TRMB - BACSU - GREMLIN Contacts

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TRMB - tRNA (guanine-N(7)-)-methyltransferase

UniProt:	O34522	Sequences: MRMRHKPWADDFLAENADIAISNPADYKGKWNTVFGNDNPIHIEVGTGKGQFISGMAKQNPDINYIGIELFKSVIVTAVQKVKDSEAQNVKLLNIDADTLTDVFEPGEVKRVYLNFSDPWPKKRHEKRRLTYSHFLKKYEEVMGKGGSIHFKTDNRGLFEYSLKSFSEYGLLLTYVSLDLHNSNLEGNIMTEYEEKFSALGQPIYRAEVEWRT	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	213 (192)
Sequences:	3862 (2517)
Seq/√Len:	181.7

ECOLI - TRMB
BACSU - TRMB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_K	144_G	4.189	1.00
58_K	85_S	4.134	1.00
60_N	65_Y	2.696	1.00
106_P	142_V	2.680	1.00
112_V	139_Y	2.626	1.00
173_L	210_E	2.614	1.00
156_R	160_E	2.594	1.00
82_V	90_V	2.540	1.00
106_P	141_E	2.536	1.00
30_K	33_T	2.477	1.00
42_H	63_I	2.277	1.00
114_L	117_S	2.216	1.00
114_L	149_I	2.210	1.00
151_F	162_S	2.173	1.00
37_N	64_N	2.170	1.00
143_M	147_G	2.159	1.00
53_I	67_G	2.094	1.00
137_K	169_Y	2.068	1.00
133_S	165_S	2.067	1.00
114_L	131_T	2.050	1.00
42_H	113_Y	2.038	1.00
47_T	67_G	1.990	1.00
111_R	148_S	1.904	1.00
140_E	171_L	1.899	1.00
101_T	138_K	1.891	1.00
55_G	59_Q	1.834	1.00
42_H	111_R	1.809	1.00
34_V	91_K	1.793	1.00
161_Y	165_S	1.780	1.00
40_P	110_K	1.773	1.00
190_M	195_E	1.734	1.00
156_R	203_P	1.701	1.00
23_N	26_D	1.690	1.00
167_S	209_V	1.617	1.00
60_N	63_I	1.595	1.00
101_T	141_E	1.586	1.00
51_Q	195_E	1.577	1.00
43_I	109_V	1.574	1.00
31_W	41_I	1.545	1.00
40_P	64_N	1.492	1.00
55_G	58_K	1.491	1.00
131_T	162_S	1.486	1.00
156_R	205_Y	1.484	1.00
195_E	199_A	1.483	1.00
39_N	62_D	1.482	1.00
39_N	64_N	1.475	1.00
32_N	38_D	1.469	1.00
57_A	87_A	1.460	1.00
78_A	92_L	1.455	1.00
72_K	94_N	1.444	1.00
100_L	138_K	1.430	1.00
153_T	159_F	1.421	1.00
140_E	172_L	1.404	1.00
68_I	97_A	1.375	1.00
169_Y	172_L	1.371	1.00
45_V	97_A	1.367	1.00
66_I	104_F	1.366	1.00
35_F	64_N	1.343	1.00
109_V	112_V	1.341	1.00
41_I	64_N	1.323	1.00
125_H	128_R	1.318	1.00
82_V	92_L	1.314	1.00
148_S	210_E	1.312	1.00
109_V	142_V	1.262	1.00
54_S	81_K	1.258	1.00
148_S	208_E	1.245	1.00
107_G	144_G	1.237	1.00
126_E	157_G	1.236	1.00
52_F	113_Y	1.227	1.00
175_Y	208_E	1.224	1.00
157_G	160_E	1.223	1.00
133_S	168_E	1.222	1.00
75_I	92_L	1.202	1.00
112_V	143_M	1.194	1.00
150_H	206_R	1.192	1.00
31_W	104_F	1.175	1.00
104_F	108_E	1.172	1.00
95_I	103_V	1.164	1.00
99_T	102_D	1.137	1.00
28_K	105_E	1.134	1.00
177_S	180_L	1.132	1.00
105_E	108_E	1.132	1.00
183_S	186_E	1.124	1.00
120_W	125_H	1.123	1.00
57_A	89_N	1.117	1.00
29_G	108_E	1.109	1.00
111_R	150_H	1.096	1.00
