UPF0231 - PFAM28P - GREMLIN Contacts

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UPF0231 - Uncharacterised protein family (UPF0231)

PFAM:	PF06062	Sequences: MEYEFIRDLTGQVKARFSMGHEAIGRWLNEEVGGDLAKLDELLAAIEQLKGSQEREWQLVGHEYSLLLDGEEVMVRANALDFEGDEEEELEEDMSYYDEESLAFCGLEDFLQLLESWREFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	121 (121)
Sequences:	529 (345)
Seq/√Len:	31.3
META:	0.456

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_F	113_L	5.292	1.00
68_L	73_V	4.320	1.00
97_Y	100_E	4.191	1.00
28_L	32_V	3.282	1.00
50_K	111_L	2.786	1.00
18_S	21_H	2.728	1.00
3_Y	112_Q	2.462	0.99
56_E	69_D	2.398	0.99
91_E	94_M	2.273	0.99
65_S	78_N	2.238	0.99
97_Y	101_S	2.206	0.99
13_V	29_N	2.112	0.98
35_D	38_K	2.036	0.98
26_R	64_Y	1.956	0.97
61_G	110_F	1.783	0.95
106_G	109_D	1.707	0.94
73_V	110_F	1.678	0.93
49_L	68_L	1.673	0.93
23_A	64_Y	1.531	0.89
60_V	65_S	1.511	0.89
18_S	25_G	1.502	0.88
19_M	100_E	1.501	0.88
36_L	121_I	1.454	0.87
72_E	104_F	1.417	0.85
3_Y	17_F	1.403	0.85
2_E	7_R	1.394	0.84
74_M	117_W	1.376	0.83
74_M	104_F	1.351	0.82
2_E	10_T	1.351	0.82
46_I	114_L	1.329	0.81
42_L	57_W	1.308	0.80
39_L	118_R	1.308	0.80
105_C	109_D	1.302	0.80
32_V	114_L	1.281	0.79
69_D	73_V	1.271	0.78
40_D	118_R	1.267	0.78
19_M	97_Y	1.266	0.78
17_F	114_L	1.255	0.77
3_Y	15_A	1.229	0.76
15_A	114_L	1.217	0.75
15_A	29_N	1.210	0.75
19_M	22_E	1.205	0.74
35_D	41_E	1.188	0.73
18_S	22_E	1.177	0.72
66_L	73_V	1.168	0.72
19_M	101_S	1.161	0.71
18_S	103_A	1.129	0.69
20_G	100_E	1.128	0.69
68_L	80_L	1.124	0.69
28_L	113_L	1.121	0.69
36_L	118_R	1.116	0.68
6_I	16_R	1.115	0.68
112_Q	115_E	1.113	0.68
70_G	116_S	1.098	0.67
111_L	115_E	1.061	0.64
31_E	63_E	1.057	0.64
80_L	103_A	1.051	0.64
10_T	78_N	1.048	0.63
94_M	97_Y	1.034	0.62
69_D	93_D	1.029	0.62
45_A	49_L	1.005	0.60
13_V	117_W	1.002	0.60
49_L	54_E	1.000	0.60
83_E	104_F	0.936	0.55
17_F	25_G	0.928	0.54
108_E	112_Q	0.918	0.53
7_R	15_A	0.905	0.52
23_A	76_R	0.901	0.52
3_Y	116_S	0.900	0.52
85_D	108_E	0.898	0.52
2_E	6_I	0.890	0.51
6_I	10_T	0.883	0.50
30_E	33_G	0.872	0.49
55_R	76_R	0.860	0.48
73_V	78_N	0.855	0.48
8_D	14_K	0.854	0.48
43_L	111_L	0.853	0.48
37_A	42_L	0.851	0.48
25_G	33_G	0.846	0.47
17_F	24_I	0.845	0.47
91_E	95_S	0.843	0.47
11_G	17_F	0.842	0.47
39_L	43_L	0.841	0.47
26_R	30_E	0.834	0.46
44_A	48_Q	0.830	0.46
31_E	61_G	0.825	0.46
23_A	77_A	0.823	0.45
21_H	25_G	0.814	0.45
26_R	63_E	0.810	0.44
63_E	99_E	0.809	0.44
11_G	15_A	0.787	0.43
104_F	117_W	0.782	0.42
