YTEP - BACSU - GREMLIN Contacts

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YTEP - Uncharacterized multiple-sugar transport system permease YteP

UniProt:	C0SPB3	Sequences: MKTAEAQAPAVDAVIFKKEKRKRLLIKLIQQKYLYLMILPGCIYFLLFKYVPMWGIVIAFQDYQPFLGILGSEWVGLKHFIRLFTEPTFFLLLKNTLVLFALNLAIFFPVPILLALLLNEVRIALFKKFVQTLIYIPHFMSWVIVVSLSFVLLTVDGGLINELIVFFGGEKINFLLNEEWFRPLYILQVIWREAGWSTIIYLAAITAVDPQLYEAAKMDGAGRLRQMWHITLPAIKSVIVVLLILKIGDTLELGFEHVYLLLNATNREVAEIFDTYVYTAGLKQGQFSYSTAVGVFKAAVGLILVMLANRLAKKFGEEGIY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	321 (257)
Sequences:	68795 (43271)
Seq/√Len:	2699.2

ECOLI - POTH YDCU UGPA YCJO MALF PSTC PSTA THIP MALG YCJP POTB YDCV YNJC CYSW UGPE CYST POTC POTI MODB TAUC YEHY SSUC PHNE YEHW METI PROW
BACSU - YTEP LPLB GANP MDXF ARAP AMYD YESP YURN YURM YESQ YQGH GANQ MDXG LPLC AMYC ARAQ YTCP YQGI YVGM YTLD SSUC OPUAB METP TCYB YXEN TCYL OPUCB OPUBD OPUBB OPUCD
HALSA - Q9HHQ7 Q9HP01 Q9HMT4 Q9HML6 Q9HS11 Q9HR05 Q9HHQ6 Q9HP02 Q9HPK3 Q9HNI9 Q9HS12
SULSO - Q97UZ0 Q97YY2 Q97UF3 Q97YY3 Q97UF4 Q97ZC2 Q97ZT7 Q97VC0 Q97UY9 Q97ZC1 Q97ZT6 Q97Z98

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
225_R	229_H	4.094	1.00
94_K	98_V	3.110	1.00
202_L	206_T	2.934	1.00
217_K	226_Q	2.910	1.00
59_A	80_F	2.803	1.00
91_L	94_K	2.585	1.00
92_L	276_Y	2.580	1.00
120_E	213_Y	2.568	1.00
222_G	225_R	2.532	1.00
213_Y	231_T	2.530	1.00
216_A	226_Q	2.481	1.00
102_L	186_I	2.480	1.00
106_I	190_I	2.431	1.00
78_K	81_I	2.382	1.00
204_A	238_V	2.372	1.00
90_F	94_K	2.343	1.00
81_I	85_T	2.329	1.00
104_L	243_L	2.320	1.00
271_E	279_T	2.319	1.00
224_L	228_W	2.258	1.00
201_Y	239_I	2.255	1.00
223_R	226_Q	2.226	1.00
78_K	82_R	2.224	1.00
112_I	227_M	2.093	1.00
221_A	225_R	2.063	1.00
225_R	228_W	2.018	1.00
286_Q	289_Y	1.999	1.00
205_I	235_I	1.960	1.00
197_S	242_L	1.933	1.00
119_N	206_T	1.913	1.00
212_L	234_A	1.870	1.00
216_A	221_A	1.870	1.00
57_V	61_Q	1.868	1.00
98_V	182_R	1.841	1.00
112_I	235_I	1.774	1.00
108_F	243_L	1.767	1.00
217_K	223_R	1.731	1.00
131_Q	202_L	1.721	1.00
91_L	95_N	1.719	1.00
100_F	247_I	1.709	1.00
123_I	126_F	1.702	1.00
111_P	197_S	1.693	1.00
306_M	310_R	1.680	1.00
213_Y	226_Q	1.653	1.00
82_R	289_Y	1.606	1.00
98_V	102_L	1.603	1.00
182_R	270_A	1.601	1.00
112_I	201_Y	1.598	1.00
103_N	250_T	1.587	1.00
118_L	198_T	1.585	1.00
56_I	295_V	1.583	1.00
114_L	198_T	1.577	1.00
213_Y	217_K	1.518	1.00
39_L	43_I	1.474	1.00
210_P	213_Y	1.449	1.00
264_A	269_V	1.444	1.00
126_F	129_F	1.419	1.00
76_G	79_H	1.397	1.00
99_L	272_I	1.396	1.00
82_R	85_T	1.392	1.00
232_L	239_I	1.387	1.00
197_S	246_K	1.379	1.00
241_V	245_L	1.378	1.00
115_A	201_Y	1.376	1.00
