Q97YP1 - SULSO - GREMLIN Contacts

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Q97YP1 - Oligo/dipeptide transport, permease protein (DppB-2)

UniProt:	Q97YP1	Sequences: MIKSYMGFLNYAIKRAVDRIILLLGLVILLWFVVEALPELFGVNPAIWYAPVGQLGKSASYFQNIINDITTLYGFNQPLYVQFIRYLYALFSFNLGYDFQHHEYVINEVLQYLPYTIILTLPPFIFQTLLAIVVGAYAALKRNKAVDHIISNYMILQYNIPGFFILAVLWVVFAVYIKAIPISGIQVLHLNDIVSILKVYWLPWIIQVFIFGFPVRGILMRNTMVDVLDSDFVKYARLSGLKESTVRAIARRNSIIPVITRTGIDLAFILGGIYFIEYIFGIPGMGYLGIIAATELNIPLLTGSFFFLTLYALVVLYAMDLIYPLVDPRIKLR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	333 (302)
Sequences:	20100 (12907)
Seq/√Len:	742.7

ECOLI - YEJB DPPB DDPB NIKB GSIC OPPB SAPB YEJE DPPC SAPC DDPC GSID OPPC NIKC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMI2 Q9HMX0 Q9HMW3 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97YP1 Q97UH1 Q97YQ0 Q97VK6 Q97VF8 Q97UG4 Q97VK7 Q97UG3 Q97UH2 Q97YP9 Q97VF6 Q97YP2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
77_Q	81_V	3.306	1.00
77_Q	85_R	3.249	1.00
35_E	82_Q	3.193	1.00
88_Y	92_S	2.853	1.00
71_T	76_N	2.728	1.00
84_I	88_Y	2.721	1.00
63_Q	67_N	2.690	1.00
224_M	250_A	2.678	1.00
27_V	83_F	2.617	1.00
237_R	243_E	2.480	1.00
122_P	204_W	2.428	1.00
115_Y	282_I	2.420	1.00
245_T	248_A	2.410	1.00
44_N	70_T	2.319	1.00
134_V	150_I	2.242	1.00
233_V	250_A	2.230	1.00
28_I	83_F	2.212	1.00
227_V	232_F	2.209	1.00
287_Y	291_I	2.139	1.00
80_Y	84_I	2.136	1.00
263_G	319_M	2.067	1.00
227_V	230_S	2.052	1.00
108_E	288_L	2.052	1.00
242_K	245_T	2.029	1.00
104_Y	107_N	2.029	1.00
244_S	247_R	2.012	1.00
62_F	65_I	1.947	1.00
66_I	70_T	1.939	1.00
10_N	14_K	1.935	1.00
228_L	250_A	1.919	1.00
129_L	133_V	1.900	1.00
147_D	221_R	1.894	1.00
65_I	68_D	1.893	1.00
126_F	209_F	1.842	1.00
180_I	198_K	1.814	1.00
101_H	108_E	1.811	1.00
68_D	72_L	1.793	1.00
174_A	182_I	1.777	1.00
81_V	85_R	1.776	1.00
26_L	309_T	1.772	1.00
241_L	245_T	1.767	1.00
141_K	144_K	1.740	1.00
180_I	201_W	1.730	1.00
233_V	246_V	1.727	1.00
23_L	310_L	1.724	1.00
259_I	326_V	1.695	1.00
103_E	107_N	1.693	1.00
67_N	70_T	1.691	1.00
145_A	149_I	1.688	1.00
105_V	303_G	1.678	1.00
137_Y	141_K	1.676	1.00
139_A	224_M	1.664	1.00
141_K	146_V	1.662	1.00
67_N	71_T	1.641	1.00
89_A	94_N	1.639	1.00
106_I	110_L	1.635	1.00
235_Y	239_S	1.587	1.00
171_V	176_Y	1.582	1.00
146_V	150_I	1.571	1.00
137_Y	146_V	1.559	1.00
136_A	224_M	1.559	1.00
