G-patch_2 - PFAM28P - GREMLIN Contacts

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G-patch_2 - DExH-box splicing factor binding site

PFAM:	PF12656	Sequences: EPDEEEAFKRDVESRPDEATLEDYEAVPVEEFGAALLRGMGWKEGEGLGKNGKGRVEPIEPERRPARLGLGAKPKPK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (73)
Sequences:	958 (736)
Seq/√Len:	86.2
META:	0.354

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_A	39_G	3.436	1.00
36_L	40_M	3.186	1.00
43_K	46_E	2.672	1.00
35_A	38_R	2.639	1.00
45_G	49_G	2.354	1.00
11_D	15_R	2.296	1.00
8_F	12_V	2.235	1.00
68_L	72_A	2.165	1.00
34_A	38_R	2.004	1.00
19_A	23_D	1.951	1.00
34_A	42_W	1.859	1.00
67_R	70_L	1.746	1.00
31_E	34_A	1.685	1.00
12_V	15_R	1.643	1.00
45_G	48_L	1.633	1.00
37_L	42_W	1.587	1.00
27_V	31_E	1.572	1.00
32_F	35_A	1.524	1.00
33_G	37_L	1.432	0.99
64_R	68_L	1.388	0.99
9_K	12_V	1.383	0.99
47_G	55_R	1.246	0.98
7_A	10_R	1.244	0.98
5_E	9_K	1.229	0.98
8_F	13_E	1.229	0.98
65_P	68_L	1.209	0.98
8_F	11_D	1.173	0.97
6_E	10_R	1.158	0.97
20_T	23_D	1.134	0.97
26_A	62_E	1.116	0.96
48_L	54_G	1.087	0.96
68_L	74_P	1.085	0.96
37_L	60_E	1.057	0.95
42_W	49_G	1.022	0.94
44_E	49_G	1.013	0.94
27_V	35_A	0.942	0.91
11_D	68_L	0.935	0.91
38_R	44_E	0.934	0.91
49_G	59_I	0.930	0.90
24_Y	29_V	0.923	0.90
47_G	54_G	0.907	0.89
27_V	33_G	0.902	0.89
36_L	67_R	0.880	0.88
23_D	27_V	0.871	0.87
19_A	63_R	0.840	0.85
55_R	58_P	0.833	0.85
16_P	20_T	0.818	0.84
24_Y	28_P	0.817	0.84
28_P	32_F	0.817	0.84
18_E	21_L	0.811	0.83
9_K	13_E	0.798	0.82
29_V	35_A	0.795	0.82
4_E	8_F	0.788	0.81
4_E	7_A	0.778	0.81
32_F	38_R	0.775	0.80
28_P	38_R	0.770	0.80
5_E	10_R	0.770	0.80
49_G	58_P	0.763	0.79
66_A	74_P	0.762	0.79
24_Y	65_P	0.740	0.77
24_Y	32_F	0.733	0.76
48_L	55_R	0.726	0.76
43_K	48_L	0.724	0.76
36_L	39_G	0.721	0.75
42_W	45_G	0.717	0.75
27_V	38_R	0.717	0.75
26_A	59_I	0.715	0.75
31_E	38_R	0.704	0.73
29_V	32_F	0.704	0.73
28_P	31_E	0.703	0.73
13_E	16_P	0.689	0.72
50_K	53_K	0.687	0.72
9_K	14_S	0.680	0.71
62_E	75_K	0.675	0.70
63_R	67_R	0.670	0.70
47_G	58_P	0.662	0.69
63_R	73_K	0.657	0.68
32_F	39_G	0.654	0.68
34_A	63_R	0.641	0.66
10_R	15_R	0.635	0.66
59_I	62_E	0.634	0.66
24_Y	72_A	0.633	0.65
66_A	70_L	0.632	0.65
31_E	35_A	0.624	0.64
24_Y	27_V	0.621	0.64
6_E	14_S	0.619	0.64
32_F	64_R	0.611	0.63
8_F	18_E	0.611	0.63
25_E	30_E	0.600	0.61
64_R	72_A	0.596	0.61
6_E	9_K	0.587	0.60
37_L	41_G	0.582	0.59
45_G	50_K	0.580	0.59
43_K	59_I	0.574	0.58
47_G	50_K	0.574	0.58
54_G	58_P	0.556	0.56
22_E	25_E	0.537	0.53
20_T	27_V	0.536	0.53
4_E	21_L	0.535	0.53
65_P	72_A	0.528	0.52
62_E	70_L	0.527	0.52
12_V	22_E	0.524	0.51
13_E	56_V	0.519	0.51
64_R	67_R	0.517	0.50
30_E	65_P	0.515	0.50
15_R	51_N	0.512	0.50
20_T	57_E	0.504	0.49
62_E	68_L	0.503	0.48
10_R	76_P	0.502	0.48
7_A	22_E	0.500	0.48

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
2lx9A	1	0.8312	5.3	0.891	Contact Map
2k5lA	1	0.8831	5.1	0.892	Contact Map
2k4yA	1	0.9221	4.2	0.896	Contact Map
2k5iA	1	0.8701	4.1	0.897	Contact Map
2gcxA	1	0.8312	3.9	0.898	Contact Map
2k5fA	1	0.8701	3.5	0.901	Contact Map
3mhxA	1	0.8831	3	0.904	Contact Map
2h3jA	1	0.8442	2.9	0.904	Contact Map
4o5vA	2	0.961	2.9	0.904	Contact Map
2qq9A	2	0.8831	2.5	0.908	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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