TRMY - HALSA - GREMLIN Contacts

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TRMY - tRNA (pseudouridine(54)-N(1))-methyltransferase

UniProt:	Q9HNR6	Sequences: MRQFVVLGHDAPTTPDFPLDDLPGAAGRLDVLCRCVSAALFVSHGIRDDVEVFLVLGDEVTVRIDAGAVQYMHPDERNVAGLLKQALDAKTEAIGHQEASSSPGIHVSKRGFEAVLDAVSGPVVALHEDGDALAAVDPLADPVFVLSDHRDFTAAEASLLADASDHRVRVGPTVLHADHAITVAHNHLDTAGFDAY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	196 (188)
Sequences:	185 (124)
Seq/√Len:	9.1

HALSA - TRMY

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
32_L	54_L	4.850	1.00
134_A	187_H	4.602	0.99
64_I	69_V	3.721	0.97
147_S	151_D	3.506	0.96
64_I	83_L	3.408	0.95
172_P	186_N	3.183	0.93
170_V	180_A	3.069	0.92
9_H	156_E	2.694	0.85
42_V	179_H	2.684	0.85
53_F	63_R	2.613	0.83
80_A	100_S	2.337	0.75
73_H	79_V	2.328	0.75
40_L	66_A	2.295	0.74
53_F	108_S	2.234	0.72
35_C	181_I	2.145	0.69
21_D	24_G	2.054	0.65
132_A	190_T	2.051	0.65
98_E	115_V	2.021	0.64
29_L	40_L	2.002	0.63
175_L	185_H	1.996	0.63
125_A	157_A	1.971	0.62
37_S	78_N	1.964	0.61
73_H	78_N	1.939	0.60
22_L	80_A	1.925	0.60
112_F	116_L	1.916	0.59
5_V	69_V	1.903	0.59
121_G	143_V	1.901	0.59
6_V	11_A	1.856	0.57
64_I	105_I	1.840	0.56
145_V	168_V	1.765	0.53
40_L	73_H	1.763	0.53
35_C	41_F	1.706	0.50
31_V	82_L	1.699	0.50
72_M	79_V	1.674	0.49
66_A	126_L	1.606	0.46
37_S	178_D	1.589	0.45
11_A	56_L	1.582	0.45
1_M	4_F	1.549	0.44
147_S	152_F	1.520	0.42
86_A	149_H	1.480	0.41
37_S	41_F	1.467	0.40
53_F	61_T	1.457	0.40
51_E	65_D	1.418	0.38
50_V	113_E	1.411	0.38
62_V	123_V	1.371	0.36
152_F	156_E	1.350	0.35
31_V	134_A	1.343	0.35
33_C	179_H	1.337	0.35
36_V	138_P	1.327	0.34
84_K	102_S	1.254	0.32
147_S	180_A	1.243	0.31
35_C	179_H	1.231	0.31
108_S	115_V	1.225	0.30
137_D	155_A	1.218	0.30
161_A	167_R	1.192	0.29
122_P	133_L	1.188	0.29
37_S	179_H	1.186	0.29
127_H	167_R	1.179	0.29
26_A	29_L	1.176	0.29
96_H	115_V	1.173	0.29
170_V	184_A	1.169	0.28
31_V	57_G	1.156	0.28
109_K	164_S	1.138	0.27
75_D	78_N	1.137	0.27
98_E	108_S	1.131	0.27
120_S	131_D	1.121	0.27
62_V	118_A	1.102	0.26
5_V	62_V	1.096	0.26
105_I	163_A	1.092	0.26
39_A	139_L	1.091	0.26
5_V	55_V	1.089	0.26
53_F	98_E	1.073	0.25
3_Q	143_V	1.071	0.25
53_F	115_V	1.056	0.25
28_R	34_R	1.055	0.25
30_D	34_R	1.055	0.25
3_Q	142_P	1.035	0.24
9_H	153_T	1.030	0.24
158_S	173_T	1.029	0.24
60_V	127_H	1.023	0.24
23_P	84_K	1.019	0.23
5_V	143_V	1.010	0.23
4_F	144_F	1.003	0.23
25_A	124_V	1.002	0.23
98_E	106_H	0.990	0.23
6_V	83_L	0.987	0.22
