TRMN6 - ECOLI - GREMLIN Contacts

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TRMN6 - tRNA1(Val) (adenine(37)-N6)-methyltransferase

UniProt:	P31825	Sequences: MSQSTSVLRRNGFTFKQFFVAHDRCAMKVGTDGILLGAWAPVAGVKRCLDIGAGSGLLALMLAQRTDDSVMIDAVELESEAAAQAQENINQSPWAERINVHTADIQQWITQQTVRFDLIISNPPYYQQGVECSTPQREQARYTTTLDHPSLLTCAAECITEEGFFCVVLPEQIGNGFTELALSMGWHLRLRTDVAENEARLPHRVLLAFSPQAGECFSDRLVIRGPDQNYSEAYTALTQAFYLFM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11538
Length:	245 (189)
Sequences:	6636 (5292)
Seq/√Len:	384.9

ECOLI - TRMN6 PRMB PRMC
BACSU - YABB PRMC
HALSA - Q9HQH3
SULSO - Q7LXK7 Q980C4

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
19_F	87_E	3.034	1.00
59_A	74_A	2.971	1.00
79_S	102_T	2.813	1.00
117_D	160_T	2.744	1.00
73_D	101_H	2.743	1.00
73_D	116_F	2.551	1.00
152_L	181_A	2.501	1.00
89_I	100_V	2.488	1.00
155_A	165_F	2.433	1.00
59_A	72_I	2.432	1.00
103_A	108_W	2.407	1.00
10_R	17_Q	2.358	1.00
49_L	116_F	2.348	1.00
193_D	199_A	2.199	1.00
53_A	85_A	2.185	1.00
23_D	80_E	2.117	1.00
62_L	120_I	2.109	1.00
82_A	100_V	2.086	1.00
47_R	71_M	2.026	1.00
16_K	65_R	1.961	1.00
16_K	64_Q	1.878	1.00
30_G	33_G	1.866	1.00
89_I	98_I	1.848	1.00
19_F	91_Q	1.839	1.00
76_E	82_A	1.781	1.00
53_A	59_A	1.775	1.00
12_G	17_Q	1.767	1.00
63_A	72_I	1.748	1.00
167_V	181_A	1.732	1.00
74_A	100_V	1.727	1.00
71_M	99_N	1.726	1.00
14_T	65_R	1.720	1.00
174_G	191_R	1.718	1.00
18_F	61_M	1.672	1.00
128_Q	140_A	1.656	1.00
159_I	163_G	1.622	1.00
82_A	102_T	1.620	1.00
104_D	107_Q	1.544	1.00
118_L	166_C	1.522	1.00
178_T	191_R	1.513	1.00
38_A	42_V	1.509	1.00
60_L	94_W	1.471	1.00
23_D	84_Q	1.467	1.00
77_L	137_R	1.464	1.00
152_L	180_L	1.459	1.00
104_D	150_S	1.458	1.00
66_T	70_V	1.449	1.00
59_A	98_I	1.432	1.00
73_D	99_N	1.426	1.00
21_A	84_Q	1.422	1.00
149_P	180_L	1.414	1.00
153_T	184_M	1.396	1.00
16_K	61_M	1.380	1.00
179_E	183_S	1.362	1.00
106_Q	158_C	1.344	1.00
136_Q	140_A	1.325	1.00
24_R	55_S	1.306	1.00
12_G	15_F	1.302	1.00
174_G	199_A	1.288	1.00
74_A	98_I	1.276	1.00
171_E	198_E	1.274	1.00
37_G	41_P	1.272	1.00
53_A	76_E	1.267	1.00
51_I	105_I	1.266	1.00
82_A	86_Q	1.262	1.00
105_I	148_H	1.242	1.00
137_R	141_R	1.240	1.00
154_C	157_E	1.239	1.00
48_C	70_V	1.238	1.00
127_Q	172_Q	1.221	1.00
121_S	167_V	1.207	1.00
179_E	182_L	1.204	1.00
21_A	87_E	1.196	1.00
36_L	39_W	1.196	1.00
78_E	81_A	1.194	1.00
47_R	73_D	1.189	1.00
178_T	182_L	1.188	1.00
169_L	177_F	1.178	1.00
66_T	69_S	1.167	1.00
85_A	100_V	1.153	1.00
48_C	72_I	1.148	1.00
47_R	116_F	1.147	1.00
50_D	59_A	1.140	1.00
