XYLF - ECOLI - GREMLIN Contacts

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XYLF - D-xylose-binding periplasmic protein

UniProt:	P37387	Sequences: MKIKNILLTLCTSLLLTNVAAHAKEVKIGMAIDDLRLERWQKDRDIFVKKAESLGAKVFVQSANGNEETQMSQIENMINRGVDVLVIIPYNGQVLSNVVKEAKQEGIKVLAYDRMINDADIDFYISFDNEKVGELQAKALVDIVPQGNYFLMGGSPVDNNAKLFRAGQMKVLKPYVDSGKIKVVGDQWVDGWLPENALKIMENALTANNNKIDAVVASNDATAGGAIQALSAQGLSGKVAISGQDADLAGIKRIAAGTQTMTVYKPITLLANTAAEIAVELGNGQEPKADTTLNNGLKDVPSRLLTPIDVNKNNIKDTVIKDGFHKESEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG20252
Length:	330 (283)
Sequences:	38186 (28614)
Seq/√Len:	1700.9

ECOLI - XYLF ALSB YTFQ RBSB LSRB GALR DGAL YPHF GALS IDNR LACI ARAF PURR ASCG CRA GNTR TORT CYTR MALI YCJW RBSR TRER EBGR XYLR
BACSU - RBSB CCPA RBSR DEGA KDGR NTDR YKVZ MSMR EXUR GANR ARAR YVDE 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
130_E	170_K	3.538	1.00
146_Q	213_D	3.274	1.00
84_V	278_A	2.830	1.00
136_Q	242_S	2.725	1.00
246_A	264_Y	2.645	1.00
146_Q	240_A	2.610	1.00
165_R	169_M	2.607	1.00
198_L	232_A	2.340	1.00
50_K	53_S	2.311	1.00
202_E	233_Q	2.232	1.00
50_K	276_E	2.209	1.00
134_E	171_V	2.180	1.00
134_E	170_K	2.143	1.00
138_K	171_V	2.115	1.00
202_E	229_A	2.102	1.00
131_K	135_L	2.100	1.00
273_T	276_E	2.098	1.00
51_A	275_A	2.098	1.00
134_E	178_S	2.055	1.00
140_L	214_A	2.024	1.00
132_V	244_Q	2.010	1.00
130_E	166_A	1.992	1.00
46_I	271_A	1.989	1.00
133_G	137_A	1.978	1.00
280_E	285_Q	1.976	1.00
50_K	272_N	1.976	1.00
138_K	142_D	1.954	1.00
141_V	179_G	1.953	1.00
123_F	281_L	1.932	1.00
197_A	225_G	1.914	1.00
230_L	239_V	1.885	1.00
206_T	233_Q	1.855	1.00
133_G	216_V	1.817	1.00
29_G	82_V	1.812	1.00
49_K	268_T	1.794	1.00
137_A	168_Q	1.784	1.00
134_E	138_K	1.779	1.00
150_F	212_I	1.778	1.00
138_K	179_G	1.744	1.00
198_L	229_A	1.731	1.00
217_A	226_A	1.728	1.00
151_L	218_S	1.723	1.00
201_M	226_A	1.720	1.00
50_K	54_L	1.683	1.00
235_L	238_K	1.680	1.00
266_P	269_L	1.673	1.00
112_Y	274_A	1.652	1.00
148_N	211_K	1.651	1.00
46_I	268_T	1.640	1.00
166_A	170_K	1.638	1.00
231_S	256_A	1.635	1.00
131_K	134_E	1.618	1.00
229_A	233_Q	1.599	1.00
141_V	171_V	1.559	1.00
54_L	279_V	1.559	1.00
139_A	142_D	1.540	1.00
264_Y	308_I	1.510	1.00
139_A	143_I	1.509	1.00
169_M	173_K	1.505	1.00
208_N	211_K	1.505	1.00
163_L	166_A	1.498	1.00
279_V	283_N	1.497	1.00
229_A	232_A	1.489	1.00
198_L	228_Q	1.477	1.00
128_D	131_K	1.466	1.00
191_G	196_N	1.464	1.00
26_V	83_D	1.458	1.00
269_L	273_T	1.451	1.00
269_L	272_N	1.448	1.00
50_K	275_A	1.435	1.00
137_A	141_V	1.428	1.00
5_N	9_T	1.416	1.00
148_N	213_D	1.405	1.00
148_N	182_K	1.391	1.00
133_G	167_G	1.391	1.00
230_L	235_L	1.389	1.00
150_F	204_A	1.389	1.00
202_E	232_A	1.383	1.00
201_M	215_V	1.379	1.00
148_N	184_V	1.369	1.00
29_G	77_M	1.354	1.00
198_L	202_E	1.343	1.00