77_L	81_I	1.372	1.00
119_N	202_L	1.366	1.00
205_I	231_T	1.353	1.00
276_Y	280_A	1.351	1.00
54_W	58_I	1.338	1.00
123_I	127_K	1.325	1.00
181_F	270_A	1.318	1.00
51_V	54_W	1.309	1.00
120_E	210_P	1.307	1.00
255_F	278_Y	1.305	1.00
107_F	246_K	1.299	1.00
88_T	91_L	1.296	1.00
201_Y	242_L	1.285	1.00
216_A	230_I	1.278	1.00
109_P	113_L	1.267	1.00
122_R	127_K	1.256	1.00
255_F	259_Y	1.247	1.00
188_Q	261_L	1.246	1.00
96_T	273_F	1.233	1.00
262_L	270_A	1.219	1.00
210_P	214_E	1.218	1.00
153_L	184_L	1.217	1.00
31_Q	34_L	1.215	1.00
257_H	261_L	1.214	1.00
112_I	239_I	1.214	1.00
280_A	286_Q	1.194	1.00
32_K	36_L	1.194	1.00
280_A	284_Q	1.191	1.00
116_L	205_I	1.184	1.00
80_F	295_V	1.180	1.00
222_G	226_Q	1.179	1.00
265_T	269_V	1.176	1.00
211_Q	214_E	1.173	1.00
33_Y	37_M	1.165	1.00
34_L	38_I	1.164	1.00
102_L	105_A	1.159	1.00
208_V	234_A	1.158	1.00
43_I	47_L	1.137	1.00
105_A	109_P	1.135	1.00
281_G	290_S	1.119	1.00
129_F	132_T	1.112	1.00
201_Y	238_V	1.106	1.00
65_P	74_W	1.102	1.00
36_L	40_P	1.102	1.00
108_F	239_I	1.094	1.00
271_E	276_Y	1.083	1.00
55_G	295_V	1.080	1.00
95_N	98_V	1.071	1.00
310_R	313_K	1.067	1.00
236_K	240_V	1.065	1.00
84_F	90_F	1.062	1.00
129_F	133_L	1.050	1.00
272_I	275_T	1.048	1.00
234_A	237_S	1.047	1.00
307_L	311_L	1.045	1.00
62_D	65_P	1.042	1.00
106_I	186_I	1.037	1.00
154_T	157_G	1.036	1.00
116_L	227_M	1.034	1.00
213_Y	223_R	1.030	1.00
183_P	187_L	1.024	1.00
194_A	198_T	1.024	1.00
103_N	107_F	1.023	1.00
271_E	275_T	1.022	1.00
182_R	186_I	1.017	1.00
97_L	101_A	1.015	1.00
93_L	273_F	1.014	1.00
116_L	223_R	1.012	1.00
186_I	190_I	1.011	1.00
279_T	283_K	1.006	1.00
102_L	106_I	1.004	1.00
103_N	189_V	1.003	1.00
200_I	242_L	1.002	1.00
258_V	272_I	0.994	1.00
276_Y	293_V	0.986	1.00
221_A	226_Q	0.980	1.00
119_N	205_I	0.977	1.00
151_V	155_V	0.970	1.00
226_Q	229_H	0.967	1.00
185_Y	258_V	0.966	1.00
30_Q	34_L	0.959	1.00
54_W	57_V	0.953	1.00
113_L	117_L	0.950	1.00
33_Y	36_L	0.949	1.00
89_F	293_V	0.946	1.00
79_H	288_S	0.946	1.00
127_K	206_T	0.945	1.00
35_Y	39_L	0.935	1.00
259_Y	275_T	0.933	1.00
189_V	250_T	0.929	1.00
204_A	235_I	0.925	1.00
125_L	128_K	0.920	1.00
83_L	296_F	0.914	1.00
253_L	257_H	0.911	1.00
36_L	39_L	0.909	1.00
159_L	183_P	0.909	1.00
101_A	105_A	0.907	1.00
253_L	258_V	0.906	1.00
31_Q	35_Y	0.905	1.00
103_N	186_I	0.904	1.00
98_V	183_P	0.901	1.00
58_I	291_T	0.900	1.00
82_R	86_E	0.897	1.00
38_I	42_C	0.897	1.00
46_L	50_Y	0.894	1.00
95_N	182_R	0.890	1.00
236_K	239_I	0.887	1.00
71_G	74_W	0.885	1.00
115_A	119_N	0.884	1.00
149_S	261_L	0.882	1.00
93_L	97_L	0.879	1.00
227_M	232_L	0.878	1.00
264_A	270_A	0.876	1.00
99_L	182_R	0.875	1.00
197_S	201_Y	0.875	1.00
