NRDIB - BACSU - GREMLIN Contacts

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NRDIB - SPBc2 prophage-derived protein NrdI

UniProt:	P68524	Sequences: MTYESKTGNVKRFVKALQQEFDVEAIEITDDTIINQEFIHITYTIGFGEVPERTLSFINKNKNKIRGVAVSGNKVWGDNYGLAGDKLSAKFHTPLLLKFELSGTKQDLQKIIQEVQLIDKHNTKLDQAQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	129 (119)
Sequences:	898 (578)
Seq/√Len:	53.0

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
16_A	108_L	4.348	1.00
70_V	84_G	3.559	1.00
11_K	15_K	3.286	1.00
84_G	95_L	2.673	1.00
37_E	64_K	2.632	1.00
65_I	91_F	2.618	1.00
14_V	41_I	2.591	1.00
70_V	95_L	2.327	1.00
85_D	98_K	2.180	1.00
65_I	93_T	2.164	1.00
50_V	55_L	1.965	1.00
74_K	80_Y	1.924	1.00
52_E	55_L	1.901	0.99
19_Q	112_I	1.895	0.99
8_G	102_S	1.795	0.99
40_H	58_I	1.792	0.99
50_V	86_K	1.710	0.99
109_Q	113_Q	1.702	0.99
51_P	54_T	1.689	0.99
69_A	111_I	1.684	0.99
13_F	111_I	1.665	0.99
4_E	54_T	1.615	0.98
40_H	54_T	1.542	0.98
39_I	115_V	1.505	0.97
71_S	99_F	1.501	0.97
49_E	79_N	1.483	0.97
42_T	87_L	1.482	0.97
85_D	95_L	1.466	0.97
79_N	82_L	1.465	0.97
80_Y	98_K	1.432	0.96
70_V	81_G	1.429	0.96
73_N	101_L	1.418	0.96
73_N	100_E	1.415	0.96
46_G	79_N	1.412	0.96
60_K	63_N	1.404	0.96
8_G	11_K	1.328	0.94
34_I	57_F	1.326	0.94
82_L	86_K	1.313	0.94
27_E	31_D	1.279	0.93
116_Q	119_D	1.219	0.91
96_L	114_E	1.203	0.91
113_Q	117_L	1.197	0.90
110_K	113_Q	1.182	0.90
55_L	90_K	1.180	0.90
41_I	69_A	1.172	0.89
60_K	92_H	1.171	0.89
43_Y	76_W	1.166	0.89
34_I	61_N	1.162	0.89
33_I	60_K	1.139	0.88
58_I	87_L	1.125	0.87
97_L	111_I	1.125	0.87
2_T	34_I	1.113	0.87
105_K	109_Q	1.104	0.86
70_V	85_D	1.081	0.85
25_A	28_I	1.080	0.85
55_L	86_K	1.072	0.85
12_R	102_S	1.055	0.84
4_E	43_Y	1.051	0.84
69_A	97_L	1.032	0.82
10_V	43_Y	1.027	0.82
11_K	24_E	0.990	0.80
47_F	76_W	0.987	0.80
9_N	48_G	0.984	0.79
75_V	100_E	0.950	0.77
44_T	68_V	0.949	0.77
49_E	86_K	0.943	0.76
75_V	101_L	0.935	0.76
8_G	15_K	0.934	0.76
9_N	101_L	0.917	0.74
54_T	70_V	0.911	0.74
51_P	77_G	0.909	0.74
6_K	45_I	0.890	0.72
3_Y	26_I	0.877	0.71
97_L	110_K	0.877	0.71
114_E	118_I	0.877	0.71
55_L	59_N	0.874	0.71
58_I	62_K	0.865	0.70
4_E	53_R	0.855	0.69
28_I	81_G	0.852	0.69
45_I	76_W	0.850	0.69
69_A	99_F	0.847	0.68
68_V	87_L	0.834	0.67
13_F	99_F	0.823	0.66
23_V	32_T	0.815	0.65
81_G	98_K	0.812	0.65
17_L	110_K	0.811	0.65
37_E	114_E	0.801	0.64
10_V	45_I	0.795	0.63
7_T	36_Q	0.788	0.63
13_F	45_I	0.784	0.62
40_H	87_L	0.777	0.62
