TRM56 - HALSA - GREMLIN Contacts

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

UniProt:	Q9HRC8	Sequences: MQSHPEVAVLRYGHRPGRDDRMTTHVGLTARALGADRVLFPDNATQAAETVRDITGRFGGPFDVERTTELNATIEDWPGVVVHLTMYGEQLQSVDDEIRTTHREEPVLVVVGGEKVPGDVYEAADWNVGVTNQPHSEVAGLAVFLDRLFDGRELEQGYENAERRVIPEELGKHVVDVEDGDHAEGAAAGDGD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	192 (169)
Sequences:	208 (134)
Seq/√Len:	10.3

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
22_M	138_V	3.902	0.99
53_D	57_R	2.942	0.93
120_V	143_V	2.869	0.92
94_V	128_V	2.860	0.91
131_T	140_G	2.644	0.88
74_I	81_V	2.568	0.86
23_T	40_F	2.544	0.86
12_Y	143_V	2.533	0.85
29_T	33_L	2.448	0.83
89_E	94_V	2.427	0.83
74_I	120_V	2.334	0.80
73_T	108_L	2.201	0.76
7_V	149_F	2.184	0.75
118_G	122_E	2.152	0.74
56_G	97_E	2.146	0.74
77_W	165_V	1.874	0.63
72_A	76_D	1.830	0.61
109_V	144_F	1.817	0.60
80_V	107_V	1.815	0.60
8_A	77_W	1.788	0.59
12_Y	120_V	1.758	0.58
149_F	153_E	1.740	0.57
20_D	138_V	1.734	0.57
80_V	105_E	1.725	0.56
12_Y	139_A	1.724	0.56
164_R	175_V	1.719	0.56
100_T	105_E	1.704	0.55
39_L	73_T	1.698	0.55
74_I	110_V	1.690	0.55
129_G	163_R	1.689	0.55
17_G	20_D	1.658	0.53
77_W	81_V	1.651	0.53
23_T	77_W	1.615	0.51
70_L	120_V	1.575	0.49
47_A	50_T	1.563	0.49
98_I	121_Y	1.552	0.48
50_T	58_F	1.545	0.48
27_G	51_V	1.534	0.47
9_V	36_D	1.533	0.47
39_L	91_L	1.466	0.44
97_E	107_V	1.464	0.44
117_P	120_V	1.460	0.44
7_V	175_V	1.455	0.44
70_L	119_D	1.435	0.43
131_T	153_E	1.385	0.41
22_M	44_A	1.342	0.39
114_E	146_D	1.339	0.39
129_G	165_V	1.313	0.37
75_E	169_E	1.305	0.37
82_V	107_V	1.292	0.37
109_V	165_V	1.285	0.36
36_D	149_F	1.282	0.36
74_I	90_Q	1.274	0.36
129_G	132_N	1.268	0.36
20_D	44_A	1.242	0.34
95_D	144_F	1.229	0.34
7_V	148_L	1.226	0.34
87_Y	172_K	1.217	0.33
12_Y	126_W	1.208	0.33
14_H	44_A	1.206	0.33
52_R	165_V	1.193	0.32
42_D	113_G	1.192	0.32
78_P	123_A	1.159	0.31
46_Q	113_G	1.154	0.31
30_A	143_V	1.151	0.31
124_A	130_V	1.139	0.30
82_V	144_F	1.113	0.29
16_P	23_T	1.111	0.29
89_E	129_G	1.111	0.29
44_A	163_R	1.102	0.29
155_E	165_V	1.082	0.28
93_S	109_V	1.075	0.28
100_T	159_E	1.073	0.28
58_F	78_P	1.051	0.27
40_F	77_W	1.050	0.27
8_A	37_R	1.043	0.27
90_Q	93_S	1.035	0.26
76_D	152_R	1.035	0.26
27_G	114_E	1.027	0.26
69_E	96_D	1.026	0.26
121_Y	168_E	1.020	0.26
82_V	141_L	1.016	0.26
36_D	139_A	1.009	0.25
54_I	74_I	1.008	0.25
37_R	68_T	1.007	0.25
61_P	128_V	1.001	0.25
56_G	162_E	1.001	0.25
51_V	138_V	0.997	0.25
100_T	109_V	0.990	0.25
27_G	38_V	0.987	0.25
26_V	114_E	0.982	0.24
92_Q	126_W	0.982	0.24
47_A	123_A	0.977	0.24
69_E	168_E	0.966	0.24
14_H	79_G	0.966	0.24
131_T	155_E	0.964	0.24
104_E	148_L	0.952	0.23
36_D	132_N	0.952	0.23
39_L	108_L	0.941	0.23
80_V	126_W	0.939	0.23
71_N	109_V	0.937	0.23
85_T	141_L	0.932	0.23
85_T	148_L	0.931	0.23
13_G	113_G	0.931	0.23
12_Y	70_L	0.928	0.23
37_R	65_E	0.924	0.23
132_N	139_A	0.923	0.22
164_R	177_V	0.921	0.22
41_P	57_R	0.919	0.22
81_V	124_A	0.916	0.22
118_G	131_T	0.915	0.22
58_F	70_L	0.914	0.22
96_D	130_V	0.912	0.22
20_D	170_L	0.911	0.22
54_I	71_N	0.909	0.22
168_E	173_H	0.909	0.22
131_T	139_A	0.907	0.22
26_V	111_V	0.902	0.22
72_A	89_E	0.893	0.22
89_E	169_E	0.890	0.21
73_T	155_E	0.888	0.21
33_L	81_V	0.886	0.21
69_E	130_V	0.885	0.21
26_V	138_V	0.877	0.21
64_V	160_N	0.875	0.21
52_R	145_L	0.872	0.21
13_G	135_H	0.867	0.21
48_A	52_R	0.864	0.21
