DUF3016 - PFAM28P - GREMLIN Contacts

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DUF3016 - Protein of unknown function (DUF3016)

PFAM:	PF11454	Sequences: GTVEVTFVDPEKFTDVRDSGNRRERDRERVLKELARHLQKLAARYLPPGQTLEITVTDIDLAGDFEPWRGPGADDVRIVRDIYPPRIDLRYTLTDADGKVLKEGEEKLRDMNYLMRINRYSSSDPLRYEKRMLDDWFRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	139 (137)
Sequences:	2001 (1556)
Seq/√Len:	133.0
META:	0.859

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_V	113_Y	4.781	1.00
90_R	105_E	3.473	1.00
91_Y	106_E	2.845	1.00
37_H	134_D	2.722	1.00
3_V	42_A	2.454	1.00
35_A	39_Q	2.451	1.00
53_E	94_T	2.381	1.00
55_T	90_R	2.319	1.00
88_D	107_K	2.200	1.00
38_L	133_L	2.169	1.00
124_D	127_R	2.165	1.00
88_D	105_E	2.154	1.00
52_L	93_L	2.082	1.00
92_T	103_E	2.072	1.00
124_D	130_K	1.994	1.00
9_D	12_K	1.956	1.00
6_T	55_T	1.896	1.00
56_V	87_I	1.890	1.00
87_I	132_M	1.835	1.00
116_R	135_D	1.799	1.00
4_E	53_E	1.765	1.00
7_F	35_A	1.753	1.00
66_E	80_R	1.752	1.00
41_L	137_F	1.750	1.00
95_D	99_K	1.749	1.00
8_V	55_T	1.726	1.00
37_H	130_K	1.693	1.00
53_E	92_T	1.664	1.00
110_D	116_R	1.646	1.00
28_E	32_K	1.632	1.00
57_T	90_R	1.551	1.00
38_L	56_V	1.525	1.00
57_T	88_D	1.503	1.00
84_P	111_M	1.472	1.00
81_D	114_L	1.459	1.00
88_D	109_R	1.413	1.00
87_I	129_E	1.372	1.00
4_E	51_T	1.369	1.00
64_D	83_Y	1.360	1.00
73_A	76_V	1.338	1.00
84_P	109_R	1.325	1.00
50_Q	93_L	1.308	1.00
7_F	13_F	1.308	1.00
45_Y	137_F	1.276	1.00
10_P	13_F	1.257	1.00
47_P	50_Q	1.231	1.00
79_V	114_L	1.223	1.00
30_V	61_L	1.201	1.00
85_P	113_Y	1.200	0.99
24_E	27_R	1.200	0.99
14_T	58_D	1.193	0.99
87_I	133_L	1.187	0.99
8_V	13_F	1.171	0.99
60_D	64_D	1.153	0.99
49_G	96_A	1.129	0.99
56_V	59_I	1.126	0.99
50_Q	101_L	1.091	0.99
16_V	61_L	1.066	0.99
95_D	98_G	1.062	0.99
32_K	35_A	1.059	0.99
51_T	94_T	1.057	0.99
86_R	107_K	1.045	0.99
42_A	52_L	1.040	0.99
112_N	115_M	1.022	0.98
39_Q	43_A	1.011	0.98
37_H	40_K	1.003	0.98
34_L	126_L	1.002	0.98
57_T	89_L	1.002	0.98
54_I	89_L	0.997	0.98
60_D	86_R	0.988	0.98
121_S	127_R	0.986	0.98
120_Y	127_R	0.986	0.98
45_Y	138_R	0.985	0.98
33_E	36_R	0.940	0.97
32_K	36_R	0.935	0.97
80_R	83_Y	0.934	0.97
87_I	108_L	0.929	0.97
21_N	29_R	0.928	0.97
36_R	39_Q	0.898	0.96
64_D	80_R	0.897	0.96
100_V	103_E	0.892	0.96
86_R	109_R	0.884	0.96
97_D	100_V	0.879	0.96
79_V	84_P	0.867	0.96
23_R	26_D	0.865	0.95
118_N	127_R	0.864	0.95
37_H	41_L	0.861	0.95
13_F	31_L	0.856	0.95
15_D	60_D	0.856	0.95
8_V	57_T	0.855	0.95
135_D	138_R	0.851	0.95
114_L	128_Y	0.850	0.95
81_D	115_M	0.837	0.95
126_L	130_K	0.831	0.94
66_E	69_R	0.830	0.94
40_K	43_A	0.828	0.94
50_Q	96_A	0.825	0.94
58_D	88_D	0.820	0.94
16_V	31_L	0.815	0.94
31_L	35_A	0.807	0.93
5_V	54_I	0.801	0.93
28_E	35_A	0.800	0.93
56_V	89_L	0.797	0.93
61_L	129_E	0.796	0.93
7_F	15_D	0.796	0.93