114_L	130_L	1.066	1.00
126_E	161_Y	1.058	1.00
58_K	87_A	1.054	1.00
123_K	126_E	1.052	1.00
107_G	145_K	1.048	1.00
134_H	137_K	1.033	1.00
137_K	140_E	1.032	1.00
196_K	200_L	1.031	1.00
43_I	68_I	1.030	1.00
179_D	182_N	1.017	0.99
35_F	66_I	1.008	0.99
43_I	112_V	1.005	0.99
140_E	169_Y	1.003	0.99
37_N	41_I	0.999	0.99
190_M	198_S	0.998	0.99
136_L	165_S	0.994	0.99
149_I	166_F	0.990	0.99
198_S	204_I	0.979	0.99
56_M	60_N	0.973	0.99
45_V	112_V	0.970	0.99
67_G	78_A	0.961	0.99
197_F	202_Q	0.961	0.99
27_Y	30_K	0.939	0.99
138_K	141_E	0.937	0.99
42_H	56_M	0.907	0.99
52_F	56_M	0.902	0.99
38_D	64_N	0.901	0.99
49_K	77_T	0.896	0.99
202_Q	205_Y	0.890	0.99
130_L	135_F	0.890	0.99
151_F	158_L	0.885	0.99
54_S	82_V	0.882	0.99
132_Y	161_Y	0.881	0.98
133_S	137_K	0.875	0.98
63_I	111_R	0.874	0.98
47_T	78_A	0.872	0.98
163_L	176_V	0.859	0.98
51_Q	81_K	0.859	0.98
52_F	115_N	0.858	0.98
56_M	113_Y	0.852	0.98
163_L	209_V	0.847	0.98
42_H	65_Y	0.847	0.98
75_I	94_N	0.844	0.98
47_T	69_E	0.836	0.98
82_V	87_A	0.829	0.98
56_M	189_I	0.828	0.98
54_S	78_A	0.828	0.98
162_S	207_A	0.826	0.98
51_Q	192_E	0.825	0.98
81_K	85_S	0.823	0.98
77_T	81_K	0.821	0.98
68_I	93_L	0.816	0.98
121_P	126_E	0.810	0.97
53_I	90_V	0.807	0.97
193_Y	196_K	0.806	0.97
41_I	66_I	0.798	0.97
120_W	128_R	0.796	0.97
114_L	139_Y	0.788	0.97
197_F	200_L	0.787	0.97
188_N	206_R	0.784	0.97
42_H	60_N	0.782	0.97
135_F	139_Y	0.778	0.97
73_S	77_T	0.777	0.97
166_F	207_A	0.775	0.97
77_T	80_Q	0.771	0.97
130_L	139_Y	0.768	0.96
136_L	149_I	0.760	0.96
27_Y	34_V	0.755	0.96
30_K	108_E	0.752	0.96
55_G	189_I	0.747	0.96
122_K	125_H	0.740	0.96
54_S	87_A	0.739	0.96
19_I	22_S	0.739	0.96
80_Q	84_D	0.734	0.95
49_K	192_E	0.732	0.95
63_I	110_K	0.729	0.95
54_S	58_K	0.723	0.95
118_D	122_K	0.723	0.95
31_W	108_E	0.722	0.95
56_M	65_Y	0.722	0.95
175_Y	210_E	0.722	0.95
38_D	88_Q	0.717	0.95
195_E	198_S	0.717	0.95
126_E	132_Y	0.716	0.95
41_I	110_K	0.715	0.95
157_G	161_Y	0.714	0.95
138_K	142_V	0.713	0.95
159_F	207_A	0.705	0.94
104_F	142_V	0.699	0.94
36_G	39_N	0.698	0.94
166_F	209_V	0.696	0.94
160_E	178_L	0.695	0.94
24_P	27_Y	0.693	0.94
40_P	63_I	0.692	0.94
80_Q	83_K	0.688	0.94
71_F	74_V	0.687	0.93
112_V	147_G	0.684	0.93
134_H	138_K	0.684	0.93
133_S	169_Y	0.681	0.93
32_N	41_I	0.678	0.93
194_E	198_S	0.676	0.93
156_R	202_Q	0.676	0.93
45_V	114_L	0.675	0.93
43_I	104_F	0.671	0.93
76_V	80_Q	0.669	0.93
51_Q	55_G	0.664	0.92
124_R	128_R	0.663	0.92
65_Y	113_Y	0.660	0.92
124_R	127_K	0.658	0.92
164_K	168_E	0.655	0.92
156_R	178_L	0.651	0.92
116_F	152_K	0.651	0.92
87_A	90_V	0.645	0.91
