DUF2829 - PFAM28P - GREMLIN Contacts

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DUF2829 - Protein of unknown function (DUF2829)

PFAM:	PF11195	Sequences: NFGEALEALKAGKKVARKGWNGKGMFLFLQPGSDGTSKMYLPYIDMKTADGKIVVPWLASQTDMLAEDWEIV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	72 (70)
Sequences:	4401 (3641)
Seq/√Len:	435.1
META:	0.911

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
16_A	70_E	3.079	1.00
8_A	13_K	2.546	1.00
4_E	8_A	2.375	1.00
1_N	7_E	2.193	1.00
18_K	70_E	2.151	1.00
10_K	67_E	2.141	1.00
9_L	15_V	1.988	1.00
47_K	51_G	1.985	1.00
5_A	15_V	1.830	1.00
2_F	64_M	1.827	1.00
4_E	7_E	1.803	1.00
41_L	52_K	1.768	1.00
30_Q	45_D	1.665	1.00
8_A	71_I	1.566	1.00
27_L	44_I	1.524	1.00
1_N	4_E	1.517	1.00
3_G	7_E	1.497	1.00
29_L	65_L	1.486	1.00
2_F	6_L	1.430	1.00
28_F	45_D	1.423	1.00
59_A	64_M	1.421	1.00
8_A	11_A	1.411	1.00
3_G	6_L	1.310	1.00
44_I	59_A	1.264	1.00
40_Y	45_D	1.232	1.00
47_K	53_I	1.229	1.00
9_L	44_I	1.184	1.00
34_D	37_S	1.173	1.00
17_R	66_A	1.168	1.00
7_E	11_A	1.153	1.00
28_F	53_I	1.150	1.00
8_A	15_V	1.145	1.00
30_Q	33_S	1.117	1.00
4_E	11_A	1.115	1.00
17_R	68_D	1.114	1.00
25_M	46_M	1.102	1.00
40_Y	43_Y	1.100	1.00
45_D	53_I	1.089	1.00
43_Y	56_P	1.052	1.00
15_V	27_L	1.043	1.00
13_K	71_I	0.962	1.00
14_K	26_F	0.959	1.00
41_L	62_T	0.953	1.00
30_Q	43_Y	0.949	1.00
61_Q	64_M	0.947	1.00
3_G	10_K	0.905	1.00
33_S	40_Y	0.883	1.00
34_D	38_K	0.879	1.00
14_K	28_F	0.876	1.00
48_T	55_V	0.851	1.00
39_M	52_K	0.841	1.00
21_N	25_M	0.818	1.00
26_F	47_K	0.806	1.00
6_L	64_M	0.763	1.00
58_L	61_Q	0.760	1.00
33_S	45_D	0.757	1.00
41_L	48_T	0.755	1.00
9_L	29_L	0.735	1.00
28_F	33_S	0.715	1.00
48_T	62_T	0.709	1.00
33_S	37_S	0.694	1.00
22_G	25_M	0.692	1.00
55_V	62_T	0.690	1.00
48_T	52_K	0.686	1.00
44_I	64_M	0.672	1.00
44_I	65_L	0.670	1.00
40_Y	53_I	0.664	1.00
56_P	61_Q	0.659	1.00
33_S	43_Y	0.651	0.99
15_V	71_I	0.649	0.99
4_E	71_I	0.648	0.99
6_L	9_L	0.647	0.99
6_L	65_L	0.647	0.99
4_E	70_E	0.645	0.99
32_G	42_P	0.642	0.99
28_F	38_K	0.639	0.99
25_M	49_A	0.637	0.99
45_D	56_P	0.636	0.99
35_G	38_K	0.629	0.99
58_L	62_T	0.622	0.99
33_S	39_M	0.597	0.99
28_F	40_Y	0.586	0.99
2_F	59_A	0.582	0.99
49_A	53_I	0.580	0.99
58_L	64_M	0.576	0.99
6_L	10_K	0.576	0.99
59_A	62_T	0.574	0.99
38_K	53_I	0.571	0.99
3_G	65_L	0.571	0.99
41_L	55_V	0.568	0.99
30_Q	39_M	0.557	0.98
35_G	40_Y	0.554	0.98
25_M	62_T	0.549	0.98
57_W	61_Q	0.543	0.98
57_W	63_D	0.533	0.98
31_P	37_S	0.532	0.98
3_G	9_L	0.528	0.98
21_N	24_G	0.526	0.98
30_Q	40_Y	0.524	0.98
55_V	61_Q	0.523	0.98
38_K	45_D	0.522	0.98
39_M	45_D	0.514	0.97
34_D	40_Y	0.505	0.97
19_G	25_M	0.504	0.97
46_M	49_A	0.500	0.97

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
3nrlA	2	0.75	12.6	0.853	Contact Map
2owlA	2	0.9167	9	0.862	Contact Map
5aj3j	1	0.9861	8.6	0.864	Contact Map
2owyA	2	0.9167	8.6	0.864	Contact Map
2y0nA	2	0.2917	7.8	0.867	Contact Map
2f5jA	2	0.2778	5.8	0.874	Contact Map
2vkjA	2	0.5417	4.3	0.881	Contact Map
2xtzA	1	0.9861	4.2	0.882	Contact Map
4gkvA	4	0.3333	3.7	0.886	Contact Map
2anuA	5	0.3056	3.6	0.886	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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