RSMA - HALSA - GREMLIN Contacts

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RSMA - Probable ribosomal RNA small subunit methyltransferase A

UniProt:	Q9HQH1	Sequences: MTAPRDPDALIRRAGRPNPDFDQHFLIDDRVLDRIPTYADGFDRGHVLEIGAGTGALTDRLLSVADRVTAVERDESYASFLREEFADAIAAGDLDVVAGDALAVDLPAFTCAVSNLPYGVASEVTFRLLPAGKPMVLMYQLEFAERMAADPGTSEYGRLSVATQHYADVSIVETVPAAAFDPQPRVESAVVRVTPRDPDYVVADEAFFLSFVKALFTQRRKTTRNAIRNTAHISGLDDPDAVVAAVDDDVLGTRPGSLSPATFAALANVAWGVETAPGPDPQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	282 (248)
Sequences:	4635 (2949)
Seq/√Len:	187.3

ECOLI - RSMA
BACSU - RSMA
HALSA - RSMA
SULSO - Q7LXK6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
253_T	257_S	3.561	1.00
62_L	94_L	3.134	1.00
253_T	262_T	2.865	1.00
259_S	262_T	2.863	1.00
46_H	69_T	2.726	1.00
67_R	95_D	2.587	1.00
144_A	189_A	2.562	1.00
262_T	265_A	2.507	1.00
249_D	252_G	2.473	1.00
78_A	98_A	2.383	1.00
28_D	179_A	2.353	1.00
105_D	108_A	2.256	1.00
69_T	97_V	2.241	1.00
34_R	173_E	2.208	1.00
118_Y	188_S	2.165	1.00
170_S	192_R	2.157	1.00
168_D	194_T	2.146	1.00
145_E	171_I	2.120	1.00
168_D	196_R	2.075	1.00
61_L	113_V	2.074	1.00
215_L	263_F	2.054	1.00
170_S	194_T	2.045	1.00
160_S	164_Q	2.044	1.00
177_A	187_E	2.031	1.00
141_L	174_T	2.024	1.00
148_A	169_V	1.970	1.00
60_R	63_S	1.956	1.00
24_H	183_Q	1.921	1.00
37_T	64_V	1.906	1.00
222_T	252_G	1.905	1.00
75_E	98_A	1.903	1.00
176_P	179_A	1.878	1.00
45_G	111_C	1.878	1.00
167_A	193_V	1.876	1.00
258_L	262_T	1.771	1.00
33_D	60_R	1.760	1.00
174_T	189_A	1.759	1.00
211_F	267_A	1.750	1.00
65_A	68_V	1.720	1.00
171_I	174_T	1.716	1.00
172_V	192_R	1.714	1.00
52_A	70_A	1.704	1.00
203_A	268_N	1.698	1.00
42_F	45_G	1.655	1.00
71_V	104_V	1.634	1.00
111_C	134_P	1.612	1.00
161_V	212_V	1.600	1.00
147_M	163_T	1.597	1.00
59_D	84_E	1.588	1.00
126_F	162_A	1.572	1.00
134_P	192_R	1.567	1.00
82_R	98_A	1.542	1.00
171_I	189_A	1.538	1.00
101_A	106_L	1.530	1.00
125_T	139_Y	1.520	1.00
27_I	181_D	1.513	1.00
59_D	85_F	1.511	1.00
71_V	101_A	1.509	1.00
222_T	225_N	1.499	1.00
138_M	175_V	1.489	1.00
61_L	68_V	1.476	1.00
161_V	260_P	1.472	1.00
163_T	169_V	1.468	1.00
249_D	253_T	1.449	1.00
101_A	124_V	1.423	1.00
141_L	145_E	1.409	1.00
32_L	60_R	1.408	1.00
38_Y	172_V	1.406	1.00
265_A	268_N	1.394	1.00
17_P	181_D	1.391	1.00
136_V	192_R	1.381	1.00
127_R	131_A	1.361	1.00
18_N	76_S	1.356	1.00
240_D	244_A	1.351	1.00
112_A	128_L	1.316	1.00
248_D	253_T	1.313	1.00
