GLNK - ECOLI - GREMLIN Contacts

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GLNK - Nitrogen regulatory protein P-II 2

UniProt:	P0AC55	Sequences: MKLVTVIIKPFKLEDVREALSSIGIQGLTVTEVKGFGRQKGHAELYRGAEYSVNFLPKVKIDVAIADDQLDEVIDIVSKAAYTGKIGDGKIFVAELQRVIRIRTGEADEAAL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12191
Length:	112 (112)
Sequences:	2942 (1589)
Seq/√Len:	150.2

ECOLI - GLNK GLNB
BACSU - NRGB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
98_R	107_A	4.476	1.00
64_A	96_L	3.673	1.00
98_R	108_D	3.607	1.00
65_I	73_V	3.091	1.00
66_A	109_E	2.659	1.00
12_K	15_D	2.524	1.00
69_Q	72_E	2.440	1.00
16_V	81_A	2.286	1.00
78_S	82_Y	2.260	1.00
6_V	77_V	2.236	1.00
23_I	76_I	2.168	1.00
29_T	33_V	2.137	1.00
5_T	94_A	1.987	1.00
76_I	80_A	1.919	1.00
75_D	79_K	1.901	1.00
66_A	69_Q	1.800	1.00
74_I	93_V	1.797	1.00
3_L	64_A	1.677	1.00
8_I	16_V	1.651	1.00
71_D	75_D	1.642	1.00
13_L	30_V	1.559	1.00
31_T	62_D	1.523	1.00
16_V	61_I	1.383	1.00
72_E	76_I	1.375	1.00
4_V	73_V	1.332	1.00
31_T	60_K	1.307	1.00
67_D	109_E	1.293	1.00
2_K	67_D	1.266	1.00
75_D	78_S	1.261	1.00
74_I	91_I	1.253	1.00
78_S	107_A	1.232	1.00
78_S	91_I	1.229	1.00
3_L	94_A	1.215	1.00
18_E	22_S	1.207	1.00
8_I	61_I	1.194	1.00
4_V	65_I	1.193	1.00
19_A	22_S	1.186	1.00
5_T	60_K	1.161	1.00
64_A	92_F	1.158	1.00
72_E	79_K	1.154	1.00
7_I	29_T	1.123	0.99
101_R	106_E	1.122	0.99
30_V	55_F	1.109	0.99
2_K	95_E	1.102	0.99
19_A	79_K	1.096	0.99
2_K	70_L	1.090	0.99
65_I	70_L	1.090	0.99
82_Y	105_G	1.090	0.99
39_Q	56_L	1.087	0.99
71_D	107_A	1.085	0.99
8_I	13_L	1.084	0.99
70_L	74_I	1.083	0.99
9_K	86_I	1.080	0.99
17_R	28_L	1.079	0.99
78_S	100_I	1.073	0.99
2_K	93_V	1.071	0.99
71_D	98_R	1.063	0.99
19_A	80_A	1.055	0.99
5_T	64_A	1.046	0.99
92_F	102_I	1.022	0.99
2_K	97_Q	1.014	0.99
39_Q	58_K	1.014	0.99
103_R	106_E	0.983	0.99
20_L	63_V	0.973	0.99
13_L	59_V	0.966	0.98
72_E	75_D	0.953	0.98
21_S	36_F	0.947	0.98
83_T	88_D	0.938	0.98
84_G	88_D	0.933	0.98
42_H	54_N	0.931	0.98
36_F	42_H	0.908	0.98
9_K	33_V	0.905	0.98
25_I	63_V	0.904	0.98
4_V	77_V	0.898	0.97
99_V	111_A	0.878	0.97
36_F	54_N	0.877	0.97
19_A	76_I	0.873	0.97
63_V	73_V	0.868	0.97
69_Q	73_V	0.862	0.97
23_I	72_E	0.859	0.97
27_G	36_F	0.829	0.96
43_A	50_E	0.807	0.95
45_L	49_A	0.785	0.95
100_I	107_A	0.770	0.94
46_Y	49_A	0.770	0.94
