TADA - ECOLI - GREMLIN Contacts

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TADA - tRNA-specific adenosine deaminase

UniProt:	P68398	Sequences: MSEVEFSHEYWMRHALTLAKRAWDEREVPVGAVLVHNNRVIGEGWNRPIGRHDPTAHAEIMALRQGGLVMQNYRLIDATLYVTLEPCVMCAGAMIHSRIGRVVFGARDAKTGAAGSLMDVLHHPGMNHRVEITEGILADECAALLSDFFRMRRQEIKAQKKAQSSTD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11372
Length:	167 (144)
Sequences:	8022 (5251)
Seq/√Len:	437.6

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
14_H	43_E	3.249	1.00
101_R	131_E	2.410	1.00
13_R	137_L	2.394	1.00
14_H	17_T	2.243	1.00
80_L	94_M	2.190	1.00
105_G	141_C	2.165	1.00
53_D	64_R	2.120	1.00
77_D	100_G	2.071	1.00
79_T	103_V	2.057	1.00
79_T	101_R	1.949	1.00
11_W	35_V	1.942	1.00
47_R	61_M	1.941	1.00
92_G	120_V	1.922	1.00
104_F	107_R	1.917	1.00
11_W	40_V	1.901	1.00
18_L	43_E	1.899	1.00
101_R	133_T	1.879	1.00
106_A	149_F	1.872	1.00
138_A	142_A	1.851	1.00
107_R	134_E	1.847	1.00
47_R	51_R	1.831	1.00
137_L	140_E	1.804	1.00
8_H	101_R	1.775	1.00
36_H	39_R	1.667	1.00
18_L	21_R	1.663	1.00
34_L	62_A	1.648	1.00
21_R	45_W	1.632	1.00
92_G	96_H	1.552	1.00
32_A	80_L	1.546	1.00
8_H	133_T	1.539	1.00
13_R	140_E	1.531	1.00
119_D	122_H	1.518	1.00
142_A	153_R	1.505	1.00
119_D	127_N	1.482	1.00
36_H	78_A	1.480	1.00
104_F	118_M	1.457	1.00
104_F	134_E	1.448	1.00
143_A	147_D	1.437	1.00
14_H	40_V	1.427	1.00
8_H	81_Y	1.410	1.00
94_M	102_V	1.384	1.00
79_T	100_G	1.368	1.00
20_K	144_L	1.365	1.00
18_L	45_W	1.319	1.00
35_V	81_Y	1.309	1.00
42_G	65_Q	1.286	1.00
48_P	55_T	1.267	1.00
8_H	103_V	1.263	1.00
143_A	146_S	1.254	1.00
15_A	83_T	1.246	1.00
147_D	151_M	1.244	1.00
142_A	146_S	1.232	1.00
84_L	145_L	1.232	1.00
23_W	151_M	1.192	1.00
36_H	77_D	1.191	1.00
56_A	64_R	1.180	1.00
80_L	99_I	1.174	1.00
135_G	138_A	1.157	1.00
44_G	61_M	1.157	1.00
25_E	45_W	1.153	1.00
60_I	93_A	1.152	1.00
36_H	41_I	1.138	1.00
9_E	137_L	1.136	1.00
22_A	45_W	1.133	1.00
106_A	142_A	1.127	1.00
14_H	18_L	1.107	1.00
147_D	150_R	1.091	1.00
34_L	66_G	1.087	1.00
20_K	140_E	1.084	1.00
93_A	97_S	1.081	1.00
117_L	125_G	1.078	1.00
49_I	73_Y	1.067	1.00
115_G	119_D	1.059	1.00
76_I	98_R	1.050	1.00
20_K	23_W	1.041	1.00
42_G	62_A	1.040	1.00
17_T	20_K	1.035	1.00
30_V	84_L	1.026	1.00
54_P	67_G	1.022	1.00
61_M	65_Q	1.017	1.00
56_A	61_M	1.011	1.00
23_W	29_P	1.004	1.00
60_I	64_R	0.996	1.00
133_T	136_I	0.986	1.00
41_I	78_A	0.980	1.00
149_F	153_R	0.962	1.00
91_A	120_V	0.961	1.00
47_R	50_G	0.958	1.00
48_P	73_Y	0.958	1.00
42_G	69_V	0.956	1.00
16_L	141_C	0.950	1.00
37_N	77_D	0.937	1.00
34_L	80_L	0.931	1.00
10_Y	14_H	0.927	1.00
19_A	144_L	0.925	1.00
16_L	20_K	0.914	1.00
13_R	17_T	0.893	1.00
15_A	31_G	0.881	1.00
34_L	78_A	0.880	1.00
63_L	75_L	0.873	1.00
139_D	143_A	0.859	1.00
20_K	24_D	0.859	1.00
95_I	130_V	0.858	1.00
9_E	13_R	0.856	1.00
63_L	97_S	0.855	1.00
8_H	79_T	0.851	1.00
95_I	120_V	0.845	1.00
44_G	62_A	0.844	1.00
63_L	93_A	0.837	1.00
