SMP - PFAM28P - GREMLIN Contacts

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SMP - Seed maturation protein

PFAM:	PF04927	Sequences: ITIGDVLEATAGLLADKPVTPEDAAAVQAAEARATGDNQTQPGGVAASAQSAARLNERA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (58)
Sequences:	591 (372)
Seq/√Len:	48.9
META:	0.103

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_Q	50_Q	3.995	1.00
27_V	49_A	2.617	1.00
19_V	49_A	2.510	1.00
22_E	57_E	2.097	1.00
24_A	46_A	2.070	1.00
25_A	47_A	1.943	0.99
38_N	41_Q	1.867	0.99
3_I	7_L	1.808	0.99
28_Q	51_S	1.690	0.98
26_A	34_A	1.589	0.97
13_L	16_D	1.579	0.97
31_E	44_G	1.578	0.97
28_Q	47_A	1.515	0.97
29_A	46_A	1.513	0.97
53_A	56_N	1.479	0.96
23_D	44_G	1.413	0.95
52_A	56_N	1.369	0.94
19_V	24_A	1.277	0.91
9_A	13_L	1.134	0.86
51_S	54_R	1.102	0.84
8_E	27_V	1.067	0.82
36_G	51_S	1.058	0.81
4_G	18_P	1.057	0.81
3_I	58_R	1.051	0.81
31_E	34_A	1.050	0.81
23_D	30_A	1.041	0.80
19_V	27_V	1.040	0.80
25_A	38_N	1.039	0.80
37_D	41_Q	1.035	0.80
32_A	48_S	1.021	0.79
23_D	31_E	1.000	0.78
6_V	49_A	0.998	0.77
19_V	26_A	0.959	0.74
2_T	5_D	0.953	0.74
18_P	28_Q	0.934	0.73
32_A	37_D	0.934	0.73
19_V	31_E	0.932	0.72
8_E	22_E	0.931	0.72
41_Q	54_R	0.909	0.70
16_D	44_G	0.887	0.69
29_A	33_R	0.882	0.68
33_R	41_Q	0.875	0.67
21_P	51_S	0.855	0.66
12_G	42_P	0.848	0.65
20_T	34_A	0.841	0.64
20_T	53_A	0.827	0.63
32_A	40_T	0.822	0.63
4_G	35_T	0.810	0.61
8_E	11_A	0.797	0.60
12_G	54_R	0.776	0.58
17_K	45_V	0.775	0.58
16_D	55_L	0.768	0.57
43_G	58_R	0.748	0.55
12_G	21_P	0.724	0.53
30_A	53_A	0.719	0.52
1_I	55_L	0.715	0.52
45_V	48_S	0.706	0.51
30_A	44_G	0.686	0.49
1_I	38_N	0.680	0.48
20_T	24_A	0.677	0.48
5_D	13_L	0.665	0.47
18_P	58_R	0.656	0.46
26_A	55_L	0.634	0.44
29_A	43_G	0.627	0.43
50_Q	58_R	0.625	0.43
17_K	33_R	0.617	0.42
19_V	48_S	0.605	0.41
2_T	29_A	0.604	0.41
22_E	32_A	0.603	0.41
26_A	57_E	0.590	0.40
28_Q	35_T	0.587	0.39
24_A	53_A	0.587	0.39
11_A	18_P	0.577	0.38
1_I	4_G	0.577	0.38
4_G	49_A	0.574	0.38
20_T	36_G	0.567	0.37
30_A	52_A	0.556	0.36
42_P	53_A	0.545	0.35
10_T	39_Q	0.536	0.34
47_A	51_S	0.529	0.34
18_P	27_V	0.521	0.33
12_G	55_L	0.520	0.33
5_D	49_A	0.516	0.33
35_T	50_Q	0.507	0.32
35_T	43_G	0.503	0.31
33_R	43_G	0.503	0.31
14_L	49_A	0.500	0.31

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
4y0bA	1	0.2542	2.8	0.893	Contact Map
4xy3A	1	0.7797	2.8	0.893	Contact Map
2vz8A	2	1	2.5	0.896	Contact Map
2gt1A	1	0.339	2.2	0.9	Contact Map
2loqA	1	0.9661	1.9	0.902	Contact Map
3zeyZ	1	0.339	1.9	0.903	Contact Map
2p5dA	1	0.4915	1.7	0.905	Contact Map
4fioA	3	1	1.7	0.906	Contact Map
3j7yZ	1	0.3729	1.7	0.906	Contact Map
4irfA	1	0.3051	1.6	0.907	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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