DUF2905 - PFAM28P - GREMLIN Contacts

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DUF2905 - Protein of unknown function (DUF2905)

PFAM:	PF11146	Sequences: GKLLIVLGLVLVVVGLLLPLGGRPLGRLPGDIRIERGNFTFYFPLVTSILLSVVLTLLLWLF	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	62 (62)
Sequences:	22816 (13994)
Seq/√Len:	1777.2
META:	0.959

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_E	40_T	3.515	1.00
33_R	40_T	2.699	1.00
5_I	12_V	2.427	1.00
5_I	19_P	2.102	1.00
1_G	19_P	2.067	1.00
36_R	39_F	1.969	1.00
56_T	60_W	1.866	1.00
3_L	7_L	1.859	1.00
9_L	12_V	1.728	1.00
31_D	47_T	1.721	1.00
30_G	46_V	1.613	1.00
33_R	42_Y	1.558	1.00
57_L	60_W	1.492	1.00
6_V	10_V	1.421	1.00
52_S	56_T	1.380	1.00
7_L	11_L	1.342	1.00
27_R	33_R	1.298	1.00
34_I	39_F	1.283	1.00
4_L	18_L	1.271	1.00
49_I	53_V	1.243	1.00
19_P	23_R	1.170	1.00
9_L	13_V	1.169	1.00
26_G	47_T	1.142	1.00
10_V	14_V	1.136	1.00
16_L	20_L	1.112	1.00
4_L	11_L	1.112	1.00
53_V	57_L	1.093	1.00
48_S	52_S	1.080	1.00
42_Y	46_V	1.071	1.00
19_P	22_G	1.043	1.00
5_I	16_L	1.032	1.00
1_G	18_L	1.008	1.00
17_L	21_G	0.999	1.00
16_L	19_P	0.965	1.00
5_I	15_G	0.961	1.00
55_L	59_L	0.960	1.00
9_L	16_L	0.952	1.00
8_G	12_V	0.927	1.00
33_R	36_R	0.926	1.00
48_S	60_W	0.907	1.00
43_F	46_V	0.905	1.00
28_L	31_D	0.887	1.00
6_V	9_L	0.884	1.00
56_T	59_L	0.879	1.00
58_L	62_F	0.868	1.00
46_V	50_L	0.863	1.00
57_L	61_L	0.862	1.00
13_V	16_L	0.857	1.00
3_L	6_V	0.851	1.00
32_I	45_L	0.836	1.00
53_V	60_W	0.824	1.00
20_L	23_R	0.819	1.00
31_D	46_V	0.810	1.00
13_V	17_L	0.803	1.00
34_I	37_G	0.783	1.00
12_V	19_P	0.782	1.00
54_V	58_L	0.760	1.00
48_S	56_T	0.752	1.00
34_I	41_F	0.746	1.00
21_G	24_P	0.733	1.00
24_P	27_R	0.730	1.00
4_L	14_V	0.719	1.00
3_L	19_P	0.718	1.00
28_L	46_V	0.702	1.00
33_R	37_G	0.701	1.00
45_L	49_I	0.684	1.00
18_L	22_G	0.676	1.00
43_F	48_S	0.673	1.00
25_L	51_L	0.670	1.00
2_K	19_P	0.643	1.00
18_L	23_R	0.629	1.00
4_L	7_L	0.627	1.00
39_F	42_Y	0.626	1.00
7_L	10_V	0.614	1.00
4_L	12_V	0.600	1.00
50_L	54_V	0.594	1.00
3_L	10_V	0.593	1.00
5_I	9_L	0.593	1.00
37_G	40_T	0.591	1.00
26_G	31_D	0.587	1.00
31_D	42_Y	0.582	1.00
36_R	41_F	0.563	1.00
10_V	13_V	0.556	1.00
17_L	23_R	0.541	1.00
6_V	13_V	0.541	1.00
25_L	47_T	0.529	1.00
45_L	48_S	0.528	1.00
14_V	18_L	0.522	1.00
2_K	8_G	0.520	1.00
4_L	9_L	0.513	1.00
42_Y	47_T	0.509	1.00
35_E	39_F	0.503	1.00
2_K	23_R	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
4ev6A	3	0.8871	9	0.84	Contact Map
4i0uA	4	0.8871	7.3	0.847	Contact Map
1zoyC	1	0.9839	6.1	0.852	Contact Map
4ysxC	1	0.9839	4.6	0.86	Contact Map
4ytpC	1	0.9839	4.2	0.863	Contact Map
3j9pD	4	1	2.9	0.874	Contact Map
2wdqC	1	0.9355	2.5	0.878	Contact Map
4bbjA	1	0.9032	2.5	0.878	Contact Map
2m59A	2	0.4355	2.4	0.879	Contact Map
2h88C	2	0.9194	2.3	0.88	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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