YNEF - BACSU - GREMLIN Contacts

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YNEF - UPF0154 protein YneF

UniProt:	P45708	Sequences: MTLWVGILVGVVALLIGVALGFFIARKYMMSYLKKNPPINEQMLRMMMMQMGMKPSQKKINQMMKAMNNQTK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	72 (67)
Sequences:	345 (193)
Seq/√Len:	23.6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_S	35_K	3.752	1.00
53_M	59_K	3.407	1.00
6_G	10_G	2.887	0.99
50_Q	66_A	2.653	0.99
20_L	24_I	2.614	0.99
5_V	9_V	2.371	0.98
57_Q	61_N	2.292	0.97
45_R	57_Q	2.187	0.96
44_L	63_M	2.186	0.96
27_K	30_M	2.080	0.95
6_G	9_V	1.934	0.93
17_G	21_G	1.914	0.93
4_W	8_L	1.817	0.90
45_R	61_N	1.507	0.80
10_G	13_A	1.294	0.68
49_M	60_I	1.286	0.68
44_L	60_I	1.275	0.67
18_V	24_I	1.274	0.67
20_L	27_K	1.264	0.66
15_L	19_A	1.244	0.65
40_N	68_N	1.229	0.64
16_I	19_A	1.165	0.60
49_M	54_K	1.114	0.56
21_G	25_A	1.114	0.56
13_A	17_G	1.081	0.54
9_V	13_A	1.063	0.53
50_Q	63_M	1.057	0.52
56_S	67_M	1.041	0.51
22_F	25_A	0.963	0.46
6_G	55_P	0.944	0.45
29_M	63_M	0.941	0.44
4_W	7_I	0.937	0.44
26_R	30_M	0.936	0.44
33_L	40_N	0.904	0.42
50_Q	62_Q	0.900	0.41
45_R	49_M	0.895	0.41
34_K	42_Q	0.892	0.41
22_F	67_M	0.877	0.40
48_M	55_P	0.869	0.39
29_M	32_Y	0.861	0.39
4_W	68_N	0.849	0.38
41_E	61_N	0.837	0.37
34_K	64_M	0.836	0.37
40_N	61_N	0.830	0.37
57_Q	66_A	0.815	0.36
28_Y	54_K	0.812	0.36
26_R	53_M	0.803	0.35
46_M	49_M	0.771	0.33
14_L	21_G	0.761	0.32
22_F	26_R	0.758	0.32
40_N	44_L	0.756	0.32
65_K	68_N	0.750	0.32
43_M	64_M	0.750	0.32
29_M	48_M	0.741	0.31
38_P	64_M	0.730	0.31
14_L	18_V	0.723	0.30
46_M	54_K	0.717	0.30
8_L	13_A	0.704	0.29
8_L	20_L	0.694	0.28
25_A	58_K	0.693	0.28
38_P	41_E	0.687	0.28
15_L	20_L	0.679	0.28
17_G	61_N	0.666	0.27
32_Y	48_M	0.655	0.26
48_M	62_Q	0.653	0.26
60_I	63_M	0.645	0.26
22_F	39_I	0.642	0.26
59_K	62_Q	0.640	0.25
44_L	67_M	0.636	0.25
46_M	62_Q	0.635	0.25
11_V	56_S	0.621	0.24
24_I	27_K	0.619	0.24
39_I	43_M	0.618	0.24
14_L	17_G	0.604	0.24
5_V	8_L	0.603	0.23
45_R	60_I	0.602	0.23
30_M	60_I	0.601	0.23
25_A	29_M	0.600	0.23
60_I	65_K	0.598	0.23
53_M	70_Q	0.597	0.23
66_A	70_Q	0.595	0.23
11_V	23_F	0.595	0.23
5_V	10_G	0.591	0.23
39_I	61_N	0.587	0.23
22_F	43_M	0.581	0.22
47_M	57_Q	0.578	0.22
30_M	33_L	0.575	0.22
34_K	65_K	0.569	0.22
58_K	67_M	0.561	0.21
43_M	66_A	0.558	0.21
30_M	50_Q	0.557	0.21
65_K	69_N	0.555	0.21
41_E	64_M	0.533	0.20
36_N	39_I	0.532	0.20
8_L	40_N	0.526	0.20
48_M	67_M	0.524	0.20
31_S	64_M	0.516	0.19
61_N	65_K	0.513	0.19
46_M	66_A	0.504	0.19
32_Y	68_N	0.500	0.19

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
3zg1A	2	0.4444	53.1	0.889	Contact Map
3layA	5	0.6389	53	0.889	Contact Map
2m8rA	1	0.3472	36.4	0.9	Contact Map
2f95B	2	0.2917	33.3	0.901	Contact Map
1scfA	4	0	30.8	0.903	Contact Map
4n5xA	1	0.6528	26.9	0.906	Contact Map
2lk9A	1	0.3333	26.4	0.906	Contact Map
4gycB	2	0.3472	26.2	0.906	Contact Map
3qnqA	2	0.6111	22.9	0.909	Contact Map
1bu3A	2	0.3194	20.2	0.912	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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