YPHF - ECOLI - GREMLIN Contacts

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YPHF - ABC transporter periplasmic-binding protein YphF

UniProt:	P77269	Sequences: MPTKMRTTRNLLLMATLLGSALFARAAEKEMTIGAIYLDTQGYYAGVRQGVQDAAKDSSVQVQLIETNAQGDISKESTFVDTLVARNVDAIILSAVSENGSSRTVRRASEAGIPVICYNTCINQKGVDKYVSAYLVGDPLEFGKKLGNAAADYFIANKIDQPKIAVINCEAFEVCVQRRKGFEEVLKSRVPGAQIVANQEGTVLDKAISVGEKLIISTPDLNAIMGESGGATLGAVKAVRNQNQAGKIAVFGSDMTTEIAQELENNQVLKAVVDISGKKMGNAVFAQTLKVINKQADGEKVIQVPIDLYTKTEDGKQWLATHVDGLP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13467
Length:	327 (288)
Sequences:	39123 (29780)
Seq/√Len:	1754.8

ECOLI - YPHF XYLF GALR PURR GALS CYTR IDNR ALSB RBSB GNTR LACI LSRB ASCG MALI CRA DGAL YTFQ RBSR YCJW ARAF TORT EBGR TRER XYLR
BACSU - CCPA KDGR DEGA RBSR NTDR MSMR RBSB YKVZ ARAR EXUR GANR 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
140_L	184_E	3.444	1.00
161_Q	222_N	3.313	1.00
90_A	288_T	2.778	1.00
179_R	183_E	2.634	1.00
146_L	251_F	2.631	1.00
255_M	274_D	2.564	1.00
133_A	291_V	2.508	1.00
161_Q	249_A	2.457	1.00
144_K	188_S	2.340	1.00
54_A	57_D	2.283	1.00
208_I	241_N	2.269	1.00
212_E	242_Q	2.215	1.00
144_K	184_E	2.155	1.00
144_K	185_V	2.147	1.00
54_A	286_A	2.143	1.00
148_N	185_V	2.137	1.00
9_R	13_L	2.101	1.00
283_A	286_A	2.075	1.00
141_E	145_K	2.071	1.00
212_E	238_A	2.060	1.00
55_A	285_F	2.015	1.00
140_L	180_K	1.991	1.00
150_A	223_A	1.983	1.00
142_F	253_S	1.966	1.00
54_A	282_N	1.946	1.00
50_G	281_G	1.923	1.00
290_K	295_Q	1.894	1.00
143_G	147_G	1.883	1.00
163_K	194_Q	1.882	1.00
207_A	234_G	1.869	1.00
148_N	152_D	1.839	1.00
151_A	189_R	1.834	1.00
148_N	189_R	1.829	1.00
153_Y	314_D	1.814	1.00
34_G	88_V	1.785	1.00
165_A	221_L	1.770	1.00
144_K	148_N	1.754	1.00
147_G	182_F	1.750	1.00
274_D	307_D	1.745	1.00
53_D	278_K	1.744	1.00
216_I	242_Q	1.742	1.00
143_G	225_M	1.741	1.00
239_V	248_I	1.718	1.00
226_G	235_A	1.718	1.00
166_V	227_E	1.694	1.00
208_I	238_A	1.679	1.00
276_S	279_K	1.667	1.00
211_G	235_A	1.643	1.00
141_E	144_K	1.641	1.00
283_A	302_I	1.635	1.00
118_Y	284_V	1.632	1.00
149_A	153_Y	1.631	1.00
20_S	23_F	1.623	1.00
54_A	58_S	1.621	1.00
50_G	278_K	1.610	1.00
180_K	184_E	1.609	1.00
244_Q	247_K	1.599	1.00
145_K	306_I	1.593	1.00
149_A	152_D	1.555	1.00
238_A	242_Q	1.543	1.00
