YFLH - BACSU - GREMLIN Contacts

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YFLH - Uncharacterized protein YflH

UniProt:	O34306	Sequences: MNRDQEKIQIENEMNAMHGTIKEDILKDFEEFKGYLKKQVNRGKKLGLDDGKLVKSAAILGDYLAKHEEPQNGEEMLLQELWSVADEDEKEHLAQLLVKLVDKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	104 (79)
Sequences:	266 (177)
Seq/√Len:	19.9

BACSU - YFLH YMFJ

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
92_H	96_L	4.257	1.00
87_E	90_K	2.939	0.99
89_E	99_K	2.535	0.98
79_Q	83_S	2.211	0.94
57_A	98_V	2.181	0.94
32_F	97_L	2.031	0.91
91_E	96_L	1.956	0.90
39_Q	42_R	1.847	0.87
44_K	102_D	1.703	0.82
85_A	93_L	1.643	0.80
37_K	101_V	1.639	0.79
69_E	76_M	1.623	0.79
56_S	60_L	1.489	0.72
76_M	79_Q	1.459	0.71
84_V	100_L	1.451	0.70
85_A	96_L	1.451	0.70
70_P	76_M	1.405	0.68
43_G	48_L	1.368	0.66
68_E	71_Q	1.354	0.65
84_V	99_K	1.347	0.64
58_A	90_K	1.259	0.59
58_A	62_D	1.244	0.58
80_E	83_S	1.240	0.58
32_F	68_E	1.232	0.57
40_V	46_L	1.223	0.57
38_K	42_R	1.194	0.55
81_L	96_L	1.185	0.54
91_E	95_Q	1.182	0.54
40_V	101_V	1.181	0.54
49_D	52_K	1.180	0.54
32_F	61_G	1.179	0.54
32_F	35_Y	1.137	0.51
25_I	35_Y	1.129	0.51
25_I	97_L	1.099	0.49
43_G	53_L	1.090	0.48
77_L	93_L	1.087	0.48
51_G	90_K	1.085	0.48
28_D	38_K	1.072	0.47
37_K	40_V	1.059	0.46
86_D	89_E	1.041	0.45
26_L	75_E	1.023	0.44
64_L	78_L	1.012	0.43
29_F	74_E	1.002	0.43
34_G	83_S	0.987	0.42
44_K	70_P	0.983	0.41
29_F	80_E	0.982	0.41
33_K	101_V	0.979	0.41
24_D	27_K	0.977	0.41
77_L	89_E	0.963	0.40
74_E	80_E	0.955	0.40
31_E	70_P	0.949	0.39
35_Y	97_L	0.946	0.39
54_V	95_Q	0.945	0.39
27_K	73_G	0.943	0.39
29_F	39_Q	0.926	0.38
27_K	92_H	0.922	0.38
79_Q	86_D	0.909	0.37
70_P	79_Q	0.904	0.37
34_G	41_N	0.904	0.37
52_K	91_E	0.902	0.36
33_K	81_L	0.894	0.36
77_L	80_E	0.890	0.36
52_K	59_I	0.882	0.35
63_Y	90_K	0.881	0.35
26_L	39_Q	0.865	0.34
28_D	75_E	0.861	0.34
58_A	91_E	0.856	0.34
58_A	87_E	0.847	0.33
59_I	65_A	0.841	0.33
63_Y	75_E	0.832	0.32
30_E	66_K	0.829	0.32
86_D	99_K	0.827	0.32
55_K	90_K	0.813	0.31
53_L	91_E	0.789	0.30
59_I	62_D	0.782	0.30
73_G	76_M	0.768	0.29
34_G	38_K	0.746	0.28
52_K	60_L	0.717	0.26
26_L	78_L	0.709	0.26
41_N	45_K	0.706	0.26
56_S	59_I	0.696	0.25
31_E	62_D	0.692	0.25
56_S	97_L	0.690	0.25
26_L	71_Q	0.659	0.23
41_N	81_L	0.636	0.22
30_E	33_K	0.629	0.22
92_H	95_Q	0.623	0.22
49_D	53_L	0.621	0.22
32_F	53_L	0.604	0.21
38_K	85_A	0.602	0.21
69_E	83_S	0.598	0.21
65_A	83_S	0.586	0.20
80_E	85_A	0.584	0.20
40_V	76_M	0.583	0.20
56_S	83_S	0.571	0.20
53_L	61_G	0.568	0.19
68_E	79_Q	0.567	0.19
98_V	101_V	0.560	0.19
54_V	93_L	0.558	0.19
76_M	83_S	0.555	0.19
45_K	50_D	0.555	0.19
65_A	100_L	0.553	0.19
48_L	98_V	0.539	0.18
71_Q	75_E	0.537	0.18
65_A	84_V	0.535	0.18
77_L	96_L	0.529	0.18
81_L	85_A	0.528	0.18
24_D	45_K	0.519	0.18
31_E	49_D	0.517	0.17
50_D	55_K	0.516	0.17
55_K	61_G	0.515	0.17
25_I	76_M	0.515	0.17
51_G	95_Q	0.514	0.17
29_F	54_V	0.505	0.17
45_K	83_S	0.502	0.17
89_E	95_Q	0.501	0.17
32_F	55_K	0.501	0.17
40_V	77_L	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
3d0wA	2	0.8269	100	0.045	Contact Map
3viuA	1	0.5481	19.8	0.927	Contact Map
2q01A	3	0.8846	19.5	0.927	Contact Map
1o2dA	1	0.6731	19.1	0.928	Contact Map
3mzyA	1	0.6827	17.6	0.929	Contact Map
1or7A	2	0.6538	16.4	0.93	Contact Map
1xkpA	1	0.5577	16.3	0.93	Contact Map
1m7sA	4	0.5769	16.2	0.93	Contact Map
3q23A	1	0.9519	15.5	0.931	Contact Map
1mw9X	1	0.5096	14	0.932	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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