DUF4386 - PFAM28P - GREMLIN Contacts

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DUF4386 - Domain of unknown function (DUF4386)

PFAM:	PF14329	Sequences: IAGVLYLLTFVAGIFAELYLPGPLIVPGDAAATAANIAAHETLFRLGILLELIGALAFIGLAVALYPLLKPVNEGLALLAVAFRLVEAAIIAVGVLNLLAALTLLQGAAAFGAPQLQAALALLLLALHDWGFLLGLIFFGLWLLLLGYLLYRSGLLPRWLGVLGLIGGVLYLVGSLAVLLFPDYSALVPLLALPAALGELSLGLWLLVKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	210 (210)
Sequences:	20802 (15312)
Seq/√Len:	1056.6
META:	0.952

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
204_L	208_V	3.316	1.00
70_K	74_E	3.173	1.00
151_Y	162_V	3.143	1.00
41_E	45_R	3.039	1.00
113_A	117_Q	2.817	1.00
82_A	85_L	2.760	1.00
114_P	117_Q	2.649	1.00
112_G	116_L	2.609	1.00
62_A	84_R	2.285	1.00
150_L	156_L	2.209	1.00
112_G	115_Q	2.197	1.00
114_P	118_A	2.126	1.00
115_Q	118_A	2.107	1.00
113_A	116_L	2.058	1.00
76_L	145_L	2.047	1.00
86_V	89_A	2.011	1.00
184_Y	187_L	2.005	1.00
147_G	164_G	1.978	1.00
29_D	32_A	1.884	1.00
111_F	115_Q	1.806	1.00
198_G	203_G	1.790	1.00
198_G	202_L	1.780	1.00
196_A	200_L	1.770	1.00
66_Y	78_L	1.763	1.00
76_L	148_Y	1.762	1.00
2_A	64_A	1.733	1.00
13_G	54_G	1.658	1.00
154_G	158_R	1.634	1.00
84_R	142_W	1.596	1.00
109_A	112_G	1.587	1.00
124_L	128_H	1.585	1.00
74_E	78_L	1.578	1.00
105_L	108_A	1.567	1.00
49_L	176_L	1.561	1.00
150_L	161_G	1.558	1.00
17_E	21_P	1.555	1.00
80_A	146_L	1.537	1.00
35_A	38_A	1.512	1.00
80_A	145_L	1.511	1.00
4_V	8_L	1.510	1.00
188_V	192_A	1.509	1.00
15_F	19_Y	1.493	1.00
179_L	182_P	1.455	1.00
110_A	118_A	1.447	1.00
151_Y	158_R	1.437	1.00
12_A	54_G	1.435	1.00
37_I	44_F	1.432	1.00
84_R	87_E	1.430	1.00
146_L	202_L	1.409	1.00
55_A	91_I	1.403	1.00
63_V	82_A	1.400	1.00
4_V	207_L	1.391	1.00
94_G	97_N	1.374	1.00
73_N	76_L	1.373	1.00
32_A	36_N	1.372	1.00
15_F	20_L	1.365	1.00
42_T	46_L	1.361	1.00
100_A	127_L	1.336	1.00
31_A	35_A	1.317	1.00
198_G	205_W	1.317	1.00
67_P	75_G	1.313	1.00
111_F	116_L	1.308	1.00
143_L	164_G	1.307	1.00
32_A	35_A	1.304	1.00
144_L	168_G	1.297	1.00
151_Y	161_G	1.296	1.00
77_A	81_V	1.293	1.00
116_L	119_A	1.291	1.00
111_F	114_P	1.267	1.00
35_A	39_A	1.254	1.00
67_P	78_L	1.245	1.00
10_F	14_I	1.202	1.00
58_F	87_E	1.200	1.00
58_F	84_R	1.182	1.00
140_G	168_G	1.181	1.00
136_L	139_F	1.179	1.00
67_P	70_K	1.169	1.00
73_N	149_L	1.167	1.00
111_F	117_Q	1.166	1.00
190_L	194_P	1.160	1.00
28_G	32_A	1.149	1.00
190_L	193_L	1.149	1.00
115_Q	119_A	1.147	1.00
123_L	126_A	1.125	1.00
33_T	36_N	1.123	1.00
147_G	161_G	1.115	1.00
5_L	64_A	1.102	1.00
160_L	201_S	1.101	1.00
112_G	117_Q	1.099	1.00
165_L	169_V	1.095	1.00
36_N	39_A	1.088	1.00
110_A	114_P	1.087	1.00
118_A	121_A	1.072	1.00
8_L	57_A	1.071	1.00
58_F	91_I	1.070	1.00
66_Y	74_E	1.068	1.00
