DUF3119 - PFAM28P - GREMLIN Contacts

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DUF3119 - Protein of unknown function (DUF3119)

PFAM:	PF11317	Sequences: VELAPSYRLPLVLVLLGLPLLLLQPWLGLVIALFGLFLLVQTATLRLQFTETALDVYRGSSGENLIRGGKNRFPYSEWQNWRIFWPPVPILFYFKEVKSKPEGQIHFLPILFDPKQLRECLEQRCP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	126 (113)
Sequences:	517 (364)
Seq/√Len:	34.3
META:	0.702

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_L	12_V	4.523	1.00
14_V	35_G	3.522	1.00
113_D	116_Q	3.269	1.00
47_L	54_L	3.031	1.00
59_G	63_E	2.824	1.00
9_L	13_L	2.725	1.00
45_L	56_V	2.597	1.00
34_F	45_L	2.517	1.00
118_R	122_E	2.455	1.00
17_G	32_A	2.400	1.00
10_P	42_T	2.365	0.99
53_A	72_R	2.233	0.99
80_N	95_K	2.036	0.98
9_L	111_L	1.890	0.97
79_Q	95_K	1.829	0.97
57_Y	66_I	1.793	0.96
120_C	123_Q	1.705	0.95
49_F	54_L	1.672	0.94
2_E	48_Q	1.671	0.94
48_Q	55_D	1.572	0.92
26_W	29_L	1.557	0.92
77_E	97_V	1.549	0.92
36_L	40_V	1.537	0.91
29_L	123_Q	1.500	0.90
80_N	107_F	1.435	0.88
56_V	66_I	1.421	0.88
45_L	59_G	1.389	0.87
91_L	105_I	1.381	0.86
34_F	37_F	1.376	0.86
22_L	87_P	1.294	0.82
13_L	17_G	1.280	0.82
13_L	16_L	1.247	0.80
20_L	31_I	1.246	0.80
73_F	78_W	1.238	0.79
14_V	36_L	1.228	0.79
106_H	109_P	1.222	0.79
92_F	108_L	1.218	0.78
8_R	12_V	1.210	0.78
55_D	65_L	1.182	0.76
7_Y	57_Y	1.175	0.76
78_W	117_L	1.168	0.75
65_L	72_R	1.164	0.75
34_F	44_T	1.157	0.75
29_L	32_A	1.127	0.73
45_L	72_R	1.122	0.72
25_P	30_V	1.118	0.72
72_R	124_R	1.115	0.72
34_F	38_L	1.094	0.70
42_T	115_K	1.077	0.69
9_L	77_E	1.073	0.69
11_L	29_L	1.055	0.68
2_E	80_N	1.016	0.65
78_W	92_F	1.009	0.64
34_F	66_I	0.999	0.63
99_S	121_L	0.975	0.61
52_T	56_V	0.964	0.60
7_Y	43_A	0.954	0.60
35_G	39_L	0.933	0.58
20_L	23_L	0.930	0.58
1_V	124_R	0.924	0.57
25_P	28_G	0.924	0.57
80_N	125_C	0.921	0.57
36_L	42_T	0.915	0.56
36_L	48_Q	0.908	0.56
17_G	35_G	0.900	0.55
9_L	16_L	0.897	0.55
76_S	97_V	0.886	0.54
50_T	72_R	0.882	0.54
8_R	11_L	0.876	0.53
73_F	92_F	0.867	0.52
117_L	121_L	0.859	0.52
75_Y	78_W	0.857	0.52
18_L	32_A	0.855	0.51
74_P	77_E	0.844	0.50
2_E	7_Y	0.841	0.50
85_W	105_I	0.837	0.50
4_A	8_R	0.836	0.50
64_N	124_R	0.832	0.49
53_A	75_Y	0.830	0.49
18_L	22_L	0.825	0.49
12_V	16_L	0.824	0.49
1_V	123_Q	0.812	0.48
120_C	125_C	0.809	0.47
6_S	9_L	0.805	0.47
92_F	99_S	0.795	0.46
22_L	35_G	0.791	0.46
11_L	15_L	0.781	0.45
