BDBB - BACSU - GREMLIN Contacts

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BDBB - SPBc2 prophage-derived disulfide bond formation protein B

UniProt:	P68571	Sequences: MNTRYVKSFFLLLFFLSFFGTMASLFYSEIMHFKPCVLCWYQRIFLYPIPIILLIGLLKKDLNSIFYVVFLSSIGLIIAFYHYIIQLTQSKSVVCEIGTNSCAKIEVEYLGFITLPLMSSVCFALIFGIGLKLIIKSKKLKQNQHVYN	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	148 (128)
Sequences:	450 (343)
Seq/√Len:	30.3

BACSU - BDBB BDBC

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
79_A	119_S	3.605	1.00
68_V	130_G	3.159	1.00
26_F	31_M	3.138	1.00
27_Y	107_V	2.992	1.00
83_Y	117_L	2.984	1.00
41_Y	45_F	2.970	1.00
16_L	125_L	2.708	1.00
110_L	113_I	2.673	1.00
76_L	124_A	2.634	1.00
73_S	127_F	2.626	1.00
72_S	127_F	2.553	0.99
27_Y	118_M	2.397	0.99
24_S	28_S	2.338	0.99
83_Y	87_L	2.139	0.98
24_S	47_Y	2.080	0.98
59_K	66_F	2.011	0.97
12_L	16_L	1.894	0.96
28_S	47_Y	1.797	0.95
73_S	77_I	1.734	0.94
34_K	37_V	1.699	0.93
81_Y	85_I	1.656	0.92
59_K	67_Y	1.626	0.91
108_E	112_F	1.597	0.90
76_L	80_F	1.589	0.90
61_D	67_Y	1.575	0.90
13_L	53_L	1.543	0.89
51_I	71_L	1.518	0.88
76_L	120_S	1.506	0.88
65_I	134_I	1.488	0.87
10_F	56_G	1.480	0.87
56_G	64_S	1.439	0.85
12_L	129_I	1.370	0.82
19_F	50_P	1.369	0.82
24_S	27_Y	1.352	0.81
49_I	70_F	1.351	0.81
10_F	64_S	1.346	0.81
52_I	64_S	1.340	0.81
13_L	130_G	1.338	0.80
69_V	127_F	1.316	0.79
84_I	88_T	1.316	0.79
26_F	30_I	1.314	0.79
12_L	125_L	1.298	0.78
27_Y	33_F	1.274	0.77
109_Y	118_M	1.247	0.75
20_G	23_A	1.238	0.75
14_F	54_L	1.171	0.71
37_V	41_Y	1.122	0.67
70_F	130_G	1.115	0.67
83_Y	86_Q	1.113	0.67
23_A	115_L	1.112	0.67
20_G	122_C	1.108	0.66
7_K	60_K	1.104	0.66
17_S	50_P	1.092	0.65
21_T	44_I	1.073	0.64
76_L	127_F	1.044	0.62
92_S	95_C	1.026	0.60
53_L	67_Y	0.999	0.58
13_L	67_Y	0.995	0.58
80_F	84_I	0.985	0.57
128_G	131_L	0.978	0.57
113_I	117_L	0.956	0.55
33_F	47_Y	0.951	0.54
107_V	118_M	0.945	0.54
52_I	131_L	0.943	0.54
72_S	76_L	0.935	0.53
86_Q	114_T	0.930	0.53
49_I	54_L	0.927	0.53
15_F	121_V	0.922	0.52
107_V	117_L	0.910	0.51
68_V	134_I	0.899	0.50
121_V	125_L	0.890	0.50
16_L	129_I	0.890	0.50
79_A	120_S	0.882	0.49
27_Y	109_Y	0.878	0.49
38_L	78_I	0.874	0.48
28_S	114_T	0.873	0.48
65_I	68_V	0.864	0.47
82_H	119_S	0.848	0.46
21_T	41_Y	0.846	0.46
81_Y	98_G	0.839	0.45
109_Y	112_F	0.838	0.45
16_L	19_F	0.837	0.45
118_M	121_V	0.824	0.44
20_G	46_L	0.824	0.44
45_F	74_I	0.821	0.44
45_F	76_L	0.817	0.44
55_I	66_F	0.811	0.43
23_A	46_L	0.806	0.43
49_I	68_V	0.802	0.43
21_T	50_P	0.787	0.41
13_L	49_I	0.782	0.41
80_F	110_L	0.780	0.41
112_F	117_L	0.771	0.40
11_L	57_L	0.771	0.40
19_F	121_V	0.768	0.40
53_L	68_V	0.768	0.40
