TSAE - ECOLI - GREMLIN Contacts

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TSAE - tRNA threonylcarbamoyladenosine biosynthesis protein TsaE

UniProt:	P0AF67	Sequences: MMNRVIPLPDEQATLDLGERVAKACDGATVIYLYGDLGAGKTTFSRGFLQALGHQGNVKSPTYTLVEPYTLDNLMVYHFDLYRLADPEELEFMGIRDYFANDAICLVEWPQQGTGVLPDPDVEIHIDYQAQGREARVSAVSSAGELLLARLAG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11757
Length:	153 (136)
Sequences:	4117 (2979)
Seq/√Len:	255.4

ECOLI - TSAE
BACSU - TSAE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
34_Y	123_E	2.501	1.00
8_L	14_T	2.487	1.00
45_S	106_L	2.358	1.00
10_D	13_A	2.332	1.00
25_C	48_F	2.255	1.00
44_F	48_F	2.193	1.00
9_P	13_A	2.090	1.00
127_D	134_E	2.058	1.00
48_F	106_L	2.016	1.00
34_Y	111_Q	2.006	1.00
127_D	136_R	1.998	1.00
34_Y	125_H	1.972	1.00
33_L	45_S	1.948	1.00
17_L	135_A	1.922	1.00
18_G	44_F	1.919	1.00
126_I	135_A	1.882	1.00
49_L	76_V	1.822	1.00
15_L	50_Q	1.804	1.00
68_P	77_Y	1.751	1.00
15_L	47_G	1.736	1.00
94_G	97_D	1.720	1.00
77_Y	103_A	1.700	1.00
19_E	50_Q	1.686	1.00
32_Y	110_P	1.674	1.00
49_L	58_V	1.671	1.00
15_L	46_R	1.657	1.00
25_C	31_I	1.655	1.00
81_L	113_G	1.625	1.00
21_V	44_F	1.565	1.00
59_K	67_E	1.544	1.00
34_Y	110_P	1.541	1.00
18_G	47_G	1.529	1.00
125_H	136_R	1.519	1.00
8_L	135_A	1.514	1.00
11_E	15_L	1.488	1.00
125_H	138_S	1.467	1.00
123_E	138_S	1.455	1.00
11_E	47_G	1.417	1.00
26_D	29_T	1.410	1.00
8_L	17_L	1.400	1.00
16_D	20_R	1.377	1.00
54_H	58_V	1.370	1.00
49_L	54_H	1.348	1.00
32_Y	121_D	1.344	1.00
79_F	95_I	1.341	1.00
99_F	105_C	1.322	1.00
47_G	51_A	1.321	1.00
9_P	132_G	1.320	1.00
7_P	132_G	1.320	1.00
87_P	115_G	1.315	1.00
129_Q	132_G	1.281	1.00
44_F	126_I	1.259	1.00
7_P	134_E	1.237	1.00
8_L	13_A	1.226	1.00
17_L	137_V	1.188	1.00
19_E	23_K	1.180	1.00
90_L	95_I	1.177	1.00
11_E	43_T	1.158	1.00
16_D	19_E	1.143	1.00
22_A	52_L	1.129	1.00
81_L	110_P	1.129	1.00
31_I	106_L	1.114	1.00
121_D	141_S	1.109	1.00
66_V	79_F	1.093	1.00
129_Q	134_E	1.086	1.00
74_L	104_I	1.082	1.00
22_A	51_A	1.072	1.00
85_A	112_Q	1.069	1.00
36_D	128_Y	1.068	1.00
91_E	96_R	1.047	1.00
68_P	98_Y	1.044	1.00
123_E	140_V	1.028	1.00
19_E	51_A	1.014	1.00
29_T	104_I	1.004	1.00
71_L	74_L	1.002	1.00
37_L	82_Y	0.998	1.00
76_V	106_L	0.989	1.00
25_C	29_T	0.988	1.00
14_T	18_G	0.986	1.00
79_F	105_C	0.982	1.00
117_L	121_D	0.979	1.00
70_T	75_M	0.976	1.00
95_I	99_F	0.964	1.00
90_L	113_G	0.953	1.00
99_F	107_V	0.952	1.00
75_M	103_A	0.950	1.00
122_V	139_A	0.931	1.00
7_P	129_Q	0.928	1.00
86_D	89_E	0.920	1.00
71_L	75_M	0.918	1.00
32_Y	123_E	0.917	1.00
88_E	91_E	0.917	1.00
79_F	98_Y	0.896	1.00
30_V	107_V	0.896	1.00
66_V	98_Y	0.878	1.00
20_R	24_A	0.868	1.00
48_F	104_I	0.863	1.00
89_E	112_Q	0.862	1.00
85_A	89_E	0.859	0.99
14_T	135_A	0.859	0.99
77_Y	105_C	0.856	0.99
75_M	101_N	0.846	0.99
