YRKI - BACSU - GREMLIN Contacts

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YRKI - UPF0033 protein YrkI

UniProt:	P54436	Sequences: MKSDKVLDAKGLACPMPIVRTKKAMNELESGQILEVHATDKGAKNDLTAWSKSGGHDLLEQTDEGDILKFWIQKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	75 (72)
Sequences:	1201 (708)
Seq/√Len:	83.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
57_D	73_Q	3.382	1.00
29_E	32_Q	3.043	1.00
4_D	32_Q	3.015	1.00
10_K	67_I	2.883	1.00
35_E	69_K	2.648	1.00
6_V	35_E	2.303	1.00
33_I	71_W	2.025	1.00
10_K	37_H	1.964	1.00
51_S	72_I	1.902	1.00
5_K	27_E	1.704	1.00
5_K	28_L	1.628	1.00
63_D	66_D	1.597	1.00
28_L	32_Q	1.551	1.00
37_H	67_I	1.497	0.99
36_V	47_L	1.467	0.99
10_K	39_T	1.443	0.99
21_T	34_L	1.417	0.99
33_I	59_L	1.384	0.99
48_T	52_K	1.322	0.99
21_T	47_L	1.244	0.98
58_L	70_F	1.242	0.98
6_V	37_H	1.239	0.98
5_K	32_Q	1.216	0.98
44_K	61_Q	1.215	0.98
19_V	50_W	1.201	0.97
43_A	70_F	1.144	0.96
43_A	68_L	1.135	0.96
44_K	63_D	1.132	0.96
12_L	20_R	1.130	0.96
23_K	27_E	1.125	0.96
25_M	50_W	1.109	0.96
16_M	19_V	1.095	0.95
37_H	69_K	1.066	0.95
35_E	71_W	1.051	0.94
38_A	43_A	1.030	0.94
22_K	26_N	1.013	0.93
62_T	69_K	1.012	0.93
60_E	71_W	1.012	0.93
33_I	73_Q	0.997	0.92
51_S	55_G	0.991	0.92
24_A	27_E	0.989	0.92
24_A	28_L	0.974	0.92
44_K	68_L	0.945	0.90
21_T	36_V	0.932	0.90
16_M	20_R	0.925	0.89
18_I	53_S	0.915	0.89
41_K	68_L	0.915	0.89
22_K	42_G	0.881	0.87
61_Q	70_F	0.871	0.86
7_L	34_L	0.842	0.84
38_A	68_L	0.830	0.84
5_K	24_A	0.819	0.83
18_I	22_K	0.817	0.83
19_V	25_M	0.815	0.82
7_L	24_A	0.807	0.82
12_L	16_M	0.801	0.81
48_T	70_F	0.787	0.80
4_D	28_L	0.784	0.80
13_A	22_K	0.751	0.77
28_L	34_L	0.743	0.76
25_M	28_L	0.737	0.76
30_S	74_K	0.735	0.75
51_S	58_L	0.733	0.75
44_K	48_T	0.709	0.73
64_E	69_K	0.705	0.72
64_E	67_I	0.704	0.72
7_L	36_V	0.691	0.71
3_S	35_E	0.689	0.71
63_D	68_L	0.672	0.69
45_N	49_A	0.672	0.69
37_H	71_W	0.662	0.68
48_T	61_Q	0.662	0.68
3_S	6_V	0.660	0.67
18_I	21_T	0.658	0.67
22_K	43_A	0.656	0.67
41_K	53_S	0.650	0.66
19_V	43_A	0.641	0.65
58_L	68_L	0.631	0.64
9_A	21_T	0.626	0.63
42_G	49_A	0.615	0.62
25_M	53_S	0.613	0.62
45_N	54_G	0.612	0.62
25_M	74_K	0.612	0.62
45_N	48_T	0.609	0.61
18_I	42_G	0.607	0.61
13_A	43_A	0.607	0.61
42_G	50_W	0.604	0.61
22_K	54_G	0.600	0.60
44_K	47_L	0.597	0.60
62_T	71_W	0.591	0.59
3_S	71_W	0.590	0.59
39_T	54_G	0.583	0.58
5_K	20_R	0.582	0.58
28_L	74_K	0.572	0.56
33_I	60_E	0.567	0.56
18_I	23_K	0.562	0.55
38_A	73_Q	0.552	0.54
21_T	74_K	0.536	0.52
26_N	56_H	0.531	0.51
6_V	69_K	0.526	0.50
26_N	50_W	0.525	0.50
24_A	36_V	0.525	0.50
61_Q	71_W	0.523	0.50
18_I	54_G	0.521	0.50
9_A	49_A	0.517	0.49
13_A	16_M	0.508	0.48
27_E	65_G	0.503	0.47
70_F	74_K	0.500	0.47

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
1je3A	1	0.9867	99.9	0.297	Contact Map
1jdqA	1	1	99.9	0.297	Contact Map
1pavA	1	1	99.9	0.306	Contact Map
3lvjC	1	1	99.9	0.306	Contact Map
3hz7A	1	0.96	99.9	0.335	Contact Map
2lxrA	1	0.92	99.8	0.405	Contact Map
1okgA	1	0.7333	98.6	0.676	Contact Map
2vd8A	2	0.9333	32.3	0.899	Contact Map
1xfcA	2	0.96	31.5	0.9	Contact Map
4bhyA	2	0.92	22.2	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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