MIAA - BACSU - GREMLIN Contacts

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MIAA - tRNA dimethylallyltransferase

UniProt:	O31795	Sequences: MNNTKQPVVILVGPTAVGKTNLSIQLAKSLNAEIISGDSMQIYKGMDIGTAKITEQEMEGVPHHLIDILDPQDSFSTADYQSLVRNKISEIANRGKLPMIVGGTGLYIQSVLYDYTFTEEANDPVFRESMQMAAEREGADFLHAKLAAADPEAAAAIHPNNTRRVIRALEILHTSGKTMSQHLKEQKRELLYNAVLIGLTMDRDTLYERINQRVDLMMQSGLLPEVKRLYDKNVRDCQSIQAIGYKELYAYFDGFVTLSDAVEQLKQNSRRYAKRQLTWFRNKMQVTWFDMTPPVDMELKKKEIFTHIAGKLEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	314 (289)
Sequences:	4857 (3634)
Seq/√Len:	213.8

ECOLI - MIAA
BACSU - MIAA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_K	60_G	3.438	1.00
75_F	83_L	3.276	1.00
215_D	266_K	3.067	1.00
149_A	172_L	2.890	1.00
250_A	255_F	2.840	1.00
223_L	248_L	2.770	1.00
257_T	260_D	2.741	1.00
129_S	173_H	2.731	1.00
133_A	145_K	2.695	1.00
33_E	64_H	2.640	1.00
215_D	262_V	2.566	1.00
218_M	262_V	2.552	1.00
224_P	227_K	2.530	1.00
90_E	94_R	2.505	1.00
133_A	137_E	2.425	1.00
211_N	266_K	2.248	1.00
208_E	212_Q	2.158	1.00
264_Q	267_Q	2.086	1.00
16_A	210_I	2.084	1.00
7_P	193_N	2.066	1.00
44_K	70_D	2.054	1.00
267_Q	271_R	2.043	1.00
268_N	271_R	1.989	1.00
198_G	286_V	1.907	1.00
109_Q	113_Y	1.887	1.00
230_Y	249_Y	1.880	1.00
144_A	147_A	1.867	1.00
145_K	148_A	1.866	1.00
81_Q	85_R	1.858	1.00
100_I	111_V	1.835	1.00
145_K	173_H	1.825	1.00
52_K	67_D	1.824	1.00
54_T	57_E	1.824	1.00
55_E	58_M	1.822	1.00
171_I	179_M	1.816	1.00
248_L	261_A	1.806	1.00
153_A	157_I	1.797	1.00
40_M	50_T	1.755	1.00
247_E	268_N	1.681	1.00
47_D	52_K	1.664	1.00
109_Q	283_K	1.663	1.00
28_K	59_E	1.659	1.00
250_A	256_V	1.649	1.00
37_G	100_I	1.618	1.00
137_E	141_F	1.608	1.00
45_G	232_K	1.605	1.00
91_I	94_R	1.585	1.00
214_V	265_L	1.585	1.00
235_R	253_D	1.579	1.00
31_N	96_K	1.575	1.00
20_T	23_S	1.553	1.00
198_G	288_W	1.551	1.00
33_E	94_R	1.548	1.00
227_K	231_D	1.540	1.00
223_L	258_L	1.533	1.00
132_M	136_R	1.531	1.00
23_S	101_V	1.530	1.00
69_L	79_D	1.509	1.00
178_T	181_Q	1.505	1.00
127_R	170_E	1.493	1.00
251_Y	258_L	1.487	1.00
216_L	220_S	1.479	1.00
87_K	90_E	1.474	1.00
258_L	261_A	1.460	1.00
230_Y	253_D	1.459	1.00
36_S	66_I	1.452	1.00
134_A	162_T	1.449	1.00
64_H	87_K	1.446	1.00
