RBSB - BACSU - GREMLIN Contacts

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RBSB - D-ribose-binding protein

UniProt:	P36949	Sequences: MKKAVSVILTLSLFLLTACSLEPPQWAKPSNSGNKKEFTIGLSVSTLNNPFFVSLKKGIEKEAKKRGMKVIIVDAQNDSSKQTSDVEDLIQQGVDALLINPTDSSAISTAVESANAVGVPVVTIDRSAEQGKVETLVASDNVKGGEMAAAFIADKLGKGAKVAELEGVPGASATRERGSGFHNIADQKLQVVTKQSADFDRTKGLTVMENLLQGHPDIQAVFAHNDEMALGALEAINSSGKDILVIGFDGNKDALASIKDRKLSATVAQQPELIGKLATEAADDILHGKKVQKTISAPLKLETQK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (278)
Sequences:	38741 (28944)
Seq/√Len:	1735.9

ECOLI - RBSB XYLF ALSB LSRB YTFQ DGAL TORT MALI CYTR GALS LACI GALR CRA IDNR PURR YCJW ASCG GNTR YPHF RBSR ARAF TRER EBGR XYLR
BACSU - RBSB KDGR CCPA RBSR NTDR DEGA MSMR YKVZ ARAR EXUR YVDE GANR CCPB

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
142_V	183_N	3.417	1.00
159_G	219_Q	3.166	1.00
96_A	282_A	2.827	1.00
178_G	182_H	2.690	1.00
148_A	246_I	2.640	1.00
159_G	244_L	2.577	1.00
250_G	268_A	2.572	1.00
135_T	285_I	2.460	1.00
146_E	187_Q	2.349	1.00
209_E	239_S	2.314	1.00
62_E	65_K	2.287	1.00
205_L	238_S	2.272	1.00
150_A	184_I	2.251	1.00
209_E	235_A	2.173	1.00
146_E	184_I	2.169	1.00
62_E	280_E	2.167	1.00
146_E	183_N	2.165	1.00
143_K	147_M	2.147	1.00
277_L	280_E	2.070	1.00
152_I	220_A	2.052	1.00
142_V	179_S	2.022	1.00
62_E	276_K	2.021	1.00
63_A	279_T	2.008	1.00
16_L	20_S	1.989	1.00
144_G	248_F	1.975	1.00
145_G	149_A	1.949	1.00
284_D	289_K	1.888	1.00
58_G	275_G	1.868	1.00
151_F	155_K	1.868	1.00
149_A	181_F	1.838	1.00
41_G	94_V	1.829	1.00
163_A	218_I	1.829	1.00
204_G	231_G	1.818	1.00
145_G	222_F	1.799	1.00
223_A	232_A	1.782	1.00
61_K	272_E	1.761	1.00
164_E	224_H	1.758	1.00
268_A	300_K	1.751	1.00
213_Q	239_S	1.742	1.00
146_E	150_A	1.729	1.00
150_A	154_D	1.727	1.00
208_M	232_A	1.721	1.00
205_L	235_A	1.719	1.00
236_I	243_I	1.710	1.00
270_Q	273_L	1.692	1.00
235_A	239_S	1.673	1.00
62_E	66_R	1.667	1.00
124_I	278_A	1.660	1.00
151_F	154_D	1.648	1.00
143_K	146_E	1.642	1.00
237_N	260_D	1.636	1.00
58_G	272_E	1.625	1.00
179_S	183_N	1.610	1.00
161_K	217_D	1.572	1.00
147_M	299_L	1.540	1.00
153_A	184_I	1.533	1.00
66_R	283_D	1.530	1.00
38_F	95_D	1.520	1.00
283_D	287_H	1.519	1.00
182_H	186_D	1.514	1.00
235_A	238_S	1.512	1.00
205_L	234_E	1.510	1.00
184_I	187_Q	1.505	1.00
176_E	179_S	1.496	1.00
273_L	277_L	1.477	1.00
277_L	295_I	1.461	1.00
198_D	203_K	1.433	1.00
161_K	219_Q	1.418	1.00
273_L	276_K	1.408	1.00
62_E	279_T	1.397	1.00
140_D	143_K	1.394	1.00
205_L	209_E	1.377	1.00
161_K	190_Q	1.363	1.00
195_Q	210_N	1.363	1.00
163_A	211_L	1.359	1.00
145_G	180_G	1.359	1.00
161_K	192_V	1.357	1.00
149_A	153_A	1.355	1.00
142_V	146_E	1.345	1.00
208_M	236_I	1.337	1.00
149_A	184_I	1.323	1.00
209_E	213_Q	1.318	1.00
