DUF3018 - PFAM28P - GREMLIN Contacts

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DUF3018 - Protein of unknown function (DUF3018)

PFAM:	PF11455	Sequences: RERVRAHRERLRAQGLRPVQIWVPDTRSPGFAAEARRQSLAVAASPHEAEDQAFIDAVSDWDGW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (61)
Sequences:	4423 (2456)
Seq/√Len:	314.5
META:	0.949

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
6_A	10_R	2.609	1.00
34_E	37_R	2.400	1.00
5_R	9_E	2.267	1.00
34_E	38_Q	2.194	1.00
11_L	18_P	2.187	1.00
36_R	40_L	2.143	1.00
35_A	39_S	2.056	1.00
54_F	58_V	1.774	1.00
7_H	11_L	1.770	1.00
52_Q	56_D	1.653	1.00
7_H	10_R	1.614	1.00
37_R	41_A	1.568	1.00
26_T	31_F	1.541	1.00
17_R	27_R	1.541	1.00
19_V	23_V	1.495	1.00
50_E	54_F	1.357	1.00
4_V	7_H	1.339	1.00
47_H	51_D	1.335	1.00
2_E	5_R	1.334	1.00
9_E	13_A	1.287	1.00
6_A	9_E	1.275	1.00
48_E	52_Q	1.273	1.00
49_A	53_A	1.245	1.00
52_Q	55_I	1.243	1.00
51_D	55_I	1.232	1.00
39_S	43_A	1.213	1.00
11_L	14_Q	1.212	1.00
48_E	51_D	1.167	1.00
45_S	48_E	1.151	1.00
51_D	58_V	1.116	1.00
31_F	35_A	1.109	1.00
2_E	6_A	1.013	1.00
17_R	26_T	0.961	1.00
30_G	33_A	0.950	1.00
10_R	14_Q	0.929	1.00
11_L	16_L	0.919	1.00
46_P	50_E	0.910	1.00
55_I	59_S	0.901	1.00
8_R	15_G	0.888	1.00
44_A	47_H	0.862	1.00
51_D	54_F	0.858	1.00
15_G	22_W	0.851	1.00
45_S	51_D	0.848	1.00
29_P	33_A	0.847	1.00
12_R	20_Q	0.845	1.00
59_S	62_D	0.828	1.00
44_A	48_E	0.821	1.00
55_I	61_W	0.819	1.00
47_H	50_E	0.817	1.00
30_G	34_E	0.816	1.00
44_A	49_A	0.799	1.00
11_L	20_Q	0.793	1.00
42_V	46_P	0.787	1.00
12_R	18_P	0.785	1.00
36_R	39_S	0.774	1.00
19_V	22_W	0.768	0.99
42_V	48_E	0.753	0.99
21_I	24_P	0.743	0.99
3_R	6_A	0.733	0.99
18_P	21_I	0.726	0.99
46_P	49_A	0.725	0.99
33_A	36_R	0.713	0.99
8_R	20_Q	0.693	0.99
34_E	41_A	0.681	0.99
2_E	9_E	0.676	0.99
3_R	7_H	0.663	0.98
38_Q	42_V	0.649	0.98
40_L	44_A	0.647	0.98
32_A	36_R	0.630	0.98
55_I	58_V	0.625	0.98
28_S	31_F	0.622	0.98
2_E	13_A	0.621	0.98
45_S	49_A	0.604	0.97
57_A	61_W	0.596	0.97
17_R	20_Q	0.594	0.97
53_A	57_A	0.594	0.97
48_E	55_I	0.593	0.97
4_V	11_L	0.591	0.97
3_R	10_R	0.581	0.96
42_V	51_D	0.566	0.96
35_A	43_A	0.559	0.96
7_H	20_Q	0.554	0.95
29_P	32_A	0.539	0.95
16_L	24_P	0.537	0.95
26_T	35_A	0.524	0.94
12_R	15_G	0.521	0.94
4_V	20_Q	0.521	0.94
40_L	43_A	0.517	0.93
29_P	37_R	0.513	0.93
22_W	31_F	0.507	0.93
56_D	59_S	0.502	0.92
17_R	23_V	0.500	0.92

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
4mijA	1	0.875	11	0.877	Contact Map
4ekfA	1	0.9375	9.3	0.881	Contact Map
3r3pA	3	0.6875	9.3	0.881	Contact Map
4n8yA	1	0.8438	7.5	0.886	Contact Map
4ovrA	1	0.8438	6.7	0.889	Contact Map
4n4jA	3	0.875	6.2	0.891	Contact Map
4p1lA	1	0.875	6.1	0.891	Contact Map
4xfeA	1	0.8438	5.9	0.892	Contact Map
3kfwX	4	0.9688	5.8	0.892	Contact Map
4ay3A	2	0.3438	5.7	0.892	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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