DUF384 - PFAM28P - GREMLIN Contacts

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DUF384 - Domain of unknown function (DUF384)

PFAM:	PF04064	Sequences: TLLLLCTTREGREYLREKGVYPILRELHLWEEDEDVREACERLVQVLIRDEEEED	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	55 (54)
Sequences:	671 (445)
Seq/√Len:	60.6
META:	0.411

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_L	30_W	2.735	1.00
19_G	22_P	2.635	1.00
9_R	13_E	2.418	1.00
8_T	11_G	2.284	1.00
28_H	41_E	2.272	1.00
26_E	29_L	2.225	1.00
6_C	46_V	2.172	1.00
13_E	17_E	2.085	1.00
41_E	45_Q	2.021	1.00
14_Y	18_K	1.960	1.00
15_L	20_V	1.661	0.99
22_P	25_R	1.645	0.99
19_G	23_I	1.534	0.98
7_T	42_R	1.504	0.98
50_D	54_E	1.418	0.97
27_L	31_E	1.401	0.97
3_L	43_L	1.372	0.97
22_P	26_E	1.361	0.97
45_Q	49_R	1.252	0.95
14_Y	17_E	1.171	0.92
40_C	44_V	1.170	0.92
24_L	43_L	1.113	0.90
2_L	43_L	1.100	0.90
16_R	21_Y	1.021	0.86
18_K	23_I	1.007	0.85
3_L	44_V	0.986	0.84
49_R	54_E	0.954	0.82
12_R	16_R	0.932	0.80
36_V	44_V	0.930	0.80
1_T	5_L	0.926	0.80
34_E	38_E	0.877	0.76
27_L	36_V	0.853	0.74
10_E	17_E	0.843	0.73
4_L	44_V	0.841	0.73
43_L	46_V	0.835	0.73
28_H	37_R	0.835	0.73
23_I	41_E	0.828	0.72
21_Y	28_H	0.817	0.71
27_L	40_C	0.814	0.71
12_R	51_E	0.812	0.70
2_L	15_L	0.783	0.68
20_V	44_V	0.779	0.67
6_C	15_L	0.767	0.66
34_E	37_R	0.751	0.64
6_C	37_R	0.747	0.64
11_G	15_L	0.726	0.62
39_A	46_V	0.711	0.60
31_E	37_R	0.703	0.59
4_L	42_R	0.699	0.59
19_G	29_L	0.697	0.59
9_R	50_D	0.682	0.57
30_W	40_C	0.679	0.57
31_E	41_E	0.678	0.56
21_Y	51_E	0.669	0.55
28_H	42_R	0.661	0.55
37_R	41_E	0.642	0.52
7_T	46_V	0.635	0.52
29_L	40_C	0.631	0.51
20_V	24_L	0.622	0.50
22_P	48_I	0.615	0.49
8_T	46_V	0.608	0.49
49_R	53_E	0.603	0.48
4_L	23_I	0.590	0.47
13_E	16_R	0.588	0.46
1_T	42_R	0.576	0.45
19_G	54_E	0.573	0.45
24_L	46_V	0.567	0.44
13_E	32_E	0.562	0.43
16_R	49_R	0.561	0.43
36_V	40_C	0.551	0.42
16_R	51_E	0.546	0.42
17_E	47_L	0.541	0.41
49_R	52_E	0.539	0.41
21_Y	25_R	0.531	0.40
32_E	36_V	0.524	0.39
7_T	47_L	0.513	0.38
1_T	33_D	0.513	0.38
26_E	40_C	0.510	0.38
39_A	43_L	0.506	0.37
1_T	54_E	0.501	0.37
32_E	35_D	0.500	0.37

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
2dkaA	1	0.7636	29.6	0.829	Contact Map
3tpoA	1	0.8545	23	0.837	Contact Map
1wa5B	1	0.9273	22.3	0.839	Contact Map
3nowA	3	1	19.7	0.843	Contact Map
2f7lA	4	0.8727	18.9	0.844	Contact Map
4ev8A	1	0.8364	17.7	0.846	Contact Map
4bjuA	1	0.9455	16.9	0.847	Contact Map
4uafB	1	0.8545	16.4	0.848	Contact Map
2jdqA	2	0.9455	14.1	0.853	Contact Map
3nmzA	2	1	14	0.853	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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