GvpO - PFAM28P - GREMLIN Contacts

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GvpO - Gas vesicle synthesis protein GvpO

PFAM:	PF05800	Sequences: SDSSSSRSRGRLSAAEAARRAREQLAELTGREPESVSGLERTDDGWRVTVEVVELRRIPDTTDVLASYEVELDDDGELLGYRRTRRYRRGQAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	93 (86)
Sequences:	2616 (1748)
Seq/√Len:	188.5
META:	0.838

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_R	71_E	3.162	1.00
38_G	49_T	2.727	1.00
37_S	67_S	2.408	1.00
47_R	69_E	2.380	1.00
56_R	60_D	2.368	1.00
71_E	80_G	2.236	1.00
51_E	87_Y	2.198	1.00
12_L	17_A	1.957	1.00
14_A	39_L	1.924	1.00
40_E	82_R	1.720	1.00
60_D	63_D	1.705	1.00
15_A	27_E	1.656	1.00
56_R	63_D	1.627	1.00
73_D	77_E	1.608	1.00
32_E	56_R	1.595	1.00
49_T	67_S	1.580	1.00
40_E	47_R	1.552	1.00
57_R	62_T	1.520	1.00
15_A	19_R	1.469	1.00
88_R	91_Q	1.468	1.00
42_T	71_E	1.456	1.00
20_R	24_Q	1.442	1.00
42_T	47_R	1.435	1.00
64_V	92_A	1.429	1.00
58_I	61_T	1.391	1.00
63_D	89_R	1.381	1.00
54_E	66_A	1.367	1.00
19_R	27_E	1.364	1.00
13_S	16_E	1.342	1.00
34_E	53_V	1.328	1.00
40_E	80_G	1.301	1.00
18_A	22_R	1.264	1.00
53_V	65_L	1.255	1.00
55_L	60_D	1.229	1.00
13_S	77_E	1.207	1.00
26_A	33_P	1.203	1.00
18_A	39_L	1.195	1.00
21_A	26_A	1.191	1.00
25_L	29_T	1.173	1.00
49_T	69_E	1.168	1.00
41_R	74_D	1.165	1.00
31_R	52_V	1.150	1.00
34_E	63_D	1.149	1.00
7_R	10_G	1.079	1.00
25_L	81_Y	1.076	1.00
58_I	62_T	1.028	1.00
55_L	61_T	0.997	0.99
55_L	62_T	0.988	0.99
37_S	51_E	0.985	0.99
69_E	82_R	0.975	0.99
62_T	88_R	0.975	0.99
24_Q	77_E	0.964	0.99
19_R	23_E	0.945	0.99
29_T	52_V	0.936	0.99
12_L	20_R	0.926	0.99
17_A	72_L	0.915	0.99
69_E	84_T	0.908	0.99
42_T	45_G	0.895	0.99
26_A	32_E	0.889	0.99
21_A	72_L	0.865	0.98
31_R	35_S	0.854	0.98
51_E	67_S	0.848	0.98
7_R	74_D	0.847	0.98
88_R	92_A	0.845	0.98
36_V	50_V	0.837	0.98
25_L	50_V	0.835	0.98
22_R	33_P	0.821	0.98
17_A	30_G	0.816	0.98
20_R	72_L	0.803	0.98
64_V	88_R	0.802	0.98
55_L	64_V	0.781	0.97
47_R	82_R	0.765	0.97
61_T	91_Q	0.757	0.97
33_P	52_V	0.734	0.96
73_D	79_L	0.731	0.96
67_S	85_R	0.729	0.96
15_A	24_Q	0.726	0.96
55_L	66_A	0.723	0.95
25_L	70_V	0.715	0.95
13_S	27_E	0.713	0.95
70_V	82_R	0.694	0.94
60_D	90_G	0.691	0.94
64_V	90_G	0.691	0.94
18_A	38_G	0.683	0.94
82_R	85_R	0.683	0.94
48_V	63_D	0.669	0.93
48_V	72_L	0.667	0.93
17_A	41_R	0.658	0.93
19_R	22_R	0.657	0.93
22_R	30_G	0.650	0.92
22_R	72_L	0.644	0.92
31_R	56_R	0.640	0.92
34_E	67_S	0.636	0.91
34_E	62_T	0.622	0.90
17_A	48_V	0.621	0.90
23_E	27_E	0.614	0.90
7_R	11_R	0.610	0.90
29_T	50_V	0.609	0.90
16_E	20_R	0.608	0.89
21_A	78_L	0.598	0.89
16_E	19_R	0.590	0.88
49_T	66_A	0.574	0.87
68_Y	89_R	0.574	0.87
11_R	74_D	0.560	0.85
79_L	84_T	0.557	0.85
59_P	62_T	0.556	0.85
9_R	12_L	0.553	0.85
53_V	61_T	0.553	0.85
40_E	65_L	0.552	0.84
22_R	92_A	0.550	0.84
54_E	83_R	0.547	0.84
34_E	37_S	0.547	0.84
8_S	11_R	0.541	0.83
21_A	48_V	0.537	0.83
55_L	58_I	0.536	0.83
18_A	21_A	0.535	0.83
81_Y	91_Q	0.528	0.82
20_R	23_E	0.528	0.82
40_E	49_T	0.526	0.81
40_E	92_A	0.524	0.81
21_A	41_R	0.523	0.81
34_E	52_V	0.523	0.81
38_G	48_V	0.522	0.81
22_R	36_V	0.517	0.80
50_V	70_V	0.512	0.80
22_R	37_S	0.511	0.80
50_V	80_G	0.505	0.79
25_L	68_Y	0.502	0.78
51_E	60_D	0.500	0.78

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
1jnsA	1	0.5914	26	0.887	Contact Map
4exrA	2	0.828	25.3	0.888	Contact Map
3tc5A	1	0.5699	24.2	0.889	Contact Map
2mntA	1	0.5699	23.2	0.89	Contact Map
2pv1A	1	0.5914	23.1	0.89	Contact Map
1yw5A	1	0.5699	22.6	0.891	Contact Map
2lj4A	1	0.5699	19.1	0.894	Contact Map
1j6yA	1	0.5699	17.9	0.896	Contact Map
4tnsA	1	0.5699	17.3	0.897	Contact Map
3i6cA	1	0.5699	15.4	0.899	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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