DUF2973 - PFAM28P - GREMLIN Contacts

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DUF2973 - Protein of unknown function (DUF2973)

PFAM:	PF11189	Sequences: LFPLLYILAFTVLLWLAFRVMIRGLIALSRESQRSSNNSNDRTGRYTIHPELLDKSGNITDEELLTVR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	68 (68)
Sequences:	781 (443)
Seq/√Len:	53.8
META:	0.836

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
41_D	44_G	3.157	1.00
48_I	53_L	2.410	1.00
16_L	19_R	2.189	1.00
63_E	66_T	1.988	1.00
13_L	59_I	1.982	1.00
4_L	11_T	1.852	0.99
54_D	58_N	1.789	0.99
47_T	67_V	1.629	0.98
15_W	20_V	1.613	0.98
7_I	10_F	1.607	0.98
47_T	53_L	1.572	0.98
24_G	28_L	1.509	0.97
42_R	45_R	1.505	0.97
35_S	38_N	1.502	0.97
15_W	19_R	1.437	0.96
63_E	67_V	1.432	0.96
5_L	9_A	1.416	0.96
40_N	58_N	1.399	0.96
26_I	64_L	1.373	0.95
16_L	67_V	1.360	0.95
5_L	36_S	1.321	0.94
10_F	54_D	1.302	0.94
65_L	68_R	1.258	0.93
19_R	60_T	1.248	0.92
41_D	45_R	1.227	0.92
44_G	47_T	1.218	0.91
45_R	48_I	1.198	0.91
27_A	30_R	1.165	0.90
21_M	54_D	1.146	0.89
30_R	33_Q	1.117	0.87
29_S	34_R	1.113	0.87
13_L	17_A	1.108	0.87
3_P	7_I	1.104	0.87
36_S	40_N	1.090	0.86
36_S	39_S	1.087	0.86
22_I	54_D	1.087	0.86
11_T	25_L	1.078	0.85
18_F	31_E	1.069	0.85
6_Y	52_L	1.041	0.83
62_E	65_L	1.040	0.83
48_I	66_T	1.010	0.82
46_Y	55_K	1.001	0.81
46_Y	58_N	0.998	0.81
35_S	39_S	0.996	0.81
35_S	40_N	0.988	0.80
20_V	63_E	0.976	0.79
2_F	15_W	0.962	0.78
7_I	21_M	0.938	0.76
33_Q	68_R	0.935	0.76
54_D	63_E	0.932	0.76
40_N	45_R	0.928	0.76
4_L	33_Q	0.924	0.75
32_S	61_D	0.921	0.75
28_L	31_E	0.866	0.71
34_R	38_N	0.862	0.70
8_L	30_R	0.845	0.69
39_S	42_R	0.819	0.66
13_L	27_A	0.814	0.66
21_M	26_I	0.810	0.65
53_L	65_L	0.803	0.65
1_L	46_Y	0.770	0.61
15_W	60_T	0.765	0.61
24_G	27_A	0.755	0.60
29_S	32_S	0.745	0.59
32_S	37_N	0.740	0.58
37_N	40_N	0.732	0.58
6_Y	15_W	0.727	0.57
4_L	31_E	0.711	0.55
38_N	46_Y	0.692	0.53
20_V	23_R	0.684	0.52
4_L	7_I	0.674	0.51
2_F	18_F	0.671	0.51
60_T	64_L	0.662	0.50
31_E	34_R	0.651	0.49
62_E	68_R	0.643	0.48
7_I	26_I	0.634	0.47
4_L	8_L	0.633	0.47
18_F	22_I	0.632	0.47
17_A	23_R	0.611	0.45
37_N	41_D	0.607	0.44
24_G	65_L	0.606	0.44
30_R	34_R	0.599	0.43
1_L	24_G	0.598	0.43
43_T	47_T	0.586	0.42
24_G	67_V	0.584	0.42
12_V	41_D	0.577	0.41
9_A	55_K	0.573	0.41
39_S	61_D	0.570	0.40
45_R	68_R	0.569	0.40
28_L	32_S	0.565	0.40
20_V	24_G	0.559	0.39
47_T	59_I	0.555	0.39
1_L	26_I	0.547	0.38
4_L	32_S	0.545	0.38
35_S	55_K	0.539	0.37
15_W	18_F	0.534	0.37
6_Y	10_F	0.528	0.36
26_I	56_S	0.525	0.36
10_F	20_V	0.525	0.36
24_G	63_E	0.512	0.35
15_W	59_I	0.503	0.34
6_Y	53_L	0.500	0.34

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
2wadA	1	0.3971	45.6	0.847	Contact Map
4ovdA	2	0.3529	37.2	0.855	Contact Map
4cbcA	3	0.4412	25.6	0.866	Contact Map
4ltoA	3	0.9265	17.8	0.875	Contact Map
3rvyA	3	0.4412	14.7	0.88	Contact Map
2j5lA	1	0	10.4	0.888	Contact Map
4c2mA	1	0.7794	9.7	0.889	Contact Map
1uf2A	7	0.9118	9.4	0.89	Contact Map
3j9pD	4	0.8824	9.1	0.891	Contact Map
3riqA	3	0.8676	6.5	0.898	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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