DUF2185 - PFAM28P - GREMLIN Contacts

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DUF2185 - Protein of unknown function (DUF2185)

PFAM:	PF09951	Sequences: CIASDRITVDGRPVGYMYREEPDNEEDSGWRFFSGDESDEYMDDPDNFAIYDVNTIANYDPSIIPLLDAPVGSAFERDETGEFEK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	85 (82)
Sequences:	2712 (2150)
Seq/√Len:	237.4
META:	0.895

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
39_D	43_D	2.823	1.00
6_R	36_D	2.618	1.00
17_M	66_L	2.418	1.00
42_M	48_F	2.342	1.00
33_F	42_M	2.311	1.00
5_D	9_V	2.243	1.00
41_Y	47_N	2.156	1.00
69_A	75_F	2.119	1.00
2_I	48_F	2.074	1.00
27_D	31_R	2.043	1.00
18_Y	31_R	1.989	1.00
20_E	31_R	1.968	1.00
12_R	36_D	1.965	1.00
62_S	77_R	1.885	1.00
5_D	49_A	1.783	1.00
6_R	12_R	1.746	1.00
4_S	48_F	1.714	1.00
54_N	58_N	1.634	1.00
6_R	10_D	1.630	1.00
51_Y	55_T	1.603	1.00
8_T	51_Y	1.566	1.00
69_A	73_S	1.556	1.00
57_A	64_I	1.535	1.00
23_D	31_R	1.496	1.00
17_M	32_F	1.462	1.00
8_T	56_I	1.376	1.00
6_R	34_S	1.355	1.00
69_A	72_G	1.325	1.00
33_F	48_F	1.302	1.00
78_D	81_G	1.233	1.00
60_D	77_R	1.164	1.00
54_N	57_A	1.157	1.00
14_V	60_D	1.155	1.00
66_L	75_F	1.118	1.00
13_P	62_S	1.117	1.00
44_D	47_N	1.110	1.00
3_A	56_I	1.101	1.00
55_T	59_Y	1.095	1.00
79_E	82_E	1.051	1.00
3_A	8_T	1.036	1.00
28_S	53_V	1.004	1.00
32_F	56_I	0.993	1.00
2_I	23_D	0.970	1.00
38_S	41_Y	0.940	1.00
70_P	73_S	0.928	1.00
14_V	32_F	0.903	1.00
58_N	64_I	0.875	0.99
55_T	58_N	0.869	0.99
54_N	64_I	0.869	0.99
26_E	52_D	0.862	0.99
21_E	71_V	0.860	0.99
53_V	56_I	0.851	0.99
54_N	59_Y	0.848	0.99
11_G	59_Y	0.837	0.99
7_I	32_F	0.831	0.99
78_D	82_E	0.828	0.99
32_F	53_V	0.822	0.99
2_I	50_I	0.819	0.99
32_F	63_I	0.810	0.99
8_T	49_A	0.808	0.99
22_P	28_S	0.799	0.99
32_F	66_L	0.798	0.99
52_D	55_T	0.786	0.99
76_E	79_E	0.775	0.99
4_S	42_M	0.766	0.98
23_D	26_E	0.764	0.98
12_R	34_S	0.750	0.98
5_D	47_N	0.739	0.98
57_A	63_I	0.737	0.98
63_I	67_L	0.729	0.98
16_Y	74_A	0.708	0.97
56_I	63_I	0.696	0.97
4_S	34_S	0.691	0.97
19_R	29_G	0.685	0.97
3_A	51_Y	0.685	0.97
53_V	57_A	0.683	0.97
9_V	49_A	0.681	0.97
14_V	63_I	0.676	0.97
15_G	36_D	0.667	0.96
39_D	42_M	0.660	0.96
10_D	36_D	0.659	0.96
18_Y	33_F	0.655	0.96
22_P	27_D	0.648	0.96
32_F	67_L	0.641	0.95
3_A	7_I	0.635	0.95
38_S	61_P	0.630	0.95
14_V	17_M	0.619	0.95
24_N	50_I	0.615	0.94
50_I	55_T	0.615	0.94
4_S	33_F	0.613	0.94
58_N	63_I	0.608	0.94
13_P	60_D	0.600	0.94
51_Y	56_I	0.597	0.93
10_D	39_D	0.597	0.93
16_Y	72_G	0.596	0.93
46_D	49_A	0.595	0.93
69_A	74_A	0.593	0.93
64_I	67_L	0.592	0.93
4_S	41_Y	0.588	0.93
73_S	77_R	0.586	0.93
28_S	67_L	0.577	0.92
20_E	23_D	0.574	0.92
21_E	78_D	0.572	0.92
62_S	81_G	0.567	0.92
6_R	41_Y	0.556	0.91
7_I	34_S	0.555	0.91
57_A	67_L	0.554	0.91
16_Y	33_F	0.551	0.90
15_G	34_S	0.551	0.90
2_I	40_E	0.550	0.90
21_E	70_P	0.549	0.90
24_N	74_A	0.542	0.90
35_G	38_S	0.534	0.89
23_D	27_D	0.532	0.89
17_M	63_I	0.521	0.88
7_I	13_P	0.517	0.87
42_M	76_E	0.513	0.87
48_F	53_V	0.512	0.87
17_M	75_F	0.512	0.87
17_M	62_S	0.505	0.86
21_E	25_E	0.501	0.86
24_N	71_V	0.501	0.86
1_C	57_A	0.500	0.86

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
2lydA	1	0.5882	39.6	0.864	Contact Map
2qklA	1	0.4588	37.9	0.866	Contact Map
4b6hA	1	0.5412	16.9	0.887	Contact Map
1q67A	2	0.4706	15.1	0.889	Contact Map
4qhwA	1	0.9529	8.5	0.901	Contact Map
2cr3A	1	0.3412	7	0.905	Contact Map
3j7aI	1	0.4941	4.9	0.911	Contact Map
4ioyX	1	0.2588	3	0.92	Contact Map
4h63K	1	0.4471	2.9	0.921	Contact Map
4khoA	1	0.4	2.8	0.921	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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