YdjO - PFAM28P - GREMLIN Contacts

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YdjO - Cold-inducible protein YdjO

PFAM:	PF14169	Sequences: MYFRKKPQEEIPEEETKVWSCTSEDCNGWMRDNFSFEEEPTCPLCGSPMVKGTRMLPVL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	59 (58)
Sequences:	532 (360)
Seq/√Len:	47.3
META:	0.457

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_G	44_L	4.414	1.00
22_T	50_V	3.121	1.00
2_Y	5_K	2.407	1.00
36_F	40_P	2.400	1.00
43_P	48_P	2.151	1.00
15_E	53_T	2.122	1.00
3_F	15_E	2.070	1.00
4_R	7_P	1.981	0.99
16_T	56_L	1.814	0.99
32_D	51_K	1.607	0.97
17_K	32_D	1.567	0.97
4_R	10_E	1.542	0.97
20_S	52_G	1.528	0.96
8_Q	13_E	1.469	0.95
37_E	57_P	1.468	0.95
20_S	54_R	1.398	0.94
15_E	55_M	1.338	0.93
48_P	58_V	1.291	0.91
34_F	40_P	1.245	0.90
48_P	57_P	1.206	0.88
3_F	53_T	1.187	0.87
3_F	43_P	1.120	0.84
2_Y	6_K	1.092	0.82
13_E	55_M	1.083	0.82
3_F	35_S	1.082	0.82
41_T	48_P	1.077	0.81
19_W	40_P	1.026	0.78
10_E	37_E	1.019	0.78
6_K	33_N	0.982	0.75
22_T	47_S	0.970	0.74
17_K	51_K	0.968	0.74
12_P	36_F	0.962	0.73
3_F	7_P	0.906	0.69
25_D	37_E	0.885	0.67
20_S	46_G	0.874	0.66
13_E	34_F	0.869	0.66
22_T	48_P	0.848	0.64
19_W	36_F	0.845	0.63
27_N	32_D	0.836	0.63
38_E	51_K	0.825	0.62
30_M	52_G	0.802	0.59
5_K	30_M	0.798	0.59
9_E	47_S	0.782	0.57
24_E	50_V	0.769	0.56
32_D	54_R	0.739	0.53
28_G	34_F	0.737	0.53
7_P	43_P	0.729	0.52
30_M	36_F	0.719	0.51
13_E	30_M	0.719	0.51
7_P	14_E	0.706	0.50
19_W	49_M	0.699	0.49
27_N	44_L	0.695	0.49
5_K	18_V	0.691	0.48
5_K	8_Q	0.685	0.48
24_E	27_N	0.681	0.47
53_T	57_P	0.678	0.47
18_V	52_G	0.673	0.47
23_S	47_S	0.667	0.46
25_D	54_R	0.664	0.46
37_E	59_L	0.635	0.43
10_E	49_M	0.630	0.42
20_S	57_P	0.628	0.42
17_K	53_T	0.626	0.42
35_S	59_L	0.615	0.41
23_S	56_L	0.614	0.41
14_E	23_S	0.608	0.40
24_E	34_F	0.602	0.40
31_R	57_P	0.585	0.38
6_K	10_E	0.581	0.38
14_E	33_N	0.573	0.37
8_Q	25_D	0.573	0.37
39_E	48_P	0.572	0.37
17_K	49_M	0.568	0.36
13_E	56_L	0.557	0.35
30_M	54_R	0.549	0.35
41_T	44_L	0.546	0.34
5_K	50_V	0.545	0.34
14_E	34_F	0.535	0.33
36_F	55_M	0.531	0.33
9_E	24_E	0.524	0.33
22_T	53_T	0.521	0.32
2_Y	43_P	0.520	0.32
2_Y	15_E	0.510	0.31
41_T	46_G	0.510	0.31
9_E	12_P	0.505	0.31
16_T	31_R	0.503	0.31
55_M	58_V	0.500	0.30

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
2kn9A	1	0.8814	38.9	0.859	Contact Map
4aybP	1	0.6441	38.5	0.859	Contact Map
4e2xA	1	0.339	37.7	0.86	Contact Map
1s24A	1	0.6949	36.2	0.861	Contact Map
1lkoA	3	0.9153	34.5	0.863	Contact Map
4d02A	2	0	33.8	0.863	Contact Map
1yk4A	1	0.6271	31.6	0.865	Contact Map
2v3bB	1	0.6441	26.5	0.87	Contact Map
4tpuA	3	0.8814	24.6	0.872	Contact Map
6rxnA	1	0.6271	20.4	0.877	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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