DUF3297 - PFAM28P - GREMLIN Contacts

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DUF3297 - Protein of unknown function (DUF3297)

PFAM:	PF11730	Sequences: PDRLSVDPRSPHYDAAVLERGVGIRFNGVERTNVEEYCVSEGWVRVAAGKTLDRKGNPLTIKLKGKVEPYF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	71 (71)
Sequences:	3420 (635)
Seq/√Len:	75.4
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
48_A	51_T	3.159	1.00
27_N	66_K	2.705	1.00
24_I	69_P	2.579	1.00
9_R	57_N	2.390	1.00
16_A	19_E	2.388	1.00
39_V	69_P	2.363	1.00
7_D	57_N	2.355	1.00
52_L	55_K	2.320	1.00
29_V	33_N	2.181	1.00
45_R	62_K	1.971	1.00
15_A	19_E	1.933	1.00
46_V	63_L	1.846	1.00
20_R	71_F	1.834	1.00
17_V	21_G	1.771	1.00
51_T	59_L	1.726	1.00
28_G	66_K	1.645	1.00
35_E	47_A	1.499	0.99
45_R	60_T	1.415	0.99
17_V	20_R	1.407	0.99
25_R	68_E	1.400	0.99
52_L	57_N	1.394	0.99
34_V	44_V	1.326	0.98
26_F	44_V	1.250	0.97
51_T	55_K	1.234	0.97
49_G	60_T	1.227	0.97
13_Y	19_E	1.206	0.96
17_V	71_F	1.172	0.96
7_D	35_E	1.096	0.94
27_N	64_K	1.089	0.94
33_N	61_I	1.081	0.93
6_V	18_L	1.032	0.92
24_I	30_E	1.028	0.92
24_I	46_V	1.020	0.91
6_V	35_E	0.962	0.89
29_V	32_T	0.945	0.88
33_N	46_V	0.945	0.88
14_D	18_L	0.939	0.88
50_K	59_L	0.935	0.87
14_D	17_V	0.932	0.87
53_D	57_N	0.911	0.86
3_R	38_C	0.881	0.84
31_R	63_L	0.862	0.83
26_F	31_R	0.852	0.82
48_A	61_I	0.850	0.82
35_E	57_N	0.845	0.81
42_G	64_K	0.826	0.80
47_A	52_L	0.814	0.79
66_K	69_P	0.804	0.78
24_I	27_N	0.803	0.78
66_K	70_Y	0.797	0.77
3_R	12_H	0.791	0.77
47_A	58_P	0.783	0.76
55_K	59_L	0.739	0.72
14_D	20_R	0.739	0.72
35_E	45_R	0.738	0.72
58_P	63_L	0.735	0.72
18_L	21_G	0.727	0.71
5_S	15_A	0.725	0.70
47_A	60_T	0.714	0.69
3_R	17_V	0.713	0.69
2_D	38_C	0.712	0.69
48_A	60_T	0.710	0.69
30_E	70_Y	0.707	0.69
44_V	63_L	0.701	0.68
52_L	58_P	0.689	0.67
31_R	46_V	0.680	0.66
6_V	13_Y	0.676	0.65
25_R	70_Y	0.676	0.65
47_A	50_K	0.674	0.65
48_A	52_L	0.673	0.65
59_L	64_K	0.671	0.65
33_N	38_C	0.667	0.64
5_S	47_A	0.666	0.64
7_D	10_S	0.657	0.63
28_G	31_R	0.638	0.61
6_V	17_V	0.638	0.61
18_L	22_V	0.622	0.59
14_D	69_P	0.609	0.57
30_E	47_A	0.605	0.57
46_V	61_I	0.601	0.56
5_S	11_P	0.596	0.55
6_V	22_V	0.595	0.55
26_F	63_L	0.593	0.55
39_V	67_V	0.591	0.55
50_K	53_D	0.587	0.54
32_T	49_G	0.572	0.52
49_G	52_L	0.569	0.52
40_S	60_T	0.567	0.52
19_E	35_E	0.561	0.51
6_V	9_R	0.561	0.51
8_P	13_Y	0.559	0.51
29_V	55_K	0.559	0.51
1_P	4_L	0.557	0.51
24_I	29_V	0.556	0.50
22_V	32_T	0.554	0.50
44_V	64_K	0.553	0.50
2_D	40_S	0.549	0.50
3_R	40_S	0.541	0.49
30_E	34_V	0.538	0.48
35_E	38_C	0.534	0.48
38_C	44_V	0.530	0.47
14_D	21_G	0.517	0.46
18_L	55_K	0.515	0.45
42_G	55_K	0.514	0.45
13_Y	16_A	0.509	0.45
13_Y	27_N	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
3e59A	1	0.662	11.9	0.931	Contact Map
2hzmB	1	0.2817	11.4	0.931	Contact Map
1ky9A	5	0.8169	10.6	0.932	Contact Map
4bjpA	2	0.3099	10.5	0.932	Contact Map
3eopA	1	0.8873	10	0.933	Contact Map
1lcyA	3	0.9014	9.7	0.933	Contact Map
3pv2A	6	0.8451	9.1	0.934	Contact Map
1ng7A	2	0.7183	8.7	0.935	Contact Map
4aw7A	1	0.9014	7.7	0.936	Contact Map
2vmhA	1	0.507	7.3	0.937	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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