RBSB - ECOLI - GREMLIN Contacts

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RBSB - D-ribose-binding periplasmic protein

UniProt:	P02925	Sequences: MNMKKLATLVSAVALSATVSANAMAKDTIALVVSTLNNPFFVSLKDGAQKEADKLGYNLVVLDSQNNPAKELANVQDLTVRGTKILLINPTDSDAVGNAVKMANQANIPVITLDRQATKGEVVSHIASDNVLGGKIAGDYIAKKAGEGAKVIELQGIAGTSAARERGEGFQQAVAAHKFNVLASQPADFDRIKGLNVMQNLLTAHPDVQAVFAQNDEMALGALRALQTAGKSDVMVVGFDGTPDGEKAVNDGKLAATIAQLPDQIGAKGVETADKVLKGEKVQAKYPVDLKLVVKQ	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10815
Length:	296 (279)
Sequences:	38439 (28922)
Seq/√Len:	1731.5

ECOLI - RBSB ALSB XYLF YTFQ LSRB LACI GALR CRA GALS IDNR ASCG CYTR PURR MALI YCJW GNTR RBSR YPHF TORT DGAL ARAF TRER EBGR XYLR
BACSU - RBSB KDGR RBSR CCPA DEGA NTDR YKVZ MSMR YVDE EXUR GANR ARAR 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
131_V	172_Q	3.424	1.00
148_G	209_Q	3.278	1.00
85_I	273_A	2.796	1.00
137_A	237_V	2.699	1.00
167_G	171_Q	2.634	1.00
241_G	259_A	2.625	1.00
148_G	235_M	2.616	1.00
124_S	276_V	2.523	1.00
135_K	176_A	2.301	1.00
51_E	54_K	2.258	1.00
195_L	228_T	2.253	1.00
199_Q	229_A	2.235	1.00
139_D	173_A	2.177	1.00
135_K	172_Q	2.166	1.00
51_E	271_E	2.156	1.00
135_K	173_A	2.141	1.00
199_Q	225_A	2.101	1.00
132_L	136_I	2.094	1.00
142_A	177_H	2.079	1.00
268_K	271_E	2.052	1.00
141_I	210_A	2.051	1.00
52_A	270_V	2.048	1.00
133_G	239_F	2.002	1.00
134_G	138_G	1.989	1.00
51_E	267_A	1.982	1.00
131_V	168_E	1.960	1.00
47_G	266_G	1.903	1.00
194_G	221_G	1.868	1.00
139_D	143_K	1.843	1.00
140_Y	144_K	1.828	1.00
30_A	83_T	1.818	1.00
138_G	170_F	1.813	1.00
134_G	212_F	1.801	1.00
152_I	208_V	1.773	1.00
139_D	177_H	1.769	1.00
203_T	229_A	1.744	1.00
213_A	222_A	1.737	1.00
153_E	214_Q	1.734	1.00
226_L	234_V	1.733	1.00
198_M	222_A	1.722	1.00
275_K	280_E	1.720	1.00
135_K	139_D	1.720	1.00
259_A	291_K	1.717	1.00
50_K	263_D	1.713	1.00
195_L	225_A	1.711	1.00
113_L	269_G	1.668	1.00
51_E	55_L	1.651	1.00
261_L	264_Q	1.649	1.00
47_G	263_D	1.622	1.00
150_K	207_D	1.607	1.00
132_L	135_K	1.602	1.00
225_A	229_A	1.601	1.00
168_E	172_Q	1.589	1.00
227_Q	251_D	1.581	1.00
140_Y	143_K	1.576	1.00
142_A	173_A	1.527	1.00
55_L	274_D	1.527	1.00
136_I	290_L	1.525	1.00
6_L	10_V	1.510	1.00
274_D	278_K	1.508	1.00
237_V	256_A	1.490	1.00
225_A	228_T	1.488	1.00
27_D	84_K	1.469	1.00
195_L	224_R	1.467	1.00
171_Q	175_A	1.462	1.00
165_E	168_E	1.450	1.00
188_D	193_K	1.445	1.00
264_Q	268_K	1.442	1.00
181_V	184_S	1.432	1.00
129_D	132_L	1.396	1.00
150_K	209_Q	1.388	1.00
134_G	169_G	1.385	1.00
264_Q	267_A	1.383	1.00
173_A	176_A	1.379	1.00
268_K	286_Y	1.374	1.00
51_E	270_V	1.366	1.00
150_K	182_L	1.357	1.00
226_L	231_K	1.356	1.00
195_L	199_Q	1.342	1.00
205_H	208_V	1.342	1.00
138_G	169_G	1.338	1.00
138_G	142_A	1.335	1.00
