PE_PPE_C - PFAM28P - GREMLIN Contacts

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PE_PPE_C - Polymorphic PE/PPE proteins C terminal

PFAM:	PF12484	Sequences: SAGLGQAASVGGLSVPPSWAAAAPAARPAAAALPGTGAAAAAAAAGAGLGGMPLAGMAGRGGAGGAAPRYGFRPTVMPRP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	80 (79)
Sequences:	2339 (1780)
Seq/√Len:	200.3
META:	0.681

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
46_G	49_L	2.124	1.00
51_G	56_G	2.028	1.00
34_P	37_G	1.941	1.00
59_G	62_G	1.938	1.00
45_A	48_G	1.854	1.00
34_P	38_A	1.797	1.00
57_M	60_R	1.781	1.00
47_A	50_G	1.738	1.00
57_M	61_G	1.697	1.00
34_P	41_A	1.672	1.00
54_L	60_R	1.669	1.00
28_P	31_A	1.614	1.00
45_A	49_L	1.571	1.00
6_Q	9_S	1.544	1.00
30_A	33_L	1.506	1.00
56_G	62_G	1.505	1.00
46_G	50_G	1.444	1.00
6_Q	17_P	1.412	1.00
27_R	30_A	1.410	1.00
7_A	14_S	1.360	1.00
66_A	69_R	1.343	1.00
55_A	60_R	1.341	1.00
68_P	77_M	1.328	1.00
73_R	79_R	1.324	1.00
71_G	77_M	1.279	1.00
55_A	59_G	1.212	1.00
56_G	60_R	1.199	1.00
38_A	41_A	1.196	1.00
9_S	12_G	1.175	1.00
53_P	56_G	1.166	1.00
39_A	42_A	1.163	1.00
68_P	75_T	1.159	1.00
3_G	6_Q	1.152	1.00
70_Y	76_V	1.150	1.00
3_G	8_A	1.149	1.00
17_P	20_A	1.127	1.00
51_G	62_G	1.122	1.00
65_G	69_R	1.120	1.00
5_G	9_S	1.113	1.00
70_Y	78_P	1.100	1.00
51_G	54_L	1.079	1.00
25_A	28_P	1.077	1.00
70_Y	74_P	1.070	1.00
74_P	77_M	1.060	1.00
35_G	39_A	1.056	1.00
51_G	61_G	1.051	1.00
38_A	43_A	1.042	1.00
68_P	74_P	1.028	1.00
36_T	41_A	1.027	1.00
67_A	75_T	1.001	1.00
44_A	48_G	0.991	1.00
63_A	71_G	0.981	1.00
34_P	44_A	0.964	0.99
75_T	79_R	0.960	0.99
51_G	55_A	0.959	0.99
29_A	32_A	0.953	0.99
29_A	33_L	0.948	0.99
27_R	33_L	0.928	0.99
27_R	32_A	0.928	0.99
6_Q	12_G	0.928	0.99
26_A	30_A	0.914	0.99
65_G	71_G	0.894	0.99
8_A	15_V	0.883	0.99
69_R	72_F	0.877	0.99
54_L	59_G	0.869	0.99
65_G	70_Y	0.869	0.99
67_A	70_Y	0.834	0.98
22_A	25_A	0.834	0.98
55_A	58_A	0.833	0.98
42_A	47_A	0.830	0.98
34_P	40_A	0.828	0.98
58_A	61_G	0.818	0.98
44_A	47_A	0.806	0.98
42_A	46_G	0.802	0.98
71_G	78_P	0.782	0.98
27_R	31_A	0.781	0.98
75_T	78_P	0.772	0.97
34_P	39_A	0.764	0.97
23_A	26_A	0.761	0.97
21_A	32_A	0.759	0.97
35_G	40_A	0.752	0.97
22_A	27_R	0.751	0.97
51_G	60_R	0.741	0.97
65_G	68_P	0.730	0.96
72_F	75_T	0.728	0.96
8_A	32_A	0.719	0.96
69_R	77_M	0.718	0.96
53_P	58_A	0.711	0.96
38_A	42_A	0.710	0.96
37_G	41_A	0.710	0.96
40_A	44_A	0.709	0.96
39_A	44_A	0.694	0.95
36_T	39_A	0.685	0.95
8_A	22_A	0.668	0.94
33_L	44_A	0.667	0.94
36_T	40_A	0.659	0.94
60_R	63_A	0.647	0.93
42_A	49_L	0.632	0.92
71_G	76_V	0.632	0.92
66_A	78_P	0.631	0.92
37_G	46_G	0.629	0.92
7_A	28_P	0.628	0.92
35_G	38_A	0.624	0.92
63_A	75_T	0.616	0.91
54_L	61_G	0.616	0.91
10_V	64_G	0.613	0.91
24_P	27_R	0.573	0.88
21_A	24_P	0.547	0.86
2_A	5_G	0.539	0.85
65_G	77_M	0.538	0.85
41_A	50_G	0.529	0.84
17_P	73_R	0.528	0.84
31_A	46_G	0.524	0.83
26_A	29_A	0.523	0.83
25_A	31_A	0.507	0.81
65_G	75_T	0.506	0.81
55_A	62_G	0.503	0.81
55_A	79_R	0.500	0.80

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
1dnvA	6	0.0875	1.3	0.909	Contact Map
3cp8A	2	0.3125	1	0.914	Contact Map
4jweC	1	0.1	1	0.915	Contact Map
2lkwA	1	0.125	0.9	0.918	Contact Map
3tk2A	1	0.2	0.7	0.923	Contact Map
4mguA	6	0.075	0.7	0.924	Contact Map
4x0qA	1	0.3	0.5	0.931	Contact Map
2al3A	1	0.225	0.5	0.933	Contact Map
3etoA	1	0.3375	0.5	0.933	Contact Map
4illA	2	0.275	0.4	0.935	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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