DUF4184 - PFAM28P - GREMLIN Contacts

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DUF4184 - Domain of unknown function (DUF4184)

PFAM:	PF13803	Sequences: MPFTLSHPAAVLPLRRLRRRRLSLSALVIGSMAPDFEYFLRLRPLGTFTHTLLGLFTFDLPLGLLLLLLFHLLLRPPLIALLPAPLRRRLAAPWRRRSLRRWLLVLLSLLIGAATHLLWDSFTHEDGWGVRHLPALREPVGGGLPLYKLLQHGSSVLGLAVLAVWLLRWLRRPPRLSPRRRLAYWLALALLALVVAALRAAFGLAALGTLVVGAISGLLLGLLLYSV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	227 (224)
Sequences:	2449 (2093)
Seq/√Len:	139.8
META:	0.747

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
63_G	109_L	5.448	1.00
119_W	154_S	4.862	1.00
5_L	8_P	4.358	1.00
23_S	108_S	4.237	1.00
55_L	113_A	3.090	1.00
6_S	159_L	3.086	1.00
127_G	130_V	3.010	1.00
58_F	62_L	2.896	1.00
60_L	110_L	2.856	1.00
152_H	155_S	2.800	1.00
10_A	115_T	2.800	1.00
25_S	71_H	2.772	1.00
11_V	31_S	2.588	1.00
217_G	221_G	2.322	1.00
37_E	41_R	2.236	1.00
33_A	63_G	2.213	1.00
46_G	49_T	2.211	1.00
71_H	75_R	2.191	1.00
29_I	63_G	2.111	1.00
123_T	150_L	2.104	1.00
52_L	56_F	2.030	1.00
59_D	113_A	1.996	1.00
213_G	217_G	1.988	1.00
55_L	114_A	1.968	1.00
208_G	212_V	1.910	1.00
140_V	146_L	1.908	1.00
38_Y	46_G	1.902	1.00
148_K	152_H	1.863	1.00
86_L	166_L	1.848	1.00
159_L	163_A	1.843	1.00
212_V	216_S	1.811	1.00
128_W	132_H	1.806	1.00
29_I	32_M	1.788	1.00
22_L	108_S	1.763	1.00
121_S	129_G	1.757	1.00
122_F	129_G	1.754	1.00
105_V	109_L	1.740	1.00
118_L	122_F	1.740	1.00
8_P	32_M	1.729	1.00
63_G	113_A	1.726	1.00
177_S	181_R	1.717	1.00
196_A	199_R	1.699	1.00
28_V	31_S	1.697	1.00
109_L	113_A	1.632	1.00
26_A	109_L	1.590	1.00
124_H	151_Q	1.575	1.00
25_S	67_L	1.476	1.00
23_S	26_A	1.410	1.00
183_A	186_L	1.388	1.00
15_R	19_R	1.381	1.00
98_S	101_R	1.374	1.00
84_A	88_R	1.357	1.00
155_S	159_L	1.347	1.00
118_L	129_G	1.331	1.00
51_T	54_G	1.331	1.00
148_K	153_G	1.325	1.00
130_V	147_Y	1.323	1.00
67_L	105_V	1.316	1.00
216_S	220_L	1.314	1.00
29_I	67_L	1.304	1.00
104_L	108_S	1.303	1.00
144_L	148_K	1.301	1.00
29_I	66_L	1.295	1.00
181_R	184_Y	1.269	1.00
29_I	33_A	1.269	1.00
41_R	44_P	1.257	1.00
164_V	168_R	1.256	1.00
33_A	109_L	1.237	1.00
38_Y	154_S	1.233	1.00
54_G	57_T	1.230	1.00
37_E	49_T	1.210	1.00
179_R	183_A	1.193	1.00
55_L	59_D	1.175	1.00
38_Y	54_G	1.168	0.99
49_T	58_F	1.168	0.99
180_R	184_Y	1.153	0.99
130_V	137_R	1.147	0.99
10_A	119_W	1.143	0.99
57_T	61_P	1.142	0.99
18_R	22_L	1.109	0.99
68_L	72_L	1.102	0.99
54_G	59_D	1.075	0.99
94_W	101_R	1.074	0.99
41_R	45_L	1.070	0.99
71_H	94_W	1.067	0.99
32_M	36_F	1.065	0.99
6_S	160_A	1.063	0.99
119_W	158_G	1.059	0.99
41_R	46_G	1.059	0.99
184_Y	188_L	1.054	0.99
180_R	183_A	1.048	0.99
200_A	203_G	1.041	0.99
129_G	133_L	1.039	0.99
56_F	61_P	1.035	0.99
133_L	136_L	1.026	0.99
199_R	203_G	1.023	0.99
85_P	89_R	1.021	0.99
84_A	87_R	1.018	0.99
67_L	109_L	1.014	0.99
64_L	105_V	1.010	0.99
26_A	67_L	1.009	0.99
3_F	6_S	1.006	0.98
213_G	216_S	1.002	0.98