16_V	80_A	0.767	0.94
74_I	100_I	0.763	0.94
41_G	58_K	0.762	0.94
36_F	55_F	0.749	0.93
6_V	81_A	0.743	0.93
42_H	49_A	0.740	0.93
7_I	92_F	0.736	0.92
60_K	92_F	0.728	0.92
6_V	63_V	0.723	0.92
13_L	54_N	0.721	0.92
3_L	96_L	0.721	0.92
20_L	77_V	0.720	0.92
28_L	61_I	0.700	0.90
48_G	51_Y	0.696	0.90
42_H	45_L	0.696	0.90
25_I	73_V	0.695	0.90
11_F	15_D	0.690	0.90
47_R	51_Y	0.676	0.89
37_G	90_K	0.676	0.89
5_T	62_D	0.671	0.89
33_V	60_K	0.664	0.88
11_F	56_L	0.662	0.88
8_I	77_V	0.654	0.87
20_L	73_V	0.653	0.87
45_L	85_K	0.653	0.87
13_L	55_F	0.653	0.87
45_L	50_E	0.649	0.87
66_A	73_V	0.640	0.86
21_S	40_K	0.639	0.86
15_D	80_A	0.634	0.86
8_I	12_K	0.634	0.86
92_F	99_V	0.634	0.86
43_A	52_S	0.628	0.85
41_G	44_E	0.618	0.84
42_H	50_E	0.614	0.84
70_L	95_E	0.611	0.83
71_D	78_S	0.611	0.83
67_D	70_L	0.607	0.83
3_L	92_F	0.604	0.83
79_K	82_Y	0.599	0.82
30_V	61_I	0.594	0.82
32_E	59_V	0.590	0.81
5_T	99_V	0.588	0.81
34_K	46_Y	0.588	0.81
17_R	54_N	0.585	0.81
22_S	79_K	0.584	0.81
1_M	67_D	0.582	0.80
20_L	61_I	0.581	0.80
27_G	99_V	0.579	0.80
38_R	102_I	0.573	0.79
9_K	82_Y	0.573	0.79
36_F	102_I	0.567	0.79
57_P	85_K	0.564	0.78
91_I	100_I	0.564	0.78
11_F	49_A	0.561	0.78
27_G	56_L	0.559	0.78
76_I	79_K	0.556	0.77
17_R	21_S	0.553	0.77
25_I	42_H	0.553	0.77
70_L	98_R	0.551	0.77
11_F	55_F	0.543	0.76
45_L	54_N	0.542	0.76
20_L	72_E	0.541	0.75
77_V	81_A	0.535	0.75
11_F	32_E	0.534	0.74
96_L	99_V	0.532	0.74
39_Q	86_I	0.530	0.74
38_R	44_E	0.530	0.74
53_V	112_L	0.530	0.74
28_L	52_S	0.529	0.74
41_G	56_L	0.522	0.73
100_I	106_E	0.522	0.73
13_L	61_I	0.519	0.72
50_E	85_K	0.519	0.72
100_I	111_A	0.517	0.72
44_E	49_A	0.517	0.72
2_K	8_I	0.512	0.71
28_L	62_D	0.508	0.71
70_L	93_V	0.508	0.71
13_L	52_S	0.506	0.71
20_L	23_I	0.505	0.70
42_H	85_K	0.501	0.70
85_K	102_I	0.500	0.70

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
4ozjA	3	0.875	100	0.177	Contact Map
3t9zA	3	0.875	100	0.188	Contact Map
2o66A	5	0.8661	100	0.189	Contact Map
3ncqA	4	1	100	0.196	Contact Map
1hwuA	6	0.9554	100	0.206	Contact Map
1vfjA	3	1	100	0.209	Contact Map
4r25A	3	1	100	0.21	Contact Map
3bzqA	3	0.8661	100	0.211	Contact Map
3l7pA	4	0.8125	100	0.212	Contact Map
2ns1B	3	1	100	0.221	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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