GlpM - PFAM28P - GREMLIN Contacts

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GlpM - GlpM protein

PFAM:	PF06942	Sequences: LKALLGALVVLLIALLSKSKNYYIAGLVPLFPTFALIAHYIVGSERGAAALRTTALFGLWSLIPYAAYLLAVYYLSDRLSLPLALLGATLAWLVAAAVLILLWSRFH	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	107 (105)
Sequences:	563 (374)
Seq/√Len:	36.5
META:	0.696

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_L	66_A	4.964	1.00
52_R	77_D	4.253	1.00
71_A	91_A	3.452	1.00
39_H	68_Y	2.613	1.00
47_G	50_A	2.496	1.00
72_V	88_A	2.350	1.00
67_A	95_A	2.216	0.99
55_A	72_V	2.182	0.99
67_A	91_A	2.167	0.99
3_A	11_L	2.048	0.99
101_L	105_R	1.881	0.98
90_L	97_A	1.851	0.97
36_L	85_L	1.845	0.97
29_P	65_Y	1.831	0.97
62_L	66_A	1.653	0.95
79_L	84_A	1.632	0.95
61_S	65_Y	1.628	0.95
29_P	34_F	1.595	0.94
58_G	65_Y	1.593	0.94
43_G	81_L	1.523	0.92
28_V	54_T	1.515	0.92
80_S	84_A	1.495	0.92
34_F	38_A	1.480	0.91
46_R	50_A	1.479	0.91
87_G	98_V	1.468	0.91
3_A	7_A	1.323	0.86
75_L	87_G	1.276	0.84
43_G	73_Y	1.268	0.83
72_V	76_S	1.244	0.82
4_L	73_Y	1.240	0.82
36_L	89_T	1.233	0.81
49_A	86_L	1.204	0.80
83_L	87_G	1.194	0.79
5_L	35_A	1.173	0.78
27_L	96_A	1.164	0.77
17_S	56_L	1.154	0.77
15_L	19_S	1.098	0.73
63_I	67_A	1.095	0.73
74_Y	91_A	1.067	0.71
27_L	71_A	1.063	0.71
91_A	95_A	1.050	0.70
80_S	83_L	1.047	0.70
67_A	87_G	1.039	0.69
71_A	75_L	1.027	0.68
59_L	70_L	1.025	0.68
94_V	98_V	1.024	0.68
51_L	68_Y	1.021	0.68
64_P	68_Y	1.018	0.67
44_S	47_G	1.007	0.66
44_S	95_A	1.002	0.66
74_Y	86_L	0.990	0.65
1_L	101_L	0.985	0.65
66_A	84_A	0.984	0.65
58_G	62_L	0.981	0.64
40_Y	85_L	0.977	0.64
24_I	61_S	0.970	0.64
72_V	84_A	0.965	0.63
10_V	58_G	0.963	0.63
65_Y	69_L	0.957	0.62
68_Y	72_V	0.939	0.61
68_Y	81_L	0.929	0.60
1_L	9_V	0.929	0.60
23_Y	31_F	0.924	0.60
67_A	77_D	0.915	0.59
71_A	82_P	0.907	0.58
29_P	33_T	0.902	0.58
23_Y	40_Y	0.894	0.57
48_A	74_Y	0.888	0.57
55_A	59_L	0.868	0.55
71_A	79_L	0.853	0.54
55_A	66_A	0.852	0.54
9_V	45_E	0.848	0.53
20_K	27_L	0.843	0.53
75_L	91_A	0.832	0.52
75_L	88_A	0.819	0.51
30_L	65_Y	0.818	0.51
55_A	84_A	0.818	0.51
38_A	45_E	0.817	0.50
4_L	12_L	0.811	0.50
8_L	74_Y	0.811	0.50
15_L	18_K	0.806	0.49
62_L	94_V	0.796	0.49
11_L	70_L	0.791	0.48
47_G	60_W	0.791	0.48
55_A	80_S	0.788	0.48
16_L	21_N	0.784	0.48
17_S	55_A	0.778	0.47
57_F	64_P	0.778	0.47
43_G	47_G	0.776	0.47
9_V	28_V	0.768	0.46
79_L	87_G	0.768	0.46
40_Y	47_G	0.767	0.46
9_V	18_K	0.753	0.45
99_L	103_W	0.749	0.45
97_A	102_L	0.745	0.44
57_F	61_S	0.735	0.43
6_G	16_L	0.731	0.43
5_L	49_A	0.724	0.42
97_A	100_I	0.719	0.42
34_F	37_I	0.716	0.42
98_V	102_L	0.712	0.41
93_L	104_S	0.707	0.41
7_A	14_A	0.704	0.41
79_L	100_I	0.693	0.40
13_I	30_L	0.689	0.39
62_L	78_R	0.687	0.39
48_A	77_D	0.686	0.39
17_S	38_A	0.682	0.39
39_H	51_L	0.680	0.39
59_L	71_A	0.673	0.38
15_L	104_S	0.670	0.38
10_V	14_A	0.661	0.37
29_P	42_V	0.649	0.36
48_A	97_A	0.649	0.36
3_A	85_L	0.647	0.36
23_Y	72_V	0.646	0.36
10_V	25_A	0.640	0.35
4_L	8_L	0.630	0.35
101_L	104_S	0.630	0.35
56_L	89_T	0.626	0.34
11_L	74_Y	0.613	0.33
25_A	81_L	0.608	0.33
92_W	96_A	0.608	0.33
78_R	94_V	0.607	0.33
8_L	105_R	0.601	0.32
90_L	101_L	0.600	0.32
27_L	67_A	0.600	0.32
44_S	102_L	0.583	0.31
44_S	62_L	0.579	0.31
70_L	83_L	0.577	0.31
87_G	90_L	0.574	0.30
74_Y	83_L	0.573	0.30
28_V	59_L	0.570	0.30
24_I	84_A	0.569	0.30
3_A	40_Y	0.567	0.30
48_A	80_S	0.562	0.29
94_V	102_L	0.561	0.29
90_L	104_S	0.560	0.29
29_P	39_H	0.557	0.29
24_I	48_A	0.554	0.29
4_L	10_V	0.552	0.29
46_R	54_T	0.552	0.29
24_I	86_L	0.550	0.29
27_L	57_F	0.545	0.28
91_A	100_I	0.545	0.28
19_S	34_F	0.544	0.28
21_N	40_Y	0.539	0.28
53_T	86_L	0.539	0.28
39_H	57_F	0.532	0.27
15_L	42_V	0.530	0.27
94_V	105_R	0.522	0.27
31_F	65_Y	0.517	0.26
65_Y	92_W	0.509	0.26
83_L	97_A	0.509	0.26
14_A	38_A	0.506	0.26
49_A	82_P	0.503	0.25
35_A	41_I	0.502	0.25
1_L	90_L	0.500	0.25

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
3rceA	1	0.8879	4	0.927	Contact Map
3zuxA	1	0.9533	3.5	0.929	Contact Map
2xq2A	2	0.9159	3.1	0.931	Contact Map
2gfpA	2	0.8411	2.7	0.933	Contact Map
4n7wA	2	0.9439	2.7	0.933	Contact Map
4ldsA	2	0.785	2.3	0.936	Contact Map
3rkoM	1	0.8972	1.9	0.938	Contact Map
3w4tA	1	0.9626	1.7	0.94	Contact Map
3wdoA	1	0.8598	1.6	0.941	Contact Map
4humA	1	0.972	1.4	0.943	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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