152_I	201_L	1.329	1.00
185_Q	200_N	1.316	1.00
199_Q	228_T	1.308	1.00
138_G	173_A	1.308	1.00
131_V	135_K	1.307	1.00
87_L	269_G	1.300	1.00
198_M	226_L	1.296	1.00
30_A	78_L	1.291	1.00
150_K	180_N	1.290	1.00
62_L	74_N	1.276	1.00
136_I	139_D	1.269	1.00
62_L	78_L	1.267	1.00
199_Q	203_T	1.267	1.00
101_K	105_Q	1.265	1.00
169_G	173_A	1.261	1.00
52_A	59_L	1.259	1.00
27_D	57_Y	1.251	1.00
133_G	290_L	1.249	1.00
148_G	210_A	1.247	1.00
28_T	58_N	1.246	1.00
271_E	275_K	1.241	1.00
198_M	211_V	1.235	1.00
227_Q	253_K	1.232	1.00
76_Q	102_M	1.229	1.00
29_I	52_A	1.229	1.00
48_A	270_V	1.213	1.00
28_T	60_V	1.212	1.00
15_L	18_T	1.208	1.00
16_S	19_V	1.196	1.00
263_D	267_A	1.190	1.00
6_L	9_L	1.189	1.00
55_L	271_E	1.179	1.00
221_G	225_A	1.178	1.00
140_Y	256_A	1.163	1.00
149_A	209_Q	1.154	1.00
153_E	167_G	1.148	1.00
31_L	48_A	1.148	1.00
200_N	204_A	1.143	1.00
131_V	169_G	1.139	1.00
49_Q	53_D	1.138	1.00
173_A	177_H	1.134	1.00
223_L	236_V	1.130	1.00
7_A	10_V	1.128	1.00
170_F	174_V	1.126	1.00
171_Q	181_V	1.110	1.00
170_F	212_F	1.109	1.00
197_V	200_N	1.109	1.00
131_V	165_E	1.105	1.00
139_D	176_A	1.104	1.00
216_D	257_T	1.101	1.00
192_I	196_N	1.099	1.00
31_L	59_L	1.097	1.00
190_D	193_K	1.088	1.00
154_L	222_A	1.088	1.00
211_V	222_A	1.083	1.00
45_K	49_Q	1.077	1.00
164_R	168_E	1.069	1.00
137_A	212_F	1.066	1.00
268_K	272_T	1.065	1.00
266_G	270_V	1.064	1.00
72_L	76_Q	1.064	1.00
151_V	174_V	1.063	1.00
168_E	171_Q	1.055	1.00
172_Q	176_A	1.055	1.00
53_D	70_K	1.054	1.00
191_R	224_R	1.052	1.00
48_A	87_L	1.049	1.00
70_K	73_A	1.046	1.00
142_A	179_F	1.041	1.00
213_A	218_M	1.037	1.00
267_A	271_E	1.033	1.00
216_D	238_G	1.031	1.00
14_A	19_V	1.027	1.00
150_K	206_P	1.013	1.00
15_L	21_A	1.011	1.00
193_K	196_N	1.005	1.00
57_Y	274_D	0.995	1.00
196_N	200_N	0.992	1.00
144_K	235_M	0.985	1.00
223_L	250_N	0.984	1.00
198_M	202_L	0.981	1.00
137_A	258_I	0.979	1.00
273_A	277_L	0.979	1.00
213_A	219_A	0.978	1.00
161_S	165_E	0.975	1.00
194_G	198_M	0.970	1.00
76_Q	80_V	0.965	1.00
46_D	50_K	0.964	1.00
124_S	272_T	0.962	1.00
55_L	278_K	0.958	1.00
54_K	267_A	0.956	1.00
143_K	177_H	0.954	1.00
97_G	101_K	0.954	1.00
151_V	210_A	0.949	1.00
138_G	174_V	0.948	1.00
67_N	70_K	0.946	1.00
149_A	179_F	0.945	1.00
17_A	20_S	0.943	1.00
272_T	286_Y	0.939	1.00
156_G	189_F	0.933	1.00
18_T	21_A	0.930	1.00
87_L	273_A	0.922	1.00
40_F	262_P	0.913	1.00
185_Q	197_V	0.911	1.00
158_A	186_P	0.907	1.00
29_I	87_L	0.903	1.00
216_D	241_G	0.897	1.00
211_V	234_V	0.891	1.00
231_K	234_V	0.886	1.00
193_K	197_V	0.879	1.00
159_G	164_R	0.878	1.00
130_N	166_R	0.874	1.00
142_A	149_A	0.869	1.00
48_A	266_G	0.868	1.00
85_I	277_L	0.865	1.00
128_S	261_L	0.863	1.00
268_K	288_V	0.862	1.00
50_K	54_K	0.862	1.00
196_N	199_Q	0.861	1.00