78_A	82_R	1.306	1.00
177_A	185_R	1.291	1.00
207_F	267_A	1.289	1.00
152_G	257_S	1.286	1.00
70_A	96_V	1.281	1.00
121_A	139_Y	1.279	1.00
147_M	191_V	1.266	1.00
17_P	54_T	1.261	1.00
241_A	245_A	1.259	1.00
21_F	73_R	1.258	1.00
208_F	212_V	1.254	1.00
141_L	187_E	1.252	1.00
215_L	255_P	1.248	1.00
175_V	190_V	1.241	1.00
145_E	155_E	1.221	1.00
97_V	104_V	1.219	1.00
134_P	194_T	1.188	1.00
116_L	137_L	1.185	1.00
245_A	269_V	1.184	1.00
46_H	67_R	1.184	1.00
174_T	187_E	1.182	1.00
41_G	47_V	1.170	1.00
129_L	167_A	1.148	1.00
139_Y	144_A	1.142	1.00
165_H	208_F	1.141	1.00
44_R	66_D	1.140	1.00
178_A	183_Q	1.134	1.00
31_V	179_A	1.129	1.00
164_Q	169_V	1.129	1.00
200_Y	264_A	1.127	1.00
217_T	226_A	1.127	1.00
207_F	270_A	1.125	1.00
248_D	251_L	1.117	1.00
202_V	268_N	1.114	1.00
167_A	195_P	1.112	1.00
99_G	104_V	1.102	1.00
220_R	256_G	1.092	1.00
154_S	256_G	1.090	1.00
69_T	95_D	1.087	1.00
36_P	113_V	1.082	1.00
136_V	190_V	1.075	1.00
100_D	103_A	1.073	1.00
70_A	94_L	1.070	1.00
41_G	45_G	1.069	1.00
246_V	269_V	1.068	1.00
39_A	47_V	1.064	1.00
147_M	169_V	1.064	1.00
30_R	179_A	1.063	1.00
48_L	71_V	1.056	1.00
249_D	257_S	1.053	1.00
198_P	201_V	1.048	1.00
21_F	76_S	1.048	1.00
148_A	171_I	1.048	1.00
121_A	143_F	1.045	1.00
242_V	270_A	1.040	1.00
173_E	190_V	1.036	1.00
29_D	60_R	1.034	1.00
71_V	109_F	1.027	1.00
215_L	226_A	1.027	1.00
196_R	199_D	1.025	1.00
39_A	114_S	1.022	1.00
215_L	223_T	1.017	1.00
33_D	37_T	1.008	1.00
30_R	33_D	1.005	0.99
132_G	205_E	0.999	0.99
114_S	137_L	0.996	0.99
167_A	196_R	0.988	0.99
58_T	68_V	0.987	0.99
41_G	65_A	0.980	0.99
62_L	93_D	0.976	0.99
78_A	96_V	0.966	0.99
224_R	240_D	0.961	0.99
46_H	66_D	0.961	0.99
39_A	113_V	0.957	0.99
22_D	119_G	0.954	0.99
150_D	153_T	0.950	0.99
166_Y	209_L	0.949	0.99
54_T	80_F	0.932	0.99
54_T	77_Y	0.927	0.99
261_A	265_A	0.923	0.99
99_G	103_A	0.919	0.99
247_D	265_A	0.913	0.99
38_Y	173_E	0.912	0.99
244_A	251_L	0.909	0.99
111_C	133_K	0.904	0.99
165_H	205_E	0.903	0.99
36_P	41_G	0.901	0.99
202_V	264_A	0.899	0.99
204_D	207_F	0.899	0.99
141_L	189_A	0.894	0.99
102_L	120_V	0.894	0.99
29_D	59_D	0.887	0.99
226_A	255_P	0.884	0.99
165_H	260_P	0.877	0.99
264_A	268_N	0.871	0.99
241_A	244_A	0.870	0.99
204_D	268_N	0.869	0.99
79_S	82_R	0.868	0.98
52_A	81_L	0.863	0.98
32_L	56_A	0.863	0.98
211_F	215_L	0.858	0.98
50_I	112_A	0.858	0.98
83_E	86_A	0.855	0.98
39_A	136_V	0.844	0.98
70_A	81_L	0.838	0.98
214_A	255_P	0.838	0.98
18_N	21_F	0.831	0.98
