RSGA - BACSU - GREMLIN Contacts

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RSGA - Putative ribosome biogenesis GTPase RsgA

UniProt:	O34530	Sequences: MPEGKIIKALSGFYYVLDESEDSDKVIQCRGRGIFRKNKITPLVGDYVVYQAENDKEGYLMEIKERTNELIRPPICNVDQAVLVFSAVQPSFSTALLDRFLVLVEANDIQPIICITKMDLIEDQDTEDTIQAYAEDYRNIGYDVYLTSSKDQDSLADIIPHFQDKTTVFAGQSGVGKSSLLNAISPELGLRTNEISEHLGRGKHTTRHVELIHTSGGLVADTPGFSSLEFTDIEEEELGYTFPDIREKSSSCKFRGCLHLKEPKCAVKQAVEDGELKQYRYDHYVEFMTEIKDRKPRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	298 (280)
Sequences:	4016 (2773)
Seq/√Len:	165.7

ECOLI - RSGA
BACSU - RSGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
278_Q	282_D	4.027	1.00
49_V	62_E	3.757	1.00
49_V	64_K	3.546	1.00
51_Q	61_M	3.329	1.00
5_K	47_Y	3.322	1.00
80_Q	167_T	3.164	1.00
110_Q	143_D	3.041	1.00
269_Q	273_D	3.031	1.00
17_L	213_H	2.802	1.00
87_A	115_I	2.732	1.00
253_K	264_K	2.655	1.00
196_S	199_L	2.607	1.00
3_E	64_K	2.588	1.00
81_A	104_V	2.576	1.00
105_E	142_Y	2.532	1.00
190_L	212_I	2.328	1.00
143_D	161_H	2.323	1.00
248_K	270_A	2.234	1.00
82_V	112_I	2.233	1.00
82_V	167_T	2.182	1.00
4_G	16_V	2.179	1.00
112_I	161_H	2.158	1.00
18_D	50_Y	2.139	1.00
29_C	33_G	2.115	1.00
80_Q	165_K	2.087	1.00
116_T	149_S	2.058	1.00
260_L	285_V	2.054	1.00
79_D	165_K	1.986	1.00
82_V	114_C	1.972	1.00
82_V	169_F	1.970	1.00
98_D	283_H	1.963	1.00
29_C	58_G	1.953	1.00
75_I	220_A	1.940	1.00
67_T	79_D	1.938	1.00
258_L	261_K	1.895	1.00
15_Y	28_Q	1.876	1.00
81_A	168_V	1.834	1.00
8_K	210_E	1.811	1.00
135_E	138_R	1.796	1.00
149_S	179_S	1.786	1.00
281_Y	285_V	1.784	1.00
266_A	270_A	1.699	1.00
16_V	50_Y	1.681	1.00
248_K	276_L	1.680	1.00
151_D	154_S	1.672	1.00
78_V	168_V	1.671	1.00
3_E	49_V	1.646	1.00
159_I	215_S	1.643	1.00
81_A	109_I	1.637	1.00
6_I	42_P	1.607	1.00
134_A	138_R	1.607	1.00
3_E	47_Y	1.605	1.00
260_L	288_M	1.583	1.00
106_A	237_E	1.567	1.00
27_I	50_Y	1.563	1.00
266_A	269_Q	1.545	1.00
268_K	272_E	1.533	1.00
145_Y	161_H	1.486	1.00
169_F	219_V	1.484	1.00
18_D	25_K	1.472	1.00
103_L	228_L	1.461	1.00
135_E	139_N	1.452	1.00
271_V	281_Y	1.450	1.00
6_I	16_V	1.443	1.00
89_Q	200_G	1.426	1.00
14_Y	60_L	1.419	1.00
244_D	280_R	1.410	1.00
98_D	137_Y	1.407	1.00
193_N	203_K	1.406	1.00
154_S	157_D	1.404	1.00
245_I	249_S	1.396	1.00
182_N	192_T	1.388	1.00
110_Q	165_K	1.384	1.00
85_F	97_L	1.368	1.00
190_L	208_H	1.359	1.00
148_S	179_S	1.352	1.00
213_H	218_L	1.347	1.00
5_K	166_T	1.343	1.00
251_S	266_A	1.333	1.00
80_Q	112_I	1.324	1.00
289_T	293_D	1.312	1.00
70_L	109_I	1.306	1.00
131_Q	134_A	1.301	1.00
136_D	277_K	1.294	1.00
97_L	113_I	1.284	1.00
80_Q	162_F	1.273	1.00
248_K	266_A	1.269	1.00
152_Q	183_A	1.258	1.00
42_P	63_I	1.252	1.00
131_Q	135_E	1.250	1.00
