OPENSEQ.org - YRDD - ECOLI GREMLIN

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YRDD - Uncharacterized protein YrdD

UniProt:	P45771	Sequence MAKSALFTVRNNESCPKCGAELVIRSGKHGPFLGCSQYPACDYVRPLKSSADGHIVKVLEGQVCPACGANLVLRQGRFGMFIGCINYPECEHTELIDKPDETAITCPQCRTGHLVQRRSRYGKTFHSCDRYPECQFAINFKPIAGECPECHYPLLIEKKTAQGVKHFCASKQCGKPVSAE	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG12841
Length:	180 (177)
Sequences:	381
Seq/Len:	2.15

YRDD
Paralog alert: 0.02 [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
69_A	86_N	4.555	1.00
22_L	43_Y	3.778	1.00
20_A	37_Q	3.623	1.00
17_K	42_D	2.951	1.00
16_P	43_Y	2.696	1.00
71_L	82_I	2.605	1.00
16_P	22_L	2.562	1.00
143_I	166_H	2.446	1.00
108_Q	135_Q	2.37	1.00
65_P	71_L	2.105	0.99
13_E	45_R	2.092	0.99
27_G	30_G	1.991	0.99
65_P	92_H	1.88	0.99
71_L	92_H	1.849	0.98
113_H	129_D	1.727	0.97
141_K	157_E	1.717	0.97
147_C	168_C	1.639	0.96
168_C	173_C	1.632	0.96
5_A	10_R	1.487	0.92
150_C	168_C	1.48	0.91
81_F	87_Y	1.475	0.91
136_F	170_S	1.461	0.91
65_P	82_I	1.44	0.90
147_C	150_C	1.431	0.89
4_S	9_V	1.356	0.86
7_F	11_N	1.338	0.85
78_F	118_R	1.328	0.84
152_Y	169_A	1.29	0.82
112_G	130_R	1.276	0.81
21_E	36_S	1.268	0.80
17_K	43_Y	1.253	0.79
43_Y	120_R	1.253	0.79
68_G	86_N	1.248	0.79
106_C	122_G	1.229	0.77
136_F	152_Y	1.222	0.77
128_C	134_C	1.215	0.76
123_K	139_N	1.213	0.76
78_F	126_H	1.193	0.74
145_G	155_L	1.179	0.73
34_G	44_V	1.175	0.73
150_C	173_C	1.175	0.73
67_C	79_G	1.172	0.72
23_V	36_S	1.168	0.72
44_V	57_K	1.165	0.72
4_S	8_T	1.159	0.71
130_R	133_E	1.159	0.71
111_T	130_R	1.158	0.71
82_I	92_H	1.158	0.71
115_V	129_D	1.146	0.70
114_L	136_F	1.144	0.70
152_Y	170_S	1.138	0.69
2_A	11_N	1.136	0.69
33_L	55_I	1.135	0.69
9_V	12_N	1.134	0.69
47_L	76_G	1.131	0.68
22_L	33_L	1.126	0.68
171_K	174_G	1.122	0.68
24_I	47_L	1.109	0.66
26_S	76_G	1.106	0.66
2_A	8_T	1.097	0.65
5_A	9_V	1.095	0.65
6_L	28_K	1.082	0.63
13_E	109_C	1.076	0.63
71_L	78_F	1.074	0.63
37_Q	40_A	1.072	0.62
103_A	148_P	1.069	0.62
61_G	70_N	1.067	0.62
148_P	177_V	1.067	0.62
125_F	158_K	1.066	0.62
166_H	177_V	1.037	0.59
106_C	134_C	1.035	0.58
25_R	34_G	1.026	0.57
61_G	152_Y	1.022	0.57
127_S	130_R	1.018	0.56
100_D	116_Q	1.006	0.55
5_A	8_T	1.004	0.55
66_A	92_H	1	0.54

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
2gaiA	2	0.4944	99.6	0.735	Contact Map	0.356
3qt1I	1	0.5	88.8	0.919	Contact Map	0.686
4c2mI	2	0.4833	84.6	0.924	Contact Map	0.262
3h0gI	2	0.4611	83.5	0.925	Contact Map	0.489
1twfI	1	0.6278	80.3	0.927	Contact Map	0.611
1vq8Z	1	0.3222	69.5	0.933	Contact Map	0.687
2jrpA	1	0.3556	35.4	0.946	Contact Map	0.381
3j20Y	1	0.2389	30.3	0.948	Contact Map	0.046
4aybP	1	0.2611	27.2	0.949	Contact Map	0
2k4xA	1	0.2722	26.3	0.949	Contact Map	0.226

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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