DUF3019 - PFAM28P - GREMLIN Contacts

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DUF3019 - Protein of unknown function (DUF3019)

PFAM:	PF11456	Sequences: LTVKPRLCVALRQGQTCYTTVRISWQSPEAGSYCLYISDRPEPLRCWENASSGSYSYELESSEDLTFQLRDPDSGQVLASAKVEVAWVAYKYRRRRRRPWRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	102 (102)
Sequences:	847 (664)
Seq/√Len:	65.8
META:	0.78

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_Y	70_R	2.875	1.00
35_L	47_W	2.767	1.00
90_Y	101_R	2.753	1.00
3_V	81_A	2.747	1.00
11_L	18_Y	2.680	1.00
3_V	23_I	2.439	1.00
61_S	65_L	2.436	1.00
37_I	67_F	2.349	1.00
25_W	53_G	2.326	1.00
87_W	101_R	2.226	1.00
5_P	8_C	2.123	1.00
68_Q	77_V	2.094	1.00
87_W	90_Y	1.923	1.00
47_W	53_G	1.889	1.00
96_R	101_R	1.725	1.00
25_W	47_W	1.722	1.00
11_L	87_W	1.605	0.99
14_G	18_Y	1.535	0.99
66_T	80_S	1.525	0.99
1_L	79_A	1.525	0.99
88_V	101_R	1.495	0.99
98_R	101_R	1.485	0.99
33_Y	78_L	1.475	0.98
83_V	98_R	1.434	0.98
57_Y	67_F	1.415	0.98
11_L	14_G	1.396	0.98
25_W	69_L	1.368	0.97
33_Y	61_S	1.365	0.97
4_K	26_Q	1.363	0.97
53_G	69_L	1.326	0.97
67_F	83_V	1.308	0.97
8_C	17_C	1.304	0.97
30_A	51_S	1.287	0.96
3_V	83_V	1.283	0.96
50_A	53_G	1.262	0.96
40_R	64_D	1.220	0.95
96_R	99_P	1.212	0.95
7_L	11_L	1.202	0.95
45_R	53_G	1.190	0.94
37_I	40_R	1.186	0.94
27_S	33_Y	1.183	0.94
24_S	82_K	1.146	0.93
71_D	85_V	1.143	0.93
14_G	87_W	1.137	0.93
68_Q	80_S	1.137	0.93
5_P	17_C	1.124	0.92
15_Q	18_Y	1.094	0.91
32_S	53_G	1.060	0.90
61_S	102_L	1.054	0.90
45_R	52_S	1.043	0.89
59_L	67_F	1.031	0.89
93_R	96_R	1.021	0.88
29_E	78_L	0.983	0.86
1_L	37_I	0.941	0.84
94_R	99_P	0.912	0.82
84_E	94_R	0.903	0.81
37_I	65_L	0.897	0.81
25_W	46_C	0.895	0.80
6_R	10_A	0.894	0.80
44_L	67_F	0.880	0.79
98_R	102_L	0.875	0.79
31_G	71_D	0.871	0.79
59_L	85_V	0.870	0.79
86_A	102_L	0.851	0.77
6_R	16_T	0.839	0.76
22_R	54_S	0.827	0.75
59_L	83_V	0.823	0.75
59_L	92_Y	0.820	0.74
92_Y	98_R	0.819	0.74
72_P	76_Q	0.814	0.74
27_S	47_W	0.813	0.74
28_P	48_E	0.805	0.73
15_Q	98_R	0.799	0.72
18_Y	101_R	0.799	0.72
3_V	21_V	0.797	0.72
18_Y	87_W	0.796	0.72
66_T	82_K	0.793	0.72
94_R	101_R	0.787	0.71
3_V	73_D	0.774	0.70
93_R	101_R	0.773	0.70
2_T	24_S	0.771	0.70
71_D	74_S	0.764	0.69
19_T	83_V	0.760	0.69
45_R	71_D	0.759	0.69
64_D	82_K	0.758	0.68
91_K	96_R	0.756	0.68
22_R	29_E	0.754	0.68
10_A	87_W	0.753	0.68
26_Q	51_S	0.750	0.68
59_L	101_R	0.745	0.67
23_I	67_F	0.741	0.67
39_D	73_D	0.736	0.66
21_V	43_P	0.726	0.65
19_T	81_A	0.725	0.65
26_Q	69_L	0.721	0.65
58_E	101_R	0.721	0.65
75_G	83_V	0.717	0.64
13_Q	18_Y	0.714	0.64
10_A	14_G	0.713	0.64
10_A	32_S	0.706	0.63
7_L	85_V	0.697	0.62
55_Y	63_E	0.694	0.62
50_A	56_S	0.694	0.62
56_S	74_S	0.693	0.61
85_V	97_R	0.684	0.60
36_Y	68_Q	0.680	0.60
22_R	56_S	0.680	0.60
15_Q	19_T	0.656	0.57
17_C	34_C	0.652	0.57
13_Q	19_T	0.649	0.56
60_E	78_L	0.640	0.55
89_A	92_Y	0.637	0.55
4_K	37_I	0.637	0.55
70_R	77_V	0.636	0.55
5_P	34_C	0.628	0.54
93_R	99_P	0.626	0.54
60_E	85_V	0.626	0.54
8_C	34_C	0.624	0.54
93_R	97_R	0.623	0.53
12_R	22_R	0.620	0.53
21_V	36_Y	0.620	0.53
71_D	76_Q	0.620	0.53
1_L	7_L	0.614	0.52
95_R	100_W	0.608	0.52
59_L	88_V	0.597	0.50
12_R	15_Q	0.595	0.50
3_V	6_R	0.588	0.49
20_T	58_E	0.584	0.49
64_D	84_E	0.584	0.49
16_T	60_E	0.583	0.49
33_Y	68_Q	0.582	0.49
15_Q	20_T	0.576	0.48
92_Y	95_R	0.573	0.48
32_S	71_D	0.572	0.47
88_V	102_L	0.565	0.47
7_L	87_W	0.564	0.46
34_C	100_W	0.563	0.46
97_R	102_L	0.555	0.45
46_C	94_R	0.553	0.45
11_L	78_L	0.551	0.45
21_V	92_Y	0.548	0.45
59_L	65_L	0.546	0.44
38_S	94_R	0.544	0.44
25_W	98_R	0.542	0.44
31_G	73_D	0.539	0.44
20_T	56_S	0.533	0.43
27_S	71_D	0.522	0.42
48_E	78_L	0.518	0.41
25_W	78_L	0.512	0.40
7_L	101_R	0.511	0.40
30_A	75_G	0.509	0.40
61_S	83_V	0.500	0.39
3_V	11_L	0.500	0.39

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
4lk4A	1	0.5294	17.4	0.895	Contact Map
2kr0A	1	0.8431	5	0.918	Contact Map
3w5mA	1	0.8039	2.9	0.927	Contact Map
4jjnK	1	0.2549	2.7	0.928	Contact Map
2ifsA	1	0.7549	2.3	0.931	Contact Map
2bc4A	2	0.3725	2	0.933	Contact Map
2eeaA	1	0.8922	2	0.933	Contact Map
1iakA	1	0.2549	1.8	0.935	Contact Map
2d7oA	1	0.951	1.7	0.936	Contact Map
2wv9A	1	0.1961	1.6	0.936	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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