DUF2489 - PFAM28P - GREMLIN Contacts

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DUF2489 - Protein of unknown function (DUF2489)

PFAM:	PF10675	Sequences: IAALAFYAGYLLRQLKKQKQQQQAQQQALQERRANILESIRIIARAMLQEQCDLSEGAIRIKVLLDQLDPELLEDEDYPAFFELYEATKHMPTHEARKALSKKERMKLDLEREKLEAELEDAILAAAKQL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	130 (130)
Sequences:	928 (674)
Seq/√Len:	59.1
META:	0.603

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
47_M	57_G	3.579	1.00
100_L	105_R	3.220	1.00
92_P	108_L	3.146	1.00
109_D	112_R	2.987	1.00
3_A	7_Y	2.738	1.00
91_M	108_L	2.580	1.00
87_A	118_E	2.459	1.00
55_S	88_T	2.395	1.00
90_H	111_E	2.325	1.00
101_S	104_E	2.252	1.00
8_A	11_L	2.232	1.00
6_F	10_Y	2.211	1.00
7_Y	11_L	2.196	1.00
95_E	99_A	2.167	1.00
97_R	109_D	2.005	1.00
43_I	61_I	1.907	1.00
120_E	124_L	1.895	1.00
16_K	20_Q	1.856	1.00
91_M	97_R	1.770	0.99
30_Q	34_A	1.768	0.99
55_S	112_R	1.751	0.99
4_L	8_A	1.733	0.99
10_Y	14_Q	1.732	0.99
27_Q	31_E	1.689	0.99
58_A	84_L	1.626	0.99
8_A	15_L	1.619	0.99
58_A	81_F	1.582	0.99
97_R	108_L	1.581	0.99
55_S	97_R	1.541	0.98
12_L	15_L	1.452	0.98
86_E	89_K	1.451	0.98
11_L	14_Q	1.436	0.97
104_E	107_K	1.432	0.97
39_S	43_I	1.404	0.97
6_F	9_G	1.402	0.97
83_E	122_A	1.392	0.97
103_K	106_M	1.379	0.97
9_G	13_R	1.362	0.96
52_C	81_F	1.343	0.96
105_R	108_L	1.313	0.95
61_I	81_F	1.290	0.95
53_D	113_E	1.274	0.95
15_L	19_K	1.264	0.94
36_I	67_Q	1.242	0.94
80_A	126_A	1.241	0.94
43_I	46_A	1.240	0.94
63_V	67_Q	1.232	0.94
41_R	45_R	1.201	0.93
39_S	64_L	1.182	0.92
97_R	105_R	1.161	0.91
106_M	117_A	1.155	0.91
63_V	66_D	1.134	0.90
77_D	129_Q	1.130	0.90
53_D	97_R	1.126	0.90
12_L	16_K	1.100	0.89
7_Y	18_Q	1.094	0.89
9_G	12_L	1.091	0.89
84_L	112_R	1.084	0.88
32_R	35_N	1.075	0.88
83_E	87_A	1.074	0.88
4_L	11_L	1.065	0.88
100_L	108_L	1.063	0.87
107_K	111_E	1.059	0.87
87_A	115_L	1.049	0.87
96_A	99_A	1.033	0.86
106_M	110_L	1.020	0.85
28_A	31_E	1.001	0.84
47_M	54_L	1.001	0.84
119_L	122_A	0.990	0.83
62_K	66_D	0.982	0.83
48_L	128_K	0.979	0.83
59_I	62_K	0.979	0.83
114_K	118_E	0.963	0.82
91_M	112_R	0.958	0.81
24_A	28_A	0.951	0.81
35_N	67_Q	0.945	0.80
122_A	125_A	0.941	0.80
101_S	106_M	0.939	0.80
106_M	113_E	0.931	0.79
83_E	119_L	0.887	0.76
16_K	19_K	0.885	0.76
97_R	112_R	0.884	0.76
108_L	112_R	0.865	0.74
13_R	17_K	0.862	0.74
52_C	85_Y	0.857	0.73
39_S	42_I	0.855	0.73
24_A	27_Q	0.848	0.73
59_I	84_L	0.841	0.72
40_I	61_I	0.838	0.72
1_I	4_L	0.822	0.70
33_R	69_D	0.797	0.68
7_Y	10_Y	0.796	0.68
4_L	7_Y	0.791	0.67
47_M	127_A	0.790	0.67
11_L	15_L	0.777	0.66
55_S	108_L	0.772	0.65
54_L	57_G	0.768	0.65
84_L	115_L	0.765	0.65