98_V	101_A	0.875	1.00
105_A	243_L	0.856	1.00
106_I	109_P	0.854	1.00
307_L	310_R	0.853	1.00
228_W	232_L	0.852	1.00
118_L	131_Q	0.852	1.00
235_I	238_V	0.850	1.00
188_Q	257_H	0.843	1.00
201_Y	235_I	0.842	1.00
61_Q	65_P	0.831	1.00
246_K	250_T	0.831	1.00
111_P	198_T	0.830	1.00
55_G	294_G	0.829	1.00
58_I	61_Q	0.828	1.00
115_A	205_I	0.823	1.00
59_A	63_Y	0.822	1.00
107_F	111_P	0.822	1.00
289_Y	293_V	0.814	1.00
60_F	75_V	0.808	1.00
149_S	188_Q	0.806	1.00
146_V	260_L	0.806	1.00
276_Y	279_T	0.804	1.00
128_K	131_Q	0.803	1.00
280_A	293_V	0.803	1.00
94_K	97_L	0.802	1.00
135_Y	199_I	0.799	1.00
99_L	189_V	0.796	1.00
142_W	192_R	0.795	1.00
208_V	235_I	0.795	1.00
280_A	289_Y	0.794	1.00
212_L	230_I	0.791	1.00
303_I	307_L	0.785	1.00
102_L	190_I	0.781	1.00
86_E	90_F	0.780	1.00
150_F	154_T	0.774	1.00
82_R	286_Q	0.772	1.00
226_Q	231_T	0.766	1.00
60_F	76_G	0.765	1.00
55_G	291_T	0.764	1.00
115_A	198_T	0.763	1.00
107_F	193_E	0.759	1.00
223_R	227_M	0.758	1.00
183_P	186_I	0.757	1.00
96_T	274_D	0.747	1.00
277_V	293_V	0.745	1.00
118_L	130_V	0.744	1.00
107_F	197_S	0.738	1.00
92_L	95_N	0.738	1.00
40_P	43_I	0.730	1.00
108_F	201_Y	0.729	1.00
210_P	217_K	0.728	1.00
158_G	161_N	0.728	1.00
308_A	311_L	0.725	1.00
181_F	184_L	0.725	1.00
227_M	231_T	0.724	1.00
92_L	273_F	0.724	1.00
81_I	84_F	0.722	1.00
161_N	264_A	0.721	1.00
253_L	272_I	0.720	1.00
100_F	104_L	0.717	1.00
201_Y	205_I	0.717	1.00
184_L	188_Q	0.714	1.00
104_L	247_I	0.713	1.00
58_I	62_D	0.708	1.00
265_T	271_E	0.702	1.00
239_I	242_L	0.702	1.00
291_T	295_V	0.702	1.00
301_G	305_V	0.698	1.00
114_L	194_A	0.698	1.00
62_D	73_E	0.698	1.00
118_L	202_L	0.698	1.00
62_D	74_W	0.697	1.00
273_F	297_K	0.697	1.00
135_Y	138_H	0.696	1.00
236_K	311_L	0.694	1.00
75_V	78_K	0.694	1.00
262_L	271_E	0.690	1.00
142_W	256_E	0.684	1.00
221_A	229_H	0.684	1.00
65_P	73_E	0.683	1.00
37_M	40_P	0.682	1.00
104_L	108_F	0.675	1.00
37_M	41_G	0.675	1.00
256_E	260_L	0.675	1.00
110_V	194_A	0.675	1.00
193_E	246_K	0.669	1.00
99_L	185_Y	0.668	1.00
61_Q	72_S	0.668	1.00
45_F	49_K	0.667	1.00
80_F	292_A	0.667	1.00
61_Q	74_W	0.666	1.00
287_F	291_T	0.664	1.00
215_A	219_D	0.657	1.00
83_L	289_Y	0.657	1.00
145_V	191_W	0.657	1.00
35_Y	38_I	0.654	1.00
90_F	93_L	0.653	1.00
107_F	250_T	0.652	1.00
87_P	91_L	0.651	1.00
146_V	256_E	0.651	1.00
42_C	46_L	0.650	1.00
274_D	297_K	0.649	1.00
288_S	291_T	0.648	1.00
99_L	186_I	0.648	1.00
278_Y	282_L	0.647	1.00
287_F	290_S	0.647	1.00
59_A	292_A	0.646	1.00
193_E	249_D	0.646	1.00
111_P	201_Y	0.643	1.00
184_L	261_L	0.642	1.00
200_I	238_V	0.641	1.00
239_I	243_L	0.639	1.00
238_V	242_L	0.639	1.00
32_K	35_Y	0.638	1.00
30_Q	33_Y	0.636	1.00
