DUF3515 - PFAM28P - GREMLIN Contacts

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DUF3515 - Protein of unknown function (DUF3515)

PFAM:	PF12028	Sequences: VALAVALVVAVLAAAALLSAAASTGPVAVVAVPAPDADAAACAALLAALPDTLGGLPRRPVAEPASPGTAAWGDPAGEPIVLRCGVPRPAEFTPTSPLQEVNGVDWFVVEDDDPGSDGTTWTTVDREVYVEVTVPAGSGPTPLQDLSDAIAATLPARP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	158 (142)
Sequences:	1788 (1397)
Seq/√Len:	117.2
META:	0.521

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
83_R	131_E	3.794	1.00
88_R	129_Y	3.008	1.00
72_W	82_L	2.966	1.00
45_L	82_L	2.897	1.00
100_E	105_D	2.743	1.00
132_V	146_L	2.595	1.00
102_N	148_D	2.352	1.00
36_D	39_A	2.291	1.00
14_A	17_L	2.255	1.00
49_L	70_A	2.218	1.00
138_S	141_T	2.095	1.00
32_V	35_P	2.085	1.00
29_V	32_V	2.023	1.00
58_R	70_A	1.712	1.00
98_L	123_T	1.704	1.00
109_V	120_T	1.685	1.00
118_G	133_T	1.668	1.00
53_L	149_A	1.654	1.00
14_A	18_L	1.647	1.00
61_V	71_A	1.637	1.00
59_R	73_G	1.624	1.00
111_D	120_T	1.610	1.00
75_P	135_P	1.605	1.00
10_A	13_A	1.600	1.00
61_V	69_T	1.585	1.00
45_L	130_V	1.555	1.00
91_E	109_V	1.548	1.00
34_A	37_A	1.520	1.00
109_V	122_T	1.504	1.00
10_A	14_A	1.454	1.00
145_D	148_D	1.434	1.00
86_V	122_T	1.420	1.00
113_D	136_A	1.419	1.00
120_T	133_T	1.414	1.00
108_V	119_T	1.402	1.00
123_T	150_I	1.391	1.00
86_V	131_E	1.389	1.00
53_L	145_D	1.383	1.00
13_A	16_A	1.328	1.00
122_T	131_E	1.325	1.00
61_V	65_A	1.296	1.00
123_T	129_Y	1.292	1.00
66_S	69_T	1.273	0.99
149_A	153_T	1.266	0.99
104_V	123_T	1.238	0.99
27_V	30_V	1.230	0.99
91_E	96_S	1.210	0.99
83_R	86_V	1.208	0.99
111_D	118_G	1.206	0.99
92_F	95_T	1.200	0.99
10_A	17_L	1.189	0.99
92_F	124_V	1.187	0.99
8_V	11_V	1.184	0.99
35_P	38_D	1.178	0.99
56_L	80_I	1.173	0.99
121_W	134_V	1.165	0.99
12_L	16_A	1.160	0.99
8_V	12_L	1.158	0.99
104_V	147_S	1.156	0.99
9_V	17_L	1.154	0.99
41_A	44_A	1.147	0.99
88_R	92_F	1.136	0.99
48_A	153_T	1.120	0.99
120_T	131_E	1.114	0.99
101_V	143_L	1.102	0.98
46_L	70_A	1.098	0.98
128_V	155_P	1.090	0.98
11_V	17_L	1.087	0.98
145_D	149_A	1.063	0.98
94_P	107_F	1.042	0.98
7_L	15_A	1.035	0.98
92_F	107_F	1.024	0.98
46_L	67_P	1.024	0.98
91_E	107_F	1.021	0.98
100_E	103_G	1.008	0.97
137_G	140_P	1.007	0.97
108_V	121_W	0.991	0.97
24_T	27_V	0.975	0.97
52_T	55_G	0.965	0.96
21_A	24_T	0.964	0.96
39_A	68_G	0.963	0.96
123_T	126_R	0.961	0.96
48_A	152_A	0.957	0.96
106_W	147_S	0.954	0.96
59_R	76_A	0.944	0.96
92_F	96_S	0.929	0.96
28_A	32_V	0.923	0.95
17_L	20_A	0.920	0.95
98_L	125_D	0.917	0.95
25_G	29_V	0.912	0.95
12_L	17_L	0.906	0.95
13_A	17_L	0.904	0.95
98_L	105_D	0.903	0.95
7_L	10_A	0.902	0.95
139_G	142_P	0.900	0.95
27_V	32_V	0.895	0.95
137_G	141_T	0.889	0.94
56_L	74_D	0.877	0.94
83_R	133_T	0.871	0.94
110_E	119_T	0.862	0.94
51_D	58_R	0.861	0.93
33_P	87_P	0.857	0.93
40_A	68_G	0.854	0.93
151_A	156_A	0.849	0.93
89_P	107_F	0.837	0.92
7_L	18_L	0.828	0.92
16_A	19_S	0.817	0.92