141_L	144_F	0.864	0.21
92_Q	131_T	0.854	0.20
64_V	111_V	0.854	0.20
82_V	85_T	0.853	0.20
109_V	156_Q	0.824	0.19
74_I	161_A	0.822	0.19
29_T	43_N	0.822	0.19
54_I	109_V	0.817	0.19
85_T	144_F	0.812	0.19
58_F	165_V	0.805	0.19
15_R	21_R	0.794	0.19
15_R	18_R	0.794	0.19
18_R	21_R	0.794	0.19
15_R	19_D	0.794	0.19
45_T	97_E	0.790	0.18
135_H	139_A	0.782	0.18
73_T	81_V	0.776	0.18
33_L	173_H	0.767	0.18
86_M	142_A	0.745	0.17
144_F	151_G	0.743	0.17
27_G	147_R	0.732	0.17
94_V	97_E	0.731	0.17
37_R	50_T	0.729	0.17
12_Y	39_L	0.726	0.17
9_V	69_E	0.726	0.17
115_K	146_D	0.724	0.17
72_A	157_G	0.712	0.16
61_P	143_V	0.699	0.16
40_F	91_L	0.697	0.16
38_V	51_V	0.693	0.16
47_A	163_R	0.690	0.16
7_V	43_N	0.687	0.16
107_V	147_R	0.686	0.16
143_V	155_E	0.686	0.16
49_E	52_R	0.685	0.16
27_G	53_D	0.685	0.16
8_A	92_Q	0.684	0.16
7_V	156_Q	0.682	0.16
37_R	92_Q	0.678	0.16
91_L	114_E	0.670	0.15
148_L	153_E	0.670	0.15
14_H	77_W	0.668	0.15
65_E	126_W	0.663	0.15
112_G	137_E	0.662	0.15
85_T	153_E	0.661	0.15
66_R	113_G	0.660	0.15
17_G	44_A	0.659	0.15
33_L	162_E	0.654	0.15
61_P	64_V	0.654	0.15
169_E	175_V	0.654	0.15
49_E	169_E	0.653	0.15
138_V	174_V	0.652	0.15
12_Y	42_D	0.646	0.15
29_T	150_D	0.642	0.15
75_E	123_A	0.639	0.15
37_R	63_D	0.637	0.15
44_A	47_A	0.637	0.15
99_R	150_D	0.634	0.15
111_V	143_V	0.634	0.15
87_Y	151_G	0.632	0.14
112_G	136_S	0.630	0.14
76_D	159_E	0.629	0.14
44_A	79_G	0.627	0.14
49_E	150_D	0.623	0.14
107_V	146_D	0.622	0.14
32_A	62_F	0.622	0.14
55_T	165_V	0.621	0.14
70_L	117_P	0.619	0.14
63_D	166_I	0.604	0.14
13_G	114_E	0.604	0.14
168_E	171_G	0.602	0.14
123_A	163_R	0.601	0.14
16_P	37_R	0.601	0.14
90_Q	129_G	0.597	0.14
77_W	108_L	0.597	0.14
52_R	98_I	0.596	0.14
53_D	105_E	0.594	0.14
119_D	123_A	0.594	0.14
122_E	138_V	0.593	0.14
40_F	81_V	0.591	0.14
49_E	164_R	0.585	0.13
70_L	106_P	0.584	0.13
51_V	55_T	0.584	0.13
46_Q	173_H	0.582	0.13
20_D	40_F	0.577	0.13
69_E	150_D	0.577	0.13
81_V	123_A	0.576	0.13
38_V	120_V	0.573	0.13
26_V	146_D	0.572	0.13
152_R	160_N	0.571	0.13
69_E	119_D	0.566	0.13
22_M	143_V	0.564	0.13
26_V	130_V	0.563	0.13
71_N	100_T	0.563	0.13
83_H	136_S	0.561	0.13
9_V	122_E	0.559	0.13
7_V	108_L	0.557	0.13
81_V	140_G	0.557	0.13
91_L	107_V	0.554	0.13
75_E	95_D	0.551	0.13
29_T	165_V	0.548	0.13
140_G	163_R	0.545	0.13
44_A	158_Y	0.540	0.12
40_F	47_A	0.538	0.12
37_R	54_I	0.533	0.12
12_Y	58_F	0.530	0.12
65_E	73_T	0.529	0.12
144_F	153_E	0.523	0.12
37_R	158_Y	0.521	0.12
48_A	130_V	0.520	0.12
138_V	147_R	0.519	0.12
20_D	140_G	0.518	0.12
104_E	107_V	0.516	0.12
29_T	100_T	0.515	0.12
23_T	165_V	0.514	0.12
37_R	165_V	0.514	0.12
39_L	107_V	0.508	0.12
40_F	54_I	0.507	0.12
51_V	62_F	0.506	0.12
16_P	114_E	0.505	0.12
91_L	151_G	0.501	0.12
11_R	21_R	0.500	0.12
11_R	18_R	0.500	0.12
11_R	15_R	0.500	0.12
11_R	19_D	0.500	0.12
32_A	148_L	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	0.901	100	0.068	Contact Map
2o3aA	2	0.849	100	0.097	Contact Map
1v2xA	2	0.849	97.9	0.905	Contact Map
2ha8A	2	0.7083	97.6	0.91	Contact Map
3dcmX	2	0.7708	97.3	0.916	Contact Map
1zjrA	2	0.8438	97	0.919	Contact Map
4kgnA	2	0.7396	96.7	0.922	Contact Map
1gz0A	2	0.7135	96.6	0.923	Contact Map
3n4jA	2	0.7396	96.2	0.926	Contact Map
3nk6A	2	0.7708	95.7	0.929	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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