DUF2087 - PFAM28P - GREMLIN Contacts

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DUF2087 - Uncharacterized protein conserved in bacteria (DUF2087)

PFAM:	PF09860	Sequences: RLKSIPAKRKKRLVVLRYLAQRFEPGRRYTEKEVNEILKRFHDDYATLRRYLVDEGLLDRTRDGGEYWR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	69 (69)
Sequences:	11016 (6863)
Seq/√Len:	826.2
META:	0.897

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_R	66_E	3.805	1.00
22_R	41_F	2.615	1.00
23_F	34_V	2.210	1.00
39_K	45_Y	2.110	1.00
28_R	68_W	2.063	1.00
13_L	55_E	1.877	1.00
61_T	65_G	1.849	1.00
18_Y	22_R	1.775	1.00
30_T	33_E	1.774	1.00
18_Y	21_Q	1.715	1.00
59_D	68_W	1.710	1.00
47_T	51_Y	1.631	1.00
9_R	55_E	1.623	1.00
35_N	45_Y	1.598	1.00
9_R	13_L	1.592	1.00
2_L	15_V	1.500	1.00
61_T	66_E	1.482	1.00
24_E	29_Y	1.474	1.00
20_A	57_L	1.464	1.00
19_L	41_F	1.432	1.00
18_Y	41_F	1.420	1.00
31_E	35_N	1.405	1.00
24_E	27_R	1.399	1.00
12_R	51_Y	1.388	1.00
36_E	39_K	1.299	1.00
22_R	37_I	1.268	1.00
53_V	59_D	1.249	1.00
42_H	48_L	1.202	1.00
51_Y	55_E	1.199	1.00
13_L	17_R	1.198	1.00
36_E	40_R	1.197	1.00
53_V	58_L	1.191	1.00
51_Y	54_D	1.175	1.00
34_V	58_L	1.168	1.00
33_E	36_E	1.054	1.00
32_K	36_E	1.014	1.00
23_F	29_Y	0.998	1.00
22_R	40_R	0.991	1.00
23_F	37_I	0.940	1.00
7_A	11_K	0.919	1.00
27_R	33_E	0.914	1.00
8_K	11_K	0.903	1.00
5_I	12_R	0.902	1.00
14_V	17_R	0.901	1.00
5_I	47_T	0.900	1.00
4_S	7_A	0.891	1.00
10_K	14_V	0.865	1.00
23_F	58_L	0.859	1.00
19_L	48_L	0.853	1.00
50_R	60_R	0.849	1.00
39_K	43_D	0.847	1.00
16_L	51_Y	0.846	1.00
17_R	20_A	0.808	1.00
27_R	37_I	0.791	1.00
17_R	57_L	0.789	1.00
25_P	69_R	0.780	1.00
35_N	46_A	0.771	1.00
13_L	57_L	0.766	1.00
62_R	65_G	0.731	1.00
16_L	57_L	0.720	1.00
38_L	48_L	0.715	1.00
5_I	48_L	0.710	1.00
37_I	40_R	0.703	1.00
5_I	16_L	0.696	1.00
9_R	12_R	0.694	1.00
17_R	21_Q	0.692	1.00
63_D	66_E	0.689	1.00
19_L	22_R	0.682	1.00
31_E	49_R	0.674	1.00
12_R	55_E	0.673	1.00
6_P	11_K	0.656	1.00
12_R	19_L	0.653	1.00
9_R	51_Y	0.652	1.00
50_R	53_V	0.649	1.00
52_L	57_L	0.642	1.00
29_Y	34_V	0.623	1.00
28_R	61_T	0.622	1.00
5_I	51_Y	0.621	1.00
46_A	50_R	0.610	1.00
56_G	59_D	0.609	1.00
4_S	11_K	0.601	1.00
12_R	47_T	0.600	1.00
16_L	55_E	0.596	1.00
52_L	58_L	0.594	1.00
11_K	15_V	0.581	1.00
19_L	38_L	0.574	1.00
48_L	52_L	0.571	1.00
20_A	69_R	0.564	1.00
53_V	56_G	0.563	1.00
20_A	52_L	0.561	1.00
11_K	14_V	0.554	1.00
29_Y	37_I	0.549	1.00
33_E	37_I	0.539	1.00
45_Y	54_D	0.533	1.00
53_V	60_R	0.527	1.00
35_N	49_R	0.520	1.00
4_S	8_K	0.513	1.00
7_A	12_R	0.508	1.00
16_L	20_A	0.508	1.00
31_E	60_R	0.507	1.00
39_K	46_A	0.503	1.00
5_I	42_H	0.503	1.00
2_L	19_L	0.503	1.00
2_L	5_I	0.500	1.00

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
2lnbA	1	0.9275	63.8	0.808	Contact Map
2jt1A	1	0.913	52	0.821	Contact Map
3f8mA	2	0.8406	49.8	0.824	Contact Map
3eetA	2	0.8841	48.5	0.825	Contact Map
2ra5A	2	0.087	45.1	0.829	Contact Map
1sfuA	1	0.942	42.9	0.831	Contact Map
2o03A	2	0.942	41.4	0.833	Contact Map
4mtdA	2	0.9565	39.6	0.835	Contact Map
3bwgA	2	0.942	38.5	0.835	Contact Map
3edpA	2	0.8696	36.8	0.837	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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