PLD_C - PFAM28P - GREMLIN Contacts

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PLD_C - Phospholipase D C terminal

PFAM:	PF12357	Sequences: DDCFLEPESLECVRRVNEIAEENWKLYASEEVTELPGHLLKYPVEVDRDGKVTPLPGCEFFPDTGGKVLGSK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (71)
Sequences:	677 (442)
Seq/√Len:	52.4
META:	0.235

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
17_N	20_A	4.333	1.00
1_D	15_R	4.312	1.00
44_V	69_L	3.022	1.00
16_V	20_A	2.741	1.00
29_S	33_T	2.228	1.00
54_P	69_L	2.219	1.00
32_V	35_L	2.115	1.00
15_R	39_L	1.904	0.99
21_E	41_K	1.825	0.99
47_D	53_T	1.708	0.99
22_E	26_L	1.665	0.98
28_A	31_E	1.592	0.98
17_N	69_L	1.555	0.98
47_D	54_P	1.529	0.97
58_C	68_V	1.524	0.97
29_S	32_V	1.447	0.96
44_V	52_V	1.437	0.96
2_D	49_D	1.286	0.93
22_E	25_K	1.208	0.91
10_L	14_R	1.169	0.89
26_L	40_L	1.155	0.88
14_R	31_E	1.138	0.88
26_L	32_V	1.124	0.87
38_H	56_P	1.120	0.87
32_V	68_V	1.106	0.86
12_C	62_P	1.094	0.86
21_E	45_E	1.028	0.82
2_D	52_V	1.027	0.82
27_Y	56_P	1.009	0.81
2_D	5_L	1.006	0.80
19_I	22_E	1.003	0.80
60_F	64_T	0.997	0.80
23_N	37_G	0.988	0.79
61_F	68_V	0.988	0.79
29_S	71_S	0.981	0.79
20_A	41_K	0.971	0.78
47_D	51_K	0.970	0.78
59_E	67_K	0.967	0.78
23_N	34_E	0.908	0.73
26_L	35_L	0.905	0.73
20_A	39_L	0.889	0.72
48_R	53_T	0.882	0.71
10_L	41_K	0.880	0.71
21_E	59_E	0.875	0.70
23_N	54_P	0.869	0.70
13_V	20_A	0.862	0.69
6_E	22_E	0.859	0.69
38_H	61_F	0.857	0.69
10_L	51_K	0.855	0.69
24_W	42_Y	0.845	0.68
45_E	54_P	0.842	0.67
9_S	25_K	0.835	0.67
54_P	59_E	0.833	0.66
17_N	40_L	0.822	0.65
51_K	71_S	0.804	0.64
10_L	25_K	0.803	0.64
63_D	70_G	0.783	0.62
49_D	69_L	0.775	0.61
19_I	36_P	0.768	0.60
22_E	28_A	0.764	0.60
1_D	34_E	0.756	0.59
9_S	30_E	0.749	0.58
28_A	35_L	0.737	0.57
24_W	35_L	0.734	0.57
8_E	46_V	0.723	0.56
36_P	66_G	0.719	0.55
42_Y	50_G	0.712	0.54
5_L	26_L	0.694	0.53
44_V	55_L	0.694	0.53
1_D	4_F	0.668	0.50
8_E	41_K	0.662	0.49
33_T	40_L	0.657	0.49
10_L	53_T	0.655	0.48
57_G	68_V	0.647	0.48
3_C	29_S	0.647	0.48
39_L	52_V	0.643	0.47
20_A	69_L	0.635	0.46
13_V	56_P	0.620	0.45
5_L	36_P	0.614	0.44
40_L	62_P	0.613	0.44
11_E	47_D	0.611	0.44
13_V	19_I	0.608	0.44
26_L	33_T	0.608	0.44
28_A	40_L	0.607	0.43
13_V	64_T	0.607	0.43
53_T	71_S	0.605	0.43
60_F	65_G	0.594	0.42
42_Y	49_D	0.590	0.42
24_W	28_A	0.576	0.40
22_E	32_V	0.575	0.40
18_E	69_L	0.572	0.40
8_E	37_G	0.570	0.40
17_N	35_L	0.556	0.38
3_C	19_I	0.544	0.37
1_D	18_E	0.534	0.36
14_R	18_E	0.530	0.36
46_V	61_F	0.530	0.36
32_V	36_P	0.528	0.36
18_E	45_E	0.526	0.35
6_E	60_F	0.522	0.35
35_L	40_L	0.509	0.34
24_W	63_D	0.507	0.34
5_L	30_E	0.503	0.33
32_V	58_C	0.501	0.33
44_V	71_S	0.501	0.33
7_P	12_C	0.500	0.33

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
4p78A	2	0.4028	25.6	0.896	Contact Map
3echC	1	0.3194	11.4	0.912	Contact Map
1t62A	2	0.5417	8.3	0.917	Contact Map
4g1gA	2	0.5833	6.5	0.921	Contact Map
3iagC	1	0.7778	6.4	0.921	Contact Map
3gvxA	2	0.5278	5.4	0.924	Contact Map
3mi0A	3	0.375	5.4	0.924	Contact Map
1e5xA	2	0.9028	4.9	0.926	Contact Map
3n7zA	4	0.9861	4.7	0.926	Contact Map
3ln7A	2	1	4.6	0.927	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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