231_T	234_A	0.634	1.00
46_L	49_K	0.631	1.00
126_F	130_V	0.630	1.00
66_F	69_I	0.630	1.00
258_V	275_T	0.629	1.00
121_V	127_K	0.628	1.00
117_L	123_I	0.628	1.00
110_V	190_I	0.624	1.00
79_H	82_R	0.621	1.00
95_N	270_A	0.621	1.00
185_Y	262_L	0.616	1.00
114_L	134_I	0.615	1.00
275_T	279_T	0.613	1.00
87_P	90_F	0.611	1.00
117_L	121_V	0.608	1.00
153_L	160_I	0.606	1.00
83_L	293_V	0.603	1.00
149_S	152_L	0.603	1.00
96_T	251_L	0.602	1.00
138_H	195_G	0.602	1.00
215_A	218_M	0.597	1.00
122_R	125_L	0.596	1.00
151_V	154_T	0.596	1.00
138_H	196_W	0.595	1.00
222_G	228_W	0.594	1.00
143_V	260_L	0.592	1.00
107_F	190_I	0.591	1.00
154_T	160_I	0.591	1.00
282_L	285_G	0.589	1.00
88_T	276_Y	0.588	1.00
56_I	60_F	0.581	1.00
134_I	195_G	0.580	1.00
100_F	250_T	0.580	1.00
249_D	252_E	0.577	1.00
108_F	112_I	0.577	1.00
131_Q	199_I	0.575	1.00
41_G	45_F	0.575	1.00
265_T	270_A	0.574	1.00
74_W	78_K	0.572	1.00
59_A	295_V	0.572	1.00
63_Y	72_S	0.572	1.00
226_Q	230_I	0.568	1.00
70_L	73_E	0.564	1.00
99_L	103_N	0.563	1.00
77_L	80_F	0.562	1.00
152_L	160_I	0.562	1.00
128_K	132_T	0.562	1.00
185_Y	189_V	0.561	1.00
302_L	306_M	0.558	1.00
115_A	202_L	0.556	1.00
74_W	77_L	0.555	1.00
130_V	134_I	0.551	1.00
240_V	243_L	0.551	1.00
192_R	257_H	0.549	1.00
86_E	289_Y	0.548	1.00
189_V	253_L	0.548	1.00
72_S	75_V	0.546	1.00
100_F	251_L	0.546	1.00
125_L	129_F	0.546	1.00
61_Q	73_E	0.545	1.00
291_T	294_G	0.544	1.00
248_G	252_E	0.542	1.00
297_K	301_G	0.542	1.00
103_N	190_I	0.541	1.00
104_L	250_T	0.539	1.00
208_V	213_Y	0.538	1.00
243_L	246_K	0.538	1.00
142_W	146_V	0.537	1.00
122_R	210_P	0.536	1.00
277_V	294_G	0.536	1.00
57_V	60_F	0.535	1.00
132_T	136_I	0.535	1.00
192_R	195_G	0.532	1.00
137_P	195_G	0.526	1.00
140_M	144_I	0.525	1.00
116_L	231_T	0.518	1.00
275_T	278_Y	0.515	1.00
80_F	84_F	0.514	1.00
256_E	259_Y	0.513	1.00
60_F	77_L	0.511	1.00
131_Q	206_T	0.507	1.00
114_L	117_L	0.507	1.00
89_F	276_Y	0.506	1.00
228_W	231_T	0.505	1.00
84_F	296_F	0.503	1.00
95_N	272_I	0.503	1.00
93_L	296_F	0.502	1.00
58_I	63_Y	0.501	1.00
44_Y	48_F	0.501	1.00
88_T	271_E	0.500	1.00
246_K	249_D	0.500	1.00
109_P	112_I	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
4tquM	1	0.8847	100	0.31	Contact Map
2onkC	2	0.7819	100	0.365	Contact Map
3d31C	2	0.7726	100	0.372	Contact Map
3rlfF	1	0.9346	100	0.381	Contact Map
3rlfG	1	0.838	100	0.415	Contact Map
4tquN	1	0.8224	100	0.427	Contact Map
4ymuD	2	0.6667	99.9	0.547	Contact Map
3tuiA	2	0.6542	99.9	0.559	Contact Map
4ytpC	1	0.4081	12.8	0.952	Contact Map
1zoyC	1	0.3489	12.6	0.952	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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