DUF2840 - PFAM28P - GREMLIN Contacts

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DUF2840 - Protein of unknown function (DUF2840)

PFAM:	PF11000	Sequences: LTHVELTWIEKRIEHWIRFGRPAREQILDRRRRVASFAPGSVFAFVRWAANDYGTVLSRIDILRAVAPGEPYQTVPGVRPGGEILLRASGWPKVERVLQAIDAIEALGIDPADVAPDYWRHVHNRLAAGEPPRPYTRERHRAWLLRRR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	148 (147)
Sequences:	1364 (664)
Seq/√Len:	54.7
META:	0.795

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
29_D	32_R	5.626	1.00
3_H	36_S	4.260	1.00
63_L	82_G	3.776	1.00
22_P	35_A	3.691	1.00
63_L	75_V	3.346	1.00
141_R	145_L	3.197	1.00
18_R	105_E	3.025	1.00
109_I	114_V	2.701	1.00
64_R	83_E	2.677	1.00
95_E	99_Q	2.569	1.00
43_F	65_A	2.406	1.00
100_A	118_Y	2.340	1.00
66_V	72_Y	2.285	1.00
60_I	97_V	2.238	1.00
104_I	114_V	2.176	1.00
44_A	60_I	2.097	1.00
58_S	91_W	1.977	1.00
51_N	55_T	1.970	1.00
28_L	34_V	1.968	1.00
48_W	55_T	1.965	1.00
8_W	14_E	1.872	0.99
21_R	113_D	1.859	0.99
88_A	97_V	1.852	0.99
64_R	70_E	1.736	0.99
136_T	139_R	1.585	0.98
21_R	110_D	1.538	0.98
26_Q	34_V	1.490	0.97
7_T	77_G	1.484	0.97
49_A	57_L	1.393	0.96
17_I	22_P	1.382	0.96
17_I	35_A	1.381	0.96
115_A	118_Y	1.359	0.95
84_I	87_R	1.343	0.95
4_V	43_F	1.330	0.95
23_A	38_A	1.311	0.94
115_A	139_R	1.302	0.94
61_D	75_V	1.299	0.94
127_A	141_R	1.299	0.94
96_R	99_Q	1.295	0.94
75_V	79_R	1.267	0.93
18_R	46_V	1.236	0.92
104_I	107_L	1.235	0.92
63_L	83_E	1.230	0.92
107_L	112_A	1.226	0.92
137_R	141_R	1.216	0.92
96_R	131_P	1.214	0.92
7_T	15_H	1.189	0.91
4_V	37_F	1.125	0.88
40_G	67_A	1.108	0.88
100_A	122_V	1.106	0.87
75_V	84_I	1.096	0.87
60_I	94_V	1.086	0.86
18_R	94_V	1.085	0.86
118_Y	122_V	1.080	0.86
104_I	139_R	1.064	0.85
45_F	77_G	1.052	0.85
122_V	132_P	1.044	0.84
67_A	70_E	1.038	0.84
11_K	17_I	1.037	0.84
14_E	58_S	1.035	0.84
22_P	26_Q	1.027	0.83
26_Q	32_R	1.022	0.83
24_R	36_S	1.021	0.83
26_Q	36_S	1.018	0.83
4_V	65_A	1.014	0.82
22_P	118_Y	1.012	0.82
138_E	141_R	1.000	0.82
25_E	33_R	0.999	0.81
73_Q	84_I	0.995	0.81
76_P	129_G	0.994	0.81
24_R	38_A	0.993	0.81
135_Y	140_H	0.980	0.80
73_Q	77_G	0.968	0.79
66_V	83_E	0.963	0.79
50_A	57_L	0.960	0.79
125_R	128_A	0.959	0.79
5_E	11_K	0.957	0.79
28_L	32_R	0.956	0.78
30_R	55_T	0.955	0.78
104_I	111_P	0.955	0.78
3_H	9_I	0.941	0.77
2_T	65_A	0.936	0.77
73_Q	89_S	0.928	0.76
73_Q	104_I	0.920	0.76
88_A	127_A	0.919	0.76
29_D	94_V	0.891	0.73
42_V	95_E	0.888	0.73
16_W	120_R	0.887	0.73
86_L	97_V	0.887	0.73
23_A	36_S	0.882	0.73
5_E	34_V	0.878	0.72
39_P	98_L	0.869	0.72
137_R	144_L	0.857	0.70
48_W	53_Y	0.854	0.70
78_V	128_A	0.846	0.69
50_A	53_Y	0.844	0.69
139_R	143_W	0.820	0.67
15_H	45_F	0.819	0.67
83_E	120_R	0.813	0.66
136_T	141_R	0.808	0.66
16_W	25_E	0.803	0.65
107_L	137_R	0.794	0.65
114_V	118_Y	0.793	0.64
37_F	41_S	0.791	0.64
27_I	31_R	0.783	0.63
44_A	91_W	0.783	0.63
93_K	102_D	0.781	0.63
48_W	90_G	0.777	0.63
115_A	143_W	0.776	0.63
39_P	116_P	0.774	0.63
66_V	77_G	0.772	0.62
