DUF3716 - PFAM28P - GREMLIN Contacts

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DUF3716 - Protein of unknown function (DUF3716)

PFAM:	PF12511	Sequences: ALLIQARGEVAPQPCTRCAKGRGPFAECVVVPDDPGPGLFGGACANCHWNGQGSRCSLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (53)
Sequences:	526 (457)
Seq/√Len:	62.7
META:	0.517

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
5_Q	45_A	4.756	1.00
11_A	30_V	4.255	1.00
4_I	45_A	3.209	1.00
48_H	51_G	2.229	1.00
50_N	53_G	1.873	1.00
4_I	40_F	1.761	0.99
4_I	31_V	1.710	0.99
3_L	9_E	1.665	0.99
40_F	48_H	1.509	0.98
27_E	46_N	1.440	0.98
1_A	25_F	1.402	0.97
5_Q	27_E	1.346	0.97
4_I	48_H	1.331	0.96
9_E	13_Q	1.275	0.96
17_R	50_N	1.267	0.95
18_C	28_C	1.249	0.95
25_F	49_W	1.207	0.94
10_V	27_E	1.167	0.93
20_K	45_A	1.147	0.92
8_G	15_C	1.131	0.92
2_L	51_G	1.086	0.90
3_L	6_A	1.081	0.90
52_Q	55_R	1.054	0.89
43_A	48_H	1.048	0.88
3_L	58_L	1.042	0.88
10_V	31_V	1.040	0.88
17_R	52_Q	0.983	0.85
17_R	55_R	0.956	0.83
24_P	46_N	0.940	0.82
2_L	10_V	0.923	0.81
5_Q	24_P	0.906	0.80
15_C	18_C	0.882	0.78
23_G	50_N	0.871	0.77
19_A	22_R	0.857	0.76
7_R	29_V	0.856	0.76
50_N	55_R	0.845	0.75
43_A	58_L	0.839	0.74
11_A	14_P	0.826	0.73
10_V	19_A	0.808	0.71
3_L	38_G	0.784	0.69
16_T	19_A	0.782	0.69
18_C	44_C	0.741	0.65
18_C	47_C	0.711	0.62
16_T	22_R	0.708	0.61
44_C	56_C	0.706	0.61
23_G	30_V	0.704	0.61
40_F	51_G	0.677	0.58
13_Q	57_S	0.675	0.58
24_P	51_G	0.674	0.57
13_Q	22_R	0.669	0.57
45_A	49_W	0.667	0.57
9_E	26_A	0.663	0.56
20_K	23_G	0.652	0.55
19_A	39_L	0.649	0.55
41_G	54_S	0.647	0.54
2_L	6_A	0.639	0.53
9_E	43_A	0.625	0.52
39_L	42_G	0.623	0.52
6_A	10_V	0.623	0.52
14_P	29_V	0.613	0.50
6_A	39_L	0.608	0.50
7_R	42_G	0.591	0.48
49_W	54_S	0.590	0.48
37_P	53_G	0.586	0.47
7_R	41_G	0.581	0.47
3_L	51_G	0.573	0.46
16_T	37_P	0.571	0.46
16_T	20_K	0.565	0.45
48_H	53_G	0.561	0.45
38_G	41_G	0.560	0.44
2_L	37_P	0.552	0.43
31_V	45_A	0.538	0.42
8_G	11_A	0.528	0.41
16_T	57_S	0.526	0.41
20_K	50_N	0.519	0.40
4_I	54_S	0.515	0.39
16_T	46_N	0.511	0.39
23_G	46_N	0.510	0.39
15_C	56_C	0.510	0.39
10_V	30_V	0.500	0.38

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
2e84A	1	1	15.9	0.832	Contact Map
2cvcA	1	1	7.7	0.854	Contact Map
3oueA	1	0.8305	5.9	0.862	Contact Map
3ov0A	3	0.8305	5.6	0.864	Contact Map
1ofwA	2	1	3.6	0.875	Contact Map
1f4sP	1	0.8983	3.6	0.875	Contact Map
1zmeC	2	0.5593	3.5	0.876	Contact Map
1co4A	1	0.4407	3.4	0.877	Contact Map
1z1nX	1	0.8983	3.4	0.877	Contact Map
3ouqA	2	0.8644	2.9	0.881	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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