DUF328 - PFAM28P - GREMLIN Contacts

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DUF328 - Protein of unknown function (DUF328)

PFAM:	PF03883	Sequences: MLILLSPAKTLDFETPLPTLKHTQPEFLDEAEELIDVLRKLSPADLAKLMGISDKLAELNVERFQAWSTAENAKPAILAFTGDVYDGLDAASLSEADLDYAQDHLRILSGLYGLLRPLDLIQPYRLEMGTKLPNGRNLYAFWGDRITDALNEDEVLVNLASNEYFKAVDPKALKARVITPVFKDEKNGKYKVISFFAKKARGLMARYIIENRITDPEDLKGFDLEGYRFDEE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	232 (232)
Sequences:	11757 (8033)
Seq/√Len:	527.4
META:	0.756

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
30_E	145_R	4.328	1.00
89_D	92_S	3.470	1.00
78_L	98_L	2.814	1.00
94_S	97_D	2.722	1.00
206_R	210_E	2.707	1.00
97_D	210_E	2.634	1.00
47_A	54_D	2.536	1.00
100_Y	104_H	2.438	1.00
60_N	63_R	2.388	1.00
203_L	225_E	2.336	1.00
52_I	56_L	2.282	1.00
13_F	79_A	2.244	1.00
62_E	66_A	2.226	1.00
144_D	148_D	2.223	1.00
26_E	149_A	2.193	1.00
61_V	65_Q	2.156	1.00
3_I	208_I	2.131	1.00
81_T	91_A	2.104	1.00
37_V	41_L	2.102	1.00
97_D	212_R	2.094	1.00
146_I	167_A	2.094	1.00
58_E	62_E	2.093	1.00
185_E	190_Y	2.088	1.00
137_N	140_A	2.062	1.00
215_D	218_D	2.023	1.00
93_L	206_R	2.015	1.00
157_V	208_I	2.006	1.00
10_T	81_T	1.979	1.00
101_A	209_I	1.975	1.00
17_L	74_K	1.959	1.00
42_S	45_D	1.954	1.00
47_A	57_A	1.895	1.00
4_L	156_L	1.890	1.00
43_P	58_E	1.820	1.00
72_N	122_Q	1.804	1.00
27_F	149_A	1.725	1.00
149_A	152_E	1.684	1.00
35_I	64_F	1.624	1.00
143_G	169_D	1.623	1.00
151_N	174_K	1.613	1.00
155_V	176_R	1.585	1.00
37_V	132_L	1.581	1.00
5_L	84_V	1.570	1.00
38_L	64_F	1.568	1.00
169_D	172_A	1.552	1.00
192_V	197_A	1.546	1.00
181_V	192_V	1.537	1.00
81_T	86_D	1.520	1.00
217_E	220_K	1.517	1.00
54_D	58_E	1.513	1.00
102_Q	118_L	1.505	1.00
33_E	141_F	1.487	1.00
218_D	221_G	1.476	1.00
28_L	31_A	1.434	1.00
77_I	88_L	1.433	1.00
213_I	218_D	1.425	1.00
88_L	205_A	1.418	1.00
74_K	79_A	1.416	1.00
97_D	209_I	1.413	1.00
165_F	170_P	1.412	1.00
37_V	134_N	1.399	1.00
203_L	224_L	1.393	1.00
5_L	105_L	1.377	1.00
43_P	61_V	1.373	1.00
2_L	106_R	1.365	1.00
128_M	167_A	1.359	1.00
98_L	118_L	1.345	1.00
106_R	114_L	1.319	1.00
30_E	141_F	1.302	1.00
33_E	37_V	1.300	1.00
210_E	224_L	1.291	1.00
77_I	98_L	1.286	1.00
5_L	205_A	1.281	1.00
83_D	195_F	1.280	1.00
