DUF3772 - PFAM28P - GREMLIN Contacts

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DUF3772 - Protein of unknown function (DUF3772)

PFAM:	PF12607	Sequences: QARLLAVRADQLIARIDALRRARFTRRLLERSPSPLSPAFWRDAAAALPDDLRRLGALVAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	61 (58)
Sequences:	3303 (2395)
Seq/√Len:	314.5
META:	0.858

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_L	23_R	2.655	1.00
3_R	7_V	2.185	1.00
7_V	11_Q	2.078	1.00
42_R	46_A	2.065	1.00
4_L	11_Q	2.051	1.00
37_S	40_F	1.849	1.00
49_P	52_L	1.837	1.00
25_T	29_L	1.808	1.00
10_D	14_A	1.783	1.00
18_A	22_A	1.747	1.00
20_R	24_F	1.689	1.00
8_R	12_L	1.686	1.00
56_G	59_V	1.614	1.00
51_D	54_R	1.556	1.00
31_R	34_S	1.526	1.00
20_R	23_R	1.506	1.00
52_L	56_G	1.451	1.00
53_R	56_G	1.418	1.00
13_I	35_P	1.382	1.00
6_A	10_D	1.351	1.00
38_P	42_R	1.218	1.00
13_I	17_D	1.186	1.00
50_D	54_R	1.181	1.00
27_R	30_E	1.145	1.00
43_D	46_A	1.133	1.00
17_D	38_P	1.109	1.00
33_P	40_F	1.104	1.00
10_D	17_D	1.045	1.00
12_L	15_R	1.037	1.00
11_Q	15_R	1.029	1.00
38_P	45_A	1.021	1.00
53_R	57_A	0.999	1.00
2_A	55_L	0.978	1.00
11_Q	26_R	0.950	1.00
47_A	51_D	0.947	1.00
12_L	57_A	0.933	1.00
23_R	27_R	0.895	1.00
32_S	40_F	0.886	1.00
24_F	27_R	0.883	1.00
4_L	15_R	0.873	1.00
9_A	12_L	0.870	1.00
8_R	51_D	0.868	1.00
43_D	47_A	0.854	1.00
11_Q	28_L	0.847	1.00
34_S	44_A	0.832	1.00
6_A	14_A	0.816	1.00
18_A	31_R	0.806	1.00
5_L	11_Q	0.784	1.00
23_R	29_L	0.783	1.00
19_L	22_A	0.781	1.00
54_R	57_A	0.766	0.99
33_P	37_S	0.765	0.99
5_L	12_L	0.765	0.99
3_R	6_A	0.758	0.99
9_A	13_I	0.738	0.99
15_R	35_P	0.728	0.99
40_F	43_D	0.716	0.99
26_R	31_R	0.709	0.99
16_I	38_P	0.683	0.99
21_R	24_F	0.671	0.99
49_P	53_R	0.662	0.98
33_P	43_D	0.661	0.98
50_D	53_R	0.650	0.98
12_L	48_L	0.648	0.98
13_I	59_V	0.635	0.98
3_R	26_R	0.630	0.98
4_L	30_E	0.624	0.98
29_L	51_D	0.621	0.98
13_I	32_S	0.616	0.98
48_L	52_L	0.614	0.97
55_L	59_V	0.611	0.97
50_D	56_G	0.611	0.97
23_R	30_E	0.595	0.97
4_L	18_A	0.578	0.96
5_L	39_A	0.571	0.96
40_F	58_L	0.565	0.96
49_P	54_R	0.550	0.95
31_R	36_L	0.547	0.95
46_A	49_P	0.545	0.95
47_A	53_R	0.544	0.95
44_A	47_A	0.528	0.94
36_L	42_R	0.518	0.93
4_L	31_R	0.518	0.93
16_I	20_R	0.515	0.93
8_R	25_T	0.506	0.93
45_A	49_P	0.504	0.93
52_L	59_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
3wh1A	1	0.7705	4.3	0.848	Contact Map
4wmuA	1	0.9672	4	0.851	Contact Map
3g13A	2	0.5246	3.1	0.858	Contact Map
2v0oA	2	0.4918	2.8	0.862	Contact Map
3fs3A	2	0.9836	2.8	0.862	Contact Map
2zd7A	2	0.9016	2.6	0.864	Contact Map
2b82A	4	0.4918	2.2	0.869	Contact Map
3l39A	3	0.9836	2.1	0.871	Contact Map
3cuqA	1	0.8361	2.1	0.871	Contact Map
1hz4A	2	0.2787	2	0.871	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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