DUF1838 - PFAM28P - GREMLIN Contacts

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DUF1838 - Protein of unknown function (DUF1838)

PFAM:	PF08894	Sequences: NEPVVYWWSGTVYGRVPGERDKPLFGVEGMNVRRCVPVEDGKRGDGYRLVSREVGFYTDPKTGEILDTWENPWTGETVEVVHVANDPVNGRIKPFPLPWQVLGDTVWLTFDIPLFYPNPLAEPGEYPRESGGPTYHASELFTFFGSLADLLDPDLTSAPATGSWTRISPWLPWMKMGGRPGHLVYHAAGRKLDSFDELPPDLRAYIEKNYPEYLEAPPEDDERPNETSWTYFKKHF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	236 (224)
Sequences:	1422 (1016)
Seq/√Len:	67.9
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
200_P	204_A	4.778	1.00
76_E	175_K	4.146	1.00
152_D	155_L	3.928	1.00
14_G	73_W	3.541	1.00
70_E	75_G	3.412	1.00
70_E	77_T	3.235	1.00
149_D	159_P	3.067	1.00
26_G	63_G	2.983	1.00
68_T	77_T	2.875	1.00
203_R	207_E	2.802	1.00
68_T	79_E	2.582	1.00
69_W	174_M	2.549	1.00
205_Y	209_N	2.548	1.00
193_D	197_E	2.516	1.00
26_G	58_T	2.474	1.00
106_V	150_L	2.395	1.00
226_E	230_T	2.362	1.00
194_S	197_E	2.329	1.00
23_P	60_P	2.292	1.00
146_S	149_D	2.273	1.00
149_D	152_D	2.267	1.00
128_R	175_K	2.262	1.00
157_S	191_K	2.252	1.00
23_P	26_G	2.156	1.00
19_E	22_K	2.109	1.00
105_T	146_S	2.038	1.00
207_E	214_L	1.985	1.00
17_P	180_P	1.977	1.00
101_V	147_L	1.952	1.00
16_V	19_E	1.942	1.00
121_A	124_G	1.907	1.00
129_E	232_F	1.896	1.00
28_E	58_T	1.849	1.00
162_G	189_G	1.841	1.00
67_D	209_N	1.806	1.00
59_D	62_T	1.798	1.00
40_D	46_G	1.746	1.00
11_T	23_P	1.731	1.00
5_V	32_V	1.682	0.99
118_N	131_G	1.650	0.99
192_L	197_E	1.601	0.99
26_G	60_P	1.600	0.99
16_V	180_P	1.584	0.99
149_D	155_L	1.575	0.99
201_D	204_A	1.566	0.99
123_P	130_S	1.561	0.99
226_E	231_Y	1.543	0.99
60_P	63_G	1.526	0.99
204_A	208_K	1.516	0.99
155_L	158_A	1.471	0.99
147_L	151_L	1.468	0.99
67_D	205_Y	1.465	0.99
41_G	46_G	1.464	0.99
7_W	28_E	1.434	0.98
115_F	134_T	1.409	0.98
200_P	203_R	1.403	0.98
30_M	206_I	1.386	0.98
74_T	176_M	1.386	0.98
76_E	128_R	1.370	0.98
38_V	48_R	1.361	0.98
38_V	46_G	1.353	0.98
117_P	134_T	1.314	0.97
19_E	73_W	1.311	0.97
145_G	158_A	1.287	0.97
12_V	183_L	1.264	0.96
64_E	201_D	1.258	0.96
106_V	147_L	1.254	0.96
205_Y	208_K	1.251	0.96
121_A	127_P	1.240	0.96
22_K	73_W	1.239	0.96
126_Y	233_K	1.231	0.96
24_L	69_W	1.215	0.95
85_N	166_R	1.190	0.95
105_T	161_T	1.186	0.95
153_P	156_T	1.178	0.94
124_G	127_P	1.163	0.94
155_L	159_P	1.160	0.94
71_N	176_M	1.155	0.94
195_F	203_R	1.153	0.94
168_S	185_Y	1.147	0.94
71_N	74_T	1.127	0.93
53_E	85_N	1.125	0.93
14_G	22_K	1.119	0.93
123_P	132_G	1.094	0.92
14_G	24_L	1.092	0.92
104_D	148_A	1.091	0.92
228_S	231_Y	1.089	0.92
11_T	26_G	1.079	0.91
95_F	99_W	1.073	0.91
99_W	103_G	1.069	0.91
55_G	83_V	1.069	0.91
139_E	166_R	1.068	0.91
94_P	99_W	1.061	0.91
116_Y	141_F	1.045	0.90
65_I	205_Y	1.040	0.90
56_F	206_I	1.035	0.90
31_N	53_E	1.034	0.90
204_A	207_E	1.021	0.89
84_A	210_Y	1.020	0.89
69_W	78_V	1.019	0.89
129_E	175_K	1.017	0.89
57_Y	171_L	1.012	0.89
31_N	51_S	1.012	0.89
