OPENSEQ.org - YDHY - ECOLI GREMLIN

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YDHY - Uncharacterized ferredoxin-like protein YdhY

UniProt:	P0AAL6	Sequence MNPVDRPLLDIGLTRLEFLRISGKGLAGLTIAPALLSLLGCKQEDIDSGTVGLINTPKGVLVTQRARCTGCHRCEISCTNFNDGSVGTFFSRIKIHRNYFFGDNGVGSGGGLYGDLNYTADTCRQCKEPQCMNVCPIGAITWQQKEGCITVDHKRCIGCSACTTACPWMMATVNTESKKSSKCVLCGECANACPTGALKIIEWKDITV	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13959
Length:	208 (197)
Sequences:	404
Seq/Len:	2.05

YDHY
Paralog alert: 0.73 [within 20: 0.12] - ratio of genomes with paralogs
Cluster includes: DMSB HYCB HYDN HYFA NRFC YDHX YDHY YGFS YNFG YSAA

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
143_Q	146_E	3.884	1.00
68_C	71_C	2.606	1.00
68_C	74_C	2.481	1.00
71_C	74_C	2.433	1.00
71_C	193_C	2.429	1.00
68_C	193_C	2.381	1.00
134_V	161_A	2.374	1.00
74_C	193_C	2.17	1.00
79_T	84_G	1.858	0.98
129_P	142_W	1.847	0.98
190_A	198_L	1.762	0.97
61_L	185_L	1.712	0.97
124_R	140_I	1.64	0.95
163_T	180_S	1.598	0.94
171_A	206_I	1.563	0.93
70_G	74_C	1.553	0.93
140_I	171_A	1.548	0.93
122_T	134_V	1.536	0.93
60_V	203_W	1.507	0.92
182_K	194_P	1.497	0.91
70_G	193_C	1.487	0.91
172_T	181_S	1.446	0.89
160_S	163_T	1.441	0.89
72_H	75_E	1.42	0.88
174_N	177_S	1.4	0.87
17_E	20_R	1.398	0.87
120_A	198_L	1.367	0.85
93_I	198_L	1.314	0.82
155_R	160_S	1.303	0.82
81_F	93_I	1.297	0.81
23_G	27_A	1.286	0.80
161_A	197_A	1.259	0.78
77_S	192_A	1.253	0.78
152_D	155_R	1.253	0.78
154_K	160_S	1.241	0.77
149_I	201_I	1.231	0.76
144_Q	204_K	1.23	0.76
69_T	195_T	1.228	0.76
134_V	168_W	1.224	0.76
173_V	177_S	1.206	0.74
19_L	22_S	1.199	0.73
61_L	168_W	1.195	0.73
132_M	205_D	1.179	0.72
83_D	179_K	1.178	0.72
125_Q	187_G	1.178	0.72
174_N	179_K	1.156	0.69
92_R	151_V	1.15	0.69
173_V	180_S	1.147	0.69
174_N	199_K	1.139	0.68
63_T	198_L	1.139	0.68
160_S	178_K	1.137	0.68
171_A	181_S	1.135	0.67
61_L	137_I	1.132	0.67
124_R	137_I	1.123	0.66
157_I	173_V	1.121	0.66
153_H	177_S	1.113	0.65
42_K	46_I	1.112	0.65
72_H	76_I	1.106	0.65
82_N	118_Y	1.098	0.64
122_T	140_I	1.087	0.63
181_S	184_V	1.081	0.62
138_G	151_V	1.077	0.61
121_D	176_E	1.075	0.61
173_V	205_D	1.073	0.61
69_T	125_Q	1.072	0.61
174_N	181_S	1.063	0.60
124_R	161_A	1.06	0.60
28_G	115_D	1.059	0.60
143_Q	187_G	1.054	0.59
14_T	79_T	1.05	0.59
133_N	152_D	1.05	0.59
168_W	181_S	1.048	0.58
69_T	157_I	1.042	0.58
36_L	112_L	1.038	0.57
17_E	21_I	1.035	0.57
143_Q	148_C	1.034	0.57
160_S	192_A	1.031	0.56
46_I	145_K	1.026	0.56
105_G	112_L	1.024	0.56
122_T	168_W	1.019	0.55
34_A	42_K	1.015	0.55
84_G	175_T	1.012	0.54
40_G	44_E	1.008	0.54
118_Y	175_T	1.007	0.54
69_T	180_S	1.003	0.53
148_C	168_W	1.003	0.53
60_V	192_A	1.002	0.53

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
2ivfB	1	0.8077	100	0.517	Contact Map	0.316
1ti6B	6	0.6875	100	0.518	Contact Map	0.257
1h0hB	2	0.6923	100	0.525	Contact Map	0.294
1kqfB	1	0.8221	100	0.526	Contact Map	0.301
2vpzB	2	0.6779	100	0.561	Contact Map	0.352
1q16B	1	0.75	100	0.615	Contact Map	0.267
3mm5B	2	0.8894	99.6	0.758	Contact Map	0.172
3gyxB	6	0.2933	99.3	0.801	Contact Map	0.169
2c42A	2	0.9423	99.2	0.812	Contact Map	0.116
1rgvA	1	0.2885	99.1	0.819	Contact Map	0.167

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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