YLBA - BACSU - GREMLIN Contacts

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YLBA - Uncharacterized protein YlbA

UniProt:	O34743	Sequences: MLKFTESGLEGVKAELSWLDDLMESKGLIRAGQWDYERVTYDKKFSTIEGTFYLRIQGIAAEGDVGSGRAVIQLMSPLLGKHYYPHGVEYGETEEFPVQVVTKSKALIQDIANMLKTVQM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	120 (112)
Sequences:	177 (121)
Seq/√Len:	11.4

BACSU - YLBA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_D	30_R	5.238	1.00
32_G	40_T	3.278	0.97
56_I	108_I	3.009	0.95
30_R	41_Y	2.831	0.93
112_A	116_K	2.787	0.92
65_V	72_I	2.699	0.91
58_G	72_I	2.314	0.83
16_L	20_D	2.149	0.78
45_F	107_L	2.144	0.78
20_D	41_Y	2.099	0.76
11_G	73_Q	2.001	0.73
16_L	72_I	1.989	0.72
51_T	82_H	1.942	0.70
8_G	112_A	1.939	0.70
39_V	58_G	1.938	0.70
79_L	101_V	1.869	0.67
54_L	108_I	1.769	0.63
58_G	74_L	1.747	0.62
28_L	43_K	1.734	0.61
29_I	75_M	1.732	0.61
4_F	81_K	1.609	0.55
6_E	105_K	1.606	0.55
43_K	107_L	1.593	0.54
46_S	51_T	1.545	0.52
4_F	108_I	1.529	0.51
52_F	112_A	1.477	0.49
3_K	57_Q	1.450	0.47
13_K	73_Q	1.420	0.46
83_Y	94_E	1.373	0.44
106_A	109_Q	1.367	0.43
12_V	21_D	1.356	0.43
102_T	105_K	1.334	0.42
26_K	114_M	1.316	0.41
89_E	94_E	1.243	0.37
80_G	90_Y	1.230	0.37
19_L	74_L	1.204	0.36
25_S	69_R	1.196	0.35
17_S	68_G	1.193	0.35
60_A	79_L	1.188	0.35
84_Y	94_E	1.177	0.35
100_V	109_Q	1.167	0.34
7_S	10_E	1.162	0.34
98_V	106_A	1.136	0.33
25_S	114_M	1.126	0.32
35_D	77_P	1.118	0.32
97_P	115_L	1.115	0.32
14_A	53_Y	1.109	0.32
16_L	30_R	1.087	0.31
75_M	108_I	1.085	0.31
110_D	113_N	1.062	0.30
3_K	76_S	1.031	0.28
106_A	113_N	1.019	0.28
35_D	82_H	1.016	0.28
13_K	30_R	1.007	0.27
3_K	78_L	1.006	0.27
43_K	52_F	0.961	0.26
83_Y	89_E	0.952	0.25
61_A	109_Q	0.924	0.24
65_V	88_V	0.918	0.24
15_E	21_D	0.912	0.24
88_V	94_E	0.906	0.24
56_I	113_N	0.906	0.24
37_E	84_Y	0.902	0.24
105_K	109_Q	0.897	0.23
41_Y	61_A	0.896	0.23
13_K	22_L	0.890	0.23
7_S	111_I	0.874	0.23
75_M	111_I	0.866	0.22
3_K	106_A	0.864	0.22
100_V	104_S	0.861	0.22
71_V	109_Q	0.856	0.22
38_R	90_Y	0.856	0.22
38_R	83_Y	0.855	0.22
57_Q	78_L	0.846	0.22
63_G	90_Y	0.830	0.21
38_R	80_G	0.814	0.21
53_Y	94_E	0.803	0.20
63_G	80_G	0.800	0.20
5_T	109_Q	0.798	0.20
48_I	102_T	0.797	0.20
45_F	100_V	0.792	0.20
4_F	106_A	0.792	0.20
9_L	102_T	0.783	0.20
26_K	52_F	0.783	0.20
27_G	54_L	0.776	0.19
54_L	111_I	0.771	0.19