166_F	172_L	0.645	0.91
70_L	98_D	0.640	0.91
121_P	155_N	0.640	0.91
148_S	174_T	0.633	0.90
144_G	147_G	0.631	0.90
73_S	132_Y	0.631	0.90
32_N	110_K	0.631	0.90
140_E	145_K	0.630	0.90
163_L	174_T	0.629	0.90
47_T	53_I	0.627	0.90
24_P	102_D	0.626	0.90
137_K	141_E	0.620	0.89
22_S	93_L	0.617	0.89
82_V	86_E	0.610	0.89
41_I	109_V	0.608	0.89
78_A	95_I	0.606	0.88
43_I	100_L	0.606	0.88
71_F	96_D	0.606	0.88
133_S	161_Y	0.605	0.88
100_L	142_V	0.600	0.88
47_T	92_L	0.600	0.88
70_L	94_N	0.599	0.88
24_P	103_V	0.598	0.88
78_A	90_V	0.593	0.87
167_S	178_L	0.592	0.87
187_G	208_E	0.588	0.87
68_I	96_D	0.588	0.87
170_G	173_L	0.587	0.87
53_I	65_Y	0.585	0.87
197_F	204_I	0.583	0.86
152_K	159_F	0.579	0.86
25_A	102_D	0.577	0.86
198_S	202_Q	0.576	0.86
69_E	205_Y	0.575	0.86
131_T	139_Y	0.574	0.86
69_E	97_A	0.574	0.86
47_T	71_F	0.574	0.86
150_H	185_L	0.574	0.86
137_K	170_G	0.572	0.85
98_D	138_K	0.572	0.85
93_L	103_V	0.571	0.85
174_T	210_E	0.569	0.85
118_D	127_K	0.567	0.85
123_K	164_K	0.565	0.85
79_V	83_K	0.563	0.84
57_A	60_N	0.562	0.84
114_L	136_L	0.562	0.84
141_E	145_K	0.562	0.84
116_F	204_I	0.559	0.84
65_Y	89_N	0.558	0.84
136_L	166_F	0.558	0.84
149_I	171_L	0.556	0.84
54_S	85_S	0.555	0.84
136_L	169_Y	0.552	0.83
32_N	210_E	0.551	0.83
131_T	166_F	0.551	0.83
121_P	125_H	0.550	0.83
164_K	167_S	0.549	0.83
118_D	128_R	0.545	0.83
126_E	165_S	0.542	0.82
44_E	120_W	0.541	0.82
152_K	194_E	0.536	0.81
162_S	209_V	0.535	0.81
117_S	158_L	0.534	0.81
189_I	204_I	0.532	0.81
29_G	105_E	0.529	0.81
44_E	47_T	0.527	0.80
115_N	192_E	0.527	0.80
19_I	23_N	0.524	0.80
74_V	118_D	0.523	0.80
21_I	79_V	0.522	0.80
73_S	76_V	0.520	0.80
163_L	178_L	0.516	0.79
167_S	174_T	0.515	0.79
53_I	78_A	0.511	0.78
152_K	188_N	0.510	0.78
158_L	162_S	0.509	0.78
177_S	181_H	0.509	0.78
163_L	167_S	0.508	0.78
155_N	197_F	0.507	0.78
192_E	197_F	0.507	0.78
74_V	193_Y	0.506	0.78
52_F	192_E	0.506	0.78
120_W	124_R	0.505	0.78
27_Y	33_T	0.504	0.77
110_K	146_G	0.503	0.77
36_G	88_Q	0.503	0.77
74_V	79_V	0.500	0.77

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
2fcaA	2	0.9624	100	0.503	Contact Map
2vdvE	2	0.9108	100	0.528	Contact Map
3ckkA	1	0.8451	100	0.529	Contact Map
1yzhA	1	0.9671	100	0.552	Contact Map
3dxyA	1	0.9531	100	0.567	Contact Map
4rwzA	1	0.8545	99.6	0.748	Contact Map
3p2eA	1	0.8498	99.6	0.753	Contact Map
1o54A	4	0.8967	99.5	0.765	Contact Map
1i9gA	3	0.9108	99.5	0.767	Contact Map
3mb5A	3	0.9061	99.5	0.769	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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