RSMD - ECOLI - GREMLIN Contacts

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RSMD - Ribosomal RNA small subunit methyltransferase D

UniProt:	P0ADX9	Sequences: MKKPNHSGSGQIRIIGGQWRGRKLPVPDSPGLRPTTDRVRETLFNWLAPVIVDAQCLDCFAGSGALGLEALSRYAAGATLIEMDRAVSQQLIKNLATLKAGNARVVNSNAMSFLAQKGTPHNIVFVDPPFRRGLLEETINLLEDNGWLADEALIYVESEVENGLPTVPANWSLHREKVAGQVAYRLYQREAQGESDAD	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10343
Length:	198 (178)
Sequences:	4174 (3084)
Seq/√Len:	231.1

ECOLI - RSMD
BACSU - YLBH

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
67_G	80_L	3.242	1.00
68_L	95_L	2.869	1.00
25_P	93_K	2.750	1.00
14_I	68_L	2.659	1.00
19_W	100_A	2.612	1.00
43_L	184_Y	2.346	1.00
158_S	185_R	2.346	1.00
40_R	65_A	2.336	1.00
22_R	97_T	2.335	1.00
55_Q	77_G	2.257	1.00
79_T	121_H	2.164	1.00
85_R	107_N	2.123	1.00
18_Q	102_N	2.104	1.00
148_L	152_A	2.058	1.00
56_C	66_L	2.033	1.00
95_L	103_A	2.021	1.00
71_L	103_A	1.940	1.00
77_G	104_R	1.898	1.00
61_A	80_L	1.894	1.00
71_L	78_A	1.856	1.00
41_E	45_N	1.826	1.00
173_L	187_Y	1.815	1.00
82_E	88_S	1.809	1.00
46_W	186_L	1.799	1.00
88_S	105_V	1.774	1.00
79_T	106_V	1.773	1.00
176_E	183_A	1.767	1.00
122_N	149_A	1.760	1.00
42_T	179_A	1.717	1.00
39_V	182_V	1.666	1.00
95_L	105_V	1.661	1.00
89_Q	93_K	1.637	1.00
57_L	121_H	1.630	1.00
55_Q	119_T	1.625	1.00
32_L	87_V	1.610	1.00
59_C	81_I	1.559	1.00
22_R	99_K	1.555	1.00
178_V	183_A	1.542	1.00
60_F	138_T	1.495	1.00
88_S	107_N	1.489	1.00
85_R	89_Q	1.470	1.00
19_W	98_L	1.469	1.00
13_R	37_D	1.458	1.00
124_V	152_A	1.457	1.00
67_G	78_A	1.428	1.00
42_T	45_N	1.372	1.00
108_S	113_F	1.358	1.00
35_T	157_E	1.358	1.00
131_R	159_E	1.354	1.00
142_L	152_A	1.352	1.00
173_L	185_R	1.351	1.00
51_I	54_A	1.347	1.00
173_L	176_E	1.341	1.00
81_I	113_F	1.335	1.00
93_K	96_A	1.333	1.00
160_V	178_V	1.321	1.00
46_W	175_R	1.304	1.00
56_C	70_A	1.284	1.00
66_L	125_F	1.279	1.00
134_L	138_T	1.277	1.00
77_G	119_T	1.275	1.00
71_L	80_L	1.259	1.00
149_A	152_A	1.252	1.00
89_Q	92_I	1.209	1.00
143_E	170_N	1.204	1.00
43_L	66_L	1.193	1.00
82_E	87_V	1.189	1.00
167_V	187_Y	1.187	1.00
134_L	137_E	1.183	1.00
109_N	112_S	1.180	1.00
86_A	89_Q	1.176	1.00
174_H	188_Q	1.172	1.00
59_C	110_A	1.156	1.00
80_L	103_A	1.153	1.00
124_V	142_L	1.142	1.00
53_D	76_A	1.112	1.00
22_R	98_L	1.101	1.00
61_A	91_L	1.099	1.00
136_E	140_N	1.097	1.00
120_P	149_A	1.094	1.00
