YDBB - BACSU - GREMLIN Contacts

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YDBB - Uncharacterized protein YdbB

UniProt:	P96597	Sequences: MSKMQNLLAIANEVKEKHANFSISEVNDHCVRLAVFTGEYDWHHHPDSDELFIVLEGELLIDFKDKETAVLKANDSLLIPKGTVHRTRSYVRTVNLCVEHKQAETVIIEEQPC	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	113 (101)
Sequences:	774 (489)
Seq/√Len:	48.7

BACSU - YDBB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
64_K	84_V	3.752	1.00
6_N	75_D	3.656	1.00
36_F	95_N	3.500	1.00
56_E	94_V	3.411	1.00
62_D	86_R	3.233	1.00
24_S	78_L	3.101	1.00
62_D	88_R	2.308	1.00
58_E	72_K	2.238	1.00
59_L	93_T	2.192	1.00
60_L	68_T	2.127	1.00
63_F	77_L	1.975	0.99
40_Y	105_T	1.809	0.99
61_I	71_L	1.788	0.99
62_D	68_T	1.772	0.99
25_E	101_K	1.752	0.99
27_N	100_H	1.742	0.99
11_A	94_V	1.673	0.98
17_K	37_T	1.627	0.98
48_S	102_Q	1.626	0.98
11_A	55_L	1.601	0.97
29_H	48_S	1.597	0.97
58_E	70_V	1.545	0.97
37_T	91_V	1.545	0.97
42_W	64_K	1.501	0.96
16_E	19_A	1.499	0.96
32_R	50_E	1.442	0.95
60_L	70_V	1.420	0.95
17_K	92_R	1.377	0.94
17_K	35_V	1.355	0.93
56_E	73_A	1.352	0.93
4_M	69_A	1.334	0.93
68_T	86_R	1.316	0.92
66_K	69_A	1.313	0.92
87_T	97_C	1.256	0.91
30_C	101_K	1.241	0.90
7_L	53_I	1.204	0.89
36_F	59_L	1.179	0.88
26_V	29_H	1.151	0.86
34_A	95_N	1.109	0.84
29_H	100_H	1.096	0.83
58_E	91_V	1.050	0.81
31_V	51_L	1.048	0.81
22_S	30_C	1.037	0.80
60_L	88_R	1.016	0.78
60_L	90_Y	1.014	0.78
9_A	13_E	1.007	0.78
39_E	88_R	1.004	0.78
10_I	23_I	0.984	0.76
63_F	69_A	0.964	0.75
59_L	95_N	0.958	0.74
28_D	101_K	0.951	0.74
34_A	103_A	0.950	0.74
53_I	96_L	0.931	0.72
51_L	96_L	0.928	0.72
80_P	83_T	0.921	0.71
11_A	14_V	0.917	0.71
50_E	85_H	0.916	0.71
69_A	77_L	0.908	0.70
61_I	77_L	0.895	0.69
33_L	97_C	0.879	0.68
26_V	50_E	0.877	0.68
66_K	77_L	0.876	0.67
4_M	70_V	0.864	0.66
14_V	21_F	0.861	0.66
8_L	23_I	0.844	0.65
17_K	95_N	0.842	0.64
44_H	84_V	0.841	0.64
71_L	75_D	0.839	0.64
42_W	84_V	0.839	0.64
30_C	48_S	0.819	0.62
11_A	33_L	0.808	0.61
83_T	91_V	0.794	0.60
19_A	93_T	0.769	0.57
20_N	34_A	0.766	0.57
12_N	81_K	0.762	0.57
9_A	12_N	0.762	0.57
24_S	76_S	0.756	0.56
18_H	89_S	0.744	0.55
10_I	13_E	0.743	0.55
61_I	79_I	0.737	0.54
56_E	91_V	0.731	0.54
5_Q	75_D	0.726	0.53
53_I	76_S	0.721	0.52
24_S	31_V	0.715	0.52
71_L	77_L	0.715	0.52
10_I	14_V	0.711	0.51
16_E	21_F	0.707	0.51
35_V	92_R	0.707	0.51
63_F	66_K	0.700	0.50
54_V	75_D	0.699	0.50
53_I	98_V	0.698	0.50
66_K	72_K	0.696	0.50
61_I	69_A	0.689	0.49
31_V	53_I	0.682	0.49
4_M	77_L	0.678	0.48
26_V	100_H	0.676	0.48
42_W	61_I	0.669	0.47
37_T	81_K	0.668	0.47
39_E	62_D	0.660	0.46
8_L	12_N	0.650	0.45
39_E	70_V	0.647	0.45
14_V	17_K	0.638	0.44
48_S	103_A	0.636	0.44
7_L	96_L	0.632	0.44
7_L	55_L	0.618	0.42
26_V	98_V	0.616	0.42
8_L	73_A	0.613	0.42
4_M	71_L	0.612	0.42
22_S	25_E	0.605	0.41
31_V	98_V	0.594	0.40
33_L	96_L	0.592	0.40
80_P	100_H	0.591	0.40
68_T	90_Y	0.584	0.39
25_E	28_D	0.582	0.39
28_D	81_K	0.582	0.39
32_R	104_E	0.578	0.38
22_S	32_R	0.578	0.38
44_H	61_I	0.573	0.38
20_N	35_V	0.573	0.38
36_F	71_L	0.567	0.37
22_S	51_L	0.565	0.37
10_I	92_R	0.564	0.37
14_V	33_L	0.559	0.36
34_A	50_E	0.557	0.36
13_E	16_E	0.556	0.36
56_E	81_K	0.549	0.36
62_D	70_V	0.548	0.35
89_S	92_R	0.547	0.35
52_F	87_T	0.543	0.35
10_I	21_F	0.538	0.35
51_L	86_R	0.538	0.35
15_K	68_T	0.535	0.34
36_F	66_K	0.535	0.34
15_K	91_V	0.533	0.34
29_H	98_V	0.531	0.34
46_P	72_K	0.529	0.34
22_S	37_T	0.527	0.34
102_Q	105_T	0.526	0.33
6_N	9_A	0.523	0.33
5_Q	23_I	0.523	0.33
61_I	87_T	0.520	0.33
20_N	87_T	0.519	0.33
12_N	39_E	0.516	0.33
26_V	51_L	0.516	0.33
40_Y	104_E	0.514	0.32
55_L	94_V	0.513	0.32
53_I	90_Y	0.511	0.32
34_A	97_C	0.507	0.32
42_W	71_L	0.506	0.32
93_T	97_C	0.504	0.31
71_L	85_H	0.503	0.31
27_N	48_S	0.500	0.31

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
2qnkA	1	0.9823	100	0.454	Contact Map
1zvfA	2	0.9912	99.8	0.577	Contact Map
4l2nA	2	0.9912	99.8	0.581	Contact Map
2i45A	2	0.885	99.7	0.636	Contact Map
3d82A	2	0.885	99.6	0.653	Contact Map
3d0jA	2	0.9204	99.6	0.669	Contact Map
2o8qA	3	0.9646	99	0.745	Contact Map
3myxA	1	0.9646	99	0.746	Contact Map
3rnsA	1	0.9027	99	0.753	Contact Map
1zrrA	1	0.9912	98.9	0.756	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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