DUF4385 - PFAM28P - GREMLIN Contacts

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DUF4385 - Domain of unknown function (DUF4385)

PFAM:	PF14328	Sequences: DYSLDYKNIDFREHPELYRIGRGEQGVLLVEPYKSEILPHWRFKTPEIARESSEKIYEMFLDYLEQGDFVGMDMARKFLQMGFTRARRYANHKGGRKYDKDGGVKPQEPDEEDPEKAESARIFKEKWDKAREDEKYLRMKKEHREK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (145)
Sequences:	1197 (689)
Seq/√Len:	57.2
META:	0.715

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_L	72_M	4.441	1.00
31_E	35_S	3.605	1.00
40_H	59_M	3.543	1.00
124_K	128_D	3.429	1.00
53_S	126_K	3.148	1.00
60_F	130_A	2.956	1.00
37_I	56_I	2.741	1.00
57_Y	61_L	2.735	1.00
64_L	133_D	2.575	1.00
45_T	48_I	2.515	1.00
46_P	119_S	2.380	1.00
87_R	117_A	2.287	1.00
86_A	119_S	2.194	1.00
37_I	59_M	2.186	1.00
72_M	133_D	2.176	1.00
6_Y	11_F	2.053	1.00
40_H	55_K	2.038	1.00
126_K	129_K	1.994	1.00
128_D	132_E	1.991	1.00
79_L	130_A	1.979	1.00
10_D	13_E	1.837	0.99
83_F	127_W	1.808	0.99
55_K	59_M	1.802	0.99
117_A	120_A	1.796	0.99
118_E	121_R	1.790	0.99
57_Y	126_K	1.720	0.99
128_D	131_R	1.657	0.99
46_P	118_E	1.645	0.99
50_R	54_E	1.643	0.99
44_K	48_I	1.628	0.99
5_D	8_N	1.606	0.99
76_R	80_Q	1.602	0.99
24_E	76_R	1.596	0.99
46_P	115_E	1.583	0.98
6_Y	9_I	1.480	0.98
31_E	34_K	1.450	0.97
93_K	116_K	1.446	0.97
110_D	113_D	1.434	0.97
46_P	122_I	1.428	0.97
135_K	138_R	1.404	0.97
67_G	135_K	1.382	0.96
24_E	80_Q	1.381	0.96
119_S	122_I	1.377	0.96
107_Q	110_D	1.377	0.96
56_I	59_M	1.327	0.95
107_Q	111_E	1.303	0.95
55_K	58_E	1.279	0.94
37_I	40_H	1.267	0.94
92_H	112_E	1.263	0.94
12_R	36_E	1.244	0.93
138_R	142_E	1.230	0.93
140_K	144_R	1.215	0.93
135_K	139_M	1.182	0.92
1_D	5_D	1.156	0.91
11_F	30_V	1.155	0.91
54_E	126_K	1.152	0.90
93_K	114_P	1.116	0.89
4_L	17_L	1.116	0.89
131_R	143_H	1.109	0.89
131_R	137_L	1.092	0.88
38_L	78_F	1.082	0.87
53_S	129_K	1.072	0.87
132_E	137_L	1.066	0.87
142_E	145_E	1.057	0.86
62_D	66_Q	1.052	0.86
99_D	103_G	1.042	0.85
93_K	111_E	1.029	0.85
4_L	19_R	1.027	0.85
10_D	15_P	1.004	0.83
12_R	15_P	1.004	0.83
94_G	111_E	0.997	0.83
105_K	108_E	0.995	0.83
56_I	79_L	0.968	0.81
57_Y	129_K	0.965	0.81
52_S	123_F	0.961	0.80
124_K	127_W	0.959	0.80
104_V	108_E	0.959	0.80
87_R	120_A	0.957	0.80
60_F	72_M	0.939	0.79
45_T	119_S	0.875	0.74
50_R	125_E	0.855	0.72
139_M	143_H	0.849	0.72
43_F	52_S	0.839	0.71
137_L	143_H	0.836	0.70
56_I	75_A	0.834	0.70
13_E	17_L	0.826	0.69
8_N	30_V	0.823	0.69
1_D	4_L	0.820	0.69
94_G	112_E	0.820	0.69
104_V	107_Q	0.815	0.68
38_L	80_Q	0.811	0.68
42_R	48_I	0.801	0.67
104_V	110_D	0.798	0.67
131_R	140_K	0.797	0.67
61_L	126_K	0.790	0.66
96_R	103_G	0.786	0.66
141_K	144_R	0.785	0.65
55_K	62_D	0.783	0.65
141_K	145_E	0.779	0.65
137_L	140_K	0.777	0.65
121_R	124_K	0.777	0.65
4_L	29_L	0.771	0.64
30_V	74_M	0.769	0.64
127_W	140_K	0.758	0.63
76_R	98_Y	0.757	0.63
121_R	125_E	0.748	0.62
47_E	115_E	0.747	0.62
20_I	23_G	0.746	0.61
36_E	63_Y	0.737	0.61
19_R	24_E	0.737	0.61
