DUF3460 - PFAM28P - GREMLIN Contacts

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DUF3460 - Protein of unknown function (DUF3460)

PFAM:	PF11943	Sequences: HYESDHTQFIRELKAKKPELEAEQRAGRALLWDKPIDLEAQAEFREARVPQKPYVYQT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	58 (57)
Sequences:	3156 (1485)
Seq/√Len:	196.7
META:	0.921

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
3_E	11_R	3.465	1.00
12_E	16_K	2.877	1.00
13_L	20_L	2.351	1.00
17_K	23_E	2.110	1.00
14_K	21_E	2.048	1.00
51_Q	55_V	2.043	1.00
19_E	23_E	1.979	1.00
23_E	26_A	1.962	1.00
22_A	26_A	1.789	1.00
44_F	47_A	1.785	1.00
6_H	10_I	1.708	1.00
40_A	44_F	1.640	1.00
37_D	40_A	1.604	1.00
39_E	43_E	1.576	1.00
8_Q	12_E	1.544	1.00
36_I	41_Q	1.523	1.00
3_E	8_Q	1.432	1.00
27_G	30_L	1.398	1.00
41_Q	45_R	1.385	1.00
52_K	57_Q	1.346	1.00
28_R	33_D	1.240	1.00
21_E	25_R	1.208	1.00
20_L	23_E	1.199	1.00
13_L	17_K	1.139	1.00
14_K	24_Q	1.048	1.00
40_A	43_E	1.031	1.00
36_I	40_A	1.028	1.00
42_A	46_E	1.027	1.00
27_G	31_L	1.026	1.00
10_I	14_K	1.021	1.00
19_E	22_A	1.020	1.00
41_Q	44_F	1.019	1.00
17_K	20_L	1.010	1.00
22_A	25_R	0.962	0.99
25_R	31_L	0.952	0.99
38_L	44_F	0.877	0.99
35_P	38_L	0.861	0.99
21_E	24_Q	0.838	0.98
12_E	15_A	0.818	0.98
31_L	36_I	0.795	0.98
7_T	11_R	0.791	0.98
50_P	53_P	0.787	0.98
23_E	27_G	0.766	0.97
41_Q	48_R	0.753	0.97
5_D	9_F	0.752	0.97
49_V	52_K	0.749	0.97
3_E	6_H	0.742	0.97
45_R	48_R	0.734	0.96
53_P	57_Q	0.727	0.96
39_E	42_A	0.727	0.96
26_A	29_A	0.727	0.96
3_E	7_T	0.713	0.96
20_L	55_V	0.713	0.96
49_V	55_V	0.651	0.93
52_K	55_V	0.649	0.93
5_D	8_Q	0.632	0.92
43_E	47_A	0.627	0.92
11_R	15_A	0.624	0.91
6_H	11_R	0.609	0.90
6_H	13_L	0.601	0.90
20_L	30_L	0.600	0.90
7_T	10_I	0.597	0.90
24_Q	27_G	0.594	0.89
42_A	45_R	0.592	0.89
38_L	41_Q	0.587	0.89
38_L	42_A	0.587	0.89
19_E	26_A	0.585	0.89
35_P	41_Q	0.580	0.88
25_R	37_D	0.573	0.88
43_E	46_E	0.568	0.87
14_K	20_L	0.553	0.86
6_H	9_F	0.550	0.85
6_H	14_K	0.538	0.84
28_R	34_K	0.530	0.83
38_L	45_R	0.528	0.83
26_A	34_K	0.528	0.83
6_H	30_L	0.526	0.83
33_D	42_A	0.523	0.83
49_V	57_Q	0.520	0.82
23_E	31_L	0.519	0.82
27_G	34_K	0.518	0.82
24_Q	28_R	0.515	0.82
27_G	57_Q	0.513	0.81
31_L	55_V	0.511	0.81
29_A	34_K	0.503	0.80
13_L	30_L	0.500	0.80

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
1dquA	4	0.9828	7.4	0.893	Contact Map
3kfuF	2	0	6.8	0.895	Contact Map
1geaA	1	0.2759	4.9	0.902	Contact Map
3sgzA	4	0.431	4.8	0.902	Contact Map
4d10F	1	0.4138	4.4	0.905	Contact Map
3dmnA	1	0.8621	4.1	0.906	Contact Map
1odzA	1	0.3793	4.1	0.906	Contact Map
2v62A	1	0.7759	4	0.906	Contact Map
2f6mB	1	0.4655	3.4	0.91	Contact Map
2p22B	2	0.2069	3.3	0.91	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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