GvpK - PFAM28P - GREMLIN Contacts

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GvpK - Gas vesicle protein K

PFAM:	PF05121	Sequences: RINADPEDVERGLAQLVLTLVELLRQLMERQAIRRMEGGTLTDEEIERLGLALMRLEERMEELKERFGLTPEDLNLDLGPLGRLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (83)
Sequences:	4028 (1572)
Seq/√Len:	172.6
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_K	71_P	4.852	1.00
77_D	83_R	3.208	1.00
45_E	48_R	2.980	1.00
59_R	62_E	2.902	1.00
61_E	64_K	2.888	1.00
51_L	55_R	2.850	1.00
42_T	45_E	2.433	1.00
61_E	71_P	1.943	1.00
44_E	48_R	1.857	1.00
55_R	58_E	1.857	1.00
22_E	25_R	1.852	1.00
27_L	30_R	1.766	1.00
12_G	15_Q	1.763	1.00
14_A	67_F	1.602	1.00
5_D	8_D	1.567	1.00
14_A	66_R	1.521	1.00
8_D	12_G	1.399	1.00
60_M	64_K	1.386	1.00
22_E	56_L	1.372	1.00
33_I	36_M	1.350	1.00
21_V	60_M	1.346	1.00
41_L	46_I	1.316	1.00
25_R	56_L	1.303	1.00
62_E	66_R	1.294	1.00
52_A	59_R	1.239	1.00
47_E	51_L	1.202	1.00
43_D	46_I	1.190	1.00
10_E	14_A	1.174	1.00
36_M	46_I	1.161	1.00
36_M	53_L	1.144	1.00
55_R	59_R	1.134	1.00
54_M	57_E	1.130	1.00
26_Q	30_R	1.124	1.00
17_V	20_L	1.112	1.00
20_L	23_L	1.103	1.00
9_V	52_A	1.075	1.00
53_L	56_L	1.072	1.00
14_A	21_V	1.070	1.00
28_M	53_L	1.055	1.00
59_R	66_R	1.053	1.00
28_M	38_G	1.036	0.99
15_Q	19_T	1.010	0.99
35_R	45_E	0.980	0.99
57_E	61_E	0.975	0.99
39_G	43_D	0.974	0.99
22_E	26_Q	0.959	0.99
77_D	82_G	0.926	0.99
4_A	8_D	0.915	0.99
69_L	73_D	0.907	0.99
23_L	75_N	0.903	0.98
65_E	70_T	0.901	0.98
20_L	24_L	0.875	0.98
33_I	37_E	0.873	0.98
6_P	9_V	0.868	0.98
79_G	82_G	0.866	0.98
40_T	53_L	0.864	0.98
32_A	49_L	0.833	0.97
49_L	53_L	0.832	0.97
19_T	23_L	0.821	0.97
32_A	50_G	0.812	0.97
75_N	79_G	0.790	0.96
75_N	82_G	0.788	0.96
10_E	59_R	0.767	0.96
76_L	79_G	0.746	0.95
22_E	53_L	0.744	0.95
61_E	65_E	0.742	0.95
25_R	53_L	0.739	0.95
2_I	12_G	0.733	0.95
29_E	34_R	0.724	0.94
39_G	42_T	0.721	0.94
77_D	80_P	0.712	0.94
26_Q	75_N	0.693	0.93
38_G	46_I	0.693	0.93
25_R	60_M	0.692	0.93
18_L	25_R	0.686	0.93
28_M	32_A	0.682	0.92
13_L	21_V	0.681	0.92
54_M	66_R	0.680	0.92
2_I	13_L	0.678	0.92
4_A	12_G	0.676	0.92
26_Q	57_E	0.673	0.92
12_G	28_M	0.673	0.92
38_G	83_R	0.670	0.92
7_E	11_R	0.659	0.91
31_Q	52_A	0.656	0.91
30_R	59_R	0.652	0.91
8_D	11_R	0.628	0.89
57_E	71_P	0.628	0.89
75_N	84_L	0.628	0.89
6_P	55_R	0.621	0.88
45_E	49_L	0.619	0.88
13_L	60_M	0.582	0.85
43_D	61_E	0.577	0.84
48_R	68_G	0.574	0.84
76_L	80_P	0.572	0.84
48_R	51_L	0.572	0.84
14_A	20_L	0.567	0.83
11_R	68_G	0.566	0.83
66_R	70_T	0.560	0.83
64_K	69_L	0.554	0.82
58_E	61_E	0.553	0.82
4_A	19_T	0.551	0.82
22_E	60_M	0.550	0.81
25_R	31_Q	0.544	0.81
51_L	54_M	0.541	0.80
48_R	70_T	0.540	0.80
63_L	70_T	0.537	0.80
30_R	34_R	0.532	0.79
2_I	10_E	0.532	0.79
37_E	40_T	0.531	0.79
10_E	21_V	0.530	0.79
16_L	19_T	0.526	0.78
5_D	9_V	0.526	0.78
39_G	44_E	0.525	0.78
19_T	75_N	0.520	0.78
18_L	21_V	0.520	0.78
15_Q	74_L	0.519	0.78
77_D	81_L	0.517	0.77
38_G	49_L	0.516	0.77
19_T	64_K	0.510	0.76
39_G	63_L	0.508	0.76
6_P	48_R	0.502	0.75
63_L	66_R	0.500	0.75
3_N	8_D	0.500	0.75

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
4gofA	2	0.6118	32.2	0.885	Contact Map
4asvA	2	0.7294	31.6	0.885	Contact Map
4cpgA	2	0.7059	30.1	0.887	Contact Map
3zdmA	4	0.7176	24.7	0.891	Contact Map
2l0kA	1	0.5647	14.1	0.903	Contact Map
3lsgA	2	0.8706	12.8	0.905	Contact Map
3mn2A	1	0.9176	11.5	0.907	Contact Map
3oouA	1	0.9059	10.6	0.908	Contact Map
4qu2A	2	0.5529	8.1	0.913	Contact Map
3qx3A	2	0.9647	7.9	0.913	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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