60_L	89_I	1.132	1.00
31_T	34_I	1.126	1.00
150_S	154_C	1.106	1.00
86_Q	90_N	1.103	1.00
143_T	149_P	1.099	1.00
63_A	98_I	1.068	1.00
144_T	149_P	1.067	1.00
115_R	160_T	1.066	1.00
169_L	174_G	1.066	1.00
58_L	120_I	1.060	1.00
156_A	186_W	1.050	1.00
39_W	42_V	1.038	1.00
90_N	95_A	1.038	1.00
10_R	91_Q	1.029	1.00
105_I	150_S	1.028	1.00
155_A	186_W	1.024	1.00
132_C	137_R	1.015	1.00
52_G	105_I	1.005	1.00
106_Q	150_S	1.004	1.00
142_Y	147_D	0.997	1.00
51_I	151_L	0.995	1.00
52_G	121_S	0.993	1.00
36_L	40_A	0.993	1.00
75_V	103_A	0.986	1.00
60_L	92_S	0.975	1.00
47_R	114_V	0.974	1.00
64_Q	94_W	0.959	1.00
40_A	166_C	0.958	1.00
24_R	27_M	0.948	1.00
75_V	109_I	0.945	1.00
175_N	179_E	0.933	1.00
138_E	142_Y	0.928	1.00
46_K	70_V	0.915	1.00
18_F	60_L	0.902	1.00
159_I	165_F	0.900	1.00
27_M	30_G	0.893	1.00
87_E	90_N	0.889	1.00
39_W	192_T	0.884	1.00
79_S	83_A	0.881	1.00
135_P	138_E	0.879	1.00
151_L	165_F	0.873	1.00
174_G	178_T	0.870	1.00
173_I	176_G	0.868	1.00
127_Q	130_V	0.868	1.00
118_L	164_F	0.867	1.00
48_C	118_L	0.866	1.00
181_A	186_W	0.862	1.00
59_A	63_A	0.860	1.00
103_A	107_Q	0.841	1.00
83_A	86_Q	0.835	1.00
87_E	91_Q	0.822	1.00
149_P	183_S	0.819	1.00
154_C	158_C	0.813	1.00
116_F	119_I	0.799	1.00
150_S	153_T	0.799	1.00
152_L	184_M	0.795	1.00
146_L	176_G	0.794	1.00
153_T	156_A	0.790	1.00
89_I	94_W	0.789	1.00
49_L	119_I	0.787	1.00
130_V	172_Q	0.786	1.00
59_A	120_I	0.784	1.00
14_T	61_M	0.784	1.00
48_C	62_L	0.783	1.00
33_G	195_A	0.782	1.00
170_P	173_I	0.781	1.00
18_F	57_L	0.778	1.00
192_T	201_L	0.778	1.00
36_L	42_V	0.774	1.00
106_Q	154_C	0.765	1.00
45_V	71_M	0.765	1.00
132_C	141_R	0.763	1.00
105_I	154_C	0.756	1.00
78_E	137_R	0.754	1.00
138_E	141_R	0.751	1.00
149_P	184_M	0.751	1.00
131_E	135_P	0.749	1.00
167_V	177_F	0.748	1.00
86_Q	89_I	0.741	1.00
156_A	184_M	0.741	1.00
169_L	191_R	0.738	1.00
30_G	34_I	0.735	1.00
18_F	94_W	0.734	1.00
126_Y	170_P	0.733	1.00
53_A	100_V	0.732	1.00
50_D	53_A	0.729	1.00
61_M	65_R	0.728	1.00
128_Q	142_Y	0.728	1.00
147_D	150_S	0.721	1.00
131_E	138_E	0.717	1.00
135_P	141_R	0.713	1.00
131_E	141_R	0.711	1.00
165_F	181_A	0.707	1.00
146_L	151_L	0.707	1.00
137_R	140_A	0.705	1.00
133_S	137_R	0.704	1.00
43_A	46_K	0.701	1.00
53_A	74_A	0.699	1.00
119_I	158_C	0.698	1.00
72_I	98_I	0.691	0.99
34_I	37_G	0.691	0.99
20_V	24_R	0.690	0.99
50_D	120_I	0.690	0.99
49_L	75_V	0.689	0.99
31_T	58_L	0.687	0.99
148_H	167_V	0.682	0.99
73_D	114_V	0.681	0.99
74_A	85_A	0.676	0.99
33_G	37_G	0.669	0.99
138_E	144_T	0.669	0.99
64_Q	92_S	0.666	0.99
37_G	192_T	0.665	0.99
