OPENSEQ.org - NRDI - ECOLI GREMLIN

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NRDI - Protein NrdI

UniProt:	P0A772	Sequence MSQLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQRQPQNA	Download Alignment We filter this alignment to remove sites that have > 75% gaps before running GREMLIN.
EcoGene:	EG13287
Length:	136 (133)
Sequences:	426
Seq/Len:	3.20

NRDI
Paralog alert: 0.07 [within 20: 0.01] - 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
20_R	118_I	2.589	1.00
75_L	101_C	2.34	1.00
80_A	94_G	2.324	1.00
43_I	125_V	2.322	1.00
37_Q	68_D	2.25	1.00
15_Q	19_E	2.109	1.00
5_V	38_V	2.061	1.00
15_Q	27_R	1.846	0.99
4_L	45_I	1.734	0.99
53_G	56_G	1.653	0.98
41_P	74_L	1.636	0.98
80_A	105_W	1.627	0.98
44_L	66_L	1.538	0.97
18_I	45_I	1.525	0.97
8_S	62_V	1.44	0.95
75_L	103_V	1.436	0.95
3_Q	40_E	1.415	0.94
58_V	96_V	1.393	0.94
95_D	105_W	1.389	0.93
38_V	65_F	1.386	0.93
12_E	54_T	1.36	0.93
17_F	121_V	1.327	0.91
83_N	110_E	1.317	0.91
85_N	111_L	1.311	0.91
59_P	62_V	1.298	0.90
24_P	40_E	1.294	0.90
83_N	111_L	1.262	0.88
92_R	96_V	1.25	0.88
57_A	89_A	1.243	0.87
30_L	61_Q	1.239	0.87
14_T	47_P	1.196	0.84
4_L	129_W	1.189	0.84
34_E	98_A	1.188	0.84
36_I	115_Q	1.174	0.83
18_I	90_Y	1.173	0.83
94_G	105_W	1.17	0.83
3_Q	24_P	1.167	0.82
123_K	127_E	1.167	0.82
70_H	73_A	1.167	0.82
126_T	129_W	1.162	0.82
95_D	108_R	1.153	0.81
44_L	97_I	1.148	0.81
85_N	110_E	1.144	0.81
17_F	49_Y	1.141	0.80
44_L	62_V	1.141	0.80
20_R	84_R	1.13	0.79
41_P	101_C	1.124	0.79
60_R	63_I	1.122	0.79
58_V	63_I	1.116	0.78
11_S	114_T	1.112	0.78
49_Y	86_F	1.111	0.78
2_S	132_Q	1.109	0.78
84_R	90_Y	1.109	0.78
12_E	112_M	1.097	0.77
80_A	95_D	1.09	0.76
48_S	78_V	1.082	0.75
23_L	125_V	1.079	0.75
83_N	86_F	1.066	0.74
77_G	106_L	1.06	0.73
54_T	130_Q	1.032	0.70
42_Y	130_Q	1.02	0.69
69_E	73_A	1.009	0.68
28_I	98_A	1.006	0.67
46_V	131_R	1.004	0.67
5_V	39_D	1	0.67

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
3n3aC	2	0.9779	99.9	0.51	Contact Map	0.659
1rljA	1	0.9338	99.8	0.603	Contact Map	0.614
2xodA	1	0.875	99.7	0.652	Contact Map	0.622
3hr4A	4	0.9632	99.3	0.73	Contact Map	0.417
2bpoA	2	0.9632	99.3	0.732	Contact Map	0.347
1bvyF	1	0.9632	99.3	0.735	Contact Map	0.353
2bmvA	1	0.9485	99.3	0.735	Contact Map	0.395
3qe2A	2	0.9559	99.3	0.738	Contact Map	0.35
1ykgA	1	0.9559	99.2	0.747	Contact Map	0.354
1tllA	2	0.9559	99.2	0.748	Contact Map	0.383

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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