DUF3955 - PFAM28P - GREMLIN Contacts

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DUF3955 - Protein of unknown function (DUF3955)

PFAM:	PF13127	Sequences: KYILGLLLLLLGVACLIAFNLIGSYVDEDGVLHEPFFLIPLGYLFLLLGIILLLISLIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (55)
Sequences:	926 (742)
Seq/√Len:	100.1
META:	0.676

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
12_G	46_L	2.863	1.00
16_L	42_G	2.859	1.00
27_D	31_V	2.807	1.00
27_D	33_H	2.693	1.00
9_L	49_G	2.315	1.00
19_F	24_S	2.195	1.00
22_I	35_P	2.181	1.00
35_P	38_L	1.849	1.00
24_S	35_P	1.762	1.00
19_F	35_P	1.519	1.00
41_L	45_F	1.508	1.00
8_L	48_L	1.457	1.00
11_L	14_A	1.372	0.99
52_L	56_S	1.348	0.99
5_G	52_L	1.348	0.99
44_L	47_L	1.347	0.99
8_L	45_F	1.327	0.99
18_A	22_I	1.144	0.98
49_G	53_L	1.134	0.98
19_F	34_E	1.118	0.98
23_G	35_P	1.106	0.97
15_C	45_F	1.078	0.97
12_G	49_G	1.078	0.97
19_F	39_I	1.040	0.96
30_G	33_H	1.009	0.96
21_L	37_F	0.990	0.95
22_I	38_L	0.981	0.95
26_V	30_G	0.978	0.95
51_I	55_I	0.960	0.94
6_L	41_L	0.915	0.93
5_G	8_L	0.912	0.93
12_G	42_G	0.910	0.93
11_L	45_F	0.899	0.92
15_C	37_F	0.884	0.91
24_S	34_E	0.859	0.90
6_L	9_L	0.846	0.90
19_F	23_G	0.841	0.89
26_V	31_V	0.832	0.89
12_G	16_L	0.828	0.89
16_L	20_N	0.825	0.88
17_I	21_L	0.799	0.87
5_G	9_L	0.796	0.87
10_L	50_I	0.786	0.86
37_F	40_P	0.784	0.86
28_E	56_S	0.774	0.85
3_I	48_L	0.760	0.84
30_G	36_F	0.754	0.83
36_F	39_I	0.747	0.83
5_G	53_L	0.744	0.83
15_C	41_L	0.739	0.82
12_G	45_F	0.726	0.81
23_G	39_I	0.726	0.81
19_F	37_F	0.711	0.80
16_L	43_Y	0.695	0.78
15_C	38_L	0.694	0.78
3_I	7_L	0.688	0.77
18_A	38_L	0.684	0.77
10_L	48_L	0.680	0.77
6_L	10_L	0.675	0.76
40_P	43_Y	0.667	0.75
19_F	22_I	0.651	0.73
19_F	26_V	0.643	0.73
48_L	52_L	0.642	0.72
13_V	46_L	0.635	0.72
46_L	50_I	0.626	0.71
21_L	26_V	0.618	0.70
18_A	45_F	0.604	0.68
14_A	41_L	0.598	0.67
7_L	55_I	0.595	0.67
17_I	55_I	0.578	0.64
18_A	35_P	0.571	0.64
54_L	57_L	0.551	0.61
10_L	37_F	0.541	0.59
18_A	37_F	0.535	0.59
16_L	46_L	0.519	0.56
42_G	49_G	0.515	0.56
11_L	17_I	0.511	0.55
13_V	43_Y	0.509	0.55
25_Y	33_H	0.506	0.54
5_G	36_F	0.503	0.54
3_I	28_E	0.502	0.54
33_H	42_G	0.500	0.54

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
3mk7C	2	0.9831	2.8	0.884	Contact Map
2mfrA	1	0.7119	2.4	0.889	Contact Map
3ixzA	1	0.8475	2.1	0.893	Contact Map
2bs2C	2	0.7119	1.9	0.894	Contact Map
4p02A	1	0.9661	1.7	0.896	Contact Map
2zxeA	1	0.8475	1.7	0.898	Contact Map
4q4hA	1	0.9831	1.6	0.899	Contact Map
3j01B	1	0.8475	1.5	0.901	Contact Map
4d8pB	1	0	1.4	0.902	Contact Map
3hunA	1	0.2712	1.4	0.902	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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