89_L	106_E	0.794	0.93
85_P	110_D	0.790	0.93
7_F	59_I	0.788	0.93
110_D	131_R	0.776	0.92
117_I	128_Y	0.773	0.92
6_T	53_E	0.773	0.92
108_L	132_M	0.758	0.91
26_D	61_L	0.756	0.91
114_L	117_I	0.755	0.91
56_V	133_L	0.754	0.91
18_D	23_R	0.753	0.91
69_R	73_A	0.735	0.90
94_T	100_V	0.734	0.90
42_A	137_F	0.734	0.90
38_L	54_I	0.729	0.89
62_A	128_Y	0.728	0.89
46_L	49_G	0.726	0.89
131_R	135_D	0.720	0.89
30_V	33_E	0.718	0.89
89_L	108_L	0.717	0.89
133_L	137_F	0.713	0.88
69_R	78_I	0.708	0.88
23_R	27_R	0.704	0.88
26_D	30_V	0.700	0.88
59_I	87_I	0.699	0.87
69_R	74_D	0.699	0.87
43_A	48_P	0.683	0.86
85_P	128_Y	0.678	0.86
21_N	61_L	0.671	0.85
68_W	78_I	0.670	0.85
41_L	44_R	0.669	0.85
57_T	105_E	0.667	0.85
68_W	71_P	0.664	0.85
15_D	30_V	0.662	0.84
22_R	25_R	0.658	0.84
106_E	133_L	0.654	0.84
131_R	134_D	0.654	0.84
38_L	137_F	0.653	0.84
9_D	13_F	0.647	0.83
84_P	132_M	0.645	0.83
18_D	26_D	0.631	0.82
16_V	21_N	0.628	0.81
37_H	54_I	0.626	0.81
93_L	101_L	0.624	0.81
110_D	113_Y	0.623	0.81
89_L	93_L	0.623	0.81
27_R	31_L	0.621	0.81
92_T	100_V	0.620	0.80
127_R	130_K	0.619	0.80
41_L	45_Y	0.607	0.79
111_M	118_N	0.602	0.78
108_L	114_L	0.601	0.78
17_R	30_V	0.596	0.78
41_L	134_D	0.589	0.77
16_V	30_V	0.587	0.77
31_L	56_V	0.586	0.77
7_F	30_V	0.585	0.76
118_N	121_S	0.584	0.76
70_G	73_A	0.582	0.76
34_L	59_I	0.579	0.76
21_N	26_D	0.572	0.75
38_L	46_L	0.569	0.74
68_W	75_D	0.568	0.74
5_V	89_L	0.566	0.74
18_D	21_N	0.562	0.74
76_V	79_V	0.561	0.73
31_L	59_I	0.558	0.73
60_D	63_G	0.557	0.73
84_P	127_R	0.556	0.73
129_E	132_M	0.555	0.73
43_A	47_P	0.553	0.72
108_L	120_Y	0.553	0.72
14_T	86_R	0.552	0.72
91_Y	104_G	0.546	0.71
21_N	25_R	0.544	0.71
30_V	60_D	0.538	0.70
87_I	106_E	0.537	0.70
67_P	73_A	0.535	0.70
65_F	81_D	0.532	0.69
37_H	124_D	0.531	0.69
120_Y	124_D	0.530	0.69
33_E	126_L	0.530	0.69
90_R	103_E	0.529	0.69
111_M	114_L	0.529	0.69
133_L	136_W	0.524	0.68
10_P	31_L	0.524	0.68
42_A	46_L	0.524	0.68
14_T	60_D	0.522	0.68
104_G	108_L	0.521	0.68
33_E	125_P	0.521	0.68
49_G	67_P	0.521	0.68
46_L	54_I	0.520	0.68
50_Q	102_K	0.517	0.67
16_V	55_T	0.516	0.67
2_T	12_K	0.516	0.67
45_Y	60_D	0.514	0.67
6_T	15_D	0.509	0.66
7_F	31_L	0.508	0.66
55_T	67_P	0.505	0.66
95_D	101_L	0.503	0.65
13_F	57_T	0.500	0.65

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
4kwyA	1	0.7914	16.9	0.935	Contact Map
4r86A	1	0.4532	15.5	0.936	Contact Map
3ck1A	4	0.8705	11.6	0.939	Contact Map
1iuqA	1	0.4604	11.4	0.94	Contact Map
3qy3A	4	0.8561	10.6	0.941	Contact Map
4qd8A	3	0.7482	9.3	0.942	Contact Map
2k49A	1	0.4604	9.2	0.942	Contact Map
2essA	2	0.8345	9.2	0.942	Contact Map
1j3mA	2	0.3094	9.1	0.942	Contact Map
1sc0A	1	0.7554	7.8	0.944	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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