DUF2884 - PFAM28P - GREMLIN Contacts

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DUF2884 - Protein of unknown function (DUF2884)

PFAM:	PF11101	Sequences: CDVDSDYDVTIDPDSLEFTRAGGPKLVINHDGQLFVDGKAVALSAAQQQRLREYERGLRALVPEVKAIAREGVDIAFDALDEVAAGLLGDDSNARARLTALLDQLKAQLKRRIYQSGDGFTLGAQAFDQFDDAFEQEFEQAVEELVPESVGSILQAAGNAMLSGDGDNLAALEARMEGLGEEIEAEVEARAQALEARAEALCPRLQALDELEQQLQQRIPELKPLDLI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	228 (227)
Sequences:	845 (576)
Seq/√Len:	38.2
META:	0.555

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_L	41_V	4.806	1.00
71_E	197_R	4.686	1.00
24_P	27_V	3.467	1.00
64_E	197_R	3.183	1.00
43_L	51_L	3.049	1.00
34_L	51_L	2.986	1.00
32_G	55_E	2.653	1.00
221_E	225_L	2.630	1.00
209_D	226_D	2.584	1.00
75_I	187_V	2.481	1.00
11_I	59_R	2.375	1.00
72_G	76_A	2.371	1.00
35_F	40_A	2.291	1.00
43_L	47_Q	2.274	1.00
134_F	138_F	2.251	0.99
79_A	83_V	2.226	0.99
155_Q	158_G	2.166	0.99
82_E	186_E	2.142	0.99
123_G	127_F	2.043	0.99
63_P	69_A	2.013	0.99
64_E	204_R	1.984	0.99
47_Q	218_R	1.957	0.98
183_I	187_V	1.937	0.98
207_A	210_E	1.935	0.98
44_S	47_Q	1.930	0.98
149_S	153_I	1.900	0.98
105_L	110_K	1.882	0.98
150_V	161_M	1.859	0.98
172_L	176_M	1.857	0.98
24_P	29_N	1.838	0.98
158_G	162_L	1.826	0.98
29_N	33_Q	1.824	0.98
106_K	109_L	1.793	0.97
58_L	203_P	1.790	0.97
98_L	105_L	1.789	0.97
23_G	26_L	1.747	0.97
33_Q	40_A	1.734	0.97
101_L	106_K	1.718	0.97
12_D	138_F	1.702	0.96
43_L	52_R	1.685	0.96
141_A	149_S	1.661	0.96
36_V	41_V	1.623	0.95
57_G	207_A	1.617	0.95
219_I	222_L	1.579	0.94
166_G	169_L	1.578	0.94
89_G	92_S	1.574	0.94
27_V	35_F	1.573	0.94
154_L	176_M	1.535	0.93
32_G	47_Q	1.507	0.93
146_V	171_A	1.498	0.93
109_L	112_R	1.476	0.92
140_Q	150_V	1.466	0.92
190_R	209_D	1.459	0.92
102_L	106_K	1.446	0.91
134_F	140_Q	1.443	0.91
68_I	71_E	1.441	0.91
49_Q	53_E	1.440	0.91
10_T	17_E	1.396	0.90
155_Q	162_L	1.371	0.89
54_Y	212_E	1.363	0.89
142_V	183_I	1.355	0.88
71_E	139_E	1.354	0.88
155_Q	159_N	1.353	0.88
179_L	183_I	1.353	0.88
83_V	87_L	1.352	0.88
80_L	122_L	1.344	0.88
37_D	52_R	1.335	0.88
153_I	158_G	1.296	0.86
88_L	94_A	1.273	0.85
16_L	59_R	1.271	0.85
192_Q	207_A	1.268	0.85
47_Q	50_R	1.265	0.85
84_A	88_L	1.263	0.84
222_L	227_L	1.259	0.84
26_L	29_N	1.258	0.84
43_L	212_E	1.253	0.84
41_V	51_L	1.239	0.83
68_I	75_I	1.234	0.83
72_G	197_R	1.221	0.82
157_A	160_A	1.211	0.82
212_E	226_D	1.191	0.81
104_Q	107_A	1.180	0.80
83_V	191_A	1.161	0.79
112_R	116_S	1.157	0.79
142_V	146_V	1.134	0.77
137_E	150_V	1.127	0.77
26_L	47_Q	1.114	0.76
223_K	226_D	1.113	0.76
189_A	206_Q	1.101	0.75
18_F	26_L	1.098	0.75
185_A	189_A	1.092	0.75
106_K	110_K	1.075	0.73
109_L	159_N	1.073	0.73
24_P	28_I	1.070	0.73
138_F	143_E	1.063	0.73
28_I	55_E	1.061	0.72
211_L	223_K	1.061	0.72
103_D	107_A	1.059	0.72
104_Q	108_Q	1.055	0.72
123_G	126_A	1.055	0.72
68_I	198_A	1.054	0.72
74_D	78_D	1.050	0.72
55_E	59_R	1.047	0.71
120_F	123_G	1.038	0.71
47_Q	55_E	1.031	0.70
