YQBS - BACSU - GREMLIN Contacts

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YQBS - Uncharacterized protein YqbS

UniProt:	P45934	Sequences: MALSPEIEFEDIEDDSEVIETSQTYKIDFENGRITNEIITGLEAIKQFVYLSLHTERYAYSVYSHDIGNELQDVLADNETTDAYKKMEIPRLIEEALIYDDRISAVTDFEIEKQGESFRVSFTVETDEGTLEIEEVLGEDV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	141 (120)
Sequences:	354 (320)
Seq/√Len:	29.2

BACSU - YQBS XKDS

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
107_T	125_E	4.819	1.00
88_E	91_R	4.272	1.00
45_I	49_V	3.275	1.00
109_F	122_F	3.094	1.00
45_I	126_T	2.920	1.00
47_Q	100_D	2.599	0.99
43_E	46_K	2.456	0.99
51_L	67_I	2.373	0.99
52_S	96_A	2.309	0.99
51_L	63_Y	2.009	0.97
53_L	129_G	1.996	0.97
89_I	92_L	1.984	0.97
22_S	45_I	1.932	0.96
51_L	55_T	1.893	0.96
24_T	47_Q	1.782	0.94
88_E	95_E	1.780	0.94
59_A	64_S	1.757	0.93
90_P	111_I	1.656	0.91
59_A	72_Q	1.652	0.91
48_F	100_D	1.648	0.91
49_V	103_I	1.584	0.89
21_T	102_R	1.481	0.86
27_I	51_L	1.478	0.85
93_I	109_F	1.472	0.85
82_D	113_K	1.441	0.84
24_T	100_D	1.418	0.83
27_I	47_Q	1.393	0.82
74_V	92_L	1.381	0.81
24_T	102_R	1.367	0.81
49_V	124_V	1.362	0.80
26_K	43_E	1.316	0.78
69_N	93_I	1.297	0.77
56_E	69_N	1.291	0.77
57_R	70_E	1.289	0.76
22_S	100_D	1.229	0.73
96_A	129_G	1.208	0.72
89_I	118_F	1.205	0.71
45_I	103_I	1.203	0.71
20_E	102_R	1.160	0.68
62_V	99_Y	1.153	0.68
27_I	34_I	1.150	0.68
124_V	131_L	1.147	0.68
71_L	89_I	1.126	0.66
86_K	111_I	1.125	0.66
108_D	121_S	1.114	0.65
101_D	124_V	1.065	0.62
108_D	123_T	1.064	0.62
108_D	122_F	1.059	0.61
27_I	32_G	1.049	0.61
41_G	115_G	1.047	0.60
112_E	119_R	1.044	0.60
19_I	127_D	1.041	0.60
22_S	102_R	1.011	0.58
41_G	129_G	1.004	0.57
27_I	100_D	0.997	0.57
13_E	114_Q	0.995	0.56
45_I	120_V	0.995	0.56
11_D	14_D	0.981	0.55
104_S	127_D	0.959	0.54
84_Y	93_I	0.948	0.53
40_T	102_R	0.939	0.52
21_T	24_T	0.933	0.52
18_V	104_S	0.929	0.51
23_Q	38_I	0.919	0.50
46_K	124_V	0.919	0.50
22_S	34_I	0.917	0.50
86_K	118_F	0.908	0.50
114_Q	117_S	0.885	0.48
48_F	99_Y	0.875	0.47
37_E	96_A	0.872	0.47
40_T	47_Q	0.868	0.47
12_I	127_D	0.853	0.45
28_D	31_N	0.853	0.45
56_E	72_Q	0.849	0.45
105_A	125_E	0.842	0.44
51_L	91_R	0.837	0.44
42_L	49_V	0.837	0.44
48_F	101_D	0.836	0.44
62_V	101_D	0.834	0.44
69_N	75_L	0.828	0.43
20_E	127_D	0.822	0.43
28_D	75_L	0.821	0.43
41_G	86_K	0.819	0.43
86_K	113_K	0.812	0.42
94_E	105_A	0.812	0.42
42_L	46_K	0.810	0.42
91_R	95_E	0.807	0.42
69_N	96_A	0.807	0.42
45_I	53_L	0.801	0.41
14_D	127_D	0.797	0.41
71_L	74_V	0.797	0.41