185_I	282_I	1.554	1.00
44_N	47_I	1.549	1.00
322_I	325_L	1.549	1.00
130_L	133_V	1.545	1.00
8_F	12_A	1.536	1.00
85_R	88_Y	1.509	1.00
204_W	209_F	1.497	1.00
130_L	213_F	1.496	1.00
231_D	234_K	1.496	1.00
289_G	304_S	1.493	1.00
17_V	21_I	1.472	1.00
260_T	323_Y	1.464	1.00
227_V	254_S	1.453	1.00
127_Q	212_G	1.447	1.00
227_V	233_V	1.429	1.00
103_E	111_Q	1.416	1.00
232_F	253_N	1.400	1.00
19_R	313_L	1.392	1.00
90_L	95_L	1.389	1.00
172_V	176_Y	1.388	1.00
24_L	83_F	1.375	1.00
164_F	168_V	1.371	1.00
85_R	89_A	1.364	1.00
128_T	262_T	1.359	1.00
115_Y	185_I	1.359	1.00
95_L	303_G	1.342	1.00
292_A	300_L	1.340	1.00
118_I	185_I	1.333	1.00
169_L	207_Q	1.332	1.00
227_V	250_A	1.318	1.00
143_N	147_D	1.316	1.00
81_V	84_I	1.313	1.00
69_I	72_L	1.302	1.00
69_I	73_Y	1.302	1.00
131_A	220_M	1.300	1.00
111_Q	114_P	1.298	1.00
24_L	28_I	1.291	1.00
118_I	122_P	1.289	1.00
95_L	106_I	1.288	1.00
131_A	216_R	1.281	1.00
74_G	77_Q	1.280	1.00
239_S	249_I	1.278	1.00
115_Y	118_I	1.269	1.00
209_F	213_F	1.269	1.00
108_E	300_L	1.265	1.00
216_R	265_D	1.257	1.00
77_Q	80_Y	1.256	1.00
46_A	66_I	1.255	1.00
27_V	86_Y	1.247	1.00
135_G	139_A	1.245	1.00
78_P	81_V	1.243	1.00
221_R	225_V	1.241	1.00
124_F	262_T	1.229	1.00
9_L	12_A	1.229	1.00
13_I	17_V	1.225	1.00
140_L	243_E	1.224	1.00
103_E	108_E	1.217	1.00
157_Q	214_P	1.209	1.00
97_Y	104_Y	1.200	1.00
141_K	243_E	1.198	1.00
288_L	300_L	1.185	1.00
219_L	261_R	1.177	1.00
91_F	94_N	1.176	1.00
160_I	165_I	1.173	1.00
135_G	220_M	1.163	1.00
172_V	177_I	1.162	1.00
150_I	217_G	1.157	1.00
304_S	308_L	1.155	1.00
220_M	258_V	1.150	1.00
47_I	66_I	1.134	1.00
256_I	323_Y	1.130	1.00
118_I	200_Y	1.120	1.00
138_A	150_I	1.119	1.00
139_A	228_L	1.114	1.00
28_I	32_F	1.094	1.00
154_M	217_G	1.073	1.00
145_A	148_H	1.070	1.00
74_G	85_R	1.067	1.00
321_L	325_L	1.064	1.00
107_N	111_Q	1.061	1.00
290_I	294_T	1.059	1.00
267_A	312_A	1.058	1.00
315_V	319_M	1.056	1.00
89_A	92_S	1.048	1.00
24_L	87_L	1.044	1.00
162_G	276_I	1.040	1.00
220_M	224_M	1.035	1.00
201_W	205_I	1.034	1.00
134_V	217_G	1.033	1.00
23_L	313_L	1.031	1.00
139_A	225_V	1.027	1.00
110_L	114_P	1.026	1.00
207_Q	211_F	1.021	1.00
173_F	177_I	1.020	1.00
168_V	172_V	1.020	1.00
27_V	306_F	1.013	1.00
100_Q	295_E	1.010	1.00
236_A	241_L	1.002	1.00
16_A	20_I	1.001	1.00
186_Q	199_V	1.000	1.00
19_R	317_Y	0.997	1.00
123_P	209_F	0.989	1.00
98_D	297_N	0.981	1.00
166_L	207_Q	0.981	1.00
