PSD3 - PFAM28P - GREMLIN Contacts

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PSD3 - Protein of unknown function (DUF1587)

PFAM:	PF07626	Sequences: RRLNRAEYANTIRDLLGLDVDPADLLPADDSGYGFDNIADVLSVSPLLLERYLSAAEKIARLAVA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (64)
Sequences:	43359 (18136)
Seq/√Len:	2267.0
META:	0.991

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_A	22_P	2.503	1.00
9_A	23_A	2.482	1.00
9_A	21_D	2.140	1.00
13_R	19_D	2.128	1.00
21_D	24_D	1.962	1.00
8_Y	56_A	1.895	1.00
58_K	62_L	1.829	1.00
44_V	49_L	1.750	1.00
51_R	54_S	1.746	1.00
12_I	59_I	1.663	1.00
18_L	62_L	1.640	1.00
25_L	58_K	1.530	1.00
45_S	48_L	1.508	1.00
32_G	41_V	1.491	1.00
60_A	64_V	1.487	1.00
53_L	57_E	1.457	1.00
47_L	50_E	1.388	1.00
33_Y	38_I	1.368	1.00
44_V	48_L	1.336	1.00
6_A	10_N	1.299	1.00
10_N	14_D	1.297	1.00
33_Y	43_S	1.274	1.00
27_P	51_R	1.273	1.00
16_L	59_I	1.249	1.00
9_A	24_D	1.221	1.00
10_N	13_R	1.192	1.00
8_Y	12_I	1.187	1.00
56_A	60_A	1.173	1.00
2_R	42_L	1.163	1.00
26_L	55_A	1.159	1.00
48_L	52_Y	1.157	1.00
57_E	60_A	1.130	1.00
16_L	63_A	1.072	1.00
6_A	36_D	1.063	1.00
50_E	54_S	1.042	1.00
50_E	53_L	1.022	1.00
58_K	61_R	1.008	1.00
30_D	43_S	0.997	1.00
48_L	51_R	0.987	1.00
28_A	31_S	0.975	1.00
43_S	47_L	0.969	1.00
27_P	48_L	0.968	1.00
5_R	28_A	0.944	1.00
46_P	50_E	0.942	1.00
25_L	55_A	0.921	1.00
8_Y	52_Y	0.908	1.00
54_S	58_K	0.895	1.00
5_R	29_D	0.864	1.00
7_E	37_N	0.861	1.00
9_A	20_V	0.858	1.00
38_I	41_V	0.857	1.00
47_L	51_R	0.854	1.00
5_R	26_L	0.838	1.00
32_G	38_I	0.831	1.00
18_L	21_D	0.784	1.00
57_E	61_R	0.775	1.00
39_A	42_L	0.769	1.00
49_L	53_L	0.735	1.00
40_D	43_S	0.733	1.00
9_A	13_R	0.728	1.00
11_T	14_D	0.718	1.00
5_R	52_Y	0.709	1.00
25_L	54_S	0.707	1.00
2_R	29_D	0.707	1.00
22_P	25_L	0.705	1.00
17_G	20_V	0.695	1.00
43_S	50_E	0.679	1.00
11_T	15_L	0.672	1.00
21_D	25_L	0.672	1.00
20_V	25_L	0.662	1.00
25_L	51_R	0.636	1.00
20_V	62_L	0.635	1.00
3_L	11_T	0.634	1.00
1_R	4_N	0.631	1.00
36_D	39_A	0.626	1.00
30_D	33_Y	0.607	1.00
18_L	53_L	0.598	1.00
37_N	42_L	0.596	1.00
44_V	52_Y	0.596	1.00
1_R	7_E	0.589	1.00
55_A	59_I	0.585	1.00
31_S	43_S	0.583	1.00
38_I	42_L	0.577	1.00
31_S	36_D	0.568	1.00
28_A	33_Y	0.561	1.00
13_R	18_L	0.549	1.00
49_L	52_Y	0.548	1.00
45_S	49_L	0.538	1.00
54_S	57_E	0.534	1.00
29_D	42_L	0.534	1.00
47_L	54_S	0.521	1.00
32_G	40_D	0.517	1.00
31_S	37_N	0.516	1.00
33_Y	40_D	0.510	1.00
31_S	34_G	0.508	1.00
4_N	36_D	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
2ijaA	1	0.5385	11.5	0.845	Contact Map
4nv8A	2	0.5538	10.6	0.847	Contact Map
3k9gA	2	0.6615	9.4	0.851	Contact Map
4guzA	2	0.5385	8.7	0.852	Contact Map
3lnbA	1	0.2923	7.8	0.855	Contact Map
3ayfA	2	0.8923	7.6	0.857	Contact Map
3d9wA	2	0.5538	7.4	0.857	Contact Map
2fgyA	2	0.8769	7.1	0.858	Contact Map
1e2tA	5	0.6	6.1	0.862	Contact Map
1w4tA	1	0.5385	5.3	0.867	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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