144_D	169_D	1.276	1.00
208_I	219_L	1.264	1.00
31_A	67_W	1.262	1.00
73_A	120_L	1.246	1.00
144_D	172_A	1.226	1.00
32_E	36_D	1.219	1.00
27_F	31_A	1.218	1.00
93_L	210_E	1.214	1.00
220_K	229_F	1.212	1.00
100_Y	212_R	1.206	1.00
162_N	166_K	1.205	1.00
92_S	206_R	1.205	1.00
87_G	199_K	1.183	1.00
114_L	149_A	1.175	1.00
52_I	57_A	1.173	1.00
30_E	136_R	1.169	1.00
93_L	98_L	1.169	1.00
12_D	15_T	1.160	1.00
99_D	103_D	1.158	1.00
59_L	63_R	1.156	1.00
12_D	81_T	1.155	1.00
147_T	169_D	1.152	1.00
77_I	90_A	1.144	1.00
185_E	188_G	1.123	1.00
183_K	190_Y	1.120	1.00
207_Y	222_F	1.120	1.00
30_E	33_E	1.114	1.00
84_V	159_L	1.112	1.00
38_L	41_L	1.104	1.00
96_A	99_D	1.094	1.00
151_N	175_A	1.089	1.00
37_V	135_G	1.086	1.00
12_D	74_K	1.064	1.00
34_L	134_N	1.063	1.00
100_Y	209_I	1.062	1.00
37_V	40_K	1.050	1.00
93_L	97_D	1.050	1.00
31_A	35_I	1.043	1.00
3_I	205_A	1.041	1.00
148_D	172_A	1.028	1.00
45_D	48_K	1.022	1.00
90_A	93_L	1.021	1.00
154_E	176_R	1.019	1.00
185_E	189_K	1.019	1.00
116_R	119_D	1.017	1.00
170_P	177_V	1.016	1.00
13_F	74_K	1.006	1.00
147_T	172_A	1.005	1.00
165_F	177_V	0.998	1.00
147_T	151_N	0.997	1.00
184_D	196_F	0.997	1.00
33_E	36_D	0.993	1.00
4_L	165_F	0.991	1.00
157_V	180_P	0.989	1.00
105_L	205_A	0.988	1.00
2_L	154_E	0.984	1.00
41_L	45_D	0.983	1.00
208_I	213_I	0.979	1.00
139_Y	166_K	0.978	1.00
155_V	216_P	0.974	1.00
162_N	179_T	0.974	1.00
77_I	101_A	0.972	1.00
35_I	111_L	0.967	1.00
73_A	122_Q	0.966	1.00
159_L	204_M	0.966	1.00
95_E	99_D	0.952	1.00
22_H	75_P	0.950	1.00
205_A	209_I	0.948	1.00
93_L	101_A	0.945	1.00
147_T	168_V	0.944	1.00
143_G	148_D	0.942	1.00
33_E	135_G	0.934	1.00
88_L	93_L	0.933	1.00
54_D	57_A	0.933	1.00
207_Y	221_G	0.932	1.00
112_Y	122_Q	0.932	1.00
106_R	149_A	0.926	1.00
86_D	199_K	0.917	1.00
146_I	168_V	0.915	1.00
37_V	133_P	0.912	1.00
32_E	69_T	0.906	1.00
15_T	74_K	0.906	1.00
23_T	102_Q	0.905	1.00
145_R	148_D	0.891	1.00
68_S	122_Q	0.890	1.00
183_K	192_V	0.890	1.00
105_L	209_I	0.886	1.00
46_L	52_I	0.885	1.00
74_K	91_A	0.878	1.00
214_T	218_D	0.871	1.00
77_I	117_P	0.861	1.00
106_R	117_P	0.859	1.00
199_K	203_L	0.859	1.00
8_A	11_L	0.857	1.00
94_S	210_E	0.849	1.00
197_A	201_R	0.848	1.00
96_A	212_R	0.841	1.00
203_L	207_Y	0.837	1.00
158_N	179_T	0.837	1.00