117_G	225_L	1.028	0.70
178_G	182_E	1.025	0.70
101_L	183_I	1.022	0.70
177_E	192_Q	1.017	0.69
37_D	46_A	1.010	0.69
23_G	128_D	1.008	0.68
53_E	60_A	1.006	0.68
43_L	48_Q	1.004	0.68
212_E	217_Q	1.000	0.68
145_L	153_I	0.999	0.68
67_A	197_R	0.991	0.67
62_V	159_N	0.980	0.66
11_I	62_V	0.974	0.66
13_P	93_N	0.971	0.66
12_D	15_S	0.967	0.65
219_I	224_P	0.966	0.65
194_L	198_A	0.961	0.65
27_V	130_F	0.959	0.65
13_P	59_R	0.952	0.64
79_A	208_L	0.944	0.63
113_I	209_D	0.944	0.63
184_E	212_E	0.942	0.63
151_G	155_Q	0.936	0.63
71_E	191_A	0.935	0.63
59_R	69_A	0.934	0.62
145_L	159_N	0.930	0.62
84_A	188_E	0.929	0.62
69_A	73_V	0.928	0.62
22_G	53_E	0.927	0.62
214_Q	217_Q	0.917	0.61
46_A	53_E	0.915	0.61
156_A	160_A	0.912	0.61
222_L	225_L	0.910	0.60
192_Q	200_A	0.910	0.60
39_K	192_Q	0.909	0.60
18_F	211_L	0.906	0.60
94_A	98_L	0.898	0.59
71_E	190_R	0.893	0.59
191_A	198_A	0.893	0.59
93_N	171_A	0.886	0.58
132_D	135_E	0.883	0.58
95_R	99_T	0.881	0.58
43_L	63_P	0.866	0.57
211_L	226_D	0.861	0.56
42_A	46_A	0.852	0.55
186_E	220_P	0.851	0.55
14_D	183_I	0.846	0.55
50_R	55_E	0.841	0.54
20_R	105_L	0.838	0.54
160_A	164_G	0.836	0.54
93_N	100_A	0.833	0.54
62_V	120_F	0.830	0.53
110_K	113_I	0.827	0.53
169_L	172_L	0.825	0.53
209_D	213_Q	0.820	0.53
66_K	80_L	0.809	0.52
94_A	101_L	0.806	0.51
22_G	28_I	0.804	0.51
102_L	105_L	0.804	0.51
76_A	80_L	0.803	0.51
58_L	126_A	0.803	0.51
54_Y	62_V	0.802	0.51
113_I	122_L	0.802	0.51
191_A	195_E	0.799	0.51
75_I	190_R	0.791	0.50
5_S	222_L	0.790	0.50
69_A	72_G	0.789	0.50
10_T	16_L	0.788	0.50
3_V	183_I	0.787	0.50
172_L	175_R	0.782	0.49
154_L	158_G	0.782	0.49
86_G	94_A	0.775	0.48
71_E	75_I	0.774	0.48
106_K	111_R	0.773	0.48
115_Q	118_D	0.773	0.48
122_L	145_L	0.772	0.48
199_E	219_I	0.770	0.48
214_Q	224_P	0.764	0.48
187_V	191_A	0.763	0.47
43_L	76_A	0.763	0.47
113_I	116_S	0.761	0.47
151_G	193_A	0.757	0.47
37_D	225_L	0.756	0.47
184_E	195_E	0.756	0.47
192_Q	195_E	0.753	0.47
41_V	187_V	0.752	0.46
58_L	87_L	0.751	0.46
87_L	148_E	0.750	0.46
32_G	50_R	0.749	0.46
36_V	139_E	0.747	0.46
138_F	147_P	0.746	0.46
42_A	178_G	0.744	0.46
143_E	158_G	0.734	0.45
105_L	113_I	0.733	0.45
103_D	106_K	0.729	0.44
49_Q	87_L	0.728	0.44
40_A	48_Q	0.724	0.44
160_A	190_R	0.723	0.44
210_E	224_P	0.713	0.43
111_R	221_E	0.708	0.43
172_L	180_G	0.702	0.42
136_Q	159_N	0.698	0.42
50_R	74_D	0.697	0.42
14_D	132_D	0.696	0.41
80_L	90_D	0.694	0.41
177_E	180_G	0.694	0.41
10_T	19_T	0.692	0.41
133_A	137_E	0.690	0.41
48_Q	52_R	0.690	0.41
50_R	218_R	0.689	0.41
131_D	136_Q	0.686	0.41
39_K	45_A	0.683	0.40
39_K	188_E	0.680	0.40
163_S	172_L	0.679	0.40
137_E	140_Q	0.678	0.40
64_E	186_E	0.678	0.40
16_L	20_R	0.675	0.40
62_V	66_K	0.671	0.39
32_G	44_S	0.671	0.39
34_L	200_A	0.666	0.39
65_V	69_A	0.666	0.39
138_F	141_A	0.664	0.39
152_S	156_A	0.659	0.38
213_Q	226_D	0.657	0.38
7_Y	20_R	0.655	0.38
54_Y	58_L	0.655	0.38
66_K	109_L	0.654	0.38
144_E	148_E	0.651	0.38
26_L	30_H	0.645	0.37
33_Q	191_A	0.645	0.37
