OPENSEQ.org - YBGA - ECOLI GREMLIN

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YBGA - Uncharacterized protein YbgA

UniProt:	P24252	Sequence MNLQRFDDSTLIRIFALHELHRLKEHGLTRGALLDYHSRYKLVFLAHSQPEYRKLGPFVADIHQWQNLDDYYNQYRQRVVVLLSHPANPRDHTNVLMHVQGYFRPHIDSTERQQLAALIDSYRRGEQPLLAPLMRIKHYMALYPDAWLSGQRYFELWPRVINLRHSGVL	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG11108
Length:	169 (166)
Sequences:	324
Seq/Len:	1.95

YBGA
Paralog alert: 0.04 [within 20: 0.00] - 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
42_L	102_Y	3.165	1.00
16_A	79_V	2.906	1.00
92_H	153_Y	2.599	1.00
34_L	59_V	2.223	1.00
98_H	101_G	1.994	0.99
16_A	40_Y	1.965	0.99
19_E	40_Y	1.961	0.99
55_L	78_R	1.855	0.98
48_S	51_E	1.846	0.98
44_F	82_L	1.815	0.98
121_S	159_R	1.803	0.97
40_Y	152_R	1.738	0.97
111_E	142_L	1.642	0.95
139_Y	143_Y	1.634	0.95
20_L	76_R	1.617	0.94
115_L	119_I	1.582	0.93
17_L	76_R	1.546	0.92
130_L	165_H	1.521	0.91
7_D	161_I	1.51	0.91
56_G	98_H	1.472	0.90
41_K	56_G	1.466	0.89
162_N	165_H	1.466	0.89
56_G	101_G	1.44	0.88
104_R	112_R	1.379	0.85
37_H	75_Y	1.367	0.84
41_K	98_H	1.346	0.83
94_N	98_H	1.325	0.82
35_D	150_G	1.322	0.82
41_K	101_G	1.322	0.82
94_N	101_G	1.31	0.81
162_N	166_S	1.301	0.80
100_Q	116_A	1.29	0.79
46_A	147_W	1.285	0.79
48_S	85_H	1.279	0.79
12_I	104_R	1.273	0.78
23_L	28_L	1.268	0.78
45_L	112_R	1.258	0.77
114_Q	138_H	1.247	0.76
140_M	148_L	1.231	0.75
54_K	133_L	1.23	0.75
30_R	62_I	1.219	0.74
148_L	151_Q	1.216	0.74
80_V	134_M	1.211	0.73
33_L	71_Y	1.176	0.70
59_V	76_R	1.169	0.69
100_Q	115_L	1.163	0.69
79_V	137_K	1.161	0.68
52_Y	164_R	1.155	0.68
31_G	35_D	1.153	0.68
101_G	147_W	1.152	0.68
103_F	148_L	1.136	0.66
98_H	147_W	1.135	0.66
82_L	154_F	1.132	0.66
18_H	22_R	1.129	0.65
103_F	140_M	1.129	0.65
98_H	102_Y	1.118	0.64
13_R	47_H	1.116	0.64
97_M	116_A	1.114	0.64
43_V	108_D	1.104	0.63
21_H	55_L	1.096	0.62
33_L	43_V	1.093	0.62
42_L	99_V	1.088	0.61
56_G	147_W	1.085	0.61
28_L	72_Y	1.073	0.60
112_R	142_L	1.07	0.59
58_F	78_R	1.064	0.59
15_F	149_S	1.06	0.58
103_F	139_Y	1.06	0.58
114_Q	135_R	1.059	0.58
26_H	32_A	1.042	0.56
108_D	111_E	1.032	0.55
96_L	132_P	1.029	0.55
120_D	123_R	1.029	0.55
100_Q	166_S	1.022	0.54
33_L	65_W	1.02	0.54
62_I	71_Y	1.019	0.54
14_I	17_L	1.011	0.53
88_N	91_D	1.009	0.53
21_H	99_V	1.009	0.53
28_L	68_L	1.006	0.52
89_P	125_G	1.006	0.52
1_M	8_D	1.003	0.52
154_F	157_W	1.002	0.52

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
4fqnA	4	0.4852	50.4	0.94	Contact Map	0.497
3pxia	3	0.5503	19	0.952	Contact Map	0.18
2ld7B	1	0.4438	17.3	0.953	Contact Map	0.274
3jtpA	4	0.5266	14.4	0.955	Contact Map	0.245
3j3t1	6	0.5503	12.8	0.956	Contact Map	0.332
3jtnA	2	0.4852	9.3	0.958	Contact Map	0.294
2vlaA	1	0.7041	8.2	0.96	Contact Map	0.209
1dlyA	1	0.6213	8	0.96	Contact Map	0.111
3lysA	6	0.6095	6.7	0.961	Contact Map	0.34
1t3wA	2	0.6864	6	0.962	Contact Map	0.313

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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