153_L	174_H	1.089	1.00
83_M	109_N	1.083	1.00
143_E	171_W	1.080	1.00
176_E	185_R	1.068	1.00
56_C	75_A	1.065	1.00
141_L	145_N	1.063	1.00
120_P	146_G	1.056	1.00
115_A	141_L	1.055	1.00
140_N	144_D	1.051	1.00
137_E	140_N	1.047	1.00
93_K	97_T	1.037	1.00
26_V	29_S	1.030	1.00
56_C	123_I	1.028	1.00
56_C	78_A	1.023	1.00
108_S	112_S	1.005	1.00
159_E	181_Q	1.004	1.00
12_I	26_V	0.994	1.00
18_Q	100_A	0.993	1.00
92_I	107_N	0.991	1.00
15_I	41_E	0.983	1.00
51_I	123_I	0.979	1.00
26_V	63_S	0.969	1.00
39_V	42_T	0.957	1.00
35_T	127_D	0.954	1.00
24_L	94_N	0.954	1.00
88_S	91_L	0.953	1.00
71_L	95_L	0.948	1.00
56_C	125_F	0.941	1.00
27_P	90_Q	0.941	1.00
61_A	67_G	0.939	1.00
51_I	75_A	0.937	1.00
15_I	37_D	0.934	1.00
106_V	113_F	0.932	1.00
172_S	188_Q	0.928	1.00
55_Q	120_P	0.920	1.00
46_W	177_K	0.911	1.00
96_A	101_G	0.911	1.00
81_I	108_S	0.907	1.00
39_V	184_Y	0.905	0.99
79_T	113_F	0.904	0.99
79_T	104_R	0.903	0.99
55_Q	149_A	0.892	0.99
126_V	154_I	0.891	0.99
135_L	156_V	0.886	0.99
28_D	86_A	0.885	0.99
131_R	161_E	0.880	0.99
19_W	22_R	0.879	0.99
126_V	156_V	0.876	0.99
42_T	46_W	0.873	0.99
81_I	110_A	0.869	0.99
44_F	70_A	0.868	0.99
55_Q	76_A	0.868	0.99
55_Q	79_T	0.866	0.99
55_Q	121_H	0.862	0.99
108_S	116_Q	0.847	0.99
159_E	162_N	0.845	0.99
143_E	189_R	0.845	0.99
179_A	184_Y	0.832	0.99
160_V	183_A	0.831	0.99
177_K	184_Y	0.829	0.99
135_L	158_S	0.828	0.99
57_L	124_V	0.817	0.99
79_T	119_T	0.808	0.99
113_F	117_K	0.808	0.99
38_R	41_E	0.804	0.99
88_S	92_I	0.796	0.99
124_V	148_L	0.791	0.99
48_A	73_R	0.789	0.99
110_A	138_T	0.789	0.99
43_L	155_Y	0.786	0.99
158_S	162_N	0.784	0.99
90_Q	94_N	0.781	0.99
92_I	96_A	0.781	0.99
104_R	119_T	0.777	0.98
133_G	136_E	0.769	0.98
114_L	141_L	0.747	0.98
29_S	32_L	0.747	0.98
57_L	79_T	0.746	0.98
44_F	125_F	0.745	0.98
165_P	168_P	0.745	0.98
14_I	95_L	0.742	0.98
60_F	134_L	0.737	0.98
61_A	82_E	0.737	0.98
36_T	39_V	0.737	0.98
31_G	84_D	0.733	0.98
112_S	115_A	0.733	0.98
139_I	154_I	0.723	0.98
46_W	184_Y	0.720	0.97
150_D	189_R	0.719	0.97
68_L	103_A	0.718	0.97
48_A	51_I	0.716	0.97
158_S	183_A	0.714	0.97
125_F	155_Y	0.713	0.97
14_I	40_R	0.712	0.97
24_L	98_L	0.709	0.97
111_M	137_E	0.706	0.97
80_L	95_L	0.682	0.97
47_L	155_Y	0.680	0.96
36_T	182_V	0.680	0.96
25_P	90_Q	0.680	0.96
141_L	144_D	0.677	0.96
49_P	54_A	0.673	0.96
82_E	91_L	0.670	0.96
120_P	147_W	0.669	0.96
151_E	188_Q	0.668	0.96
