DOG1 - PFAM28P - GREMLIN Contacts

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DOG1 - Seed dormancy control

PFAM:	PF14144	Sequences: QINELRAALQAHASDNELRLLVDKVLAHYDEYFRLKSAAAKADVFHLLSGMWKTPAERCFLWIGGFRPSELLKLLYS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	77 (75)
Sequences:	791 (468)
Seq/√Len:	54.1
META:	0.078

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
33_F	72_L	3.073	1.00
32_Y	50_G	2.759	1.00
63_I	68_P	2.311	1.00
67_R	76_Y	2.291	1.00
29_Y	45_F	2.182	1.00
60_F	75_L	2.054	1.00
23_D	67_R	1.885	0.99
31_E	54_T	1.858	0.99
15_D	19_R	1.849	0.99
29_Y	36_K	1.787	0.99
36_K	39_A	1.785	0.99
48_L	59_C	1.650	0.99
59_C	74_L	1.630	0.98
13_A	74_L	1.616	0.98
3_N	7_A	1.570	0.98
19_R	27_A	1.476	0.97
56_A	59_C	1.470	0.97
66_F	70_E	1.453	0.97
28_H	44_V	1.445	0.97
36_K	45_F	1.394	0.96
27_A	55_P	1.379	0.96
46_H	55_P	1.356	0.95
49_S	60_F	1.337	0.95
58_R	66_F	1.296	0.94
45_F	66_F	1.239	0.92
17_E	60_F	1.238	0.92
18_L	23_D	1.231	0.92
20_L	59_C	1.208	0.91
53_K	59_C	1.200	0.91
14_S	17_E	1.151	0.89
11_A	75_L	1.137	0.88
8_A	13_A	1.132	0.88
32_Y	61_L	1.111	0.87
16_N	20_L	1.103	0.87
34_R	38_A	1.097	0.87
66_F	71_L	1.094	0.86
27_A	51_M	1.093	0.86
11_A	15_D	1.050	0.84
62_W	67_R	1.042	0.84
36_K	65_G	1.028	0.83
21_L	25_V	1.022	0.82
54_T	70_E	1.018	0.82
33_F	66_F	0.992	0.81
4_E	74_L	0.975	0.79
28_H	55_P	0.975	0.79
26_L	67_R	0.973	0.79
36_K	66_F	0.959	0.78
18_L	63_I	0.959	0.78
48_L	64_G	0.953	0.78
12_H	26_L	0.953	0.78
35_L	71_L	0.928	0.76
9_L	69_S	0.925	0.76
53_K	73_K	0.909	0.74
46_H	59_C	0.900	0.74
60_F	70_E	0.895	0.73
3_N	11_A	0.890	0.73
57_E	62_W	0.882	0.72
4_E	10_Q	0.844	0.69
41_K	44_V	0.825	0.67
70_E	73_K	0.815	0.66
34_R	42_A	0.799	0.65
41_K	53_K	0.799	0.65
13_A	17_E	0.795	0.64
35_L	73_K	0.790	0.64
62_W	65_G	0.784	0.63
3_N	74_L	0.776	0.62
29_Y	51_M	0.737	0.58
2_I	25_V	0.731	0.58
6_R	9_L	0.722	0.57
59_C	66_F	0.708	0.55
66_F	76_Y	0.692	0.54
3_N	9_L	0.689	0.53
65_G	76_Y	0.678	0.52
7_A	11_A	0.676	0.52
17_E	35_L	0.673	0.52
33_F	36_K	0.667	0.51
2_I	7_A	0.666	0.51
44_V	69_S	0.665	0.51
73_K	76_Y	0.661	0.50
11_A	43_D	0.657	0.50
6_R	22_V	0.652	0.49
13_A	16_N	0.648	0.49
17_E	20_L	0.646	0.49
32_Y	74_L	0.639	0.48
39_A	58_R	0.630	0.47
19_R	38_A	0.628	0.47
21_L	34_R	0.623	0.46
63_I	72_L	0.613	0.45
50_G	61_L	0.598	0.44
51_M	73_K	0.574	0.41
29_Y	71_L	0.574	0.41
44_V	56_A	0.573	0.41
35_L	55_P	0.564	0.40
8_A	11_A	0.562	0.40
2_I	10_Q	0.553	0.39
9_L	24_K	0.551	0.39
50_G	58_R	0.544	0.38
3_N	31_E	0.543	0.38
24_K	38_A	0.542	0.38
6_R	39_A	0.537	0.37
66_F	69_S	0.537	0.37
18_L	22_V	0.536	0.37
32_Y	37_S	0.532	0.37
23_D	27_A	0.529	0.37
45_F	49_S	0.513	0.35
59_C	73_K	0.511	0.35
22_V	38_A	0.511	0.35
27_A	34_R	0.509	0.35
14_S	75_L	0.508	0.34
17_E	23_D	0.504	0.34
53_K	61_L	0.500	0.34
33_F	47_L	0.500	0.34

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
3h0gD	1	0.961	29.5	0.889	Contact Map
3lj5A	3	0.6623	18	0.9	Contact Map
1vt0M	4	0.6623	15.6	0.902	Contact Map
1slqA	6	0.3506	10.1	0.91	Contact Map
4d6kA	2	0.8312	10	0.91	Contact Map
2c35A	1	0.974	8.5	0.913	Contact Map
4ywtA	1	0.8571	8.3	0.913	Contact Map
2arhA	3	0.4416	7.4	0.915	Contact Map
3b21A	1	0.8052	6.7	0.917	Contact Map
4rp3A	2	0.8442	5.9	0.919	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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