NRDI - ECOLI - GREMLIN Contacts

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NRDI - Protein NrdI

UniProt:	P0A772	Sequences: MSQLVYFSSSSENTQRFIERLGLPAVRIPLNERERIQVDEPYILIVPSYGGGGTAGAVPRQVIRFLNDEHNRALLRGVIASGNRNFGEAYGRAGDVIARKCGVPWLYRFELMGTQSDIENVRKGVTEFWQRQPQNA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13287
Length:	136 (125)
Sequences:	898 (578)
Seq/√Len:	51.7

ECOLI - NRDI
BACSU - NRDIB NRDI

GREMLIN Results:

Legend: The darker and larger the blue dots, the higher coevolution strength.

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
20_R	118_I	4.395	1.00
15_Q	19_E	3.455	1.00
80_A	94_G	3.390	1.00
75_L	101_C	2.627	1.00
94_G	105_W	2.606	1.00
37_Q	68_D	2.593	1.00
41_P	74_L	2.583	1.00
18_I	45_I	2.482	1.00
69_E	73_A	2.330	1.00
80_A	105_W	2.224	1.00
5_V	38_V	2.171	1.00
95_D	108_R	2.146	1.00
84_R	90_Y	1.928	0.99
58_V	63_I	1.892	0.99
75_L	103_V	1.884	0.99
119_E	123_K	1.872	0.99
17_F	121_V	1.801	0.99
79_I	121_V	1.798	0.99
8_S	62_V	1.768	0.99
60_R	63_I	1.710	0.99
15_Q	27_R	1.699	0.99
44_L	66_L	1.654	0.98
46_V	97_I	1.648	0.98
4_L	45_I	1.629	0.98
44_L	62_V	1.548	0.97
23_L	122_R	1.541	0.97
12_E	112_M	1.532	0.97
80_A	91_G	1.506	0.97
92_R	96_V	1.428	0.96
95_D	105_W	1.417	0.96
50_G	89_A	1.409	0.96
59_P	62_V	1.406	0.95
58_V	96_V	1.359	0.95
89_A	92_R	1.347	0.94
38_V	65_F	1.328	0.94
43_I	125_V	1.314	0.93
90_Y	108_R	1.305	0.93
81_S	109_F	1.282	0.93
57_A	89_A	1.276	0.92
70_H	73_A	1.255	0.92
12_E	15_Q	1.218	0.91
48_S	78_V	1.203	0.90
106_L	124_G	1.178	0.89
63_I	100_K	1.166	0.89
83_N	111_L	1.147	0.88
79_I	107_Y	1.141	0.87
8_S	47_P	1.132	0.87
107_Y	121_V	1.130	0.87
52_G	81_S	1.121	0.87
120_N	123_K	1.086	0.85
17_F	109_F	1.072	0.84
78_V	97_I	1.067	0.84
53_G	89_A	1.067	0.84
6_Y	38_V	1.064	0.84
66_L	97_I	1.062	0.83
45_I	79_I	1.026	0.81
62_V	80_A	1.019	0.81
8_S	61_Q	1.016	0.81
47_P	86_F	1.008	0.80
123_K	127_E	0.999	0.79
14_T	47_P	0.994	0.79
63_I	96_V	0.989	0.79
33_R	91_G	0.986	0.79
107_Y	120_N	0.976	0.78
115_Q	119_E	0.968	0.77
32_E	35_R	0.965	0.77
37_Q	70_H	0.965	0.77
38_V	71_N	0.961	0.77
124_G	128_F	0.957	0.76
46_V	52_G	0.946	0.76
16_R	112_M	0.945	0.76
126_T	129_W	0.939	0.75
10_S	49_Y	0.936	0.75
49_Y	86_F	0.932	0.74
64_R	68_D	0.927	0.74
6_Y	28_I	0.902	0.72
83_N	110_E	0.897	0.72
63_I	67_N	0.893	0.71
59_P	87_G	0.892	0.71
91_G	108_R	0.883	0.70
80_A	95_D	0.881	0.70
81_S	106_L	0.869	0.69
70_H	102_G	0.868	0.69
11_S	40_E	0.863	0.69
22_G	25_A	0.862	0.69
8_S	49_Y	0.861	0.68
56_G	89_A	0.859	0.68
51_G	86_F	0.858	0.68
30_L	61_Q	0.853	0.68
46_V	53_G	0.846	0.67
88_E	91_G	0.839	0.66
66_L	72_R	0.824	0.65
54_T	89_A	0.823	0.65
13_N	111_L	0.820	0.65
12_E	19_E	0.817	0.64
85_N	111_L	0.813	0.64
17_F	49_Y	0.810	0.64
41_P	124_G	0.805	0.63
99_R	102_G	0.804	0.63
67_N	94_G	0.792	0.62
53_G	95_D	0.791	0.62
24_P	40_E	0.786	0.61
9_S	81_S	0.781	0.61
12_E	54_T	0.778	0.61
43_I	106_L	0.773	0.60
35_R	68_D	0.751	0.58
57_A	129_W	0.750	0.58
19_E	22_G	0.749	0.58
123_K	126_T	0.747	0.57
44_L	97_I	0.739	0.57
57_A	92_R	0.731	0.56
42_Y	114_T	0.723	0.55
51_G	94_G	0.722	0.55
41_P	76_R	0.719	0.55
75_L	108_R	0.715	0.54
35_R	64_R	0.707	0.53
21_L	120_N	0.707	0.53
54_T	96_V	0.697	0.52
56_G	60_R	0.694	0.52
5_V	40_E	0.694	0.52
81_S	91_G	0.691	0.52
79_I	109_F	0.682	0.51
17_F	118_I	0.678	0.50
35_R	127_E	0.663	0.49
66_L	103_V	0.663	0.49
77_G	117_D	0.657	0.48
33_R	46_V	0.654	0.48
53_G	56_G	0.652	0.48
85_N	110_E	0.648	0.47
32_E	64_R	0.648	0.47
64_R	123_K	0.639	0.46
14_T	49_Y	0.638	0.46
43_I	77_G	0.632	0.46
18_I	25_A	0.630	0.45
49_Y	107_Y	0.625	0.45
5_V	68_D	0.623	0.45
11_S	57_A	0.615	0.44
74_L	122_R	0.614	0.44
98_A	116_S	0.613	0.44
90_Y	95_D	0.603	0.43
91_G	106_L	0.600	0.42
18_I	124_G	0.600	0.42
37_Q	40_E	0.595	0.42
95_D	99_R	0.593	0.42
50_G	59_P	0.590	0.41
29_P	61_Q	0.589	0.41
73_A	127_E	0.588	0.41
53_G	81_S	0.588	0.41
41_P	101_C	0.583	0.41
78_V	91_G	0.583	0.41
6_Y	100_K	0.582	0.40
17_F	117_D	0.576	0.40
107_Y	117_D	0.576	0.40
35_R	53_G	0.573	0.40
83_N	86_F	0.571	0.39
101_C	108_R	0.565	0.39
107_Y	128_F	0.563	0.39
25_A	74_L	0.561	0.38
34_E	68_D	0.557	0.38
23_L	126_T	0.556	0.38
44_L	87_G	0.556	0.38
83_N	109_F	0.552	0.37
125_V	128_F	0.546	0.37
72_R	93_A	0.545	0.37
77_G	124_G	0.542	0.36
72_R	101_C	0.542	0.36
61_Q	100_K	0.541	0.36
70_H	98_A	0.539	0.36
59_P	93_A	0.538	0.36
80_A	98_A	0.536	0.36
94_G	108_R	0.536	0.36
8_S	86_F	0.533	0.36
105_W	116_S	0.533	0.36
34_E	126_T	0.531	0.35
7_F	20_R	0.528	0.35
67_N	100_K	0.519	0.34
35_R	123_K	0.517	0.34
42_Y	103_V	0.514	0.34
91_G	105_W	0.511	0.34
73_A	76_R	0.511	0.34
43_I	124_G	0.509	0.33
48_S	103_V	0.508	0.33
14_T	81_S	0.508	0.33
105_W	108_R	0.507	0.33
47_P	61_Q	0.507	0.33
52_G	69_E	0.506	0.33
23_L	26_V	0.503	0.33
73_A	115_Q	0.500	0.33