132_L	289_D	0.859	1.00
219_A	238_G	0.858	1.00
152_I	211_V	0.855	1.00
155_Q	167_G	0.855	1.00
28_T	81_R	0.849	1.00
144_K	148_G	0.848	1.00
224_R	227_Q	0.847	1.00
226_L	236_V	0.846	1.00
261_L	291_K	0.843	1.00
50_K	267_A	0.841	1.00
202_L	225_A	0.840	1.00
128_S	260_Q	0.839	1.00
44_L	113_L	0.837	1.00
45_K	61_V	0.836	1.00
31_L	45_K	0.833	1.00
70_K	74_N	0.825	1.00
272_T	275_K	0.824	1.00
187_A	218_M	0.819	1.00
12_A	18_T	0.816	1.00
126_I	272_T	0.811	1.00
172_Q	175_A	0.810	1.00
238_G	257_T	0.810	1.00
60_V	83_T	0.808	1.00
48_A	59_L	0.807	1.00
141_I	237_V	0.804	1.00
129_D	287_P	0.803	1.00
174_V	181_V	0.803	1.00
270_V	274_D	0.800	1.00
104_N	123_V	0.798	1.00
12_A	15_L	0.796	1.00
60_V	81_R	0.793	1.00
46_D	49_Q	0.787	1.00
73_A	76_Q	0.785	1.00
102_M	105_Q	0.782	1.00
125_H	285_K	0.779	1.00
261_L	288_V	0.776	1.00
153_E	212_F	0.773	1.00
198_M	225_A	0.771	1.00
47_G	267_A	0.769	1.00
202_L	229_A	0.762	1.00
240_D	260_Q	0.760	1.00
32_V	74_N	0.760	1.00
207_D	231_K	0.760	1.00
174_V	179_F	0.760	1.00
65_Q	70_K	0.758	1.00
26_K	84_K	0.757	1.00
154_L	213_A	0.755	1.00
99_A	102_M	0.755	1.00
127_A	285_K	0.753	1.00
198_M	201_L	0.752	1.00
132_L	290_L	0.751	1.00
34_S	41_F	0.747	1.00
43_S	263_D	0.746	1.00
165_E	169_G	0.745	1.00
128_S	290_L	0.744	1.00
13_V	80_V	0.743	1.00
248_A	253_K	0.742	1.00
127_A	287_P	0.738	1.00
47_G	51_E	0.738	1.00
124_S	284_A	0.735	1.00
200_N	203_T	0.734	1.00
87_L	113_L	0.733	1.00
79_T	106_A	0.730	1.00
135_K	169_G	0.725	1.00
85_I	111_I	0.723	1.00
116_Q	285_K	0.721	1.00
216_D	219_A	0.718	1.00
140_Y	292_L	0.712	1.00
224_R	253_K	0.711	1.00
103_A	110_V	0.709	1.00
163_A	189_F	0.709	1.00
30_A	86_L	0.703	1.00
101_K	104_N	0.700	1.00
72_L	99_A	0.699	1.00
38_N	217_E	0.696	1.00
112_T	117_A	0.693	1.00
26_K	58_N	0.692	1.00
189_F	214_Q	0.690	1.00
215_N	240_D	0.687	1.00
136_I	258_I	0.685	1.00
245_G	254_L	0.684	1.00
49_Q	59_L	0.681	1.00
156_G	163_A	0.678	1.00
69_A	73_A	0.676	1.00
153_E	170_F	0.674	1.00
129_D	289_D	0.674	1.00
187_A	193_K	0.672	1.00
13_V	76_Q	0.671	1.00
170_F	181_V	0.671	1.00
8_T	11_S	0.667	1.00
114_D	162_A	0.665	1.00
111_I	276_V	0.664	1.00
29_I	270_V	0.663	1.00
13_V	17_A	0.662	1.00
224_R	228_T	0.655	1.00
212_F	237_V	0.653	1.00
209_Q	235_M	0.652	1.00
25_A	84_K	0.650	1.00
75_V	86_L	0.648	1.00
77_D	81_R	0.647	1.00
215_N	218_M	0.647	1.00
142_A	174_V	0.644	1.00
112_T	125_H	0.642	1.00
204_A	208_V	0.641	1.00
79_T	108_I	0.637	1.00
223_L	227_Q	0.636	1.00
85_I	269_G	0.632	1.00
216_D	242_T	0.631	1.00
52_A	57_Y	0.630	1.00
43_S	262_P	0.629	1.00
25_A	278_K	0.624	1.00
212_F	239_F	0.621	1.00
194_G	197_V	0.618	1.00
198_M	221_G	0.616	1.00
151_V	209_Q	0.616	1.00
86_L	108_I	0.615	1.00
204_A	207_D	0.614	1.00
114_D	130_N	0.614	1.00
68_P	72_L	0.613	1.00
191_R	244_D	0.612	1.00
