YTFQ - ECOLI - GREMLIN Contacts

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YTFQ - ABC transporter periplasmic-binding protein YtfQ

UniProt:	P39325	Sequences: MWKRLLIVSAVSAAMSSMALAAPLTVGFSQVGSESGWRAAETNVAKSEAEKRGITLKIADGQQKQENQIKAVRSFVAQGVDAIFIAPVVATGWEPVLKEAKDAEIPVFLLDRSIDVKDKSLYMTTVTADNILEGKLIGDWLVKEVNGKPCNVVELQGTVGASVAIDRKKGFAEAIKNAPNIKIIRSQSGDFTRSKGKEVMESFIKAENNGKNICMVYAHNDDMVIGAIQAIKEAGLKPGKDILTGSIDGVPDIYKAMMDGEANASVELTPNMAGPAFDALEKYKKDGTMPEKLTLTKSTLYLPDTAKEELEKKKNMGY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG12517
Length:	318 (277)
Sequences:	38410 (28583)
Seq/√Len:	1717.4

ECOLI - YTFQ LACI ALSB GALS XYLF GALR CYTR PURR CRA RBSB IDNR ASCG GNTR MALI ARAF RBSR LSRB DGAL YCJW TORT YPHF EBGR TRER XYLR
BACSU - DEGA CCPA KDGR RBSR NTDR YKVZ RBSB EXUR MSMR ARAR 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
131_I	173_E	3.422	1.00
148_K	214_C	3.189	1.00
237_K	240_K	3.075	1.00
82_A	280_L	2.771	1.00
137_I	245_G	2.713	1.00
168_K	172_A	2.622	1.00
249_G	267_E	2.573	1.00
148_K	243_L	2.520	1.00
124_T	283_Y	2.469	1.00
135_K	177_N	2.332	1.00
197_K	233_E	2.256	1.00
48_E	51_K	2.256	1.00
201_E	234_A	2.233	1.00
139_D	174_A	2.168	1.00
48_E	278_D	2.124	1.00
135_K	173_E	2.124	1.00
201_E	230_A	2.123	1.00
135_K	174_A	2.121	1.00
142_V	178_A	2.103	1.00
132_L	136_L	2.068	1.00
275_P	278_D	2.059	1.00
49_A	277_F	2.010	1.00
133_E	247_I	1.990	1.00
141_L	215_M	1.988	1.00
44_V	273_A	1.987	1.00
48_E	274_G	1.966	1.00
131_I	169_K	1.960	1.00
134_G	138_G	1.929	1.00
196_G	226_G	1.870	1.00
282_K	287_G	1.829	1.00
139_D	143_K	1.814	1.00
134_G	217_Y	1.796	1.00
138_G	171_F	1.795	1.00
267_E	299_T	1.782	1.00
153_V	213_I	1.773	1.00
27_G	80_V	1.769	1.00
139_D	178_A	1.753	1.00
218_A	227_A	1.746	1.00
154_E	219_H	1.734	1.00
135_K	139_D	1.724	1.00
197_K	230_A	1.719	1.00
205_K	234_A	1.718	1.00
207_E	211_K	1.716	1.00
200_M	227_A	1.708	1.00
231_I	242_I	1.675	1.00
110_L	276_A	1.669	1.00
232_K	259_D	1.641	1.00
136_L	298_S	1.637	1.00
236_L	241_D	1.619	1.00
275_P	294_T	1.608	1.00
230_A	234_A	1.606	1.00
132_L	135_K	1.601	1.00
169_K	173_E	1.584	1.00
48_E	52_R	1.552	1.00
151_N	212_N	1.552	1.00
237_K	241_D	1.530	1.00
261_E	304_D	1.529	1.00
140_W	143_K	1.526	1.00
142_V	174_A	1.517	1.00
230_A	233_E	1.497	1.00
281_E	285_K	1.491	1.00
271_N	275_P	1.470	1.00
166_D	169_K	1.462	1.00
140_W	302_L	1.457	1.00
172_A	176_K	1.451	1.00
197_K	229_Q	1.443	1.00
129_D	132_L	1.439	1.00
52_R	281_E	1.437	1.00
24_L	81_D	1.434	1.00
48_E	277_F	1.397	1.00
140_W	144_E	1.393	1.00
190_D	195_K	1.391	1.00
151_N	214_C	1.388	1.00
207_E	212_N	1.386	1.00
249_G	303_P	1.382	1.00
174_A	177_N	1.370	1.00
133_E	298_S	1.367	1.00
134_G	170_G	1.362	1.00
231_I	236_L	1.351	1.00
271_N	274_G	1.348	1.00