10_T	86_D	0.833	1.00
22_H	120_L	0.832	1.00
26_E	116_R	0.827	1.00
108_L	114_L	0.826	1.00
25_P	28_L	0.824	1.00
35_I	39_R	0.824	1.00
8_A	81_T	0.819	1.00
43_P	54_D	0.818	1.00
21_K	99_D	0.806	1.00
195_F	199_K	0.801	1.00
55_K	58_E	0.800	1.00
92_S	210_E	0.796	1.00
186_K	196_F	0.795	1.00
194_S	197_A	0.794	1.00
44_A	47_A	0.793	1.00
196_F	199_K	0.791	1.00
15_T	18_P	0.785	1.00
190_Y	230_D	0.783	1.00
29_D	33_E	0.779	1.00
28_L	32_E	0.779	1.00
8_A	86_D	0.776	1.00
131_K	137_N	0.762	1.00
207_Y	224_L	0.756	1.00
115_L	121_I	0.755	1.00
72_N	120_L	0.749	1.00
31_A	111_L	0.745	1.00
38_L	132_L	0.745	1.00
158_N	165_F	0.743	1.00
128_M	163_E	0.741	1.00
157_V	219_L	0.740	1.00
49_L	130_T	0.736	1.00
220_K	231_E	0.735	1.00
83_D	86_D	0.732	1.00
207_Y	211_N	0.730	1.00
50_M	64_F	0.728	1.00
173_L	177_V	0.727	1.00
83_D	199_K	0.726	1.00
86_D	195_F	0.725	1.00
27_F	30_E	0.723	1.00
44_A	48_K	0.714	1.00
207_Y	210_E	0.712	1.00
101_A	105_L	0.709	1.00
62_E	65_Q	0.708	1.00
186_K	193_I	0.708	1.00
24_Q	28_L	0.704	1.00
106_R	150_L	0.699	1.00
46_L	61_V	0.697	1.00
83_D	194_S	0.694	1.00
101_A	205_A	0.694	1.00
63_R	66_A	0.686	1.00
98_L	102_Q	0.682	1.00
186_K	189_K	0.682	1.00
156_L	175_A	0.681	1.00
90_A	98_L	0.675	1.00
14_E	17_L	0.674	1.00
41_L	46_L	0.670	1.00
110_G	128_M	0.670	1.00
207_Y	213_I	0.667	1.00
155_V	178_I	0.666	1.00
161_S	164_Y	0.666	1.00
35_I	67_W	0.664	1.00
88_L	206_R	0.661	1.00
22_H	70_A	0.660	1.00
184_D	193_I	0.658	1.00
154_E	174_K	0.656	1.00
181_V	184_D	0.656	1.00
78_L	90_A	0.655	1.00
75_P	78_L	0.653	1.00
26_E	31_A	0.645	1.00
228_R	231_E	0.641	1.00
110_G	127_E	0.640	1.00
12_D	16_P	0.639	1.00
43_P	57_A	0.638	1.00
60_N	64_F	0.634	1.00
24_Q	27_F	0.627	1.00
35_I	46_L	0.626	1.00
43_P	47_A	0.625	1.00
170_P	179_T	0.624	1.00
13_F	121_I	0.619	1.00
199_K	225_E	0.618	1.00
147_T	170_P	0.617	1.00
216_P	220_K	0.617	1.00
153_D	176_R	0.614	1.00
186_K	191_K	0.613	1.00
4_L	150_L	0.609	1.00
36_D	39_R	0.608	1.00
40_K	135_G	0.607	1.00
187_N	191_K	0.606	1.00
104_H	214_T	0.606	1.00
44_A	54_D	0.604	1.00
61_V	64_F	0.604	1.00
18_P	78_L	0.602	1.00
193_I	196_F	0.602	1.00
3_I	214_T	0.597	1.00
53_S	56_L	0.596	1.00
108_L	168_V	0.595	1.00
79_A	121_I	0.595	1.00
178_I	216_P	0.590	0.99
59_L	62_E	0.589	0.99
