DUF4357 - PFAM28P - GREMLIN Contacts

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DUF4357 - Domain of unknown function (DUF4357)

PFAM:	PF14267	Sequences: REKLIEDGVLVEEGDKLVFTKDYLFSSPSAAAAVVLGRSANGRTEWKDKDGKTL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	54 (54)
Sequences:	7559 (5706)
Seq/√Len:	776.5
META:	0.916

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_A	40_A	3.350	1.00
9_V	23_Y	2.564	1.00
11_V	20_T	2.379	1.00
9_V	21_K	2.330	1.00
13_E	18_V	2.227	1.00
40_A	45_E	2.161	1.00
36_L	40_A	2.153	1.00
48_D	52_K	2.091	1.00
19_F	35_V	2.090	1.00
3_K	7_D	2.086	1.00
19_F	23_Y	1.919	1.00
27_S	30_A	1.833	1.00
29_S	42_G	1.707	1.00
2_E	6_E	1.665	1.00
25_F	34_V	1.509	1.00
36_L	45_E	1.442	1.00
5_I	17_L	1.360	1.00
28_P	43_R	1.358	1.00
38_R	45_E	1.356	1.00
11_V	18_V	1.353	1.00
26_S	30_A	1.334	1.00
41_N	44_T	1.116	1.00
13_E	16_K	1.044	1.00
10_L	17_L	1.011	1.00
33_A	40_A	1.006	1.00
10_L	19_F	0.984	1.00
12_E	17_L	0.971	1.00
30_A	34_V	0.883	1.00
28_P	54_L	0.883	1.00
12_E	15_D	0.853	1.00
4_L	34_V	0.846	1.00
44_T	53_T	0.835	1.00
33_A	39_S	0.817	1.00
8_G	11_V	0.814	1.00
24_L	36_L	0.797	1.00
2_E	5_I	0.788	1.00
29_S	33_A	0.786	1.00
19_F	34_V	0.783	1.00
4_L	9_V	0.776	1.00
12_E	16_K	0.746	1.00
7_D	21_K	0.734	1.00
1_R	22_D	0.730	1.00
1_R	17_L	0.669	1.00
10_L	35_V	0.661	1.00
3_K	6_E	0.658	1.00
32_A	45_E	0.647	1.00
14_G	18_V	0.647	1.00
30_A	33_A	0.644	1.00
1_R	37_G	0.639	1.00
32_A	36_L	0.638	1.00
23_Y	34_V	0.630	1.00
5_I	12_E	0.629	1.00
21_K	24_L	0.628	1.00
19_F	25_F	0.623	1.00
4_L	23_Y	0.620	1.00
4_L	8_G	0.609	1.00
24_L	35_V	0.598	1.00
29_S	41_N	0.598	1.00
5_I	39_S	0.593	1.00
28_P	41_N	0.584	1.00
33_A	38_R	0.584	1.00
31_A	46_W	0.569	1.00
40_A	44_T	0.561	1.00
30_A	43_R	0.556	1.00
25_F	30_A	0.556	1.00
49_K	52_K	0.555	1.00
27_S	31_A	0.554	1.00
22_D	37_G	0.545	1.00
19_F	22_D	0.531	1.00
17_L	35_V	0.531	1.00
37_G	48_D	0.530	1.00
38_R	44_T	0.526	1.00
35_V	46_W	0.525	1.00
4_L	10_L	0.521	1.00
13_E	20_T	0.519	1.00
36_L	44_T	0.519	1.00
43_R	54_L	0.518	1.00
22_D	34_V	0.504	1.00
33_A	43_R	0.504	1.00
24_L	38_R	0.503	1.00
9_V	19_F	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
4rf6A	1	0.7407	8.9	0.855	Contact Map
1zn6A	1	0.9259	8.9	0.856	Contact Map
3bv4A	2	0.9815	6.5	0.864	Contact Map
2yewB	4	0.963	6.2	0.865	Contact Map
3muuA	3	0.963	6.2	0.865	Contact Map
3j0fE	4	0.963	5.8	0.868	Contact Map
4yiiA	1	0.3704	5.7	0.868	Contact Map
1oh4A	1	0.5556	5.7	0.868	Contact Map
3j0cA	4	0.963	5.7	0.868	Contact Map
3t5xA	1	0.5741	5.5	0.868	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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