57_L	61_M	0.662	0.99
75_V	101_H	0.658	0.99
51_I	106_Q	0.655	0.99
99_N	114_V	0.653	0.99
47_R	160_T	0.652	0.99
63_A	89_I	0.650	0.99
17_Q	91_Q	0.644	0.99
121_S	151_L	0.644	0.99
36_L	166_C	0.641	0.99
77_L	139_Q	0.640	0.99
24_R	28_K	0.640	0.99
193_D	197_N	0.638	0.99
133_S	140_A	0.638	0.99
132_C	142_Y	0.637	0.99
20_V	84_Q	0.634	0.99
48_C	66_T	0.628	0.99
144_T	147_D	0.627	0.99
152_L	167_V	0.626	0.99
83_A	87_E	0.626	0.99
113_T	157_E	0.624	0.99
46_K	117_D	0.622	0.99
174_G	198_E	0.620	0.99
180_L	184_M	0.620	0.99
194_V	200_R	0.618	0.99
119_I	159_I	0.615	0.99
141_R	148_H	0.614	0.99
139_Q	145_T	0.611	0.99
46_K	69_S	0.611	0.99
105_I	151_L	0.610	0.99
149_P	153_T	0.609	0.99
36_L	41_P	0.606	0.99
15_F	64_Q	0.604	0.99
44_G	69_S	0.599	0.98
197_N	200_R	0.598	0.98
30_G	196_E	0.594	0.98
28_K	31_T	0.593	0.98
182_L	187_H	0.590	0.98
176_G	179_E	0.587	0.98
32_D	36_L	0.586	0.98
173_I	177_F	0.583	0.98
45_V	69_S	0.582	0.98
132_C	140_A	0.582	0.98
39_W	166_C	0.577	0.98
84_Q	88_N	0.576	0.98
132_C	135_P	0.574	0.98
25_C	84_Q	0.573	0.98
119_I	165_F	0.570	0.98
52_G	148_H	0.564	0.98
171_E	174_G	0.561	0.98
131_E	142_Y	0.560	0.98
182_L	189_R	0.558	0.98
10_R	19_F	0.557	0.98
146_L	180_L	0.553	0.97
63_A	95_A	0.552	0.97
24_R	84_Q	0.552	0.97
46_K	66_T	0.551	0.97
61_M	64_Q	0.547	0.97
23_D	26_A	0.543	0.97
60_L	64_Q	0.543	0.97
25_C	28_K	0.538	0.97
180_L	183_S	0.538	0.97
80_E	83_A	0.538	0.97
47_R	117_D	0.537	0.97
178_T	189_R	0.531	0.97
67_D	70_V	0.531	0.97
136_Q	141_R	0.526	0.97
133_S	141_R	0.526	0.97
26_A	81_A	0.524	0.96
132_C	136_Q	0.524	0.96
63_A	94_W	0.524	0.96
51_I	158_C	0.523	0.96
127_Q	176_G	0.521	0.96
127_Q	173_I	0.520	0.96
17_Q	92_S	0.520	0.96
39_W	43_A	0.520	0.96
40_A	120_I	0.519	0.96
12_G	19_F	0.519	0.96
133_S	138_E	0.518	0.96
62_L	70_V	0.518	0.96
116_F	158_C	0.516	0.96
49_L	109_I	0.514	0.96
152_L	177_F	0.511	0.96
168_V	194_V	0.511	0.96
21_A	24_R	0.509	0.96
43_A	164_F	0.508	0.96
60_L	88_N	0.505	0.96
78_E	82_A	0.503	0.96
141_R	147_D	0.503	0.96
89_I	92_S	0.500	0.95

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
3lpmA	2	0.8816	100	0.387	Contact Map
2ozvA	2	0.7878	100	0.43	Contact Map
2b3tA	1	0.8286	100	0.527	Contact Map
1nv8A	1	0.8041	100	0.548	Contact Map
3evzA	1	0.751	100	0.585	Contact Map
4dzrA	2	0.6204	99.9	0.618	Contact Map
2ih2A	1	0.8408	99.9	0.637	Contact Map
4dcmA	1	0.7388	99.9	0.638	Contact Map
3v97A	1	0.7755	99.9	0.639	Contact Map
2h00A	1	0.7592	99.9	0.644	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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