10_I	108_I	1.437	1.00
277_L	281_R	1.422	1.00
140_D	144_A	1.406	1.00
32_A	99_M	1.394	1.00
260_D	263_E	1.386	1.00
263_E	267_Q	1.380	1.00
177_K	185_E	1.378	1.00
260_D	264_Q	1.374	1.00
207_Y	270_R	1.368	1.00
87_K	91_I	1.367	1.00
196_L	283_K	1.365	1.00
258_L	262_V	1.358	1.00
45_G	70_D	1.350	1.00
37_G	108_I	1.346	1.00
248_L	252_F	1.345	1.00
64_H	94_R	1.345	1.00
207_Y	271_R	1.339	1.00
126_F	173_H	1.334	1.00
143_H	147_A	1.333	1.00
218_M	258_L	1.330	1.00
139_A	162_T	1.324	1.00
205_T	208_E	1.318	1.00
12_V	108_I	1.311	1.00
208_E	211_N	1.307	1.00
25_Q	29_S	1.297	1.00
144_A	148_A	1.294	1.00
152_E	155_A	1.267	1.00
84_V	111_V	1.262	1.00
9_V	97_L	1.244	1.00
68_I	83_L	1.243	1.00
126_F	130_M	1.241	1.00
203_R	207_Y	1.222	1.00
212_Q	216_L	1.219	1.00
211_N	270_R	1.218	1.00
73_D	79_D	1.216	1.00
207_Y	267_Q	1.213	1.00
128_E	132_M	1.212	1.00
201_M	205_T	1.208	1.00
269_S	272_Y	1.203	1.00
203_R	277_L	1.195	1.00
79_D	82_S	1.193	1.00
200_T	277_L	1.193	1.00
65_L	87_K	1.191	1.00
40_M	242_A	1.190	1.00
88_I	92_A	1.187	1.00
145_K	149_A	1.184	1.00
12_V	198_G	1.180	1.00
149_A	173_H	1.169	1.00
223_L	227_K	1.168	1.00
17_V	199_L	1.167	1.00
17_V	201_M	1.166	1.00
138_G	141_F	1.162	1.00
49_G	245_Y	1.156	1.00
76_S	79_D	1.153	1.00
85_R	191_L	1.148	1.00
218_M	223_L	1.142	1.00
25_Q	28_K	1.138	1.00
33_E	91_I	1.136	1.00
177_K	181_Q	1.127	1.00
28_K	61_V	1.120	1.00
69_L	73_D	1.118	1.00
149_A	169_L	1.117	1.00
58_M	67_D	1.116	1.00
33_E	96_K	1.110	1.00
226_V	252_F	1.108	1.00
24_I	60_G	1.103	1.00
128_E	131_Q	1.102	1.00
137_E	145_K	1.096	1.00
72_Q	234_V	1.078	1.00
112_L	194_A	1.073	1.00
86_N	90_E	1.070	1.00
158_H	161_N	1.067	1.00
133_A	173_H	1.064	1.00
7_P	92_A	1.057	1.00
129_S	133_A	1.050	1.00
153_A	179_M	1.049	1.00
14_P	17_V	1.045	1.00
197_I	289_F	1.043	1.00
124_P	128_E	1.043	1.00
179_M	183_L	1.043	1.00
113_Y	285_Q	1.040	1.00
256_V	264_Q	1.039	1.00
216_L	219_Q	1.035	1.00
35_I	91_I	1.034	1.00
91_I	96_K	1.031	1.00
30_L	97_L	1.027	1.00
83_L	86_N	1.024	1.00
133_A	142_L	1.014	1.00
207_Y	211_N	1.010	1.00
105_G	280_F	1.009	1.00
46_M	50_T	1.009	1.00
133_A	141_F	1.002	1.00
21_N	25_Q	1.002	1.00
274_K	278_T	1.000	1.00
6_Q	92_A	0.993	1.00
134_A	139_A	0.991	1.00
53_I	58_M	0.984	1.00
79_D	83_L	0.982	1.00