108_E	111_Q	0.977	1.00
68_D	71_T	0.974	1.00
224_M	254_S	0.973	1.00
31_W	113_L	0.973	1.00
169_L	202_L	0.971	1.00
71_T	77_Q	0.967	1.00
9_L	13_I	0.964	1.00
126_F	204_W	0.964	1.00
243_E	246_V	0.960	1.00
12_A	321_L	0.959	1.00
180_I	202_L	0.956	1.00
236_A	246_V	0.955	1.00
197_L	201_W	0.952	1.00
98_D	103_E	0.952	1.00
323_Y	327_D	0.946	1.00
293_A	296_L	0.945	1.00
153_Y	157_Q	0.945	1.00
28_I	79_L	0.940	1.00
133_V	136_A	0.938	1.00
35_E	79_L	0.934	1.00
254_S	257_P	0.934	1.00
64_N	68_D	0.930	1.00
291_I	295_E	0.924	1.00
107_N	110_L	0.919	1.00
241_L	246_V	0.919	1.00
97_Y	102_H	0.918	1.00
16_A	317_Y	0.918	1.00
266_L	315_V	0.915	1.00
200_Y	204_W	0.914	1.00
298_I	302_T	0.913	1.00
50_A	69_I	0.913	1.00
318_A	322_I	0.912	1.00
147_D	225_V	0.909	1.00
120_T	269_I	0.907	1.00
288_L	292_A	0.906	1.00
142_R	229_D	0.903	1.00
39_E	296_L	0.903	1.00
151_S	217_G	0.903	1.00
25_G	29_L	0.903	1.00
32_F	79_L	0.902	1.00
173_F	180_I	0.896	1.00
237_R	246_V	0.896	1.00
11_Y	324_P	0.895	1.00
259_I	319_M	0.886	1.00
17_V	321_L	0.883	1.00
90_L	306_F	0.883	1.00
112_Y	288_L	0.879	1.00
289_G	292_A	0.879	1.00
143_N	148_H	0.878	1.00
136_A	251_R	0.867	1.00
149_I	153_Y	0.864	1.00
64_N	67_N	0.861	1.00
109_V	303_G	0.860	1.00
131_A	135_G	0.854	1.00
99_F	299_P	0.853	1.00
278_Y	287_Y	0.849	1.00
32_F	35_E	0.847	1.00
324_P	330_I	0.844	1.00
314_V	318_A	0.842	1.00
88_Y	91_F	0.831	1.00
246_V	250_A	0.830	1.00
116_T	120_T	0.828	1.00
236_A	249_I	0.828	1.00
132_I	220_M	0.826	1.00
83_F	87_L	0.824	1.00
166_L	279_I	0.822	1.00
50_A	61_Y	0.821	1.00
123_P	208_V	0.820	1.00
140_L	247_R	0.820	1.00
124_F	266_L	0.818	1.00
63_Q	66_I	0.812	1.00
247_R	250_A	0.810	1.00
134_V	213_F	0.810	1.00
118_I	121_L	0.806	1.00
121_L	125_I	0.804	1.00
148_H	151_S	0.804	1.00
46_A	50_A	0.803	1.00
84_I	87_L	0.797	1.00
205_I	209_F	0.796	1.00
226_D	230_S	0.796	1.00
128_T	133_V	0.793	1.00
223_T	254_S	0.788	1.00
123_P	127_Q	0.784	1.00
146_V	149_I	0.783	1.00
267_A	315_V	0.781	1.00
122_P	282_I	0.781	1.00
21_I	24_L	0.778	1.00
44_N	50_A	0.777	1.00
87_L	91_F	0.777	1.00
213_F	217_G	0.775	1.00
131_A	217_G	0.774	1.00
158_Y	214_P	0.771	1.00
35_E	298_I	0.769	1.00
86_Y	90_L	0.767	1.00
135_G	224_M	0.765	1.00
323_Y	330_I	0.762	1.00
29_L	33_V	0.761	1.00
45_P	48_W	0.758	1.00
223_T	227_V	0.758	1.00
220_M	254_S	0.758	1.00
165_I	210_I	0.755	1.00
212_G	215_V	0.755	1.00
142_R	225_V	0.755	1.00
87_L	90_L	0.754	1.00
