DUF2909 - PFAM28P - GREMLIN Contacts

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DUF2909 - Protein of unknown function (DUF2909)

PFAM:	PF11137	Sequences: MKILIVLLLLAILASLGSALFFLVRDKGDSKRMVKALTVRVGLSVALFLLLLLAYYLGWI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (60)
Sequences:	7672 (4111)
Seq/√Len:	530.8
META:	0.923

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
23_L	33_M	3.136	1.00
34_V	38_T	2.912	1.00
31_K	35_K	2.241	1.00
6_V	10_L	2.104	1.00
54_A	59_W	2.017	1.00
53_L	57_L	1.973	1.00
19_A	36_A	1.721	1.00
12_I	44_S	1.707	1.00
26_D	30_S	1.587	1.00
39_V	43_L	1.504	1.00
49_L	53_L	1.496	1.00
12_I	47_L	1.476	1.00
35_K	38_T	1.454	1.00
21_F	25_R	1.442	1.00
3_I	7_L	1.375	1.00
48_F	52_L	1.361	1.00
18_S	22_F	1.356	1.00
15_S	39_V	1.241	1.00
22_F	32_R	1.239	1.00
4_L	8_L	1.236	1.00
26_D	32_R	1.199	1.00
10_L	14_A	1.183	1.00
50_L	54_A	1.179	1.00
14_A	39_V	1.176	1.00
12_I	43_L	1.172	1.00
17_G	20_L	1.151	1.00
38_T	41_V	1.151	1.00
42_G	46_A	1.149	1.00
11_A	43_L	1.143	1.00
14_A	18_S	1.130	1.00
52_L	56_Y	1.110	1.00
17_G	21_F	1.055	1.00
4_L	50_L	1.048	1.00
54_A	57_L	1.033	1.00
38_T	42_G	1.030	1.00
6_V	9_L	1.028	1.00
13_L	17_G	1.025	1.00
8_L	47_L	1.022	1.00
35_K	39_V	0.986	1.00
9_L	13_L	0.968	1.00
39_V	42_G	0.939	1.00
22_F	26_D	0.906	1.00
53_L	56_Y	0.890	1.00
7_L	11_A	0.882	1.00
19_A	33_M	0.872	1.00
46_A	50_L	0.858	1.00
15_S	18_S	0.855	1.00
45_V	48_F	0.854	1.00
8_L	11_A	0.823	1.00
27_K	30_S	0.816	1.00
14_A	17_G	0.813	1.00
17_G	24_V	0.797	1.00
15_S	20_L	0.766	1.00
18_S	21_F	0.764	1.00
20_L	24_V	0.764	1.00
44_S	48_F	0.755	1.00
8_L	46_A	0.732	1.00
1_M	54_A	0.724	1.00
11_A	15_S	0.711	1.00
1_M	59_W	0.708	1.00
13_L	16_L	0.705	1.00
21_F	24_V	0.683	1.00
19_A	22_F	0.672	1.00
52_L	55_Y	0.648	1.00
47_L	50_L	0.639	1.00
45_V	49_L	0.636	1.00
41_V	48_F	0.628	1.00
22_F	36_A	0.625	1.00
53_L	59_W	0.622	1.00
50_L	59_W	0.587	0.99
5_I	60_I	0.578	0.99
33_M	37_L	0.572	0.99
56_Y	59_W	0.567	0.99
42_G	45_V	0.566	0.99
51_L	55_Y	0.561	0.99
33_M	36_A	0.558	0.99
43_L	48_F	0.558	0.99
34_V	45_V	0.553	0.99
2_K	6_V	0.551	0.99
41_V	44_S	0.538	0.99
31_K	34_V	0.534	0.99
11_A	14_A	0.533	0.99
28_G	32_R	0.532	0.99
18_S	32_R	0.531	0.99
55_Y	59_W	0.527	0.99
9_L	41_V	0.520	0.99
42_G	49_L	0.514	0.99
24_V	33_M	0.511	0.99
3_I	6_V	0.509	0.98
20_L	43_L	0.500	0.98

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
2lonA	1	0.9833	82.2	0.719	Contact Map
2lomA	1	0.9833	78.8	0.728	Contact Map
4ev6A	3	0.9	22.1	0.814	Contact Map
4i0uA	4	0.8667	16.7	0.825	Contact Map
1rz2A	1	0.0167	9.8	0.842	Contact Map
4p02B	1	0.45	6.2	0.856	Contact Map
1zoyC	1	0.9167	5.3	0.86	Contact Map
2kseA	1	0.55	4.5	0.864	Contact Map
2wdqC	1	0.9333	4.4	0.866	Contact Map
2h88C	2	0.9167	4.4	0.866	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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