169_L	173_H	0.978	1.00
8_V	88_I	0.977	1.00
223_L	252_F	0.976	1.00
32_A	98_P	0.974	1.00
256_V	260_D	0.973	1.00
218_M	261_A	0.972	1.00
143_H	154_A	0.971	1.00
126_F	169_L	0.968	1.00
215_D	219_Q	0.965	1.00
226_V	248_L	0.964	1.00
41_Q	53_I	0.953	1.00
83_L	87_K	0.952	1.00
131_Q	135_E	0.949	1.00
20_T	53_I	0.946	1.00
228_R	232_K	0.946	1.00
147_A	155_A	0.938	0.99
198_G	280_F	0.936	0.99
243_I	272_Y	0.933	0.99
24_I	28_K	0.927	0.99
11_L	26_L	0.924	0.99
24_I	53_I	0.917	0.99
275_R	278_T	0.914	0.99
214_V	266_K	0.911	0.99
24_I	63_H	0.911	0.99
131_Q	166_I	0.908	0.99
262_V	266_K	0.906	0.99
256_V	261_A	0.906	0.99
6_Q	89_S	0.905	0.99
162_T	165_V	0.902	0.99
250_A	264_Q	0.899	0.99
126_F	174_T	0.899	0.99
223_L	251_Y	0.899	0.99
123_D	174_T	0.893	0.99
77_T	81_Q	0.890	0.99
109_Q	282_N	0.889	0.99
130_M	166_I	0.888	0.99
112_L	196_L	0.888	0.99
222_L	248_L	0.885	0.99
143_H	165_V	0.884	0.99
210_I	273_A	0.880	0.99
54_T	58_M	0.880	0.99
152_E	184_K	0.880	0.99
156_A	161_N	0.880	0.99
202_D	205_T	0.878	0.99
152_E	178_T	0.870	0.99
45_G	71_P	0.869	0.99
207_Y	277_L	0.866	0.99
21_N	216_L	0.865	0.99
21_N	57_E	0.859	0.99
157_I	161_N	0.858	0.99
47_D	67_D	0.848	0.99
207_Y	266_K	0.847	0.99
249_Y	253_D	0.841	0.99
90_E	93_N	0.837	0.99
146_L	168_A	0.833	0.99
218_M	248_L	0.833	0.99
46_M	229_L	0.828	0.99
290_D	293_P	0.824	0.99
71_P	239_S	0.824	0.99
140_D	159_P	0.823	0.99
10_I	112_L	0.822	0.99
54_T	220_S	0.815	0.99
204_D	208_E	0.812	0.99
261_A	265_L	0.810	0.98
130_M	173_H	0.807	0.98
11_L	99_M	0.802	0.98
47_D	58_M	0.799	0.98
37_G	80_Y	0.799	0.98
31_N	97_L	0.799	0.98
132_M	135_E	0.792	0.98
172_L	179_M	0.790	0.98
259_S	263_E	0.789	0.98
32_A	97_L	0.787	0.98
36_S	65_L	0.786	0.98
81_Q	114_D	0.786	0.98
14_P	277_L	0.785	0.98
12_V	37_G	0.779	0.98
146_L	165_V	0.776	0.98
27_A	61_V	0.775	0.98
143_H	159_P	0.774	0.98
139_A	143_H	0.769	0.98
167_R	170_E	0.769	0.98
26_L	99_M	0.768	0.98
9_V	195_V	0.767	0.98
10_I	194_A	0.766	0.98
125_V	129_S	0.766	0.98
264_Q	268_N	0.765	0.98
70_D	232_K	0.760	0.98
123_D	126_F	0.759	0.98
89_S	92_A	0.759	0.98
91_I	98_P	0.756	0.98
156_A	183_L	0.755	0.98
69_L	75_F	0.754	0.98
161_N	165_V	0.751	0.98
248_L	265_L	0.751	0.98
226_V	230_Y	0.743	0.97
139_A	165_V	0.743	0.97