116_Q	119_E	0.757	0.43
112_F	121_L	0.756	0.43
74_P	78_W	0.745	0.42
14_V	43_A	0.745	0.42
39_L	43_A	0.729	0.41
73_F	108_L	0.725	0.40
6_S	44_T	0.718	0.40
9_L	88_V	0.709	0.39
18_L	83_I	0.708	0.39
22_L	27_L	0.707	0.39
64_N	76_S	0.703	0.39
73_F	99_S	0.701	0.38
97_V	107_F	0.697	0.38
87_P	118_R	0.695	0.38
32_A	113_D	0.683	0.37
14_V	40_V	0.679	0.37
50_T	53_A	0.671	0.36
8_R	13_L	0.670	0.36
6_S	114_P	0.666	0.36
44_T	58_R	0.666	0.36
4_A	116_Q	0.665	0.36
82_R	111_L	0.660	0.35
86_P	118_R	0.660	0.35
35_G	95_K	0.659	0.35
110_I	114_P	0.659	0.35
40_V	98_K	0.657	0.35
99_S	108_L	0.643	0.34
48_Q	63_E	0.639	0.34
81_W	112_F	0.639	0.34
40_V	91_L	0.637	0.33
37_F	40_V	0.632	0.33
98_K	107_F	0.631	0.33
119_E	123_Q	0.623	0.32
12_V	48_Q	0.620	0.32
118_R	124_R	0.619	0.32
56_V	81_W	0.617	0.32
21_L	39_L	0.615	0.32
19_P	22_L	0.614	0.32
78_W	81_W	0.614	0.32
45_L	55_D	0.614	0.32
67_R	92_F	0.611	0.32
47_L	92_F	0.611	0.32
34_F	125_C	0.607	0.31
75_Y	85_W	0.606	0.31
74_P	112_F	0.603	0.31
20_L	24_Q	0.603	0.31
44_T	56_V	0.601	0.31
10_P	110_I	0.590	0.30
6_S	110_I	0.587	0.30
15_L	22_L	0.586	0.30
82_R	107_F	0.585	0.30
35_G	91_L	0.585	0.30
25_P	64_N	0.584	0.30
4_A	10_P	0.582	0.29
37_F	112_F	0.578	0.29
10_P	13_L	0.566	0.28
5_P	16_L	0.564	0.28
47_L	73_F	0.563	0.28
25_P	29_L	0.562	0.28
22_L	25_P	0.560	0.28
30_V	123_Q	0.557	0.28
119_E	122_E	0.549	0.27
56_V	108_L	0.548	0.27
116_Q	123_Q	0.547	0.27
17_G	120_C	0.547	0.27
39_L	87_P	0.544	0.27
1_V	25_P	0.543	0.27
47_L	108_L	0.540	0.27
18_L	122_E	0.539	0.27
40_V	44_T	0.530	0.26
55_D	63_E	0.528	0.26
21_L	25_P	0.527	0.26
86_P	116_Q	0.523	0.25
85_W	88_V	0.520	0.25
19_P	23_L	0.515	0.25
115_K	118_R	0.513	0.25
21_L	28_G	0.513	0.25
8_R	88_V	0.513	0.25
39_L	111_L	0.510	0.25
56_V	65_L	0.508	0.25
110_I	121_L	0.506	0.24
73_F	121_L	0.505	0.24
43_A	58_R	0.500	0.24

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
1j0wA	1	0.6587	10	0.95	Contact Map
1ciiA	1	0.4444	8.6	0.952	Contact Map
3hrgA	1	0.9048	5	0.957	Contact Map
3fm7C	1	0.2143	4.1	0.959	Contact Map
3glwZ	2	0.1349	3.7	0.959	Contact Map
2p8iA	2	0.3095	3.5	0.96	Contact Map
1g8mA	2	0.5	3.3	0.96	Contact Map
2dlwA	1	0.6984	3.3	0.96	Contact Map
1xr0B	1	0.6587	3	0.961	Contact Map
1yumA	4	0.9683	3	0.961	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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