MadM - PFAM28P - GREMLIN Contacts

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MadM - Malonate/sodium symporter MadM subunit

PFAM:	PF03818	Sequences: EILEKVLTKNGLVTAFAVVGLIMWLSYWLSKKLTRGRIHGSAIAILIGLVLAYVGGVVT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (59)
Sequences:	1339 (846)
Seq/√Len:	110.1
META:	0.875

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_W	32_K	3.082	1.00
27_Y	40_G	2.767	1.00
12_L	16_F	2.351	1.00
22_I	51_L	2.280	1.00
54_V	58_V	2.207	1.00
50_V	54_V	2.169	1.00
5_K	9_K	2.028	1.00
7_L	14_T	1.971	1.00
16_F	19_V	1.719	1.00
51_L	55_G	1.677	1.00
24_W	28_W	1.638	1.00
29_L	33_L	1.534	1.00
13_V	53_Y	1.503	1.00
4_E	8_T	1.395	1.00
26_S	43_I	1.377	1.00
1_E	4_E	1.289	0.99
25_L	47_I	1.280	0.99
46_L	50_V	1.257	0.99
23_M	27_Y	1.249	0.99
36_G	39_H	1.205	0.99
8_T	11_G	1.198	0.99
13_V	23_M	1.163	0.99
31_K	36_G	1.118	0.98
38_I	46_L	1.099	0.98
5_K	11_G	1.088	0.98
55_G	58_V	1.067	0.98
26_S	44_A	1.053	0.97
18_V	22_I	1.050	0.97
30_S	34_T	1.045	0.97
27_Y	31_K	1.035	0.97
56_G	59_T	1.003	0.97
34_T	39_H	0.987	0.96
22_I	48_G	0.984	0.96
23_M	42_A	0.962	0.96
3_L	14_T	0.957	0.96
47_I	50_V	0.947	0.95
28_W	31_K	0.938	0.95
27_Y	39_H	0.919	0.94
13_V	17_A	0.919	0.94
34_T	48_G	0.891	0.94
5_K	8_T	0.883	0.93
15_A	18_V	0.876	0.93
41_S	53_Y	0.863	0.92
17_A	36_G	0.862	0.92
6_V	9_K	0.862	0.92
14_T	43_I	0.832	0.91
53_Y	57_V	0.823	0.91
22_I	26_S	0.807	0.90
47_I	51_L	0.779	0.88
24_W	27_Y	0.766	0.87
21_L	37_R	0.748	0.86
37_R	46_L	0.746	0.86
19_V	55_G	0.740	0.85
12_L	19_V	0.739	0.85
29_L	47_I	0.728	0.84
17_A	21_L	0.721	0.84
44_A	55_G	0.710	0.83
29_L	34_T	0.703	0.82
15_A	19_V	0.700	0.82
12_L	15_A	0.695	0.81
20_G	39_H	0.678	0.80
30_S	36_G	0.667	0.79
23_M	26_S	0.658	0.78
4_E	46_L	0.632	0.75
17_A	41_S	0.623	0.74
28_W	58_V	0.615	0.73
17_A	39_H	0.614	0.73
7_L	15_A	0.601	0.71
4_E	7_L	0.592	0.70
2_I	5_K	0.589	0.70
14_T	39_H	0.588	0.70
20_G	57_V	0.586	0.69
35_R	53_Y	0.583	0.69
20_G	30_S	0.578	0.68
41_S	45_I	0.577	0.68
21_L	28_W	0.570	0.67
6_V	10_N	0.548	0.64
22_I	47_I	0.543	0.64
1_E	9_K	0.542	0.63
28_W	50_V	0.537	0.63
10_N	38_I	0.525	0.61
20_G	33_L	0.520	0.60
18_V	51_L	0.520	0.60
41_S	54_V	0.515	0.59
9_K	35_R	0.510	0.59
9_K	13_V	0.504	0.58
10_N	14_T	0.501	0.57
3_L	7_L	0.500	0.57

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
4bwzA	2	0.8136	6.9	0.888	Contact Map
4cz8A	2	0.8475	6.8	0.889	Contact Map
3qe7A	2	0.9153	6.3	0.89	Contact Map
2xq2A	2	0.7288	5.2	0.895	Contact Map
3ug9A	2	0.8644	3.9	0.9	Contact Map
4r2fA	1	0	3.7	0.902	Contact Map
3p5nA	2	0.9661	3.6	0.902	Contact Map
4czbA	2	0.8305	3.5	0.903	Contact Map
4mt1A	3	0.8475	3.3	0.904	Contact Map
4a01A	2	1	3.3	0.905	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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