147_M	150_A	1.318	1.00
98_L	278_A	1.305	1.00
209_E	238_S	1.303	1.00
180_G	184_I	1.298	1.00
149_A	180_G	1.290	1.00
41_G	89_L	1.288	1.00
237_N	262_K	1.284	1.00
160_A	219_Q	1.282	1.00
73_V	85_D	1.279	1.00
38_F	68_M	1.275	1.00
280_E	284_D	1.274	1.00
63_A	70_V	1.269	1.00
16_L	19_C	1.269	1.00
39_T	69_K	1.268	1.00
112_E	116_A	1.268	1.00
144_G	299_L	1.264	1.00
87_E	113_S	1.254	1.00
73_V	89_L	1.251	1.00
272_E	276_K	1.236	1.00
39_T	71_I	1.234	1.00
59_I	279_T	1.229	1.00
159_G	220_A	1.210	1.00
66_R	280_E	1.203	1.00
17_T	21_L	1.189	1.00
215_H	218_I	1.186	1.00
42_L	59_I	1.184	1.00
208_M	221_V	1.174	1.00
40_I	63_A	1.173	1.00
142_V	180_G	1.165	1.00
164_E	178_G	1.159	1.00
60_E	64_K	1.159	1.00
202_T	206_T	1.158	1.00
231_G	235_A	1.147	1.00
200_D	203_K	1.145	1.00
210_N	214_G	1.145	1.00
142_V	176_E	1.143	1.00
233_L	245_V	1.142	1.00
150_A	187_Q	1.138	1.00
207_V	210_N	1.135	1.00
182_H	191_V	1.124	1.00
181_F	185_A	1.123	1.00
175_R	179_S	1.123	1.00
153_A	189_L	1.119	1.00
246_I	264_S	1.102	1.00
56_K	60_E	1.101	1.00
181_F	222_F	1.099	1.00
42_L	70_V	1.089	1.00
203_K	206_T	1.081	1.00
148_A	222_F	1.081	1.00
226_D	266_T	1.079	1.00
179_S	182_H	1.078	1.00
183_N	187_Q	1.078	1.00
201_R	234_E	1.077	1.00
64_K	81_K	1.076	1.00
221_V	232_A	1.074	1.00
277_L	281_A	1.072	1.00
18_A	21_L	1.068	1.00
276_K	280_E	1.066	1.00
162_V	185_A	1.061	1.00
223_A	228_M	1.051	1.00
226_D	247_G	1.049	1.00
172_S	176_E	1.047	1.00
160_A	189_L	1.046	1.00
165_L	232_A	1.043	1.00
59_I	98_L	1.039	1.00
83_T	87_E	1.036	1.00
275_G	279_T	1.035	1.00
81_K	84_S	1.033	1.00
68_M	283_D	1.024	1.00
169_P	196_S	1.016	1.00
66_R	287_H	1.015	1.00
161_K	216_P	1.014	1.00
282_A	286_L	1.014	1.00
28_K	31_N	1.010	1.00
155_K	244_L	1.010	1.00
206_T	210_N	1.003	1.00
108_S	112_E	1.000	1.00
162_V	220_A	0.998	1.00
223_A	229_A	0.996	1.00
135_T	281_A	0.995	1.00
26_W	32_S	0.993	1.00
65_K	276_K	0.990	1.00
29_P	32_S	0.988	1.00
87_E	91_Q	0.987	1.00
149_A	185_A	0.985	1.00
57_K	61_K	0.985	1.00
281_A	295_I	0.977	1.00
195_Q	207_V	0.969	1.00
204_G	208_M	0.968	1.00
148_A	267_V	0.962	1.00
167_G	199_F	0.954	1.00
17_T	20_S	0.953	1.00
208_M	212_L	0.950	1.00
51_F	271_P	0.948	1.00
151_F	264_S	0.943	1.00
143_K	298_P	0.941	1.00
98_L	282_A	0.929	1.00
233_L	259_K	0.927	1.00
221_V	243_I	0.920	1.00
78_D	81_K	0.917	1.00
61_K	65_K	0.910	1.00
206_T	209_E	0.900	1.00
153_A	160_A	0.899	1.00
40_I	98_L	0.896	1.00
55_L	124_I	0.893	1.00
229_A	247_G	0.890	1.00
141_N	177_R	0.881	1.00
277_L	297_A	0.880	1.00
96_A	286_L	0.880	1.00
59_I	275_G	0.880	1.00
155_K	159_G	0.879	1.00
234_E	237_N	0.875	1.00
163_A	221_V	0.868	1.00
166_E	178_G	0.867	1.00
61_K	276_K	0.861	1.00
236_I	245_V	0.860	1.00
203_K	207_V	0.859	1.00
281_A	284_D	0.859	1.00
270_Q	300_K	0.857	1.00
