DUF422 - PFAM28P - GREMLIN Contacts

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DUF422 - Protein of unknown function (DUF422)

PFAM:	PF04240	Sequences: GGVVLVLLGAAALLLHAVRRLGWRRALLFLAIAFLIGFAAELLGVRTGFPFGHYHYTDTLGPKLFGLVPLLIPLAWFMLAYPSYLLARLLLGPRARRRWLRALLAALLMVAWDLVLDPVAVRLGFWIWEDGGGYFGVPLSNFLGWFLVGLVLLALLRLLLRRRPLRARRAALLLPLALYLLFLLFFLGLNLAFGLWLPALLGLLLGVG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	208 (193)
Sequences:	6004 (4757)
Seq/√Len:	342.4
META:	0.877

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
105_A	153_L	3.585	1.00
102_A	150_L	3.000	1.00
79_L	109_M	2.781	1.00
38_F	42_L	2.718	1.00
40_A	148_V	2.536	1.00
106_A	150_L	2.374	1.00
195_L	198_P	2.232	1.00
106_A	146_F	2.172	1.00
55_H	129_E	2.171	1.00
39_A	43_L	2.110	1.00
42_L	46_R	2.022	1.00
134_Y	142_F	2.018	1.00
50_P	140_S	1.989	1.00
182_F	186_F	1.979	1.00
102_A	106_A	1.970	1.00
42_L	65_F	1.961	1.00
106_A	110_V	1.958	1.00
178_L	181_L	1.927	1.00
175_P	179_Y	1.914	1.00
109_M	149_G	1.879	1.00
144_G	148_V	1.866	1.00
179_Y	182_F	1.836	1.00
102_A	154_A	1.832	1.00
150_L	154_A	1.805	1.00
55_H	127_I	1.755	1.00
12_A	16_H	1.745	1.00
110_V	146_F	1.741	1.00
58_D	63_K	1.738	1.00
196_W	199_A	1.732	1.00
6_V	9_G	1.716	1.00
182_F	185_F	1.692	1.00
33_A	152_L	1.657	1.00
139_L	143_L	1.647	1.00
40_A	51_F	1.646	1.00
13_L	16_H	1.643	1.00
87_A	104_L	1.619	1.00
30_L	77_F	1.595	1.00
50_P	144_G	1.576	1.00
29_F	33_A	1.544	1.00
17_A	26_A	1.512	1.00
112_W	116_L	1.494	1.00
178_L	182_F	1.492	1.00
46_R	66_G	1.470	1.00
113_D	141_N	1.416	1.00
83_S	109_M	1.414	1.00
179_Y	183_L	1.408	1.00
83_S	108_L	1.400	1.00
43_L	47_T	1.386	1.00
7_L	11_A	1.371	1.00
176_L	179_Y	1.354	1.00
175_P	182_F	1.349	1.00
38_F	73_P	1.338	1.00
140_S	144_G	1.333	1.00
125_F	128_W	1.312	1.00
53_H	129_E	1.311	1.00
156_L	160_L	1.296	1.00
33_A	77_F	1.295	1.00
179_Y	186_F	1.294	1.00
181_L	185_F	1.294	1.00
24_R	28_L	1.292	1.00
32_I	155_L	1.285	1.00
107_L	146_F	1.280	1.00
80_A	109_M	1.280	1.00
191_L	199_A	1.277	1.00
154_A	158_L	1.257	1.00
175_P	178_L	1.253	1.00
186_F	190_N	1.235	1.00
34_F	77_F	1.225	1.00
57_T	127_I	1.224	1.00
9_G	12_A	1.216	1.00
13_L	17_A	1.194	1.00
10_A	13_L	1.192	1.00
173_L	177_A	1.174	1.00
84_Y	153_L	1.174	1.00
174_L	177_A	1.173	1.00
80_A	153_L	1.172	1.00
9_G	17_A	1.171	1.00
181_L	186_F	1.162	1.00
14_L	17_A	1.154	1.00
167_A	170_A	1.147	1.00
98_R	101_R	1.146	1.00
143_L	147_L	1.122	1.00
194_G	199_A	1.115	1.00
195_L	199_A	1.113	1.00
83_S	87_A	1.107	1.00
91_L	104_L	1.106	1.00
174_L	178_L	1.097	1.00
121_V	137_V	1.095	1.00
