RDOA - ECOLI - GREMLIN Contacts

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RDOA - Protein RdoA

UniProt:	P0C0K3	Sequences: MNNSAFTFQTLHPDTIMDALFEHGIRVDSGLTPLNSYENRVYQFQDEDRRRFVVKFYRPERWTADQILEEHQFALQLVNDEVPVAAPVAFNGQTLLNHQGFYFAVFPSVGGRQFEADNIDQMEAVGRYLGRMHQTGRKQLFIHRPTIGLNEYLIEPRKLFEDATLIPSGLKAAFLKATDELIAAVTAHWREDFTVLRLHGDCHAGNILWRDGPMFVDLDDARNGPAVQDLWMLLNGDKAEQRMQLETIIEAYEEFSEFDTAEIGLIEPLRAMRLVYYLAWLMRRWADPAFPKNFPWLTGEDYWLRQTATFIEQAKVLQEPPLQLTPMY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11831
Length:	328 (274)
Sequences:	7242 (5536)
Seq/√Len:	334.4

ECOLI - RDOA
BACSU - YERI COTS COTI YSXE

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
43_Q	51_R	3.635	1.00
86_A	107_P	3.599	1.00
126_G	251_A	3.162	1.00
45_Q	51_R	3.155	1.00
123_E	251_A	3.081	1.00
88_V	107_P	3.040	1.00
43_Q	108_S	2.979	1.00
109_V	214_M	2.909	1.00
124_A	127_R	2.783	1.00
127_R	251_A	2.717	1.00
131_R	255_F	2.673	1.00
127_R	254_E	2.663	1.00
53_V	108_S	2.560	1.00
184_A	188_H	2.533	1.00
32_T	43_Q	2.368	1.00
129_L	202_C	2.345	1.00
130_G	255_F	2.323	1.00
54_V	105_V	2.310	1.00
30_G	45_Q	2.292	1.00
78_V	86_A	2.262	1.00
51_R	108_S	2.257	1.00
198_L	224_G	2.251	1.00
196_L	226_A	2.220	1.00
127_R	255_F	2.185	1.00
74_A	87_P	2.168	1.00
233_L	248_I	2.115	1.00
123_E	250_E	2.086	1.00
134_Q	256_S	2.018	1.00
208_L	216_V	1.974	1.00
51_R	110_G	1.963	1.00
177_A	180_E	1.948	1.00
170_L	173_A	1.892	1.00
46_D	52_F	1.868	1.00
154_I	158_K	1.866	1.00
128_Y	215_F	1.855	1.00
123_E	254_E	1.851	1.00
125_V	207_I	1.850	1.00
133_H	252_Y	1.829	1.00
75_L	89_A	1.784	1.00
76_Q	139_Q	1.775	1.00
126_G	248_I	1.770	1.00
80_D	138_K	1.767	1.00
183_A	187_A	1.750	1.00
44_F	105_V	1.743	1.00
202_C	215_F	1.730	1.00
246_E	250_E	1.724	1.00
113_Q	208_L	1.715	1.00
167_P	170_L	1.698	1.00
17_M	21_F	1.673	1.00
71_H	87_P	1.666	1.00
124_A	212_G	1.650	1.00
127_R	131_R	1.628	1.00
81_E	131_R	1.607	1.00
251_A	254_E	1.604	1.00
253_E	263_I	1.602	1.00
130_G	256_S	1.593	1.00
52_F	88_V	1.576	1.00
32_T	45_Q	1.560	1.00
134_Q	255_F	1.551	1.00
119_I	247_T	1.533	1.00
46_D	50_R	1.520	1.00
68_L	72_Q	1.519	1.00
259_D	262_E	1.503	1.00
73_F	221_A	1.478	1.00
123_E	126_G	1.477	1.00
56_F	101_F	1.472	1.00
20_L	105_V	1.426	1.00
244_Q	247_T	1.412	1.00
250_E	254_E	1.411	1.00
164_T	168_S	1.409	1.00
136_G	139_Q	1.406	1.00
34_L	53_V	1.390	1.00
231_W	270_R	1.374	1.00
230_L	249_I	1.360	1.00
179_D	183_A	1.356	1.00
31_L	44_F	1.349	1.00
74_A	218_L	1.335	1.00
110_G	210_R	1.326	1.00
123_E	127_R	1.326	1.00
19_A	89_A	1.321	1.00
283_R	287_D	1.313	1.00
171_K	175_L	1.307	1.00
50_R	107_P	1.304	1.00
109_V	213_P	1.301	1.00
247_T	251_A	1.299	1.00
147_I	151_E	1.296	1.00
