YRKD - BACSU - GREMLIN Contacts

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YRKD - Uncharacterized protein YrkD

UniProt:	P54431	Sequences: MMEQGKDCREVVTQLAASRNAIDRAMGLIVSTNLEHCVRESLEKGEDTQNLVKEAVDLLVKSR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	63 (63)
Sequences:	211 (115)
Seq/√Len:	14.5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
35_E	39_R	3.542	0.99
18_S	22_I	3.272	0.99
19_R	23_D	3.185	0.98
27_G	38_V	2.281	0.89
13_T	24_R	2.178	0.87
31_S	38_V	2.002	0.82
53_K	56_V	1.971	0.81
31_S	56_V	1.948	0.80
11_V	15_L	1.750	0.72
30_V	34_L	1.736	0.71
48_T	52_V	1.635	0.66
48_T	51_L	1.457	0.57
15_L	22_I	1.410	0.55
51_L	56_V	1.392	0.54
22_I	58_L	1.326	0.50
23_D	63_R	1.325	0.50
19_R	63_R	1.293	0.48
31_S	46_E	1.208	0.44
38_V	41_S	1.169	0.42
24_R	27_G	1.160	0.41
2_M	6_K	1.154	0.41
1_M	52_V	1.144	0.40
53_K	57_D	1.138	0.40
15_L	29_I	1.137	0.40
32_T	58_L	1.135	0.40
2_M	42_L	1.100	0.38
22_I	42_L	1.094	0.38
12_V	42_L	1.070	0.36
3_E	52_V	1.053	0.35
20_N	57_D	1.024	0.34
28_L	31_S	1.011	0.33
36_H	41_S	1.006	0.33
34_L	56_V	1.004	0.33
4_Q	16_A	0.952	0.31
7_D	40_E	0.944	0.30
4_Q	39_R	0.916	0.29
12_V	60_V	0.914	0.29
15_L	26_M	0.909	0.29
27_G	57_D	0.906	0.28
7_D	58_L	0.880	0.27
32_T	56_V	0.869	0.27
19_R	30_V	0.867	0.27
12_V	18_S	0.866	0.27
12_V	35_E	0.864	0.27
3_E	44_K	0.836	0.25
31_S	51_L	0.834	0.25
27_G	56_V	0.834	0.25
18_S	42_L	0.822	0.25
10_E	32_T	0.821	0.25
4_Q	50_N	0.808	0.24
40_E	63_R	0.805	0.24
35_E	38_V	0.781	0.23
49_Q	53_K	0.776	0.23
13_T	50_N	0.769	0.23
43_E	47_D	0.763	0.22
45_G	60_V	0.757	0.22
36_H	42_L	0.756	0.22
2_M	29_I	0.752	0.22
9_R	12_V	0.752	0.22
6_K	52_V	0.751	0.22
56_V	59_L	0.744	0.22
25_A	28_L	0.740	0.22
13_T	16_A	0.736	0.21
12_V	26_M	0.715	0.21
5_G	48_T	0.696	0.20
18_S	41_S	0.669	0.19
3_E	25_A	0.663	0.19
25_A	50_N	0.639	0.18
40_E	44_K	0.629	0.18
12_V	32_T	0.620	0.17
1_M	35_E	0.615	0.17
9_R	60_V	0.611	0.17
7_D	43_E	0.610	0.17
10_E	43_E	0.606	0.17
6_K	51_L	0.603	0.17
27_G	60_V	0.598	0.17
21_A	49_Q	0.595	0.17
5_G	11_V	0.579	0.16
23_D	60_V	0.578	0.16
28_L	47_D	0.575	0.16
5_G	47_D	0.563	0.16
48_T	59_L	0.547	0.15
2_M	20_N	0.545	0.15
31_S	58_L	0.543	0.15
6_K	19_R	0.530	0.15
2_M	53_K	0.529	0.15
50_N	57_D	0.526	0.15
36_H	50_N	0.522	0.15
3_E	50_N	0.520	0.14
49_Q	63_R	0.516	0.14
1_M	54_E	0.511	0.14
1_M	10_E	0.510	0.14
45_G	48_T	0.501	0.14
42_L	48_T	0.500	0.14

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
4m1pA	3	0.9841	99.3	0.544	Contact Map
2hh7A	3	0.9524	99.3	0.545	Contact Map
4adzA	4	1	99.3	0.547	Contact Map
3aaiA	3	0.8413	99.3	0.552	Contact Map
3kxeC	2	0.619	21.7	0.899	Contact Map
1l6nA	1	0.873	11.1	0.912	Contact Map
1paqA	1	0.9841	8	0.917	Contact Map
3a11A	4	0.9365	7.7	0.918	Contact Map
2ve8A	1	0.2857	7.6	0.918	Contact Map
1vb5A	3	0.9206	7.4	0.919	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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