145_K	169_L	0.735	0.97
24_I	61_V	0.731	0.97
181_Q	184_K	0.729	0.97
27_A	99_M	0.729	0.97
263_E	266_K	0.726	0.97
12_V	286_V	0.725	0.97
181_Q	185_E	0.725	0.97
8_V	100_I	0.720	0.97
257_T	263_E	0.719	0.97
153_A	156_A	0.716	0.97
110_S	115_Y	0.715	0.97
24_I	34_I	0.714	0.97
106_L	115_Y	0.714	0.97
142_L	145_K	0.713	0.97
205_T	292_T	0.712	0.97
248_L	258_L	0.712	0.97
247_E	265_L	0.712	0.97
72_Q	232_K	0.711	0.97
199_L	291_M	0.710	0.97
130_M	142_L	0.706	0.96
51_A	217_M	0.702	0.96
201_M	291_M	0.701	0.96
283_K	286_V	0.700	0.96
234_V	237_C	0.699	0.96
143_H	157_I	0.698	0.96
6_Q	96_K	0.697	0.96
58_M	61_V	0.696	0.96
121_A	174_T	0.695	0.96
82_S	86_N	0.694	0.96
92_A	192_Y	0.694	0.96
153_A	168_A	0.694	0.96
84_V	88_I	0.691	0.96
65_L	83_L	0.689	0.96
53_I	60_G	0.687	0.96
11_L	23_S	0.686	0.96
23_S	53_I	0.684	0.96
250_A	261_A	0.682	0.96
211_N	214_V	0.679	0.96
34_I	61_V	0.679	0.96
90_E	96_K	0.677	0.95
230_Y	252_F	0.676	0.95
130_M	169_L	0.674	0.95
141_F	144_A	0.674	0.95
84_V	87_K	0.674	0.95
218_M	265_L	0.670	0.95
125_V	128_E	0.669	0.95
212_Q	219_Q	0.667	0.95
8_V	194_A	0.664	0.95
35_I	87_K	0.664	0.95
118_T	182_H	0.661	0.95
129_S	132_M	0.660	0.95
44_K	67_D	0.659	0.95
130_M	145_K	0.658	0.95
42_I	75_F	0.657	0.95
149_A	178_T	0.654	0.95
46_M	239_S	0.654	0.95
49_G	222_L	0.653	0.94
195_V	289_F	0.653	0.94
68_I	75_F	0.648	0.94
57_E	60_G	0.645	0.94
8_V	92_A	0.644	0.94
134_A	142_L	0.642	0.94
113_Y	283_K	0.640	0.94
58_M	62_P	0.634	0.94
200_T	288_W	0.632	0.93
234_V	240_I	0.631	0.93
151_P	155_A	0.630	0.93
70_D	73_D	0.622	0.93
24_I	59_E	0.620	0.93
168_A	179_M	0.615	0.93
32_A	91_I	0.615	0.93
171_I	183_L	0.612	0.92
88_I	100_I	0.611	0.92
64_H	91_I	0.610	0.92
201_M	292_T	0.609	0.92
205_T	209_R	0.606	0.92
47_D	55_E	0.605	0.92
88_I	111_V	0.605	0.92
177_K	182_H	0.602	0.92
20_T	24_I	0.600	0.92
40_M	272_Y	0.599	0.92
266_K	270_R	0.596	0.91
137_E	142_L	0.596	0.91
143_H	158_H	0.594	0.91
237_C	240_I	0.594	0.91
150_D	180_S	0.592	0.91
142_L	165_V	0.591	0.91
172_L	175_S	0.589	0.91
147_A	154_A	0.583	0.90
8_V	111_V	0.580	0.90
87_K	94_R	0.580	0.90
211_N	262_V	0.580	0.90
211_N	263_E	0.579	0.90
130_M	133_A	0.578	0.90
172_L	180_S	0.577	0.90
40_M	241_Q	0.577	0.90
41_Q	272_Y	0.576	0.90
