YUKE - BACSU - GREMLIN Contacts

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YUKE - Uncharacterized protein YukE

UniProt:	C0SP85	Sequences: MAGLIRVTPEELRAMAKQYGVESQEVLNQVDRLNRMISDLKSMWEGASSEAFADQYEQLKPSFIKMSDLLQDVNQQLDQTANTLESTDQDIANQIRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	97 (93)
Sequences:	126 (87)
Seq/√Len:	9.0

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
13_R	85_E	4.416	0.99
47_A	50_E	2.369	0.76
62_S	66_M	2.354	0.76
55_Q	76_Q	2.331	0.75
34_N	56_Y	2.081	0.66
15_M	36_M	2.069	0.66
6_R	40_L	2.055	0.65
86_S	90_D	2.049	0.65
47_A	89_Q	2.022	0.64
10_E	89_Q	1.964	0.61
68_D	72_D	1.905	0.59
79_Q	82_N	1.804	0.54
3_G	51_A	1.640	0.47
83_T	87_T	1.592	0.45
43_M	73_V	1.591	0.45
37_I	52_F	1.574	0.45
14_A	68_D	1.548	0.43
68_D	71_Q	1.539	0.43
34_N	58_Q	1.526	0.42
43_M	95_I	1.517	0.42
27_L	67_S	1.462	0.40
87_T	91_I	1.449	0.39
26_V	29_Q	1.448	0.39
23_S	70_L	1.437	0.39
42_S	89_Q	1.370	0.36
52_F	76_Q	1.364	0.36
24_Q	75_Q	1.331	0.34
6_R	45_E	1.317	0.34
36_M	56_Y	1.301	0.33
22_E	26_V	1.298	0.33
7_V	43_M	1.230	0.31
7_V	36_M	1.218	0.30
65_K	75_Q	1.192	0.29
52_F	55_Q	1.179	0.29
6_R	60_K	1.178	0.29
51_A	92_A	1.164	0.28
8_T	84_L	1.162	0.28
21_V	25_E	1.154	0.28
12_L	70_L	1.140	0.27
80_T	83_T	1.138	0.27
11_E	70_L	1.133	0.27
24_Q	68_D	1.129	0.27
6_R	80_T	1.127	0.27
55_Q	66_M	1.123	0.27
12_L	33_L	1.104	0.26
52_F	95_I	1.100	0.26
49_S	74_N	1.100	0.26
14_A	28_N	1.092	0.26
36_M	48_S	1.087	0.26
25_E	60_K	1.083	0.25
41_K	53_A	1.078	0.25
25_E	68_D	1.077	0.25
19_Y	77_L	1.027	0.24
12_L	55_Q	0.991	0.22
82_N	85_E	0.987	0.22
18_Q	72_D	0.986	0.22
37_I	66_M	0.967	0.22
36_M	40_L	0.963	0.22
33_L	70_L	0.956	0.21
30_V	62_S	0.952	0.21
22_E	94_Q	0.949	0.21
12_L	74_N	0.923	0.20
54_D	64_I	0.910	0.20
7_V	95_I	0.855	0.19
63_F	92_A	0.848	0.18
20_G	74_N	0.835	0.18
28_N	38_S	0.829	0.18
7_V	56_Y	0.824	0.18
21_V	42_S	0.823	0.18
63_F	66_M	0.821	0.18
48_S	73_V	0.814	0.18
15_M	18_Q	0.812	0.18
31_D	86_S	0.809	0.17
49_S	63_F	0.784	0.17
52_F	67_S	0.780	0.17
37_I	49_S	0.776	0.17
15_M	43_M	0.764	0.16
19_Y	59_L	0.763	0.16
37_I	55_Q	0.763	0.16
18_Q	33_L	0.751	0.16
4_L	45_E	0.744	0.16
57_E	68_D	0.744	0.16
34_N	60_K	0.744	0.16
86_S	89_Q	0.740	0.16
28_N	42_S	0.738	0.16
26_V	70_L	0.728	0.16
4_L	36_M	0.725	0.15
74_N	78_D	0.722	0.15
12_L	76_Q	0.717	0.15
45_E	80_T	0.705	0.15
67_S	71_Q	0.700	0.15
55_Q	70_L	0.694	0.15
16_A	87_T	0.693	0.15
12_L	66_M	0.689	0.15
56_Y	90_D	0.688	0.15
19_Y	56_Y	0.685	0.15
63_F	91_I	0.680	0.14
27_L	31_D	0.678	0.14
11_E	52_F	0.673	0.14
48_S	86_S	0.671	0.14
53_A	91_I	0.670	0.14
40_L	61_P	0.649	0.14
42_S	50_E	0.642	0.14
13_R	16_A	0.635	0.13
17_K	54_D	0.634	0.13
8_T	86_S	0.628	0.13
68_D	89_Q	0.625	0.13
23_S	27_L	0.624	0.13
37_I	76_Q	0.621	0.13
25_E	47_A	0.619	0.13
23_S	71_Q	0.618	0.13
57_E	60_K	0.612	0.13
25_E	78_D	0.610	0.13
36_M	45_E	0.607	0.13
31_D	35_R	0.605	0.13
80_T	91_I	0.605	0.13
20_G	78_D	0.590	0.13
37_I	62_S	0.586	0.13
65_K	71_Q	0.585	0.13
65_K	68_D	0.575	0.12
11_E	73_V	0.566	0.12
19_Y	81_A	0.565	0.12
50_E	57_E	0.550	0.12
40_L	49_S	0.549	0.12
78_D	90_D	0.548	0.12
8_T	29_Q	0.544	0.12
62_S	92_A	0.538	0.12
24_Q	28_N	0.538	0.12
40_L	80_T	0.535	0.12
66_M	76_Q	0.533	0.12
13_R	81_A	0.515	0.11
31_D	89_Q	0.510	0.11
12_L	19_Y	0.510	0.11
33_L	52_F	0.510	0.11
66_M	74_N	0.509	0.11
87_T	94_Q	0.505	0.11
9_P	59_L	0.503	0.11
15_M	40_L	0.503	0.11
12_L	49_S	0.502	0.11
50_E	58_Q	0.500	0.11

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
3ogiB	1	0.9175	99.8	0.517	Contact Map
3gwkC	2	1	99.7	0.539	Contact Map
4lwsA	1	0.9691	99.7	0.54	Contact Map
3zbhA	2	1	99.7	0.54	Contact Map
4lwsB	1	0.8763	99.7	0.549	Contact Map
3h6pC	1	0.5773	99.7	0.555	Contact Map
3favA	1	0.9278	99.6	0.571	Contact Map
3favB	1	0.8041	99.6	0.587	Contact Map
2vs0A	2	0.8763	99.6	0.588	Contact Map
4i0xB	1	0.9072	99.5	0.6	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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