48_F	1.115	1.00
17_E	84_K	1.115	1.00
38_T	67_D	1.086	1.00
32_K	60_L	1.072	1.00
38_T	74_L	1.067	1.00
37_T	66_V	1.058	1.00
24_L	28_K	1.044	1.00
58_A	87_L	1.023	1.00
14_I	27_A	1.020	1.00
60_L	64_R	1.006	1.00
24_L	53_N	0.999	1.00
38_T	42_K	0.966	1.00
22_D	25_S	0.952	1.00
55_L	87_L	0.950	1.00
36_F	41_V	0.933	1.00
19_F	50_F	0.932	1.00
51_E	54_R	0.915	1.00
43_Q	46_Q	0.910	1.00
42_K	73_Q	0.909	1.00
87_L	90_Y	0.899	1.00
71_Y	74_L	0.888	1.00
85_D	89_E	0.868	1.00
44_L	57_L	0.867	1.00
18_S	79_T	0.834	1.00
31_F	61_A	0.830	1.00
19_F	80_F	0.823	1.00
7_F	40_Q	0.815	1.00
83_S	86_E	0.808	1.00
75_Y	84_K	0.802	1.00
84_K	88_N	0.792	1.00
74_L	87_L	0.792	1.00
86_E	89_E	0.789	1.00
12_Q	15_K	0.784	1.00
56_E	59_K	0.779	1.00
37_T	40_Q	0.775	1.00
6_D	9_Q	0.773	1.00
59_K	90_Y	0.772	1.00
23_K	47_L	0.764	1.00
80_F	83_S	0.752	1.00
58_A	78_F	0.746	1.00
55_L	78_F	0.737	1.00
72_Y	75_Y	0.729	1.00
42_K	74_L	0.729	1.00
78_F	84_K	0.720	1.00
39_A	43_Q	0.710	1.00
35_C	64_R	0.701	1.00
32_K	64_R	0.701	1.00
58_A	74_L	0.691	1.00
12_Q	16_N	0.690	1.00
22_D	81_S	0.688	1.00
7_F	11_L	0.679	1.00
4_D	43_Q	0.667	1.00
5_A	9_Q	0.650	1.00
85_D	88_N	0.639	1.00
24_L	56_E	0.634	1.00
24_L	57_L	0.632	1.00
27_A	44_L	0.630	1.00
26_V	30_A	0.622	1.00
6_D	34_N	0.615	1.00
14_I	44_L	0.611	1.00
55_L	83_S	0.603	1.00
19_F	22_D	0.587	0.99
5_A	8_N	0.580	0.99
24_L	48_F	0.578	0.99
14_I	47_L	0.574	0.99
61_A	65_V	0.566	0.99
38_T	65_V	0.566	0.99
20_D	48_F	0.566	0.99
75_Y	87_L	0.550	0.99
54_R	77_A	0.548	0.99
13_S	26_V	0.547	0.99
81_S	84_K	0.546	0.99
11_L	44_L	0.543	0.99
14_I	26_V	0.538	0.99
8_N	12_Q	0.534	0.99
62_Y	68_P	0.532	0.99
19_F	23_K	0.531	0.99
9_Q	12_Q	0.526	0.99
8_N	43_Q	0.520	0.99
52_S	82_S	0.518	0.99
62_Y	65_V	0.517	0.99
2_M	34_N	0.513	0.98
14_I	23_K	0.511	0.98
78_F	83_S	0.507	0.98
52_S	56_E	0.506	0.98
61_A	71_Y	0.504	0.98
56_E	60_L	0.502	0.98
71_Y	87_L	0.500	0.98

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
3dtpE	2	0.967	21.8	0.835	Contact Map
1m45A	1	0.967	17.4	0.842	Contact Map
1w7jB	1	0.9341	16.5	0.844	Contact Map
4fhnB	1	0.978	16.3	0.844	Contact Map
4ociA	2	1	16	0.845	Contact Map
4mzjA	1	0.978	16	0.845	Contact Map
1wdcB	1	0.978	15.8	0.845	Contact Map
3j04B	1	0.978	15.6	0.846	Contact Map
4wpxA	1	1	15.6	0.846	Contact Map
4i2yA	1	1	15.6	0.846	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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