57_Y	164_W	1.010	0.88
5_V	195_F	1.010	0.88
198_L	206_I	0.978	0.87
78_V	175_K	0.978	0.87
126_Y	175_K	0.976	0.87
16_V	73_W	0.967	0.86
140_L	186_H	0.967	0.86
195_F	207_E	0.959	0.86
126_Y	129_E	0.952	0.85
67_D	82_H	0.951	0.85
34_R	216_A	0.949	0.85
58_T	201_D	0.941	0.85
97_L	103_G	0.939	0.85
106_V	145_G	0.935	0.84
12_V	25_F	0.932	0.84
55_G	187_A	0.930	0.84
167_I	182_H	0.928	0.84
95_F	98_P	0.917	0.83
72_P	176_M	0.917	0.83
27_V	187_A	0.915	0.83
107_W	144_F	0.914	0.83
123_P	178_G	0.912	0.83
56_F	65_I	0.911	0.83
52_R	86_D	0.911	0.83
14_G	170_W	0.907	0.82
52_R	164_W	0.897	0.82
36_V	50_V	0.894	0.81
14_G	19_E	0.891	0.81
227_T	230_T	0.890	0.81
150_L	158_A	0.878	0.80
230_T	233_K	0.873	0.80
174_M	183_L	0.870	0.80
8_W	29_G	0.866	0.79
104_D	146_S	0.863	0.79
64_E	204_A	0.863	0.79
111_D	140_L	0.861	0.79
48_R	91_R	0.861	0.79
170_W	181_G	0.857	0.79
123_P	126_Y	0.854	0.78
53_E	87_P	0.854	0.78
15_R	21_D	0.853	0.78
167_I	184_V	0.850	0.78
12_V	185_Y	0.850	0.78
96_P	99_W	0.841	0.77
169_P	177_G	0.840	0.77
218_P	221_D	0.833	0.77
125_E	233_K	0.827	0.76
52_R	217_P	0.823	0.76
101_V	106_V	0.821	0.76
205_Y	210_Y	0.815	0.75
48_R	220_D	0.814	0.75
138_S	184_V	0.812	0.75
59_D	63_G	0.806	0.74
225_N	230_T	0.802	0.74
108_L	143_F	0.790	0.73
198_L	203_R	0.790	0.73
85_N	139_E	0.786	0.72
51_S	90_G	0.784	0.72
203_R	214_L	0.777	0.72
195_F	214_L	0.776	0.71
112_I	141_F	0.774	0.71
52_R	166_R	0.767	0.71
85_N	89_N	0.763	0.70
9_S	28_E	0.760	0.70
16_V	22_K	0.758	0.70
169_P	178_G	0.754	0.69
15_R	182_H	0.752	0.69
196_D	214_L	0.751	0.69
164_W	185_Y	0.751	0.69
127_P	130_S	0.750	0.69
24_L	73_W	0.749	0.69
111_D	186_H	0.749	0.69
54_V	213_Y	0.747	0.69
56_F	202_L	0.746	0.68
5_V	8_W	0.746	0.68
8_W	55_G	0.745	0.68
7_W	61_K	0.742	0.68
206_I	210_Y	0.739	0.68
163_S	186_H	0.732	0.67
70_E	74_T	0.732	0.67
145_G	191_K	0.729	0.67
200_P	208_K	0.728	0.67
108_L	117_P	0.728	0.67
24_L	170_W	0.722	0.66
90_G	110_F	0.722	0.66
123_P	131_G	0.721	0.66
27_V	35_C	0.713	0.65
170_W	176_M	0.711	0.65
224_P	230_T	0.709	0.65
100_Q	103_G	0.705	0.64
57_Y	166_R	0.698	0.63
9_S	100_Q	0.696	0.63
74_T	78_V	0.693	0.63
52_R	85_N	0.693	0.63
196_D	203_R	0.692	0.63
168_S	228_S	0.691	0.63
83_V	164_W	0.684	0.62
73_W	170_W	0.682	0.62
219_E	222_E	0.681	0.61
158_A	191_K	0.679	0.61
226_E	232_F	0.674	0.61
202_L	206_I	0.672	0.60
58_T	65_I	0.672	0.60
94_P	97_L	0.672	0.60
128_R	134_T	0.671	0.60
135_Y	164_W	0.671	0.60
194_S	198_L	0.668	0.60
86_D	116_Y	0.664	0.59
105_T	110_F	0.664	0.59
165_T	184_V	0.659	0.59
53_E	172_P	0.658	0.59
33_R	47_Y	0.658	0.59
124_G	133_P	0.656	0.59
16_V	20_R	0.656	0.59
118_N	121_A	0.653	0.58
118_N	130_S	0.651	0.58
194_S	199_P	0.650	0.58
103_G	107_W	0.647	0.57
215_E	218_P	0.643	0.57
120_L	164_W	0.643	0.57
166_R	185_Y	0.641	0.57
140_L	163_S	0.641	0.57
58_T	63_G	0.637	0.56
85_N	88_V	0.637	0.56
54_V	203_R	0.637	0.56
85_N	185_Y	0.634	0.56
86_D	89_N	0.632	0.56
67_D	208_K	0.631	0.56