14_L	18_V	1.092	1.00
10_A	16_H	1.077	1.00
175_P	186_F	1.074	1.00
190_N	195_L	1.067	1.00
180_L	184_L	1.065	1.00
181_L	184_L	1.060	1.00
15_L	18_V	1.056	1.00
42_L	68_V	1.054	1.00
32_I	36_I	1.052	1.00
59_T	63_K	1.043	1.00
80_A	152_L	1.030	1.00
56_Y	72_I	1.024	1.00
176_L	180_L	1.022	1.00
121_V	124_G	1.019	1.00
22_G	26_A	1.017	1.00
87_A	105_A	1.012	1.00
38_F	65_F	1.010	1.00
118_P	121_V	1.004	1.00
178_L	185_F	1.000	1.00
185_F	189_L	1.000	1.00
40_A	151_V	0.995	1.00
37_G	152_L	0.992	1.00
9_G	13_L	0.988	1.00
18_V	23_W	0.981	1.00
109_M	153_L	0.978	1.00
110_V	149_G	0.972	1.00
16_H	81_Y	0.971	1.00
157_R	160_L	0.967	1.00
86_L	108_L	0.963	1.00
37_G	148_V	0.944	1.00
103_L	146_F	0.944	1.00
128_W	137_V	0.943	1.00
190_N	193_F	0.938	1.00
105_A	157_R	0.936	1.00
40_A	50_P	0.934	1.00
97_R	101_R	0.934	1.00
129_E	132_G	0.932	1.00
101_R	157_R	0.932	1.00
177_A	181_L	0.928	1.00
189_L	193_F	0.925	1.00
62_P	70_L	0.923	1.00
36_I	148_V	0.920	1.00
88_R	101_R	0.915	1.00
184_L	187_L	0.913	1.00
36_I	152_L	0.909	1.00
194_G	197_L	0.909	1.00
44_G	54_Y	0.907	1.00
194_G	198_P	0.888	1.00
103_L	150_L	0.884	1.00
117_D	137_V	0.875	1.00
112_W	120_A	0.873	1.00
158_L	161_R	0.873	1.00
84_Y	157_R	0.868	1.00
185_F	190_N	0.865	1.00
83_S	153_L	0.864	1.00
79_L	112_W	0.860	1.00
57_T	124_G	0.855	1.00
173_L	181_L	0.846	1.00
47_T	50_P	0.845	1.00
59_T	125_F	0.842	1.00
108_L	111_A	0.841	1.00
40_A	144_G	0.841	1.00
13_L	18_V	0.839	1.00
182_F	187_L	0.829	1.00
121_V	128_W	0.825	1.00
178_L	186_F	0.820	1.00
97_R	100_L	0.817	1.00
183_L	186_F	0.803	1.00
186_F	189_L	0.803	1.00
9_G	14_L	0.800	1.00
173_L	176_L	0.800	1.00
38_F	68_V	0.798	1.00
180_L	187_L	0.790	1.00
172_L	177_A	0.787	1.00
53_H	130_D	0.785	1.00
180_L	183_L	0.780	1.00
44_G	76_W	0.780	1.00
113_D	126_W	0.779	1.00
182_F	189_L	0.778	1.00
6_V	10_A	0.778	1.00
181_L	188_G	0.778	1.00
178_L	183_L	0.773	1.00
149_G	153_L	0.771	1.00
116_L	120_A	0.771	1.00
172_L	175_P	0.770	1.00
185_F	188_G	0.763	1.00
184_L	188_G	0.759	1.00
106_A	153_L	0.758	1.00
71_L	74_L	0.753	1.00
175_P	181_L	0.751	1.00
75_A	78_M	0.750	1.00
174_L	181_L	0.749	1.00
25_R	28_L	0.744	1.00
35_L	39_A	0.740	0.99
19_R	22_G	0.727	0.99
45_V	66_G	0.725	0.99
173_L	178_L	0.722	0.99
34_F	73_P	0.720	0.99
190_N	198_P	0.718	0.99
177_A	180_L	0.714	0.99
60_L	63_K	0.714	0.99
153_L	157_R	0.711	0.99
36_I	39_A	0.710	0.99
33_A	36_I	0.707	0.99
36_I	40_A	0.707	0.99
179_Y	190_N	0.704	0.99
133_G	139_L	0.704	0.99
36_I	155_L	0.702	0.99
73_P	120_A	0.699	0.99
23_W	27_L	0.695	0.99
174_L	182_F	0.695	0.99
175_P	185_F	0.694	0.99