163_K	220_D	1.521	1.00
151_A	185_V	1.510	1.00
289_L	293_N	1.506	1.00
58_S	289_L	1.504	1.00
251_F	271_A	1.482	1.00
8_T	11_L	1.475	1.00
183_E	187_K	1.474	1.00
238_A	241_N	1.465	1.00
177_Q	180_K	1.452	1.00
279_K	283_A	1.448	1.00
31_M	89_D	1.440	1.00
208_I	237_K	1.436	1.00
138_D	141_E	1.432	1.00
8_T	12_L	1.427	1.00
199_Q	213_K	1.394	1.00
163_K	222_N	1.390	1.00
185_V	188_S	1.386	1.00
255_M	311_K	1.376	1.00
54_A	285_F	1.373	1.00
279_K	282_N	1.373	1.00
34_G	83_L	1.371	1.00
165_A	214_L	1.371	1.00
143_G	181_G	1.370	1.00
149_A	310_T	1.362	1.00
142_F	306_I	1.354	1.00
147_G	151_A	1.351	1.00
240_R	264_E	1.349	1.00
10_N	14_M	1.348	1.00
239_V	244_Q	1.343	1.00
218_T	221_L	1.336	1.00
106_R	110_E	1.322	1.00
208_I	212_E	1.320	1.00
212_E	241_N	1.314	1.00
140_L	144_K	1.314	1.00
147_G	181_G	1.313	1.00
266_N	312_T	1.313	1.00
286_A	290_K	1.296	1.00
211_G	239_V	1.293	1.00
55_A	62_V	1.290	1.00
81_D	107_R	1.289	1.00
147_G	185_V	1.269	1.00
92_I	284_V	1.269	1.00
145_K	148_N	1.245	1.00
181_G	185_V	1.242	1.00
211_G	224_I	1.229	1.00
161_Q	223_A	1.228	1.00
212_E	216_I	1.228	1.00
260_A	265_N	1.227	1.00
162_P	222_N	1.216	1.00
51_V	285_F	1.207	1.00
52_Q	56_K	1.191	1.00
32_T	61_Q	1.183	1.00
58_S	286_A	1.181	1.00
32_T	63_Q	1.180	1.00
31_M	60_V	1.177	1.00
194_Q	197_A	1.177	1.00
278_K	282_N	1.173	1.00
33_I	55_A	1.172	1.00
35_A	51_V	1.169	1.00
234_G	238_A	1.165	1.00
19_G	22_L	1.154	1.00
166_V	179_R	1.151	1.00
213_K	217_S	1.150	1.00
182_F	186_L	1.134	1.00
236_V	250_V	1.131	1.00
149_A	314_D	1.125	1.00
67_T	79_F	1.123	1.00
205_D	209_S	1.116	1.00
140_L	181_G	1.114	1.00
229_G	272_V	1.109	1.00
249_A	314_D	1.109	1.00
152_D	189_R	1.108	1.00
140_L	177_Q	1.104	1.00
182_F	225_M	1.102	1.00
210_V	213_K	1.102	1.00
203_V	206_K	1.096	1.00
176_V	180_K	1.083	1.00
261_Q	265_N	1.080	1.00
48_R	52_Q	1.070	1.00
287_Q	302_I	1.069	1.00
169_C	202_T	1.068	1.00
51_V	92_I	1.068	1.00
184_E	188_S	1.065	1.00
148_N	188_S	1.064	1.00
224_I	235_A	1.060	1.00
10_N	13_L	1.060	1.00
226_G	231_A	1.058	1.00
167_I	235_A	1.057	1.00
164_I	186_L	1.054	1.00
153_Y	249_A	1.050	1.00
204_L	237_K	1.049	1.00
146_L	225_M	1.049	1.00
229_G	252_G	1.045	1.00
180_K	183_E	1.044	1.00
77_S	81_D	1.038	1.00
283_A	287_Q	1.030	1.00
281_G	285_F	1.023	1.00
56_K	75_K	1.022	1.00