45_F	78_I	0.768	0.40
27_Y	106_E	0.762	0.39
70_F	127_F	0.760	0.39
12_L	132_K	0.755	0.39
120_S	124_A	0.755	0.39
26_F	94_V	0.747	0.38
105_I	108_E	0.743	0.38
55_I	70_F	0.743	0.38
28_S	33_F	0.737	0.38
83_Y	119_S	0.730	0.37
56_G	67_Y	0.728	0.37
33_F	114_T	0.727	0.37
108_E	115_L	0.727	0.37
8_S	96_E	0.723	0.37
8_S	57_L	0.716	0.36
55_I	64_S	0.713	0.36
27_Y	114_T	0.711	0.36
57_L	129_I	0.710	0.36
41_Y	44_I	0.709	0.36
90_S	94_V	0.709	0.36
24_S	114_T	0.707	0.35
103_A	130_G	0.693	0.34
62_L	133_L	0.692	0.34
46_L	123_F	0.691	0.34
24_S	106_E	0.689	0.34
27_Y	115_L	0.688	0.34
79_A	82_H	0.686	0.34
25_L	47_Y	0.683	0.34
77_I	91_K	0.682	0.34
54_L	57_L	0.682	0.34
66_F	70_F	0.681	0.34
23_A	27_Y	0.680	0.33
13_L	61_D	0.678	0.33
86_Q	106_E	0.667	0.33
47_Y	106_E	0.667	0.33
51_I	72_S	0.661	0.32
23_A	107_V	0.657	0.32
79_A	101_S	0.656	0.32
11_L	65_I	0.654	0.32
27_Y	108_E	0.639	0.31
94_V	97_I	0.633	0.30
74_I	78_I	0.625	0.30
37_V	78_I	0.623	0.30
77_I	131_L	0.616	0.29
15_F	51_I	0.609	0.29
121_V	124_A	0.605	0.28
94_V	103_A	0.600	0.28
85_I	97_I	0.600	0.28
101_S	104_K	0.600	0.28
85_I	94_V	0.597	0.28
66_F	134_I	0.593	0.28
80_F	122_C	0.592	0.28
80_F	120_S	0.589	0.27
65_I	85_I	0.589	0.27
31_M	37_V	0.588	0.27
7_K	134_I	0.586	0.27
87_L	108_E	0.583	0.27
55_I	74_I	0.579	0.27
105_I	117_L	0.578	0.27
51_I	60_K	0.575	0.26
70_F	95_C	0.572	0.26
33_F	106_E	0.570	0.26
85_I	93_V	0.566	0.26
16_L	68_V	0.565	0.26
74_I	119_S	0.562	0.26
49_I	53_L	0.560	0.26
35_P	46_L	0.557	0.25
57_L	62_L	0.556	0.25
40_W	46_L	0.556	0.25
31_M	105_I	0.553	0.25
67_Y	130_G	0.551	0.25
11_L	90_S	0.549	0.25
38_L	53_L	0.545	0.25
61_D	129_I	0.543	0.25
65_I	130_G	0.542	0.24
84_I	90_S	0.542	0.24
9_F	125_L	0.541	0.24
55_I	67_Y	0.540	0.24
13_L	16_L	0.540	0.24
92_S	97_I	0.538	0.24
52_I	67_Y	0.537	0.24
29_E	46_L	0.536	0.24
129_I	132_K	0.536	0.24
14_F	56_G	0.534	0.24
88_T	93_V	0.528	0.24
21_T	45_F	0.527	0.24
36_C	43_R	0.522	0.23
14_F	69_V	0.519	0.23
13_L	65_I	0.517	0.23
51_I	74_I	0.514	0.23
65_I	70_F	0.514	0.23
53_L	130_G	0.512	0.23
9_F	129_I	0.511	0.23
28_S	106_E	0.508	0.22
88_T	94_V	0.507	0.22
49_I	63_N	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
2hi7B	1	0.75	100	0.578	Contact Map
4nv5A	1	0.527	88.2	0.922	Contact Map
2l0lA	1	0.1824	56.4	0.941	Contact Map
4xnvA	1	0.6149	21.4	0.953	Contact Map
4yayA	1	0.5068	21.1	0.953	Contact Map
2ks1B	1	0.2973	18.1	0.954	Contact Map
4p6vD	1	0.7973	14.6	0.956	Contact Map
4xt1A	1	0.5676	13.7	0.957	Contact Map
4ldeA	1	0.5878	12.4	0.958	Contact Map
2z73A	2	0.6216	12.2	0.958	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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