DUF116 - PFAM28P - GREMLIN Contacts

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DUF116 - Protein of unknown function DUF116

PFAM:	PF01976	Sequences: LAKLLGRLLGIDKDHLDMSFIELNNRLVREKFAKVPPERRLLLLPHCLRNSDCPAKITEDGLNCKRCGKCSIGDLLELAEKLGYKVYVAPGGTLARKIIKEGRPDAIVGVACERELESGIQDLYPLPVPGQGVPLPKGGCVNTTVDLEEVEEAI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	154 (148)
Sequences:	3832 (2405)
Seq/√Len:	197.7
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_R	105_D	5.031	1.00
71_S	144_T	4.634	1.00
44_L	110_V	3.718	1.00
66_R	80_E	3.656	1.00
145_V	150_V	3.174	1.00
66_R	77_E	3.038	1.00
66_R	76_L	2.895	1.00
52_D	69_K	2.856	1.00
149_E	152_E	2.661	1.00
85_K	102_G	2.533	1.00
81_K	151_E	2.314	1.00
51_S	142_N	2.259	1.00
44_L	86_V	2.027	1.00
73_G	77_E	1.987	1.00
75_L	150_V	1.946	1.00
14_D	17_D	1.830	1.00
42_L	84_Y	1.821	1.00
72_I	88_V	1.806	1.00
71_S	74_D	1.804	1.00
66_R	73_G	1.786	1.00
137_K	144_T	1.785	1.00
78_L	151_E	1.771	1.00
97_K	101_E	1.751	1.00
93_T	115_E	1.728	1.00
136_P	146_D	1.725	1.00
36_P	39_R	1.614	1.00
48_L	72_I	1.563	1.00
139_G	143_T	1.507	1.00
106_A	129_P	1.503	1.00
35_V	106_A	1.463	1.00
96_R	122_D	1.448	1.00
42_L	79_A	1.443	1.00
78_L	81_K	1.438	1.00
58_T	63_N	1.431	1.00
56_K	65_K	1.430	1.00
29_R	33_A	1.421	1.00
50_N	69_K	1.419	1.00
74_D	147_L	1.414	1.00
87_Y	98_I	1.387	1.00
146_D	149_E	1.374	1.00
77_E	81_K	1.366	1.00
24_N	28_V	1.342	1.00
148_E	151_E	1.319	1.00
55_A	65_K	1.315	1.00
35_V	40_R	1.306	1.00
111_A	116_L	1.304	1.00
43_L	89_A	1.298	1.00
76_L	80_E	1.288	1.00
62_L	79_A	1.256	1.00
92_G	118_S	1.255	1.00
54_P	65_K	1.234	1.00
111_A	115_E	1.232	1.00
99_I	107_I	1.231	1.00
43_L	95_A	1.192	1.00
137_K	142_N	1.175	1.00
87_Y	102_G	1.164	1.00
15_H	18_M	1.155	1.00
21_I	113_E	1.153	1.00
79_A	84_Y	1.136	1.00
37_P	40_R	1.120	1.00
17_D	117_E	1.115	1.00
22_E	26_R	1.094	1.00
20_F	24_N	1.094	1.00
93_T	96_R	1.088	1.00
32_F	35_V	1.071	1.00
131_Q	153_A	1.045	1.00
74_D	77_E	1.022	1.00
14_D	18_M	1.009	1.00
108_V	131_Q	1.007	1.00
75_L	86_V	1.005	1.00
37_P	84_Y	0.987	1.00
25_N	32_F	0.985	1.00
78_L	82_L	0.974	0.99
39_R	85_K	0.967	0.99
54_P	69_K	0.967	0.99
148_E	152_E	0.951	0.99
65_K	69_K	0.928	0.99
31_K	35_V	0.922	0.99
62_L	80_E	0.919	0.99
68_G	73_G	0.917	0.99
114_R	118_S	0.910	0.99
38_E	105_D	0.906	0.99
29_R	106_A	0.905	0.99
51_S	141_V	0.901	0.99
82_L	151_E	0.895	0.99
92_G	115_E	0.881	0.99
24_N	120_I	0.872	0.99
134_P	144_T	0.870	0.99
110_V	150_V	0.863	0.99
37_P	106_A	0.854	0.99
7_R	13_K	0.853	0.99
91_G	95_A	0.843	0.98
89_A	95_A	0.843	0.98
134_P	146_D	0.842	0.98
135_L	138_G	0.837	0.98
26_R	29_R	0.837	0.98
61_G	86_V	0.836	0.98
6_G	16_L	0.832	0.98
43_L	109_G	0.819	0.98
89_A	94_L	0.816	0.98
46_H	91_G	0.816	0.98
44_L	72_I	0.812	0.98
26_R	30_E	0.811	0.98
60_D	63_N	0.805	0.98
19_S	23_L	0.804	0.98
134_P	149_E	0.800	0.98
46_H	57_I	0.799	0.98
46_H	115_E	0.798	0.98
16_L	19_S	0.790	0.98
117_E	121_Q	0.789	0.98
24_N	27_L	0.777	0.97
92_G	122_D	0.773	0.97
