TADA - BACSU - GREMLIN Contacts

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TADA - tRNA-specific adenosine deaminase

UniProt:	P21335	Sequences: MTQDELYMKEAIKEAKKAEEKGEVPIGAVLVINGEIIARAHNLRETEQRSIAHAEMLVIDEACKALGTWRLEGATLYVTLEPCPMCAGAVVLSRVEKVVFGAFDPKGGCSGTLMNLLQEERFNHQAEVVSGVLEEECGGMLSAFFRELRKKKKAARKNLSE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	161 (141)
Sequences:	8155 (5220)
Seq/√Len:	439.6

ECOLI - TADA RIBD
BACSU - TADA GUAD COMEB RIBD

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
10_E	39_R	3.314	1.00
97_K	127_E	2.443	1.00
9_K	133_L	2.391	1.00
10_E	13_K	2.288	1.00
76_L	90_V	2.245	1.00
49_R	60_D	2.195	1.00
101_G	137_C	2.187	1.00
73_G	96_E	2.082	1.00
75_T	99_V	2.077	1.00
43_L	57_L	2.009	1.00
88_G	116_L	1.967	1.00
7_Y	31_V	1.962	1.00
7_Y	36_I	1.962	1.00
75_T	97_K	1.942	1.00
102_A	145_F	1.930	1.00
100_F	103_F	1.923	1.00
134_E	138_G	1.910	1.00
14_E	39_R	1.894	1.00
97_K	129_V	1.877	1.00
43_L	47_E	1.875	1.00
103_F	130_S	1.862	1.00
133_L	136_E	1.820	1.00
14_E	17_K	1.711	1.00
4_D	97_K	1.711	1.00
30_L	58_V	1.660	1.00
17_K	41_H	1.639	1.00
28_A	76_L	1.616	1.00
9_K	136_E	1.602	1.00
115_N	118_Q	1.570	1.00
138_G	149_R	1.518	1.00
88_G	92_L	1.518	1.00
115_N	123_N	1.505	1.00
4_D	129_V	1.474	1.00
100_F	114_M	1.469	1.00
10_E	36_I	1.461	1.00
90_V	98_V	1.438	1.00
100_F	130_S	1.432	1.00
139_G	143_A	1.425	1.00
38_A	61_E	1.412	1.00
14_E	41_H	1.365	1.00
75_T	96_E	1.348	1.00
16_K	140_M	1.326	1.00
31_V	77_Y	1.317	1.00
32_I	73_G	1.313	1.00
44_R	51_I	1.275	1.00
11_A	79_T	1.271	1.00
32_I	74_A	1.266	1.00
80_L	141_L	1.265	1.00
4_D	99_V	1.262	1.00
139_G	142_S	1.262	1.00
143_A	147_E	1.226	1.00
4_D	77_Y	1.217	1.00
40_A	57_L	1.198	1.00
138_G	142_S	1.198	1.00
18_A	41_H	1.195	1.00
131_G	134_E	1.180	1.00
76_L	95_V	1.173	1.00
52_A	60_D	1.166	1.00
19_E	147_E	1.157	1.00
56_M	89_A	1.156	1.00
38_A	58_V	1.148	1.00
45_E	69_W	1.145	1.00
16_K	136_E	1.125	1.00
10_E	14_E	1.122	1.00
72_E	94_R	1.110	1.00
21_K	41_H	1.106	1.00
89_A	93_S	1.092	1.00
5_E	133_L	1.090	1.00
102_A	138_G	1.089	1.00
143_A	146_R	1.074	1.00
111_G	115_N	1.073	1.00
26_I	80_L	1.072	1.00
57_L	61_E	1.055	1.00
19_E	25_P	1.045	1.00
129_V	132_V	1.042	1.00
30_L	62_A	1.039	1.00
50_S	63_C	1.034	1.00
16_K	19_E	1.026	1.00
30_L	76_L	1.016	1.00
52_A	57_L	1.002	1.00
13_K	16_K	0.988	1.00
32_I	37_I	0.986	1.00
56_M	60_D	0.968	1.00
44_R	69_W	0.965	1.00
33_N	73_G	0.951	1.00
87_A	116_L	0.941	1.00
12_I	137_C	0.940	1.00
15_A	140_M	0.939	1.00
37_I	74_A	0.936	1.00
12_I	16_K	0.924	1.00
145_F	149_R	0.919	1.00
11_A	27_G	0.917	1.00
135_E	139_G	0.917	1.00
9_K	13_K	0.911	1.00
87_A	91_V	0.898	1.00
91_V	116_L	0.898	1.00
59_I	93_S	0.896	1.00
22_G	148_L	0.886	1.00
59_I	71_L	0.876	1.00
6_L	10_E	0.865	1.00
62_A	71_L	0.865	1.00
16_K	20_E	0.857	1.00
59_I	89_A	0.853	1.00
91_V	126_A	0.852	1.00
25_P	141_L	0.851	1.00
30_L	74_A	0.851	1.00