13_R	16_K	0.761	0.64
53_D	112_R	0.745	0.63
52_C	57_G	0.744	0.63
22_Q	26_Q	0.744	0.63
110_L	117_A	0.730	0.61
97_R	100_L	0.730	0.61
50_E	106_M	0.730	0.61
43_I	64_L	0.728	0.61
10_Y	17_K	0.723	0.60
13_R	19_K	0.723	0.60
32_R	63_V	0.721	0.60
32_R	36_I	0.719	0.60
55_S	116_E	0.713	0.59
1_I	31_E	0.710	0.59
40_I	53_D	0.709	0.59
59_I	67_Q	0.698	0.58
34_A	38_E	0.698	0.58
3_A	10_Y	0.697	0.58
79_P	126_A	0.693	0.57
62_K	82_F	0.692	0.57
43_I	57_G	0.690	0.57
41_R	127_A	0.689	0.57
100_L	104_E	0.680	0.56
7_Y	79_P	0.671	0.55
51_Q	115_L	0.670	0.55
58_A	80_A	0.667	0.54
36_I	40_I	0.662	0.54
91_M	105_R	0.661	0.54
40_I	92_P	0.658	0.53
53_D	94_H	0.656	0.53
52_C	127_A	0.655	0.53
101_S	107_K	0.653	0.53
39_S	59_I	0.643	0.52
21_Q	25_Q	0.640	0.51
59_I	63_V	0.638	0.51
23_Q	27_Q	0.633	0.51
83_E	118_E	0.630	0.50
8_A	14_Q	0.627	0.50
26_Q	30_Q	0.626	0.50
113_E	117_A	0.623	0.49
70_P	129_Q	0.614	0.48
112_R	123_I	0.610	0.48
70_P	73_L	0.609	0.48
2_A	27_Q	0.608	0.48
53_D	96_A	0.607	0.48
5_A	9_G	0.607	0.48
1_I	5_A	0.605	0.47
47_M	123_I	0.600	0.47
58_A	73_L	0.599	0.47
11_L	18_Q	0.598	0.47
29_L	33_R	0.597	0.46
15_L	18_Q	0.593	0.46
125_A	128_K	0.593	0.46
38_E	101_S	0.587	0.45
37_L	40_I	0.586	0.45
47_M	52_C	0.582	0.45
87_A	119_L	0.580	0.45
117_A	121_D	0.578	0.44
12_L	17_K	0.577	0.44
84_L	94_H	0.574	0.44
81_F	127_A	0.574	0.44
53_D	88_T	0.572	0.44
60_R	100_L	0.572	0.44
126_A	129_Q	0.571	0.44
7_Y	12_L	0.570	0.44
5_A	20_Q	0.566	0.43
70_P	74_E	0.566	0.43
91_M	115_L	0.553	0.42
2_A	6_F	0.553	0.42
37_L	66_D	0.553	0.42
6_F	17_K	0.549	0.41
80_A	83_E	0.547	0.41
87_A	90_H	0.544	0.41
51_Q	59_I	0.543	0.41
10_Y	16_K	0.539	0.40
78_Y	129_Q	0.538	0.40
85_Y	89_K	0.538	0.40
88_T	97_R	0.537	0.40
124_L	128_K	0.533	0.40
102_K	106_M	0.528	0.39
80_A	119_L	0.526	0.39
14_Q	18_Q	0.526	0.39
39_S	112_R	0.525	0.39
32_R	82_F	0.522	0.38
70_P	77_D	0.521	0.38
55_S	105_R	0.519	0.38
32_R	46_A	0.519	0.38
80_A	122_A	0.518	0.38
54_L	124_L	0.514	0.38
31_E	35_N	0.509	0.37
5_A	8_A	0.508	0.37
1_I	22_Q	0.505	0.37
52_C	84_L	0.504	0.36
36_I	78_Y	0.504	0.36
56_E	60_R	0.502	0.36
5_A	19_K	0.501	0.36
51_Q	98_K	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
2micA	2	0.1615	14.3	0.925	Contact Map
2ks1B	1	0.1615	10.3	0.929	Contact Map
2l2tA	2	0.1692	10	0.93	Contact Map
2x3vA	2	0.3769	8.3	0.932	Contact Map
3m3wA	2	0.3692	7.9	0.933	Contact Map
2jwaA	2	0.1538	7.4	0.934	Contact Map
1jv1A	2	0.4231	6.5	0.935	Contact Map
2yqcA	1	0.4231	6.4	0.936	Contact Map
4n3yB	2	0.3	6.1	0.936	Contact Map
3abhA	2	0.3692	5.6	0.937	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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