185_S	188_L	1.249	1.00
179_S	192_T	1.242	1.00
47_Y	67_T	1.239	1.00
95_A	283_H	1.236	1.00
245_I	248_K	1.235	1.00
157_D	160_P	1.232	1.00
16_V	29_C	1.222	1.00
122_E	125_D	1.222	1.00
8_K	15_Y	1.218	1.00
7_I	17_L	1.217	1.00
86_S	89_Q	1.214	1.00
234_E	237_E	1.211	1.00
30_R	33_G	1.195	1.00
87_A	118_M	1.185	1.00
258_L	288_M	1.183	1.00
82_V	158_I	1.179	1.00
104_V	111_P	1.175	1.00
105_E	243_P	1.175	1.00
156_A	159_I	1.173	1.00
114_C	158_I	1.157	1.00
50_Y	58_G	1.153	1.00
148_S	154_S	1.133	1.00
181_L	219_V	1.127	1.00
25_K	29_C	1.126	1.00
238_L	288_M	1.112	1.00
239_G	245_I	1.105	1.00
269_Q	272_E	1.104	1.00
178_S	190_L	1.092	1.00
29_C	32_R	1.083	1.00
68_N	79_D	1.076	1.00
86_S	175_V	1.072	0.99
244_D	276_L	1.062	0.99
270_A	275_E	1.053	0.99
95_A	286_E	1.052	0.99
118_M	146_L	1.051	0.99
101_L	142_Y	1.049	0.99
43_L	69_E	1.044	0.99
284_Y	288_M	1.037	0.99
248_K	275_E	1.036	0.99
15_Y	26_V	1.034	0.99
268_K	281_Y	1.033	0.99
28_Q	33_G	1.030	0.99
162_F	167_T	1.028	0.99
182_N	190_L	1.022	0.99
160_P	163_Q	1.017	0.99
4_G	50_Y	1.015	0.99
233_I	238_L	1.015	0.99
84_V	116_T	1.010	0.99
89_Q	195_I	1.004	0.99
279_Y	283_H	1.003	0.99
249_S	267_V	0.999	0.99
80_Q	161_H	0.997	0.99
272_E	278_Q	0.997	0.99
102_V	242_F	0.996	0.99
82_V	162_F	0.988	0.99
17_L	26_V	0.988	0.99
164_D	216_G	0.985	0.99
186_P	189_G	0.982	0.99
134_A	146_L	0.981	0.99
254_F	263_P	0.976	0.99
26_V	33_G	0.968	0.99
86_S	92_F	0.967	0.99
18_D	27_I	0.966	0.99
86_S	195_I	0.962	0.99
155_L	159_I	0.960	0.99
163_Q	216_G	0.958	0.99
105_E	246_R	0.952	0.99
147_T	179_S	0.952	0.99
47_Y	166_T	0.951	0.99
267_V	281_Y	0.948	0.99
48_V	60_L	0.942	0.99
4_G	58_G	0.937	0.99
68_N	78_V	0.935	0.99
100_F	170_A	0.929	0.99
8_K	208_H	0.928	0.99
4_G	29_C	0.928	0.99
80_Q	110_Q	0.924	0.98
136_D	279_Y	0.921	0.98
74_P	209_V	0.921	0.98
116_T	180_L	0.918	0.98
238_L	291_I	0.915	0.98
149_S	183_A	0.913	0.98
168_V	222_T	0.908	0.98
84_V	180_L	0.905	0.98
94_T	133_Y	0.899	0.98
250_S	266_A	0.893	0.98
143_D	157_D	0.891	0.98
271_V	278_Q	0.887	0.98
4_G	18_D	0.886	0.98
88_V	91_S	0.886	0.98
250_S	267_V	0.880	0.98
112_I	145_Y	0.870	0.98
17_L	218_L	0.870	0.98
155_L	183_A	0.865	0.98
19_E	24_D	0.863	0.98
82_V	161_H	0.863	0.98
246_R	249_S	0.863	0.98
130_I	134_A	0.859	0.98
102_V	241_T	0.856	0.98
211_L	218_L	0.851	0.97
51_Q	59_Y	0.850	0.97
118_M	153_D	0.847	0.97
95_A	99_R	0.843	0.97
92_F	172_Q	0.841	0.97
7_I	26_V	0.841	0.97
283_H	287_F	0.837	0.97
114_C	147_T	0.836	0.97
71_I	231_T	0.836	0.97
131_Q	146_L	0.834	0.97
242_F	283_H	0.827	0.97
70_L	168_V	0.826	0.97
138_R	143_D	0.821	0.97
99_R	290_E	0.817	0.97
106_A	241_T	0.817	0.97
270_A	276_L	0.817	0.97
86_S	90_P	0.815	0.97
27_I	52_A	0.813	0.97
121_I	125_D	0.810	0.97