219_A	254_L	0.609	1.00
141_I	212_F	0.609	1.00
29_I	277_L	0.605	1.00
136_I	140_Y	0.604	1.00
224_R	251_D	0.602	1.00
111_I	273_A	0.596	1.00
29_I	85_I	0.596	1.00
41_F	89_N	0.595	1.00
220_L	250_N	0.595	1.00
104_N	110_V	0.595	1.00
98_N	101_K	0.591	1.00
46_D	263_D	0.589	1.00
110_V	123_V	0.589	1.00
62_L	77_D	0.589	1.00
111_I	126_I	0.589	1.00
47_G	262_P	0.588	1.00
116_Q	125_H	0.588	1.00
57_Y	84_K	0.587	1.00
201_L	205_H	0.587	1.00
226_L	229_A	0.586	1.00
12_A	16_S	0.586	1.00
140_Y	237_V	0.586	1.00
148_G	178_K	0.585	1.00
163_A	214_Q	0.581	1.00
49_Q	63_D	0.581	1.00
130_N	162_A	0.580	1.00
192_I	195_L	0.580	1.00
137_A	210_A	0.578	1.00
241_G	245_G	0.578	1.00
112_T	123_V	0.576	1.00
40_F	44_L	0.573	1.00
224_R	248_A	0.572	1.00
263_D	266_G	0.571	1.00
150_K	208_V	0.571	1.00
185_Q	204_A	0.571	1.00
197_V	201_L	0.570	1.00
216_D	245_G	0.569	1.00
111_I	272_T	0.567	1.00
74_N	77_D	0.567	1.00
166_R	260_Q	0.566	1.00
120_G	123_V	0.565	1.00
127_A	130_N	0.564	1.00
130_N	165_E	0.562	1.00
189_F	218_M	0.560	1.00
102_M	106_A	0.557	1.00
213_A	238_G	0.557	1.00
111_I	269_G	0.555	1.00
44_L	262_P	0.555	1.00
29_I	57_Y	0.554	1.00
73_A	77_D	0.554	1.00
239_F	260_Q	0.554	1.00
114_D	265_I	0.550	1.00
77_D	80_V	0.548	1.00
150_K	205_H	0.548	1.00
185_Q	201_L	0.548	1.00
15_L	19_V	0.547	1.00
250_N	253_K	0.547	1.00
28_T	83_T	0.543	1.00
220_L	242_T	0.541	1.00
210_A	235_M	0.541	1.00
151_V	170_F	0.537	1.00
202_L	226_L	0.536	1.00
46_D	65_Q	0.535	1.00
191_R	221_G	0.531	1.00
272_T	276_V	0.530	1.00
19_V	23_A	0.529	1.00
195_L	198_M	0.529	1.00
28_T	84_K	0.529	1.00
195_L	221_G	0.528	1.00
287_P	290_L	0.527	1.00
135_K	138_G	0.526	1.00
72_L	102_M	0.525	1.00
27_D	277_L	0.520	1.00
98_N	102_M	0.520	1.00
64_S	71_E	0.519	1.00
57_Y	277_L	0.519	1.00
78_L	83_T	0.515	1.00
268_K	275_K	0.515	1.00
256_A	292_L	0.515	1.00
222_A	226_L	0.510	1.00
154_L	197_V	0.510	1.00
128_S	239_F	0.510	1.00
139_D	142_A	0.509	1.00
245_G	257_T	0.507	1.00
109_P	277_L	0.507	1.00
52_A	274_D	0.507	1.00
12_A	17_A	0.506	1.00
191_R	217_E	0.506	1.00
16_S	20_S	0.505	1.00
47_G	50_K	0.505	1.00
275_K	284_A	0.504	1.00
39_P	217_E	0.503	1.00
27_D	278_K	0.502	1.00
219_A	236_V	0.500	1.00
76_Q	79_T	0.500	1.00
154_L	198_M	0.500	1.00
208_V	231_K	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
3dbiA	2	0.8986	100	0.126	Contact Map
2hsgA	1	0.9628	100	0.126	Contact Map
4o5aA	2	0.8784	100	0.128	Contact Map
2iksA	2	0.8986	100	0.132	Contact Map
1qpzA	2	0.9764	100	0.133	Contact Map
3huuA	2	0.8649	100	0.133	Contact Map
3bilA	2	0.8412	100	0.139	Contact Map
1jyeA	2	0.8851	100	0.14	Contact Map
3e3mA	2	0.8716	100	0.141	Contact Map
3kjxA	2	0.973	100	0.142	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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