273_I	276_I	0.750	1.00
109_V	304_S	0.749	1.00
133_V	137_Y	0.748	1.00
119_L	204_W	0.748	1.00
46_A	69_I	0.746	1.00
61_Y	66_I	0.743	1.00
185_I	200_Y	0.736	1.00
310_L	314_V	0.736	1.00
132_I	258_V	0.736	1.00
28_I	80_Y	0.734	1.00
173_F	202_L	0.734	1.00
303_G	307_F	0.731	1.00
201_W	204_W	0.729	1.00
121_L	266_L	0.727	1.00
30_L	305_F	0.726	1.00
173_F	179_A	0.725	1.00
236_A	239_S	0.722	1.00
321_L	324_P	0.722	1.00
117_I	121_L	0.716	1.00
223_T	226_D	0.711	1.00
150_I	154_M	0.710	1.00
105_V	300_L	0.708	1.00
127_Q	209_F	0.708	1.00
162_G	210_I	0.707	1.00
130_L	134_V	0.701	1.00
220_M	223_T	0.701	1.00
170_W	182_I	0.701	1.00
114_P	118_I	0.700	1.00
88_Y	93_F	0.698	1.00
114_P	117_I	0.697	1.00
31_W	35_E	0.697	1.00
49_Y	69_I	0.696	1.00
61_Y	65_I	0.688	1.00
207_Q	276_I	0.688	1.00
105_V	288_L	0.684	1.00
302_T	305_F	0.684	1.00
278_Y	290_I	0.673	1.00
130_L	209_F	0.666	1.00
176_Y	179_A	0.664	1.00
17_V	20_I	0.661	1.00
312_A	316_L	0.658	1.00
110_L	113_L	0.654	1.00
20_I	24_L	0.653	1.00
292_A	301_L	0.653	1.00
324_P	331_K	0.652	1.00
214_P	217_G	0.648	1.00
15_R	18_D	0.646	1.00
108_E	112_Y	0.645	1.00
291_I	294_T	0.643	1.00
23_L	27_V	0.642	1.00
149_I	152_N	0.642	1.00
288_L	304_S	0.642	1.00
259_I	322_I	0.641	1.00
138_A	147_D	0.640	1.00
113_L	117_I	0.640	1.00
162_G	166_L	0.637	1.00
308_L	312_A	0.635	1.00
183_S	281_G	0.633	1.00
234_K	237_R	0.632	1.00
46_A	70_T	0.631	1.00
162_G	165_I	0.631	1.00
184_G	199_V	0.628	1.00
154_M	214_P	0.628	1.00
157_Q	210_I	0.627	1.00
283_P	287_Y	0.625	1.00
38_P	107_N	0.625	1.00
20_I	314_V	0.624	1.00
181_P	184_G	0.623	1.00
70_T	76_N	0.622	1.00
171_V	175_V	0.617	1.00
57_K	61_Y	0.615	1.00
123_P	273_I	0.612	1.00
216_R	261_R	0.611	1.00
128_T	216_R	0.610	1.00
112_Y	287_Y	0.610	1.00
289_G	308_L	0.606	1.00
202_L	207_Q	0.605	1.00
241_L	249_I	0.605	1.00
129_L	132_I	0.604	1.00
301_L	305_F	0.604	1.00
70_T	75_F	0.604	1.00
46_A	49_Y	0.604	1.00
93_F	97_Y	0.602	1.00
21_I	25_G	0.602	1.00
181_P	199_V	0.602	1.00
98_D	101_H	0.598	1.00
147_D	151_S	0.597	1.00
26_L	30_L	0.597	1.00
57_K	60_S	0.595	1.00
32_F	36_A	0.593	1.00
215_V	261_R	0.592	1.00
152_N	156_L	0.591	1.00
27_V	87_L	0.589	1.00
152_N	155_I	0.588	1.00
67_N	76_N	0.587	1.00
122_P	201_W	0.587	1.00
278_Y	291_I	0.587	1.00
79_L	82_Q	0.586	1.00
22_L	313_L	0.584	1.00
148_H	152_N	0.584	1.00
255_I	259_I	0.583	1.00
122_P	126_F	0.582	1.00
44_N	49_Y	0.582	1.00
56_G	61_Y	0.582	1.00