227_K	230_Y	0.576	0.90
238_Q	241_Q	0.576	0.90
42_I	104_T	0.572	0.90
30_L	99_M	0.571	0.90
118_T	121_A	0.571	0.90
205_T	290_D	0.568	0.89
81_Q	111_V	0.566	0.89
17_V	200_T	0.565	0.89
223_L	261_A	0.565	0.89
69_L	83_L	0.564	0.89
49_G	229_L	0.563	0.89
53_I	66_I	0.560	0.89
45_G	228_R	0.559	0.89
243_I	268_N	0.557	0.88
35_I	88_I	0.556	0.88
12_V	280_F	0.554	0.88
12_V	196_L	0.554	0.88
89_S	191_L	0.554	0.88
195_V	287_T	0.553	0.88
109_Q	112_L	0.553	0.88
48_I	220_S	0.550	0.88
229_L	240_I	0.549	0.88
45_G	233_N	0.547	0.87
196_L	285_Q	0.546	0.87
78_A	82_S	0.544	0.87
84_V	100_I	0.542	0.87
114_D	119_E	0.540	0.87
226_V	249_Y	0.537	0.87
251_Y	256_V	0.536	0.86
135_E	162_T	0.535	0.86
44_K	68_I	0.535	0.86
109_Q	196_L	0.534	0.86
226_V	245_Y	0.533	0.86
75_F	79_D	0.533	0.86
246_K	250_A	0.532	0.86
106_L	279_W	0.532	0.86
238_Q	242_A	0.532	0.86
207_Y	274_K	0.531	0.86
259_S	262_V	0.529	0.86
80_Y	272_Y	0.528	0.86
85_R	192_Y	0.528	0.86
227_K	258_L	0.527	0.85
222_L	246_K	0.527	0.85
34_I	101_V	0.526	0.85
65_L	68_I	0.525	0.85
141_F	145_K	0.524	0.85
228_R	231_D	0.523	0.85
154_A	158_H	0.522	0.85
200_T	291_M	0.522	0.85
95_G	98_P	0.520	0.85
10_I	37_G	0.517	0.84
110_S	113_Y	0.517	0.84
291_M	294_P	0.516	0.84
140_D	162_T	0.515	0.84
126_F	129_S	0.515	0.84
229_L	245_Y	0.514	0.84
9_V	30_L	0.513	0.84
62_P	94_R	0.512	0.84
11_L	32_A	0.510	0.84
55_E	59_E	0.510	0.84
241_Q	246_K	0.509	0.83
39_S	42_I	0.509	0.83
30_L	197_I	0.508	0.83
243_I	265_L	0.508	0.83
146_L	150_D	0.507	0.83
224_P	228_R	0.505	0.83
26_L	30_L	0.505	0.83
248_L	251_Y	0.504	0.83
88_I	98_P	0.503	0.83
138_G	162_T	0.503	0.83
46_M	71_P	0.502	0.83
240_I	249_Y	0.501	0.83
139_A	160_N	0.500	0.82
190_L	194_A	0.500	0.82

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
3exaA	2	0.9427	100	0.198	Contact Map
3fozA	2	0.9618	100	0.203	Contact Map
3d3qA	1	0.9713	100	0.21	Contact Map
3ephA	2	0.9777	100	0.227	Contact Map
3crmA	1	0.742	100	0.286	Contact Map
3a8tA	1	0.7643	100	0.416	Contact Map
2ze6A	1	0.6592	100	0.579	Contact Map
1ckeA	1	0.6624	99.8	0.804	Contact Map
2qmhA	5	0.5127	99.7	0.834	Contact Map
3tqfA	3	0.4745	99.4	0.859	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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