158_G	161_M	0.644	0.37
65_V	76_A	0.644	0.37
214_Q	226_D	0.644	0.37
7_Y	123_G	0.643	0.37
151_G	154_L	0.643	0.37
209_D	212_E	0.643	0.37
172_L	195_E	0.643	0.37
182_E	186_E	0.642	0.37
146_V	154_L	0.639	0.37
48_Q	182_E	0.638	0.37
186_E	201_L	0.638	0.37
160_A	168_N	0.637	0.36
101_L	114_Y	0.636	0.36
128_D	143_E	0.634	0.36
161_M	168_N	0.634	0.36
95_R	179_L	0.632	0.36
165_D	172_L	0.629	0.36
102_L	146_V	0.623	0.35
160_A	167_D	0.622	0.35
136_Q	139_E	0.621	0.35
173_E	176_M	0.619	0.35
34_L	47_Q	0.612	0.34
135_E	153_I	0.611	0.34
195_E	220_P	0.610	0.34
139_E	173_E	0.609	0.34
155_Q	180_G	0.606	0.34
85_A	135_E	0.606	0.34
174_A	177_E	0.606	0.34
4_D	46_A	0.604	0.34
99_T	113_I	0.603	0.34
44_S	128_D	0.602	0.34
72_G	193_A	0.599	0.33
34_L	129_Q	0.595	0.33
169_L	173_E	0.595	0.33
83_V	183_I	0.594	0.33
172_L	183_I	0.593	0.33
83_V	128_D	0.590	0.33
34_L	100_A	0.590	0.33
108_Q	188_E	0.590	0.33
18_F	47_Q	0.588	0.33
133_A	138_F	0.587	0.32
55_E	113_I	0.585	0.32
3_V	127_F	0.585	0.32
51_L	55_E	0.584	0.32
138_F	153_I	0.584	0.32
16_L	19_T	0.577	0.32
3_V	19_T	0.574	0.31
217_Q	222_L	0.570	0.31
68_I	156_A	0.569	0.31
7_Y	55_E	0.568	0.31
105_L	112_R	0.568	0.31
156_A	209_D	0.568	0.31
176_M	180_G	0.564	0.31
51_L	85_A	0.564	0.31
102_L	112_R	0.564	0.31
134_F	152_S	0.563	0.31
84_A	157_A	0.562	0.30
47_Q	222_L	0.562	0.30
52_R	199_E	0.558	0.30
187_V	201_L	0.550	0.30
33_Q	195_E	0.550	0.30
187_V	197_R	0.550	0.30
65_V	165_D	0.549	0.30
56_R	171_A	0.549	0.30
136_Q	146_V	0.548	0.29
8_D	186_E	0.548	0.29
28_I	58_L	0.547	0.29
156_A	164_G	0.546	0.29
65_V	109_L	0.546	0.29
136_Q	177_E	0.545	0.29
68_I	186_E	0.542	0.29
154_L	172_L	0.541	0.29
82_E	86_G	0.540	0.29
131_D	137_E	0.540	0.29
146_V	183_I	0.540	0.29
171_A	180_G	0.539	0.29
8_D	71_E	0.537	0.29
109_L	150_V	0.536	0.29
37_D	108_Q	0.535	0.28
37_D	139_E	0.535	0.28
188_E	192_Q	0.535	0.28
113_I	168_N	0.533	0.28
73_V	169_L	0.532	0.28
72_G	194_L	0.531	0.28
87_L	109_L	0.530	0.28
187_V	213_Q	0.530	0.28
74_D	98_L	0.530	0.28
89_G	154_L	0.529	0.28
57_G	204_R	0.526	0.28
25_K	71_E	0.523	0.28
11_I	16_L	0.523	0.28
22_G	208_L	0.523	0.28
84_A	118_D	0.522	0.28
120_F	157_A	0.521	0.27
149_S	156_A	0.518	0.27
158_G	172_L	0.517	0.27
217_Q	225_L	0.517	0.27
41_V	44_S	0.514	0.27
111_R	157_A	0.513	0.27
185_A	196_A	0.512	0.27
8_D	164_G	0.504	0.26
62_V	180_G	0.504	0.26
215_L	219_I	0.504	0.26
16_L	36_V	0.503	0.26
42_A	45_A	0.500	0.26

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
4etpB	1	0.2544	40.6	0.936	Contact Map
4etpA	1	0.2588	31.7	0.94	Contact Map
1mzkA	1	0.2851	28.7	0.941	Contact Map
3ounA	1	0.25	21.3	0.945	Contact Map
3uv0A	2	0.3026	21.3	0.945	Contact Map
3r2pA	2	0.6974	16.9	0.947	Contact Map
3rjpA	1	0.3904	16.8	0.947	Contact Map
3witA	3	0.2105	15.5	0.948	Contact Map
2hqnA	1	0.4474	14.8	0.949	Contact Map
4mtkA	4	0.3509	14.3	0.949	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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