45_F	58_S	0.770	0.62
21_R	108_G	0.766	0.62
127_A	145_L	0.765	0.62
7_T	75_V	0.760	0.61
51_N	56_V	0.746	0.60
7_T	10_E	0.744	0.59
30_R	46_V	0.743	0.59
70_E	77_G	0.732	0.58
25_E	87_R	0.730	0.58
9_I	12_R	0.726	0.58
26_Q	72_Y	0.724	0.57
8_W	11_K	0.719	0.57
21_R	112_A	0.719	0.57
27_I	30_R	0.714	0.56
95_E	139_R	0.710	0.56
1_L	23_A	0.708	0.56
112_A	115_A	0.689	0.54
54_G	102_D	0.689	0.54
60_I	78_V	0.686	0.53
52_D	110_D	0.683	0.53
49_A	56_V	0.678	0.53
45_F	60_I	0.671	0.52
129_G	145_L	0.670	0.52
84_I	145_L	0.668	0.51
42_V	65_A	0.664	0.51
12_R	50_A	0.662	0.51
100_A	104_I	0.660	0.51
138_E	147_R	0.660	0.51
98_L	107_L	0.658	0.50
111_P	114_V	0.657	0.50
35_A	96_R	0.657	0.50
23_A	67_A	0.656	0.50
41_S	65_A	0.655	0.50
144_L	147_R	0.644	0.49
106_A	115_A	0.639	0.48
22_P	27_I	0.638	0.48
57_L	87_R	0.637	0.48
75_V	78_V	0.635	0.48
13_I	147_R	0.634	0.48
34_V	111_P	0.630	0.47
59_R	77_G	0.626	0.47
3_H	26_Q	0.626	0.47
22_P	87_R	0.618	0.46
38_A	108_G	0.613	0.46
98_L	113_D	0.613	0.46
67_A	72_Y	0.612	0.45
51_N	54_G	0.610	0.45
5_E	28_L	0.606	0.45
100_A	114_V	0.603	0.45
131_P	138_E	0.600	0.44
29_D	33_R	0.600	0.44
110_D	117_D	0.599	0.44
45_F	53_Y	0.597	0.44
13_I	29_D	0.594	0.44
86_L	114_V	0.594	0.44
61_D	87_R	0.594	0.44
50_A	55_T	0.592	0.43
88_A	93_K	0.585	0.43
54_G	58_S	0.585	0.43
99_Q	136_T	0.583	0.42
77_G	145_L	0.581	0.42
9_I	27_I	0.579	0.42
46_V	105_E	0.576	0.42
15_H	77_G	0.575	0.42
134_P	143_W	0.575	0.42
42_V	64_R	0.574	0.41
53_Y	87_R	0.573	0.41
14_E	91_W	0.571	0.41
143_W	146_R	0.570	0.41
101_I	111_P	0.564	0.40
13_I	32_R	0.563	0.40
44_A	102_D	0.560	0.40
136_T	145_L	0.555	0.39
40_G	70_E	0.553	0.39
38_A	41_S	0.552	0.39
55_T	120_R	0.551	0.39
3_H	79_R	0.550	0.39
25_E	31_R	0.547	0.39
60_I	88_A	0.546	0.39
121_H	133_R	0.544	0.38
96_R	128_A	0.544	0.38
43_F	47_R	0.540	0.38
22_P	127_A	0.539	0.38
23_A	41_S	0.537	0.38
129_G	132_P	0.535	0.37
41_S	96_R	0.535	0.37
95_E	147_R	0.532	0.37
45_F	72_Y	0.528	0.37
130_E	134_P	0.524	0.36
108_G	112_A	0.524	0.36
99_Q	134_P	0.522	0.36
42_V	103_A	0.521	0.36
15_H	96_R	0.520	0.36
27_I	82_G	0.520	0.36
30_R	44_A	0.519	0.36
56_V	92_P	0.518	0.36
48_W	54_G	0.518	0.36
44_A	129_G	0.517	0.36
22_P	100_A	0.513	0.35
134_P	138_E	0.512	0.35
37_F	122_V	0.511	0.35
111_P	117_D	0.511	0.35
99_Q	109_I	0.508	0.35
34_V	141_R	0.507	0.35
25_E	34_V	0.505	0.34
67_A	108_G	0.505	0.34
30_R	129_G	0.501	0.34
99_Q	139_R	0.501	0.34
75_V	131_P	0.500	0.34

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
2y8uA	1	0.7905	26.4	0.94	Contact Map
2c1iA	1	0.8041	21.7	0.942	Contact Map
2j13A	1	0.6689	20.9	0.943	Contact Map
2cc0A	2	0.7703	16.8	0.945	Contact Map
4qlxA	2	0.9054	9.2	0.951	Contact Map
1ny1A	1	0.7973	9	0.951	Contact Map
2iw0A	1	0.8851	8.1	0.952	Contact Map
4m1bA	1	0.7365	6.8	0.954	Contact Map
1o65A	1	0.8378	6.4	0.955	Contact Map
1vm6A	4	0.4257	6.1	0.955	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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