66_L	170_W	0.630	0.55
160_A	189_G	0.628	0.55
49_L	90_G	0.626	0.55
85_N	164_W	0.624	0.55
225_N	231_Y	0.623	0.55
67_D	79_E	0.622	0.55
112_I	116_Y	0.621	0.54
5_V	192_L	0.620	0.54
170_W	179_R	0.619	0.54
52_R	141_F	0.619	0.54
34_R	50_V	0.617	0.54
141_F	166_R	0.616	0.54
134_T	177_G	0.615	0.54
72_P	181_G	0.613	0.53
118_N	127_P	0.611	0.53
31_N	141_F	0.609	0.53
227_T	233_K	0.609	0.53
38_V	41_G	0.606	0.53
103_G	152_D	0.605	0.53
116_Y	119_P	0.604	0.52
105_T	144_F	0.603	0.52
102_L	107_W	0.601	0.52
166_R	172_P	0.599	0.52
80_V	173_W	0.597	0.52
69_W	80_V	0.595	0.51
72_P	150_L	0.593	0.51
61_K	190_R	0.591	0.51
26_G	29_G	0.590	0.51
140_L	184_V	0.590	0.51
74_T	179_R	0.588	0.50
86_D	139_E	0.588	0.50
131_G	178_G	0.588	0.50
85_N	174_M	0.588	0.50
103_G	197_E	0.587	0.50
187_A	206_I	0.584	0.50
97_L	110_F	0.584	0.50
15_R	184_V	0.583	0.50
24_L	232_F	0.582	0.50
75_G	94_P	0.581	0.50
97_L	108_L	0.580	0.50
50_V	89_N	0.579	0.49
70_E	76_E	0.579	0.49
32_V	195_F	0.579	0.49
163_S	189_G	0.579	0.49
37_P	47_Y	0.578	0.49
71_N	181_G	0.578	0.49
5_V	9_S	0.578	0.49
12_V	27_V	0.578	0.49
31_N	85_N	0.578	0.49
123_P	133_P	0.577	0.49
47_Y	145_G	0.574	0.49
11_T	60_P	0.570	0.48
57_Y	228_S	0.567	0.48
99_W	104_D	0.564	0.48
31_N	52_R	0.560	0.47
57_Y	185_Y	0.559	0.47
76_E	179_R	0.558	0.47
124_G	130_S	0.556	0.47
148_A	154_D	0.552	0.46
131_G	135_Y	0.548	0.46
136_H	182_H	0.548	0.46
53_E	174_M	0.546	0.45
222_E	227_T	0.545	0.45
103_G	106_V	0.542	0.45
119_P	177_G	0.542	0.45
51_S	189_G	0.541	0.45
142_T	186_H	0.540	0.45
176_M	179_R	0.539	0.45
127_P	131_G	0.538	0.45
110_F	143_F	0.537	0.44
86_D	166_R	0.533	0.44
145_G	150_L	0.532	0.44
51_S	84_A	0.531	0.44
89_N	164_W	0.528	0.43
6_Y	33_R	0.528	0.43
100_Q	107_W	0.528	0.43
226_E	229_W	0.527	0.43
166_R	171_L	0.526	0.43
193_D	215_E	0.525	0.43
165_T	186_H	0.525	0.43
94_P	102_L	0.523	0.43
8_W	31_N	0.522	0.43
49_L	143_F	0.522	0.43
222_E	230_T	0.522	0.43
34_R	53_E	0.521	0.43
113_P	132_G	0.521	0.43
99_W	169_P	0.518	0.42
160_A	163_S	0.518	0.42
225_N	229_W	0.518	0.42
145_G	149_D	0.516	0.42
102_L	105_T	0.516	0.42
139_E	164_W	0.515	0.42
61_K	154_D	0.515	0.42
107_W	188_A	0.515	0.42
87_P	137_A	0.515	0.42
25_F	69_W	0.513	0.42
17_P	130_S	0.512	0.41
214_L	219_E	0.512	0.41
137_A	166_R	0.511	0.41
118_N	135_Y	0.510	0.41
36_V	48_R	0.505	0.41
90_G	165_T	0.505	0.41
100_Q	146_S	0.502	0.40
81_V	231_Y	0.500	0.40
159_P	193_D	0.500	0.40

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
4pjoK	1	0.178	9.6	0.96	Contact Map
3elgA	1	0.2034	8.8	0.961	Contact Map
4dsdA	1	0.1949	7	0.962	Contact Map
1wizA	1	0.322	5.2	0.965	Contact Map
3db7A	2	0.2034	5.1	0.965	Contact Map
4qoaA	2	0.1992	5	0.965	Contact Map
2gu3A	1	0.2627	4.8	0.965	Contact Map
2mxeA	1	0.1568	4.6	0.966	Contact Map
4cfgA	2	0	3.4	0.968	Contact Map
2o4aA	1	0.2542	3.3	0.968	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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