DUF2854 - PFAM28P - GREMLIN Contacts

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DUF2854 - Protein of unknown function (DUF2854)

PFAM:	PF11016	Sequences: IGFVAYFTGNATLSLPGFFYGIPILLGGLALKAAELKPVPFSQPTSPEVLALREQQATPTQNQIRKDVTRYRYGQEAHLDSSLEALGLSPTDEERPQLTGIREEETDGAYALVLEFDSPLVPLERWQEKQEKLERFFGPGVRAEVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	146 (145)
Sequences:	502 (303)
Seq/√Len:	25.1
META:	0.685

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
123_L	145_V	3.591	1.00
81_S	85_A	3.415	1.00
18_F	22_I	3.387	1.00
68_V	98_L	2.975	1.00
106_T	111_A	2.809	1.00
3_F	7_F	2.627	0.99
63_Q	136_F	2.611	0.99
62_N	65_R	2.418	0.98
51_A	55_Q	2.305	0.98
32_K	35_E	2.288	0.98
133_L	141_V	2.136	0.97
133_L	143_A	2.105	0.96
72_R	79_L	2.070	0.96
42_S	100_G	2.066	0.96
102_R	115_E	1.966	0.94
49_V	105_E	1.768	0.91
76_E	80_D	1.676	0.88
104_E	111_A	1.671	0.88
68_V	72_R	1.657	0.87
90_P	95_R	1.654	0.87
42_S	115_E	1.648	0.87
103_E	110_Y	1.642	0.87
121_V	129_K	1.632	0.87
99_T	117_D	1.619	0.86
8_T	16_P	1.568	0.84
76_E	133_L	1.557	0.84
65_R	112_L	1.521	0.82
12_T	15_L	1.519	0.82
12_T	16_P	1.513	0.82
37_K	76_E	1.495	0.81
102_R	113_V	1.476	0.80
122_P	135_R	1.449	0.79
131_E	135_R	1.424	0.78
72_R	136_F	1.416	0.78
76_E	89_S	1.409	0.77
130_Q	134_E	1.393	0.76
100_G	115_E	1.391	0.76
97_Q	121_V	1.374	0.75
10_N	15_L	1.352	0.74
83_L	116_F	1.329	0.73
4_V	34_A	1.329	0.73
104_E	113_V	1.320	0.72
56_Q	114_L	1.317	0.72
53_R	103_E	1.312	0.72
124_E	128_E	1.311	0.72
11_A	15_L	1.294	0.71
127_Q	130_Q	1.292	0.71
64_I	121_V	1.270	0.69
103_E	112_L	1.261	0.69
95_R	121_V	1.245	0.68
15_L	19_F	1.191	0.64
63_Q	72_R	1.189	0.64
48_E	105_E	1.187	0.64
29_L	88_L	1.169	0.63
9_G	18_F	1.164	0.62
3_F	9_G	1.154	0.62
89_S	95_R	1.151	0.62
85_A	143_A	1.146	0.61
53_R	110_Y	1.131	0.60
7_F	11_A	1.126	0.60
59_P	136_F	1.120	0.59
53_R	112_L	1.120	0.59
91_T	121_V	1.119	0.59
27_G	30_A	1.109	0.59
34_A	92_D	1.109	0.59
128_E	143_A	1.099	0.58
22_I	25_L	1.089	0.57
68_V	101_I	1.087	0.57
64_I	141_V	1.082	0.57
34_A	76_E	1.081	0.57
141_V	145_V	1.077	0.56
58_T	62_N	1.075	0.56
12_T	17_G	1.066	0.56
15_L	33_A	1.058	0.55
82_S	133_L	1.052	0.55
98_L	133_L	1.047	0.54
84_E	108_G	1.024	0.53
13_L	19_F	1.013	0.52
79_L	136_F	1.013	0.52
24_I	32_K	1.008	0.51
8_T	11_A	1.000	0.51
86_L	129_K	0.993	0.50
132_K	143_A	0.984	0.50
61_Q	111_A	0.973	0.49
36_L	75_Q	0.965	0.48
34_A	72_R	0.957	0.48
2_G	5_A	0.953	0.47
65_R	103_E	0.941	0.47
20_Y	28_G	0.937	0.46
58_T	138_G	0.934	0.46
117_D	124_E	0.931	0.46
80_D	140_G	0.924	0.45
6_Y	35_E	0.913	0.45
91_T	120_L	0.913	0.45
23_P	26_L	0.902	0.44
82_S	85_A	0.879	0.42
18_F	122_P	0.871	0.42
48_E	69_T	0.870	0.41
24_I	84_E	0.869	0.41
55_Q	99_T	0.869	0.41
52_L	105_E	0.868	0.41
4_V	8_T	0.858	0.41
85_A	133_L	0.854	0.40
36_L	110_Y	0.849	0.40
61_Q	83_L	0.843	0.40
56_Q	109_A	0.842	0.40
39_V	77_A	0.835	0.39
7_F	27_G	0.834	0.39
33_A	75_Q	0.823	0.38
82_S	134_E	0.819	0.38
