DUF4266 - PFAM28P - GREMLIN Contacts

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DUF4266 - Domain of unknown function (DUF4266)

PFAM:	PF14086	Sequences: VKPWERGRLADPIMQLDRDPLEAAFEEHVYFSREGASGGGGVGGGGCGCN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	50 (50)
Sequences:	8128 (3456)
Seq/√Len:	488.8
META:	0.969

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
27_E	40_G	4.168	1.00
2_K	5_E	2.923	1.00
8_R	11_D	2.734	1.00
17_D	23_A	2.215	1.00
21_L	24_A	2.147	1.00
22_E	26_E	1.996	1.00
27_E	31_F	1.901	1.00
26_E	29_V	1.556	1.00
10_A	46_G	1.460	1.00
34_E	38_G	1.381	1.00
28_H	32_S	1.336	1.00
6_R	10_A	1.333	1.00
31_F	37_S	1.328	1.00
26_E	30_Y	1.296	1.00
6_R	9_L	1.284	1.00
38_G	41_G	1.227	1.00
12_P	15_Q	1.225	1.00
23_A	27_E	1.221	1.00
7_G	10_A	1.200	1.00
13_I	16_L	1.193	1.00
22_E	25_F	1.156	1.00
3_P	6_R	1.155	1.00
7_G	12_P	1.128	1.00
31_F	40_G	1.118	1.00
23_A	40_G	1.107	1.00
12_P	18_R	1.097	1.00
19_D	22_E	1.013	1.00
37_S	42_V	0.995	1.00
16_L	33_R	0.927	1.00
29_V	32_S	0.914	1.00
33_R	45_G	0.901	1.00
28_H	48_G	0.876	1.00
24_A	27_E	0.867	1.00
29_V	33_R	0.838	1.00
28_H	45_G	0.812	1.00
27_E	30_Y	0.791	1.00
28_H	50_N	0.779	1.00
13_I	18_R	0.772	1.00
30_Y	33_R	0.742	1.00
3_P	28_H	0.738	1.00
5_E	42_V	0.725	1.00
38_G	43_G	0.705	1.00
15_Q	18_R	0.698	1.00
46_G	49_C	0.697	1.00
21_L	26_E	0.690	1.00
41_G	44_G	0.690	1.00
25_F	48_G	0.685	1.00
11_D	32_S	0.682	1.00
38_G	42_V	0.674	1.00
18_R	22_E	0.665	1.00
36_A	39_G	0.657	1.00
23_A	26_E	0.655	1.00
43_G	50_N	0.652	1.00
5_E	19_D	0.630	1.00
4_W	32_S	0.624	1.00
25_F	29_V	0.614	0.99
24_A	31_F	0.612	0.99
12_P	19_D	0.609	0.99
3_P	10_A	0.606	0.99
15_Q	20_P	0.598	0.99
24_A	42_V	0.587	0.99
6_R	30_Y	0.563	0.99
33_R	50_N	0.551	0.99
7_G	24_A	0.544	0.99
18_R	21_L	0.538	0.99
4_W	7_G	0.538	0.99
19_D	23_A	0.531	0.98
9_L	12_P	0.529	0.98
37_S	40_G	0.527	0.98
25_F	32_S	0.522	0.98
21_L	29_V	0.519	0.98
8_R	15_Q	0.516	0.98
24_A	33_R	0.516	0.98
37_S	44_G	0.500	0.98
11_D	33_R	0.500	0.98

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
3au7A	1	0.5	6.1	0.874	Contact Map
3n44F	1	0	5.9	0.874	Contact Map
3j4sA	6	0.64	5.2	0.877	Contact Map
4qc8A	6	0	4.9	0.879	Contact Map
1w5fA	2	0.28	4.8	0.88	Contact Map
4ywtA	1	0.74	4.7	0.88	Contact Map
1nwbA	1	0.6	3.9	0.885	Contact Map
1r94A	3	0.68	3.7	0.886	Contact Map
3cymA	1	0.38	3.6	0.887	Contact Map
2d2aA	2	0.78	3.3	0.888	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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