61_G	75_V	0.780	0.42
81_D	87_E	0.751	0.40
15_A	113_L	0.750	0.40
107_L	119_E	0.748	0.39
18_S	61_G	0.744	0.39
59_L	107_L	0.736	0.39
82_F	92_E	0.735	0.38
4_E	10_T	0.724	0.38
63_E	72_E	0.723	0.38
63_E	78_N	0.722	0.37
108_E	111_L	0.702	0.36
48_Q	51_G	0.698	0.36
12_Q	37_A	0.698	0.36
52_S	70_G	0.697	0.36
115_E	119_E	0.697	0.36
64_Y	77_A	0.695	0.35
107_L	121_I	0.694	0.35
81_D	90_L	0.683	0.35
2_E	49_L	0.683	0.35
10_T	14_K	0.669	0.34
1_M	5_F	0.665	0.33
115_E	118_R	0.664	0.33
72_E	120_F	0.662	0.33
40_D	51_G	0.661	0.33
8_D	64_Y	0.656	0.33
8_D	12_Q	0.655	0.33
103_A	116_S	0.653	0.32
37_A	48_Q	0.648	0.32
80_L	98_D	0.642	0.32
52_S	66_L	0.640	0.31
23_A	110_F	0.639	0.31
20_G	119_E	0.638	0.31
47_E	98_D	0.635	0.31
3_Y	22_E	0.634	0.31
25_G	30_E	0.627	0.31
8_D	59_L	0.627	0.31
9_L	14_K	0.619	0.30
24_I	52_S	0.617	0.30
84_G	90_L	0.611	0.29
79_A	98_D	0.611	0.29
44_A	89_E	0.607	0.29
88_E	93_D	0.604	0.29
36_L	40_D	0.599	0.29
87_E	115_E	0.596	0.28
30_E	64_Y	0.594	0.28
28_L	116_S	0.592	0.28
77_A	94_M	0.591	0.28
87_E	91_E	0.588	0.28
73_V	107_L	0.587	0.28
77_A	101_S	0.585	0.28
43_L	115_E	0.584	0.28
45_A	57_W	0.583	0.28
11_G	64_Y	0.580	0.27
87_E	90_L	0.579	0.27
3_Y	34_G	0.578	0.27
42_L	114_L	0.575	0.27
49_L	111_L	0.570	0.27
5_F	28_L	0.569	0.27
48_Q	119_E	0.569	0.27
38_K	59_L	0.567	0.27
92_E	95_S	0.567	0.27
68_L	107_L	0.564	0.26
2_E	121_I	0.562	0.26
10_T	25_G	0.560	0.26
77_A	99_E	0.556	0.26
12_Q	20_G	0.554	0.26
41_E	59_L	0.553	0.26
13_V	77_A	0.548	0.25
10_T	16_R	0.546	0.25
49_L	53_Q	0.545	0.25
61_G	78_N	0.544	0.25
24_I	53_Q	0.544	0.25
15_A	25_G	0.542	0.25
83_E	89_E	0.538	0.25
88_E	102_L	0.533	0.25
22_E	97_Y	0.533	0.25
46_I	110_F	0.529	0.24
65_S	75_V	0.529	0.24
4_E	9_L	0.528	0.24
16_R	40_D	0.527	0.24
23_A	97_Y	0.526	0.24
62_H	71_E	0.521	0.24
16_R	39_L	0.520	0.24
52_S	55_R	0.519	0.24
23_A	101_S	0.517	0.24
21_H	31_E	0.517	0.24
5_F	72_E	0.512	0.23
67_L	74_M	0.511	0.23
27_W	77_A	0.503	0.23
42_L	49_L	0.500	0.23

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
1q67A	2	0.4132	13.5	0.928	Contact Map
4kmdA	2	0.5785	12.1	0.93	Contact Map
2lydA	1	0.3636	7.1	0.937	Contact Map
1dvoA	1	0.3884	6.8	0.937	Contact Map
1nnvA	1	0.4711	6.2	0.938	Contact Map
3bidA	2	0.4876	6	0.939	Contact Map
4b6hA	1	0.3636	5.7	0.94	Contact Map
2qklA	1	0.3554	3.8	0.945	Contact Map
2k7iA	2	0.4959	2.8	0.948	Contact Map
3zk4A	5	0.3388	2.5	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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