72_M	130_A	0.734	0.60
67_G	139_M	0.731	0.60
43_F	123_F	0.731	0.60
100_K	103_G	0.727	0.60
87_R	91_N	0.718	0.59
125_E	129_K	0.718	0.59
92_H	110_D	0.717	0.58
50_R	65_E	0.711	0.58
5_D	30_V	0.709	0.58
140_K	143_H	0.708	0.57
131_R	144_R	0.707	0.57
48_I	51_E	0.699	0.57
116_K	120_A	0.698	0.56
107_Q	113_D	0.698	0.56
21_G	25_Q	0.695	0.56
11_F	29_L	0.694	0.56
134_E	138_R	0.692	0.56
15_P	70_V	0.690	0.56
88_R	95_G	0.688	0.55
59_M	62_D	0.682	0.55
4_L	9_I	0.678	0.54
60_F	75_A	0.676	0.54
117_A	121_R	0.675	0.54
61_L	129_K	0.660	0.52
108_E	111_E	0.654	0.52
103_G	106_P	0.654	0.52
115_E	118_E	0.653	0.52
133_D	139_M	0.651	0.51
111_E	114_P	0.645	0.51
83_F	110_D	0.640	0.50
47_E	54_E	0.633	0.49
6_Y	29_L	0.633	0.49
108_E	113_D	0.629	0.49
34_K	80_Q	0.624	0.48
99_D	106_P	0.623	0.48
62_D	65_E	0.623	0.48
34_K	38_L	0.619	0.48
20_I	131_R	0.616	0.47
57_Y	130_A	0.615	0.47
6_Y	30_V	0.612	0.47
94_G	108_E	0.611	0.47
66_Q	118_E	0.610	0.47
53_S	125_E	0.607	0.46
42_R	52_S	0.605	0.46
24_E	98_Y	0.604	0.46
110_D	114_P	0.603	0.46
54_E	125_E	0.601	0.46
127_W	131_R	0.595	0.45
47_E	129_K	0.593	0.45
103_G	108_E	0.592	0.45
50_R	118_E	0.587	0.44
15_P	36_E	0.586	0.44
80_Q	83_F	0.586	0.44
114_P	118_E	0.586	0.44
4_L	8_N	0.574	0.43
35_S	39_P	0.573	0.43
51_E	62_D	0.573	0.43
22_R	124_K	0.572	0.43
100_K	104_V	0.571	0.43
57_Y	67_G	0.570	0.42
10_D	142_E	0.568	0.42
80_Q	127_W	0.566	0.42
48_I	53_S	0.562	0.42
92_H	106_P	0.561	0.41
25_Q	44_K	0.561	0.41
45_T	118_E	0.560	0.41
43_F	46_P	0.555	0.41
109_P	112_E	0.555	0.41
64_L	135_K	0.553	0.41
54_E	58_E	0.551	0.40
96_R	100_K	0.550	0.40
124_K	132_E	0.544	0.40
43_F	119_S	0.543	0.40
92_H	108_E	0.541	0.39
96_R	104_V	0.539	0.39
72_M	76_R	0.539	0.39
101_D	104_V	0.539	0.39
138_R	141_K	0.537	0.39
134_E	137_L	0.534	0.39
75_A	130_A	0.534	0.39
61_L	133_D	0.532	0.38
62_D	121_R	0.531	0.38
36_E	39_P	0.531	0.38
65_E	106_P	0.527	0.38
119_S	123_F	0.527	0.38
123_F	127_W	0.525	0.38
108_E	112_E	0.525	0.38
14_H	17_L	0.523	0.38
53_S	61_L	0.523	0.38
86_A	94_G	0.516	0.37
92_H	107_Q	0.516	0.37
78_F	96_R	0.516	0.37
67_G	142_E	0.516	0.37
3_S	7_K	0.516	0.37
64_L	130_A	0.515	0.37
39_P	63_Y	0.515	0.37
134_E	139_M	0.511	0.36
105_K	113_D	0.510	0.36
93_K	112_E	0.510	0.36
47_E	142_E	0.510	0.36
28_L	91_N	0.509	0.36
61_L	65_E	0.507	0.36
7_K	11_F	0.505	0.36
104_V	113_D	0.503	0.35
79_L	134_E	0.503	0.35
106_P	110_D	0.502	0.35
115_E	122_I	0.502	0.35
9_I	17_L	0.500	0.35

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
4h41A	3	0.4041	11.1	0.961	Contact Map
1gwmA	1	0.3151	4.3	0.968	Contact Map
3r3jA	5	0.4315	4.3	0.968	Contact Map
2b7eA	1	0.2192	4.2	0.968	Contact Map
4x86A	1	0.2329	3.8	0.969	Contact Map
3v76A	2	0.3356	3	0.97	Contact Map
2dkhA	2	0.3836	2.7	0.971	Contact Map
1uzcA	1	0.2877	2.4	0.972	Contact Map
1i60A	1	0.4247	2.1	0.973	Contact Map
2basA	2	0.4863	2	0.973	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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