245_I	267_V	0.810	0.97
261_K	268_K	0.810	0.97
116_T	147_T	0.809	0.97
169_F	180_L	0.808	0.96
86_S	172_Q	0.801	0.96
95_A	201_R	0.794	0.96
97_L	133_Y	0.785	0.96
155_L	180_L	0.785	0.96
89_Q	197_E	0.784	0.96
253_K	263_P	0.783	0.96
195_I	199_L	0.782	0.96
114_C	145_Y	0.780	0.96
145_Y	157_D	0.780	0.96
96_L	172_Q	0.780	0.96
48_V	63_I	0.777	0.96
245_I	276_L	0.776	0.96
53_E	57_E	0.772	0.95
235_E	292_K	0.770	0.95
162_F	217_G	0.767	0.95
282_D	285_V	0.766	0.95
132_A	136_D	0.766	0.95
87_A	121_I	0.763	0.95
93_S	201_R	0.755	0.95
237_E	240_Y	0.750	0.95
262_E	268_K	0.750	0.95
245_I	250_S	0.749	0.95
113_I	142_Y	0.740	0.94
136_D	139_N	0.738	0.94
53_E	56_K	0.733	0.94
209_V	220_A	0.733	0.94
260_L	289_T	0.733	0.94
240_Y	246_R	0.733	0.94
83_L	170_A	0.728	0.94
85_F	172_Q	0.727	0.94
95_A	279_Y	0.726	0.94
260_L	268_K	0.725	0.94
92_F	133_Y	0.724	0.94
152_Q	155_L	0.724	0.94
113_I	137_Y	0.721	0.94
93_S	172_Q	0.718	0.93
19_E	47_Y	0.717	0.93
147_T	180_L	0.714	0.93
28_Q	31_G	0.706	0.93
230_F	291_I	0.704	0.93
101_L	243_P	0.703	0.93
88_V	121_I	0.702	0.93
134_A	144_V	0.699	0.92
285_V	288_M	0.699	0.92
101_L	105_E	0.697	0.92
138_R	146_L	0.697	0.92
166_T	218_L	0.695	0.92
113_I	144_V	0.695	0.92
31_G	42_P	0.694	0.92
264_K	268_K	0.694	0.92
5_K	218_L	0.686	0.92
230_F	287_F	0.684	0.92
24_D	33_G	0.682	0.91
131_Q	138_R	0.679	0.91
132_A	135_E	0.679	0.91
99_R	204_H	0.679	0.91
239_G	246_R	0.678	0.91
238_L	287_F	0.676	0.91
149_S	154_S	0.675	0.91
237_E	241_T	0.675	0.91
214_T	217_G	0.674	0.91
167_T	217_G	0.672	0.91
70_L	104_V	0.671	0.91
90_P	200_G	0.670	0.91
19_E	25_K	0.669	0.91
43_L	76_C	0.666	0.91
108_D	237_E	0.666	0.91
110_Q	243_P	0.664	0.90
78_V	109_I	0.663	0.90
102_V	291_I	0.663	0.90
28_Q	57_E	0.661	0.90
87_A	146_L	0.660	0.90
246_R	250_S	0.659	0.90
105_E	141_G	0.659	0.90
199_L	283_H	0.658	0.90
240_Y	249_S	0.657	0.90
13_F	30_R	0.654	0.90
153_D	156_A	0.654	0.90
260_L	292_K	0.653	0.90
54_N	57_E	0.652	0.90
271_V	276_L	0.650	0.89
133_Y	137_Y	0.647	0.89
94_T	279_Y	0.646	0.89
31_G	41_T	0.646	0.89
115_I	118_M	0.646	0.89
195_I	200_G	0.644	0.89
108_D	112_I	0.641	0.89
213_H	217_G	0.636	0.88
150_K	154_S	0.635	0.88
28_Q	32_R	0.635	0.88
116_T	148_S	0.630	0.88
148_S	155_L	0.629	0.88
114_C	227_S	0.623	0.87
88_V	125_D	0.620	0.87
73_P	225_F	0.619	0.87
33_G	262_E	0.619	0.87
13_F	28_Q	0.619	0.87
247_E	250_S	0.618	0.87
154_S	183_A	0.615	0.87
159_I	184_I	0.615	0.87
85_F	96_L	0.614	0.87
281_Y	284_Y	0.614	0.87
243_P	248_K	0.614	0.87
140_I	244_D	0.613	0.87
102_V	287_F	0.613	0.87
24_D	29_C	0.612	0.86
75_I	78_V	0.611	0.86
185_S	189_G	0.611	0.86
201_R	222_T	0.609	0.86
10_L	13_F	0.605	0.86
166_T	211_L	0.605	0.86
197_E	200_G	0.604	0.86
17_L	24_D	0.604	0.86
96_L	209_V	0.603	0.86
