DUF3072 - PFAM28P - GREMLIN Contacts

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DUF3072 - Protein of unknown function (DUF3072)

PFAM:	PF11272	Sequences: TEKDPDDWVTGDEPMTGAQASYLKTLAEEAGEEDAFDEDLTKAEASKRIDELQEKTGR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (55)
Sequences:	3937 (1231)
Seq/√Len:	166.0
META:	0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_R	51_E	3.412	1.00
6_D	47_K	3.280	1.00
15_M	20_A	2.541	1.00
32_E	55_K	2.328	1.00
24_K	36_F	2.171	1.00
24_K	28_E	1.936	1.00
44_E	47_K	1.931	1.00
20_A	24_K	1.883	1.00
32_E	48_R	1.776	1.00
27_A	36_F	1.653	1.00
18_A	28_E	1.573	1.00
30_A	56_T	1.572	1.00
4_D	7_D	1.540	1.00
23_L	26_L	1.513	1.00
20_A	38_E	1.476	1.00
53_Q	58_R	1.395	1.00
21_S	25_T	1.374	1.00
53_Q	56_T	1.338	1.00
2_E	9_V	1.257	1.00
10_T	13_E	1.135	1.00
17_G	21_S	1.115	1.00
29_E	56_T	1.092	1.00
12_D	41_T	1.083	1.00
15_M	36_F	1.080	1.00
24_K	38_E	1.075	1.00
22_Y	53_Q	1.013	0.99
22_Y	46_S	1.009	0.99
25_T	29_E	1.005	0.99
32_E	51_E	0.978	0.99
42_K	46_S	0.965	0.99
22_Y	25_T	0.956	0.99
8_W	42_K	0.928	0.99
51_E	55_K	0.915	0.98
46_S	50_D	0.914	0.98
20_A	36_F	0.893	0.98
3_K	9_V	0.883	0.98
13_E	42_K	0.860	0.98
36_F	39_D	0.856	0.98
41_T	44_E	0.852	0.97
44_E	48_R	0.829	0.97
24_K	27_A	0.807	0.96
9_V	28_E	0.775	0.96
36_F	48_R	0.773	0.96
48_R	52_L	0.736	0.94
16_T	19_Q	0.729	0.94
11_G	40_L	0.723	0.94
2_E	6_D	0.696	0.92
7_D	28_E	0.689	0.92
29_E	58_R	0.682	0.92
18_A	21_S	0.676	0.91
46_S	53_Q	0.662	0.90
10_T	56_T	0.658	0.90
21_S	50_D	0.648	0.89
15_M	40_L	0.636	0.88
13_E	16_T	0.632	0.88
23_L	40_L	0.609	0.86
22_Y	42_K	0.608	0.86
18_A	50_D	0.607	0.86
27_A	32_E	0.605	0.86
8_W	13_E	0.604	0.86
43_A	50_D	0.598	0.85
13_E	46_S	0.593	0.85
22_Y	31_G	0.592	0.85
28_E	33_E	0.588	0.84
14_P	26_L	0.585	0.84
27_A	48_R	0.584	0.84
18_A	22_Y	0.582	0.84
36_F	40_L	0.577	0.83
23_L	45_A	0.572	0.83
5_P	18_A	0.565	0.82
15_M	37_D	0.537	0.79
3_K	17_G	0.534	0.78
16_T	49_I	0.534	0.78
13_E	53_Q	0.531	0.78
30_A	53_Q	0.529	0.77
2_E	7_D	0.517	0.76
23_L	36_F	0.516	0.76
2_E	18_A	0.514	0.75
54_E	57_G	0.508	0.75
30_A	55_K	0.504	0.74
20_A	48_R	0.503	0.74
20_A	54_E	0.500	0.73

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
2qt7A	3	0.8621	16.6	0.856	Contact Map
3mfqA	1	0.9828	12.1	0.865	Contact Map
4pzjA	2	0.7586	12	0.865	Contact Map
3j3iA	6	0.931	11.6	0.866	Contact Map
4htiA	1	0.8621	11.5	0.866	Contact Map
1al3A	1	0	11.1	0.867	Contact Map
1ykdA	2	0.7586	11	0.867	Contact Map
1ixcA	4	0.7586	10.5	0.868	Contact Map
2h98A	2	0	10.4	0.869	Contact Map
4r60A	2	0.7586	10	0.87	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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