33_Q	97_P	0.770	0.19
54_L	97_P	0.762	0.19
39_V	79_L	0.761	0.19
5_T	112_A	0.761	0.19
56_I	82_H	0.756	0.19
48_I	104_S	0.755	0.19
14_A	98_V	0.751	0.19
37_E	83_Y	0.738	0.18
37_E	94_E	0.731	0.18
52_F	69_R	0.725	0.18
77_P	82_H	0.722	0.18
28_L	68_G	0.715	0.18
65_V	96_F	0.713	0.18
19_L	41_Y	0.702	0.17
9_L	116_K	0.702	0.17
7_S	116_K	0.696	0.17
84_Y	111_I	0.695	0.17
61_A	114_M	0.684	0.17
48_I	112_A	0.680	0.17
40_T	70_A	0.680	0.17
33_Q	91_G	0.670	0.16
66_G	91_G	0.667	0.16
20_D	86_H	0.663	0.16
102_T	106_A	0.661	0.16
83_Y	88_V	0.661	0.16
69_R	73_Q	0.659	0.16
33_Q	59_I	0.657	0.16
52_F	105_K	0.657	0.16
11_G	59_I	0.652	0.16
74_L	91_G	0.652	0.16
9_L	56_I	0.644	0.16
11_G	18_W	0.644	0.16
9_L	113_N	0.642	0.16
45_F	103_K	0.640	0.16
41_Y	66_G	0.639	0.16
9_L	106_A	0.635	0.15
84_Y	89_E	0.625	0.15
109_Q	113_N	0.622	0.15
5_T	27_G	0.621	0.15
48_I	101_V	0.617	0.15
88_V	96_F	0.617	0.15
52_F	115_L	0.614	0.15
35_D	83_Y	0.612	0.15
74_L	99_Q	0.612	0.15
4_F	53_Y	0.611	0.15
28_L	41_Y	0.610	0.15
50_G	54_L	0.601	0.15
22_L	29_I	0.589	0.14
98_V	102_T	0.585	0.14
5_T	38_R	0.583	0.14
108_I	112_A	0.580	0.14
56_I	78_L	0.578	0.14
30_R	66_G	0.575	0.14
9_L	73_Q	0.574	0.14
65_V	84_Y	0.574	0.14
26_K	89_E	0.572	0.14
26_K	29_I	0.569	0.14
43_K	100_V	0.568	0.14
57_Q	107_L	0.558	0.14
34_W	97_P	0.558	0.14
51_T	96_F	0.558	0.14
18_W	43_K	0.540	0.13
39_V	100_V	0.539	0.13
12_V	57_Q	0.537	0.13
12_V	16_L	0.535	0.13
17_S	45_F	0.534	0.13
83_Y	96_F	0.533	0.13
74_L	77_P	0.533	0.13
47_T	50_G	0.532	0.13
16_L	66_G	0.529	0.13
49_E	73_Q	0.526	0.13
10_E	60_A	0.523	0.13
21_D	41_Y	0.514	0.13
84_Y	96_F	0.512	0.13
62_E	113_N	0.511	0.13
28_L	47_T	0.511	0.13
4_F	37_E	0.510	0.13
105_K	114_M	0.506	0.12
39_V	78_L	0.505	0.12
9_L	74_L	0.503	0.12
12_V	116_K	0.501	0.12
86_H	108_I	0.500	0.12

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
2r5xA	1	0.975	100	0.243	Contact Map
2pwwA	1	0.9583	100	0.259	Contact Map
1t6aA	1	0.8833	23.9	0.946	Contact Map
1yrtA	1	0.8833	19.3	0.948	Contact Map
3rfyA	2	0.6333	18	0.949	Contact Map
3ottA	2	0.675	15	0.951	Contact Map
1y791	1	0.3833	10.5	0.954	Contact Map
2wn9A	3	0.4083	10.4	0.954	Contact Map
4zk1A	4	0.5167	9.1	0.955	Contact Map
2im5A	1	0.9	8.1	0.956	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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