YlzJ - PFAM28P - GREMLIN Contacts

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YlzJ - YlzJ-like protein

PFAM:	PF14035	Sequences: LYTIMPLELVFEGEEEEEPEYQEIEYGGVTLLVEPLGDGQYRIVRLLSTDPQDYLNPELQPGSII	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	65 (65)
Sequences:	1203 (1030)
Seq/√Len:	127.7
META:	0.692

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_E	42_R	3.457	1.00
29_V	53_D	2.729	1.00
50_D	53_D	2.202	1.00
7_L	11_F	2.146	1.00
25_E	30_T	2.097	1.00
22_Q	35_P	2.024	1.00
23_E	32_L	1.840	1.00
1_L	5_M	1.829	1.00
32_L	45_R	1.821	1.00
48_S	51_P	1.760	1.00
35_P	41_Y	1.689	1.00
42_R	64_I	1.627	1.00
21_Y	32_L	1.602	1.00
6_P	9_L	1.563	1.00
29_V	46_L	1.490	1.00
40_Q	64_I	1.475	1.00
43_I	63_S	1.461	1.00
1_L	10_V	1.415	1.00
36_L	64_I	1.388	1.00
34_E	44_V	1.354	1.00
30_T	47_L	1.350	1.00
56_N	59_L	1.288	1.00
26_Y	59_L	1.288	1.00
36_L	42_R	1.278	1.00
37_G	40_Q	1.261	1.00
33_V	41_Y	1.244	1.00
24_I	33_V	1.218	0.99
46_L	59_L	1.209	0.99
4_I	9_L	1.178	0.99
19_P	34_E	1.166	0.99
5_M	9_L	1.157	0.99
48_S	53_D	1.117	0.99
23_E	47_L	1.089	0.99
36_L	40_Q	1.064	0.99
15_E	24_I	1.021	0.98
7_L	10_V	1.021	0.98
5_M	10_V	1.020	0.98
31_L	43_I	0.970	0.97
29_V	59_L	0.970	0.97
23_E	45_R	0.954	0.97
31_L	59_L	0.920	0.96
29_V	43_I	0.917	0.96
38_D	41_Y	0.896	0.96
15_E	19_P	0.864	0.95
26_Y	31_L	0.862	0.95
9_L	12_E	0.837	0.94
27_G	58_E	0.819	0.93
2_Y	51_P	0.813	0.93
23_E	30_T	0.804	0.93
18_E	21_Y	0.797	0.92
29_V	50_D	0.793	0.92
21_Y	44_V	0.791	0.92
31_L	49_T	0.733	0.89
57_P	60_Q	0.718	0.88
1_L	49_T	0.712	0.87
27_G	59_L	0.701	0.86
34_E	43_I	0.691	0.86
23_E	27_G	0.685	0.85
46_L	60_Q	0.669	0.84
10_V	14_E	0.664	0.83
21_Y	34_E	0.664	0.83
4_I	7_L	0.662	0.83
22_Q	40_Q	0.659	0.83
46_L	53_D	0.659	0.83
12_E	27_G	0.652	0.82
3_T	7_L	0.641	0.81
58_E	63_S	0.637	0.81
36_L	54_Y	0.635	0.81
26_Y	58_E	0.633	0.80
19_P	42_R	0.630	0.80
22_Q	33_V	0.627	0.80
17_E	20_E	0.627	0.80
20_E	35_P	0.621	0.79
10_V	53_D	0.618	0.79
29_V	56_N	0.617	0.79
11_F	14_E	0.610	0.78
3_T	9_L	0.603	0.77
40_Q	60_Q	0.600	0.77
24_I	31_L	0.600	0.77
3_T	29_V	0.594	0.76
51_P	54_Y	0.590	0.76
3_T	10_V	0.589	0.75
25_E	29_V	0.588	0.75
19_P	36_L	0.583	0.75
11_F	41_Y	0.582	0.75
2_Y	9_L	0.575	0.74
44_V	54_Y	0.561	0.72
52_Q	63_S	0.547	0.70
20_E	64_I	0.545	0.70
9_L	13_G	0.544	0.70
43_I	60_Q	0.542	0.69
53_D	56_N	0.535	0.68
39_G	59_L	0.532	0.68
33_V	65_I	0.531	0.68
2_Y	18_E	0.529	0.67
43_I	59_L	0.516	0.66
14_E	17_E	0.504	0.64
21_Y	46_L	0.500	0.63

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
3pbtA	1	0.9538	28.3	0.845	Contact Map
3equA	1	0.9538	26.2	0.847	Contact Map
4bjpA	2	0.9538	24	0.85	Contact Map
3ue3A	1	0.9538	19.9	0.855	Contact Map
4ztkA	1	0.9538	18.3	0.858	Contact Map
4ovdA	2	0.9077	18.1	0.859	Contact Map
1qmeA	1	0.9538	15.5	0.862	Contact Map
1dzfA	1	0.7692	12.6	0.868	Contact Map
4ye5A	1	0.9538	12	0.869	Contact Map
4r23A	1	0.8615	11.1	0.871	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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