TRM56 - SULSO - GREMLIN Contacts

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TRM56 - tRNA (cytidine(56)-2'-O)-methyltransferase

UniProt:	Q980M4	Sequences: MTTHVILVARAFGAKGVYIEGKDEKMVKSILKVIDSWGGSSYFLVKEIENGKSIVNEWKEKGGTIIHLTMYGININDFQDRFEKIKYPLLIIVGAEKVEGWYYHNADYNIAIGNQPHSEVAALAIFLDRIYKGRELYMEFEDAKIKILPQKAGKKVIRSG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	160 (151)
Sequences:	204 (139)
Seq/√Len:	11.3

HALSA - TRM56
SULSO - TRM56

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
1_M	120_V	4.206	0.99
32_K	36_S	3.239	0.97
102_Y	125_I	3.102	0.96
78_F	110_I	2.976	0.95
113_G	122_A	2.778	0.92
55_V	65_I	2.742	0.92
8_V	12_F	2.638	0.90
55_V	102_Y	2.625	0.90
58_W	63_G	2.508	0.88
73_I	78_F	2.504	0.87
100_G	104_H	2.282	0.82
2_T	19_I	2.183	0.79
54_I	90_L	2.150	0.78
91_I	126_F	2.132	0.77
64_T	87_Y	2.033	0.74
55_V	92_I	1.924	0.69
18_Y	54_I	1.884	0.68
53_S	57_E	1.838	0.66
146_K	157_I	1.833	0.65
131_Y	135_E	1.828	0.65
35_D	81_R	1.803	0.64
111_A	145_I	1.762	0.62
64_T	89_L	1.700	0.59
58_W	147_I	1.692	0.59
84_K	87_Y	1.681	0.58
58_W	65_I	1.664	0.58
99_E	102_Y	1.648	0.57
91_I	147_I	1.645	0.57
26_M	29_S	1.643	0.57
18_Y	75_I	1.640	0.56
29_S	37_W	1.629	0.56
51_G	102_Y	1.598	0.54
2_T	58_W	1.593	0.54
111_A	114_N	1.584	0.54
1_M	23_D	1.541	0.52
56_N	151_K	1.498	0.49
51_G	101_W	1.478	0.48
6_I	30_I	1.447	0.47
8_V	22_K	1.388	0.44
106_A	112_I	1.340	0.42
73_I	111_A	1.333	0.42
66_I	89_L	1.316	0.41
79_Q	126_F	1.288	0.39
31_L	147_I	1.268	0.38
57_E	134_R	1.253	0.38
16_G	49_E	1.250	0.38
52_K	91_I	1.249	0.38
66_I	126_F	1.246	0.37
15_K	131_Y	1.235	0.37
113_G	135_E	1.223	0.36
35_D	144_K	1.187	0.35
96_E	128_D	1.186	0.35
55_V	74_N	1.179	0.34
6_I	96_E	1.166	0.34
59_K	105_N	1.148	0.33
23_D	145_I	1.147	0.33
5_V	96_E	1.145	0.33
71_Y	154_K	1.137	0.33
103_Y	150_Q	1.134	0.32
25_K	95_A	1.118	0.32
37_W	51_G	1.108	0.31
33_V	52_K	1.094	0.31
18_Y	90_L	1.092	0.31
137_Y	147_I	1.090	0.31
69_T	130_I	1.075	0.30
84_K	91_I	1.056	0.29
20_E	36_S	1.052	0.29
76_N	108_Y	1.031	0.28
26_M	105_N	1.018	0.28
37_W	59_K	1.012	0.27
84_K	141_E	1.008	0.27
10_R	13_G	1.000	0.27
15_K	121_A	0.985	0.26
27_V	31_L	0.980	0.26
113_G	121_A	0.974	0.26
19_I	58_W	0.973	0.26
5_V	93_V	0.953	0.25
111_A	147_I	0.945	0.25
117_H	121_A	0.940	0.25
31_L	127_L	0.939	0.25
16_G	44_L	0.937	0.25
82_F	103_Y	0.934	0.25
150_Q	155_K	0.932	0.24
16_G	29_S	0.924	0.24
45_V	93_V	0.923	0.24
16_G	46_K	0.920	0.24
66_I	123_L	0.917	0.24
54_I	137_Y	0.912	0.24
51_G	99_E	0.911	0.24
66_I	69_T	0.904	0.23
50_N	150_Q	0.901	0.23
16_G	76_N	0.898	0.23
93_V	123_L	0.896	0.23
76_N	113_G	0.894	0.23
40_S	125_I	0.894	0.23
100_G	113_G	0.893	0.23
64_T	108_Y	0.883	0.23
23_D	26_M	0.882	0.23
9_A	125_I	0.881	0.23
69_T	126_F	0.874	0.22
64_T	85_I	0.873	0.22
23_D	63_G	0.863	0.22
69_T	123_L	0.862	0.22
85_I	108_Y	0.853	0.22
65_I	106_A	0.853	0.22
96_E	114_N	0.842	0.21
74_N	77_D	0.833	0.21
4_H	7_L	0.830	0.21
113_G	137_Y	0.829	0.21
53_S	73_I	0.825	0.21
30_I	34_I	0.824	0.21
81_R	89_L	0.821	0.21
37_W	147_I	0.820	0.21