114_A	118_L	1.001	0.98
10_A	154_S	0.988	0.98
2_P	7_H	0.986	0.98
60_L	113_A	0.985	0.98
146_L	150_L	0.985	0.98
16_R	19_R	0.981	0.98
188_L	192_A	0.980	0.98
11_V	27_L	0.979	0.98
138_E	146_L	0.976	0.98
72_L	95_R	0.969	0.98
106_L	109_L	0.967	0.98
9_A	12_L	0.966	0.98
208_G	215_I	0.959	0.98
176_L	181_R	0.952	0.98
201_A	204_L	0.949	0.98
179_R	184_Y	0.945	0.98
208_G	211_V	0.941	0.98
48_F	57_T	0.937	0.98
55_L	110_L	0.934	0.98
111_I	115_T	0.931	0.97
60_L	106_L	0.928	0.97
25_S	70_F	0.928	0.97
212_V	215_I	0.927	0.97
132_H	137_R	0.927	0.97
37_E	43_R	0.922	0.97
25_S	94_W	0.919	0.97
80_A	90_L	0.915	0.97
44_P	49_T	0.908	0.97
40_L	44_P	0.908	0.97
24_L	165_W	0.906	0.97
86_L	89_R	0.904	0.97
33_A	66_L	0.898	0.97
121_S	127_G	0.897	0.97
221_G	225_Y	0.894	0.97
178_P	181_R	0.893	0.97
121_S	132_H	0.874	0.96
53_L	57_T	0.873	0.96
195_V	199_R	0.864	0.96
121_S	128_W	0.863	0.96
76_P	161_V	0.861	0.96
70_F	75_R	0.859	0.96
24_L	63_G	0.859	0.96
59_D	63_G	0.859	0.96
157_L	161_V	0.850	0.96
53_L	56_F	0.848	0.96
162_L	166_L	0.844	0.96
214_A	218_L	0.842	0.95
12_L	24_L	0.841	0.95
26_A	105_V	0.840	0.95
37_E	42_L	0.838	0.95
134_P	137_R	0.836	0.95
178_P	182_L	0.833	0.95
9_A	165_W	0.832	0.95
4_T	7_H	0.830	0.95
96_R	99_L	0.816	0.95
9_A	162_L	0.811	0.94
19_R	22_L	0.805	0.94
126_D	131_R	0.804	0.94
176_L	180_R	0.798	0.94
27_L	111_I	0.796	0.94
51_T	113_A	0.795	0.94
122_F	151_Q	0.794	0.94
144_L	156_V	0.791	0.94
1_M	4_T	0.788	0.94
182_L	192_A	0.785	0.93
182_L	185_W	0.784	0.93
24_L	28_V	0.780	0.93
196_A	200_A	0.777	0.93
209_T	212_V	0.776	0.93
197_A	201_A	0.773	0.93
33_A	113_A	0.771	0.93
182_L	186_L	0.770	0.93
129_G	136_L	0.765	0.93
49_T	54_G	0.764	0.92
124_H	150_L	0.763	0.92
135_A	146_L	0.763	0.92
17_L	20_R	0.762	0.92
186_L	190_L	0.759	0.92
187_A	191_L	0.759	0.92
104_L	107_L	0.754	0.92
56_F	59_D	0.754	0.92
113_A	117_L	0.752	0.92
94_W	97_R	0.750	0.92
127_G	131_R	0.749	0.92
195_V	198_L	0.746	0.92
102_W	106_L	0.742	0.91
189_A	193_L	0.741	0.91
8_P	11_V	0.739	0.91
48_F	54_G	0.738	0.91
200_A	204_L	0.737	0.91
119_W	152_H	0.730	0.91
145_P	148_K	0.725	0.90
94_W	98_S	0.724	0.90
48_F	51_T	0.723	0.90
168_R	172_R	0.721	0.90
189_A	192_A	0.717	0.90
61_P	70_F	0.713	0.90
129_G	132_H	0.705	0.89
174_P	180_R	0.704	0.89
8_P	31_S	0.702	0.89
195_V	200_A	0.695	0.88
208_G	219_L	0.694	0.88
54_G	61_P	0.691	0.88
71_H	108_S	0.688	0.88
209_T	215_I	0.687	0.88
75_R	92_A	0.684	0.88
55_L	117_L	0.683	0.88
174_P	193_L	0.679	0.87
133_L	137_R	0.679	0.87
22_L	104_L	0.679	0.87
30_G	34_P	0.677	0.87
187_A	193_L	0.676	0.87
156_V	159_L	0.676	0.87
6_S	15_R	0.674	0.87
159_L	162_L	0.668	0.86
3_F	159_L	0.667	0.86
144_L	149_L	0.666	0.86
210_L	220_L	0.665	0.86
123_T	151_Q	0.665	0.86
210_L	219_L	0.665	0.86
164_V	186_L	0.664	0.86
135_A	138_E	0.663	0.86
178_P	183_A	0.659	0.86
24_L	108_S	0.658	0.86
164_V	167_L	0.657	0.86
181_R	188_L	0.653	0.85
4_T	151_Q	0.653	0.85
68_L	98_S	0.652	0.85
