Sof1 - PFAM28P - GREMLIN Contacts

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Sof1 - Sof1-like domain

PFAM:	PF04158	Sequences: ANASEKLGVLSPRERAALEYREALKERYKHMPEIRRIARHRHVPKAIKKAAKIKREMLEAIKRKEENRRKHSKPGSVPRVPERKKHV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (87)
Sequences:	755 (506)
Seq/√Len:	54.3
META:	0.419

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
65_E	69_R	3.490	1.00
2_N	22_E	3.228	1.00
63_R	67_N	3.206	1.00
17_A	21_R	3.175	1.00
25_K	38_A	2.866	1.00
26_E	29_K	2.693	1.00
2_N	5_E	2.574	1.00
69_R	78_P	2.396	1.00
22_E	25_K	2.124	1.00
55_R	59_E	2.048	1.00
51_A	55_R	1.894	0.99
57_M	60_A	1.872	0.99
53_I	57_M	1.869	0.99
56_E	60_A	1.830	0.99
54_K	58_L	1.824	0.99
57_M	61_I	1.780	0.99
36_R	40_H	1.712	0.99
60_A	64_K	1.675	0.99
23_A	26_E	1.659	0.99
48_K	52_K	1.560	0.98
72_S	75_G	1.560	0.98
11_S	14_E	1.450	0.97
66_E	70_K	1.434	0.97
27_R	46_A	1.397	0.96
43_V	47_I	1.338	0.95
15_R	19_E	1.306	0.94
46_A	50_A	1.304	0.94
18_L	84_K	1.216	0.92
48_K	57_M	1.205	0.91
50_A	53_I	1.151	0.89
49_K	52_K	1.146	0.89
34_I	41_R	1.120	0.88
62_K	66_E	1.094	0.87
82_E	86_H	1.062	0.85
62_K	65_E	1.045	0.84
82_E	85_K	1.031	0.83
8_G	14_E	1.029	0.83
23_A	60_A	1.025	0.83
80_V	84_K	1.002	0.81
53_I	56_E	0.995	0.81
5_E	8_G	0.988	0.80
65_E	68_R	0.953	0.78
58_L	62_K	0.921	0.76
27_R	67_N	0.903	0.74
66_E	79_R	0.885	0.73
62_K	71_H	0.884	0.72
32_P	67_N	0.877	0.72
28_Y	77_V	0.867	0.71
69_R	79_R	0.864	0.71
72_S	76_S	0.863	0.71
6_K	14_E	0.859	0.70
73_K	81_P	0.854	0.70
1_A	5_E	0.846	0.69
32_P	53_I	0.842	0.69
10_L	14_E	0.841	0.69
21_R	53_I	0.831	0.68
50_A	71_H	0.823	0.67
22_E	34_I	0.814	0.66
20_Y	70_K	0.802	0.65
64_K	71_H	0.797	0.64
3_A	83_R	0.787	0.63
5_E	56_E	0.779	0.63
71_H	74_P	0.764	0.61
33_E	36_R	0.759	0.61
36_R	42_H	0.758	0.61
74_P	77_V	0.752	0.60
25_K	28_Y	0.750	0.60
65_E	77_V	0.749	0.60
8_G	56_E	0.747	0.59
40_H	64_K	0.744	0.59
35_R	84_K	0.741	0.59
64_K	68_R	0.736	0.58
7_L	29_K	0.726	0.57
29_K	50_A	0.724	0.57
68_R	72_S	0.716	0.56
49_K	62_K	0.712	0.56
81_P	84_K	0.692	0.54
23_A	61_I	0.690	0.53
56_E	59_E	0.687	0.53
4_S	18_L	0.682	0.53
67_N	71_H	0.681	0.53
73_K	76_S	0.664	0.51
29_K	56_E	0.661	0.50
41_R	83_R	0.659	0.50
12_P	16_A	0.653	0.50
81_P	85_K	0.652	0.49
50_A	57_M	0.652	0.49
53_I	60_A	0.646	0.49
13_R	39_R	0.645	0.49
24_L	38_A	0.632	0.47
35_R	39_R	0.628	0.47
80_V	87_V	0.625	0.47
14_E	26_E	0.609	0.45
16_A	19_E	0.608	0.45
46_A	49_K	0.608	0.45
50_A	54_K	0.599	0.44
31_M	48_K	0.594	0.43
7_L	64_K	0.586	0.42
42_H	52_K	0.586	0.42
48_K	51_A	0.585	0.42
56_E	63_R	0.579	0.42
15_R	69_R	0.572	0.41
27_R	49_K	0.570	0.41
27_R	60_A	0.565	0.40
56_E	80_V	0.563	0.40
33_E	66_E	0.561	0.40
20_Y	24_L	0.560	0.40
30_H	49_K	0.560	0.40
60_A	67_N	0.551	0.39
24_L	73_K	0.546	0.38
37_I	87_V	0.542	0.38
46_A	53_I	0.541	0.38
17_A	31_M	0.539	0.38
43_V	51_A	0.531	0.37
5_E	32_P	0.529	0.37
79_R	87_V	0.528	0.37
21_R	61_I	0.526	0.36
47_I	75_G	0.523	0.36
40_H	43_V	0.521	0.36
6_K	31_M	0.520	0.36
2_N	10_L	0.519	0.36
33_E	80_V	0.517	0.35
29_K	45_K	0.516	0.35
18_L	25_K	0.515	0.35
9_V	30_H	0.513	0.35
66_E	69_R	0.511	0.35
22_E	39_R	0.508	0.35
7_L	51_A	0.504	0.34
28_Y	52_K	0.501	0.34
56_E	79_R	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
4uerb	1	0.092	5.6	0.914	Contact Map
3flvA	1	0.3333	5	0.916	Contact Map
4z29A	1	0.3563	2.8	0.926	Contact Map
4flaA	2	0.3678	2.6	0.927	Contact Map
2zaiA	2	0.6207	2.4	0.929	Contact Map
2jpfA	1	0.3333	2.3	0.929	Contact Map
3vu1A	2	0.6782	2.2	0.93	Contact Map
1ji8A	1	0.8391	2	0.932	Contact Map
3b5mA	2	0.3218	1.5	0.936	Contact Map
2lbbA	1	0.3333	1.4	0.937	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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