119_A	122_L	1.059	1.00
55_A	92_A	1.057	1.00
151_Y	165_L	1.056	1.00
8_L	12_A	1.052	1.00
142_W	146_L	1.051	1.00
117_Q	121_A	1.048	1.00
193_L	197_L	1.040	1.00
14_I	18_L	1.039	1.00
147_G	165_L	1.038	1.00
36_N	40_H	1.037	1.00
128_H	132_F	1.025	1.00
41_E	106_Q	1.024	1.00
147_G	168_G	1.020	1.00
116_L	120_L	1.020	1.00
126_A	129_D	1.018	1.00
203_G	207_L	1.016	1.00
21_P	51_E	1.008	1.00
109_A	114_P	1.008	1.00
101_A	105_L	1.002	1.00
197_L	201_S	1.002	1.00
9_T	57_A	1.001	1.00
103_T	106_Q	1.000	1.00
72_V	149_L	0.995	1.00
194_P	197_L	0.990	1.00
58_F	88_A	0.984	1.00
192_A	195_A	0.981	1.00
112_G	119_A	0.972	1.00
123_L	127_L	0.966	1.00
66_Y	77_A	0.958	1.00
33_T	37_I	0.954	1.00
30_A	34_A	0.949	1.00
96_L	131_G	0.947	1.00
51_E	91_I	0.944	1.00
20_L	23_P	0.942	1.00
117_Q	120_L	0.941	1.00
191_L	195_A	0.940	1.00
63_V	79_L	0.933	1.00
54_G	57_A	0.932	1.00
169_V	173_V	0.932	1.00
111_F	118_A	0.931	1.00
71_P	74_E	0.924	1.00
103_T	130_W	0.924	1.00
12_A	50_L	0.924	1.00
201_S	205_W	0.921	1.00
13_G	16_A	0.912	1.00
66_Y	70_K	0.911	1.00
19_Y	23_P	0.904	1.00
171_Y	174_G	0.904	1.00
54_G	58_F	0.901	1.00
122_L	126_A	0.899	1.00
48_I	99_L	0.897	1.00
167_G	171_Y	0.896	1.00
83_F	141_L	0.891	1.00
69_L	149_L	0.884	1.00
14_I	17_E	0.884	1.00
167_G	170_L	0.867	1.00
162_V	166_I	0.863	1.00
159_W	162_V	0.845	1.00
55_A	88_A	0.842	1.00
188_V	191_L	0.841	1.00
130_W	133_L	0.834	1.00
34_A	38_A	0.834	1.00
141_L	145_L	0.829	1.00
72_V	153_S	0.828	1.00
11_V	14_I	0.828	1.00
13_G	17_E	0.825	1.00
109_A	117_Q	0.823	1.00
112_G	118_A	0.821	1.00
51_E	95_V	0.820	1.00
110_A	119_A	0.818	1.00
193_L	196_A	0.818	1.00
97_N	101_A	0.815	1.00
2_A	65_L	0.814	1.00
159_W	201_S	0.812	1.00
94_G	131_G	0.810	1.00
159_W	163_L	0.808	1.00
95_V	98_L	0.805	1.00
199_E	202_L	0.804	1.00
98_L	128_H	0.804	1.00
189_P	192_A	0.804	1.00
118_A	122_L	0.804	1.00
77_A	149_L	0.803	1.00
79_L	83_F	0.797	1.00
67_P	74_E	0.796	1.00
7_L	10_F	0.794	1.00
44_F	48_I	0.790	1.00
5_L	60_G	0.788	1.00
184_Y	188_V	0.782	1.00
94_G	135_G	0.782	1.00
173_V	177_A	0.778	1.00
62_A	88_A	0.777	1.00
26_V	33_T	0.777	1.00
195_A	198_G	0.775	1.00
21_P	25_I	0.775	1.00
10_F	203_G	0.774	1.00
170_L	195_A	0.763	1.00
17_E	22_G	0.762	1.00
46_L	50_L	0.760	1.00
114_P	119_A	0.758	1.00
66_Y	81_V	0.755	1.00
179_L	183_D	0.753	1.00
21_P	24_L	0.752	1.00
195_A	203_G	0.750	1.00
91_I	135_G	0.745	1.00
110_A	117_Q	0.743	1.00
26_V	29_D	0.742	1.00
59_I	86_V	0.741	1.00
140_G	172_L	0.740	1.00
150_L	202_L	0.735	1.00
76_L	152_R	0.734	1.00
15_F	46_L	0.730	1.00
10_F	13_G	0.730	1.00
80_A	142_W	0.730	1.00
34_A	37_I	0.726	1.00
187_L	191_L	0.721	1.00
87_E	91_I	0.719	1.00
132_F	136_L	0.713	1.00
48_I	95_V	0.713	1.00
148_Y	152_R	0.713	1.00
63_V	75_G	0.712	1.00
97_N	124_L	0.710	1.00
186_A	190_L	0.707	1.00
