DUF4035 - PFAM28P - GREMLIN Contacts

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DUF4035 - Protein of unknown function (DUF4035)

PFAM:	PF13227	Sequences: AYDRLEPFGDERADLRAAQIASTIAGSKGKKFKLSDFMPKFGKEEEEEEDD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	51 (48)
Sequences:	758 (661)
Seq/√Len:	95.4
META:	0.85

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_A	16_R	4.028	1.00
3_D	8_F	3.452	1.00
17_A	20_I	2.594	1.00
10_D	13_A	2.547	1.00
26_G	29_G	2.500	1.00
10_D	16_R	2.497	1.00
19_Q	39_P	2.154	1.00
18_A	34_L	2.034	1.00
22_S	34_L	1.708	1.00
18_A	22_S	1.608	1.00
11_E	15_L	1.588	1.00
25_A	37_F	1.350	0.99
6_E	10_D	1.330	0.99
20_I	23_T	1.322	0.99
40_K	43_K	1.222	0.98
32_F	37_F	1.157	0.98
25_A	32_F	1.092	0.97
44_E	47_E	1.035	0.96
26_G	30_K	0.971	0.94
3_D	9_G	0.949	0.93
15_L	19_Q	0.931	0.93
15_L	41_F	0.928	0.92
17_A	24_I	0.899	0.91
8_F	41_F	0.887	0.91
17_A	21_A	0.855	0.89
43_K	47_E	0.844	0.88
45_E	48_E	0.842	0.88
43_K	46_E	0.839	0.88
19_Q	23_T	0.823	0.87
2_Y	10_D	0.820	0.87
33_K	47_E	0.792	0.85
16_R	39_P	0.784	0.84
18_A	36_D	0.779	0.84
1_A	5_L	0.777	0.84
2_Y	41_F	0.766	0.83
30_K	44_E	0.747	0.81
11_E	38_M	0.736	0.80
26_G	31_K	0.709	0.78
4_R	28_K	0.684	0.75
17_A	23_T	0.680	0.75
13_A	17_A	0.665	0.73
25_A	31_K	0.659	0.73
5_L	36_D	0.658	0.72
44_E	48_E	0.657	0.72
27_S	30_K	0.654	0.72
43_K	48_E	0.653	0.72
11_E	40_K	0.639	0.70
25_A	28_K	0.636	0.70
9_G	30_K	0.633	0.70
15_L	39_P	0.606	0.66
14_D	39_P	0.606	0.66
35_S	42_G	0.605	0.66
10_D	41_F	0.596	0.65
31_K	42_G	0.592	0.64
34_L	39_P	0.588	0.64
5_L	48_E	0.584	0.63
33_K	38_M	0.584	0.63
20_I	24_I	0.584	0.63
5_L	42_G	0.578	0.63
15_L	38_M	0.576	0.62
22_S	32_F	0.571	0.62
16_R	19_Q	0.561	0.60
19_Q	25_A	0.559	0.60
3_D	11_E	0.554	0.59
21_A	37_F	0.551	0.59
11_E	35_S	0.523	0.55
1_A	48_E	0.519	0.54
4_R	44_E	0.519	0.54
9_G	26_G	0.518	0.54
9_G	38_M	0.506	0.53
23_T	32_F	0.506	0.53
6_E	12_R	0.500	0.52

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
4wd8A	3	0.7451	11	0.851	Contact Map
3v3tA	1	0	4.1	0.878	Contact Map
1p9iA	2	0.5686	2.7	0.888	Contact Map
1zh8A	2	0.7451	2.5	0.89	Contact Map
4iovA	7	0	2.4	0.891	Contact Map
3dtpE	2	0.9804	2.2	0.894	Contact Map
4bzjA	2	0.8824	2	0.897	Contact Map
1nthA	5	0.4902	1.9	0.898	Contact Map
4ui9I	1	0.7451	1.8	0.898	Contact Map
1ej6D	1	0.5882	1.7	0.9	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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