175_R	186_L	0.665	0.96
66_L	155_Y	0.664	0.96
117_K	147_W	0.650	0.95
50_V	54_A	0.648	0.95
25_P	97_T	0.645	0.95
59_C	126_V	0.644	0.95
36_T	179_A	0.643	0.95
155_Y	184_Y	0.637	0.95
85_R	88_S	0.637	0.95
161_E	181_Q	0.634	0.95
29_S	87_V	0.632	0.95
59_C	114_L	0.629	0.95
37_D	41_E	0.629	0.95
132_R	162_N	0.626	0.94
54_A	75_A	0.622	0.94
43_L	125_F	0.617	0.94
16_G	73_R	0.608	0.94
143_E	169_A	0.606	0.93
35_T	39_V	0.604	0.93
166_T	173_L	0.604	0.93
16_G	40_R	0.603	0.93
19_W	71_L	0.603	0.93
29_S	84_D	0.601	0.93
68_L	98_L	0.599	0.93
114_L	147_W	0.599	0.93
137_E	141_L	0.597	0.93
170_N	189_R	0.595	0.93
42_T	184_Y	0.594	0.93
78_A	103_A	0.593	0.93
19_W	102_N	0.590	0.93
126_V	138_T	0.589	0.92
40_R	66_L	0.589	0.92
26_V	32_L	0.582	0.92
155_Y	186_L	0.581	0.92
135_L	162_N	0.580	0.92
100_A	103_A	0.577	0.92
115_A	145_N	0.575	0.92
136_E	166_T	0.574	0.91
110_A	114_L	0.570	0.91
54_A	122_N	0.569	0.91
157_E	182_V	0.569	0.91
49_P	52_V	0.568	0.91
165_P	187_Y	0.568	0.91
38_R	42_T	0.563	0.91
84_D	87_V	0.563	0.91
32_L	90_Q	0.562	0.91
135_L	159_E	0.560	0.90
135_L	139_I	0.558	0.90
146_G	189_R	0.557	0.90
111_M	138_T	0.557	0.90
23_K	97_T	0.557	0.90
66_L	186_L	0.553	0.90
35_T	65_A	0.548	0.89
138_T	142_L	0.547	0.89
94_N	97_T	0.543	0.89
126_V	135_L	0.542	0.89
171_W	189_R	0.542	0.89
43_L	186_L	0.539	0.89
143_E	172_S	0.539	0.89
60_F	109_N	0.537	0.89
81_I	106_V	0.537	0.89
111_M	134_L	0.535	0.88
133_G	162_N	0.534	0.88
106_V	116_Q	0.531	0.88
75_A	123_I	0.527	0.88
26_V	90_Q	0.525	0.87
130_F	182_V	0.524	0.87
60_F	110_A	0.523	0.87
27_P	88_S	0.520	0.87
18_Q	74_Y	0.519	0.87
66_L	70_A	0.519	0.87
83_M	107_N	0.518	0.87
68_L	94_N	0.517	0.87
21_G	177_K	0.517	0.87
13_R	23_K	0.516	0.87
35_T	41_E	0.514	0.86
155_Y	179_A	0.512	0.86
17_G	72_S	0.510	0.86
114_L	145_N	0.505	0.85
121_H	124_V	0.503	0.85
48_A	52_V	0.502	0.85
46_W	155_Y	0.500	0.85

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
2fpoA	1	0.9192	100	0.561	Contact Map
1ws6A	1	0.8434	100	0.567	Contact Map
2iftA	1	0.8838	100	0.588	Contact Map
2fhpA	1	0.9091	100	0.6	Contact Map
4bluA	2	0.904	99.9	0.624	Contact Map
3x0dA	1	0.9596	99.9	0.638	Contact Map
3p9nA	1	0.8939	99.9	0.642	Contact Map
2oo3A	1	0.9242	99.9	0.642	Contact Map
2esrA	2	0.803	99.9	0.645	Contact Map
4dcmA	1	0.904	99.8	0.684	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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