OPENSEQ.org - YMFS - ECOLI GREMLIN

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YMFS - Uncharacterized protein YmfS

UniProt:	P09154	Sequence MKIYCCLNTVGFFMDGCGVIPPDSKEITAEHWQSLLKSQAEGGVIDFSVFPPSIKEVIRTHDDEVADANFQKQMLISDATDFINSRQWQGKAALGRLKEDELKQYNLWLDYLEALELVDTSSAPDIEWPTPPAVQAR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG14337
Length:	137 (136)
Sequences:	214
Seq/Len:	1.57

YMFS
Paralog alert: 0.49 [within 20: 0.19] - ratio of genomes with paralogs
Cluster includes: TFAS YFDK YMFS

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
6_C	23_D	2.489	1.00
39_Q	45_I	2.216	0.99
90_G	112_L	2.129	0.99
109_L	112_L	2.128	0.99
71_Q	75_L	2.024	0.98
90_G	93_A	1.776	0.96
35_L	53_S	1.75	0.95
113_E	117_L	1.718	0.94
88_W	91_K	1.71	0.94
38_S	53_S	1.593	0.91
123_A	126_I	1.512	0.88
35_L	39_Q	1.51	0.88
45_I	53_S	1.495	0.87
97_L	113_E	1.435	0.84
109_L	113_E	1.432	0.83
80_T	112_L	1.406	0.82
35_L	40_A	1.401	0.82
65_V	69_N	1.397	0.81
93_A	112_L	1.375	0.80
91_K	97_L	1.364	0.79
87_Q	93_A	1.358	0.79
87_Q	101_E	1.343	0.78
91_K	101_E	1.317	0.76
6_C	12_F	1.286	0.73
35_L	45_I	1.27	0.72
76_I	115_L	1.265	0.72
101_E	117_L	1.251	0.70
31_H	35_L	1.238	0.69
97_L	117_L	1.211	0.67
101_E	113_E	1.205	0.66
12_F	51_P	1.201	0.66
5_C	24_S	1.201	0.66
59_R	67_D	1.198	0.66
43_G	55_K	1.193	0.65
83_I	112_L	1.171	0.63
118_V	128_W	1.167	0.63
38_S	45_I	1.166	0.62
105_Y	109_L	1.165	0.62
87_Q	110_D	1.16	0.62
9_T	26_E	1.159	0.62
92_A	97_L	1.158	0.62
27_I	36_L	1.154	0.61
9_T	13_F	1.152	0.61
87_Q	116_E	1.149	0.61
71_Q	74_M	1.149	0.61
79_A	83_I	1.137	0.60
91_K	113_E	1.13	0.59
113_E	116_E	1.116	0.57
110_D	117_L	1.114	0.57
43_G	48_S	1.113	0.57
79_A	108_W	1.1	0.56
39_Q	53_S	1.096	0.55
120_T	133_A	1.09	0.55
93_A	106_N	1.088	0.55
14_M	17_C	1.084	0.54
90_G	109_L	1.072	0.53
86_R	116_E	1.069	0.53
69_N	120_T	1.056	0.51
40_A	45_I	1.056	0.51
69_N	75_L	1.038	0.49
85_S	116_E	1.034	0.49
97_L	101_E	1.024	0.48
90_G	97_L	1.023	0.48
12_F	23_D	1.022	0.48
11_G	35_L	1.022	0.48
86_R	97_L	1.016	0.47
112_L	115_L	1.014	0.47
86_R	105_Y	1.014	0.47
86_R	98_K	1.014	0.47
35_L	38_S	1.01	0.46
36_L	39_Q	1.005	0.46
85_S	91_K	1.003	0.46
122_S	131_P	1	0.45

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
2kz6A	1	0.6788	99.7	0.597	Contact Map	0.232
2hh6A	1	0.5912	6.4	0.946	Contact Map	0.34
3al0C	1	0.4453	5.1	0.948	Contact Map	0.389
3lnpA	1	0.5839	3.8	0.951	Contact Map	0.435
3mduA	1	0.562	3.5	0.952	Contact Map	0.216
4gbdA	2	0.5912	3.3	0.952	Contact Map	0.405
3zx7A	1	0.3577	3.3	0.953	Contact Map	0
3buxB	2	0.4015	3	0.954	Contact Map	0.285
2pstX	1	0.4891	2.7	0.955	Contact Map	0
4f0lA	2	0.562	2.6	0.955	Contact Map	0.329

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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