170_G	175_R	0.855	1.00
39_T	92_Q	0.853	1.00
139_S	270_Q	0.853	1.00
226_D	250_G	0.852	1.00
56_K	72_I	0.848	1.00
212_L	235_A	0.847	1.00
71_I	92_Q	0.844	1.00
136_L	294_T	0.831	1.00
71_I	94_V	0.830	1.00
279_T	283_D	0.830	1.00
84_S	87_E	0.828	1.00
152_I	246_I	0.828	1.00
197_A	228_M	0.826	1.00
19_C	22_E	0.825	1.00
139_S	269_Q	0.825	1.00
140_D	296_S	0.824	1.00
183_N	186_D	0.822	1.00
81_K	85_D	0.821	1.00
42_L	56_K	0.817	1.00
25_Q	30_S	0.813	1.00
208_M	235_A	0.805	1.00
115_N	132_K	0.805	1.00
113_S	116_A	0.799	1.00
24_P	91_Q	0.798	1.00
137_V	281_A	0.796	1.00
110_A	113_S	0.794	1.00
57_K	60_E	0.792	1.00
257_S	262_K	0.791	1.00
59_I	70_V	0.790	1.00
212_L	239_S	0.788	1.00
185_A	189_L	0.783	1.00
138_A	296_S	0.782	1.00
76_Q	81_K	0.780	1.00
45_S	52_F	0.780	1.00
185_A	191_V	0.778	1.00
153_A	185_A	0.778	1.00
58_G	276_K	0.777	1.00
139_S	299_L	0.769	1.00
43_S	85_D	0.768	1.00
58_G	62_E	0.765	1.00
143_K	299_L	0.763	1.00
164_E	222_F	0.763	1.00
27_A	30_S	0.761	1.00
127_S	294_T	0.754	1.00
165_L	223_A	0.753	1.00
54_S	272_E	0.752	1.00
96_A	122_V	0.751	1.00
256_A	260_D	0.750	1.00
208_M	211_L	0.746	1.00
98_L	124_I	0.746	1.00
138_A	294_T	0.743	1.00
114_A	121_V	0.743	1.00
146_E	180_G	0.741	1.00
247_G	266_T	0.741	1.00
90_I	117_V	0.740	1.00
176_E	180_G	0.738	1.00
210_N	213_Q	0.738	1.00
256_A	259_K	0.738	1.00
26_W	29_P	0.734	1.00
60_E	70_V	0.732	1.00
123_T	133_V	0.728	1.00
112_E	115_N	0.722	1.00
270_Q	297_A	0.720	1.00
37_E	69_K	0.717	1.00
234_E	262_K	0.714	1.00
123_T	128_A	0.712	1.00
41_G	97_L	0.711	1.00
226_D	229_A	0.711	1.00
284_D	288_G	0.707	1.00
83_T	110_A	0.706	1.00
122_V	285_I	0.706	1.00
80_S	84_S	0.703	1.00
147_M	267_V	0.703	1.00
199_F	224_H	0.703	1.00
140_D	298_P	0.702	1.00
24_P	87_E	0.701	1.00
37_E	95_D	0.701	1.00
151_F	301_L	0.700	1.00
36_K	95_D	0.696	1.00
249_D	269_Q	0.692	1.00
234_E	238_S	0.692	1.00
178_G	194_K	0.687	1.00
40_I	279_T	0.686	1.00
174_T	199_F	0.685	1.00
49_N	227_E	0.681	1.00
214_G	217_D	0.678	1.00
225_N	249_D	0.673	1.00
250_G	256_A	0.672	1.00
181_F	191_V	0.671	1.00
135_T	293_K	0.670	1.00
233_L	237_N	0.669	1.00
79_S	83_T	0.667	1.00
36_K	287_H	0.666	1.00
222_F	246_I	0.664	1.00
230_L	259_K	0.660	1.00
219_Q	244_L	0.659	1.00
125_D	173_A	0.656	1.00
244_L	264_S	0.653	1.00
123_T	136_L	0.652	1.00
164_E	181_F	0.650	1.00
204_G	207_V	0.647	1.00
40_I	96_A	0.647	1.00
63_A	68_M	0.641	1.00
225_N	228_M	0.641	1.00
167_G	174_T	0.641	1.00
90_I	119_V	0.640	1.00
162_V	219_Q	0.636	1.00
96_A	278_A	0.636	1.00
54_S	271_P	0.632	1.00
222_F	248_F	0.632	1.00
122_V	282_A	0.632	1.00
226_D	251_N	0.631	1.00
86_V	97_L	0.628	1.00
115_N	121_V	0.628	1.00
19_C	23_P	0.627	1.00
97_L	119_V	0.627	1.00
40_I	286_L	0.626	1.00
234_E	260_D	0.621	1.00
195_Q	214_G	0.620	1.00
197_A	203_K	0.620	1.00
