PSD2 - PFAM28P - GREMLIN Contacts

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PSD2 - Protein of unknown function (DUF1585)

PFAM:	PF07624	Sequences: DGTKFDGPAELRQALLARPDQFVRTLTEKLLTYALGRGLEYYDMPAVRAIVRDAAADDYRFSSLVLGIVKSDPF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	74 (74)
Sequences:	74178 (44860)
Seq/√Len:	5214.8
META:	0.993

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
66_L	70_K	2.583	1.00
53_D	67_G	2.313	1.00
6_D	10_E	2.067	1.00
18_R	21_Q	1.948	1.00
55_A	59_Y	1.892	1.00
49_A	53_D	1.852	1.00
57_D	63_S	1.837	1.00
3_T	17_A	1.803	1.00
24_R	51_V	1.680	1.00
23_V	59_Y	1.637	1.00
25_T	29_K	1.633	1.00
63_S	66_L	1.559	1.00
20_D	55_A	1.506	1.00
46_A	49_A	1.483	1.00
32_T	38_G	1.458	1.00
27_T	51_V	1.458	1.00
7_G	10_E	1.409	1.00
63_S	67_G	1.388	1.00
53_D	70_K	1.354	1.00
60_R	63_S	1.319	1.00
32_T	39_L	1.302	1.00
54_A	64_L	1.289	1.00
5_F	10_E	1.260	1.00
19_P	23_V	1.259	1.00
62_S	66_L	1.250	1.00
5_F	14_A	1.240	1.00
5_F	11_L	1.234	1.00
13_Q	16_L	1.230	1.00
29_K	32_T	1.230	1.00
51_V	55_A	1.229	1.00
67_G	70_K	1.225	1.00
16_L	19_P	1.216	1.00
37_R	43_D	1.216	1.00
9_A	13_Q	1.201	1.00
28_E	39_L	1.111	1.00
8_P	12_R	1.100	1.00
3_T	18_R	1.092	1.00
24_R	48_R	1.089	1.00
53_D	56_A	1.088	1.00
52_R	56_A	1.085	1.00
46_A	73_P	1.078	1.00
45_P	49_A	1.071	1.00
53_D	57_D	1.061	1.00
31_L	39_L	1.046	1.00
57_D	60_R	1.007	1.00
57_D	67_G	0.999	1.00
27_T	64_L	0.987	1.00
49_A	52_R	0.984	1.00
9_A	12_R	0.964	1.00
26_L	61_F	0.949	1.00
39_L	47_V	0.945	1.00
31_L	47_V	0.922	1.00
31_L	68_I	0.917	1.00
44_M	48_R	0.898	1.00
10_E	13_Q	0.895	1.00
28_E	32_T	0.883	1.00
14_A	17_A	0.883	1.00
46_A	72_D	0.880	1.00
52_R	55_A	0.879	1.00
31_L	73_P	0.868	1.00
23_V	51_V	0.861	1.00
24_R	28_E	0.854	1.00
26_L	64_L	0.840	1.00
13_Q	17_A	0.839	1.00
10_E	14_A	0.825	1.00
15_L	22_F	0.819	1.00
28_E	44_M	0.796	1.00
31_L	35_L	0.788	1.00
51_V	54_A	0.783	1.00
66_L	69_V	0.755	1.00
20_D	52_R	0.750	1.00
48_R	52_R	0.748	1.00
21_Q	24_R	0.733	1.00
27_T	50_I	0.728	1.00
30_L	68_I	0.724	1.00
54_A	59_Y	0.720	1.00
20_D	24_R	0.708	1.00
12_R	16_L	0.708	1.00
48_R	51_V	0.703	1.00
3_T	14_A	0.701	1.00
21_Q	25_T	0.687	1.00
54_A	67_G	0.679	1.00
42_Y	46_A	0.676	1.00
47_V	51_V	0.674	1.00
11_L	15_L	0.658	1.00
56_A	59_Y	0.656	1.00
31_L	46_A	0.646	1.00
20_D	23_V	0.644	1.00
53_D	63_S	0.641	1.00
27_T	31_L	0.636	1.00
50_I	67_G	0.620	1.00
54_A	60_R	0.611	1.00
25_T	28_E	0.599	1.00
30_L	65_V	0.594	1.00
14_A	18_R	0.589	1.00
23_V	54_A	0.584	1.00
30_L	34_A	0.582	1.00
69_V	72_D	0.577	1.00
6_D	9_A	0.567	1.00
27_T	47_V	0.561	1.00
61_F	65_V	0.559	1.00
30_L	61_F	0.557	1.00
8_P	11_L	0.557	1.00
35_L	68_I	0.554	1.00
35_L	39_L	0.552	1.00
45_P	48_R	0.546	1.00
22_F	25_T	0.530	1.00
25_T	32_T	0.523	1.00
17_A	20_D	0.517	1.00
32_T	61_F	0.504	1.00
37_R	40_E	0.500	1.00

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
3pruC	1	0.8919	53.4	0.792	Contact Map
3osjA	1	0.8919	48.4	0.798	Contact Map
4rcnA	6	0.9865	33.6	0.816	Contact Map
2ky4A	1	0.8919	32.7	0.817	Contact Map
3nphB	1	0.8108	30.7	0.819	Contact Map
3gf3A	4	0.9865	25.1	0.827	Contact Map
3u9rB	5	0.9865	21.5	0.832	Contact Map
3ohwB	1	0.7432	20.7	0.834	Contact Map
1vrgA	4	0.9865	19.5	0.835	Contact Map
1pixA	4	0.9865	16.2	0.841	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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