DUF2887 - PFAM28P - GREMLIN Contacts

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DUF2887 - Protein of unknown function (DUF2887)

PFAM:	PF11103	Sequences: TDSIFYRLFQTFPSLLFELLGQPPENAGGYRFSSVEVKETAFRIDGVFLPPEEDPDGPIYFVEVQFQPDEDFYWRLFAEIFLYLRQNPPRRDWQAVVIYPSRSLEPGDPPPYRELLNSGRVRRIYLDELGEIPDLSLGLALLKLIVEPEEEAPEQARQLLERAQQEILDEALQRDLLELIETILVYKFPQLSREEIEAML	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	200 (200)
Sequences:	1141 (830)
Seq/√Len:	58.7
META:	0.691

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
114_E	120_R	5.851	1.00
102_R	128_E	4.781	1.00
99_Y	106_P	3.858	1.00
72_F	76_L	3.295	1.00
92_D	113_R	3.223	1.00
36_E	43_R	3.127	1.00
77_F	121_V	2.799	1.00
36_E	41_A	2.700	1.00
69_D	75_R	2.637	1.00
76_L	95_A	2.637	1.00
182_T	186_Y	2.626	1.00
44_I	72_F	2.608	1.00
75_R	79_E	2.595	1.00
81_F	115_L	2.345	1.00
80_I	95_A	2.269	1.00
71_D	88_P	2.250	1.00
16_L	60_Y	2.230	1.00
3_S	39_E	2.103	1.00
5_F	8_L	1.916	1.00
194_E	197_E	1.898	1.00
24_P	27_A	1.886	1.00
69_D	79_E	1.857	1.00
185_V	196_I	1.848	1.00
74_W	85_R	1.809	0.99
195_E	199_M	1.796	0.99
100_P	104_L	1.743	0.99
114_E	119_G	1.741	0.99
49_L	59_I	1.734	0.99
105_E	123_R	1.703	0.99
44_I	79_E	1.667	0.99
42_F	82_L	1.639	0.99
66_F	100_P	1.627	0.99
193_R	197_E	1.590	0.99
94_Q	122_R	1.586	0.99
99_Y	105_E	1.585	0.99
42_F	85_R	1.536	0.98
47_V	59_I	1.524	0.98
61_F	112_Y	1.518	0.98
156_A	200_L	1.512	0.98
100_P	106_P	1.510	0.98
44_I	47_V	1.509	0.98
153_P	157_R	1.507	0.98
61_F	80_I	1.488	0.98
61_F	95_A	1.481	0.98
71_D	89_P	1.472	0.98
125_Y	128_E	1.444	0.97
68_P	107_G	1.376	0.96
18_E	136_S	1.352	0.96
181_E	189_P	1.349	0.96
65_Q	75_R	1.343	0.96
140_A	162_R	1.338	0.96
72_F	97_V	1.315	0.95
101_S	104_L	1.296	0.95
76_L	80_I	1.289	0.95
116_L	121_V	1.283	0.95
114_E	118_S	1.281	0.95
61_F	83_Y	1.277	0.95
135_L	143_K	1.264	0.94
152_A	156_A	1.263	0.94
147_E	151_E	1.261	0.94
35_V	47_V	1.251	0.94
113_R	117_N	1.250	0.94
98_I	117_N	1.229	0.93
163_A	167_I	1.211	0.93
113_R	120_R	1.208	0.93
77_F	81_F	1.195	0.92
149_E	157_R	1.195	0.92
9_F	13_P	1.181	0.92
152_A	184_L	1.177	0.92
140_A	143_K	1.169	0.92
89_P	111_P	1.169	0.92
4_I	187_K	1.168	0.92
143_K	147_E	1.163	0.91
39_E	82_L	1.158	0.91
37_V	44_I	1.140	0.91
71_D	85_R	1.138	0.90
39_E	186_Y	1.128	0.90
32_F	79_E	1.117	0.90
16_L	48_F	1.116	0.90
182_T	188_F	1.111	0.89
17_F	23_P	1.109	0.89
38_K	45_D	1.105	0.89
16_L	20_L	1.105	0.89
67_Q	104_L	1.103	0.89
163_A	168_L	1.098	0.89
32_F	46_G	1.098	0.89
81_F	112_Y	1.090	0.88
92_D	110_P	1.088	0.88
95_A	121_V	1.075	0.88
22_Q	26_N	1.063	0.87
188_F	196_I	1.053	0.87