137_A	167_G	1.339	1.00
75_E	101_E	1.334	1.00
28_I	51_A	1.332	1.00
137_A	171_V	1.331	1.00
86_V	274_A	1.314	1.00
130_E	134_E	1.311	1.00
100_K	104_Q	1.305	1.00
201_M	230_L	1.299	1.00
276_E	280_E	1.297	1.00
51_A	58_V	1.296	1.00
184_V	187_Q	1.294	1.00
26_V	56_A	1.294	1.00
167_G	171_V	1.288	1.00
135_L	307_P	1.272	1.00
135_L	138_K	1.268	1.00
183_V	186_D	1.257	1.00
61_Q	77_M	1.250	1.00
61_Q	73_Q	1.247	1.00
202_E	206_T	1.243	1.00
6_I	9_T	1.239	1.00
231_S	258_T	1.237	1.00
146_Q	214_A	1.235	1.00
47_F	275_A	1.229	1.00
27_K	57_K	1.225	1.00
268_T	272_N	1.209	1.00
30_M	47_F	1.208	1.00
225_G	229_A	1.198	1.00
48_V	52_E	1.194	1.00
227_I	241_I	1.193	1.00
208_N	212_I	1.189	1.00
54_L	276_E	1.179	1.00
168_Q	172_L	1.175	1.00
195_E	199_K	1.161	1.00
169_M	183_V	1.154	1.00
27_K	59_F	1.151	1.00
130_E	167_G	1.151	1.00
152_M	226_A	1.150	1.00
138_K	178_S	1.136	1.00
130_E	163_L	1.136	1.00
47_F	86_V	1.130	1.00
151_L	165_R	1.130	1.00
200_I	203_N	1.129	1.00
168_Q	216_V	1.128	1.00
220_D	262_T	1.124	1.00
30_M	58_V	1.123	1.00
203_N	207_A	1.112	1.00
14_L	20_A	1.111	1.00
308_I	311_N	1.110	1.00
242_S	260_T	1.107	1.00
162_K	166_A	1.106	1.00
215_V	226_A	1.104	1.00
141_V	181_I	1.098	1.00
171_V	178_S	1.096	1.00
136_Q	216_V	1.096	1.00
220_D	243_G	1.096	1.00
142_D	179_G	1.090	1.00
44_R	48_V	1.088	1.00
193_L	196_N	1.082	1.00
71_M	75_E	1.078	1.00
199_K	203_N	1.070	1.00
273_T	277_I	1.070	1.00
52_E	69_T	1.063	1.00
149_Y	172_L	1.061	1.00
69_T	72_S	1.058	1.00
217_A	222_T	1.057	1.00
197_A	201_M	1.056	1.00
5_N	8_L	1.045	1.00
194_P	228_Q	1.044	1.00
196_N	199_K	1.042	1.00
166_A	169_M	1.035	1.00
16_L	19_V	1.035	1.00
271_A	275_A	1.033	1.00
139_A	311_N	1.029	1.00
272_N	276_E	1.027	1.00
17_T	20_A	1.024	1.00
148_N	210_N	1.020	1.00
132_V	307_P	1.014	1.00
147_G	213_D	1.013	1.00
154_G	192_W	1.009	1.00
278_A	282_G	1.004	1.00
56_A	279_V	0.993	1.00
75_E	79_N	0.991	1.00
66_N	69_T	0.983	1.00
54_L	283_N	0.981	1.00
53_S	272_N	0.980	1.00
201_M	205_L	0.979	1.00
139_A	260_T	0.979	1.00
227_I	255_A	0.979	1.00
96_S	100_K	0.978	1.00
217_A	223_A	0.976	1.00
45_D	49_K	0.973	1.00
136_Q	263_V	0.973	1.00
149_Y	214_A	0.965	1.00
156_P	189_V	0.961	1.00
137_A	172_L	0.954	1.00
14_L	17_T	0.952	1.00
13_S	18_N	0.948	1.00
39_R	267_I	0.934	1.00
159_N	163_L	0.933	1.00
190_D	222_T	0.918	1.00
199_K	202_E	0.914	1.00
86_V	278_A	0.913	1.00
141_V	147_G	0.907	1.00
196_N	200_I	0.902	1.00
235_L	239_V	0.901	1.00
30_M	44_R	0.895	1.00
84_V	282_G	0.894	1.00
157_V	162_K	0.893	1.00
49_K	272_N	0.891	1.00
47_F	271_A	0.889	1.00
28_I	86_V	0.888	1.00
127_F	266_P	0.883	1.00
220_D	246_A	0.879	1.00
49_K	53_S	0.875	1.00
150_F	215_V	0.875	1.00
129_N	164_F	0.873	1.00
127_F	265_K	0.872	1.00
230_L	241_I	0.871	1.00
215_V	239_V	0.869	1.00
243_G	262_T	0.865	1.00
223_A	243_G	0.853	1.00
