DUF4307 - PFAM28P - GREMLIN Contacts

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DUF4307 - Domain of unknown function (DUF4307)

PFAM:	PF14155	Sequences: RRRRLVIVAAVLAVVALAWLAWAGYSHYSTPPVSAELIGFEVVDDHTVTVTFEVTRPDGSPAVCTVRALDEDGAEVGRREVTVPAGDARTVRVTVTVRTTRRAVTGEVYGC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	111 (109)
Sequences:	3087 (2276)
Seq/√Len:	218.0
META:	0.723

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
44_D	47_T	3.322	1.00
45_D	102_R	2.928	1.00
68_A	103_A	2.710	1.00
70_D	101_R	2.707	1.00
75_E	78_R	2.457	1.00
19_W	23_A	2.377	1.00
51_T	92_R	2.261	1.00
47_T	96_T	2.162	1.00
63_V	80_E	2.151	1.00
69_L	73_G	2.114	1.00
56_R	62_A	2.092	1.00
52_F	81_V	2.041	1.00
49_T	96_T	1.952	1.00
66_V	95_V	1.901	1.00
50_V	106_G	1.869	1.00
38_I	53_E	1.844	1.00
51_T	94_T	1.829	1.00
79_R	95_V	1.823	1.00
65_T	80_E	1.736	1.00
42_V	48_V	1.689	1.00
53_E	92_R	1.685	1.00
70_D	74_A	1.611	1.00
36_E	53_E	1.577	1.00
56_R	59_G	1.574	1.00
67_R	75_E	1.523	1.00
21_A	25_Y	1.497	1.00
79_R	97_V	1.483	1.00
67_R	107_E	1.476	1.00
99_T	103_A	1.441	1.00
83_V	93_V	1.415	1.00
71_E	104_V	1.382	1.00
65_T	78_R	1.369	1.00
43_V	47_T	1.304	1.00
55_T	90_T	1.265	1.00
39_G	51_T	1.263	1.00
6_V	10_A	1.246	1.00
52_F	95_V	1.241	1.00
69_L	105_T	1.233	1.00
41_E	49_T	1.222	1.00
22_W	26_S	1.219	1.00
48_V	68_A	1.217	1.00
69_L	107_E	1.209	1.00
14_V	17_L	1.203	1.00
61_P	84_P	1.199	1.00
63_V	82_T	1.189	1.00
42_V	102_R	1.167	1.00
48_V	106_G	1.150	1.00
5_L	9_A	1.140	1.00
19_W	22_W	1.118	1.00
43_V	49_T	1.107	1.00
97_V	106_G	1.074	1.00
4_R	7_I	1.064	1.00
58_D	89_R	1.059	1.00
49_T	94_T	1.058	1.00
56_R	61_P	1.038	1.00
77_G	97_V	1.035	1.00
38_I	51_T	1.024	1.00
61_P	82_T	1.020	1.00
7_I	11_V	1.005	1.00
36_E	55_T	0.984	1.00
56_R	83_V	0.984	1.00
72_D	101_R	0.977	1.00
15_V	19_W	0.967	1.00
35_A	52_F	0.962	1.00
81_V	95_V	0.960	1.00
59_G	87_D	0.930	0.99
52_F	108_V	0.924	0.99
57_P	60_S	0.906	0.99
68_A	99_T	0.898	0.99
40_F	105_T	0.889	0.99
2_R	6_V	0.879	0.99
40_F	104_V	0.878	0.99
8_V	12_L	0.873	0.99
33_V	62_A	0.865	0.99
5_L	8_V	0.858	0.99
42_V	103_A	0.858	0.99
61_P	85_A	0.854	0.99
18_A	22_W	0.854	0.99
20_L	23_A	0.854	0.99
52_F	93_V	0.838	0.99
54_V	62_A	0.833	0.99
35_A	108_V	0.823	0.99
30_T	57_P	0.822	0.99