112_G	116_S	0.837	1.00
26_R	152_R	0.835	1.00
107_R	138_A	0.832	1.00
25_E	50_G	0.832	1.00
66_G	75_L	0.829	1.00
91_A	95_I	0.824	1.00
63_L	67_G	0.822	1.00
29_P	145_L	0.817	1.00
65_Q	69_V	0.811	1.00
40_V	43_E	0.810	1.00
65_Q	68_L	0.809	1.00
23_W	147_D	0.793	1.00
114_A	121_L	0.790	1.00
16_L	144_L	0.784	1.00
110_K	152_R	0.778	1.00
12_M	135_G	0.773	1.00
118_M	125_G	0.772	1.00
39_R	69_V	0.768	1.00
94_M	130_V	0.762	1.00
10_Y	13_R	0.762	1.00
121_L	130_V	0.759	1.00
88_V	120_V	0.740	1.00
103_V	133_T	0.738	1.00
102_V	130_V	0.737	1.00
34_L	42_G	0.734	1.00
20_K	147_D	0.733	1.00
103_V	136_I	0.732	1.00
102_V	121_L	0.730	1.00
11_W	81_Y	0.730	1.00
55_T	93_A	0.727	1.00
51_R	61_M	0.726	1.00
116_S	120_V	0.722	1.00
104_F	115_G	0.717	1.00
21_R	24_D	0.709	1.00
84_L	106_A	0.702	1.00
51_R	68_L	0.702	1.00
120_V	128_H	0.691	1.00
126_M	130_V	0.689	1.00
67_G	75_L	0.686	1.00
12_M	15_A	0.686	1.00
43_E	65_Q	0.684	1.00
44_G	65_Q	0.680	1.00
39_R	74_R	0.667	1.00
52_H	72_N	0.665	1.00
145_L	149_F	0.662	1.00
36_H	70_M	0.660	1.00
46_N	55_T	0.654	1.00
36_H	74_R	0.653	0.99
53_D	56_A	0.645	0.99
35_V	40_V	0.645	0.99
107_R	118_M	0.643	0.99
51_R	56_A	0.641	0.99
11_W	14_H	0.641	0.99
52_H	71_Q	0.641	0.99
121_L	125_G	0.638	0.99
33_V	40_V	0.637	0.99
29_P	46_N	0.635	0.99
21_R	25_E	0.635	0.99
95_I	121_L	0.632	0.99
56_A	60_I	0.624	0.99
118_M	121_L	0.624	0.99
47_R	65_Q	0.619	0.99
91_A	121_L	0.617	0.99
16_L	140_E	0.615	0.99
48_P	96_H	0.614	0.99
116_S	119_D	0.612	0.99
141_C	144_L	0.611	0.99
108_D	111_T	0.610	0.99
95_I	127_N	0.607	0.99
88_V	108_D	0.606	0.99
102_V	114_A	0.606	0.99
72_N	76_I	0.604	0.99
63_L	94_M	0.598	0.99
125_G	129_R	0.595	0.99
55_T	61_M	0.591	0.99
63_L	99_I	0.588	0.99
47_R	56_A	0.585	0.99
78_A	99_I	0.583	0.99
23_W	144_L	0.583	0.99
60_I	96_H	0.581	0.99
76_I	100_G	0.570	0.99
34_L	63_L	0.567	0.99
29_P	147_D	0.564	0.99
117_L	121_L	0.550	0.98
142_A	149_F	0.548	0.98
49_I	55_T	0.548	0.98
24_D	49_I	0.547	0.98
113_A	120_V	0.546	0.98
118_M	122_H	0.538	0.98
41_I	69_V	0.538	0.98
81_Y	103_V	0.537	0.98
134_E	138_A	0.527	0.98
32_A	58_A	0.525	0.98
140_E	143_A	0.525	0.98
61_M	64_R	0.523	0.98
113_A	118_M	0.521	0.98
84_L	108_D	0.518	0.97
118_M	126_M	0.515	0.97
138_A	141_C	0.514	0.97
25_E	29_P	0.513	0.97
22_A	29_P	0.512	0.97
17_T	21_R	0.510	0.97
113_A	116_S	0.506	0.97
14_H	33_V	0.506	0.97
146_S	150_R	0.503	0.97
33_V	43_E	0.501	0.97
113_A	126_M	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
1z3aA	2	0.9281	100	0.211	Contact Map
2nx8A	2	0.988	100	0.211	Contact Map
3dh1A	2	0.9042	100	0.222	Contact Map
2b3jA	2	0.9102	100	0.248	Contact Map
1wwrA	3	0.9341	100	0.267	Contact Map
2a8nA	2	0.8383	100	0.279	Contact Map
2g84A	2	0.9521	100	0.303	Contact Map
1wkqA	2	0.9162	100	0.321	Contact Map
1p6oA	2	0.9162	100	0.353	Contact Map
2b3zA	3	0.8802	100	0.353	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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