DUF1059 - PFAM28P - GREMLIN Contacts

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DUF1059 - Protein of unknown function (DUF1059)

PFAM:	PF06348	Sequences: MKSIDCRDVGPGCTFVIRAETEEEVLEAAAEHAVEVHGMHEDTPELREKIRAAIKD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	56 (54)
Sequences:	11280 (6184)
Seq/√Len:	841.6
META:	0.961

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_E	35_E	3.013	1.00
22_E	51_R	2.779	1.00
2_K	22_E	2.490	1.00
8_D	55_K	2.487	1.00
3_S	16_V	1.802	1.00
43_T	46_L	1.702	1.00
49_K	53_A	1.702	1.00
19_A	28_A	1.635	1.00
27_E	31_E	1.517	1.00
42_D	47_R	1.354	1.00
49_K	52_A	1.349	1.00
3_S	18_R	1.344	1.00
28_A	31_E	1.341	1.00
4_I	29_A	1.330	1.00
5_D	16_V	1.323	1.00
7_R	10_G	1.317	1.00
23_E	27_E	1.250	1.00
15_F	28_A	1.224	1.00
25_V	54_I	1.221	1.00
21_T	24_E	1.212	1.00
5_D	8_D	1.210	1.00
17_I	25_V	1.189	1.00
25_V	29_A	1.139	1.00
34_V	40_H	1.120	1.00
30_A	47_R	1.119	1.00
44_P	48_E	1.106	1.00
3_S	8_D	1.060	1.00
48_E	52_A	1.057	1.00
39_M	43_T	1.031	1.00
13_C	32_H	1.026	1.00
47_R	51_R	1.023	1.00
7_R	14_T	1.002	1.00
9_V	12_G	0.994	1.00
19_A	24_E	0.979	1.00
48_E	51_R	0.961	1.00
17_I	28_A	0.956	1.00
22_E	54_I	0.945	1.00
19_A	25_V	0.934	1.00
24_E	27_E	0.932	1.00
45_E	49_K	0.912	1.00
3_S	55_K	0.903	1.00
32_H	37_H	0.884	1.00
4_I	25_V	0.872	1.00
7_R	12_G	0.863	1.00
26_L	54_I	0.802	1.00
24_E	28_A	0.789	1.00
39_M	46_L	0.782	1.00
46_L	49_K	0.780	1.00
30_A	42_D	0.768	1.00
9_V	53_A	0.766	1.00
30_A	34_V	0.765	1.00
31_E	36_V	0.758	1.00
27_E	30_A	0.754	1.00
44_P	47_R	0.726	1.00
46_L	50_I	0.722	1.00
14_T	24_E	0.711	1.00
11_P	36_V	0.679	1.00
39_M	42_D	0.674	1.00
23_E	51_R	0.672	1.00
43_T	47_R	0.670	1.00
4_I	8_D	0.669	1.00
6_C	32_H	0.665	1.00
26_L	29_A	0.610	1.00
26_L	30_A	0.605	1.00
45_E	48_E	0.593	1.00
11_P	14_T	0.587	1.00
13_C	37_H	0.552	1.00
33_A	38_G	0.546	1.00
7_R	11_P	0.541	1.00
8_D	53_A	0.541	1.00
42_D	46_L	0.531	1.00
17_I	31_E	0.526	1.00
41_E	45_E	0.525	1.00
26_L	50_I	0.521	1.00
31_E	34_V	0.520	1.00
4_I	54_I	0.518	1.00
41_E	44_P	0.512	1.00
4_I	26_L	0.507	1.00
26_L	47_R	0.506	1.00
17_I	24_E	0.500	1.00
16_V	19_A	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
1aipC	2	0.9107	18.7	0.816	Contact Map
1tfeA	2	0.9107	13	0.829	Contact Map
4b4uA	2	0.9821	11.1	0.834	Contact Map
4lmgA	1	0.9464	9.2	0.84	Contact Map
1edzA	2	0.9464	9.2	0.84	Contact Map
3l07A	2	0.9821	8.1	0.844	Contact Map
2c2xA	2	0.9821	8	0.845	Contact Map
1b0aA	2	0.9821	7.7	0.846	Contact Map
3avxA	1	0.875	6.8	0.85	Contact Map
4a5oA	2	0.9821	6.7	0.85	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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