81_S	136_F	0.817	0.38
17_G	24_I	0.811	0.37
59_P	72_R	0.800	0.37
60_T	139_P	0.789	0.36
80_D	87_G	0.780	0.35
72_R	82_S	0.779	0.35
63_Q	85_A	0.770	0.35
98_L	114_L	0.768	0.34
13_L	17_G	0.766	0.34
64_I	143_A	0.765	0.34
1_I	16_P	0.763	0.34
82_S	93_E	0.758	0.34
134_E	143_A	0.756	0.34
41_F	45_T	0.755	0.34
4_V	7_F	0.754	0.34
101_I	134_E	0.749	0.33
99_T	144_E	0.748	0.33
1_I	145_V	0.746	0.33
30_A	78_H	0.744	0.33
47_P	54_E	0.739	0.33
52_L	139_P	0.732	0.32
27_G	32_K	0.729	0.32
2_G	6_Y	0.722	0.32
64_I	97_Q	0.720	0.31
11_A	16_P	0.720	0.31
5_A	9_G	0.719	0.31
70_R	75_Q	0.716	0.31
125_R	128_E	0.703	0.30
61_Q	112_L	0.696	0.30
29_L	36_L	0.687	0.29
49_V	60_T	0.684	0.29
128_E	133_L	0.681	0.29
7_F	18_F	0.677	0.29
134_E	142_R	0.674	0.29
4_V	27_G	0.673	0.29
89_S	121_V	0.668	0.28
130_Q	138_G	0.665	0.28
48_E	97_Q	0.659	0.28
51_A	101_I	0.656	0.28
27_G	35_E	0.656	0.28
1_I	45_T	0.647	0.27
77_A	97_Q	0.644	0.27
40_P	58_T	0.640	0.27
84_E	135_R	0.639	0.27
59_P	114_L	0.637	0.26
39_V	69_T	0.637	0.26
80_D	95_R	0.631	0.26
6_Y	32_K	0.630	0.26
52_L	138_G	0.627	0.26
40_P	112_L	0.624	0.26
21_G	26_L	0.622	0.26
57_A	62_N	0.621	0.26
72_R	98_L	0.617	0.25
3_F	18_F	0.614	0.25
100_G	113_V	0.613	0.25
17_G	118_S	0.609	0.25
125_R	145_V	0.609	0.25
59_P	66_K	0.600	0.24
68_V	79_L	0.598	0.24
47_P	134_E	0.598	0.24
26_L	69_T	0.594	0.24
118_S	126_W	0.593	0.24
84_E	106_T	0.591	0.24
58_T	139_P	0.587	0.24
117_D	145_V	0.587	0.24
87_G	95_R	0.584	0.24
44_P	129_K	0.584	0.24
48_E	130_Q	0.583	0.24
15_L	84_E	0.583	0.24
34_A	136_F	0.582	0.23
36_L	78_H	0.576	0.23
88_L	126_W	0.574	0.23
134_E	141_V	0.573	0.23
46_S	64_I	0.572	0.23
4_V	10_N	0.572	0.23
74_G	80_D	0.572	0.23
5_A	103_E	0.570	0.23
51_A	122_P	0.566	0.23
29_L	132_K	0.563	0.22
93_E	121_V	0.561	0.22
1_I	22_I	0.560	0.22
46_S	76_E	0.556	0.22
30_A	90_P	0.556	0.22
13_L	16_P	0.555	0.22
30_A	36_L	0.553	0.22
39_V	106_T	0.550	0.22
60_T	100_G	0.550	0.22
25_L	92_D	0.544	0.22
20_Y	31_L	0.538	0.21
21_G	24_I	0.535	0.21
18_F	86_L	0.535	0.21
15_L	32_K	0.531	0.21
4_V	49_V	0.530	0.21
8_T	24_I	0.530	0.21
30_A	92_D	0.530	0.21
61_Q	126_W	0.526	0.21
44_P	100_G	0.524	0.21
24_I	44_P	0.522	0.20
12_T	19_F	0.519	0.20
118_S	123_L	0.519	0.20
77_A	135_R	0.518	0.20
104_E	109_A	0.516	0.20
39_V	99_T	0.515	0.20
98_L	143_A	0.512	0.20
95_R	113_V	0.511	0.20
61_Q	110_Y	0.510	0.20
58_T	114_L	0.503	0.20
56_Q	100_G	0.500	0.19

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
3tqmA	1	0.2397	19.1	0.954	Contact Map
3v26X	1	0.2397	19	0.954	Contact Map
2ywqA	1	0.2397	18.1	0.955	Contact Map
4heiA	1	0.2397	13.6	0.957	Contact Map
2l60A	1	0.2671	11.6	0.958	Contact Map
1f8pA	1	0.2466	8.2	0.961	Contact Map
1qbfA	1	0.2466	8	0.961	Contact Map
1xatA	3	0.6301	7.3	0.962	Contact Map
4k0jA	3	0.8288	6.2	0.963	Contact Map
3v2cY	1	0.2671	5.7	0.964	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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