38_E	219_D	1.293	1.00
132_M	215_F	1.288	1.00
13_P	17_M	1.278	1.00
230_L	248_I	1.247	1.00
148_G	151_E	1.246	1.00
64_A	102_Y	1.241	1.00
128_Y	131_R	1.220	1.00
156_P	160_F	1.197	1.00
12_H	15_T	1.190	1.00
170_L	174_F	1.187	1.00
124_A	128_Y	1.179	1.00
71_H	94_T	1.178	1.00
14_D	17_M	1.174	1.00
78_V	87_P	1.170	1.00
138_K	144_R	1.168	1.00
74_A	85_A	1.149	1.00
125_V	233_L	1.144	1.00
120_D	123_E	1.139	1.00
76_Q	138_K	1.131	1.00
15_T	18_D	1.116	1.00
39_N	55_K	1.112	1.00
56_F	103_F	1.112	1.00
54_V	103_F	1.107	1.00
234_L	245_L	1.103	1.00
281_L	284_R	1.102	1.00
55_K	70_E	1.099	1.00
75_L	79_N	1.094	1.00
154_I	186_T	1.090	1.00
277_Y	280_W	1.086	1.00
210_R	213_P	1.079	1.00
41_V	53_V	1.068	1.00
123_E	247_T	1.067	1.00
251_A	255_F	1.067	1.00
135_T	140_L	1.061	1.00
89_A	94_T	1.059	1.00
194_T	262_E	1.056	1.00
194_T	226_A	1.043	1.00
175_L	179_D	1.043	1.00
75_L	87_P	1.040	1.00
129_L	133_H	1.037	1.00
109_V	208_L	1.036	1.00
67_I	70_E	1.031	1.00
182_I	186_T	1.029	1.00
82_V	132_M	1.026	1.00
281_L	285_W	1.022	1.00
277_Y	281_L	1.018	1.00
181_L	184_A	1.016	1.00
164_T	167_P	1.014	1.00
29_S	47_E	1.010	1.00
90_F	93_Q	1.004	1.00
201_D	206_N	1.000	1.00
133_H	229_D	0.996	1.00
43_Q	53_V	0.993	1.00
122_M	243_M	0.981	1.00
72_Q	75_L	0.979	1.00
46_D	49_R	0.977	1.00
250_E	253_E	0.977	1.00
247_T	250_E	0.974	1.00
208_L	213_P	0.972	1.00
71_H	104_A	0.972	1.00
137_R	256_S	0.971	1.00
166_I	171_K	0.970	1.00
18_D	22_E	0.970	1.00
194_T	258_F	0.970	1.00
178_T	182_I	0.961	1.00
249_I	253_E	0.954	1.00
253_E	257_E	0.947	1.00
180_E	183_A	0.944	1.00
194_T	256_S	0.944	1.00
128_Y	212_G	0.942	1.00
166_I	170_L	0.927	1.00
76_Q	135_T	0.922	1.00
245_L	267_E	0.922	1.00
125_V	202_C	0.917	1.00
279_A	282_M	0.916	1.00
176_K	180_E	0.913	1.00
13_P	31_L	0.902	1.00
40_R	56_F	0.901	1.00
85_A	214_M	0.898	1.00
29_S	44_F	0.897	1.00
126_G	130_G	0.896	1.00
276_Y	280_W	0.895	1.00
121_Q	209_W	0.889	1.00
184_A	268_P	0.888	1.00
280_W	284_R	0.887	1.00
118_N	121_Q	0.885	1.00
249_I	263_I	0.884	1.00
145_P	148_G	0.880	1.00
276_Y	279_A	0.880	1.00
68_L	90_F	0.879	1.00
82_V	128_Y	0.878	1.00
195_V	223_N	0.873	1.00
64_A	68_L	0.873	1.00
146_T	151_E	0.872	1.00
181_L	185_V	0.869	1.00
157_R	161_E	0.856	1.00
72_Q	139_Q	0.856	1.00
73_F	136_G	0.854	1.00
25_I	28_D	0.850	1.00
115_E	205_G	0.848	1.00
166_I	174_F	0.848	1.00
201_D	217_D	0.847	1.00
166_I	169_G	0.847	1.00
71_H	75_L	0.846	1.00
282_M	286_A	0.845	1.00
278_L	281_L	0.845	1.00
39_N	219_D	0.844	1.00
243_M	247_T	0.842	1.00
241_Q	244_Q	0.839	1.00
33_P	40_R	0.838	1.00
63_T	66_Q	0.836	1.00
278_L	282_M	0.835	1.00
206_N	217_D	0.834	1.00
192_D	261_A	0.834	1.00
150_N	155_E	0.833	1.00
52_F	105_V	0.830	1.00
