DUF2955 - PFAM28P - GREMLIN Contacts

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DUF2955 - Protein of unknown function (DUF2955)

PFAM:	PF11168	Sequences: RILRLALGTTLALAVAYGLGWPLPFLAPVLAVLLLSPPPPPPLKAGLGLVLVLALAAGAGLLLSPLLLHYPLVGLLLVGLLLFLSFYLGARGGSPLLGTLLLIGLTLIPVVGSVSPALALALALALVVGALLAVLVVWLA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	140 (138)
Sequences:	1802 (1251)
Seq/√Len:	106.5
META:	0.794

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
8_G	35_L	3.524	1.00
111_V	118_L	3.323	1.00
14_A	18_G	3.123	1.00
122_L	126_L	3.069	1.00
15_V	19_L	2.581	1.00
30_L	33_L	2.480	1.00
64_S	112_G	2.307	1.00
43_L	46_G	2.298	1.00
42_P	45_A	2.259	1.00
81_L	105_L	2.160	1.00
78_V	106_T	2.153	1.00
13_L	17_Y	2.110	1.00
21_W	24_P	2.082	1.00
88_L	93_G	2.021	1.00
53_L	130_A	1.952	1.00
73_V	76_L	1.875	1.00
109_P	113_S	1.804	1.00
67_L	77_L	1.760	1.00
89_G	98_G	1.745	1.00
9_T	32_V	1.714	1.00
17_Y	24_P	1.688	1.00
40_P	46_G	1.678	1.00
54_A	127_V	1.672	1.00
12_A	31_A	1.613	1.00
109_P	119_A	1.605	1.00
71_P	75_L	1.568	1.00
60_G	112_G	1.551	1.00
134_V	137_V	1.494	1.00
46_G	138_W	1.482	1.00
49_L	53_L	1.475	1.00
44_K	48_G	1.474	1.00
35_L	86_F	1.447	1.00
40_P	45_A	1.445	1.00
41_P	45_A	1.415	1.00
57_A	129_G	1.398	1.00
23_L	122_L	1.397	1.00
73_V	77_L	1.386	1.00
133_A	137_V	1.364	1.00
95_P	99_T	1.360	1.00
59_A	85_S	1.342	0.99
125_A	129_G	1.321	0.99
117_A	120_L	1.304	0.99
86_F	92_G	1.242	0.99
6_A	10_T	1.240	0.99
119_A	123_A	1.230	0.99
66_L	73_V	1.229	0.99
49_L	52_V	1.204	0.99
98_G	110_V	1.198	0.99
57_A	123_A	1.184	0.99
63_L	96_L	1.177	0.99
135_L	139_L	1.150	0.98
9_T	22_P	1.150	0.98
29_V	49_L	1.147	0.98
87_Y	92_G	1.147	0.98
127_V	134_V	1.137	0.98
59_A	108_I	1.107	0.98
129_G	132_L	1.105	0.98
30_L	34_L	1.099	0.98
32_V	64_S	1.091	0.98
36_S	39_P	1.083	0.98
43_L	47_L	1.070	0.97
90_A	93_G	1.059	0.97
7_L	54_A	1.042	0.97
113_S	116_P	1.040	0.97
89_G	95_P	1.039	0.97
50_V	127_V	1.028	0.97
27_A	31_A	1.026	0.97
3_L	8_G	1.026	0.97
38_P	41_P	1.012	0.96
31_A	136_V	1.012	0.96
55_L	58_G	1.011	0.96
47_L	139_L	1.000	0.96
100_L	104_G	0.985	0.96
8_G	21_W	0.985	0.96
72_L	76_L	0.984	0.96
128_V	132_L	0.984	0.96
15_V	18_G	0.971	0.96
10_T	14_A	0.968	0.95
35_L	92_G	0.963	0.95
22_P	25_F	0.956	0.95
33_L	66_L	0.949	0.95
52_V	97_L	0.943	0.95
128_V	139_L	0.942	0.95
5_L	8_G	0.941	0.95
2_I	12_A	0.928	0.94
56_A	87_Y	0.927	0.94
65_P	74_G	0.925	0.94
27_A	39_P	0.924	0.94
60_G	108_I	0.917	0.94
52_V	56_A	0.914	0.94
115_S	118_L	0.913	0.94
12_A	68_L	0.891	0.93
130_A	133_A	0.884	0.93
76_L	80_L	0.868	0.92
18_G	129_G	0.856	0.91
15_V	21_W	0.856	0.91
62_L	124_L	0.853	0.91
64_S	120_L	0.844	0.91
85_S	101_L	0.842	0.91
3_L	35_L	0.841	0.91
34_L	60_G	0.839	0.91
45_A	48_G	0.837	0.91
70_Y	76_L	0.834	0.90
111_V	122_L	0.832	0.90
18_G	117_A	0.832	0.90