42_F	79_E	1.050	0.87
73_Y	125_Y	1.049	0.87
73_Y	105_E	1.048	0.86
147_E	155_Q	1.029	0.85
185_V	192_S	1.028	0.85
130_G	135_L	1.024	0.85
40_T	43_R	1.018	0.85
160_L	180_I	1.001	0.84
78_A	81_F	0.995	0.83
2_D	5_F	0.983	0.83
69_D	72_F	0.983	0.83
69_D	97_V	0.976	0.82
118_S	121_V	0.975	0.82
74_W	88_P	0.967	0.82
48_F	76_L	0.963	0.81
23_P	28_G	0.957	0.81
40_T	61_F	0.952	0.81
77_F	112_Y	0.946	0.80
67_Q	79_E	0.945	0.80
181_E	185_V	0.933	0.79
78_A	82_L	0.933	0.79
37_V	82_L	0.932	0.79
7_R	39_E	0.931	0.79
72_F	80_I	0.930	0.79
91_R	111_P	0.913	0.78
5_F	64_V	0.904	0.77
114_E	117_N	0.901	0.77
9_F	18_E	0.898	0.77
132_I	135_L	0.894	0.76
69_D	99_Y	0.894	0.76
185_V	189_P	0.892	0.76
68_P	106_P	0.889	0.76
180_I	183_I	0.886	0.76
139_L	143_K	0.883	0.75
67_Q	100_P	0.881	0.75
20_L	98_I	0.877	0.75
31_R	51_P	0.867	0.74
33_S	86_Q	0.865	0.74
23_P	26_N	0.864	0.74
19_L	129_L	0.862	0.74
35_V	87_N	0.861	0.74
67_Q	75_R	0.853	0.73
139_L	142_L	0.846	0.72
87_N	111_P	0.833	0.71
136_S	143_K	0.827	0.71
8_L	16_L	0.822	0.70
34_S	44_I	0.815	0.69
101_S	127_D	0.814	0.69
117_N	155_Q	0.812	0.69
4_I	9_F	0.808	0.69
33_S	47_V	0.804	0.68
92_D	120_R	0.800	0.68
12_F	16_L	0.799	0.68
44_I	69_D	0.798	0.68
68_P	161_E	0.791	0.67
152_A	197_E	0.788	0.67
141_L	196_I	0.788	0.67
3_S	72_F	0.787	0.67
1_T	11_T	0.779	0.66
42_F	78_A	0.775	0.65
14_S	18_E	0.774	0.65
159_L	180_I	0.772	0.65
182_T	196_I	0.772	0.65
102_R	116_L	0.770	0.65
32_F	76_L	0.768	0.65
59_I	83_Y	0.766	0.65
172_L	184_L	0.764	0.64
135_L	162_R	0.761	0.64
112_Y	115_L	0.759	0.64
33_S	37_V	0.759	0.64
145_I	187_K	0.758	0.64
192_S	195_E	0.758	0.64
181_E	194_E	0.755	0.63
13_P	75_R	0.754	0.63
84_L	112_Y	0.751	0.63
69_D	200_L	0.750	0.63
78_A	85_R	0.748	0.63
37_V	96_V	0.747	0.63
133_P	140_A	0.743	0.62
82_L	85_R	0.743	0.62
73_Y	77_F	0.741	0.62
5_F	9_F	0.736	0.61
16_L	21_G	0.732	0.61
137_L	163_A	0.729	0.61
74_W	84_L	0.728	0.61
5_F	18_E	0.725	0.60
13_P	17_F	0.719	0.60
148_P	151_E	0.716	0.59
3_S	40_T	0.712	0.59
150_E	192_S	0.712	0.59
163_A	166_E	0.707	0.58
16_L	24_P	0.706	0.58
115_L	121_V	0.701	0.58
194_E	200_L	0.694	0.57
156_A	196_I	0.694	0.57
166_E	169_D	0.684	0.56
37_V	132_I	0.684	0.56
129_L	139_L	0.680	0.55
37_V	76_L	0.676	0.55
110_P	161_E	0.674	0.55
149_E	189_P	0.672	0.55
191_L	196_I	0.668	0.54
39_E	111_P	0.666	0.54
29_G	57_G	0.664	0.54
136_S	162_R	0.661	0.53
88_P	111_P	0.660	0.53
94_Q	117_N	0.659	0.53
4_I	179_L	0.657	0.53
60_Y	128_E	0.657	0.53
1_T	58_P	0.653	0.52
16_L	25_E	0.652	0.52
159_L	162_R	0.649	0.52
171_A	176_L	0.646	0.52
84_L	93_W	0.644	0.51
176_L	188_F	0.641	0.51
102_R	149_E	0.641	0.51
