RLMH - BACSU - GREMLIN Contacts

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RLMH - Ribosomal RNA large subunit methyltransferase H

UniProt:	Q45601	Sequences: MNINIVTIGKLKEKYLKQGIEEYTKRLSAYAKIDIIELPDEKAPENLSDQDMKIIKDKEGDRILSKISPDAHVIALAIEGKMKTSEELADTIDKLATYGKSKVTFVIGGSLGLSDTVMKRADEKLSFSKMTFPHQLMRLILVEQIYRAFRINRGEPYHK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	159 (155)
Sequences:	2665 (1830)
Seq/√Len:	147.0

ECOLI - RLMH
BACSU - RLMH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
82_M	129_K	3.366	1.00
19_G	139_L	2.433	1.00
71_A	104_T	2.416	1.00
89_A	152_N	2.271	1.00
75_A	113_L	2.189	1.00
6_V	63_I	2.184	1.00
115_D	119_K	2.132	1.00
15_Y	19_G	2.111	1.00
150_R	155_E	2.082	1.00
64_L	120_R	2.031	1.00
133_P	136_L	2.010	1.00
75_A	121_A	2.010	1.00
91_T	123_E	1.979	1.00
83_K	123_E	1.961	1.00
60_G	117_V	1.925	1.00
4_N	34_D	1.905	1.00
64_L	117_V	1.904	1.00
17_K	21_E	1.891	1.00
61_D	116_T	1.885	1.00
132_F	140_I	1.860	1.00
68_S	71_A	1.847	1.00
128_S	132_F	1.836	1.00
93_D	152_N	1.780	1.00
57_D	114_S	1.769	1.00
60_G	114_S	1.768	1.00
24_T	33_I	1.764	1.00
73_V	106_V	1.744	1.00
78_I	126_S	1.733	1.00
84_T	87_E	1.677	1.00
88_L	148_A	1.669	1.00
91_T	95_L	1.648	1.00
127_F	137_M	1.635	1.00
57_D	116_T	1.607	1.00
87_E	129_K	1.583	1.00
77_A	118_M	1.573	1.00
14_K	18_Q	1.508	1.00
41_E	62_R	1.468	1.00
51_D	54_I	1.453	1.00
30_Y	155_E	1.435	1.00
61_D	65_S	1.428	1.00
67_I	73_V	1.426	1.00
7_T	138_R	1.422	1.00
16_L	19_G	1.406	1.00
4_N	102_K	1.405	1.00
4_N	71_A	1.388	1.00
20_I	142_V	1.366	1.00
72_H	122_D	1.359	1.00
71_A	102_K	1.354	1.00
58_K	61_D	1.348	1.00
90_D	93_D	1.330	1.00
93_D	97_T	1.329	1.00
5_I	141_L	1.316	1.00
73_V	120_R	1.298	1.00
118_M	124_K	1.298	1.00
31_A	149_F	1.290	1.00
125_L	130_M	1.290	1.00
72_H	123_E	1.289	1.00
56_K	118_M	1.288	1.00
63_I	106_V	1.272	1.00
137_M	140_I	1.257	1.00
2_N	34_D	1.244	1.00
100_K	122_D	1.239	1.00
54_I	57_D	1.219	1.00
81_K	87_E	1.202	1.00
8_I	38_L	1.200	1.00
18_Q	21_E	1.189	1.00
20_I	24_T	1.155	1.00
74_I	95_L	1.148	1.00
79_E	118_M	1.147	1.00
20_I	139_L	1.137	0.99
20_I	35_I	1.136	0.99
52_M	56_K	1.129	0.99
105_F	141_L	1.117	0.99
75_A	118_M	1.111	0.99
4_N	36_I	1.106	0.99
21_E	24_T	1.095	0.99
78_I	86_E	1.087	0.99
16_L	139_L	1.087	0.99
77_A	124_K	1.083	0.99
72_H	95_L	1.082	0.99
81_K	123_E	1.078	0.99
75_A	124_K	1.072	0.99
4_N	104_T	1.051	0.99
54_I	58_K	1.008	0.99
76_L	141_L	1.002	0.99
116_T	119_K	0.987	0.99
22_E	26_R	0.986	0.99
115_D	118_M	0.973	0.98
57_D	61_D	0.961	0.98
83_K	91_T	0.953	0.98
96_A	152_N	0.953	0.98
60_G	116_T	0.949	0.98
55_I	111_L	0.946	0.98
5_I	33_I	0.945	0.98
91_T	94_K	0.941	0.98
11_L	20_I	0.919	0.98
36_I	66_K	0.916	0.98
37_E	138_R	0.908	0.97
2_N	32_K	0.908	0.97
8_I	109_G	0.903	0.97
83_K	88_L	0.899	0.97
30_Y	150_R	0.888	0.97
94_K	98_Y	0.879	0.97
110_S	159_K	0.877	0.97
35_I	138_R	0.869	0.97
76_L	137_M	0.862	0.97
60_G	64_L	0.861	0.97
70_D	102_K	0.859	0.96
5_I	145_I	0.856	0.96
73_V	122_D	0.845	0.96
5_I	107_I	0.844	0.96
69_P	120_R	0.840	0.96
139_L	142_V	0.839	0.96
150_R	156_P	0.829	0.96
33_I	142_V	0.822	0.95
14_K	17_K	0.820	0.95