42_P	138_W	0.830	0.90
47_L	76_L	0.814	0.89
43_L	50_V	0.813	0.89
40_P	75_L	0.813	0.89
121_A	125_A	0.811	0.89
84_L	88_L	0.809	0.89
108_I	123_A	0.804	0.89
128_V	131_L	0.796	0.88
98_G	114_V	0.781	0.87
10_T	131_L	0.774	0.87
133_A	136_V	0.773	0.87
26_L	44_K	0.773	0.87
18_G	60_G	0.768	0.86
23_L	26_L	0.761	0.86
88_L	107_L	0.760	0.86
69_H	102_L	0.751	0.85
48_G	51_L	0.748	0.85
57_A	127_V	0.741	0.84
46_G	134_V	0.730	0.83
63_L	78_V	0.723	0.83
122_L	127_V	0.719	0.82
56_A	89_G	0.719	0.82
53_L	100_L	0.717	0.82
134_V	139_L	0.713	0.82
25_F	37_P	0.710	0.82
15_V	136_V	0.706	0.81
118_L	121_A	0.705	0.81
106_T	110_V	0.697	0.81
26_L	38_P	0.687	0.80
122_L	125_A	0.687	0.80
125_A	132_L	0.682	0.79
9_T	12_A	0.682	0.79
60_G	74_G	0.680	0.79
74_G	78_V	0.677	0.79
22_P	121_A	0.675	0.78
88_L	95_P	0.675	0.78
116_P	129_G	0.672	0.78
68_L	105_L	0.671	0.78
30_L	130_A	0.666	0.77
135_L	138_W	0.655	0.76
46_G	137_V	0.653	0.76
56_A	68_L	0.650	0.76
4_R	7_L	0.647	0.75
85_S	89_G	0.647	0.75
121_A	129_G	0.646	0.75
35_L	137_V	0.643	0.75
50_V	53_L	0.641	0.75
74_G	77_L	0.639	0.74
75_L	79_G	0.639	0.74
102_L	109_P	0.637	0.74
64_S	109_P	0.632	0.74
34_L	68_L	0.631	0.74
5_L	12_A	0.610	0.71
16_A	24_P	0.608	0.71
85_S	98_G	0.603	0.70
12_A	136_V	0.602	0.70
88_L	94_S	0.602	0.70
124_L	128_V	0.596	0.69
105_L	111_V	0.595	0.69
11_L	20_G	0.593	0.69
55_L	59_A	0.593	0.69
72_L	75_L	0.590	0.69
39_P	99_T	0.590	0.69
66_L	74_G	0.589	0.68
17_Y	25_F	0.587	0.68
87_Y	94_S	0.587	0.68
77_L	103_I	0.587	0.68
61_L	108_I	0.585	0.68
2_I	7_L	0.583	0.68
117_A	124_L	0.582	0.67
81_L	85_S	0.572	0.66
101_L	133_A	0.571	0.66
75_L	84_L	0.569	0.66
46_G	54_A	0.567	0.65
57_A	104_G	0.566	0.65
126_L	129_G	0.566	0.65
43_L	52_V	0.563	0.65
91_R	94_S	0.561	0.65
7_L	10_T	0.560	0.65
22_P	58_G	0.557	0.64
57_A	126_L	0.549	0.63
26_L	126_L	0.542	0.62
53_L	56_A	0.542	0.62
120_L	124_L	0.541	0.62
5_L	24_P	0.541	0.62
73_V	84_L	0.537	0.61
124_L	135_L	0.534	0.61
101_L	105_L	0.534	0.61
80_L	128_V	0.529	0.60
45_A	115_S	0.529	0.60
63_L	85_S	0.528	0.60
13_L	18_G	0.526	0.60
106_T	113_S	0.522	0.59
33_L	99_T	0.520	0.59
107_L	121_A	0.520	0.59
121_A	126_L	0.519	0.59
80_L	108_I	0.517	0.58
25_F	29_V	0.509	0.57
84_L	129_G	0.509	0.57
103_I	137_V	0.508	0.57
117_A	125_A	0.503	0.56
24_P	45_A	0.500	0.56

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
1hq1A	1	0.2429	1.8	0.93	Contact Map
2jqeA	1	0.2857	1.7	0.93	Contact Map
2k44A	1	0.0714	1.3	0.934	Contact Map
2mc7A	1	0.2143	1.2	0.937	Contact Map
3k3fA	3	0.8143	1.1	0.938	Contact Map
2mpnA	2	0.3357	1	0.939	Contact Map
4f35D	2	0.6571	1	0.94	Contact Map
2ksfA	1	0.7	1	0.941	Contact Map
4wgvA	2	0.9714	0.8	0.944	Contact Map
4p02A	1	0.6929	0.8	0.945	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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