72_I	143_T	0.750	0.97
61_G	88_V	0.749	0.97
64_C	112_C	0.748	0.97
6_G	19_S	0.748	0.97
7_R	16_L	0.746	0.97
30_E	33_A	0.733	0.96
11_I	15_H	0.732	0.96
114_R	138_G	0.724	0.96
13_K	17_D	0.720	0.96
46_H	97_K	0.718	0.96
107_I	126_L	0.702	0.95
120_I	130_G	0.701	0.95
90_P	94_L	0.701	0.95
147_L	151_E	0.697	0.95
9_L	14_D	0.693	0.95
6_G	12_D	0.692	0.95
30_E	34_K	0.688	0.95
48_L	61_G	0.676	0.94
91_G	115_E	0.672	0.94
91_G	143_T	0.669	0.94
61_G	79_A	0.665	0.94
75_L	147_L	0.661	0.94
92_G	96_R	0.659	0.94
95_A	119_G	0.656	0.93
99_I	104_P	0.654	0.93
18_M	113_E	0.654	0.93
32_F	108_V	0.644	0.93
117_E	120_I	0.643	0.93
7_R	14_D	0.642	0.93
114_R	122_D	0.639	0.92
46_H	111_A	0.636	0.92
123_L	130_G	0.636	0.92
8_L	13_K	0.625	0.92
41_L	99_I	0.624	0.92
74_D	78_L	0.623	0.92
41_L	87_Y	0.619	0.91
74_D	151_E	0.618	0.91
77_E	82_L	0.616	0.91
11_I	14_D	0.615	0.91
122_D	130_G	0.613	0.91
116_L	132_G	0.612	0.91
32_F	36_P	0.610	0.91
21_I	132_G	0.610	0.91
92_G	104_P	0.609	0.91
47_C	64_C	0.608	0.91
68_G	95_A	0.605	0.90
75_L	145_V	0.602	0.90
112_C	140_C	0.599	0.90
17_D	106_A	0.598	0.90
94_L	97_K	0.598	0.90
49_R	104_P	0.597	0.90
41_L	98_I	0.593	0.89
144_T	148_E	0.589	0.89
64_C	70_C	0.589	0.89
15_H	19_S	0.588	0.89
120_I	132_G	0.585	0.89
57_I	88_V	0.582	0.89
78_L	147_L	0.581	0.88
49_R	139_G	0.578	0.88
45_P	107_I	0.577	0.88
50_N	54_P	0.577	0.88
12_D	15_H	0.576	0.88
29_R	153_A	0.575	0.88
108_V	153_A	0.575	0.88
19_S	22_E	0.574	0.88
28_V	31_K	0.572	0.88
46_H	93_T	0.569	0.87
71_S	147_L	0.568	0.87
8_L	14_D	0.567	0.87
6_G	9_L	0.567	0.87
93_T	114_R	0.560	0.87
48_L	75_L	0.560	0.87
93_T	122_D	0.559	0.86
21_I	91_G	0.556	0.86
47_C	112_C	0.554	0.86
89_A	132_G	0.554	0.86
111_A	120_I	0.550	0.86
55_A	63_N	0.549	0.86
92_G	95_A	0.548	0.85
95_A	122_D	0.548	0.85
98_I	102_G	0.548	0.85
52_D	77_E	0.548	0.85
53_C	70_C	0.547	0.85
40_R	84_Y	0.546	0.85
103_R	126_L	0.545	0.85
16_L	20_F	0.543	0.85
65_K	73_G	0.542	0.85
119_G	123_L	0.537	0.84
138_G	143_T	0.536	0.84
115_E	137_K	0.534	0.84
25_N	34_K	0.531	0.84
144_T	147_L	0.531	0.84
18_M	22_E	0.530	0.83
135_L	139_G	0.527	0.83
95_A	99_I	0.525	0.83
91_G	111_A	0.521	0.82
115_E	119_G	0.520	0.82
133_V	153_A	0.519	0.82
91_G	98_I	0.518	0.82
96_R	115_E	0.518	0.82
149_E	153_A	0.517	0.82
114_R	119_G	0.515	0.82
109_G	132_G	0.515	0.82
116_L	130_G	0.509	0.81
6_G	15_H	0.508	0.81
111_A	130_G	0.507	0.81
111_A	122_D	0.504	0.80
41_L	104_P	0.504	0.80
67_C	70_C	0.501	0.80
35_V	108_V	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
3m9wA	1	0.6558	57.2	0.914	Contact Map
2rgyA	2	0.6558	55.4	0.915	Contact Map
3clkA	2	0.6234	54.2	0.915	Contact Map
3cs3A	2	0.6753	50.1	0.917	Contact Map
2qu7A	2	0.6429	49.8	0.918	Contact Map
4rk6A	2	0.6429	49.1	0.918	Contact Map
3l6uA	2	0.6558	49.1	0.918	Contact Map
3c3kA	2	0.6558	48.1	0.918	Contact Map
3o74A	2	0.6688	48.1	0.918	Contact Map
4rk4A	2	0.6494	47.7	0.918	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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