Legend: The i and j are positions as given in the UniProt sequence. Only predictions with Prob ≥ 0.7 are listed. For all 3L/2 predictions, click on one of the links below.

Sco = ((raw_sco - min_sco)/(avg_sco - min_sco))/2 + 0.5
Prob = P(contact | Sco, seq80/√len)
seq80 = effective number of sequences, after reducing redundancy to 80% identity

Text file of predictions (all 3L/2 predictions)
Generate restraints for ROSETTA Structure Modeling
Upload PDB model overlay contacts on the model

HHsearch Results:

Legend: GREMLIN results (Prob ≥ 0.7) overlaid on top PDB hits. The grey/red filled circles underneath are pdb residue contacts (min distance < 5 Angstroms). The shade of the circles is based on the top 10 (or top 20 if e-value < 1E-20) 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	%	HHΔ
3n3aC	1	0.9632	99.9	0.52	Contact Map
1rljA	1	0.9338	99.9	0.589	Contact Map
2xodA	1	0.8676	99.8	0.64	Contact Map
4n82B	1	0.9779	99.7	0.65	Contact Map
3hr4A	2	0.9632	99.5	0.717	Contact Map
1bvyF	1	0.9632	99.4	0.723	Contact Map
2bpoA	1	0.9632	99.4	0.724	Contact Map
2bmvA	1	0.9485	99.4	0.728	Contact Map
3qe2A	1	0.9559	99.4	0.731	Contact Map
1yobA	1	0.9706	99.3	0.735	Contact Map

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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