137_R	197_R	0.823	1.00
152_Y	156_P	0.819	1.00
110_G	211_D	0.819	1.00
200_G	222_R	0.818	1.00
47_E	50_R	0.817	1.00
18_D	21_F	0.816	1.00
87_P	107_P	0.815	1.00
122_M	126_G	0.814	1.00
128_Y	202_C	0.803	1.00
226_A	256_S	0.800	1.00
186_T	189_W	0.795	1.00
153_L	156_P	0.791	1.00
281_L	289_A	0.790	1.00
209_W	213_P	0.789	1.00
36_S	40_R	0.788	1.00
171_K	174_F	0.781	1.00
146_T	149_L	0.780	1.00
122_M	244_Q	0.778	1.00
150_N	154_I	0.776	1.00
75_L	86_A	0.775	1.00
203_H	235_N	0.775	1.00
130_G	134_Q	0.772	1.00
196_L	256_S	0.771	1.00
169_G	174_F	0.770	1.00
172_A	176_K	0.769	1.00
21_F	26_R	0.757	1.00
184_A	187_A	0.756	1.00
87_P	90_F	0.755	1.00
169_G	172_A	0.754	1.00
154_I	157_R	0.749	0.99
269_L	273_R	0.746	0.99
80_D	135_T	0.744	0.99
41_V	203_H	0.744	0.99
25_I	105_V	0.742	0.99
157_R	179_D	0.741	0.99
172_A	175_L	0.736	0.99
199_H	202_C	0.731	0.99
232_M	235_N	0.730	0.99
129_L	200_G	0.723	0.99
121_Q	124_A	0.723	0.99
39_N	70_E	0.722	0.99
176_K	179_D	0.719	0.99
165_L	169_G	0.719	0.99
28_D	46_D	0.719	0.99
76_Q	79_N	0.717	0.99
126_G	233_L	0.716	0.99
259_D	263_I	0.709	0.99
161_E	164_T	0.709	0.99
40_R	101_F	0.702	0.99
73_F	197_R	0.702	0.99
129_L	229_D	0.700	0.99
137_R	140_L	0.699	0.99
14_D	18_D	0.698	0.99
111_G	211_D	0.698	0.99
37_Y	41_V	0.694	0.99
131_R	134_Q	0.690	0.99
135_T	139_Q	0.687	0.99
147_I	152_Y	0.685	0.99
65_D	68_L	0.685	0.99
70_E	74_A	0.684	0.99
149_L	153_L	0.682	0.99
151_E	155_E	0.680	0.99
240_E	243_M	0.679	0.99
183_A	186_T	0.679	0.99
206_N	219_D	0.675	0.99
222_R	228_Q	0.670	0.99
200_G	228_Q	0.668	0.99
261_A	264_G	0.667	0.99
126_G	255_F	0.667	0.99
144_R	148_G	0.665	0.99
146_T	150_N	0.662	0.99
75_L	94_T	0.662	0.99
161_E	182_I	0.661	0.99
132_M	218_L	0.661	0.99
173_A	176_K	0.661	0.99
155_E	159_L	0.656	0.99
146_T	221_A	0.654	0.99
203_H	220_D	0.653	0.99
114_F	207_I	0.651	0.99
153_L	182_I	0.649	0.99
167_P	172_A	0.647	0.99
143_H	146_T	0.646	0.99
182_I	272_M	0.645	0.98
17_M	28_D	0.644	0.98
120_D	124_A	0.643	0.98
15_T	99_Q	0.642	0.98
180_E	184_A	0.639	0.98
258_F	263_I	0.638	0.98
38_E	41_V	0.637	0.98
260_T	264_G	0.637	0.98
34_L	43_Q	0.634	0.98
70_E	224_G	0.634	0.98
71_H	90_F	0.632	0.98
75_L	78_V	0.632	0.98
92_G	95_L	0.625	0.98
57_Y	70_E	0.624	0.98
279_A	283_R	0.621	0.98
112_R	210_R	0.620	0.98
119_I	123_E	0.618	0.98
82_V	135_T	0.615	0.98
55_K	219_D	0.615	0.98
21_F	27_V	0.615	0.98
70_E	219_D	0.615	0.98
63_T	70_E	0.614	0.98
279_A	284_R	0.614	0.98
136_G	140_L	0.614	0.98
20_L	23_H	0.613	0.98
145_P	150_N	0.612	0.98
133_H	198_L	0.612	0.98
157_R	160_F	0.610	0.98
26_R	46_D	0.609	0.98
72_Q	142_I	0.609	0.98
245_L	249_I	0.608	0.98
287_D	290_F	0.608	0.98
145_P	149_L	0.606	0.98
24_G	47_E	0.603	0.98
