DUF3126 - PFAM28P - GREMLIN Contacts

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DUF3126 - Protein of unknown function (DUF3126)

PFAM:	PF11324	Sequences: EIAKLQAYLRRLFGNPRIRVVPRPKKDDSAEVYIGEEFIGVLFRDDEDGERSYNFQMAILDID	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	63 (63)
Sequences:	2899 (1227)
Seq/√Len:	154.6
META:	0.94

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_Q	10_R	3.237	1.00
44_R	51_R	3.172	1.00
32_V	55_F	3.075	1.00
21_V	33_Y	2.999	1.00
23_R	29_S	2.361	1.00
8_Y	12_L	2.157	1.00
3_A	6_Q	2.013	1.00
46_D	51_R	1.975	1.00
33_Y	36_E	1.882	1.00
14_G	17_R	1.804	1.00
29_S	41_V	1.617	1.00
34_I	39_I	1.547	1.00
17_R	35_G	1.471	1.00
20_V	30_A	1.457	1.00
15_N	34_I	1.450	1.00
40_G	57_M	1.438	1.00
23_R	41_V	1.401	1.00
32_V	42_L	1.393	1.00
38_F	41_V	1.367	1.00
47_E	50_E	1.349	1.00
23_R	31_E	1.335	1.00
54_N	58_A	1.313	1.00
18_I	34_I	1.299	1.00
7_A	11_R	1.292	1.00
19_R	36_E	1.247	1.00
40_G	55_F	1.188	1.00
1_E	44_R	1.172	1.00
10_R	16_P	1.141	1.00
23_R	28_D	1.121	1.00
10_R	15_N	1.058	0.99
29_S	43_F	1.044	0.99
55_F	59_I	1.020	0.99
51_R	54_N	1.002	0.99
5_L	9_L	0.957	0.98
18_I	32_V	0.932	0.98
31_E	38_F	0.927	0.98
4_K	8_Y	0.890	0.98
26_K	29_S	0.850	0.97
60_L	63_D	0.847	0.97
22_P	25_K	0.816	0.96
46_D	50_E	0.811	0.96
9_L	40_G	0.807	0.96
32_V	39_I	0.799	0.95
38_F	43_F	0.791	0.95
8_Y	11_R	0.790	0.95
3_A	7_A	0.771	0.94
43_F	56_Q	0.765	0.94
1_E	4_K	0.722	0.92
45_D	54_N	0.711	0.92
48_D	52_S	0.688	0.90
31_E	41_V	0.687	0.90
44_R	53_Y	0.686	0.90
26_K	43_F	0.680	0.90
40_G	45_D	0.679	0.90
23_R	43_F	0.677	0.90
44_R	50_E	0.667	0.89
12_L	37_E	0.662	0.89
10_R	18_I	0.659	0.88
1_E	53_Y	0.650	0.88
34_I	40_G	0.639	0.87
45_D	48_D	0.638	0.87
9_L	32_V	0.628	0.86
19_R	33_Y	0.627	0.86
2_I	30_A	0.624	0.86
7_A	16_P	0.616	0.85
51_R	56_Q	0.615	0.85
51_R	61_D	0.608	0.84
11_R	14_G	0.607	0.84
15_N	19_R	0.595	0.83
12_L	34_I	0.595	0.83
37_E	43_F	0.591	0.82
53_Y	62_I	0.573	0.80
14_G	22_P	0.573	0.80
29_S	37_E	0.572	0.80
14_G	19_R	0.571	0.80
44_R	49_G	0.571	0.80
3_A	14_G	0.557	0.78
23_R	42_L	0.545	0.77
28_D	38_F	0.541	0.76
3_A	10_R	0.538	0.76
21_V	24_P	0.535	0.76
50_E	53_Y	0.531	0.75
38_F	57_M	0.528	0.75
11_R	25_K	0.524	0.74
38_F	58_A	0.522	0.74
42_L	55_F	0.522	0.74
2_I	5_L	0.519	0.73
46_D	49_G	0.519	0.73
5_L	10_R	0.516	0.73
38_F	44_R	0.515	0.73
41_V	58_A	0.512	0.72
6_Q	15_N	0.511	0.72
34_I	37_E	0.508	0.72
50_E	62_I	0.500	0.71

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
4madA	1	0.9524	34.5	0.864	Contact Map
1jmxA	1	0.9841	34.2	0.865	Contact Map
3d3aA	1	0.9206	28.9	0.869	Contact Map
3w5fA	1	0.9524	27.5	0.871	Contact Map
4e8dA	2	0.9524	18.5	0.881	Contact Map
3pl5A	1	0.7302	14.6	0.886	Contact Map
3tpdA	1	0.5556	12	0.891	Contact Map
3jr7A	1	0.6349	11.3	0.892	Contact Map
2g7zA	3	0.6667	11.3	0.892	Contact Map
3fysA	1	0.6825	10.3	0.894	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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