DUF3139 - PFAM28P - GREMLIN Contacts

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DUF3139 - Protein of unknown function (DUF3139)

PFAM:	PF11337	Sequences: MKKIIIIIIILILLIVIGYIGYNPYQYLAKKVDEYLEEKGYKESDIKSIKTKYDSKKGGYYVEVVFKDEPNVTYYY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	76 (75)
Sequences:	507 (434)
Seq/√Len:	50.1
META:	0.412

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_V	66_F	2.561	1.00
32_V	36_L	2.528	1.00
10_I	14_L	2.506	1.00
66_F	70_P	2.262	1.00
69_E	72_V	2.216	1.00
41_Y	64_V	2.149	1.00
41_Y	66_F	2.102	1.00
54_D	58_G	1.934	0.99
69_E	74_Y	1.880	0.99
19_Y	23_N	1.859	0.99
39_K	68_D	1.852	0.99
6_I	45_D	1.802	0.99
41_Y	45_D	1.761	0.99
10_I	13_L	1.759	0.99
67_K	75_Y	1.655	0.98
45_D	68_D	1.512	0.97
51_T	66_F	1.467	0.96
9_I	17_I	1.452	0.96
35_Y	39_K	1.397	0.95
47_K	65_V	1.377	0.94
24_P	29_A	1.354	0.94
7_I	10_I	1.346	0.94
30_K	46_I	1.339	0.94
50_K	75_Y	1.295	0.92
10_I	17_I	1.263	0.91
57_K	62_V	1.230	0.90
51_T	55_S	1.226	0.90
51_T	62_V	1.213	0.90
30_K	34_E	1.201	0.89
54_D	57_K	1.192	0.89
50_K	63_E	1.173	0.88
36_L	41_Y	1.149	0.87
46_I	76_Y	1.148	0.87
65_V	71_N	1.073	0.83
19_Y	24_P	1.065	0.83
18_G	22_Y	1.039	0.81
35_Y	68_D	1.035	0.81
33_D	49_I	1.007	0.79
12_I	71_N	0.995	0.78
8_I	13_L	0.973	0.76
64_V	70_P	0.968	0.76
37_E	73_T	0.950	0.75
4_I	12_I	0.917	0.72
53_Y	59_G	0.911	0.72
43_E	56_K	0.911	0.72
58_G	61_Y	0.910	0.72
11_L	14_L	0.907	0.71
47_K	67_K	0.903	0.71
7_I	52_K	0.900	0.71
36_L	39_K	0.891	0.70
12_I	16_V	0.872	0.68
43_E	51_T	0.868	0.68
49_I	62_V	0.864	0.68
63_E	73_T	0.863	0.67
57_K	60_Y	0.855	0.67
51_T	59_G	0.825	0.64
42_K	61_Y	0.820	0.63
4_I	11_L	0.812	0.63
45_D	48_S	0.806	0.62
37_E	50_K	0.802	0.62
4_I	14_L	0.800	0.62
41_Y	69_E	0.792	0.61
20_I	23_N	0.781	0.60
16_V	71_N	0.777	0.59
11_L	16_V	0.777	0.59
4_I	7_I	0.765	0.58
44_S	67_K	0.760	0.58
34_E	47_K	0.758	0.57
4_I	16_V	0.757	0.57
21_G	24_P	0.743	0.56
32_V	62_V	0.715	0.53
53_Y	57_K	0.713	0.53
38_E	45_D	0.706	0.52
66_F	74_Y	0.699	0.51
63_E	71_N	0.697	0.51
32_V	61_Y	0.697	0.51
41_Y	53_Y	0.691	0.51
3_K	9_I	0.683	0.50
11_L	27_Y	0.675	0.49
23_N	26_Q	0.666	0.48
9_I	15_I	0.654	0.47
35_Y	46_I	0.648	0.46
37_E	72_V	0.646	0.46
54_D	72_V	0.633	0.45
42_K	48_S	0.632	0.45
21_G	26_Q	0.631	0.44
16_V	42_K	0.629	0.44
36_L	69_E	0.624	0.44
40_G	44_S	0.622	0.43
8_I	43_E	0.620	0.43
21_G	25_Y	0.618	0.43
53_Y	56_K	0.606	0.42
10_I	15_I	0.599	0.41
6_I	10_I	0.587	0.40
48_S	70_P	0.584	0.40
7_I	15_I	0.580	0.39
25_Y	29_A	0.568	0.38
53_Y	61_Y	0.567	0.38
42_K	67_K	0.557	0.37
33_D	37_E	0.554	0.37
19_Y	67_K	0.552	0.37
20_I	24_P	0.550	0.36
43_E	47_K	0.548	0.36
5_I	9_I	0.542	0.36
5_I	8_I	0.524	0.34
9_I	20_I	0.522	0.34
57_K	73_T	0.515	0.33
39_K	69_E	0.514	0.33
35_Y	56_K	0.509	0.33
66_F	72_V	0.509	0.33
33_D	43_E	0.502	0.32
19_Y	22_Y	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
2j5lA	1	0	47.7	0.803	Contact Map
1qqhA	2	0.6842	32	0.822	Contact Map
3hvnA	1	0.6053	16.4	0.845	Contact Map
2m8rA	1	0.3421	16.1	0.845	Contact Map
4m1bA	1	0.3553	15.4	0.847	Contact Map
2k3dA	1	0.6447	13.1	0.851	Contact Map
2w3zA	1	0.6184	7.1	0.868	Contact Map
1tueB	1	0.9342	6.9	0.869	Contact Map
2jexA	1	0.9342	6.9	0.869	Contact Map
1pfoA	2	0.6974	5.3	0.876	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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