165_L	168_S	0.601	0.98
112_R	208_L	0.601	0.98
168_S	172_A	0.598	0.98
258_F	262_E	0.596	0.97
57_Y	104_A	0.592	0.97
57_Y	67_I	0.590	0.97
68_L	93_Q	0.590	0.97
130_G	251_A	0.589	0.97
148_G	156_P	0.588	0.97
148_G	152_Y	0.587	0.97
144_R	147_I	0.586	0.97
37_Y	215_F	0.585	0.97
38_E	58_R	0.585	0.97
207_I	212_G	0.583	0.97
145_P	151_E	0.582	0.97
90_F	102_Y	0.581	0.97
83_P	128_Y	0.581	0.97
209_W	212_G	0.579	0.97
41_V	280_W	0.575	0.97
167_P	171_K	0.574	0.97
58_R	101_F	0.574	0.97
267_E	271_A	0.573	0.97
20_L	44_F	0.572	0.97
231_W	269_L	0.571	0.97
185_V	188_H	0.570	0.97
23_H	90_F	0.569	0.97
92_G	99_Q	0.569	0.97
12_H	18_D	0.569	0.97
285_W	289_A	0.568	0.97
207_I	216_V	0.566	0.97
248_I	252_Y	0.566	0.97
212_G	215_F	0.564	0.97
85_A	106_F	0.564	0.97
139_Q	142_I	0.563	0.96
274_L	277_Y	0.561	0.96
265_L	269_L	0.561	0.96
76_Q	80_D	0.561	0.96
197_R	223_N	0.560	0.96
16_I	19_A	0.559	0.96
152_Y	157_R	0.556	0.96
227_V	258_F	0.554	0.96
168_S	171_K	0.552	0.96
133_H	136_G	0.551	0.96
72_Q	145_P	0.550	0.96
85_A	107_P	0.549	0.96
234_L	267_E	0.544	0.96
134_Q	137_R	0.544	0.96
186_T	190_R	0.544	0.96
146_T	155_E	0.542	0.96
55_K	203_H	0.542	0.96
226_A	262_E	0.540	0.96
277_Y	284_R	0.540	0.96
85_A	109_V	0.538	0.95
193_F	225_P	0.538	0.95
231_W	267_E	0.537	0.95
74_A	106_F	0.535	0.95
234_L	263_I	0.535	0.95
44_F	54_V	0.534	0.95
19_A	103_F	0.534	0.95
252_Y	256_S	0.534	0.95
41_V	220_D	0.533	0.95
25_I	46_D	0.533	0.95
156_P	159_L	0.529	0.95
265_L	268_P	0.527	0.95
69_E	142_I	0.525	0.95
58_R	220_D	0.524	0.95
39_N	57_Y	0.523	0.95
29_S	45_Q	0.521	0.95
15_T	19_A	0.518	0.94
38_E	220_D	0.518	0.94
195_V	225_P	0.518	0.94
161_E	175_L	0.517	0.94
27_V	47_E	0.517	0.94
169_G	173_A	0.514	0.94
220_D	273_R	0.513	0.94
137_R	194_T	0.512	0.94
23_H	26_R	0.511	0.94
200_G	224_G	0.510	0.94
26_R	47_E	0.510	0.94
220_D	232_M	0.510	0.94
146_T	152_Y	0.509	0.94
23_H	28_D	0.508	0.94
125_V	248_I	0.508	0.94
41_V	67_I	0.507	0.94
55_K	231_W	0.506	0.94
83_P	212_G	0.506	0.94
235_N	270_R	0.504	0.94
82_V	131_R	0.504	0.94
276_Y	281_L	0.503	0.94
188_H	268_P	0.502	0.93
150_N	153_L	0.501	0.93
165_L	174_F	0.501	0.93
39_N	53_V	0.500	0.93

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
1zylA	1	0.9909	100	0.314	Contact Map
2ppqA	2	0.9085	100	0.425	Contact Map
4pdyA	1	0.9177	100	0.438	Contact Map
2q83A	1	0.8963	100	0.448	Contact Map
4ocvA	1	0.936	100	0.463	Contact Map
3dxpA	2	0.8963	100	0.518	Contact Map
3i1aA	1	0.9146	100	0.522	Contact Map
3csvA	2	0.8811	100	0.543	Contact Map
3atsA	1	0.9024	100	0.548	Contact Map
1nw1A	2	0.9207	100	0.556	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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