180_L	183_D	0.707	1.00
113_A	118_A	0.700	1.00
129_D	133_L	0.699	1.00
38_A	105_L	0.699	1.00
60_G	64_A	0.698	1.00
6_Y	9_T	0.697	1.00
142_W	145_L	0.697	1.00
42_T	45_R	0.688	1.00
18_L	22_G	0.686	1.00
81_V	85_L	0.685	1.00
26_V	36_N	0.681	1.00
143_L	147_G	0.681	1.00
65_L	146_L	0.680	1.00
171_Y	195_A	0.678	1.00
157_P	160_L	0.678	1.00
200_L	203_G	0.676	1.00
51_E	128_H	0.670	1.00
125_L	129_D	0.669	1.00
59_I	88_A	0.669	1.00
117_Q	122_L	0.668	1.00
83_F	145_L	0.661	1.00
100_A	124_L	0.658	1.00
109_A	113_A	0.651	1.00
165_L	168_G	0.646	1.00
38_A	41_E	0.645	1.00
202_L	206_L	0.645	1.00
200_L	204_L	0.643	1.00
150_L	164_G	0.643	1.00
99_L	103_T	0.642	1.00
53_I	57_A	0.641	1.00
143_L	168_G	0.638	1.00
185_S	188_V	0.635	1.00
54_G	91_I	0.632	1.00
199_E	203_G	0.630	1.00
109_A	116_L	0.630	1.00
127_L	130_W	0.629	1.00
94_G	128_H	0.624	1.00
124_L	127_L	0.623	1.00
96_L	99_L	0.616	1.00
76_L	149_L	0.613	1.00
168_G	171_Y	0.613	1.00
191_L	194_P	0.609	1.00
195_A	199_E	0.608	1.00
198_G	201_S	0.608	1.00
72_V	155_L	0.607	1.00
62_A	142_W	0.603	1.00
194_P	201_S	0.600	1.00
51_E	54_G	0.598	1.00
67_P	71_P	0.598	1.00
144_L	165_L	0.596	1.00
48_I	98_L	0.594	1.00
110_A	113_A	0.593	1.00
189_P	193_L	0.588	1.00
3_G	6_Y	0.587	1.00
192_A	196_A	0.586	1.00
9_T	13_G	0.579	1.00
80_A	150_L	0.578	1.00
60_G	79_L	0.577	1.00
80_A	84_R	0.576	1.00
89_A	92_A	0.575	1.00
204_L	209_K	0.575	1.00
75_G	79_L	0.575	1.00
204_L	207_L	0.572	1.00
195_A	201_S	0.570	1.00
135_G	139_F	0.567	1.00
16_A	50_L	0.564	1.00
166_I	169_V	0.560	1.00
40_H	43_L	0.556	1.00
146_L	150_L	0.556	1.00
6_Y	10_F	0.554	1.00
167_G	196_A	0.550	1.00
133_L	178_V	0.546	1.00
56_L	60_G	0.541	1.00
58_F	62_A	0.541	1.00
69_L	156_L	0.540	1.00
23_P	43_L	0.538	1.00
174_G	178_V	0.537	1.00
132_F	135_G	0.536	1.00
65_L	80_A	0.534	1.00
14_I	19_Y	0.531	1.00
8_L	53_I	0.531	1.00
87_E	135_G	0.523	1.00
168_G	195_A	0.523	1.00
51_E	132_F	0.517	1.00
196_A	202_L	0.516	1.00
167_G	195_A	0.516	1.00
186_A	189_P	0.516	1.00
156_L	202_L	0.516	1.00
16_A	19_Y	0.515	1.00
59_I	85_L	0.513	1.00
39_A	42_T	0.513	1.00
134_L	137_I	0.512	1.00
194_P	198_G	0.512	1.00
147_G	163_L	0.506	1.00
41_E	44_F	0.503	1.00
163_L	201_S	0.502	1.00
97_N	100_A	0.500	1.00

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
4p79A	1	0.3095	17.3	0.904	Contact Map
3wu2J	1	0.1857	7.6	0.918	Contact Map
2jafA	3	0.7476	5.5	0.923	Contact Map
4o6yA	2	0.8667	4.6	0.926	Contact Map
2xq2A	2	0.4381	4.5	0.926	Contact Map
3ux4A	3	0.6619	4.1	0.928	Contact Map
4c7rA	3	0.9476	4	0.928	Contact Map
3wfdB	1	0.6476	3.8	0.929	Contact Map
4ymuD	2	0.319	2.9	0.933	Contact Map
4djkA	2	0.9238	2.8	0.934	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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