MadL - PFAM28P - GREMLIN Contacts

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MadL - Malonate transporter MadL subunit

PFAM:	PF03817	Sequences: MIIYGVALLAFCMLLGVFLGDLLGVLLGVKANVGGVGIAMLLLILASNYLRKRGLLSPPTESGILFWSAMYIPIVVAMAAQQNVVAALSGGPVAILAGVLAVVVCFALVPLLSRIGK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	117 (116)
Sequences:	967 (581)
Seq/√Len:	53.9
META:	0.82

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
21_D	32_N	4.752	1.00
49_Y	53_R	3.036	1.00
38_I	79_A	2.832	1.00
108_L	111_L	2.586	1.00
89_S	92_P	2.500	1.00
21_D	29_V	2.458	1.00
62_S	65_L	2.455	1.00
15_L	42_L	2.168	1.00
22_L	26_L	2.146	1.00
86_A	90_G	1.937	1.00
69_A	101_A	1.919	1.00
59_P	105_C	1.893	0.99
13_M	17_V	1.882	0.99
2_I	31_A	1.849	0.99
50_L	54_G	1.846	0.99
56_L	61_E	1.834	0.99
79_A	97_A	1.819	0.99
18_F	22_L	1.761	0.99
27_L	33_V	1.695	0.99
41_L	86_A	1.679	0.99
41_L	45_L	1.671	0.99
12_C	42_L	1.624	0.98
2_I	6_V	1.611	0.98
11_F	46_A	1.596	0.98
103_V	107_A	1.524	0.98
15_L	46_A	1.516	0.97
107_A	110_P	1.510	0.97
101_A	105_C	1.491	0.97
6_V	66_F	1.457	0.97
65_L	69_A	1.445	0.97
17_V	32_N	1.394	0.96
29_V	33_V	1.371	0.95
45_L	48_N	1.343	0.95
95_I	99_V	1.304	0.94
72_I	86_A	1.291	0.94
57_S	60_T	1.288	0.94
6_V	13_M	1.286	0.94
58_P	61_E	1.252	0.93
48_N	68_S	1.247	0.92
7_A	10_A	1.242	0.92
60_T	65_L	1.223	0.92
98_G	110_P	1.213	0.91
13_M	81_Q	1.176	0.90
50_L	55_L	1.162	0.89
9_L	14_L	1.152	0.89
102_V	108_L	1.132	0.88
51_R	61_E	1.109	0.87
11_F	15_L	1.107	0.87
82_Q	85_V	1.105	0.87
46_A	49_Y	1.078	0.86
19_L	68_S	1.028	0.83
76_V	86_A	1.026	0.83
52_K	58_P	1.014	0.82
98_G	101_A	1.011	0.82
8_L	116_G	1.005	0.81
45_L	88_L	0.997	0.81
68_S	110_P	0.996	0.81
48_N	52_K	0.996	0.81
72_I	78_M	0.995	0.81
21_D	30_K	0.989	0.80
9_L	67_W	0.989	0.80
66_F	70_M	0.988	0.80
47_S	79_A	0.972	0.79
17_V	27_L	0.967	0.79
96_L	99_V	0.948	0.77
24_G	83_N	0.931	0.76
19_L	42_L	0.927	0.76
13_M	74_I	0.926	0.76
83_N	113_S	0.924	0.75
29_V	74_I	0.923	0.75
69_A	75_V	0.917	0.75
8_L	74_I	0.899	0.73
41_L	44_I	0.895	0.73
42_L	76_V	0.895	0.73
104_V	108_L	0.894	0.73
1_M	5_G	0.890	0.73
38_I	47_S	0.886	0.72
47_S	69_A	0.884	0.72
6_V	57_S	0.881	0.72
6_V	21_D	0.861	0.70
104_V	107_A	0.856	0.70
21_D	112_L	0.853	0.69
11_F	75_V	0.852	0.69
98_G	106_F	0.852	0.69
15_L	22_L	0.852	0.69
7_A	75_V	0.841	0.68
17_V	75_V	0.839	0.68
27_L	66_F	0.828	0.67
70_M	109_V	0.824	0.67