46_R	57_N	0.844	0.99
20_R	23_K	0.843	0.99
31_I	122_V	0.842	0.99
18_G	22_A	0.836	0.99
66_V	77_Y	0.830	0.99
90_L	93_M	0.828	0.99
11_E	46_R	0.825	0.99
45_S	49_L	0.809	0.99
22_A	48_F	0.805	0.99
21_V	122_V	0.801	0.99
21_V	124_I	0.796	0.99
89_E	92_F	0.783	0.99
53_G	73_N	0.772	0.99
31_I	124_I	0.771	0.99
87_P	114_T	0.770	0.99
14_T	126_I	0.768	0.99
12_Q	16_D	0.764	0.99
84_L	90_L	0.760	0.99
33_L	106_L	0.757	0.99
54_H	76_V	0.755	0.99
14_T	43_T	0.754	0.99
59_K	65_L	0.751	0.99
53_G	56_G	0.737	0.98
68_P	75_M	0.732	0.98
13_A	16_D	0.731	0.98
12_Q	15_L	0.728	0.98
96_R	100_A	0.712	0.98
15_L	19_E	0.712	0.98
66_V	93_M	0.711	0.98
25_C	104_I	0.700	0.98
77_Y	98_Y	0.690	0.98
81_L	107_V	0.686	0.98
81_L	112_Q	0.684	0.97
45_S	48_F	0.682	0.97
32_Y	113_G	0.678	0.97
72_D	75_M	0.677	0.97
39_A	128_Y	0.673	0.97
11_E	18_G	0.667	0.97
46_R	49_L	0.666	0.97
21_V	48_F	0.664	0.97
74_L	103_A	0.662	0.97
18_G	48_F	0.651	0.97
8_L	126_I	0.651	0.97
90_L	116_V	0.638	0.96
124_I	135_A	0.637	0.96
14_T	17_L	0.637	0.96
8_L	43_T	0.631	0.96
27_G	74_L	0.630	0.96
118_P	121_D	0.630	0.96
84_L	93_M	0.629	0.96
66_V	94_G	0.623	0.96
32_Y	63_Y	0.615	0.95
84_L	95_I	0.614	0.95
15_L	43_T	0.613	0.95
76_V	104_I	0.610	0.95
63_Y	120_P	0.609	0.95
28_A	103_A	0.608	0.95
32_Y	120_P	0.607	0.95
46_R	50_Q	0.605	0.95
124_I	137_V	0.605	0.95
59_K	64_T	0.604	0.95
121_D	140_V	0.602	0.95
93_M	98_Y	0.600	0.95
84_L	112_Q	0.587	0.94
44_F	47_G	0.587	0.94
64_T	67_E	0.586	0.94
36_D	127_D	0.586	0.94
43_T	46_R	0.584	0.94
8_L	47_G	0.583	0.94
71_L	76_V	0.579	0.94
89_E	93_M	0.577	0.94
120_P	141_S	0.569	0.93
17_L	21_V	0.562	0.93
14_T	47_G	0.561	0.93
19_E	47_G	0.561	0.93
111_Q	125_H	0.560	0.92
89_E	94_G	0.557	0.92
64_T	69_Y	0.555	0.92
18_G	51_A	0.554	0.92
45_S	76_V	0.554	0.92
113_G	117_L	0.554	0.92
46_R	59_K	0.552	0.92
87_P	116_V	0.551	0.92
22_A	25_C	0.550	0.92
79_F	118_P	0.539	0.91
36_D	39_A	0.539	0.91
88_E	116_V	0.527	0.90
122_V	137_V	0.525	0.90
30_V	105_C	0.524	0.90
54_H	71_L	0.518	0.89
55_Q	72_D	0.517	0.89
52_L	104_I	0.511	0.89
81_L	84_L	0.511	0.89
137_V	141_S	0.509	0.88
28_A	102_D	0.506	0.88
31_I	48_F	0.505	0.88
70_T	74_L	0.505	0.88
75_M	102_D	0.505	0.88
58_V	76_V	0.503	0.88
49_L	67_E	0.503	0.88
35_G	39_A	0.502	0.88
39_A	126_I	0.500	0.88

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
1htwA	1	1	100	0.291	Contact Map
1svmA	3	0.9869	97.4	0.844	Contact Map
2c95A	1	0.8301	97.4	0.844	Contact Map
2yogA	1	0.7516	97.3	0.845	Contact Map
3umfA	1	0.7974	97.3	0.846	Contact Map
2v54A	2	0.7974	97.3	0.847	Contact Map
1uj2A	3	0.8105	97.2	0.848	Contact Map
3kb2A	2	0.7582	97.2	0.848	Contact Map
2f6rA	1	0.915	97.2	0.848	Contact Map
2jeoA	3	0.8105	97.2	0.848	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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