OPENSEQ.org - YIDF - ECOLI GREMLIN

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YIDF - Uncharacterized protein YidF

UniProt:	P31443	Sequence MTGSQVIDAEEDRHKLVVEYKDALQPADFYHNFKQRGIRSVQLIPYLEFDDRGDLTAASVTAELWGKFLIALFECWVRADISRISIELFDATLQKWCGSENPQPRCDCQACDWHRLCPHARQETPDSVLCAGYQAFYSYSAPHMRVMRDLIKQHRSPMELMTMLR	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11694
Length:	165 (152)
Sequences:	329
Seq/Len:	2.16

YIDF
Paralog alert: 0.74 [within 20: 0.02] - 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
74_E	139_Y	2.835	1.00
27_A	71_A	2.519	1.00
105_R	126_D	2.208	1.00
96_W	144_M	2.179	1.00
26_P	71_A	2.136	1.00
72_L	86_I	2.065	0.99
96_W	115_R	2.018	0.99
65_W	132_G	1.827	0.98
160_L	164_L	1.794	0.98
70_I	74_E	1.753	0.97
47_L	129_L	1.74	0.97
22_D	29_F	1.688	0.97
112_D	138_S	1.687	0.97
96_W	116_L	1.66	0.96
150_L	159_E	1.64	0.96
16_L	44_I	1.624	0.95
16_L	33_F	1.603	0.95
113_W	138_S	1.484	0.92
70_I	135_A	1.472	0.91
17_V	46_Y	1.448	0.90
23_A	64_L	1.411	0.89
95_K	101_N	1.41	0.89
16_L	38_I	1.406	0.88
38_I	41_V	1.402	0.88
26_P	72_L	1.4	0.88
77_V	161_M	1.39	0.88
18_V	69_L	1.386	0.87
23_A	61_T	1.385	0.87
32_N	36_R	1.371	0.87
27_A	75_C	1.364	0.86
33_F	38_I	1.322	0.84
113_W	134_Q	1.319	0.84
63_E	131_A	1.315	0.83
92_T	140_S	1.293	0.82
67_K	71_A	1.272	0.81
31_H	34_K	1.268	0.80
90_D	93_L	1.266	0.80
96_W	141_A	1.253	0.79
146_V	150_L	1.223	0.77
31_H	75_C	1.197	0.75
160_L	163_M	1.195	0.75
62_A	128_V	1.175	0.73
155_R	159_E	1.175	0.73
79_A	164_L	1.163	0.72
87_E	132_G	1.149	0.70
87_E	91_A	1.139	0.69
14_H	38_I	1.137	0.69
40_S	90_D	1.136	0.69
15_K	29_F	1.127	0.68
83_R	86_I	1.108	0.66
70_I	139_Y	1.094	0.65
25_Q	28_D	1.093	0.65
146_V	157_P	1.085	0.64
106_C	110_A	1.077	0.63
155_R	161_M	1.073	0.63
146_V	159_E	1.071	0.62
69_L	136_F	1.067	0.62
153_Q	164_L	1.062	0.61
47_L	103_Q	1.057	0.61
154_H	157_P	1.044	0.60
47_L	60_V	1.043	0.59
140_S	144_M	1.037	0.59
81_I	161_M	1.037	0.59
45_P	117_C	1.032	0.58
65_W	129_L	1.03	0.58
68_F	117_C	1.025	0.57
19_E	22_D	1.022	0.57
29_F	65_W	1.021	0.57
27_A	77_V	1.017	0.57
150_L	160_L	1.015	0.56
42_Q	117_C	1.015	0.56
136_F	140_S	1.01	0.56

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
4k36A	2	0.9939	99.9	0.601	Contact Map	0.624
1tv8A	2	0.9273	86.9	0.913	Contact Map	0.206
3canA	1	0.497	12.9	0.951	Contact Map	0.403
3dtzA	5	0.3636	7.7	0.956	Contact Map	0.145
1konA	1	0.497	7.7	0.956	Contact Map	0.151
3hhwK	5	0.4364	7.2	0.957	Contact Map	0.328
1xr7A	2	0.7455	6.3	0.958	Contact Map	0.266
3n6mA	1	0.6545	6.1	0.958	Contact Map	0.258
2z2uA	1	0.5576	6	0.958	Contact Map	0.557
3fgnA	4	0.4364	5.6	0.959	Contact Map	0.122

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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