DUF2878 - PFAM28P - GREMLIN Contacts

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DUF2878 - Protein of unknown function (DUF2878)

PFAM:	PF11086	Sequences: KLINFVLFQLGWFACVLGAAHGLPWLGPLAALAFLALHLALSPRRRRELRLLLLAALLGLLVDSLLVALGLLSFPSPPPGLAPLWLVALWALFATTLNHSLRWLRGRPLLAALLGAIGGPLAYLAGARLGAVTFPDPLLLALLALALGWALLLPL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	155 (153)
Sequences:	3640 (2893)
Seq/√Len:	233.9
META:	0.833

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_G	92_L	4.120	1.00
56_A	91_A	4.080	1.00
62_V	148_G	3.303	1.00
74_F	86_L	3.000	1.00
60_L	87_V	2.670	1.00
46_R	50_R	2.641	1.00
114_L	118_G	2.415	1.00
127_A	132_V	2.373	1.00
56_A	87_V	2.333	1.00
82_A	86_L	2.099	1.00
37_L	41_L	2.082	1.00
17_L	129_L	2.066	1.00
9_Q	13_F	2.057	1.00
116_A	146_A	2.044	1.00
134_F	141_A	2.032	1.00
4_N	100_S	2.027	1.00
72_L	132_V	1.977	1.00
64_S	82_A	1.815	1.00
48_E	99_H	1.785	1.00
48_E	95_T	1.760	1.00
55_A	94_A	1.753	1.00
71_L	144_A	1.690	1.00
31_A	88_A	1.677	1.00
124_L	128_R	1.629	1.00
112_A	150_A	1.618	1.00
127_A	134_F	1.618	1.00
62_V	152_L	1.602	1.00
42_S	48_E	1.592	1.00
66_L	148_G	1.575	1.00
102_R	105_R	1.571	1.00
13_F	17_L	1.568	1.00
8_F	122_A	1.567	1.00
42_S	45_R	1.553	1.00
2_L	6_V	1.511	1.00
124_L	127_A	1.504	1.00
48_E	98_N	1.471	1.00
63_D	123_Y	1.433	1.00
7_L	34_F	1.426	1.00
47_R	50_R	1.397	1.00
11_G	34_F	1.369	1.00
115_G	119_G	1.330	1.00
121_L	125_A	1.329	1.00
143_L	146_A	1.268	1.00
16_V	132_V	1.264	1.00
28_P	84_L	1.263	1.00
118_G	122_A	1.256	1.00
38_H	48_E	1.252	1.00
96_T	100_S	1.239	1.00
86_L	89_L	1.223	1.00
35_L	39_L	1.221	1.00
111_A	115_G	1.209	1.00
120_P	146_A	1.200	1.00
98_N	105_R	1.200	1.00
60_L	82_A	1.198	1.00
4_N	96_T	1.194	1.00
11_G	15_C	1.187	1.00
65_L	69_L	1.170	1.00
23_L	26_L	1.167	1.00
67_V	74_F	1.157	1.00
24_P	27_G	1.146	1.00
116_A	150_A	1.140	1.00
69_L	73_S	1.115	1.00
52_L	91_A	1.090	1.00
116_A	120_P	1.088	1.00
136_D	141_A	1.088	1.00
8_F	96_T	1.059	1.00
15_C	18_G	1.051	1.00
112_A	154_P	1.048	1.00
141_A	145_L	1.034	1.00
44_R	47_R	1.031	1.00
137_P	140_L	1.028	1.00
105_R	108_P	1.027	1.00
4_N	98_N	1.026	1.00
123_Y	132_V	1.024	1.00
139_L	143_L	1.009	1.00
5_F	100_S	1.001	1.00
92_L	95_T	1.000	1.00
28_P	32_L	0.992	1.00
105_R	154_P	0.991	1.00
146_A	150_A	0.985	1.00
64_S	68_A	0.979	1.00
25_W	28_P	0.979	1.00
73_S	135_P	0.975	1.00
5_F	9_Q	0.971	1.00
7_L	11_G	0.955	1.00
4_N	99_H	0.943	1.00
9_Q	100_S	0.942	1.00
134_F	142_L	0.933	1.00
108_P	112_A	0.919	1.00
45_R	49_L	0.918	1.00
100_S	103_W	0.917	1.00
82_A	87_V	0.914	1.00
34_F	92_L	0.913	1.00
117_I	120_P	0.912	1.00
119_G	122_A	0.902	1.00
15_C	31_A	0.899	0.99
65_L	68_A	0.897	0.99
104_L	153_L	0.896	0.99
99_H	102_R	0.889	0.99
59_G	63_D	0.889	0.99
28_P	31_A	0.881	0.99
142_L	145_L	0.881	0.99
42_S	99_H	0.879	0.99
148_G	152_L	0.879	0.99
122_A	125_A	0.877	0.99
151_L	154_P	0.875	0.99
117_I	121_L	0.870	0.99
38_H	95_T	0.842	0.99
63_D	74_F	0.838	0.99
101_L	153_L	0.837	0.99
5_F	103_W	0.835	0.99
6_V	10_L	0.833	0.99
107_R	110_L	0.828	0.99
35_L	91_A	0.825	0.99
53_L	57_L	0.814	0.99