6_R	10_N	1.022	1.00
35_A	62_V	1.016	1.00
206_K	209_S	1.011	1.00
173_E	177_Q	1.008	1.00
67_T	83_L	1.007	1.00
11_L	14_M	1.006	1.00
209_S	213_K	1.006	1.00
282_N	286_A	1.006	1.00
75_K	78_T	0.997	1.00
171_A	200_E	0.994	1.00
153_Y	310_T	0.989	1.00
81_D	85_A	0.988	1.00
141_E	305_P	0.985	1.00
57_D	282_N	0.980	1.00
288_T	292_I	0.980	1.00
49_Q	53_D	0.978	1.00
102_S	106_R	0.976	1.00
58_S	293_N	0.967	1.00
146_L	273_V	0.967	1.00
185_V	189_R	0.956	1.00
211_G	215_I	0.945	1.00
19_G	25_R	0.945	1.00
60_V	289_L	0.944	1.00
226_G	232_T	0.943	1.00
164_I	223_A	0.941	1.00
18_L	23_F	0.941	1.00
133_A	287_Q	0.938	1.00
207_A	211_G	0.933	1.00
149_A	271_A	0.928	1.00
283_A	304_V	0.924	1.00
262_E	265_N	0.922	1.00
43_Y	277_G	0.913	1.00
147_G	186_L	0.906	1.00
199_Q	210_V	0.906	1.00
307_D	310_T	0.905	1.00
229_G	255_M	0.902	1.00
33_I	92_I	0.899	1.00
53_D	57_D	0.897	1.00
151_A	191_P	0.893	1.00
92_I	288_T	0.893	1.00
209_S	212_E	0.891	1.00
72_D	75_K	0.890	1.00
276_S	307_D	0.882	1.00
134_Y	301_V	0.878	1.00
51_V	281_G	0.871	1.00
244_Q	248_I	0.870	1.00
274_D	309_Y	0.870	1.00
53_D	282_N	0.862	1.00
239_V	250_V	0.857	1.00
137_G	275_I	0.857	1.00
9_R	12_L	0.856	1.00
215_I	238_A	0.852	1.00
165_A	224_I	0.851	1.00
206_K	210_V	0.851	1.00
90_A	292_I	0.848	1.00
153_Y	161_Q	0.848	1.00
21_A	24_A	0.847	1.00
224_I	248_I	0.843	1.00
138_D	303_Q	0.840	1.00
47_V	118_Y	0.835	1.00
32_T	86_R	0.834	1.00
137_G	276_S	0.830	1.00
75_K	79_F	0.821	1.00
139_P	178_R	0.820	1.00
35_A	48_R	0.820	1.00
70_Q	75_K	0.817	1.00
287_Q	290_K	0.815	1.00
184_E	187_K	0.813	1.00
197_A	217_S	0.808	1.00
136_V	301_V	0.808	1.00
151_A	162_P	0.808	1.00
232_T	252_G	0.802	1.00
186_L	191_P	0.801	1.00
135_L	287_Q	0.800	1.00
107_R	110_E	0.794	1.00
49_Q	52_Q	0.792	1.00
22_L	25_R	0.788	1.00
285_F	289_L	0.788	1.00
63_Q	88_V	0.786	1.00
252_G	272_V	0.782	1.00
136_V	303_Q	0.781	1.00
78_T	81_D	0.777	1.00
48_R	64_L	0.775	1.00
168_N	179_R	0.775	1.00
36_I	79_F	0.775	1.00
16_T	19_G	0.774	1.00
193_A	196_V	0.771	1.00
121_C	301_V	0.768	1.00
141_E	306_I	0.768	1.00
133_A	300_K	0.767	1.00
137_G	306_I	0.767	1.00
51_V	62_V	0.764	1.00
183_E	198_N	0.763	1.00
255_M	309_Y	0.761	1.00
167_I	226_G	0.761	1.00
254_D	275_I	0.760	1.00
38_L	44_Y	0.760	1.00
50_G	282_N	0.760	1.00
144_K	181_G	0.759	1.00