158_R	213_K	0.830	0.98
149_A	153_T	0.822	0.98
201_V	204_D	0.822	0.98
32_L	36_P	0.820	0.98
125_T	147_M	0.819	0.98
30_R	34_R	0.817	0.98
205_E	209_L	0.809	0.98
135_M	195_P	0.808	0.98
85_F	94_L	0.807	0.98
240_D	251_L	0.805	0.98
81_L	96_V	0.802	0.97
177_A	183_Q	0.797	0.97
48_L	110_T	0.796	0.97
243_V	251_L	0.795	0.97
207_F	211_F	0.795	0.97
120_V	124_V	0.790	0.97
35_I	138_M	0.786	0.97
208_F	267_A	0.783	0.97
47_V	65_A	0.781	0.97
156_Y	160_S	0.779	0.97
265_A	269_V	0.778	0.97
111_C	136_V	0.773	0.97
156_Y	263_F	0.770	0.97
141_L	171_I	0.768	0.97
101_A	116_L	0.768	0.97
158_R	162_A	0.764	0.97
29_D	33_D	0.762	0.97
130_P	209_L	0.762	0.97
207_F	210_S	0.757	0.96
35_I	190_V	0.756	0.96
206_A	210_S	0.756	0.96
157_G	256_G	0.755	0.96
17_P	25_F	0.751	0.96
205_E	208_F	0.748	0.96
148_A	189_A	0.746	0.96
32_L	138_M	0.743	0.96
161_V	263_F	0.741	0.96
196_R	200_Y	0.736	0.96
39_A	111_C	0.731	0.96
15_G	76_S	0.725	0.95
34_R	178_A	0.722	0.95
41_G	111_C	0.707	0.95
87_D	91_A	0.706	0.95
125_T	163_T	0.699	0.94
210_S	230_T	0.697	0.94
162_A	209_L	0.694	0.94
223_T	227_I	0.694	0.94
101_A	120_V	0.692	0.94
68_V	114_S	0.692	0.94
248_D	262_T	0.685	0.94
243_V	247_D	0.683	0.94
56_A	60_R	0.682	0.94
126_F	130_P	0.682	0.94
43_D	66_D	0.681	0.94
231_A	234_S	0.681	0.94
243_V	248_D	0.678	0.94
101_A	127_R	0.678	0.94
62_L	91_A	0.677	0.94
116_L	124_V	0.676	0.93
211_F	230_T	0.674	0.93
165_H	209_L	0.672	0.93
224_R	228_R	0.666	0.93
99_G	108_A	0.664	0.93
60_R	64_V	0.662	0.93
79_S	83_E	0.660	0.93
244_A	247_D	0.660	0.93
118_Y	138_M	0.659	0.93
166_Y	205_E	0.658	0.93
126_F	158_R	0.657	0.92
80_F	83_E	0.657	0.92
72_E	78_A	0.654	0.92
199_D	202_V	0.652	0.92
210_S	214_A	0.651	0.92
122_S	135_M	0.651	0.92
31_V	173_E	0.644	0.92
116_L	121_A	0.643	0.92
15_G	80_F	0.640	0.91
31_V	175_V	0.640	0.91
107_P	131_A	0.639	0.91
248_D	257_S	0.634	0.91
218_Q	226_A	0.630	0.91
112_A	137_L	0.629	0.91
16_R	76_S	0.627	0.91
176_P	187_E	0.624	0.90
255_P	263_F	0.623	0.90
34_R	37_T	0.621	0.90
38_Y	192_R	0.620	0.90
54_T	84_E	0.617	0.90
199_D	264_A	0.616	0.90
147_M	160_S	0.614	0.90
175_V	186_V	0.613	0.90
121_A	126_F	0.613	0.90
220_R	254_R	0.613	0.90
258_L	263_F	0.612	0.90
45_G	133_K	0.612	0.90
177_A	186_V	0.612	0.90
106_L	124_V	0.610	0.89
165_H	202_V	0.610	0.89
158_R	209_L	0.609	0.89
106_L	127_R	0.606	0.89
148_A	191_V	0.606	0.89
48_L	106_L	0.605	0.89
214_A	230_T	0.602	0.89
145_E	174_T	0.601	0.89
204_D	208_F	0.594	0.88
73_R	98_A	0.592	0.88
