DUF1161 - PFAM28P - GREMLIN Contacts

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DUF1161 - Protein of unknown function (DUF1161)

PFAM:	PF06649	Sequences: CEELKAEIAAKLDAKGVKGYTLEIVPKDAVKQADGKVVGSCEGGTKKIVYKR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	52 (50)
Sequences:	1998 (898)
Seq/√Len:	127.0
META:	0.868

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
9_A	13_D	4.455	1.00
22_L	48_I	2.465	1.00
27_K	47_K	2.394	1.00
4_L	7_E	2.353	1.00
8_I	48_I	2.351	1.00
26_P	29_A	2.255	1.00
28_D	47_K	1.929	1.00
42_E	46_K	1.913	1.00
37_V	49_V	1.857	1.00
8_I	38_V	1.790	1.00
12_L	15_K	1.710	1.00
35_G	49_V	1.700	1.00
7_E	11_K	1.458	1.00
13_D	20_Y	1.416	1.00
9_A	22_L	1.206	0.99
12_L	20_Y	1.188	0.99
29_A	33_A	1.176	0.99
12_L	17_V	1.056	0.98
40_S	44_G	1.051	0.98
9_A	20_Y	1.020	0.98
17_V	50_Y	1.005	0.98
4_L	40_S	0.996	0.98
10_A	14_A	0.958	0.97
26_P	46_K	0.938	0.97
30_V	35_G	0.937	0.97
30_V	34_D	0.923	0.96
6_A	10_A	0.906	0.96
27_K	40_S	0.903	0.96
2_E	5_K	0.889	0.96
34_D	51_K	0.862	0.95
43_G	52_R	0.858	0.95
7_E	14_A	0.852	0.94
25_V	37_V	0.839	0.94
30_V	33_A	0.789	0.92
26_P	33_A	0.778	0.91
15_K	36_K	0.777	0.91
13_D	18_K	0.772	0.91
13_D	19_G	0.766	0.91
4_L	8_I	0.762	0.90
11_K	17_V	0.761	0.90
27_K	45_T	0.755	0.90
5_K	24_I	0.748	0.90
16_G	50_Y	0.746	0.89
3_E	40_S	0.687	0.85
3_E	34_D	0.680	0.85
3_E	7_E	0.677	0.84
24_I	48_I	0.672	0.84
23_E	35_G	0.671	0.84
6_A	46_K	0.666	0.83
9_A	44_G	0.656	0.82
4_L	39_G	0.655	0.82
38_V	50_Y	0.642	0.81
42_E	45_T	0.636	0.80
22_L	38_V	0.619	0.79
30_V	40_S	0.598	0.76
14_A	42_E	0.581	0.74
12_L	38_V	0.581	0.74
3_E	24_I	0.578	0.74
27_K	30_V	0.576	0.74
29_A	47_K	0.565	0.72
25_V	33_A	0.564	0.72
8_I	15_K	0.564	0.72
29_A	35_G	0.560	0.72
33_A	49_V	0.556	0.71
25_V	49_V	0.550	0.70
28_D	34_D	0.546	0.70
14_A	45_T	0.543	0.69
23_E	51_K	0.539	0.69
19_G	43_G	0.523	0.66
16_G	29_A	0.520	0.66
21_T	24_I	0.510	0.64
30_V	38_V	0.509	0.64
25_V	45_T	0.509	0.64
14_A	20_Y	0.505	0.64
27_K	38_V	0.500	0.63

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
2mx4A	1	0.75	9.1	0.869	Contact Map
5bxvB	1	0.1346	6.9	0.876	Contact Map
3wkrC	2	0	6	0.879	Contact Map
2hiqA	2	0.6538	5.2	0.882	Contact Map
3hxiC	1	0.1346	5.2	0.882	Contact Map
3g4nA	1	0.4615	5.1	0.883	Contact Map
3h90A	3	0.5769	4.8	0.884	Contact Map
4aukA	2	0.8654	3.9	0.889	Contact Map
3nqwA	2	0.3462	3.7	0.89	Contact Map
4lvcA	4	0.4615	3.6	0.891	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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