YKZQ - BACSU - GREMLIN Contacts

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YKZQ - Uncharacterized protein YkzQ

UniProt:	C0H403	Sequences: MKGKIPKIRNQANKVKRTPRYMEFPVTYEVYHVESGDTLWTIAKSFEIPVQQLMNLNKLSSDRIYPGQIIKIRER	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	75 (61)
Sequences:	4620 (4057)
Seq/√Len:	519.4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_H	69_I	2.677	1.00
52_Q	56_L	2.404	1.00
40_W	44_K	2.215	1.00
43_A	50_V	2.196	1.00
38_T	41_T	2.129	1.00
53_L	70_I	2.065	1.00
31_Y	46_F	2.052	1.00
30_V	69_I	1.955	1.00
31_Y	37_D	1.818	1.00
54_M	62_D	1.760	1.00
65_Y	68_Q	1.739	1.00
31_Y	42_I	1.708	1.00
48_I	56_L	1.659	1.00
33_V	70_I	1.644	1.00
49_P	52_Q	1.610	1.00
50_V	54_M	1.568	1.00
54_M	61_S	1.494	1.00
48_I	52_Q	1.486	1.00
39_L	61_S	1.422	1.00
52_Q	55_N	1.407	1.00
51_Q	55_N	1.371	1.00
34_E	37_D	1.319	1.00
28_Y	71_K	1.234	1.00
23_E	30_V	1.217	1.00
41_T	45_S	1.215	1.00
32_H	67_G	1.176	1.00
19_P	23_E	1.163	1.00
27_T	71_K	1.117	1.00
31_Y	34_E	1.072	1.00
46_F	72_I	1.059	1.00
53_L	59_L	1.053	1.00
48_I	53_L	1.051	1.00
56_L	72_I	1.038	1.00
30_V	71_K	1.030	1.00
33_V	37_D	1.016	1.00
58_K	71_K	0.935	1.00
37_D	41_T	0.928	1.00
37_D	45_S	0.927	1.00
39_L	59_L	0.926	1.00
51_Q	54_M	0.905	1.00
43_A	48_I	0.886	1.00
39_L	54_M	0.876	1.00
39_L	50_V	0.875	1.00
12_A	15_V	0.872	1.00
20_R	23_E	0.855	1.00
56_L	71_K	0.819	1.00
54_M	59_L	0.804	1.00
39_L	53_L	0.788	1.00
40_W	43_A	0.774	1.00
42_I	70_I	0.724	1.00
29_E	46_F	0.717	1.00
18_T	22_M	0.711	1.00
54_M	60_S	0.698	1.00
38_T	44_K	0.695	1.00
31_Y	45_S	0.691	1.00
32_H	68_Q	0.688	1.00
12_A	20_R	0.685	1.00
37_D	66_P	0.680	1.00
33_V	42_I	0.674	1.00
42_I	64_I	0.669	1.00
59_L	70_I	0.658	1.00
39_L	64_I	0.631	1.00
39_L	71_K	0.628	1.00
43_A	46_F	0.623	1.00
33_V	68_Q	0.622	1.00
34_E	45_S	0.613	1.00
41_T	44_K	0.608	1.00
38_T	43_A	0.599	0.99
18_T	69_I	0.595	0.99
40_W	50_V	0.592	0.99
14_K	17_R	0.584	0.99
42_I	46_F	0.573	0.99
26_V	29_E	0.571	0.99
17_R	22_M	0.565	0.99
15_V	23_E	0.564	0.99
36_G	66_P	0.558	0.99
61_S	71_K	0.551	0.99
54_M	58_K	0.546	0.99
15_V	18_T	0.544	0.99
15_V	19_P	0.543	0.99
37_D	64_I	0.539	0.99
35_S	67_G	0.539	0.99
60_S	63_R	0.539	0.99
14_K	18_T	0.532	0.99
38_T	64_I	0.529	0.99
37_D	42_I	0.528	0.99
34_E	67_G	0.527	0.99
59_L	62_D	0.525	0.99
28_Y	56_L	0.523	0.99
13_N	17_R	0.505	0.98
59_L	64_I	0.501	0.98
35_S	66_P	0.500	0.98

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
4xcmA	2	0.6267	99.2	0.358	Contact Map
4b8vA	2	0.7067	99.2	0.371	Contact Map
2mkxA	1	0.6667	99.1	0.376	Contact Map
2djpA	1	0.8267	99.1	0.382	Contact Map
4pxvA	1	0.6267	99.1	0.388	Contact Map
2l9yA	1	1	99	0.414	Contact Map
4uz3A	1	0.64	99	0.415	Contact Map
2mpwA	1	0.9467	99	0.416	Contact Map
1e0gA	1	0.64	98.9	0.427	Contact Map
4ebyA	1	0.7067	98.8	0.442	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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