84_Y	88_R	0.687	0.99
9_G	16_H	0.685	0.99
30_L	33_A	0.681	0.99
6_V	13_L	0.679	0.99
12_A	15_L	0.677	0.99
27_L	31_A	0.676	0.99
172_L	181_L	0.675	0.99
45_V	48_G	0.673	0.99
46_R	68_V	0.669	0.99
11_A	14_L	0.669	0.99
33_A	37_G	0.669	0.99
172_L	176_L	0.666	0.99
168_R	171_A	0.663	0.99
183_L	187_L	0.662	0.99
28_L	32_I	0.661	0.99
41_E	54_Y	0.661	0.99
22_G	25_R	0.658	0.99
177_A	182_F	0.653	0.99
140_S	143_L	0.653	0.99
29_F	156_L	0.652	0.99
54_Y	113_D	0.651	0.99
157_R	161_R	0.650	0.99
49_F	53_H	0.649	0.99
187_L	190_N	0.647	0.99
59_T	62_P	0.645	0.99
183_L	189_L	0.642	0.99
181_L	190_N	0.641	0.99
181_L	189_L	0.641	0.99
151_V	154_A	0.629	0.98
163_R	166_R	0.620	0.98
80_A	149_G	0.620	0.98
173_L	179_Y	0.615	0.98
17_A	81_Y	0.610	0.98
116_L	119_V	0.608	0.98
117_D	136_G	0.608	0.98
141_N	145_W	0.603	0.98
64_L	70_L	0.603	0.98
172_L	180_L	0.602	0.98
193_F	196_W	0.600	0.98
42_L	45_V	0.599	0.98
120_A	125_F	0.596	0.98
121_V	127_I	0.593	0.98
49_F	147_L	0.591	0.98
192_A	195_L	0.582	0.97
39_A	42_L	0.580	0.97
45_V	68_V	0.578	0.97
56_Y	113_D	0.576	0.97
177_A	184_L	0.575	0.97
37_G	77_F	0.575	0.97
34_F	37_G	0.574	0.97
174_L	186_F	0.574	0.97
154_A	157_R	0.574	0.97
9_G	18_V	0.573	0.97
51_F	76_W	0.570	0.97
63_K	70_L	0.569	0.97
61_G	71_L	0.568	0.97
6_V	12_A	0.568	0.97
177_A	186_F	0.567	0.97
119_V	123_L	0.564	0.97
135_F	198_P	0.563	0.97
191_L	194_G	0.563	0.97
43_L	50_P	0.561	0.97
137_V	142_F	0.561	0.97
183_L	188_G	0.560	0.97
169_R	172_L	0.559	0.97
6_V	14_L	0.556	0.96
49_F	140_S	0.551	0.96
72_I	76_W	0.547	0.96
176_L	181_L	0.545	0.96
44_G	50_P	0.543	0.96
102_A	157_R	0.541	0.96
63_K	66_G	0.539	0.96
12_A	17_A	0.537	0.96
188_G	192_A	0.535	0.96
179_Y	185_F	0.534	0.96
43_L	49_F	0.534	0.96
8_L	15_L	0.531	0.95
179_Y	187_L	0.531	0.95
88_R	157_R	0.531	0.95
128_W	138_P	0.528	0.95
158_L	162_R	0.521	0.95
118_P	144_G	0.521	0.95
96_R	99_W	0.520	0.95
114_L	117_D	0.514	0.95
115_V	118_P	0.513	0.95
51_F	144_G	0.512	0.94
173_L	186_F	0.507	0.94
72_I	120_A	0.504	0.94
156_L	159_L	0.504	0.94
113_D	142_F	0.500	0.94

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
4qncA	2	0.3365	4.6	0.949	Contact Map
4x5mA	2	0.3462	3.1	0.953	Contact Map
1afoA	2	0.1154	2.6	0.955	Contact Map
3gd8A	4	0.4327	2.2	0.956	Contact Map
2jwaA	2	0.1202	2.1	0.957	Contact Map
2a65A	2	0.4327	1.9	0.958	Contact Map
2ks1B	1	0.125	1.7	0.959	Contact Map
4rngA	2	0.3413	1.6	0.959	Contact Map
2l2tA	2	0.1202	1.3	0.962	Contact Map
3j9tb	1	0	1.2	0.962	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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