DUF4303 - PFAM28P - GREMLIN Contacts

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DUF4303 - Domain of unknown function (DUF4303)

PFAM:	PF14136	Sequences: IAEAARAAFEELREEHPDETFYAFALYTDDDAMTVGPAANTEEALERVAAEYPEDDEYYRWSPAEWPYEFGGDELFDEVNELLRERPDELDDDEDDFEAFRELLLEAMVEALKELDAEGLFGTGEREDIVLFVSVSDDDDEEELENESAKRLNPP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	155 (153)
Sequences:	1218 (1034)
Seq/√Len:	83.6
META:	0.795

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
42_E	60_R	4.798	1.00
6_R	118_E	4.482	1.00
20_T	43_E	3.550	1.00
2_A	114_E	3.349	1.00
116_D	126_R	3.103	1.00
19_E	68_Y	2.799	1.00
62_S	65_E	2.797	1.00
113_K	151_R	2.785	1.00
12_L	39_A	2.729	1.00
40_N	66_W	2.538	1.00
5_A	9_F	2.448	1.00
107_A	111_A	2.377	1.00
61_W	130_V	2.302	1.00
113_K	117_A	1.986	1.00
23_A	66_W	1.958	1.00
17_P	21_F	1.930	1.00
100_F	104_L	1.868	1.00
115_L	121_F	1.821	1.00
132_F	149_A	1.788	1.00
11_E	15_E	1.724	1.00
27_Y	36_G	1.699	1.00
30_D	138_D	1.669	1.00
28_T	32_A	1.637	1.00
40_N	67_P	1.636	1.00
86_R	100_F	1.603	1.00
29_D	34_T	1.575	1.00
22_Y	42_E	1.561	1.00
106_E	110_E	1.534	1.00
115_L	118_E	1.522	1.00
125_E	128_D	1.481	0.99
4_A	76_F	1.451	0.99
140_D	143_E	1.422	0.99
22_Y	40_N	1.415	0.99
111_A	115_L	1.406	0.99
116_D	131_L	1.372	0.99
116_D	122_G	1.369	0.99
135_V	138_D	1.361	0.99
48_V	52_Y	1.359	0.99
24_F	37_P	1.342	0.99
34_T	65_E	1.337	0.99
9_F	37_P	1.332	0.99
52_Y	56_D	1.304	0.98
122_G	126_R	1.301	0.98
106_E	113_K	1.287	0.98
81_E	85_E	1.237	0.98
138_D	143_E	1.231	0.98
16_H	19_E	1.219	0.98
147_E	151_R	1.219	0.98
115_L	119_G	1.205	0.97
105_L	109_V	1.189	0.97
28_T	105_L	1.180	0.97
141_E	145_E	1.179	0.97
103_L	107_A	1.167	0.97
136_S	141_E	1.158	0.97
19_E	43_E	1.152	0.97
116_D	124_G	1.147	0.96
93_D	96_D	1.137	0.96
63_P	134_S	1.131	0.96
2_A	6_R	1.130	0.96
6_R	115_L	1.125	0.96
29_D	33_M	1.116	0.96
53_P	56_D	1.103	0.96
134_S	138_D	1.100	0.96
80_N	84_R	1.078	0.95
135_V	141_E	1.059	0.94
21_F	41_T	1.058	0.94
69_E	72_G	1.056	0.94
72_G	75_L	1.035	0.94
32_A	105_L	1.027	0.94
19_E	67_P	1.022	0.93
22_Y	60_R	1.022	0.93
62_S	71_G	1.017	0.93
52_Y	55_D	1.003	0.93
115_L	120_L	0.979	0.92
55_D	59_Y	0.976	0.92
19_E	47_R	0.973	0.92
10_E	14_E	0.971	0.91
134_S	148_S	0.967	0.91
141_E	144_L	0.959	0.91
120_L	129_I	0.958	0.91
30_D	64_A	0.957	0.91
86_R	104_L	0.953	0.91
63_P	66_W	0.942	0.90
108_M	111_A	0.940	0.90
3_E	6_R	0.939	0.90
109_V	151_R	0.917	0.89
47_R	50_A	0.915	0.89
40_N	44_A	0.911	0.89
124_G	129_I	0.905	0.88
53_P	58_Y	0.893	0.88
80_N	83_L	0.882	0.87
137_D	140_D	0.882	0.87
23_A	132_F	0.878	0.87
3_E	7_A	0.877	0.87
5_A	26_L	0.866	0.86
51_E	54_E	0.863	0.86
86_R	90_L	0.860	0.86
138_D	142_E	0.860	0.86
78_E	81_E	0.857	0.85
134_S	137_D	0.856	0.85
28_T	108_M	0.854	0.85
8_A	24_F	0.853	0.85
116_D	121_F	0.848	0.85
27_Y	38_A	0.848	0.85
35_V	108_M	0.847	0.85
34_T	136_S	0.847	0.85
9_F	13_R	0.845	0.85
23_A	40_N	0.841	0.84
68_Y	99_A	0.838	0.84
38_A	64_A	0.828	0.83
9_F	120_L	0.828	0.83
141_E	148_S	0.826	0.83
27_Y	37_P	0.822	0.83
38_A	61_W	0.817	0.83
29_D	136_S	0.815	0.82
