DUF3077 - PFAM28P - GREMLIN Contacts

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DUF3077 - Protein of unknown function (DUF3077)

PFAM:	PF11275	Sequences: TIGLTPFGYCGNSDQPLFRVNPGVPLEDALEHASDLLGCAKALALDAAMEDDTDRLAWAAHYLSEMAKALVDDVVKV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (73)
Sequences:	583 (325)
Seq/√Len:	38.0
META:	0.439

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_S	72_D	3.718	1.00
40_A	64_S	3.398	1.00
68_K	72_D	2.467	1.00
19_R	73_D	2.436	1.00
63_L	66_M	2.247	0.99
44_A	60_A	2.184	0.99
8_G	32_H	1.990	0.99
18_F	71_V	1.820	0.98
32_H	36_L	1.798	0.97
51_D	54_D	1.750	0.97
48_A	57_A	1.739	0.97
17_L	24_V	1.650	0.96
43_L	62_Y	1.593	0.95
31_E	63_L	1.491	0.92
47_A	56_L	1.425	0.91
59_A	63_L	1.392	0.89
15_Q	27_E	1.306	0.86
39_C	59_A	1.289	0.85
30_L	71_V	1.286	0.85
39_C	43_L	1.275	0.85
7_F	70_L	1.268	0.84
60_A	63_L	1.233	0.83
43_L	59_A	1.212	0.82
31_E	64_S	1.187	0.80
30_L	74_V	1.171	0.79
48_A	53_T	1.163	0.79
58_W	61_H	1.157	0.79
32_H	52_D	1.142	0.78
39_C	49_M	1.098	0.75
41_K	67_A	1.093	0.74
23_G	26_L	1.093	0.74
71_V	75_V	1.053	0.72
23_G	73_D	1.051	0.71
35_D	70_L	1.046	0.71
63_L	73_D	1.042	0.71
32_H	61_H	1.007	0.68
41_K	65_E	1.006	0.68
54_D	58_W	1.002	0.68
9_Y	39_C	0.999	0.68
34_S	50_E	0.995	0.67
40_A	67_A	0.973	0.65
24_V	29_A	0.972	0.65
16_P	39_C	0.956	0.64
21_N	72_D	0.946	0.63
41_K	64_S	0.945	0.63
20_V	23_G	0.939	0.63
4_L	11_G	0.917	0.61
32_H	39_C	0.903	0.60
17_L	26_L	0.894	0.59
3_G	62_Y	0.892	0.59
20_V	70_L	0.892	0.59
5_T	9_Y	0.887	0.58
46_D	61_H	0.858	0.56
22_P	73_D	0.858	0.56
17_L	53_T	0.843	0.54
62_Y	66_M	0.821	0.52
5_T	16_P	0.810	0.51
44_A	66_M	0.803	0.51
30_L	65_E	0.792	0.50
4_L	67_A	0.791	0.50
21_N	28_D	0.790	0.50
41_K	71_V	0.788	0.49
40_A	55_R	0.784	0.49
22_P	71_V	0.780	0.49
44_A	61_H	0.779	0.49
30_L	48_A	0.773	0.48
49_M	58_W	0.769	0.48
34_S	68_K	0.768	0.48
29_A	33_A	0.760	0.47
57_A	61_H	0.757	0.47
62_Y	68_K	0.751	0.46
47_A	57_A	0.740	0.45
55_R	63_L	0.718	0.43
6_P	11_G	0.716	0.43
6_P	19_R	0.711	0.43
14_D	63_L	0.701	0.42
52_D	56_L	0.696	0.41
18_F	40_A	0.681	0.40
59_A	66_M	0.655	0.38
65_E	72_D	0.647	0.37
19_R	66_M	0.644	0.37
67_A	75_V	0.632	0.36
7_F	31_E	0.632	0.36
25_P	55_R	0.616	0.35
5_T	11_G	0.615	0.35
34_S	54_D	0.614	0.34
10_C	75_V	0.611	0.34
32_H	65_E	0.610	0.34
13_S	20_V	0.608	0.34
69_A	73_D	0.607	0.34
39_C	72_D	0.599	0.33
13_S	69_A	0.592	0.33
8_G	38_G	0.587	0.32
46_D	55_R	0.584	0.32
4_L	9_Y	0.577	0.32
6_P	10_C	0.576	0.31
21_N	65_E	0.572	0.31
10_C	31_E	0.572	0.31
5_T	8_G	0.570	0.31
18_F	33_A	0.566	0.31
56_L	59_A	0.562	0.30
20_V	26_L	0.559	0.30
3_G	73_D	0.547	0.29
12_N	26_L	0.539	0.29
71_V	74_V	0.538	0.29
10_C	70_L	0.515	0.27
4_L	10_C	0.511	0.27
32_H	40_A	0.511	0.27
51_D	67_A	0.507	0.26
35_D	58_W	0.500	0.26

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
2ztjA	2	0.8701	7.9	0.905	Contact Map
1vjeA	2	0.961	7.6	0.906	Contact Map
1j98A	2	0.961	6.9	0.908	Contact Map
3ewbX	2	0.987	6	0.91	Contact Map
3rmjA	2	0.987	5.9	0.911	Contact Map
1j6xA	2	0.961	5.8	0.911	Contact Map
1j6wA	2	0.974	5.5	0.912	Contact Map
1ub0A	2	0.7013	4.9	0.914	Contact Map
4xchA	4	0.974	4.8	0.915	Contact Map
4yt2A	2	0.974	4.7	0.915	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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