70_M	124_A	0.818	0.21
6_I	32_K	0.813	0.20
33_V	55_V	0.795	0.20
78_F	81_R	0.792	0.20
6_I	17_V	0.776	0.19
44_L	50_N	0.765	0.19
25_K	155_K	0.765	0.19
49_E	75_I	0.762	0.19
50_N	142_D	0.755	0.19
30_I	120_V	0.749	0.18
80_D	112_I	0.746	0.18
16_G	140_F	0.746	0.18
50_N	80_D	0.734	0.18
15_K	114_N	0.734	0.18
125_I	137_Y	0.733	0.18
53_S	139_E	0.728	0.18
120_V	156_V	0.723	0.18
123_L	126_F	0.715	0.18
45_V	53_S	0.714	0.17
94_G	119_E	0.714	0.17
16_G	77_D	0.706	0.17
91_I	138_M	0.702	0.17
45_V	54_I	0.702	0.17
111_A	121_A	0.702	0.17
19_I	47_E	0.700	0.17
97_K	128_D	0.698	0.17
94_G	118_S	0.696	0.17
114_N	121_A	0.695	0.17
65_I	105_N	0.693	0.17
12_F	65_I	0.693	0.17
7_L	10_R	0.690	0.17
7_L	13_G	0.690	0.17
71_Y	133_G	0.687	0.17
26_M	145_I	0.684	0.17
50_N	112_I	0.680	0.17
28_K	146_K	0.678	0.17
75_I	133_G	0.675	0.16
129_R	156_V	0.673	0.16
74_N	111_A	0.672	0.16
9_A	157_I	0.666	0.16
45_V	142_D	0.662	0.16
2_T	121_A	0.656	0.16
17_V	102_Y	0.655	0.16
16_G	147_I	0.655	0.16
40_S	45_V	0.653	0.16
5_V	112_I	0.650	0.16
33_V	91_I	0.649	0.16
44_L	148_L	0.645	0.16
122_A	145_I	0.645	0.16
58_W	90_L	0.644	0.16
12_F	144_K	0.643	0.16
28_K	31_L	0.638	0.15
126_F	135_E	0.636	0.15
8_V	147_I	0.633	0.15
83_E	132_K	0.625	0.15
67_H	118_S	0.625	0.15
137_Y	144_K	0.619	0.15
45_V	88_P	0.612	0.15
73_I	151_K	0.611	0.15
65_I	122_A	0.607	0.15
5_V	120_V	0.606	0.15
23_D	140_F	0.604	0.15
28_K	132_K	0.604	0.15
2_T	147_I	0.603	0.15
111_A	150_Q	0.603	0.15
29_S	96_E	0.603	0.15
30_I	43_F	0.602	0.15
7_L	14_A	0.598	0.14
82_F	105_N	0.597	0.14
3_T	7_L	0.597	0.14
12_F	125_I	0.589	0.14
8_V	132_K	0.586	0.14
8_V	84_K	0.584	0.14
46_K	108_Y	0.582	0.14
54_I	65_I	0.580	0.14
47_E	95_A	0.579	0.14
128_D	154_K	0.578	0.14
18_Y	89_L	0.578	0.14
31_L	35_D	0.575	0.14
17_V	21_G	0.574	0.14
5_V	128_D	0.573	0.14
150_Q	153_G	0.572	0.14
1_M	122_A	0.571	0.14
57_E	141_E	0.570	0.14
35_D	150_Q	0.567	0.14
16_G	33_V	0.558	0.14
120_V	129_R	0.555	0.13
71_Y	103_Y	0.550	0.13
46_K	54_I	0.548	0.13
89_L	108_Y	0.548	0.13
98_V	119_E	0.547	0.13
94_G	98_V	0.547	0.13
77_D	91_I	0.545	0.13
6_I	21_G	0.539	0.13
55_V	143_A	0.531	0.13
32_K	87_Y	0.530	0.13
19_I	26_M	0.529	0.13
89_L	130_I	0.525	0.13
126_F	133_G	0.525	0.13
56_N	105_N	0.520	0.13
98_V	118_S	0.520	0.13
12_F	103_Y	0.518	0.13
19_I	75_I	0.518	0.13
78_F	83_E	0.516	0.13
90_L	117_H	0.513	0.13
56_N	79_Q	0.512	0.13
75_I	150_Q	0.511	0.12
75_I	131_Y	0.511	0.12
99_E	142_D	0.510	0.12
63_G	126_F	0.510	0.12
51_G	88_P	0.510	0.12
71_Y	92_I	0.505	0.12
85_I	157_I	0.500	0.12

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
2yy8A	2	0.9688	100	0.057	Contact Map
2o3aA	2	0.9125	100	0.078	Contact Map
1v2xA	2	0.9187	98.5	0.866	Contact Map
1zjrA	2	0.9313	98.3	0.875	Contact Map
2ha8A	2	0.8063	98.2	0.879	Contact Map
3dcmX	2	0.8438	97.7	0.892	Contact Map
1gz0A	2	0.7875	97.6	0.895	Contact Map
3n4jA	2	0.8313	97.5	0.896	Contact Map
4kgnA	2	0.825	97.4	0.899	Contact Map
3nk6A	2	0.8438	96.9	0.906	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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