201_G	231_A	0.759	1.00
255_M	260_A	0.759	1.00
150_A	251_F	0.758	1.00
229_G	232_T	0.756	1.00
215_I	242_Q	0.755	1.00
104_T	107_R	0.750	1.00
211_G	238_A	0.748	1.00
46_G	278_K	0.746	1.00
149_A	308_L	0.745	1.00
30_E	89_D	0.739	1.00
237_K	240_R	0.738	1.00
90_A	116_I	0.737	1.00
276_S	304_V	0.736	1.00
211_G	214_L	0.736	1.00
166_V	225_M	0.734	1.00
163_K	219_P	0.734	1.00
162_P	191_P	0.733	1.00
183_E	193_A	0.732	1.00
63_Q	86_R	0.731	1.00
50_G	54_A	0.727	1.00
17_L	85_A	0.724	1.00
202_T	227_E	0.722	1.00
271_A	308_L	0.716	1.00
138_D	305_P	0.712	1.00
34_G	91_I	0.712	1.00
195_I	198_N	0.711	1.00
310_T	314_D	0.707	1.00
92_I	118_Y	0.705	1.00
177_Q	181_G	0.705	1.00
119_N	174_V	0.703	1.00
106_R	109_S	0.700	1.00
30_E	61_Q	0.699	1.00
108_A	115_V	0.699	1.00
213_K	216_I	0.692	1.00
175_C	202_T	0.692	1.00
29_K	89_D	0.690	1.00
41_Q	230_G	0.689	1.00
12_L	15_A	0.687	1.00
117_C	122_I	0.685	1.00
236_V	263_L	0.684	1.00
80_V	91_I	0.682	1.00
151_A	190_V	0.679	1.00
163_K	197_A	0.677	1.00
74_S	78_T	0.676	1.00
84_V	111_A	0.675	1.00
109_S	132_S	0.675	1.00
220_D	244_Q	0.673	1.00
15_A	18_L	0.669	1.00
77_S	104_T	0.668	1.00
52_Q	62_V	0.667	1.00
55_A	60_V	0.658	1.00
228_S	254_D	0.658	1.00
33_I	285_F	0.656	1.00
225_M	251_F	0.653	1.00
145_K	273_V	0.652	1.00
116_I	291_V	0.651	1.00
290_K	294_K	0.648	1.00
84_V	113_I	0.648	1.00
271_A	314_D	0.644	1.00
179_R	198_N	0.644	1.00
183_E	195_I	0.635	1.00
237_K	241_N	0.633	1.00
161_Q	192_G	0.632	1.00
33_I	90_A	0.630	1.00
125_K	132_S	0.629	1.00
228_S	231_A	0.628	1.00
29_K	293_N	0.628	1.00
169_C	175_C	0.625	1.00
193_A	198_N	0.624	1.00
236_V	240_R	0.623	1.00
239_V	242_Q	0.623	1.00
17_L	81_D	0.622	1.00
151_A	186_L	0.617	1.00
207_A	210_V	0.614	1.00
119_N	139_P	0.613	1.00
90_A	284_V	0.613	1.00
229_G	256_T	0.612	1.00
166_V	182_F	0.611	1.00
117_C	134_Y	0.610	1.00
196_V	199_Q	0.608	1.00
17_L	21_A	0.604	1.00
217_S	221_L	0.603	1.00
195_I	199_Q	0.602	1.00
150_A	225_M	0.602	1.00
211_G	234_G	0.601	1.00
103_R	106_R	0.599	1.00
73_I	77_S	0.598	1.00
43_Y	47_V	0.597	1.00
199_Q	214_L	0.595	1.00
199_Q	217_S	0.595	1.00
202_T	231_A	0.593	1.00
256_T	259_I	0.592	1.00
178_R	275_I	0.588	1.00
233_L	263_L	0.588	1.00
33_I	292_I	0.584	1.00
44_Y	94_S	0.581	1.00
225_M	253_S	0.581	1.00
260_A	263_L	0.581	1.00
46_G	277_G	0.577	1.00
