OPENSEQ.org - YAFM - ECOLI GREMLIN

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YAFM - Uncharacterized protein YafM

UniProt:	Q47152	Sequence MSEYRRYYIKGGTWFFTVNLRNRRSQLLTTQYQMLRHAIIKVKRDRPFEINAWVVLPEHMHCIWTLPEGDDDFSSRWREIKKQFTHACGLKNIWQPRFWEHAIRNTKDYRHHVDYIYINPVKHGWVKQVSDWPFSTFHRDVARGLYPIDWAGDVTDFSAGERIIS	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13150
Length:	165 (152)
Sequences:	1058
Seq/Len:	6.96

YAFM
Paralog alert: 0.31 [within 20: 0.04] - ratio of genomes with paralogs

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Scaled Score	Prob
63_I	116_I	4.421	1.00
74_S	98_F	4.261	1.00
117_Y	140_D	3.119	1.00
52_A	113_V	2.904	1.00
57_P	125_W	2.507	1.00
59_H	119_N	2.496	1.00
115_Y	119_N	2.496	1.00
51_N	65_T	2.448	1.00
121_V	129_V	2.275	1.00
35_L	60_M	1.927	1.00
103_I	112_H	1.87	1.00
75_S	78_R	1.794	1.00
32_Y	57_P	1.78	1.00
28_L	88_C	1.728	1.00
137_F	141_V	1.725	1.00
48_F	76_R	1.657	1.00
49_E	65_T	1.632	1.00
61_H	119_N	1.63	1.00
59_H	115_Y	1.626	1.00
42_V	80_I	1.59	1.00
9_I	12_G	1.561	1.00
39_I	53_W	1.539	0.99
128_Q	131_D	1.534	0.99
16_F	73_F	1.533	0.99
18_V	60_M	1.496	0.99
35_L	80_I	1.458	0.99
82_K	86_H	1.409	0.99
78_R	82_K	1.386	0.99
19_N	91_K	1.378	0.99
56_L	119_N	1.355	0.98
16_F	64_W	1.33	0.98
51_N	109_Y	1.316	0.98
21_R	92_N	1.269	0.97
61_H	115_Y	1.243	0.97
118_I	122_K	1.234	0.97
57_P	132_W	1.216	0.96
7_Y	102_A	1.213	0.96
118_I	121_V	1.211	0.96
19_N	23_R	1.209	0.96
20_L	84_F	1.207	0.96
63_I	113_V	1.194	0.96
20_L	26_Q	1.189	0.95
90_L	95_Q	1.186	0.95
39_I	62_C	1.176	0.95
32_Y	55_V	1.163	0.95
43_K	50_I	1.162	0.95
34_M	87_A	1.149	0.94
54_V	122_K	1.145	0.94
125_W	132_W	1.143	0.94
25_S	57_P	1.134	0.94
56_L	123_H	1.131	0.94
56_L	120_P	1.123	0.93
101_H	108_D	1.116	0.93
46_R	75_S	1.111	0.93
48_F	64_W	1.108	0.93
94_W	117_Y	1.095	0.92
114_D	117_Y	1.093	0.92
34_M	38_A	1.083	0.91
64_W	77_W	1.083	0.91
45_D	79_E	1.074	0.91
101_H	112_H	1.069	0.91
26_Q	30_T	1.066	0.91
46_R	79_E	1.064	0.91
56_L	59_H	1.063	0.90
54_V	120_P	1.06	0.90
39_I	50_I	1.039	0.89
63_I	103_I	1.037	0.89
22_N	89_G	1.035	0.89
90_L	96_P	1.028	0.88
35_L	55_V	1.022	0.88
16_F	77_W	1.022	0.88
39_I	80_I	1.022	0.88
20_L	27_L	1.017	0.88
79_E	82_K	1.017	0.88
32_Y	134_F	1.013	0.87
23_R	115_Y	1.011	0.87

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Scaled Score = (raw_score/average(raw_scores)) > 1 are listed. For all 3L/2 predictions, click on one of the links below.

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling

HHsearch Results: GREMLIN results overlayed on top 10 PDB hits:

Legend: Blue filled circles are GREMLIN results (Scaled_score >1). The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on 10 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	P(%)	HHΔ		Acc
4er8A	1	1	100	0.183	Contact Map	0.777
2vjvA	2	0.8485	100	0.453	Contact Map	0.529
2f5gA	2	0.7576	99.9	0.483	Contact Map	0.462
2fyxA	2	0.7273	99.9	0.486	Contact Map	0.457
3cjlA	2	0.4485	37	0.932	Contact Map	0.345
2nlyA	1	0.5939	7.5	0.951	Contact Map	0.11
2i2jA	1	0.1273	3.5	0.958	Contact Map	0.502
3pr6A	1	0.6424	3.3	0.958	Contact Map	0.257
2lm0A	1	0.2667	2.8	0.96	Contact Map	0.135
2bx2L	1	0.703	2.1	0.963	Contact Map	0.225

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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