DUF1049 - PFAM28P - GREMLIN Contacts

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DUF1049 - Protein of unknown function (DUF1049)

PFAM:	PF06305	Sequences: QNTQPVTVNFLFWQFELPLALVLLLAFLLGALLGLLAGLLRRLRLRREARRLRRELRRLEKELE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	64 (61)
Sequences:	25166 (16190)
Seq/√Len:	2072.9
META:	0.915

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
31_A	34_G	2.114	1.00
23_L	26_A	1.994	1.00
52_L	56_L	1.938	1.00
45_L	49_A	1.918	1.00
17_L	22_V	1.882	1.00
7_T	16_E	1.821	1.00
55_E	60_E	1.795	1.00
27_F	33_L	1.693	1.00
6_V	19_L	1.683	1.00
49_A	52_L	1.649	1.00
27_F	30_G	1.611	1.00
35_L	38_G	1.601	1.00
56_L	59_L	1.571	1.00
48_E	52_L	1.555	1.00
43_L	47_R	1.512	1.00
56_L	60_E	1.504	1.00
5_P	16_E	1.498	1.00
47_R	51_R	1.484	1.00
26_A	30_G	1.450	1.00
9_N	12_F	1.400	1.00
18_P	21_L	1.373	1.00
22_V	26_A	1.344	1.00
48_E	53_R	1.340	1.00
38_G	42_R	1.284	1.00
42_R	45_L	1.278	1.00
31_A	37_A	1.230	1.00
8_V	22_V	1.224	1.00
4_Q	7_T	1.192	1.00
10_F	13_W	1.180	1.00
35_L	39_L	1.147	1.00
55_E	58_R	1.144	1.00
7_T	14_Q	1.134	1.00
9_N	14_Q	1.113	1.00
55_E	59_L	1.047	1.00
58_R	62_E	1.030	1.00
53_R	57_R	1.025	1.00
38_G	41_R	0.983	1.00
57_R	61_K	0.973	1.00
49_A	53_R	0.963	1.00
4_Q	19_L	0.947	1.00
39_L	43_L	0.946	1.00
51_R	55_E	0.942	1.00
47_R	50_R	0.911	1.00
30_G	34_G	0.883	1.00
10_F	15_F	0.873	1.00
27_F	31_A	0.866	1.00
54_R	58_R	0.864	1.00
3_T	20_A	0.861	1.00
42_R	46_R	0.825	1.00
50_R	54_R	0.810	1.00
41_R	45_L	0.807	1.00
52_L	55_E	0.805	1.00
40_L	43_L	0.798	1.00
5_P	18_P	0.791	1.00
19_L	23_L	0.767	1.00
50_R	57_R	0.751	1.00
54_R	57_R	0.741	1.00
57_R	60_E	0.736	1.00
46_R	50_R	0.731	1.00
9_N	13_W	0.718	1.00
36_L	40_L	0.703	1.00
46_R	49_A	0.682	1.00
11_L	14_Q	0.678	1.00
8_V	19_L	0.678	1.00
16_E	20_A	0.674	1.00
48_E	51_R	0.674	1.00
3_T	6_V	0.659	1.00
34_G	38_G	0.644	1.00
40_L	44_R	0.622	1.00
6_V	22_V	0.620	1.00
45_L	48_E	0.616	1.00
4_Q	9_N	0.612	1.00
7_T	11_L	0.605	1.00
7_T	22_V	0.599	1.00
12_F	15_F	0.594	1.00
34_G	37_A	0.594	1.00
39_L	42_R	0.593	1.00
28_L	31_A	0.593	1.00
17_L	25_L	0.576	1.00
44_R	48_E	0.558	1.00
58_R	61_K	0.558	1.00
20_A	23_L	0.557	1.00
41_R	44_R	0.556	1.00
51_R	54_R	0.552	1.00
53_R	60_E	0.546	1.00
17_L	20_A	0.533	1.00
3_T	21_L	0.528	1.00
31_A	35_L	0.518	1.00
45_L	62_E	0.518	1.00
19_L	22_V	0.511	1.00
22_V	27_F	0.504	1.00
31_A	38_G	0.500	1.00

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
2hi2A	1	0.7344	47.5	0.744	Contact Map
3sokA	1	0.75	43.4	0.749	Contact Map
4tllA	1	0.3281	41.7	0.752	Contact Map
1scfA	4	0	34.4	0.763	Contact Map
1oqwA	1	0.75	34	0.764	Contact Map
4bgnA	3	0.7188	28.9	0.772	Contact Map
2m7gA	1	0.75	28.1	0.774	Contact Map
4um9B	2	0	23.6	0.782	Contact Map
4uqqA	3	0.1719	23.2	0.783	Contact Map
5a2fA	1	0	18.3	0.793	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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