DUF2949 - PFAM28P - GREMLIN Contacts

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DUF2949 - Protein of unknown function (DUF2949)

PFAM:	PF11165	Sequences: YSRLIRFLQEELGLSESSIALALRHSEQEPGPLPMVLWQYGLITLEQLDQIFDWLE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (55)
Sequences:	898 (552)
Seq/√Len:	74.4
META:	0.744

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_I	51_I	5.358	1.00
9_Q	16_E	2.626	1.00
6_R	10_E	2.058	1.00
22_A	36_V	1.762	1.00
15_S	42_L	1.599	0.99
31_G	43_I	1.587	0.99
7_F	50_Q	1.558	0.99
28_Q	39_Q	1.510	0.99
4_L	51_I	1.464	0.99
48_L	52_F	1.451	0.99
15_S	18_S	1.397	0.99
7_F	10_E	1.392	0.98
2_S	20_A	1.379	0.98
34_P	40_Y	1.354	0.98
11_E	19_I	1.344	0.98
22_A	33_L	1.326	0.98
7_F	12_L	1.301	0.98
2_S	17_S	1.282	0.97
42_L	53_D	1.260	0.97
40_Y	48_L	1.242	0.97
18_S	44_T	1.231	0.97
42_L	46_E	1.224	0.97
34_P	38_W	1.204	0.96
14_L	47_Q	1.190	0.96
4_L	54_W	1.161	0.95
49_D	53_D	1.148	0.95
46_E	49_D	1.089	0.93
3_R	6_R	1.075	0.93
8_L	19_I	1.048	0.92
7_F	34_P	1.031	0.91
5_I	19_I	0.994	0.90
22_A	26_S	0.943	0.87
6_R	39_Q	0.931	0.87
22_A	47_Q	0.930	0.87
25_H	56_E	0.922	0.86
4_L	23_L	0.907	0.85
8_L	53_D	0.897	0.85
4_L	34_P	0.884	0.84
22_A	31_G	0.878	0.83
13_G	44_T	0.840	0.81
3_R	21_L	0.838	0.80
22_A	39_Q	0.828	0.80
24_R	29_E	0.817	0.79
26_S	42_L	0.814	0.78
27_E	31_G	0.811	0.78
4_L	25_H	0.772	0.75
29_E	32_P	0.769	0.74
25_H	52_F	0.759	0.73
12_L	51_I	0.750	0.73
22_A	45_L	0.745	0.72
42_L	45_L	0.738	0.71
13_G	33_L	0.735	0.71
9_Q	19_I	0.715	0.69
16_E	56_E	0.703	0.68
34_P	48_L	0.702	0.67
11_E	38_W	0.699	0.67
17_S	20_A	0.683	0.65
14_L	18_S	0.668	0.64
21_L	24_R	0.665	0.63
13_G	16_E	0.658	0.62
2_S	6_R	0.632	0.59
20_A	53_D	0.629	0.59
9_Q	50_Q	0.613	0.57
21_L	29_E	0.599	0.55
8_L	12_L	0.588	0.54
30_P	45_L	0.587	0.54
3_R	12_L	0.584	0.53
35_M	45_L	0.583	0.53
44_T	49_D	0.580	0.53
51_I	54_W	0.578	0.53
16_E	20_A	0.572	0.52
25_H	47_Q	0.561	0.51
2_S	11_E	0.551	0.49
7_F	41_G	0.547	0.49
4_L	22_A	0.531	0.47
39_Q	55_L	0.530	0.47
49_D	52_F	0.528	0.46
44_T	53_D	0.527	0.46
25_H	40_Y	0.519	0.45
27_E	43_I	0.514	0.45
26_S	36_V	0.505	0.44
34_P	49_D	0.500	0.43

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
2d28C	1	0.9464	80.9	0.779	Contact Map
2w84A	1	0.5536	17.1	0.86	Contact Map
3ff5A	2	0.4464	15.1	0.863	Contact Map
2pi2A	1	0	14.8	0.864	Contact Map
3mvaO	1	0.7857	8.8	0.877	Contact Map
4iuwA	1	1	8.1	0.879	Contact Map
4fp9B	2	0.7321	7.8	0.88	Contact Map
3eyiA	1	0.9821	6.6	0.884	Contact Map
4p5wA	2	0.7857	6.4	0.884	Contact Map
4dbgB	1	0.6429	6.2	0.885	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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