OAD_gamma - PFAM28P - GREMLIN Contacts

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OAD_gamma - Oxaloacetate decarboxylase, gamma chain

PFAM:	PF04277	Sequences: EEGLLLTLLGMGVVFLFLILLVLVIKLMSKIINKFAKKKAAKAAAAAAAAAAAAAAAEEEDDGELVAAIAAAIAAYR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (73)
Sequences:	12101 (9872)
Seq/√Len:	1155.4
META:	0.903

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
22_V	26_K	3.275	1.00
26_K	30_K	3.079	1.00
62_D	65_L	2.723	1.00
23_L	27_L	2.240	1.00
70_A	74_A	2.025	1.00
23_L	26_K	2.021	1.00
2_E	5_L	1.945	1.00
66_V	70_A	1.876	1.00
29_S	33_N	1.874	1.00
61_D	65_L	1.865	1.00
4_L	8_L	1.860	1.00
64_E	68_A	1.852	1.00
28_M	32_I	1.763	1.00
19_I	23_L	1.671	1.00
29_S	32_I	1.660	1.00
21_L	25_I	1.645	1.00
7_T	11_M	1.569	1.00
65_L	68_A	1.559	1.00
17_F	21_L	1.501	1.00
26_K	29_S	1.468	1.00
65_L	69_I	1.405	1.00
65_L	70_A	1.374	1.00
71_A	75_A	1.369	1.00
71_A	74_A	1.343	1.00
19_I	22_V	1.322	1.00
7_T	10_G	1.316	1.00
33_N	36_A	1.266	1.00
3_G	6_L	1.249	1.00
30_K	34_K	1.150	1.00
27_L	30_K	1.141	1.00
17_F	22_V	1.138	1.00
25_I	28_M	1.103	1.00
61_D	64_E	1.100	1.00
69_I	73_I	1.044	1.00
30_K	33_N	1.038	1.00
67_A	71_A	1.036	1.00
68_A	71_A	1.025	1.00
16_L	19_I	1.022	1.00
14_V	18_L	1.022	1.00
34_K	37_K	1.014	1.00
32_I	35_F	0.962	1.00
62_D	66_V	0.949	1.00
61_D	66_V	0.949	1.00
22_V	25_I	0.945	1.00
66_V	71_A	0.929	1.00
11_M	15_F	0.874	1.00
9_L	12_G	0.871	1.00
35_F	39_K	0.866	1.00
35_F	38_K	0.829	1.00
20_L	24_V	0.829	1.00
5_L	9_L	0.823	1.00
42_K	45_A	0.815	1.00
13_V	16_L	0.802	1.00
34_K	38_K	0.798	1.00
31_I	35_F	0.788	1.00
63_G	66_V	0.776	1.00
51_A	55_A	0.773	1.00
67_A	70_A	0.760	1.00
70_A	76_Y	0.750	1.00
50_A	54_A	0.746	1.00
16_L	20_L	0.740	1.00
48_A	51_A	0.732	1.00
9_L	13_V	0.729	1.00
15_F	19_I	0.714	1.00
47_A	50_A	0.713	1.00
6_L	25_I	0.702	1.00
16_L	23_L	0.696	1.00
46_A	49_A	0.692	1.00
64_E	67_A	0.679	1.00
21_L	29_S	0.673	1.00
38_K	42_K	0.673	1.00
45_A	48_A	0.672	1.00
13_V	25_I	0.666	1.00
70_A	73_I	0.666	1.00
13_V	17_F	0.659	1.00
10_G	17_F	0.655	1.00
6_L	28_M	0.649	1.00
63_G	67_A	0.629	1.00
19_I	26_K	0.623	1.00
40_A	43_A	0.623	1.00
45_A	51_A	0.623	1.00
36_A	39_K	0.620	1.00
5_L	8_L	0.617	1.00
4_L	17_F	0.612	1.00
38_K	41_A	0.605	1.00
11_M	17_F	0.578	1.00
4_L	7_T	0.578	1.00
40_A	44_A	0.575	1.00
49_A	55_A	0.572	1.00
24_V	27_L	0.565	1.00
68_A	72_A	0.564	1.00
47_A	52_A	0.563	1.00
52_A	55_A	0.560	1.00
24_V	28_M	0.558	1.00
5_L	25_I	0.555	1.00
60_E	63_G	0.552	1.00
10_G	13_V	0.550	1.00
48_A	52_A	0.546	1.00
42_K	46_A	0.546	1.00
42_K	50_A	0.542	1.00
37_K	40_A	0.538	1.00
49_A	52_A	0.533	1.00
58_E	61_D	0.530	1.00
12_G	19_I	0.519	1.00
41_A	45_A	0.516	1.00
59_E	62_D	0.511	1.00
50_A	53_A	0.502	1.00
53_A	58_E	0.501	1.00
2_E	6_L	0.500	1.00
18_L	25_I	0.500	1.00

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
5a2fA	1	0	28.4	0.801	Contact Map
4ij3C	1	0	14.6	0.826	Contact Map
2kncA	1	0.5974	14.5	0.826	Contact Map
2kogA	1	0.3377	10.3	0.837	Contact Map
2m3eA	1	0.5455	8.1	0.845	Contact Map
3w9iA	3	0.5325	6.6	0.851	Contact Map
4k0jA	3	0.4935	6.5	0.851	Contact Map
4tphA	2	0.4286	6.2	0.853	Contact Map
4um9B	2	0	6	0.854	Contact Map
4dx5A	3	0.5584	5.9	0.854	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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