YWBE - BACSU - GREMLIN Contacts

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YWBE - Uncharacterized protein YwbE

UniProt:	P39588	Sequences: MNGQERNSISKGLQVDIVLKADQKTGKLTRGTVKDILTKSNFHPHGIKVRLEDGRIGRDQQIVST	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	65 (62)
Sequences:	410 (227)
Seq/√Len:	28.8

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_D	50_R	3.878	1.00
16_D	30_R	3.637	1.00
22_D	27_K	3.436	1.00
14_Q	30_R	2.818	1.00
19_L	55_R	2.795	1.00
9_I	33_V	2.448	0.99
18_V	60_Q	2.048	0.97
28_L	60_Q	2.008	0.97
16_D	61_Q	1.824	0.94
11_K	35_D	1.664	0.91
45_H	60_Q	1.628	0.90
21_A	27_K	1.598	0.89
16_D	63_V	1.591	0.89
17_I	55_R	1.269	0.75
44_P	56_I	1.266	0.75
5_E	42_F	1.225	0.72
16_D	28_L	1.198	0.70
45_H	56_I	1.165	0.68
14_Q	32_T	1.159	0.68
25_T	60_Q	1.157	0.68
19_L	22_D	1.118	0.65
4_Q	44_P	1.060	0.61
9_I	36_I	1.058	0.61
39_K	44_P	1.032	0.59
10_S	13_L	1.032	0.59
2_N	8_S	1.029	0.58
42_F	45_H	1.023	0.58
40_S	44_P	1.000	0.56
7_N	10_S	0.998	0.56
9_I	13_L	0.993	0.56
40_S	45_H	0.979	0.55
14_Q	63_V	0.978	0.54
39_K	60_Q	0.969	0.54
11_K	50_R	0.960	0.53
6_R	36_I	0.900	0.48
25_T	61_Q	0.897	0.48
18_V	45_H	0.886	0.47
50_R	56_I	0.886	0.47
28_L	61_Q	0.878	0.47
7_N	41_N	0.860	0.45
2_N	5_E	0.853	0.45
5_E	8_S	0.820	0.42
21_A	55_R	0.812	0.42
32_T	52_E	0.782	0.39
3_G	24_K	0.782	0.39
50_R	54_G	0.763	0.38
5_E	10_S	0.757	0.38
36_I	39_K	0.756	0.37
18_V	28_L	0.749	0.37
34_K	50_R	0.735	0.36
11_K	52_E	0.732	0.36
17_I	49_V	0.725	0.35
16_D	62_I	0.724	0.35
4_Q	45_H	0.719	0.35
5_E	41_N	0.709	0.34
30_R	61_Q	0.692	0.33
10_S	56_I	0.691	0.33
39_K	45_H	0.688	0.33
34_K	53_D	0.683	0.32
10_S	18_V	0.675	0.32
4_Q	62_I	0.668	0.31
25_T	63_V	0.666	0.31
39_K	52_E	0.662	0.31
13_L	62_I	0.652	0.30
17_I	35_D	0.622	0.28
10_S	41_N	0.618	0.28
11_K	36_I	0.604	0.27
27_K	32_T	0.604	0.27
32_T	53_D	0.599	0.27
3_G	36_I	0.589	0.26
17_I	24_K	0.585	0.26
60_Q	63_V	0.584	0.26
14_Q	34_K	0.582	0.26
7_N	42_F	0.571	0.25
3_G	62_I	0.568	0.25
2_N	27_K	0.563	0.25
32_T	63_V	0.561	0.25
35_D	52_E	0.558	0.24
8_S	61_Q	0.556	0.24
49_V	54_G	0.554	0.24
9_I	42_F	0.551	0.24
13_L	32_T	0.546	0.24
21_A	32_T	0.540	0.23
7_N	13_L	0.537	0.23
51_L	54_G	0.534	0.23
17_I	50_R	0.533	0.23
4_Q	32_T	0.528	0.23
13_L	63_V	0.527	0.23
42_F	63_V	0.521	0.22
15_V	29_T	0.515	0.22
11_K	42_F	0.506	0.22
14_Q	53_D	0.501	0.21
17_I	51_L	0.500	0.21

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
4hikA	1	0.9077	22.3	0.903	Contact Map
4ql5A	4	0.5231	15.5	0.91	Contact Map
3dlmA	1	0.8308	13.3	0.913	Contact Map
4lduA	2	1	12.3	0.914	Contact Map
3sqrA	1	0.8154	10.2	0.917	Contact Map
1aozA	3	0.8154	10	0.917	Contact Map
2q9oA	2	0.8	9.6	0.918	Contact Map
3i4oA	1	0.5231	8.6	0.92	Contact Map
3gdcA	3	0.8	8	0.921	Contact Map
1x6vB	2	0.9231	7.8	0.921	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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