31_V	159_L	0.976	0.22
139_L	142_P	0.974	0.22
17_F	128_E	0.972	0.22
158_S	161_A	0.968	0.22
45_G	48_D	0.965	0.22
21_D	78_N	0.964	0.22
19_L	24_G	0.964	0.22
80_A	184_A	0.963	0.22
174_V	180_A	0.963	0.22
75_D	156_E	0.959	0.22
136_V	168_V	0.946	0.21
36_V	101_S	0.941	0.21
46_I	115_V	0.937	0.21
133_L	166_H	0.934	0.21
24_G	44_H	0.932	0.21
34_R	74_P	0.921	0.20
161_A	168_V	0.915	0.20
124_V	183_V	0.913	0.20
26_A	124_V	0.908	0.20
32_L	56_L	0.906	0.20
124_V	141_D	0.901	0.20
37_S	42_V	0.899	0.20
24_G	70_Q	0.899	0.20
153_T	156_E	0.898	0.20
126_L	181_I	0.897	0.20
61_T	171_G	0.888	0.20
113_E	120_S	0.883	0.19
40_L	82_L	0.880	0.19
9_H	20_D	0.880	0.19
13_T	149_H	0.876	0.19
55_V	112_F	0.875	0.19
145_V	160_L	0.870	0.19
14_T	70_Q	0.865	0.19
71_Y	81_G	0.865	0.19
54_L	112_F	0.865	0.19
21_D	44_H	0.855	0.19
59_E	152_F	0.854	0.19
3_Q	53_F	0.853	0.19
2_R	185_H	0.849	0.19
36_V	185_H	0.848	0.18
23_P	31_V	0.839	0.18
185_H	188_L	0.837	0.18
53_F	168_V	0.832	0.18
111_G	175_L	0.819	0.18
37_S	79_V	0.816	0.18
20_D	40_L	0.807	0.17
42_V	132_A	0.800	0.17
96_H	186_N	0.798	0.17
72_M	78_N	0.797	0.17
40_L	65_D	0.796	0.17
22_L	48_D	0.793	0.17
155_A	161_A	0.789	0.17
40_L	49_D	0.783	0.17
8_G	127_H	0.779	0.17
160_L	188_L	0.779	0.17
43_S	74_P	0.778	0.17
38_A	179_H	0.777	0.17
2_R	46_I	0.776	0.17
27_G	34_R	0.774	0.17
128_E	174_V	0.770	0.17
15_P	38_A	0.769	0.16
18_P	33_C	0.769	0.16
62_V	105_I	0.764	0.16
63_R	98_E	0.763	0.16
22_L	69_V	0.760	0.16
121_G	173_T	0.759	0.16
68_A	154_A	0.755	0.16
85_Q	155_A	0.755	0.16
83_L	107_V	0.753	0.16
82_L	156_E	0.750	0.16
40_L	79_V	0.747	0.16
39_A	52_V	0.746	0.16
6_V	137_D	0.746	0.16
28_R	74_P	0.746	0.16
30_D	74_P	0.746	0.16
78_N	81_G	0.744	0.16
60_V	109_K	0.744	0.16
152_F	180_A	0.740	0.16
122_P	141_D	0.737	0.16
134_A	190_T	0.722	0.15
131_D	135_A	0.718	0.15
42_V	56_L	0.716	0.15
116_L	159_L	0.716	0.15
89_A	101_S	0.715	0.15
79_V	145_V	0.712	0.15
105_I	118_A	0.709	0.15
2_R	12_P	0.709	0.15
12_P	29_L	0.708	0.15
86_A	177_A	0.704	0.15
179_H	186_N	0.703	0.15
60_V	174_V	0.700	0.15
36_V	123_V	0.699	0.15
19_L	103_P	0.698	0.15
62_V	108_S	0.696	0.15
36_V	39_A	0.694	0.15
49_D	77_R	0.690	0.15
11_A	14_T	0.688	0.15
27_G	30_D	0.685	0.15
131_D	161_A	0.681	0.14
133_L	170_V	0.680	0.14
20_D	185_H	0.679	0.14
101_S	181_I	0.679	0.14
170_V	174_V	0.677	0.14
141_D	178_D	0.676	0.14
175_L	183_V	0.673	0.14
175_L	180_A	0.673	0.14
68_A	113_E	0.673	0.14
91_T	127_H	0.670	0.14
64_I	101_S	0.664	0.14
20_D	114_A	0.662	0.14