72_S	75_E	0.852	1.00
205_L	229_A	0.851	1.00
27_K	80_R	0.846	1.00
43_D	112_Y	0.845	1.00
273_T	303_R	0.845	1.00
47_F	58_V	0.844	1.00
170_K	178_S	0.844	1.00
143_I	311_N	0.842	1.00
125_I	277_I	0.832	1.00
153_G	165_R	0.831	1.00
44_R	60_V	0.829	1.00
228_Q	231_S	0.828	1.00
277_I	280_E	0.825	1.00
275_A	279_V	0.822	1.00
277_I	303_R	0.820	1.00
12_T	79_N	0.818	1.00
170_K	173_K	0.815	1.00
140_L	242_S	0.812	1.00
15_L	18_N	0.810	1.00
31_A	73_Q	0.809	1.00
59_F	82_V	0.809	1.00
46_I	272_N	0.802	1.00
59_F	80_R	0.800	1.00
151_L	216_V	0.798	1.00
128_D	304_L	0.797	1.00
69_T	73_Q	0.795	1.00
147_G	181_I	0.794	1.00
245_D	265_K	0.793	1.00
84_V	110_L	0.791	1.00
123_F	277_I	0.790	1.00
201_M	229_A	0.789	1.00
101_E	104_Q	0.788	1.00
64_N	69_T	0.788	1.00
163_L	167_G	0.787	1.00
33_D	40_W	0.786	1.00
171_V	179_G	0.784	1.00
172_L	181_I	0.784	1.00
172_L	183_V	0.779	1.00
25_E	83_D	0.779	1.00
205_L	233_Q	0.778	1.00
45_D	48_V	0.776	1.00
152_M	217_A	0.775	1.00
220_D	223_A	0.774	1.00
201_M	204_A	0.771	1.00
98_V	101_E	0.767	1.00
211_K	235_L	0.766	1.00
42_K	268_T	0.755	1.00
253_R	258_T	0.753	1.00
134_E	167_G	0.742	1.00
203_N	206_T	0.740	1.00
252_K	256_A	0.737	1.00
29_G	85_L	0.736	1.00
190_D	196_N	0.734	1.00
78_I	107_I	0.733	1.00
46_I	50_K	0.730	1.00
7_L	10_L	0.722	1.00
24_K	283_N	0.721	1.00
68_E	72_S	0.720	1.00
102_A	109_V	0.718	1.00
207_A	210_N	0.717	1.00
24_K	83_D	0.717	1.00
131_K	306_T	0.716	1.00
86_V	112_Y	0.712	1.00
48_V	58_V	0.709	1.00
74_I	85_L	0.707	1.00
273_T	305_L	0.705	1.00
266_P	305_L	0.704	1.00
219_N	245_D	0.701	1.00
110_L	281_L	0.701	1.00
28_I	275_A	0.699	1.00
266_P	308_I	0.698	1.00
25_E	57_K	0.697	1.00
183_V	187_Q	0.697	1.00
37_L	221_A	0.697	1.00
207_A	211_K	0.696	1.00
197_A	200_I	0.694	1.00
213_D	240_A	0.693	1.00
12_T	75_E	0.691	1.00
143_I	240_A	0.691	1.00
192_W	218_S	0.690	1.00
111_A	116_I	0.690	1.00
228_Q	258_T	0.689	1.00
141_V	178_S	0.688	1.00
100_K	103_K	0.688	1.00
71_M	98_V	0.686	1.00
135_L	263_V	0.685	1.00
78_I	105_E	0.682	1.00
161_A	192_W	0.678	1.00
207_A	212_I	0.678	1.00
230_L	233_Q	0.677	1.00
216_V	242_S	0.677	1.00
201_M	225_G	0.677	1.00
154_G	161_A	0.673	1.00
141_V	172_L	0.669	1.00
111_A	121_I	0.667	1.00
151_L	168_Q	0.666	1.00
224_G	255_A	0.660	1.00
72_S	76_N	0.655	1.00
284_G	287_P	0.655	1.00
227_I	231_S	0.654	1.00
84_V	274_A	0.650	1.00
250_G	259_Q	0.650	1.00
220_D	247_D	0.650	1.00
113_D	160_N	0.650	1.00
228_Q	232_A	0.649	1.00
280_E	284_G	0.647	1.00
168_Q	183_V	0.646	1.00
111_A	124_Y	0.646	1.00
28_I	282_G	0.644	1.00
11_C	14_L	0.644	1.00
139_A	309_D	0.641	1.00
42_K	267_I	0.636	1.00
146_Q	180_K	0.633	1.00
219_N	222_T	0.633	1.00
113_D	129_N	0.630	1.00
126_S	304_L	0.627	1.00
67_E	71_M	0.626	1.00
51_A	56_A	0.623	1.00
140_L	216_V	0.621	1.00
127_F	307_P	0.620	1.00
149_Y	213_D	0.620	1.00
40_W	88_I	0.619	1.00