138_G	170_G	1.328	1.00
183_I	186_S	1.326	1.00
197_K	201_E	1.325	1.00
151_N	182_K	1.325	1.00
153_V	203_F	1.320	1.00
138_G	142_V	1.312	1.00
131_I	135_K	1.309	1.00
98_K	102_D	1.304	1.00
200_M	231_I	1.299	1.00
201_E	233_E	1.299	1.00
138_G	174_A	1.289	1.00
151_N	184_I	1.288	1.00
84_F	276_A	1.288	1.00
27_G	75_F	1.287	1.00
278_D	282_K	1.278	1.00
59_A	71_A	1.264	1.00
201_E	205_K	1.262	1.00
170_G	174_A	1.257	1.00
24_L	54_I	1.256	1.00
59_A	75_F	1.240	1.00
184_I	187_Q	1.235	1.00
136_L	139_D	1.234	1.00
148_K	215_M	1.228	1.00
200_M	216_V	1.228	1.00
45_A	277_F	1.228	1.00
26_V	49_A	1.215	1.00
73_R	99_E	1.215	1.00
49_A	56_L	1.215	1.00
232_K	261_E	1.200	1.00
140_W	306_A	1.199	1.00
28_F	45_A	1.190	1.00
15_M	18_M	1.190	1.00
25_T	55_T	1.174	1.00
172_A	183_I	1.162	1.00
207_E	213_I	1.155	1.00
226_G	230_A	1.153	1.00
171_F	175_I	1.146	1.00
243_L	306_A	1.142	1.00
131_I	170_G	1.140	1.00
25_T	57_K	1.140	1.00
131_I	166_D	1.136	1.00
46_K	50_E	1.136	1.00
228_I	244_T	1.131	1.00
154_E	168_K	1.130	1.00
194_S	198_E	1.124	1.00
52_R	278_D	1.105	1.00
245_G	263_N	1.104	1.00
174_A	178_A	1.103	1.00
199_V	202_S	1.103	1.00
216_V	227_A	1.097	1.00
14_A	17_S	1.097	1.00
202_S	206_A	1.095	1.00
192_T	195_K	1.095	1.00
173_E	177_N	1.089	1.00
139_D	177_N	1.083	1.00
28_F	56_L	1.077	1.00
273_A	277_F	1.071	1.00
45_A	84_F	1.067	1.00
67_N	70_K	1.067	1.00
171_F	217_Y	1.061	1.00
155_L	227_A	1.057	1.00
275_P	279_A	1.055	1.00
152_V	175_I	1.053	1.00
165_I	169_K	1.052	1.00
137_I	217_Y	1.049	1.00
142_V	181_I	1.046	1.00
193_R	229_Q	1.044	1.00
50_E	67_N	1.044	1.00
195_K	198_E	1.033	1.00
169_K	172_A	1.033	1.00
151_N	211_K	1.027	1.00
221_D	246_S	1.026	1.00
69_I	73_R	1.025	1.00
218_A	223_M	1.024	1.00
42_T	46_K	1.016	1.00
274_G	278_D	1.012	1.00
52_R	285_K	1.005	1.00
221_D	265_S	0.999	1.00
54_I	281_E	0.999	1.00
198_E	202_S	0.989	1.00
218_A	224_V	0.988	1.00
149_P	214_C	0.983	1.00
132_L	297_K	0.982	1.00
275_P	296_T	0.980	1.00
144_E	302_L	0.972	1.00
144_E	306_A	0.971	1.00
162_S	166_D	0.971	1.00
51_K	274_G	0.970	1.00
280_L	284_K	0.958	1.00
94_E	98_K	0.957	1.00
143_K	178_A	0.954	1.00
196_G	200_M	0.951	1.00
152_V	215_M	0.943	1.00
200_M	204_I	0.939	1.00
124_T	279_A	0.938	1.00
279_A	294_T	0.938	1.00
43_N	47_S	0.934	1.00
64_K	67_N	0.933	1.00
159_V	188_S	0.931	1.00
37_W	270_P	0.928	1.00
138_G	175_I	0.927	1.00
142_V	149_P	0.925	1.00
157_G	191_F	0.924	1.00
299_T	302_L	0.916	1.00
84_F	280_L	0.912	1.00
137_I	266_V	0.909	1.00
267_E	301_Y	0.899	1.00
130_N	167_R	0.891	1.00
269_T	299_T	0.891	1.00
45_A	273_A	0.881	1.00
26_V	84_F	0.877	1.00
149_P	181_I	0.872	1.00
160_G	165_I	0.867	1.00
221_D	249_G	0.866	1.00
216_V	242_I	0.864	1.00
228_I	258_M	0.863	1.00
128_A	269_T	0.860	1.00
73_R	77_A	0.859	1.00
198_E	201_E	0.858	1.00
156_Q	168_K	0.856	1.00