113_Q	116_Q	0.775	0.61
39_I	96_L	0.774	0.61
4_E	45_I	0.768	0.61
89_A	92_H	0.765	0.60
2_T	90_K	0.765	0.60
31_D	117_L	0.760	0.60
65_I	98_K	0.757	0.60
13_F	107_D	0.750	0.59
18_Q	21_F	0.730	0.57
5_S	71_S	0.722	0.56
63_N	105_K	0.722	0.56
10_V	71_S	0.720	0.56
59_N	84_G	0.708	0.54
71_S	96_L	0.701	0.54
19_Q	96_L	0.698	0.53
73_N	76_W	0.694	0.53
116_Q	120_K	0.694	0.53
70_V	88_S	0.687	0.52
3_Y	16_A	0.685	0.52
25_A	89_A	0.684	0.52
73_N	99_F	0.684	0.52
37_E	66_R	0.684	0.52
25_A	29_T	0.680	0.51
24_E	68_V	0.679	0.51
38_F	93_T	0.669	0.50
33_I	36_Q	0.664	0.50
64_K	112_I	0.655	0.49
39_I	67_G	0.653	0.49
78_D	81_G	0.652	0.49
71_S	81_G	0.648	0.48
14_V	114_E	0.637	0.47
48_G	101_L	0.634	0.47
80_Y	85_D	0.632	0.46
15_K	18_Q	0.632	0.46
27_E	56_S	0.625	0.46
66_R	118_I	0.625	0.46
42_T	120_K	0.624	0.46
51_P	83_A	0.614	0.45
27_E	32_T	0.608	0.44
58_I	93_T	0.608	0.44
21_F	78_D	0.606	0.44
77_G	83_A	0.602	0.43
6_K	42_T	0.602	0.43
91_F	98_K	0.597	0.43
81_G	84_G	0.589	0.42
20_E	29_T	0.588	0.42
95_L	98_K	0.586	0.42
99_F	118_I	0.583	0.41
67_G	107_D	0.582	0.41
42_T	49_E	0.576	0.41
62_K	83_A	0.573	0.40
63_N	117_L	0.572	0.40
70_V	102_S	0.570	0.40
53_R	90_K	0.570	0.40
50_V	59_N	0.569	0.40
59_N	90_K	0.565	0.40
84_G	98_K	0.564	0.39
46_G	51_P	0.563	0.39
66_R	109_Q	0.561	0.39
63_N	109_Q	0.557	0.39
8_G	52_E	0.556	0.39
38_F	61_N	0.554	0.38
59_N	91_F	0.551	0.38
65_I	87_L	0.547	0.38
45_I	97_L	0.546	0.38
104_T	114_E	0.543	0.37
9_N	46_G	0.538	0.37
8_G	120_K	0.536	0.37
19_Q	36_Q	0.536	0.37
23_V	28_I	0.536	0.37
40_H	77_G	0.535	0.37
38_F	104_T	0.534	0.36
18_Q	106_Q	0.531	0.36
52_E	86_K	0.530	0.36
39_I	66_R	0.530	0.36
43_Y	53_R	0.528	0.36
13_F	73_N	0.526	0.36
117_L	120_K	0.525	0.36
96_L	119_D	0.523	0.35
39_I	114_E	0.517	0.35
60_K	88_S	0.512	0.34
19_Q	116_Q	0.510	0.34
26_I	113_Q	0.508	0.34
67_G	114_E	0.508	0.34
38_F	60_K	0.507	0.34
4_E	76_W	0.504	0.34
22_D	25_A	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	0.9457	99.9	0.565	Contact Map
1rljA	1	0.9457	99.9	0.59	Contact Map
2xodA	1	0.8992	99.8	0.635	Contact Map
4n82B	1	0.9535	99.7	0.66	Contact Map
2bpoA	1	0.9922	99.3	0.727	Contact Map
1bvyF	1	0.9845	99.3	0.727	Contact Map
3hr4A	2	0.9922	99.3	0.733	Contact Map
2bmvA	1	0.9535	99.2	0.74	Contact Map
3qe2A	1	0.969	99.2	0.743	Contact Map
1yobA	1	0.9767	99.2	0.749	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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