13_E	19_G	0.811	0.95
70_D	100_K	0.811	0.95
24_T	28_S	0.809	0.95
85_S	151_I	0.807	0.95
15_Y	18_Q	0.803	0.95
27_L	31_A	0.798	0.95
111_L	159_K	0.797	0.95
87_E	90_D	0.795	0.95
41_E	58_K	0.793	0.95
2_N	102_K	0.791	0.94
92_I	148_A	0.771	0.94
24_T	35_I	0.769	0.94
78_I	159_K	0.763	0.93
56_K	111_L	0.762	0.93
106_V	113_L	0.759	0.93
59_E	109_G	0.758	0.93
146_Y	150_R	0.753	0.93
52_M	111_L	0.753	0.93
90_D	94_K	0.752	0.93
53_K	56_K	0.742	0.92
82_M	126_S	0.733	0.92
27_L	149_F	0.731	0.92
75_A	106_V	0.720	0.91
86_E	89_A	0.715	0.91
50_Q	54_I	0.711	0.91
53_K	57_D	0.711	0.91
4_N	68_S	0.709	0.91
127_F	130_M	0.700	0.90
74_I	91_T	0.699	0.90
88_L	130_M	0.698	0.90
6_V	104_T	0.694	0.90
41_E	55_I	0.692	0.89
74_I	103_V	0.690	0.89
125_L	141_L	0.684	0.89
76_L	127_F	0.683	0.89
78_I	110_S	0.681	0.89
92_I	103_V	0.680	0.89
27_L	145_I	0.679	0.89
117_V	120_R	0.665	0.88
126_S	129_K	0.663	0.87
136_L	139_L	0.663	0.87
18_Q	22_E	0.663	0.87
56_K	109_G	0.660	0.87
86_E	151_I	0.657	0.87
96_A	153_R	0.657	0.87
81_K	129_K	0.657	0.87
74_I	125_L	0.657	0.87
79_E	124_K	0.653	0.87
23_Y	139_L	0.652	0.87
73_V	104_T	0.650	0.86
11_L	16_L	0.649	0.86
121_A	124_K	0.649	0.86
92_I	96_A	0.646	0.86
67_I	71_A	0.637	0.85
43_A	55_I	0.634	0.85
93_D	96_A	0.633	0.85
83_K	130_M	0.632	0.85
26_R	146_Y	0.624	0.84
130_M	140_I	0.622	0.84
85_S	89_A	0.620	0.84
110_S	137_M	0.619	0.84
83_K	87_E	0.619	0.84
151_I	158_H	0.616	0.83
3_I	31_A	0.616	0.83
13_E	16_L	0.614	0.83
21_E	25_K	0.612	0.83
12_K	135_Q	0.611	0.83
12_K	40_D	0.610	0.83
43_A	156_P	0.608	0.82
78_I	124_K	0.602	0.82
68_S	102_K	0.600	0.82
44_P	110_S	0.598	0.81
16_L	136_L	0.597	0.81
74_I	123_E	0.597	0.81
136_L	140_I	0.588	0.80
81_K	91_T	0.586	0.80
148_A	152_N	0.584	0.80
23_Y	144_Q	0.584	0.80
106_V	117_V	0.581	0.80
72_H	98_Y	0.581	0.80
96_A	149_F	0.581	0.80
31_A	96_A	0.578	0.79
82_M	128_S	0.570	0.78
35_I	142_V	0.566	0.78
3_I	149_F	0.564	0.78
83_K	125_L	0.563	0.77
88_L	125_L	0.560	0.77
68_S	104_T	0.560	0.77
24_T	142_V	0.557	0.77
133_P	137_M	0.553	0.76
62_R	65_S	0.553	0.76
8_I	63_I	0.553	0.76
77_A	121_A	0.551	0.76
72_H	100_K	0.550	0.76
127_F	140_I	0.550	0.76
9_G	138_R	0.546	0.75
58_K	62_R	0.546	0.75
25_K	29_A	0.545	0.75
45_E	51_D	0.545	0.75
38_L	63_I	0.542	0.75
149_F	153_R	0.539	0.74
7_T	37_E	0.536	0.74
53_K	115_D	0.530	0.73
89_A	93_D	0.522	0.72
95_L	100_K	0.519	0.72
141_L	145_I	0.518	0.71
26_R	138_R	0.512	0.71
73_V	121_A	0.511	0.70
86_E	90_D	0.508	0.70
11_L	17_K	0.508	0.70
38_L	62_R	0.508	0.70
74_I	105_F	0.508	0.70
6_V	106_V	0.506	0.70
55_I	58_K	0.503	0.69
11_L	138_R	0.502	0.69
97_T	100_K	0.500	0.69

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
1to0A	2	0.9623	100	-0.002	Contact Map
4fakA	2	1	100	0.007	Contact Map
1ns5A	2	0.9686	100	0.022	Contact Map
1o6dA	2	0.9057	100	0.048	Contact Map
3oiiA	2	0.8302	99.7	0.664	Contact Map
3o7bA	2	0.8428	93.3	0.897	Contact Map
1oy5A	2	0.9182	92.1	0.901	Contact Map
3ky7A	2	0.8742	92	0.902	Contact Map
3knuA	2	0.9119	91.8	0.902	Contact Map
3iefA	2	0.9245	91.6	0.903	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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