25_T	78_Q	0.851	1.00
153_V	216_V	0.850	1.00
204_I	230_A	0.847	1.00
82_A	284_K	0.847	1.00
129_D	295_L	0.847	1.00
236_L	242_I	0.845	1.00
224_V	246_S	0.842	1.00
189_G	223_M	0.841	1.00
231_I	244_T	0.840	1.00
41_E	110_L	0.839	1.00
47_S	51_K	0.831	1.00
195_K	199_V	0.829	1.00
229_Q	232_K	0.820	1.00
28_F	42_T	0.819	1.00
173_E	176_K	0.818	1.00
228_I	238_P	0.817	1.00
44_V	274_G	0.816	1.00
70_K	73_R	0.809	1.00
45_A	56_L	0.808	1.00
128_A	268_L	0.807	1.00
279_A	282_K	0.807	1.00
42_T	58_I	0.806	1.00
277_F	281_E	0.801	1.00
126_V	279_A	0.801	1.00
67_N	71_A	0.800	1.00
128_A	298_S	0.794	1.00
43_N	46_K	0.793	1.00
249_G	301_Y	0.788	1.00
132_L	298_S	0.787	1.00
175_I	183_I	0.787	1.00
23_P	81_D	0.781	1.00
200_M	230_A	0.780	1.00
57_K	80_V	0.778	1.00
101_K	123_M	0.777	1.00
141_L	245_G	0.776	1.00
140_W	300_L	0.773	1.00
99_E	102_D	0.770	1.00
155_L	218_A	0.769	1.00
44_V	48_E	0.769	1.00
204_I	234_A	0.767	1.00
154_E	217_Y	0.765	1.00
269_T	296_T	0.762	1.00
127_T	295_L	0.761	1.00
57_K	78_Q	0.760	1.00
246_S	265_S	0.756	1.00
29_S	71_A	0.750	1.00
175_I	181_I	0.749	1.00
47_S	274_G	0.749	1.00
212_N	236_L	0.748	1.00
96_V	99_E	0.747	1.00
140_W	263_N	0.743	1.00
166_D	170_G	0.743	1.00
248_D	268_L	0.740	1.00
27_G	83_I	0.738	1.00
302_L	306_A	0.737	1.00
31_V	38_R	0.735	1.00
200_M	203_F	0.734	1.00
82_A	108_F	0.732	1.00
253_I	262_A	0.730	1.00
129_D	297_K	0.723	1.00
125_T	293_L	0.719	1.00
22_A	81_D	0.716	1.00
62_Q	67_N	0.713	1.00
135_K	170_G	0.713	1.00
231_I	238_P	0.712	1.00
84_F	110_L	0.711	1.00
256_A	261_E	0.711	1.00
46_K	56_L	0.710	1.00
98_K	101_K	0.708	1.00
100_A	107_V	0.700	1.00
202_S	205_K	0.699	1.00
76_V	103_A	0.697	1.00
191_F	219_H	0.697	1.00
229_Q	261_E	0.694	1.00
136_L	266_V	0.689	1.00
26_V	277_F	0.687	1.00
220_N	248_D	0.683	1.00
22_A	285_K	0.681	1.00
164_A	191_F	0.679	1.00
66_E	70_K	0.676	1.00
221_D	224_V	0.673	1.00
109_L	114_I	0.663	1.00
225_I	252_D	0.662	1.00
69_I	96_V	0.660	1.00
111_D	163_V	0.659	1.00
82_A	276_A	0.659	1.00
282_K	286_D	0.659	1.00
144_E	243_L	0.659	1.00
217_Y	245_G	0.658	1.00
154_E	171_F	0.656	1.00
183_I	187_Q	0.655	1.00
225_I	258_M	0.655	1.00
249_G	253_I	0.654	1.00
117_K	122_Y	0.651	1.00
229_Q	233_E	0.650	1.00
189_G	195_K	0.649	1.00
206_A	211_K	0.647	1.00
72_V	83_I	0.646	1.00
171_F	183_I	0.645	1.00
157_G	164_A	0.645	1.00
35_S	222_D	0.644	1.00
76_V	105_I	0.637	1.00
108_F	283_Y	0.636	1.00
142_V	175_I	0.635	1.00
40_A	270_P	0.634	1.00
44_V	270_P	0.633	1.00
152_V	214_C	0.630	1.00
221_D	250_V	0.629	1.00
193_R	252_D	0.627	1.00
23_P	55_T	0.626	1.00
187_Q	206_A	0.625	1.00
200_M	226_G	0.625	1.00
220_N	223_M	0.623	1.00
263_N	306_A	0.622	1.00
109_L	125_T	0.622	1.00
111_D	130_N	0.619	1.00
228_I	232_K	0.618	1.00
206_A	212_N	0.617	1.00
196_G	199_V	0.617	1.00