103_S	108_D	0.640	0.51
70_E	88_P	0.639	0.51
155_Q	161_E	0.632	0.50
116_L	123_R	0.631	0.50
40_T	87_N	0.630	0.50
20_L	113_R	0.629	0.50
7_R	22_Q	0.629	0.50
52_E	57_G	0.628	0.50
31_R	171_A	0.627	0.50
48_F	60_Y	0.627	0.50
2_D	6_Y	0.624	0.49
153_P	156_A	0.622	0.49
34_S	62_V	0.621	0.49
87_N	136_S	0.620	0.49
151_E	158_Q	0.619	0.49
77_F	115_L	0.618	0.49
196_I	199_M	0.614	0.48
48_F	62_V	0.613	0.48
133_P	150_E	0.613	0.48
150_E	153_P	0.612	0.48
40_T	182_T	0.612	0.48
25_E	28_G	0.607	0.47
37_V	56_D	0.605	0.47
20_L	31_R	0.603	0.47
172_L	177_L	0.599	0.46
72_F	105_E	0.596	0.46
170_E	174_R	0.596	0.46
150_E	157_R	0.592	0.46
15_L	20_L	0.590	0.45
78_A	121_V	0.589	0.45
46_G	58_P	0.587	0.45
85_R	200_L	0.582	0.45
65_Q	69_D	0.581	0.44
55_P	166_E	0.578	0.44
98_I	142_L	0.578	0.44
74_W	111_P	0.577	0.44
154_E	161_E	0.574	0.44
15_L	60_Y	0.572	0.43
42_F	182_T	0.571	0.43
94_Q	121_V	0.571	0.43
56_D	164_Q	0.571	0.43
6_Y	61_F	0.569	0.43
31_R	151_E	0.569	0.43
157_R	185_V	0.566	0.43
183_I	187_K	0.565	0.43
137_L	184_L	0.563	0.43
73_Y	123_R	0.561	0.42
180_I	190_Q	0.561	0.42
40_T	85_R	0.561	0.42
62_V	161_E	0.560	0.42
36_E	40_T	0.560	0.42
135_L	169_D	0.557	0.42
110_P	113_R	0.555	0.42
87_N	109_P	0.554	0.42
16_L	147_E	0.553	0.41
17_F	60_Y	0.552	0.41
155_Q	159_L	0.549	0.41
16_L	27_A	0.549	0.41
185_V	193_R	0.547	0.41
75_R	85_R	0.545	0.41
3_S	18_E	0.539	0.40
37_V	150_E	0.535	0.40
58_P	142_L	0.535	0.40
15_L	25_E	0.533	0.39
102_R	131_E	0.533	0.39
25_E	51_P	0.532	0.39
7_R	11_T	0.531	0.39
77_F	183_I	0.529	0.39
55_P	194_E	0.526	0.39
14_S	33_S	0.524	0.38
68_P	104_L	0.522	0.38
11_T	151_E	0.521	0.38
82_L	93_W	0.518	0.38
105_E	193_R	0.517	0.38
124_I	172_L	0.516	0.38
184_L	200_L	0.516	0.38
50_P	100_P	0.513	0.37
138_G	160_L	0.512	0.37
15_L	30_Y	0.511	0.37
103_S	122_R	0.511	0.37
53_E	57_G	0.510	0.37
28_G	31_R	0.510	0.37
196_I	200_L	0.510	0.37
101_S	143_K	0.509	0.37
4_I	40_T	0.508	0.37
2_D	9_F	0.506	0.36
107_G	119_G	0.506	0.36
5_F	30_Y	0.506	0.36
169_D	172_L	0.505	0.36
7_R	178_E	0.503	0.36
16_L	22_Q	0.501	0.36
136_S	142_L	0.500	0.36
83_Y	89_P	0.500	0.36

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
2f4mB	1	0.125	11	0.955	Contact Map
2xppB	1	0.095	7.9	0.958	Contact Map
1pveA	1	0.17	6.5	0.959	Contact Map
4r1kA	1	0.245	5.6	0.961	Contact Map
2d58A	1	0.37	5.6	0.961	Contact Map
1w9cA	2	0.35	5.4	0.961	Contact Map
4gtnA	2	0.31	5.3	0.961	Contact Map
2kkpA	1	0.285	4.5	0.962	Contact Map
2yb5A	1	0.47	4.5	0.963	Contact Map
2xpnB	1	0.1	4.5	0.963	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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