YFKK - BACSU - GREMLIN Contacts

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YFKK - UPF0435 protein YfkK

UniProt:	O35019	Sequences: MSSPNTETLTQMIEEISQKLNMLNVGVIKAEDFSDEKIEDLTYLHRMVMKKESFSPSEMQAIAQELASLRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	71 (68)
Sequences:	160 (108)
Seq/√Len:	13.1

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
51_K	58_E	2.246	0.86
42_T	46_R	2.206	0.85
22_M	34_S	2.176	0.84
40_D	43_Y	2.153	0.83
5_N	36_E	1.746	0.68
54_F	62_I	1.712	0.66
23_L	56_P	1.708	0.66
11_Q	45_H	1.700	0.65
21_N	56_P	1.697	0.65
14_E	17_S	1.695	0.65
9_L	24_N	1.614	0.61
3_S	44_L	1.613	0.61
8_T	11_Q	1.599	0.60
56_P	60_Q	1.583	0.60
15_E	45_H	1.497	0.55
15_E	18_Q	1.487	0.55
10_T	44_L	1.442	0.52
21_N	63_A	1.396	0.50
37_K	64_Q	1.381	0.49
55_S	61_A	1.354	0.48
58_E	70_R	1.278	0.44
27_V	33_F	1.275	0.44
13_I	59_M	1.254	0.43
47_M	61_A	1.248	0.42
17_S	27_V	1.241	0.42
24_N	68_S	1.236	0.42
19_K	62_I	1.235	0.42
23_L	40_D	1.235	0.42
9_L	35_D	1.225	0.41
5_N	8_T	1.221	0.41
22_M	48_V	1.172	0.38
24_N	54_F	1.154	0.38
16_I	51_K	1.146	0.37
26_G	51_K	1.141	0.37
13_I	41_L	1.139	0.37
15_E	40_D	1.099	0.35
39_E	48_V	1.084	0.34
16_I	63_A	1.070	0.33
8_T	45_H	1.066	0.33
47_M	62_I	1.051	0.33
24_N	50_K	0.999	0.30
14_E	25_V	0.996	0.30
18_Q	62_I	0.995	0.30
10_T	46_R	0.993	0.30
44_L	70_R	0.989	0.30
44_L	54_F	0.966	0.29
4_P	51_K	0.955	0.28
43_Y	46_R	0.947	0.28
18_Q	39_E	0.906	0.26
47_M	58_E	0.897	0.26
43_Y	62_I	0.896	0.26
10_T	31_E	0.893	0.26
23_L	31_E	0.886	0.26
19_K	41_L	0.885	0.25
24_N	56_P	0.848	0.24
41_L	59_M	0.848	0.24
12_M	30_A	0.785	0.22
15_E	47_M	0.776	0.21
48_V	63_A	0.768	0.21
11_Q	46_R	0.766	0.21
41_L	50_K	0.749	0.20
3_S	30_A	0.749	0.20
21_N	25_V	0.748	0.20
11_Q	49_M	0.741	0.20
17_S	70_R	0.740	0.20
24_N	31_E	0.733	0.20
3_S	50_K	0.728	0.20
48_V	67_A	0.727	0.20
50_K	64_Q	0.702	0.19
41_L	47_M	0.696	0.19
22_M	56_P	0.691	0.19
40_D	70_R	0.684	0.18
14_E	36_E	0.682	0.18
41_L	54_F	0.671	0.18
5_N	31_E	0.665	0.18
29_K	41_L	0.665	0.18
31_E	36_E	0.635	0.17
30_A	52_E	0.635	0.17
6_T	56_P	0.631	0.17
28_I	70_R	0.628	0.17
40_D	44_L	0.624	0.16
12_M	37_K	0.619	0.16
7_E	32_D	0.610	0.16
4_P	39_E	0.610	0.16
39_E	45_H	0.607	0.16
13_I	33_F	0.600	0.16
3_S	37_K	0.597	0.16
38_I	45_H	0.591	0.16
6_T	60_Q	0.577	0.15
5_N	49_M	0.575	0.15
36_E	41_L	0.574	0.15
51_K	68_S	0.572	0.15
14_E	18_Q	0.560	0.15
50_K	54_F	0.557	0.15
7_E	45_H	0.554	0.15
9_L	38_I	0.554	0.15
29_K	60_Q	0.542	0.14
29_K	59_M	0.537	0.14
16_I	27_V	0.536	0.14
51_K	57_S	0.532	0.14
12_M	32_D	0.505	0.13
4_P	35_D	0.500	0.13

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
1y14A	1	0.9718	64.6	0.875	Contact Map
4qjfB	1	0.9718	60.9	0.878	Contact Map
3h0gD	1	0.9437	59.5	0.879	Contact Map
4aybF	1	0.9014	59.2	0.879	Contact Map
2p01A	1	0.9437	46.2	0.888	Contact Map
1go3F	1	0.9014	40.3	0.892	Contact Map
2c35A	1	0.9577	31	0.898	Contact Map
4m0mA	1	0.6761	27.5	0.901	Contact Map
1g6uA	3	0.4789	27.5	0.901	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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