180_A	183_V	0.660	0.14
57_G	62_V	0.655	0.14
28_R	75_D	0.654	0.14
30_D	75_D	0.654	0.14
29_L	141_D	0.654	0.14
153_T	162_D	0.654	0.14
7_L	112_F	0.650	0.14
127_H	157_A	0.643	0.14
187_H	190_T	0.642	0.14
100_S	167_R	0.638	0.14
129_D	168_V	0.636	0.14
86_A	107_V	0.635	0.14
31_V	41_F	0.632	0.13
51_E	64_I	0.630	0.13
2_R	188_L	0.628	0.13
31_V	96_H	0.626	0.13
37_S	182_T	0.625	0.13
9_H	150_R	0.625	0.13
105_I	161_A	0.624	0.13
90_K	95_G	0.614	0.13
79_V	82_L	0.612	0.13
41_F	79_V	0.608	0.13
172_P	176_H	0.607	0.13
2_R	160_L	0.605	0.13
159_L	179_H	0.603	0.13
124_V	129_D	0.603	0.13
80_A	145_V	0.601	0.13
46_I	49_D	0.600	0.13
78_N	182_T	0.600	0.13
5_V	150_R	0.598	0.13
62_V	166_H	0.597	0.13
124_V	145_V	0.595	0.13
56_L	111_G	0.590	0.13
89_A	99_A	0.589	0.13
63_R	115_V	0.586	0.13
127_H	174_V	0.583	0.12
85_Q	105_I	0.582	0.12
13_T	41_F	0.580	0.12
96_H	107_V	0.577	0.12
86_A	172_P	0.576	0.12
22_L	34_R	0.575	0.12
21_D	34_R	0.573	0.12
48_D	122_P	0.572	0.12
35_C	177_A	0.569	0.12
5_V	119_V	0.569	0.12
47_R	104_G	0.568	0.12
78_N	136_V	0.568	0.12
2_R	124_V	0.566	0.12
133_L	141_D	0.566	0.12
38_A	156_E	0.564	0.12
52_V	123_V	0.564	0.12
49_D	107_V	0.562	0.12
86_A	103_P	0.560	0.12
122_P	163_A	0.557	0.12
66_A	128_E	0.556	0.12
130_G	146_L	0.556	0.12
23_P	73_H	0.556	0.12
42_V	170_V	0.551	0.12
108_S	184_A	0.549	0.12
12_P	132_A	0.546	0.12
31_V	184_A	0.545	0.12
70_Q	159_L	0.543	0.12
64_I	100_S	0.541	0.12
98_E	125_A	0.540	0.12
46_I	50_V	0.534	0.12
39_A	123_V	0.533	0.12
23_P	108_S	0.531	0.12
21_D	43_S	0.529	0.11
23_P	60_V	0.527	0.11
74_P	80_A	0.526	0.11
40_L	78_N	0.522	0.11
69_V	168_V	0.520	0.11
21_D	77_R	0.520	0.11
125_A	174_V	0.517	0.11
40_L	87_L	0.515	0.11
16_D	140_A	0.514	0.11
66_A	78_N	0.513	0.11
9_H	38_A	0.509	0.11
124_V	153_T	0.507	0.11
82_L	85_Q	0.506	0.11
8_G	149_H	0.506	0.11
21_D	74_P	0.504	0.11
89_A	181_I	0.504	0.11
11_A	29_L	0.502	0.11
16_D	135_A	0.501	0.11
17_F	56_L	0.500	0.11

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
2qwvA	2	0.9337	100	0.189	Contact Map
3aiaA	2	0.9694	100	0.37	Contact Map
2qmmA	2	0.9592	100	0.459	Contact Map
3oiiA	2	0.898	93.8	0.929	Contact Map
2egvA	2	0.9031	91.1	0.935	Contact Map
1z85A	2	0.8316	90.9	0.935	Contact Map
3bbdA	2	0.8929	90.5	0.936	Contact Map
4l69A	2	0.9235	87	0.94	Contact Map
1vhyA	2	0.949	86.5	0.94	Contact Map
1vhkA	3	0.9286	86.3	0.94	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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