261_E	303_P	0.614	1.00
253_I	265_S	0.613	1.00
141_L	217_Y	0.612	1.00
217_Y	247_I	0.611	1.00
70_K	74_S	0.610	1.00
127_T	293_L	0.609	1.00
26_V	284_K	0.604	1.00
41_E	270_P	0.603	1.00
83_I	105_I	0.602	1.00
101_K	107_V	0.602	1.00
16_S	20_L	0.602	1.00
54_I	81_D	0.600	1.00
229_Q	259_D	0.600	1.00
109_L	123_M	0.598	1.00
108_F	280_L	0.597	1.00
231_I	234_A	0.596	1.00
65_Q	69_I	0.594	1.00
46_K	60_D	0.591	1.00
224_V	262_A	0.589	1.00
229_Q	256_A	0.586	1.00
232_K	237_K	0.586	1.00
206_A	213_I	0.586	1.00
117_K	123_M	0.584	1.00
151_N	187_Q	0.583	1.00
26_V	82_A	0.583	1.00
37_W	41_E	0.583	1.00
203_F	207_E	0.582	1.00
101_K	122_Y	0.581	1.00
130_N	163_V	0.580	1.00
49_A	54_I	0.580	1.00
218_A	246_S	0.580	1.00
38_R	86_A	0.580	1.00
136_L	140_W	0.578	1.00
124_T	292_K	0.577	1.00
214_C	243_L	0.576	1.00
26_V	54_I	0.575	1.00
247_I	268_L	0.575	1.00
71_A	74_S	0.572	1.00
178_A	181_I	0.569	1.00
164_A	219_H	0.566	1.00
113_S	125_T	0.565	1.00
193_R	226_G	0.565	1.00
108_F	126_V	0.561	1.00
95_P	98_K	0.559	1.00
99_E	103_A	0.557	1.00
167_R	268_L	0.552	1.00
108_F	279_A	0.552	1.00
130_N	166_D	0.550	1.00
199_V	203_F	0.548	1.00
225_I	250_V	0.547	1.00
137_I	215_M	0.547	1.00
279_A	283_Y	0.547	1.00
59_A	74_S	0.546	1.00
127_T	130_N	0.546	1.00
140_W	245_G	0.545	1.00
76_V	79_G	0.545	1.00
197_K	226_G	0.544	1.00
135_K	138_G	0.544	1.00
272_M	296_T	0.544	1.00
111_D	272_M	0.542	1.00
258_M	261_E	0.539	1.00
283_Y	286_D	0.537	1.00
151_N	213_I	0.533	1.00
108_F	276_A	0.532	1.00
116_V	122_Y	0.532	1.00
17_S	20_L	0.532	1.00
194_S	197_K	0.530	1.00
238_P	241_D	0.529	1.00
69_I	99_E	0.524	1.00
54_I	284_K	0.524	1.00
253_I	256_A	0.523	1.00
49_A	281_E	0.522	1.00
152_V	171_F	0.521	1.00
107_V	123_M	0.521	1.00
161_A	164_A	0.520	1.00
221_D	253_I	0.520	1.00
43_N	62_Q	0.520	1.00
215_M	243_L	0.519	1.00
151_N	207_E	0.518	1.00
197_K	200_M	0.517	1.00
191_F	223_M	0.517	1.00
227_A	231_I	0.515	1.00
213_I	216_V	0.514	1.00
275_P	282_K	0.511	1.00
25_T	80_V	0.510	1.00
155_L	199_V	0.508	1.00
36_G	222_D	0.508	1.00
233_E	259_D	0.508	1.00
144_E	148_K	0.507	1.00
25_T	81_D	0.506	1.00
148_K	180_N	0.505	1.00
189_G	196_G	0.503	1.00
74_S	77_A	0.503	1.00
73_R	76_V	0.503	1.00
23_P	54_I	0.503	1.00
95_P	99_E	0.500	1.00
75_F	80_V	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
3huuA	2	0.8333	100	0.132	Contact Map
2hsgA	1	0.9057	100	0.14	Contact Map
2iksA	2	0.8616	100	0.143	Contact Map
4o5aA	2	0.8428	100	0.152	Contact Map
1qpzA	2	0.9403	100	0.152	Contact Map
3dbiA	2	0.8616	100	0.153	Contact Map
3e3mA	2	0.8333	100	0.153	Contact Map
3h5oA	2	0.8396	100	0.154	Contact Map
2o20A	2	0.8553	100	0.156	Contact Map
3bilA	2	0.805	100	0.156	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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