64_P	67_P	0.815	0.91
101_V	147_S	0.813	0.91
59_R	71_A	0.811	0.91
10_A	15_A	0.807	0.91
29_V	61_V	0.798	0.91
17_L	21_A	0.796	0.90
7_L	13_A	0.791	0.90
61_V	64_P	0.782	0.90
9_V	13_A	0.781	0.90
118_G	134_V	0.780	0.90
139_G	143_L	0.777	0.89
73_G	122_T	0.771	0.89
130_V	135_P	0.770	0.89
64_P	68_G	0.764	0.89
53_L	146_L	0.760	0.88
93_T	96_S	0.758	0.88
34_A	40_A	0.756	0.88
109_V	113_D	0.754	0.88
148_D	152_A	0.753	0.88
73_G	134_V	0.753	0.88
22_A	25_G	0.751	0.88
18_L	21_A	0.751	0.88
121_W	139_G	0.747	0.87
64_P	129_Y	0.745	0.87
45_L	155_P	0.741	0.87
29_V	69_T	0.740	0.87
44_A	154_L	0.736	0.87
19_S	22_A	0.736	0.87
40_A	43_A	0.731	0.86
99_Q	121_W	0.726	0.86
143_L	147_S	0.724	0.86
13_A	19_S	0.722	0.86
99_Q	150_I	0.718	0.85
95_T	98_L	0.718	0.85
8_V	16_A	0.716	0.85
131_E	150_I	0.711	0.85
22_A	28_A	0.703	0.84
141_T	144_Q	0.701	0.84
24_T	28_A	0.700	0.84
110_E	123_T	0.690	0.83
121_W	140_P	0.689	0.83
49_L	82_L	0.688	0.83
109_V	112_D	0.688	0.83
23_S	26_P	0.687	0.83
140_P	144_Q	0.686	0.83
89_P	129_Y	0.683	0.82
83_R	107_F	0.683	0.82
108_V	143_L	0.677	0.82
98_L	108_V	0.674	0.82
147_S	151_A	0.674	0.82
7_L	11_V	0.668	0.81
23_S	28_A	0.663	0.80
26_P	32_V	0.662	0.80
97_P	108_V	0.661	0.80
128_V	154_L	0.657	0.80
43_A	70_A	0.656	0.80
15_A	18_L	0.648	0.79
142_P	147_S	0.646	0.79
8_V	14_A	0.634	0.77
113_D	118_G	0.631	0.77
106_W	145_D	0.629	0.77
142_P	146_L	0.622	0.76
64_P	69_T	0.620	0.76
153_T	156_A	0.618	0.76
144_Q	150_I	0.615	0.75
98_L	124_V	0.613	0.75
52_T	72_W	0.608	0.75
33_P	41_A	0.605	0.74
43_A	68_G	0.603	0.74
44_A	48_A	0.602	0.74
10_A	16_A	0.598	0.73
105_D	125_D	0.583	0.71
32_V	37_A	0.580	0.71
13_A	18_L	0.580	0.71
11_V	18_L	0.576	0.71
80_I	101_V	0.575	0.70
86_V	89_P	0.572	0.70
87_P	131_E	0.568	0.69
105_D	124_V	0.566	0.69
16_A	20_A	0.563	0.69
124_V	150_I	0.561	0.69
36_D	40_A	0.555	0.68
30_V	36_D	0.554	0.68
63_E	70_A	0.551	0.67
53_L	138_S	0.550	0.67
42_C	84_C	0.550	0.67
106_W	132_V	0.548	0.67
91_E	94_P	0.544	0.66
61_V	66_S	0.544	0.66
25_G	60_P	0.534	0.65
23_S	30_V	0.533	0.65
11_V	14_A	0.529	0.64
30_V	33_P	0.528	0.64
43_A	67_P	0.527	0.64
102_N	144_Q	0.527	0.64
25_G	30_V	0.526	0.64
7_L	12_L	0.525	0.63
26_P	60_P	0.522	0.63
30_V	81_V	0.519	0.63
28_A	37_A	0.515	0.62
45_L	72_W	0.512	0.62
72_W	88_R	0.511	0.61
72_W	83_R	0.509	0.61
52_T	93_T	0.506	0.61
125_D	129_Y	0.503	0.60
46_L	49_L	0.500	0.60

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
4fazA	4	0.1962	6.9	0.941	Contact Map
3ry0A	4	0.1962	6.7	0.941	Contact Map
4x1cC	5	0.1962	6.7	0.941	Contact Map
2opaA	4	0.1962	6.5	0.941	Contact Map
2x4kA	4	0.2152	5.9	0.942	Contact Map
3m21A	4	0.1962	5.9	0.942	Contact Map
4fdxA	4	0.1962	5.6	0.943	Contact Map
3ej9B	3	0.1962	5.3	0.943	Contact Map
3m20A	5	0.1899	5	0.944	Contact Map
3ej9A	3	0.1962	4	0.947	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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