52_F	83_V	0.807	0.99
48_V	103_A	0.801	0.98
56_R	84_P	0.796	0.98
81_V	93_V	0.792	0.98
37_L	40_F	0.785	0.98
83_V	95_V	0.768	0.98
24_G	29_S	0.752	0.98
5_L	12_L	0.744	0.98
3_R	7_I	0.743	0.98
56_R	60_S	0.742	0.97
67_R	109_Y	0.733	0.97
4_R	8_V	0.724	0.97
53_E	90_T	0.716	0.97
67_R	73_G	0.715	0.97
32_P	57_P	0.701	0.96
67_R	78_R	0.693	0.96
20_L	27_H	0.691	0.96
10_A	17_L	0.689	0.96
16_A	20_L	0.686	0.96
43_V	96_T	0.673	0.96
52_F	94_T	0.662	0.95
76_V	101_R	0.660	0.95
10_A	14_V	0.660	0.95
7_I	10_A	0.657	0.95
50_V	97_V	0.653	0.95
20_L	24_G	0.650	0.95
9_A	13_A	0.646	0.94
38_I	92_R	0.645	0.94
19_W	26_S	0.642	0.94
21_A	24_G	0.637	0.94
62_A	83_V	0.633	0.94
37_L	105_T	0.628	0.94
107_E	110_G	0.625	0.93
58_D	61_P	0.620	0.93
11_V	18_A	0.618	0.93
13_A	17_L	0.616	0.93
52_F	66_V	0.601	0.92
76_V	99_T	0.601	0.92
70_D	100_T	0.599	0.92
61_P	83_V	0.595	0.92
100_T	104_V	0.594	0.92
9_A	24_G	0.592	0.91
6_V	9_A	0.588	0.91
13_A	16_A	0.587	0.91
35_A	80_E	0.579	0.91
41_E	51_T	0.571	0.90
3_R	18_A	0.564	0.89
36_E	90_T	0.560	0.89
21_A	26_S	0.555	0.89
23_A	27_H	0.553	0.89
56_R	91_V	0.553	0.89
8_V	16_A	0.549	0.88
10_A	26_S	0.546	0.88
40_F	106_G	0.544	0.88
65_T	75_E	0.544	0.88
12_L	19_W	0.542	0.88
17_L	24_G	0.542	0.88
12_L	15_V	0.542	0.88
25_Y	29_S	0.539	0.87
87_D	96_T	0.537	0.87
68_A	76_V	0.536	0.87
8_V	11_V	0.535	0.87
5_L	16_A	0.533	0.87
42_V	99_T	0.532	0.87
11_V	15_V	0.531	0.86
30_T	34_S	0.531	0.86
86_G	91_V	0.526	0.86
3_R	9_A	0.524	0.86
108_V	111_C	0.522	0.86
18_A	24_G	0.517	0.85
38_I	106_G	0.517	0.85
85_A	93_V	0.515	0.85
76_V	104_V	0.513	0.85
57_P	63_V	0.513	0.85
69_L	74_A	0.512	0.84
65_T	109_Y	0.507	0.84
50_V	108_V	0.506	0.84
19_W	27_H	0.504	0.84
50_V	66_V	0.501	0.83
19_W	24_G	0.501	0.83
69_L	75_E	0.500	0.83

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
3j6da	3	0	12.6	0.897	Contact Map
4i3gA	1	0.9099	6.9	0.908	Contact Map
3aqpA	1	0.9459	6.8	0.909	Contact Map
4v3iA	2	0	4.9	0.915	Contact Map
2yiuB	1	0.2793	4.5	0.916	Contact Map
3abzA	3	0.9009	4.2	0.917	Contact Map
2x41A	1	0.8829	4	0.918	Contact Map
3lb6C	1	0	3.3	0.921	Contact Map
3s88I	1	0.2703	3.1	0.922	Contact Map
4ogqD	1	0.7297	3	0.923	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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