YLBF - BACSU - GREMLIN Contacts

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YLBF - Regulatory protein YlbF

UniProt:	O34412	Sequences: MYATMESVRLQSEAQQLAEMILQSETAENYRNCYKRLQEDEEAGRIIRSFIKIKEQYEDVQRFGKYHPDYREISRKMREIKRELDLNDKVADFKRAENELQSILDEVSVEIGTAVSEHVKVPTGNPYFDGLSSCGGGCGSGGSCGCKVS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	149 (143)
Sequences:	291 (238)
Seq/√Len:	19.9

BACSU - YLBF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
72_E	76_K	4.748	1.00
59_D	73_I	4.682	1.00
101_Q	105_D	4.564	1.00
40_D	89_K	3.389	1.00
46_I	87_N	3.132	0.99
57_Y	74_S	2.516	0.97
43_A	89_K	2.362	0.96
37_L	43_A	2.345	0.96
40_D	43_A	2.332	0.96
43_A	46_I	2.317	0.96
138_C	144_C	2.310	0.96
43_A	87_N	2.073	0.92
30_Y	93_F	1.984	0.90
21_I	107_V	1.980	0.90
6_E	101_Q	1.954	0.90
108_S	122_P	1.853	0.87
40_D	87_N	1.836	0.87
15_Q	19_E	1.826	0.86
62_R	67_H	1.826	0.86
63_F	67_H	1.820	0.86
123_T	129_D	1.813	0.86
56_Q	73_I	1.789	0.85
27_A	31_R	1.784	0.85
139_G	144_C	1.780	0.85
2_Y	84_L	1.738	0.83
34_Y	38_Q	1.703	0.82
102_S	106_E	1.671	0.81
55_E	73_I	1.640	0.79
34_Y	112_G	1.625	0.79
74_S	84_L	1.624	0.79
91_A	139_G	1.527	0.74
99_E	143_S	1.511	0.73
125_N	128_F	1.473	0.71
124_G	128_F	1.469	0.71
24_S	120_K	1.458	0.71
22_L	27_A	1.457	0.71
22_L	34_Y	1.448	0.70
60_V	69_D	1.447	0.70
53_I	76_K	1.446	0.70
56_Q	59_D	1.389	0.67
88_D	92_D	1.378	0.66
95_R	99_E	1.342	0.64
43_A	93_F	1.319	0.63
57_Y	73_I	1.316	0.63
40_D	46_I	1.201	0.55
53_I	77_M	1.201	0.55
9_R	44_G	1.183	0.54
41_E	88_D	1.159	0.53
70_Y	120_K	1.146	0.52
11_Q	67_H	1.068	0.47
50_F	107_V	1.068	0.47
42_E	45_R	1.064	0.47
47_I	84_L	1.041	0.45
115_V	119_V	1.030	0.44
2_Y	7_S	1.027	0.44
15_Q	101_Q	1.025	0.44
10_L	111_I	1.021	0.44
46_I	94_K	1.020	0.44
71_R	124_G	1.020	0.44
5_M	18_A	1.019	0.44
141_G	144_C	1.016	0.43
61_Q	117_E	1.012	0.43
46_I	84_L	1.009	0.43
80_I	88_D	1.009	0.43
118_H	145_G	1.001	0.42
42_E	55_E	0.987	0.42
28_E	88_D	0.987	0.42
71_R	94_K	0.983	0.41
54_K	58_E	0.982	0.41
123_T	126_P	0.976	0.41
19_E	115_V	0.954	0.40
54_K	111_I	0.949	0.39
42_E	54_K	0.937	0.39
12_S	128_F	0.930	0.38
29_N	49_S	0.926	0.38
2_Y	34_Y	0.922	0.38
64_G	120_K	0.907	0.37
30_Y	72_E	0.897	0.36
24_S	70_Y	0.893	0.36
124_G	127_Y	0.890	0.36
109_V	112_G	0.888	0.36
137_G	140_S	0.882	0.35
96_A	121_V	0.875	0.35
31_R	34_Y	0.860	0.34
48_R	52_K	0.860	0.34
70_Y	73_I	0.859	0.34
25_E	37_L	0.851	0.33
57_Y	75_R	0.850	0.33
110_E	114_A	0.847	0.33
78_R	105_D	0.846	0.33
75_R	81_K	0.843	0.33
16_Q	88_D	0.843	0.33
78_R	81_K	0.843	0.33
18_A	21_I	0.837	0.33
74_S	78_R	0.837	0.33
23_Q	76_K	0.823	0.32
47_I	51_I	0.819	0.32
85_D	94_K	0.818	0.32
6_E	105_D	0.811	0.31
58_E	61_Q	0.809	0.31
111_I	117_E	0.808	0.31
60_V	73_I	0.807	0.31
105_D	128_F	0.796	0.30
33_C	36_R	0.794	0.30
59_D	67_H	0.790	0.30
78_R	82_R	0.788	0.30
11_Q	15_Q	0.776	0.29
65_K	146_C	0.774	0.29
14_A	120_K	0.772	0.29