172_Q	175_V	0.603	0.86
156_A	160_P	0.601	0.85
181_L	212_I	0.601	0.85
188_L	212_I	0.601	0.85
9_A	13_F	0.598	0.85
121_I	124_Q	0.597	0.85
142_Y	243_P	0.597	0.85
99_R	226_S	0.595	0.85
148_S	183_A	0.592	0.85
260_L	271_V	0.590	0.84
124_Q	146_L	0.588	0.84
288_M	292_K	0.587	0.84
186_P	190_L	0.587	0.84
100_F	228_L	0.586	0.84
11_S	209_V	0.586	0.84
100_F	207_R	0.585	0.84
254_F	264_K	0.585	0.84
91_S	172_Q	0.584	0.84
96_L	256_G	0.583	0.84
115_I	144_V	0.583	0.84
9_A	14_Y	0.582	0.84
103_L	287_F	0.582	0.84
99_R	182_N	0.581	0.84
101_L	111_P	0.578	0.83
47_Y	64_K	0.577	0.83
86_S	116_T	0.577	0.83
68_N	107_N	0.576	0.83
199_L	226_S	0.575	0.83
175_V	179_S	0.574	0.83
16_V	60_L	0.571	0.82
190_L	207_R	0.570	0.82
233_I	241_T	0.567	0.82
43_L	225_F	0.563	0.82
148_S	151_D	0.562	0.81
145_Y	162_F	0.562	0.81
152_Q	157_D	0.562	0.81
235_E	288_M	0.560	0.81
238_L	284_Y	0.560	0.81
136_D	140_I	0.560	0.81
164_D	215_S	0.559	0.81
75_I	168_V	0.559	0.81
73_P	226_S	0.555	0.81
18_D	24_D	0.555	0.81
182_N	189_G	0.554	0.81
163_Q	215_S	0.553	0.80
195_I	204_H	0.552	0.80
248_K	271_V	0.551	0.80
269_Q	275_E	0.550	0.80
67_T	215_S	0.550	0.80
248_K	251_S	0.550	0.80
258_L	262_E	0.550	0.80
116_T	179_S	0.550	0.80
52_A	58_G	0.550	0.80
151_D	156_A	0.548	0.80
147_T	154_S	0.546	0.80
103_L	242_F	0.546	0.80
105_E	111_P	0.544	0.79
239_G	249_S	0.541	0.79
5_K	17_L	0.541	0.79
27_I	56_K	0.541	0.79
9_A	12_G	0.539	0.79
118_M	130_I	0.539	0.79
158_I	161_H	0.538	0.79
41_T	63_I	0.535	0.78
25_K	33_G	0.534	0.78
201_R	226_S	0.534	0.78
182_N	212_I	0.534	0.78
10_L	15_Y	0.534	0.78
282_D	286_E	0.533	0.78
209_V	225_F	0.532	0.78
42_P	97_L	0.532	0.78
100_F	172_Q	0.531	0.78
158_I	184_I	0.526	0.77
285_V	289_T	0.525	0.77
184_I	214_T	0.522	0.77
85_F	92_F	0.522	0.77
116_T	222_T	0.521	0.76
201_R	207_R	0.520	0.76
149_S	155_L	0.517	0.76
70_L	200_G	0.515	0.76
14_Y	208_H	0.515	0.76
70_L	218_L	0.513	0.75
26_V	29_C	0.513	0.75
119_D	164_D	0.513	0.75
262_E	267_V	0.512	0.75
243_P	247_E	0.512	0.75
32_R	61_M	0.511	0.75
108_D	240_Y	0.510	0.75
288_M	291_I	0.509	0.75
159_I	163_Q	0.509	0.75
110_Q	141_G	0.506	0.74
94_T	137_Y	0.505	0.74
73_P	207_R	0.503	0.74
268_K	285_V	0.500	0.73

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
1t9hA	1	0.9362	100	0.298	Contact Map
2rcnA	2	0.896	100	0.299	Contact Map
1u0lA	1	0.9228	100	0.323	Contact Map
2yv5A	1	0.9463	100	0.339	Contact Map
3cnlA	1	0.651	99.9	0.783	Contact Map
3ec1A	1	0.7383	99.9	0.784	Contact Map
1pujA	1	0.6812	99.9	0.788	Contact Map
3h2yA	1	0.7517	99.9	0.794	Contact Map
4tmxA	1	0.8557	99.7	0.825	Contact Map
4dcuA	1	0.8121	99.7	0.826	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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