29_D	32_E	0.589	0.99
102_Q	117_P	0.587	0.99
13_F	17_L	0.586	0.99
83_D	87_G	0.585	0.99
24_Q	120_L	0.585	0.99
192_V	195_F	0.584	0.99
141_F	145_R	0.582	0.99
80_F	109_S	0.582	0.99
13_F	16_P	0.576	0.99
140_A	143_G	0.575	0.99
13_F	123_P	0.574	0.99
9_K	127_E	0.572	0.99
90_A	101_A	0.567	0.99
67_W	122_Q	0.566	0.99
90_A	206_R	0.565	0.99
16_P	19_T	0.561	0.99
24_Q	31_A	0.560	0.99
148_D	152_E	0.559	0.99
36_D	40_K	0.557	0.99
32_E	68_S	0.556	0.99
64_F	67_W	0.555	0.99
3_I	157_V	0.555	0.99
80_F	124_Y	0.554	0.99
18_P	91_A	0.553	0.99
153_D	175_A	0.553	0.99
19_T	95_E	0.552	0.99
26_E	29_D	0.552	0.99
35_I	38_L	0.550	0.99
46_L	50_M	0.548	0.99
58_E	61_V	0.546	0.99
4_L	168_V	0.545	0.99
75_P	120_L	0.544	0.99
147_T	175_A	0.544	0.99
41_L	49_L	0.544	0.99
10_T	55_K	0.544	0.99
21_K	95_E	0.543	0.99
184_D	227_Y	0.543	0.99
179_T	192_V	0.542	0.99
93_L	209_I	0.541	0.99
25_P	31_A	0.540	0.99
10_T	52_I	0.540	0.99
216_P	219_L	0.539	0.99
177_V	180_P	0.538	0.99
185_E	228_R	0.538	0.99
223_D	228_R	0.535	0.99
47_A	52_I	0.534	0.99
162_N	181_V	0.532	0.99
48_K	51_G	0.526	0.99
89_D	206_R	0.525	0.99
136_R	145_R	0.525	0.99
24_Q	29_D	0.524	0.99
31_A	38_L	0.524	0.99
70_A	120_L	0.523	0.99
143_G	147_T	0.522	0.99
221_G	224_L	0.522	0.99
46_L	64_F	0.521	0.99
151_N	173_L	0.521	0.99
207_Y	218_D	0.521	0.99
134_N	140_A	0.520	0.99
8_A	85_Y	0.518	0.99
28_L	69_T	0.517	0.99
86_D	196_F	0.517	0.99
215_D	220_K	0.517	0.99
104_H	212_R	0.516	0.99
69_T	122_Q	0.514	0.99
11_L	79_A	0.514	0.99
26_E	152_E	0.512	0.99
89_D	93_L	0.512	0.99
55_K	59_L	0.510	0.98
213_I	216_P	0.508	0.98
108_L	167_A	0.506	0.98
127_E	164_Y	0.504	0.98
68_S	71_E	0.504	0.98
17_L	75_P	0.503	0.98
183_K	230_D	0.501	0.98
3_I	209_I	0.500	0.98

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
4ou0A	1	0.2543	5.9	0.964	Contact Map
2fu2A	1	0.3103	4.9	0.965	Contact Map
2yfvC	1	0.2371	4.7	0.966	Contact Map
2m1bA	1	0.4095	4.4	0.966	Contact Map
4aaiA	2	0.2845	4.2	0.966	Contact Map
2m87A	1	0.4267	3.6	0.968	Contact Map
2hzmB	1	0.4655	3.5	0.968	Contact Map
3eyiA	1	0.2457	3.2	0.968	Contact Map
3bd1A	4	0.25	3.1	0.969	Contact Map
2cg4A	6	0.5819	3	0.969	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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