25_E	60_V	0.770	0.29
10_L	40_D	0.762	0.28
73_I	94_K	0.762	0.28
21_I	93_F	0.761	0.28
79_E	107_V	0.758	0.28
30_Y	100_L	0.752	0.28
58_E	65_K	0.748	0.28
29_N	96_A	0.745	0.28
66_Y	100_L	0.740	0.27
78_R	125_N	0.734	0.27
39_E	43_A	0.730	0.27
63_F	103_I	0.715	0.26
37_L	118_H	0.707	0.26
36_R	117_E	0.707	0.26
14_A	112_G	0.702	0.25
53_I	100_L	0.698	0.25
137_G	144_C	0.688	0.25
35_K	112_G	0.687	0.25
35_K	113_T	0.687	0.25
107_V	113_T	0.683	0.24
36_R	76_K	0.679	0.24
60_V	81_K	0.677	0.24
78_R	120_K	0.676	0.24
98_N	105_D	0.671	0.24
64_G	67_H	0.667	0.24
32_N	36_R	0.667	0.24
87_N	127_Y	0.666	0.24
82_R	86_L	0.666	0.24
57_Y	61_Q	0.663	0.24
36_R	99_E	0.661	0.23
130_G	134_C	0.661	0.23
25_E	99_E	0.659	0.23
2_Y	119_V	0.657	0.23
49_S	83_E	0.654	0.23
108_S	119_V	0.652	0.23
41_E	45_R	0.651	0.23
29_N	33_C	0.645	0.23
138_C	141_G	0.645	0.23
75_R	135_G	0.642	0.23
27_A	112_G	0.641	0.23
96_A	118_H	0.639	0.22
112_G	140_S	0.639	0.22
14_A	30_Y	0.636	0.22
25_E	47_I	0.635	0.22
66_Y	86_L	0.632	0.22
124_G	129_D	0.627	0.22
71_R	123_T	0.625	0.22
27_A	93_F	0.621	0.22
82_R	85_D	0.612	0.21
67_H	120_K	0.610	0.21
21_I	27_A	0.609	0.21
67_H	122_P	0.608	0.21
106_E	140_S	0.600	0.21
104_L	122_P	0.600	0.21
24_S	78_R	0.600	0.21
53_I	56_Q	0.599	0.21
84_L	145_G	0.598	0.21
9_R	36_R	0.597	0.21
35_K	39_E	0.597	0.21
15_Q	90_V	0.589	0.20
122_P	145_G	0.586	0.20
60_V	78_R	0.584	0.20
20_M	111_I	0.583	0.20
7_S	112_G	0.582	0.20
37_L	42_E	0.580	0.20
141_G	146_C	0.578	0.20
121_V	126_P	0.576	0.20
65_K	125_N	0.574	0.20
83_E	100_L	0.574	0.20
52_K	55_E	0.573	0.20
11_Q	62_R	0.573	0.20
20_M	62_R	0.569	0.19
15_Q	98_N	0.566	0.19
39_E	89_K	0.565	0.19
6_E	118_H	0.564	0.19
38_Q	113_T	0.558	0.19
77_M	99_E	0.554	0.19
20_M	60_V	0.551	0.19
28_E	112_G	0.550	0.19
2_Y	19_E	0.549	0.19
16_Q	110_E	0.548	0.19
103_I	107_V	0.547	0.19
60_V	67_H	0.547	0.19
30_Y	124_G	0.546	0.19
55_E	109_V	0.545	0.18
34_Y	121_V	0.542	0.18
39_E	140_S	0.541	0.18
63_F	97_E	0.540	0.18
71_R	87_N	0.534	0.18
30_Y	119_V	0.533	0.18
63_F	137_G	0.529	0.18
87_N	135_G	0.528	0.18
108_S	139_G	0.527	0.18
54_K	120_K	0.527	0.18
23_Q	88_D	0.521	0.18
12_S	36_R	0.517	0.17
127_Y	130_G	0.517	0.17
42_E	91_A	0.514	0.17
23_Q	109_V	0.513	0.17
59_D	62_R	0.505	0.17
35_K	117_E	0.505	0.17
104_L	121_V	0.504	0.17
7_S	145_G	0.503	0.17
5_M	14_A	0.500	0.17
92_D	111_I	0.500	0.17

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
2pihA	2	0.8255	100	0.49	Contact Map
2oeqA	4	0.7919	99.9	0.607	Contact Map
2oeeA	2	0.6242	99.9	0.617	Contact Map
2iazA	4	0.7584	99.9	0.649	Contact Map
1t2yA	1	0.1074	45.9	0.944	Contact Map
4rwuA	1	0.5436	37.7	0.947	Contact Map
4mxpA	1	0.8121	34.3	0.948	Contact Map
2mj3A	1	0.3087	32.9	0.948	Contact Map
1m0jA	1	0.1074	29.7	0.949	Contact Map
1qjlA	1	0.1812	26.2	0.951	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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