DUF723 - PFAM28P - GREMLIN Contacts

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DUF723 - Protein of unknown function (DUF723)

PFAM:	PF05265	Sequences: KRLTFEEAIKKFKEKFGDYSLVEYKGSKTPVTIICPIHGEFEQSPPNHHLKSKYGCPKCG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	60 (55)
Sequences:	696 (651)
Seq/√Len:	87.8
META:	0.93

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
26_G	29_T	3.982	1.00
8_A	12_F	3.643	1.00
34_I	40_E	3.178	1.00
32_T	40_E	3.092	1.00
13_K	17_G	3.026	1.00
21_L	40_E	2.128	1.00
22_V	31_V	2.090	1.00
32_T	42_E	1.931	1.00
24_Y	27_S	1.695	1.00
20_S	34_I	1.665	1.00
9_I	13_K	1.662	1.00
21_L	32_T	1.648	1.00
25_K	29_T	1.526	1.00
12_F	17_G	1.474	0.99
9_I	17_G	1.363	0.99
45_P	48_H	1.187	0.98
56_C	59_C	1.186	0.98
33_I	43_Q	1.119	0.96
46_P	49_H	1.103	0.96
19_Y	33_I	1.097	0.96
14_E	17_G	0.990	0.93
8_A	13_K	0.989	0.93
7_E	11_K	0.988	0.93
13_K	18_D	0.956	0.92
50_L	53_K	0.935	0.91
9_I	12_F	0.919	0.90
38_H	41_F	0.904	0.90
11_K	15_K	0.901	0.89
53_K	60_G	0.874	0.88
28_K	47_N	0.873	0.88
33_I	41_F	0.865	0.87
6_E	10_K	0.855	0.87
12_F	15_K	0.855	0.87
57_P	60_G	0.828	0.85
12_F	16_F	0.808	0.83
44_S	47_N	0.798	0.83
36_P	39_G	0.795	0.83
8_A	17_G	0.790	0.82
47_N	50_L	0.774	0.81
47_N	51_K	0.770	0.80
40_E	60_G	0.760	0.80
12_F	33_I	0.750	0.79
6_E	9_I	0.746	0.78
19_Y	22_V	0.732	0.77
38_H	42_E	0.709	0.75
44_S	49_H	0.677	0.71
8_A	16_F	0.675	0.71
39_G	42_E	0.666	0.70
30_P	42_E	0.652	0.68
27_S	37_I	0.633	0.66
8_A	11_K	0.632	0.66
12_F	49_H	0.618	0.64
28_K	37_I	0.614	0.64
55_G	59_C	0.602	0.62
35_C	56_C	0.584	0.60
21_L	31_V	0.583	0.60
19_Y	38_H	0.582	0.60
31_V	41_F	0.579	0.59
28_K	54_Y	0.579	0.59
23_E	32_T	0.577	0.59
35_C	39_G	0.567	0.58
28_K	32_T	0.565	0.57
24_Y	29_T	0.561	0.57
8_A	15_K	0.561	0.57
14_E	22_V	0.560	0.57
14_E	42_E	0.549	0.55
33_I	38_H	0.548	0.55
25_K	40_E	0.545	0.55
31_V	46_P	0.545	0.55
18_D	23_E	0.542	0.54
54_Y	60_G	0.541	0.54
9_I	14_E	0.537	0.54
23_E	58_K	0.534	0.53
35_C	59_C	0.527	0.52
13_K	16_F	0.522	0.52
43_Q	54_Y	0.522	0.52
7_E	37_I	0.519	0.51
26_G	30_P	0.518	0.51
28_K	46_P	0.515	0.51
7_E	10_K	0.509	0.50
47_N	52_S	0.502	0.49
18_D	21_L	0.500	0.49

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
4u3eA	2	0.7833	65.3	0.789	Contact Map
1gh9A	1	0.45	50.1	0.808	Contact Map
3wwlA	1	0.4833	46.3	0.812	Contact Map
1yuzA	2	0.8833	40	0.819	Contact Map
2au3A	1	0.9667	38.2	0.821	Contact Map
2gviA	3	0.9833	26.6	0.835	Contact Map
4cgyA	1	0.4167	25.3	0.837	Contact Map
4aybP	1	0.4333	25.2	0.837	Contact Map
3i2dA	1	0.9	24.5	0.838	Contact Map
4qiwP	1	0.4	23.3	0.84	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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