36_P	64_V	0.590	0.88
17_P	77_Y	0.590	0.88
15_G	54_T	0.589	0.88
76_S	79_S	0.588	0.88
61_L	65_A	0.587	0.88
121_A	125_T	0.587	0.88
17_P	20_D	0.586	0.87
139_Y	163_T	0.586	0.87
165_H	264_A	0.586	0.87
266_L	269_V	0.585	0.87
24_H	185_R	0.585	0.87
14_A	17_P	0.585	0.87
71_V	226_A	0.584	0.87
52_A	62_L	0.580	0.87
135_M	193_V	0.578	0.87
123_E	127_R	0.576	0.87
104_V	108_A	0.575	0.86
138_M	190_V	0.574	0.86
36_P	61_L	0.572	0.86
31_V	176_P	0.570	0.86
139_Y	147_M	0.569	0.86
122_S	126_F	0.568	0.86
50_I	128_L	0.568	0.86
223_T	258_L	0.568	0.86
173_E	189_A	0.567	0.86
211_F	266_L	0.566	0.86
138_M	188_S	0.566	0.86
50_I	137_L	0.565	0.86
75_E	78_A	0.560	0.85
47_V	68_V	0.560	0.85
132_G	195_P	0.558	0.85
211_F	263_F	0.557	0.85
146_R	149_A	0.554	0.84
32_L	57_L	0.554	0.84
169_V	191_V	0.552	0.84
32_L	113_V	0.552	0.84
164_Q	260_P	0.550	0.84
242_V	266_L	0.549	0.84
40_D	134_P	0.545	0.83
158_R	212_V	0.545	0.83
139_Y	158_R	0.541	0.83
222_T	226_A	0.539	0.83
130_P	206_A	0.538	0.83
44_R	65_A	0.538	0.83
85_F	91_A	0.535	0.82
35_I	143_F	0.535	0.82
56_A	114_S	0.534	0.82
36_P	60_R	0.532	0.82
252_G	257_S	0.530	0.82
122_S	158_R	0.530	0.82
217_T	255_P	0.529	0.82
246_V	266_L	0.528	0.82
215_L	227_I	0.528	0.82
234_S	244_A	0.526	0.81
156_Y	260_P	0.525	0.81
47_V	111_C	0.524	0.81
128_L	135_M	0.523	0.81
135_M	139_Y	0.522	0.81
177_A	189_A	0.521	0.81
228_R	240_D	0.521	0.81
47_V	64_V	0.520	0.81
165_H	196_R	0.520	0.81
230_T	233_I	0.520	0.81
175_V	179_A	0.518	0.80
168_D	197_D	0.516	0.80
41_G	66_D	0.513	0.80
242_V	269_V	0.512	0.80
34_R	38_Y	0.512	0.80
137_L	195_P	0.511	0.79
163_T	193_V	0.510	0.79
106_L	131_A	0.509	0.79
150_D	164_Q	0.509	0.79
119_G	185_R	0.507	0.79
208_F	260_P	0.507	0.79
26_L	31_V	0.507	0.79
83_E	87_D	0.505	0.79
112_A	124_V	0.504	0.78
35_I	118_Y	0.503	0.78
222_T	257_S	0.502	0.78
133_K	194_T	0.502	0.78
188_S	256_G	0.501	0.78
208_F	211_F	0.501	0.78
33_D	64_V	0.500	0.78

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
4gc5A	2	0.9823	100	0.256	Contact Map
1i4wA	1	0.9255	100	0.263	Contact Map
4jxjA	1	0.844	100	0.293	Contact Map
3futA	1	0.9184	100	0.311	Contact Map
3gruA	1	0.8901	100	0.318	Contact Map
3tqsA	1	0.8404	100	0.326	Contact Map
3uzuA	1	0.8723	100	0.333	Contact Map
1qyrA	1	0.8546	100	0.337	Contact Map
3ftdA	1	0.8262	100	0.363	Contact Map
1zq9A	2	0.8972	100	0.387	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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