89_S	93_V	0.815	0.66
16_G	20_G	0.813	0.66
23_L	27_L	0.794	0.64
55_L	59_P	0.793	0.64
51_R	115_I	0.793	0.64
6_V	9_L	0.788	0.63
21_D	25_V	0.782	0.63
27_L	70_M	0.760	0.61
29_V	69_A	0.757	0.60
25_V	30_K	0.755	0.60
92_P	96_L	0.750	0.59
18_F	25_V	0.750	0.59
49_Y	52_K	0.749	0.59
53_R	86_A	0.749	0.59
19_L	95_I	0.727	0.57
31_A	102_V	0.726	0.57
8_L	80_A	0.725	0.57
99_V	105_C	0.715	0.56
97_A	102_V	0.714	0.56
81_Q	92_P	0.708	0.55
74_I	93_V	0.701	0.54
54_G	92_P	0.699	0.54
49_Y	61_E	0.699	0.54
90_G	95_I	0.696	0.54
92_P	95_I	0.690	0.53
50_L	56_L	0.689	0.53
46_A	50_L	0.686	0.53
61_E	93_V	0.679	0.52
2_I	85_V	0.676	0.52
42_L	45_L	0.665	0.51
110_P	113_S	0.657	0.50
86_A	100_L	0.645	0.48
83_N	86_A	0.642	0.48
80_A	97_A	0.624	0.46
109_V	113_S	0.622	0.46
90_G	101_A	0.616	0.45
51_R	54_G	0.616	0.45
1_M	4_Y	0.615	0.45
72_I	113_S	0.614	0.45
38_I	101_A	0.606	0.44
46_A	55_L	0.605	0.44
10_A	47_S	0.603	0.44
2_I	69_A	0.593	0.43
66_F	116_G	0.591	0.43
81_Q	85_V	0.589	0.43
32_N	67_W	0.583	0.42
25_V	41_L	0.583	0.42
66_F	113_S	0.581	0.42
13_M	102_V	0.578	0.41
15_L	18_F	0.578	0.41
8_L	107_A	0.573	0.41
54_G	105_C	0.573	0.41
1_M	7_A	0.572	0.41
62_S	69_A	0.572	0.41
33_V	57_S	0.565	0.40
48_N	105_C	0.564	0.40
4_Y	60_T	0.563	0.40
38_I	81_Q	0.563	0.40
14_L	42_L	0.557	0.39
41_L	62_S	0.556	0.39
12_C	40_M	0.554	0.39
94_A	108_L	0.552	0.39
97_A	101_A	0.550	0.39
33_V	85_V	0.549	0.38
3_I	70_M	0.544	0.38
50_L	59_P	0.543	0.38
60_T	94_A	0.542	0.38
56_L	60_T	0.536	0.37
74_I	98_G	0.535	0.37
44_I	90_G	0.534	0.37
109_V	112_L	0.534	0.37
57_S	72_I	0.530	0.37
99_V	106_F	0.526	0.36
45_L	62_S	0.526	0.36
6_V	67_W	0.524	0.36
17_V	74_I	0.515	0.35
22_L	88_L	0.512	0.35
25_V	74_I	0.511	0.35
11_F	14_L	0.509	0.34
70_M	93_V	0.506	0.34
59_P	65_L	0.504	0.34
75_V	84_V	0.503	0.34
33_V	64_I	0.501	0.34
95_I	114_R	0.501	0.34
14_L	31_A	0.500	0.34

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
2m20A	2	0.3846	13.9	0.943	Contact Map
4djkA	2	0.4615	7.7	0.949	Contact Map
2wswA	3	0.5641	3.6	0.956	Contact Map
2qjyC	2	0.265	3.2	0.957	Contact Map
4i0uA	4	0.4615	3.2	0.957	Contact Map
4qncA	2	0.2991	2.7	0.959	Contact Map
4p6vB	1	0.3675	2.5	0.96	Contact Map
4ev6A	3	0.4786	2.5	0.96	Contact Map
3j9tb	1	0	2.4	0.96	Contact Map
2l9uA	2	0.2564	1.9	0.962	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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