135_L	139_A	0.618	1.00
39_R	43_D	0.615	1.00
240_A	260_T	0.615	1.00
252_K	255_A	0.612	1.00
223_A	259_Q	0.611	1.00
228_Q	256_A	0.607	1.00
110_L	278_A	0.607	1.00
187_Q	207_A	0.606	1.00
200_I	204_A	0.606	1.00
195_E	198_L	0.605	1.00
103_K	109_V	0.603	1.00
268_T	271_A	0.603	1.00
216_V	244_Q	0.602	1.00
12_T	16_L	0.600	1.00
43_D	267_I	0.600	1.00
115_M	124_Y	0.597	1.00
194_P	225_G	0.594	1.00
192_W	222_T	0.593	1.00
148_N	208_N	0.592	1.00
73_Q	76_N	0.592	1.00
244_Q	265_K	0.591	1.00
161_A	218_S	0.590	1.00
45_D	268_T	0.589	1.00
113_D	270_L	0.589	1.00
139_A	242_S	0.588	1.00
128_D	306_T	0.588	1.00
148_N	187_Q	0.587	1.00
85_L	107_I	0.587	1.00
164_F	265_K	0.585	1.00
110_L	125_I	0.585	1.00
28_I	84_V	0.585	1.00
224_G	247_D	0.585	1.00
148_N	212_I	0.584	1.00
61_Q	76_N	0.584	1.00
149_Y	168_Q	0.584	1.00
110_L	277_I	0.581	1.00
231_S	236_S	0.581	1.00
46_I	267_I	0.578	1.00
136_Q	214_A	0.578	1.00
129_N	163_L	0.577	1.00
56_A	83_D	0.574	1.00
97_N	100_K	0.572	1.00
77_M	82_V	0.571	1.00
18_N	22_H	0.571	1.00
28_I	56_A	0.570	1.00
217_A	243_G	0.570	1.00
129_N	160_N	0.568	1.00
48_V	62_S	0.567	1.00
212_I	235_L	0.564	1.00
304_L	307_P	0.564	1.00
246_A	252_K	0.560	1.00
214_A	240_A	0.559	1.00
101_E	105_E	0.559	1.00
277_I	281_L	0.559	1.00
27_K	83_D	0.559	1.00
76_N	79_N	0.559	1.00
126_S	129_N	0.558	1.00
255_A	258_T	0.556	1.00
198_L	201_M	0.556	1.00
232_A	256_A	0.549	1.00
134_E	137_A	0.547	1.00
51_A	279_V	0.545	1.00
281_L	287_P	0.543	1.00
82_V	85_L	0.542	1.00
228_Q	253_R	0.541	1.00
6_I	13_S	0.541	1.00
27_K	82_V	0.537	1.00
198_L	225_G	0.537	1.00
56_A	282_G	0.537	1.00
143_I	146_Q	0.537	1.00
110_L	274_A	0.535	1.00
45_D	64_N	0.535	1.00
131_K	307_P	0.535	1.00
205_L	230_L	0.534	1.00
10_L	13_S	0.533	1.00
223_A	241_I	0.531	1.00
97_N	101_E	0.528	1.00
190_D	197_A	0.527	1.00
19_V	22_H	0.524	1.00
26_V	283_N	0.524	1.00
71_M	101_E	0.521	1.00
26_V	282_G	0.520	1.00
173_K	178_S	0.519	1.00
226_A	230_L	0.515	1.00
212_I	215_V	0.514	1.00
63_A	70_Q	0.511	1.00
152_M	200_I	0.511	1.00
127_F	270_L	0.509	1.00
273_T	280_E	0.508	1.00
127_F	132_V	0.507	1.00
103_K	120_D	0.507	1.00
38_E	221_A	0.507	1.00
37_L	40_W	0.507	1.00
179_G	182_K	0.507	1.00
43_D	271_A	0.505	1.00
42_K	45_D	0.503	1.00
50_K	279_V	0.502	1.00
78_I	81_G	0.501	1.00
76_N	80_R	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
2hsgA	1	0.8788	100	0.212	Contact Map
3huuA	2	0.8	100	0.219	Contact Map
2iksA	2	0.8303	100	0.225	Contact Map
3dbiA	2	0.8303	100	0.227	Contact Map
1qpzA	2	0.9152	100	0.227	Contact Map
4o5aA	2	0.8091	100	0.229	Contact Map
2o20A	2	0.8242	100	0.23	Contact Map
3h5oA	2	0.8091	100	0.23	Contact Map
3bilA	2	0.7697	100	0.23	Contact Map
3e3mA	2	0.803	100	0.231	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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