67_L	71_H	0.649	0.85
9_A	38_Y	0.648	0.85
58_F	61_P	0.647	0.85
208_G	216_S	0.644	0.84
1_M	7_H	0.642	0.84
79_I	91_A	0.641	0.84
12_L	165_W	0.638	0.84
46_G	102_W	0.636	0.84
28_V	32_M	0.635	0.84
56_F	110_L	0.635	0.84
23_S	42_L	0.634	0.83
96_R	101_R	0.631	0.83
33_A	38_Y	0.627	0.83
175_R	181_R	0.618	0.82
87_R	181_R	0.617	0.82
79_I	87_R	0.614	0.81
36_F	215_I	0.614	0.81
18_R	24_L	0.614	0.81
18_R	21_R	0.611	0.81
196_A	201_A	0.610	0.81
212_V	220_L	0.605	0.81
14_L	20_R	0.605	0.81
165_W	169_W	0.604	0.80
180_R	188_L	0.598	0.80
56_F	114_A	0.597	0.80
29_I	105_V	0.588	0.79
149_L	152_H	0.587	0.79
185_W	188_L	0.586	0.78
211_V	215_I	0.586	0.78
75_R	79_I	0.585	0.78
199_R	202_F	0.585	0.78
67_L	94_W	0.584	0.78
222_L	225_Y	0.584	0.78
22_L	115_T	0.580	0.78
210_L	217_G	0.580	0.78
197_A	200_A	0.579	0.78
160_A	167_L	0.578	0.77
15_R	22_L	0.576	0.77
203_G	206_A	0.575	0.77
15_R	18_R	0.573	0.77
74_L	223_L	0.569	0.76
3_F	39_F	0.568	0.76
157_L	204_L	0.566	0.76
63_G	105_V	0.565	0.76
151_Q	154_S	0.564	0.76
209_T	222_L	0.562	0.75
132_H	135_A	0.560	0.75
40_L	62_L	0.555	0.75
97_R	101_R	0.555	0.75
92_A	95_R	0.552	0.74
32_M	151_Q	0.552	0.74
9_A	161_V	0.551	0.74
40_L	43_R	0.549	0.74
206_A	219_L	0.548	0.74
118_L	121_S	0.547	0.74
37_E	48_F	0.546	0.73
210_L	218_L	0.546	0.73
206_A	209_T	0.544	0.73
183_A	188_L	0.543	0.73
41_R	49_T	0.542	0.73
181_R	185_W	0.541	0.73
190_L	193_L	0.541	0.73
38_Y	129_G	0.540	0.73
140_V	149_L	0.540	0.73
195_V	221_G	0.540	0.73
176_L	184_Y	0.538	0.72
209_T	213_G	0.536	0.72
49_T	80_A	0.536	0.72
195_V	217_G	0.535	0.72
39_F	58_F	0.535	0.72
20_R	104_L	0.535	0.72
134_P	138_E	0.534	0.72
46_G	51_T	0.533	0.72
208_G	213_G	0.533	0.72
17_L	22_L	0.532	0.71
201_A	206_A	0.532	0.71
65_L	73_L	0.530	0.71
100_R	104_L	0.530	0.71
71_H	78_L	0.529	0.71
39_F	215_I	0.528	0.71
148_K	155_S	0.527	0.71
78_L	96_R	0.527	0.71
119_W	162_L	0.526	0.71
69_L	73_L	0.524	0.70
43_R	46_G	0.520	0.70
6_S	155_S	0.520	0.70
188_L	225_Y	0.519	0.70
175_R	178_P	0.518	0.69
177_S	183_A	0.516	0.69
127_G	146_L	0.516	0.69
2_P	13_P	0.515	0.69
130_V	136_L	0.515	0.69
115_T	151_Q	0.514	0.69
64_L	68_L	0.513	0.69
9_A	155_S	0.512	0.69
64_L	180_R	0.511	0.68
36_F	66_L	0.511	0.68
67_L	108_S	0.511	0.68
209_T	216_S	0.510	0.68
8_P	24_L	0.507	0.68
82_L	85_P	0.504	0.67
53_L	62_L	0.504	0.67
52_L	114_A	0.501	0.67
220_L	223_L	0.501	0.67
198_L	202_F	0.500	0.67

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
1pw4A	1	0.5859	12.9	0.954	Contact Map
1oedB	1	0.348	8.8	0.957	Contact Map
1oedC	1	0.348	8.6	0.958	Contact Map
1oedA	1	0.348	7.6	0.959	Contact Map
1oedE	1	0.3524	6.8	0.959	Contact Map
3pjsK	4	0.3789	5.6	0.961	Contact Map
4pypA	1	0.5066	5.2	0.962	Contact Map
3effK	4	0.3789	3.4	0.965	Contact Map
4av3A	2	0.3524	3	0.966	Contact Map
2m6bA	1	0.3744	2.4	0.967	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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