11_Y	317_Y	0.580	1.00
116_T	277_E	0.578	1.00
65_I	69_I	0.578	1.00
169_L	205_I	0.578	1.00
216_R	258_V	0.577	1.00
35_E	302_T	0.576	1.00
44_N	48_W	0.575	1.00
45_P	49_Y	0.575	1.00
232_F	236_A	0.575	1.00
216_R	220_M	0.574	1.00
261_R	265_D	0.573	1.00
198_K	202_L	0.572	1.00
181_P	198_K	0.569	1.00
14_K	17_V	0.569	1.00
220_M	251_R	0.568	1.00
180_I	184_G	0.567	1.00
263_G	315_V	0.565	1.00
199_V	202_L	0.564	1.00
319_M	323_Y	0.563	1.00
219_L	223_T	0.562	1.00
234_K	238_L	0.562	1.00
288_L	291_I	0.562	1.00
162_G	211_F	0.561	1.00
164_F	167_A	0.560	1.00
174_A	198_K	0.559	1.00
209_F	212_G	0.555	1.00
133_V	247_R	0.555	1.00
125_I	129_L	0.554	1.00
120_T	273_I	0.552	1.00
265_D	268_F	0.552	1.00
274_Y	278_Y	0.548	1.00
302_T	306_F	0.547	1.00
274_Y	290_I	0.547	1.00
128_T	132_I	0.546	1.00
81_V	88_Y	0.546	1.00
205_I	210_I	0.544	1.00
138_A	151_S	0.543	1.00
215_V	265_D	0.543	1.00
141_K	147_D	0.541	1.00
18_D	21_I	0.539	1.00
118_I	282_I	0.538	1.00
34_V	301_L	0.538	1.00
46_A	73_Y	0.538	1.00
256_I	330_I	0.537	1.00
215_V	219_L	0.537	1.00
100_Q	291_I	0.537	1.00
95_L	109_V	0.534	1.00
255_I	258_V	0.534	1.00
136_A	247_R	0.534	1.00
198_K	201_W	0.533	1.00
19_R	22_L	0.533	1.00
211_F	214_P	0.530	1.00
311_Y	315_V	0.530	1.00
119_L	277_E	0.530	1.00
247_R	252_R	0.528	1.00
144_K	147_D	0.526	1.00
122_P	125_I	0.525	1.00
317_Y	321_L	0.524	1.00
242_K	246_V	0.520	1.00
177_I	180_I	0.520	1.00
144_K	149_I	0.519	1.00
160_I	164_F	0.519	1.00
124_F	128_T	0.519	1.00
233_V	237_R	0.518	1.00
18_D	22_L	0.518	1.00
72_L	102_H	0.517	1.00
90_L	93_F	0.515	1.00
136_A	140_L	0.515	1.00
122_P	197_L	0.514	1.00
164_F	207_Q	0.514	1.00
116_T	273_I	0.513	1.00
126_F	205_I	0.513	1.00
300_L	304_S	0.512	1.00
309_T	313_L	0.512	1.00
224_M	228_L	0.509	1.00
50_A	56_G	0.508	1.00
101_H	300_L	0.507	1.00
230_S	234_K	0.502	1.00
62_F	67_N	0.500	1.00
247_R	251_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
3tuiA	2	0.6246	99.9	0.686	Contact Map
4tquM	1	0.8078	99.8	0.696	Contact Map
2onkC	2	0.7447	99.8	0.712	Contact Map
3rlfF	1	0.8258	99.8	0.714	Contact Map
3d31C	2	0.7387	99.8	0.715	Contact Map
4ymuD	2	0.6276	99.8	0.721	Contact Map
4tquN	1	0.7778	99.7	0.734	Contact Map
3rlfG	1	0.8228	99.6	0.754	Contact Map
3j9tb	1	0	5	0.967	Contact Map
2yevC	1	0.0871	4.8	0.967	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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