201_G	206_K	0.576	1.00
191_P	195_I	0.575	1.00
214_L	218_T	0.573	1.00
222_N	249_A	0.573	1.00
78_T	82_T	0.570	1.00
109_S	115_V	0.568	1.00
253_S	275_I	0.567	1.00
50_G	277_G	0.563	1.00
91_I	113_I	0.563	1.00
221_L	244_Q	0.562	1.00
261_Q	266_N	0.561	1.00
145_K	149_A	0.559	1.00
47_V	277_G	0.559	1.00
175_C	227_E	0.559	1.00
139_P	174_V	0.558	1.00
32_T	89_D	0.558	1.00
116_I	135_L	0.558	1.00
146_L	223_A	0.555	1.00
163_K	221_L	0.555	1.00
49_Q	278_K	0.553	1.00
31_M	292_I	0.553	1.00
237_K	266_N	0.553	1.00
107_R	111_A	0.552	1.00
164_I	222_N	0.551	1.00
13_L	16_T	0.550	1.00
186_L	193_A	0.549	1.00
259_I	263_L	0.549	1.00
116_I	288_T	0.547	1.00
208_I	211_G	0.547	1.00
240_R	245_A	0.545	1.00
163_K	218_T	0.545	1.00
7_T	16_T	0.544	1.00
226_G	252_G	0.544	1.00
119_N	280_M	0.543	1.00
60_V	89_D	0.543	1.00
139_P	177_Q	0.542	1.00
32_T	88_V	0.539	1.00
291_V	294_K	0.539	1.00
204_L	234_G	0.538	1.00
121_C	134_Y	0.537	1.00
221_L	224_I	0.537	1.00
23_F	27_A	0.537	1.00
136_V	139_P	0.536	1.00
60_V	292_I	0.536	1.00
233_L	256_T	0.536	1.00
149_A	251_F	0.535	1.00
266_N	311_K	0.532	1.00
33_I	60_V	0.532	1.00
116_I	287_Q	0.531	1.00
83_L	88_V	0.530	1.00
278_K	281_G	0.530	1.00
206_K	231_A	0.530	1.00
237_K	264_E	0.525	1.00
144_K	147_G	0.525	1.00
79_F	82_T	0.520	1.00
116_I	284_V	0.519	1.00
217_S	220_D	0.518	1.00
19_G	23_F	0.517	1.00
210_V	214_L	0.514	1.00
205_D	208_I	0.514	1.00
208_I	234_G	0.514	1.00
303_Q	306_I	0.512	1.00
165_A	197_A	0.512	1.00
223_A	249_A	0.510	1.00
103_R	107_R	0.509	1.00
287_Q	291_V	0.509	1.00
235_A	239_V	0.506	1.00
215_I	239_V	0.504	1.00
263_L	266_N	0.502	1.00
196_V	217_S	0.502	1.00
168_N	200_E	0.502	1.00
114_P	291_V	0.502	1.00
84_V	107_R	0.502	1.00
229_G	259_I	0.501	1.00
290_K	300_K	0.501	1.00
190_V	193_A	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	0.8991	100	0.194	Contact Map
3dbiA	2	0.8318	100	0.199	Contact Map
4o5aA	2	0.8104	100	0.201	Contact Map
3h5oA	2	0.8135	100	0.206	Contact Map
3e3mA	2	0.8043	100	0.207	Contact Map
3kjxA	2	0.9083	100	0.207	Contact Map
1qpzA	2	0.9327	100	0.208	Contact Map
3bilA	2	0.7706	100	0.21	Contact Map
2o20A	2	0.8257	100	0.211	Contact Map
3huuA	2	0.8012	100	0.213	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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