60_L	81_L	0.810	0.99
136_D	139_L	0.809	0.99
51_L	98_N	0.807	0.99
15_C	88_A	0.806	0.99
63_D	72_L	0.803	0.99
104_L	114_L	0.800	0.99
3_I	6_V	0.782	0.99
63_D	86_L	0.781	0.99
96_T	99_H	0.779	0.99
31_A	92_L	0.777	0.99
63_D	82_A	0.775	0.99
14_A	18_G	0.772	0.98
86_L	132_V	0.755	0.98
62_V	65_L	0.750	0.98
74_F	82_A	0.747	0.98
68_A	80_G	0.741	0.98
66_L	144_A	0.739	0.98
137_P	142_L	0.738	0.98
126_G	129_L	0.736	0.98
27_G	31_A	0.733	0.98
15_C	22_G	0.732	0.98
12_W	16_V	0.730	0.98
9_Q	125_A	0.730	0.98
4_N	48_E	0.727	0.98
107_R	111_A	0.727	0.98
34_F	95_T	0.724	0.98
86_L	145_L	0.720	0.98
30_A	33_A	0.719	0.98
62_V	66_L	0.718	0.98
4_N	38_H	0.716	0.97
135_P	139_L	0.711	0.97
71_L	136_D	0.709	0.97
67_V	80_G	0.700	0.97
14_A	30_A	0.697	0.97
11_G	30_A	0.696	0.97
147_L	150_A	0.696	0.97
20_A	131_A	0.696	0.97
118_G	153_L	0.692	0.97
49_L	53_L	0.690	0.97
8_F	92_L	0.686	0.97
17_L	20_A	0.671	0.96
34_F	99_H	0.669	0.96
13_F	125_A	0.667	0.96
77_P	84_L	0.667	0.96
140_L	143_L	0.666	0.96
119_G	145_L	0.658	0.96
127_A	130_G	0.653	0.96
18_G	27_G	0.650	0.96
64_S	81_L	0.648	0.96
50_R	53_L	0.646	0.95
19_A	131_A	0.646	0.95
124_L	142_L	0.642	0.95
134_F	145_L	0.633	0.95
126_G	131_A	0.632	0.95
143_L	147_L	0.631	0.95
78_P	81_L	0.630	0.95
103_W	119_G	0.629	0.95
27_G	88_A	0.626	0.95
20_A	130_G	0.625	0.95
119_G	148_G	0.623	0.94
120_P	145_L	0.622	0.94
71_L	141_A	0.621	0.94
31_A	35_L	0.613	0.94
68_A	81_L	0.608	0.94
7_L	37_L	0.608	0.94
15_C	92_L	0.607	0.94
3_I	7_L	0.607	0.94
56_A	60_L	0.607	0.94
124_L	138_L	0.606	0.94
32_L	36_A	0.604	0.94
123_Y	149_W	0.603	0.93
28_P	88_A	0.602	0.93
66_L	69_L	0.601	0.93
2_L	5_F	0.597	0.93
145_L	148_G	0.594	0.93
57_L	61_L	0.592	0.93
109_L	113_L	0.587	0.93
100_S	123_Y	0.586	0.92
37_L	40_A	0.580	0.92
46_R	113_L	0.578	0.92
121_L	124_L	0.574	0.92
144_A	147_L	0.572	0.92
17_L	21_H	0.571	0.91
18_G	22_G	0.570	0.91
61_L	79_P	0.570	0.91
77_P	80_G	0.569	0.91
63_D	145_L	0.568	0.91
52_L	95_T	0.567	0.91
48_E	100_S	0.564	0.91
4_N	101_L	0.560	0.91
14_A	27_G	0.557	0.90
47_R	98_N	0.557	0.90
13_F	129_L	0.555	0.90
38_H	42_S	0.552	0.90
22_G	25_W	0.551	0.90
46_R	61_L	0.549	0.90
67_V	132_V	0.545	0.90
29_L	33_A	0.545	0.90
11_G	14_A	0.541	0.89
47_R	75_P	0.538	0.89
73_S	133_T	0.538	0.89
62_V	72_L	0.531	0.88
97_L	123_Y	0.531	0.88
118_G	121_L	0.529	0.88
76_S	79_P	0.526	0.88
144_A	148_G	0.526	0.88
108_P	111_A	0.523	0.88
55_A	152_L	0.519	0.87
19_A	22_G	0.517	0.87
86_L	126_G	0.516	0.87
39_L	49_L	0.512	0.86
92_L	99_H	0.512	0.86
94_A	120_P	0.508	0.86
43_P	47_R	0.505	0.86
55_A	60_L	0.500	0.85

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
4uc1A	3	0.6903	4.4	0.936	Contact Map
4ryoA	1	0.6452	3.1	0.94	Contact Map
4m5bA	1	0.5032	2.3	0.945	Contact Map
4mt1A	3	0.3484	1.3	0.952	Contact Map
1xc0A	1	0.2129	1.3	0.952	Contact Map
4k0jA	3	0.3613	1.2	0.953	Contact Map
3w9iA	3	0.3548	1.2	0.953	Contact Map
4dx5A	3	0.3548	1.1	0.954	Contact Map
4czbA	2	0.8452	1.1	0.954	Contact Map
3orgA	2	0.3548	0.9	0.956	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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