DUF4259 - PFAM28P - GREMLIN Contacts

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DUF4259 - Domain of unknown function (DUF4259)

PFAM:	PF14078	Sequences: GAWGTGPFENDDALDWLAELEEAGPEDDLSLVEEALDAVLAADGDDYLEAPEASEALAAAEVVAALLGGPGPRDDAYGDLPEEVDEWVAAHPALPSPELVALARRALDRVLGEDSELRELWEESEDLEEWRAH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	133 (125)
Sequences:	2584 (2201)
Seq/√Len:	196.9
META:	0.824

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
4_G	9_E	5.515	1.00
7_P	57_L	3.603	1.00
12_D	54_S	3.372	1.00
6_G	9_E	3.356	1.00
12_D	51_P	3.233	1.00
57_L	107_L	2.574	1.00
37_D	102_L	2.380	1.00
31_L	35_A	2.273	1.00
56_A	106_A	2.232	1.00
87_W	91_H	2.167	1.00
16_W	20_L	2.091	1.00
116_E	120_L	2.006	1.00
7_P	61_E	1.926	1.00
38_A	52_E	1.774	1.00
124_S	127_L	1.703	1.00
127_L	131_R	1.666	1.00
118_R	131_R	1.636	1.00
2_A	54_S	1.609	1.00
64_A	68_G	1.596	1.00
33_E	102_L	1.566	1.00
1_G	11_D	1.540	1.00
67_L	100_V	1.534	1.00
11_D	15_D	1.476	1.00
104_R	108_D	1.464	1.00
118_R	122_E	1.460	1.00
18_A	21_E	1.393	1.00
36_L	102_L	1.391	1.00
114_D	118_R	1.379	1.00
65_A	71_G	1.348	1.00
122_E	131_R	1.337	1.00
12_D	55_E	1.323	1.00
12_D	49_E	1.286	1.00
23_A	31_L	1.274	1.00
117_L	130_W	1.269	1.00
63_V	100_V	1.253	1.00
100_V	104_R	1.252	1.00
33_E	99_L	1.245	1.00
120_L	123_E	1.227	1.00
61_E	68_G	1.214	1.00
111_L	131_R	1.205	1.00
33_E	37_D	1.182	1.00
70_P	73_R	1.175	1.00
53_A	115_S	1.175	1.00
59_A	103_A	1.171	1.00
126_D	129_E	1.164	1.00
51_P	54_S	1.160	1.00
29_L	33_E	1.159	1.00
48_L	53_A	1.139	1.00
84_V	87_W	1.128	1.00
16_W	62_V	1.112	1.00
48_L	109_R	1.105	1.00
53_A	110_V	1.102	1.00
10_N	50_A	1.096	1.00
16_W	35_A	1.093	1.00
62_V	84_V	1.090	1.00
122_E	127_L	1.083	1.00
39_V	48_L	1.080	1.00
14_L	18_A	1.080	1.00
36_L	60_A	1.079	1.00
32_V	36_L	1.078	1.00
47_Y	119_E	1.072	1.00
29_L	66_L	1.064	1.00
13_A	58_A	1.046	1.00
65_A	70_P	1.031	1.00
19_E	55_E	1.020	1.00
61_E	64_A	1.005	1.00
21_E	83_E	0.992	1.00
32_V	35_A	0.991	1.00
16_W	59_A	0.983	1.00
60_A	103_A	0.980	0.99
95_P	99_L	0.978	0.99
61_E	69_G	0.972	0.99
35_A	55_E	0.961	0.99
20_L	87_W	0.958	0.99
35_A	39_V	0.957	0.99
10_N	13_A	0.952	0.99
47_Y	116_E	0.950	0.99
8_F	81_P	0.949	0.99
24_G	29_L	0.944	0.99
113_E	118_R	0.944	0.99
60_A	107_L	0.929	0.99
20_L	24_G	0.926	0.99
52_E	55_E	0.918	0.99
39_V	110_V	0.902	0.99
36_L	103_A	0.900	0.99
24_G	28_D	0.885	0.99
91_H	95_P	0.878	0.99
1_G	15_D	0.865	0.99
19_E	31_L	0.864	0.99
5_T	129_E	0.827	0.98
10_N	57_L	0.817	0.98
118_R	127_L	0.814	0.98
9_E	14_L	0.812	0.98
65_A	80_L	0.807	0.98
80_L	84_V	0.801	0.98