111_I	118_F	0.796	0.41
28_D	33_R	0.795	0.41
26_K	37_E	0.794	0.41
34_I	100_D	0.792	0.41
22_S	40_T	0.785	0.40
47_Q	102_R	0.784	0.40
76_A	92_L	0.781	0.40
40_T	100_D	0.772	0.39
22_S	126_T	0.767	0.39
12_I	114_Q	0.766	0.39
93_I	120_V	0.764	0.39
70_E	99_Y	0.761	0.38
34_I	48_F	0.760	0.38
56_E	92_L	0.760	0.38
14_D	17_E	0.758	0.38
86_K	116_E	0.754	0.38
61_S	99_Y	0.752	0.38
49_V	113_K	0.745	0.37
53_L	83_A	0.737	0.37
89_I	105_A	0.731	0.36
50_Y	54_H	0.731	0.36
58_Y	70_E	0.722	0.35
124_V	130_T	0.721	0.35
24_T	48_F	0.717	0.35
34_I	83_A	0.717	0.35
31_N	125_E	0.715	0.35
38_I	69_N	0.710	0.35
55_T	67_I	0.706	0.34
52_S	69_N	0.703	0.34
62_V	84_Y	0.692	0.33
58_Y	65_H	0.691	0.33
73_D	134_E	0.685	0.33
70_E	92_L	0.683	0.33
23_Q	26_K	0.681	0.33
16_S	41_G	0.679	0.32
114_Q	119_R	0.678	0.32
103_I	113_K	0.677	0.32
57_R	65_H	0.677	0.32
44_A	64_S	0.671	0.32
69_N	92_L	0.668	0.32
47_Q	96_A	0.652	0.31
57_R	68_G	0.651	0.31
55_T	133_I	0.651	0.31
108_D	119_R	0.648	0.30
27_I	82_D	0.645	0.30
24_T	27_I	0.644	0.30
29_F	90_P	0.638	0.30
61_S	73_D	0.637	0.30
16_S	107_T	0.635	0.30
28_D	57_R	0.633	0.29
94_E	109_F	0.632	0.29
37_E	102_R	0.627	0.29
76_A	85_K	0.624	0.29
22_S	48_F	0.624	0.29
103_I	106_V	0.619	0.28
112_E	121_S	0.615	0.28
60_Y	90_P	0.611	0.28
42_L	87_M	0.610	0.28
93_I	98_I	0.609	0.28
52_S	99_Y	0.609	0.28
24_T	40_T	0.594	0.27
66_D	70_E	0.588	0.27
17_E	110_E	0.586	0.26
70_E	91_R	0.584	0.26
60_Y	118_F	0.580	0.26
93_I	122_F	0.573	0.26
56_E	84_Y	0.566	0.25
123_T	132_E	0.565	0.25
85_K	119_R	0.562	0.25
71_L	96_A	0.561	0.25
87_M	118_F	0.552	0.24
49_V	81_T	0.548	0.24
40_T	62_V	0.547	0.24
70_E	103_I	0.547	0.24
32_G	123_T	0.546	0.24
40_T	43_E	0.545	0.24
90_P	94_E	0.544	0.24
130_T	133_I	0.544	0.24
67_I	88_E	0.542	0.24
28_D	101_D	0.534	0.23
51_L	116_E	0.527	0.23
33_R	58_Y	0.522	0.23
21_T	100_D	0.516	0.22
74_V	88_E	0.516	0.22
103_I	126_T	0.514	0.22
40_T	54_H	0.505	0.22
15_D	18_V	0.504	0.22
39_I	45_I	0.504	0.22
54_H	118_F	0.500	0.22

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
4hrzA	2	0.8085	99	0.758	Contact Map
2ia7A	1	0.7163	98.9	0.765	Contact Map
2e7gA	1	0.4965	40.3	0.931	Contact Map
1josA	1	0.4113	21.8	0.939	Contact Map
3w61A	2	0.3972	16.6	0.943	Contact Map
2zztA	2	0.4043	15.7	0.943	Contact Map
2kzfA	1	0.4397	15.3	0.944	Contact Map
3bypA	2	0.4113	14.4	0.944	Contact Map
1pa4A	1	0.3972	10.1	0.948	Contact Map
1v4eA	3	0.6596	8.9	0.949	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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