103_F	134_E	0.849	1.00
4_D	75_T	0.848	1.00
40_A	58_V	0.847	1.00
59_I	63_C	0.846	1.00
5_E	9_K	0.824	1.00
8_M	131_G	0.799	1.00
110_S	117_L	0.799	1.00
61_E	64_K	0.795	1.00
106_K	148_L	0.792	1.00
98_V	117_L	0.781	1.00
36_I	39_R	0.780	1.00
99_V	132_V	0.777	1.00
32_I	35_E	0.773	1.00
19_E	143_A	0.770	1.00
6_L	9_K	0.766	1.00
12_I	140_M	0.760	1.00
84_P	116_L	0.755	1.00
109_C	113_L	0.748	1.00
30_L	38_A	0.746	1.00
51_I	89_A	0.745	1.00
122_F	126_A	0.740	1.00
90_V	126_A	0.737	1.00
17_K	21_K	0.734	1.00
43_L	61_E	0.732	1.00
7_Y	77_Y	0.728	1.00
98_V	126_A	0.723	1.00
8_M	11_A	0.720	1.00
16_K	143_A	0.716	1.00
116_L	124_H	0.715	1.00
108_G	112_T	0.713	1.00
99_V	129_V	0.712	1.00
47_E	57_L	0.708	1.00
91_V	123_N	0.702	1.00
117_L	126_A	0.701	1.00
25_P	42_N	0.692	1.00
114_M	118_Q	0.691	1.00
47_E	64_K	0.687	1.00
42_N	51_I	0.682	1.00
100_F	111_G	0.680	1.00
40_A	61_E	0.678	1.00
35_E	70_R	0.677	1.00
29_V	36_I	0.675	1.00
103_F	114_M	0.673	1.00
114_M	117_L	0.672	1.00
39_R	61_E	0.667	1.00
80_L	102_A	0.667	1.00
141_L	145_F	0.665	1.00
63_C	71_L	0.660	1.00
52_A	56_M	0.660	1.00
17_K	20_E	0.659	1.00
7_Y	10_E	0.655	1.00
47_E	52_A	0.653	1.00
49_R	52_A	0.648	0.99
109_C	112_T	0.645	0.99
104_D	107_G	0.639	0.99
59_I	90_V	0.638	0.99
137_C	140_M	0.636	0.99
48_Q	67_G	0.632	0.99
12_I	136_E	0.628	0.99
112_T	116_L	0.625	0.99
32_I	66_L	0.625	0.99
98_V	110_S	0.621	0.99
31_V	36_I	0.619	0.99
25_P	143_A	0.611	0.99
91_V	117_L	0.604	0.99
43_L	52_A	0.595	0.99
44_R	92_L	0.592	0.99
68_T	72_E	0.591	0.99
45_E	51_I	0.590	0.99
84_P	104_D	0.586	0.99
19_E	140_M	0.581	0.99
112_T	115_N	0.578	0.99
72_E	96_E	0.574	0.99
138_G	145_F	0.574	0.99
51_I	57_L	0.571	0.99
74_A	95_V	0.570	0.99
48_Q	68_T	0.565	0.99
56_M	92_L	0.561	0.98
80_L	104_D	0.560	0.98
130_S	134_E	0.552	0.98
87_A	117_L	0.552	0.98
114_M	122_F	0.551	0.98
109_C	114_M	0.547	0.98
91_V	124_H	0.546	0.98
54_A	78_V	0.545	0.98
59_I	95_V	0.543	0.98
66_L	74_A	0.541	0.98
11_A	29_V	0.541	0.98
109_C	116_L	0.538	0.98
30_L	59_I	0.529	0.98
13_K	17_K	0.527	0.98
12_I	133_L	0.525	0.98
18_A	45_E	0.524	0.98
142_S	146_R	0.519	0.98
69_W	94_R	0.518	0.97
57_L	60_D	0.514	0.97
61_E	71_L	0.512	0.97
31_V	74_A	0.511	0.97
109_C	122_F	0.509	0.97
33_N	74_A	0.503	0.97
102_A	137_C	0.503	0.97
110_S	126_A	0.502	0.97
136_E	139_G	0.502	0.97
103_F	111_G	0.501	0.97
10_E	29_V	0.501	0.97
32_I	70_R	0.500	0.97

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
2nx8A	2	1	100	0.194	Contact Map
3dh1A	2	0.913	100	0.196	Contact Map
1z3aA	2	0.9503	100	0.198	Contact Map
2b3jA	2	0.9441	100	0.209	Contact Map
2a8nA	2	0.8696	100	0.245	Contact Map
1wwrA	3	0.9441	100	0.246	Contact Map
2g84A	2	0.9627	100	0.282	Contact Map
1wkqA	2	0.9441	100	0.295	Contact Map
2b3zA	3	0.9006	100	0.325	Contact Map
2hxvA	2	0.9317	100	0.33	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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