152_I	222_F	0.614	1.00
236_I	239_S	0.614	1.00
52_F	100_N	0.607	1.00
202_T	205_L	0.607	1.00
151_F	246_I	0.606	1.00
73_V	88_D	0.605	1.00
122_V	137_V	0.605	1.00
125_D	141_N	0.604	1.00
214_G	218_I	0.604	1.00
58_G	271_P	0.604	1.00
223_A	247_G	0.601	1.00
147_M	151_F	0.601	1.00
109_T	112_E	0.600	1.00
138_A	141_N	0.598	1.00
161_K	218_I	0.598	1.00
229_A	263_L	0.598	1.00
127_S	136_L	0.596	1.00
30_S	34_N	0.593	1.00
248_F	269_Q	0.592	1.00
201_R	231_G	0.591	1.00
211_L	215_H	0.588	1.00
57_K	272_E	0.587	1.00
141_N	173_A	0.583	1.00
208_M	231_G	0.582	1.00
84_S	88_D	0.581	1.00
40_I	68_M	0.580	1.00
207_V	211_L	0.577	1.00
39_T	95_D	0.575	1.00
68_M	95_D	0.575	1.00
230_L	251_N	0.575	1.00
162_V	181_F	0.574	1.00
159_G	188_K	0.574	1.00
195_Q	211_L	0.573	1.00
60_E	74_D	0.573	1.00
113_S	117_V	0.572	1.00
161_K	215_H	0.568	1.00
141_N	176_E	0.567	1.00
122_V	281_A	0.567	1.00
174_T	224_H	0.564	1.00
39_T	94_V	0.563	1.00
150_A	153_A	0.562	1.00
232_A	236_I	0.562	1.00
51_F	55_L	0.562	1.00
109_T	113_S	0.560	1.00
83_T	113_S	0.559	1.00
85_D	88_D	0.558	1.00
148_A	220_A	0.557	1.00
38_F	286_L	0.556	1.00
55_L	271_P	0.553	1.00
177_R	269_Q	0.552	1.00
234_E	257_S	0.550	1.00
281_A	285_I	0.549	1.00
88_D	91_Q	0.549	1.00
125_D	274_I	0.546	1.00
24_P	28_K	0.544	1.00
205_L	231_G	0.544	1.00
112_E	132_K	0.541	1.00
38_F	287_H	0.539	1.00
87_E	90_I	0.539	1.00
229_A	245_V	0.539	1.00
259_K	262_K	0.538	1.00
212_L	236_I	0.538	1.00
120_P	285_I	0.538	1.00
146_E	149_A	0.538	1.00
220_A	244_L	0.537	1.00
57_K	76_Q	0.536	1.00
205_L	208_M	0.536	1.00
63_A	283_D	0.535	1.00
68_M	286_L	0.534	1.00
251_N	255_L	0.534	1.00
285_I	288_G	0.533	1.00
122_V	278_A	0.533	1.00
80_S	83_T	0.532	1.00
296_S	299_L	0.531	1.00
199_F	228_M	0.531	1.00
165_L	207_V	0.529	1.00
218_I	221_V	0.529	1.00
277_L	284_D	0.526	1.00
284_D	293_K	0.526	1.00
58_G	61_K	0.523	1.00
272_E	275_G	0.521	1.00
89_L	94_V	0.519	1.00
182_H	194_K	0.517	1.00
238_S	260_D	0.516	1.00
217_D	242_D	0.512	1.00
208_M	223_A	0.512	1.00
160_A	220_A	0.508	1.00
155_K	264_S	0.508	1.00
197_A	204_G	0.508	1.00
55_L	275_G	0.507	1.00
54_S	57_K	0.506	1.00
201_R	227_E	0.505	1.00
139_S	144_G	0.504	1.00
59_I	63_A	0.502	1.00
166_E	224_H	0.500	1.00
90_I	113_S	0.500	1.00

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
2iksA	2	0.8656	100	0.204	Contact Map
3huuA	2	0.8328	100	0.207	Contact Map
2hsgA	1	0.9639	100	0.21	Contact Map
4o5aA	2	0.8459	100	0.212	Contact Map
3brqA	2	0.859	100	0.218	Contact Map
3dbiA	2	0.8656	100	0.218	Contact Map
1qpzA	2	0.977	100	0.22	Contact Map
3e3mA	2	0.8393	100	0.224	Contact Map
3bilA	2	0.8066	100	0.225	Contact Map
3kjxA	2	0.9738	100	0.227	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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