DUF3317 - PFAM28P - GREMLIN Contacts

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DUF3317 - Protein of unknown function (DUF3317)

PFAM:	PF11779	Sequences: KNWLQRKYYQYEVTFGLYMLEPWEKFLFNSILLLLLSLLLYAAYVYLPQHIRFI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (51)
Sequences:	534 (364)
Seq/√Len:	50.9
META:	0.309

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_E	25_K	5.733	1.00
11_Y	29_N	4.610	1.00
23_W	27_L	2.349	1.00
6_R	10_Q	2.128	1.00
7_K	10_Q	1.924	0.99
3_W	7_K	1.895	0.99
4_L	8_Y	1.726	0.99
34_L	44_Y	1.649	0.98
8_Y	11_Y	1.629	0.98
21_E	27_L	1.404	0.95
22_P	26_F	1.351	0.94
10_Q	18_Y	1.349	0.94
8_Y	12_E	1.196	0.89
49_Q	52_R	1.187	0.89
42_A	48_P	1.183	0.89
16_G	28_F	1.167	0.88
34_L	37_S	1.140	0.87
15_F	18_Y	1.110	0.86
19_M	50_H	1.099	0.85
2_N	5_Q	1.093	0.85
35_L	40_L	1.022	0.80
13_V	21_E	1.021	0.80
12_E	21_E	0.968	0.77
10_Q	14_T	0.936	0.74
42_A	45_V	0.925	0.73
5_Q	8_Y	0.911	0.72
2_N	19_M	0.904	0.72
13_V	29_N	0.901	0.71
32_L	38_L	0.878	0.69
38_L	42_A	0.863	0.68
36_L	43_A	0.856	0.67
22_P	30_S	0.832	0.65
17_L	25_K	0.825	0.65
19_M	46_Y	0.817	0.64
13_V	18_Y	0.814	0.64
43_A	50_H	0.799	0.62
33_L	37_S	0.786	0.61
36_L	44_Y	0.778	0.60
5_Q	25_K	0.767	0.59
26_F	35_L	0.764	0.59
26_F	31_I	0.749	0.57
6_R	38_L	0.739	0.56
33_L	39_L	0.719	0.54
11_Y	32_L	0.716	0.54
44_Y	52_R	0.696	0.52
38_L	44_Y	0.691	0.51
31_I	41_Y	0.687	0.51
35_L	39_L	0.682	0.50
11_Y	17_L	0.671	0.49
11_Y	49_Q	0.665	0.48
8_Y	35_L	0.654	0.47
32_L	51_I	0.648	0.47
8_Y	36_L	0.648	0.47
26_F	40_L	0.636	0.45
8_Y	29_N	0.626	0.44
36_L	52_R	0.610	0.43
5_Q	23_W	0.607	0.42
6_R	9_Y	0.593	0.41
22_P	40_L	0.590	0.41
19_M	39_L	0.586	0.40
30_S	41_Y	0.586	0.40
3_W	28_F	0.564	0.38
37_S	50_H	0.561	0.38
13_V	36_L	0.550	0.37
32_L	49_Q	0.548	0.37
16_G	19_M	0.547	0.37
17_L	29_N	0.530	0.35
5_Q	14_T	0.529	0.35
42_A	46_Y	0.521	0.34
31_I	40_L	0.518	0.34
44_Y	51_I	0.516	0.34
28_F	42_A	0.509	0.33
16_G	20_L	0.506	0.33
10_Q	28_F	0.506	0.33
14_T	25_K	0.505	0.33
16_G	48_P	0.500	0.32

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
2kixA	3	0.5741	5.1	0.869	Contact Map
4q6xA	1	0.463	3.2	0.881	Contact Map
2kogA	1	0.5926	2.9	0.884	Contact Map
3mk7B	1	0.6111	2.6	0.887	Contact Map
2zxeB	1	0.6296	1.6	0.899	Contact Map
3wguB	1	1	1.4	0.903	Contact Map
3ixzB	1	0.6111	1.4	0.903	Contact Map
2l16A	1	0.6111	1.3	0.905	Contact Map
2mn6B	2	0.5926	1.2	0.906	Contact Map
3spcA	3	0.9074	1	0.912	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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