YecR - PFAM28P - GREMLIN Contacts

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YecR - YecR-like lipoprotein

PFAM:	PF13992	Sequences: GGSRADGTVRLSYEYGEFEKPQVDEAQALALATQRCAAWGYSGAEPFGGETRQCSNGGGGGCLRWRVTREYQC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	73 (73)
Sequences:	718 (585)
Seq/√Len:	68.4
META:	0.869

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_R	70_E	3.584	1.00
3_S	6_D	3.525	1.00
15_Y	21_P	2.726	1.00
52_R	65_W	2.440	1.00
33_T	43_G	2.334	1.00
54_C	62_C	2.163	1.00
25_E	69_R	2.112	1.00
14_E	64_R	1.940	1.00
10_R	51_T	1.746	1.00
29_L	33_T	1.741	1.00
55_S	66_R	1.724	1.00
15_Y	67_V	1.709	1.00
58_G	63_L	1.637	0.99
27_Q	31_L	1.611	0.99
12_S	68_T	1.560	0.99
24_D	27_Q	1.453	0.98
29_L	46_P	1.412	0.98
25_E	31_L	1.403	0.98
1_G	9_V	1.402	0.98
14_E	66_R	1.394	0.98
35_R	45_E	1.354	0.98
34_Q	45_E	1.300	0.97
34_Q	43_G	1.299	0.97
14_E	52_R	1.223	0.96
25_E	29_L	1.175	0.95
35_R	38_A	1.174	0.94
22_Q	33_T	1.153	0.94
7_G	69_R	1.146	0.94
26_A	29_L	1.143	0.94
5_A	47_F	1.136	0.93
34_Q	37_A	1.116	0.93
13_Y	67_V	1.116	0.93
26_A	30_A	1.059	0.91
57_G	61_G	1.057	0.91
58_G	61_G	1.054	0.91
10_R	68_T	1.032	0.90
12_S	66_R	1.018	0.89
12_S	49_G	1.017	0.89
4_R	39_W	1.007	0.89
6_D	47_F	1.004	0.88
46_P	49_G	0.986	0.87
5_A	41_Y	0.982	0.87
31_L	48_G	0.944	0.85
38_A	45_E	0.931	0.84
46_P	71_Y	0.923	0.84
33_T	37_A	0.920	0.84
19_E	22_Q	0.886	0.81
57_G	63_L	0.868	0.80
11_L	31_L	0.868	0.80
37_A	51_T	0.866	0.80
45_E	49_G	0.862	0.79
37_A	42_S	0.857	0.79
3_S	47_F	0.853	0.79
33_T	44_A	0.849	0.78
36_C	40_G	0.848	0.78
55_S	60_G	0.827	0.76
16_G	64_R	0.827	0.76
47_F	72_Q	0.819	0.76
1_G	4_R	0.801	0.74
12_S	35_R	0.800	0.74
37_A	55_S	0.768	0.71
57_G	60_G	0.762	0.70
16_G	19_E	0.750	0.69
24_D	40_G	0.734	0.68
2_G	5_A	0.734	0.68
17_E	63_L	0.733	0.67
28_A	45_E	0.733	0.67
18_F	65_W	0.730	0.67
56_N	63_L	0.727	0.67
15_Y	65_W	0.695	0.63
13_Y	23_V	0.689	0.63
50_E	69_R	0.686	0.62
2_G	39_W	0.675	0.61
30_A	33_T	0.674	0.61
65_W	70_E	0.664	0.60
8_T	70_E	0.643	0.57
29_L	43_G	0.629	0.56
36_C	39_W	0.625	0.55
8_T	48_G	0.614	0.54
11_L	68_T	0.608	0.53
4_R	41_Y	0.600	0.52
5_A	8_T	0.594	0.52
18_F	23_V	0.585	0.50
22_Q	52_R	0.585	0.50
24_D	65_W	0.580	0.50
19_E	24_D	0.579	0.50
3_S	35_R	0.574	0.49
29_L	42_S	0.573	0.49
38_A	49_G	0.568	0.48
16_G	61_G	0.567	0.48
51_T	70_E	0.564	0.48
53_Q	66_R	0.561	0.48
21_P	58_G	0.555	0.47
7_G	31_L	0.553	0.47
43_G	58_G	0.552	0.46
6_D	41_Y	0.549	0.46
11_L	25_E	0.547	0.46
35_R	49_G	0.541	0.45
55_S	59_G	0.529	0.44
12_S	29_L	0.526	0.43
19_E	67_V	0.524	0.43
46_P	72_Q	0.519	0.43
8_T	12_S	0.517	0.42
28_A	51_T	0.513	0.42
48_G	51_T	0.511	0.42
8_T	11_L	0.510	0.42
1_G	6_D	0.509	0.41
12_S	65_W	0.509	0.41
15_Y	22_Q	0.508	0.41
36_C	54_C	0.500	0.40

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
2jopA	1	0.9041	74.9	0.823	Contact Map
5a2eA	1	0.8356	59.9	0.84	Contact Map
2ja4A	1	0.863	56.8	0.844	Contact Map
1by2A	1	0.9452	53.8	0.846	Contact Map
2oyaA	2	0.9315	36.2	0.862	Contact Map
2xrcA	2	0.9452	29.5	0.868	Contact Map
1r02A	1	0.1507	14.6	0.886	Contact Map
1z8gA	1	0.9726	14.3	0.886	Contact Map
1cq0A	1	0.1507	7.7	0.899	Contact Map
3rziA	3	0.5616	4.5	0.91	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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