29_L	32_V	0.801	0.98
21_E	84_V	0.800	0.98
112_G	118_R	0.795	0.98
61_E	71_G	0.794	0.98
20_L	62_V	0.774	0.97
14_L	17_L	0.763	0.97
128_E	131_R	0.761	0.97
56_A	103_A	0.760	0.97
49_E	52_E	0.759	0.97
33_E	98_E	0.754	0.97
17_L	21_E	0.747	0.97
36_L	106_A	0.743	0.97
7_P	58_A	0.734	0.96
104_R	111_L	0.734	0.96
17_L	84_V	0.727	0.96
39_V	56_A	0.719	0.96
60_A	110_V	0.715	0.96
56_A	60_A	0.707	0.95
81_P	85_D	0.700	0.95
17_L	83_E	0.697	0.95
115_S	118_R	0.695	0.95
35_A	59_A	0.693	0.95
36_L	63_V	0.692	0.95
50_A	117_L	0.690	0.95
71_G	79_D	0.686	0.95
23_A	28_D	0.685	0.95
50_A	120_L	0.664	0.94
50_A	54_S	0.664	0.94
18_A	22_E	0.659	0.93
65_A	85_D	0.656	0.93
8_F	61_E	0.654	0.93
97_P	100_V	0.653	0.93
59_A	64_A	0.649	0.93
60_A	63_V	0.643	0.93
47_Y	51_P	0.642	0.93
110_V	118_R	0.638	0.92
7_P	10_N	0.632	0.92
14_L	80_L	0.630	0.92
14_L	83_E	0.630	0.92
101_A	105_R	0.630	0.92
10_N	58_A	0.628	0.92
24_G	31_L	0.623	0.91
53_A	117_L	0.620	0.91
16_W	61_E	0.618	0.91
36_L	40_L	0.616	0.91
67_L	104_R	0.605	0.90
19_E	23_A	0.604	0.90
16_W	54_S	0.600	0.90
65_A	81_P	0.598	0.90
129_E	132_A	0.594	0.89
48_L	116_E	0.592	0.89
49_E	54_S	0.588	0.89
47_Y	123_E	0.587	0.89
58_A	63_V	0.587	0.89
35_A	56_A	0.584	0.89
50_A	55_E	0.584	0.89
10_N	54_S	0.581	0.88
5_T	9_E	0.578	0.88
110_V	115_S	0.577	0.88
50_A	116_E	0.574	0.88
11_D	14_L	0.574	0.88
70_P	89_A	0.572	0.88
15_D	18_A	0.570	0.87
102_L	105_R	0.568	0.87
50_A	53_A	0.567	0.87
86_E	90_A	0.563	0.87
63_V	103_A	0.560	0.86
69_G	88_V	0.559	0.86
94_L	97_P	0.555	0.86
61_E	70_P	0.552	0.86
64_A	103_A	0.540	0.84
66_L	99_L	0.539	0.84
66_L	93_A	0.535	0.84
123_E	127_L	0.534	0.84
51_P	120_L	0.533	0.84
97_P	101_A	0.532	0.84
97_P	129_E	0.528	0.83
68_G	71_G	0.524	0.83
61_E	73_R	0.520	0.82
47_Y	52_E	0.520	0.82
63_V	107_L	0.518	0.82
117_L	121_W	0.518	0.82
91_H	96_S	0.517	0.82
16_W	103_A	0.517	0.82
5_T	124_S	0.515	0.82
30_S	33_E	0.514	0.81
38_A	55_E	0.511	0.81
57_L	110_V	0.511	0.81
12_D	50_A	0.510	0.81
81_P	88_V	0.508	0.81
120_L	124_S	0.505	0.80
38_A	86_E	0.505	0.80
16_W	58_A	0.500	0.80

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
3sl1A	5	0.4887	6.3	0.913	Contact Map
4l2hA	1	0.594	4.6	0.919	Contact Map
4iu0A	3	0.4812	4.5	0.919	Contact Map
4b3nA	1	0.8947	4.3	0.92	Contact Map
4a0dA	1	0.6842	3.5	0.923	Contact Map
3uekA	1	0.6767	3.2	0.925	Contact Map
3sigA	1	0.406	3	0.926	Contact Map
3u64A	5	0.391	2.5	0.929	Contact Map
3zn6A	1	0.1429	2.3	0.93	Contact Map
2zyoA	1	0.8271	2.1	0.932	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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