22_Y	44_A	0.808	0.82
6_R	10_E	0.802	0.81
13_R	122_G	0.796	0.81
136_S	139_D	0.794	0.81
25_A	38_A	0.789	0.80
9_F	24_F	0.787	0.80
22_Y	45_L	0.780	0.80
122_G	125_E	0.778	0.79
21_F	39_A	0.775	0.79
9_F	25_A	0.775	0.79
110_E	117_A	0.770	0.79
26_L	35_V	0.769	0.79
27_Y	64_A	0.764	0.78
22_Y	43_E	0.759	0.78
126_R	129_I	0.759	0.78
63_P	104_L	0.756	0.77
25_A	66_W	0.755	0.77
26_L	108_M	0.749	0.77
27_Y	69_E	0.742	0.76
134_S	141_E	0.728	0.75
6_R	119_G	0.722	0.74
76_F	80_N	0.719	0.74
98_E	106_E	0.715	0.73
16_H	68_Y	0.714	0.73
25_A	63_P	0.713	0.73
108_M	112_L	0.709	0.73
23_A	63_P	0.698	0.72
106_E	151_R	0.689	0.71
82_L	99_A	0.685	0.70
28_T	31_D	0.685	0.70
35_V	104_L	0.684	0.70
135_V	139_D	0.682	0.70
124_G	154_P	0.679	0.70
41_T	108_M	0.671	0.69
150_K	154_P	0.663	0.68
22_Y	61_W	0.662	0.68
137_D	142_E	0.657	0.67
50_A	53_P	0.656	0.67
131_L	134_S	0.653	0.67
79_V	82_L	0.651	0.66
48_V	51_E	0.651	0.66
138_D	148_S	0.647	0.66
25_A	110_E	0.647	0.66
44_A	60_R	0.643	0.65
145_E	148_S	0.642	0.65
5_A	35_V	0.640	0.65
20_T	42_E	0.635	0.64
69_E	73_D	0.635	0.64
107_A	110_E	0.633	0.64
78_E	95_D	0.633	0.64
13_R	116_D	0.631	0.64
71_G	75_L	0.630	0.64
4_A	79_V	0.629	0.64
18_D	78_E	0.626	0.63
13_R	110_E	0.622	0.63
14_E	99_A	0.618	0.62
42_E	46_E	0.617	0.62
39_A	116_D	0.615	0.62
9_F	115_L	0.610	0.61
23_A	109_V	0.610	0.61
102_E	142_E	0.607	0.61
40_N	61_W	0.603	0.60
16_H	21_F	0.598	0.60
132_F	145_E	0.595	0.59
65_E	139_D	0.593	0.59
33_M	97_F	0.592	0.59
132_F	148_S	0.591	0.59
138_D	141_E	0.591	0.59
76_F	82_L	0.590	0.59
3_E	11_E	0.590	0.59
13_R	24_F	0.590	0.59
26_L	32_A	0.589	0.59
78_E	117_A	0.589	0.59
25_A	132_F	0.588	0.59
3_E	135_V	0.587	0.58
46_E	49_A	0.584	0.58
134_S	145_E	0.575	0.57
44_A	67_P	0.570	0.56
24_F	121_F	0.570	0.56
8_A	72_G	0.568	0.56
56_D	59_Y	0.565	0.56
34_T	64_A	0.563	0.55
24_F	112_L	0.562	0.55
63_P	137_D	0.560	0.55
140_D	149_A	0.557	0.55
37_P	76_F	0.555	0.54
18_D	88_D	0.551	0.54
138_D	145_E	0.549	0.53
82_L	93_D	0.545	0.53
82_L	85_E	0.542	0.53
133_V	138_D	0.540	0.52
7_A	75_L	0.540	0.52
88_D	117_A	0.539	0.52
32_A	135_V	0.538	0.52
65_E	136_S	0.537	0.52
97_F	100_F	0.537	0.52
27_Y	136_S	0.534	0.51
134_S	146_N	0.534	0.51
76_F	79_V	0.532	0.51
138_D	146_N	0.530	0.51
7_A	14_E	0.525	0.50
36_G	133_V	0.523	0.50
36_G	69_E	0.523	0.50
55_D	58_Y	0.520	0.50
124_G	127_E	0.517	0.49
99_A	117_A	0.516	0.49
5_A	76_F	0.515	0.49
13_R	119_G	0.512	0.49
29_D	32_A	0.511	0.48
139_D	143_E	0.505	0.48
87_P	90_L	0.503	0.47
105_L	133_V	0.502	0.47
79_V	139_D	0.501	0.47
31_D	101_R	0.500	0.47
95_D	106_E	0.500	0.47

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
2d8bA	1	0.8645	7.9	0.918	Contact Map
3dawB	1	0.8645	5.8	0.923	Contact Map
3oeqA	3	0.5742	3.7	0.93	Contact Map
4csoA	1	0.8839	3.6	0.93	Contact Map
3zxwB	1	0.271	3	0.933	Contact Map
5csmA	2	0.4	2.7	0.935	Contact Map
1vw42	1	0.3355	2.6	0.935	Contact Map
4bx8A	1	0.9548	2.5	0.936	Contact Map
1ew4A	1	0.6065	2.4	0.936	Contact Map
3j7y8	1	0.1613	2.4	0.936	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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