DUF3008 - PFAM28P - GREMLIN Contacts

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DUF3008 - Protein of unknwon function (DUF3008)

PFAM:	PF11450	Sequences: AKSKAQQKAAGAALAAKRGETKKSELKGASKSMAKSMSEKELEDFASTKRKGLPEKK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	57 (57)
Sequences:	3191 (1371)
Seq/√Len:	181.6
META:	0.932

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
7_Q	50_R	2.271	1.00
9_A	33_M	2.264	1.00
41_E	44_D	2.143	1.00
14_L	18_R	1.978	1.00
38_S	41_E	1.957	1.00
14_L	17_K	1.902	1.00
43_E	47_S	1.845	1.00
5_A	8_K	1.728	1.00
15_A	21_T	1.675	1.00
11_G	46_A	1.541	1.00
13_A	42_L	1.519	1.00
5_A	55_E	1.519	1.00
18_R	39_E	1.506	1.00
8_K	50_R	1.502	1.00
22_K	25_E	1.405	1.00
12_A	21_T	1.401	1.00
11_G	15_A	1.394	1.00
14_L	43_E	1.359	1.00
14_L	42_L	1.329	1.00
5_A	56_K	1.320	1.00
10_A	33_M	1.288	1.00
21_T	25_E	1.231	1.00
23_K	34_A	1.229	1.00
48_T	53_L	1.220	1.00
28_G	32_S	1.199	1.00
41_E	45_F	1.194	1.00
9_A	13_A	1.182	1.00
33_M	42_L	1.149	1.00
16_A	23_K	1.138	1.00
10_A	37_M	1.096	1.00
16_A	21_T	1.077	1.00
4_K	7_Q	1.075	1.00
27_K	30_S	1.054	1.00
10_A	42_L	1.053	1.00
16_A	26_L	1.042	1.00
17_K	39_E	1.008	0.99
16_A	30_S	1.003	0.99
4_K	55_E	0.995	0.99
37_M	42_L	0.994	0.99
12_A	30_S	0.971	0.99
8_K	55_E	0.949	0.99
7_Q	48_T	0.910	0.99
4_K	53_L	0.891	0.99
7_Q	11_G	0.882	0.99
53_L	56_K	0.881	0.98
15_A	20_E	0.881	0.98
26_L	30_S	0.813	0.97
14_L	39_E	0.803	0.97
40_K	44_D	0.792	0.97
44_D	47_S	0.784	0.97
21_T	26_L	0.765	0.96
17_K	42_L	0.764	0.96
4_K	50_R	0.712	0.95
7_Q	46_A	0.703	0.94
50_R	53_L	0.696	0.94
16_A	24_S	0.695	0.94
12_A	16_A	0.694	0.94
23_K	35_K	0.685	0.93
33_M	37_M	0.660	0.92
49_K	52_G	0.643	0.91
8_K	12_A	0.642	0.91
16_A	31_K	0.626	0.90
29_A	33_M	0.625	0.90
26_L	31_K	0.623	0.90
28_G	31_K	0.617	0.89
53_L	57_K	0.612	0.89
30_S	34_A	0.605	0.88
13_A	17_K	0.598	0.88
10_A	14_L	0.598	0.88
26_L	57_K	0.576	0.86
15_A	19_G	0.575	0.86
3_S	6_Q	0.571	0.85
13_A	33_M	0.565	0.85
27_K	34_A	0.563	0.84
25_E	28_G	0.558	0.84
29_A	32_S	0.553	0.83
16_A	28_G	0.537	0.82
18_R	43_E	0.533	0.81
32_S	36_S	0.519	0.79
8_K	11_G	0.519	0.79
49_K	55_E	0.510	0.78
2_K	57_K	0.505	0.78
11_G	48_T	0.504	0.77
45_F	48_T	0.504	0.77
9_A	30_S	0.502	0.77
9_A	29_A	0.500	0.77

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
1bh9B	1	0.3684	14.2	0.858	Contact Map
4qq1A	1	0.8246	6.2	0.88	Contact Map
2ohwA	1	0.3333	6	0.88	Contact Map
4aybC	1	0.4035	5.5	0.882	Contact Map
2np9A	4	0.9825	3.3	0.895	Contact Map
2kfpA	1	0.3684	3.2	0.896	Contact Map
2ou5A	2	0.386	3.1	0.896	Contact Map
3uaqA	2	0.8246	2.9	0.897	Contact Map
3ewtE	1	0.2456	2.9	0.897	Contact Map
2ejqA	1	0.3509	2.9	0.898	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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