OPPB - ECOLI - GREMLIN Contacts

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OPPB - Oligopeptide transport system permease protein OppB

UniProt:	P0AFH2	Sequences: MLKFILRRCLEAIPTLFILITISFFMMRLAPGSPFTGERTLPPEVMANIEAKYHLNDPIMTQYFSYLKQLAHGDFGPSFKYKDYSVNDLVASSFPVSAKLGAAAFFLAVILGVSAGVIAALKQNTKWDYTVMGLAMTGVVIPSFVVAPLLVMIFAIILHWLPGGGWNGGALKFMILPMVALSLAYIASIARITRGSMIEVLHSNFIRTARAKGLPMRRIILRHALKPALLPVLSYMGPAFVGIITGSMVIETIYGLPGIGQLFVNGALNRDYSLVLSLTILVGALTILFNAIVDVLYAVIDPKIRY	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10675
Length:	306 (279)
Sequences:	22420 (14847)
Seq/√Len:	888.9

ECOLI - OPPB DPPB DDPB NIKB YEJB GSIC SAPB YEJE DPPC SAPC NIKC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMW3 Q9HMI2 Q9HMX0 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VF8 Q97VK6 Q97YQ0 Q97UH1 Q97YP1 Q97UG4 Q97VK7 Q97UG3 Q97VF6 Q97UH2 Q97YP9 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
28_R	62_Q	3.207	1.00
57_D	65_S	3.148	1.00
57_D	61_T	3.094	1.00
197_M	224_A	2.762	1.00
64_F	68_K	2.742	1.00
68_K	72_H	2.641	1.00
20_I	63_Y	2.581	1.00
51_A	56_N	2.494	1.00
43_P	47_A	2.473	1.00
103_A	178_M	2.430	1.00
210_R	216_M	2.428	1.00
96_V	256_L	2.396	1.00
218_R	222_R	2.348	1.00
115_A	131_V	2.337	1.00
200_V	205_F	2.320	1.00
261_Q	265_N	2.303	1.00
200_V	203_S	2.216	1.00
21_T	63_Y	2.187	1.00
206_I	224_A	2.186	1.00
128_D	194_R	2.167	1.00
215_P	218_R	2.128	1.00
217_R	221_L	2.109	1.00
89_L	262_L	2.086	1.00
237_G	293_V	2.026	1.00
214_L	218_R	1.995	1.00
60_M	64_F	1.982	1.00
107_L	182_S	1.977	1.00
85_S	88_D	1.974	1.00
33_S	50_E	1.951	1.00
45_V	48_N	1.945	1.00
110_I	114_S	1.870	1.00
201_L	224_A	1.838	1.00
46_M	50_E	1.833	1.00
42_P	45_V	1.820	1.00
118_I	122_K	1.801	1.00
126_K	130_T	1.798	1.00
206_I	219_I	1.788	1.00
122_K	125_T	1.771	1.00
48_N	52_K	1.764	1.00
61_T	65_S	1.750	1.00
19_L	283_G	1.729	1.00
204_N	207_R	1.713	1.00
87_N	91_A	1.687	1.00
122_K	127_W	1.680	1.00
120_A	197_M	1.678	1.00
86_V	277_S	1.669	1.00
117_V	197_M	1.667	1.00
84_Y	88_D	1.636	1.00
47_A	50_E	1.602	1.00
65_S	68_K	1.587	1.00
200_V	228_A	1.586	1.00
47_A	51_A	1.582	1.00
118_I	127_W	1.574	1.00
122_K	216_M	1.567	1.00
69_Q	74_D	1.567	1.00
189_I	239_A	1.564	1.00
111_L	114_S	1.542	1.00
127_W	131_V	1.541	1.00
205_F	227_P	1.535	1.00
178_M	182_S	1.507	1.00
111_L	186_I	1.484	1.00
121_L	220_I	1.482	1.00
121_L	216_M	1.479	1.00
108_A	185_Y	1.476	1.00
208_T	212_K	1.475	1.00
263_F	278_L	1.463	1.00
200_V	224_A	1.459	1.00
233_L	300_I	1.455	1.00
99_K	103_A	1.443	1.00
234_S	297_Y	1.431	1.00
109_V	236_M	1.431	1.00
266_G	274_L	1.422	1.00
92_S	95_P	1.415	1.00
54_H	57_D	1.415	1.00
296_L	299_V	1.407	1.00
145_V	149_L	1.403	1.00
71_A	74_D	1.400	1.00
75_F	277_S	1.375	1.00
170_A	173_F	1.372	1.00
96_V	99_K	1.369	1.00
200_V	206_I	1.368	1.00
84_Y	92_S	1.356	1.00
150_L	180_A	1.353	1.00
65_S	69_Q	1.344	1.00
78_S	84_Y	1.341	1.00
112_G	193_T	1.324	1.00
16_L	284_A	1.319	1.00
131_V	190_A	1.304	1.00
112_G	189_I	1.303	1.00
105_F	236_M	1.290	1.00
33_S	36_T	1.288	1.00
10_L	14_P	1.283	1.00
70_L	75_F	1.280	1.00
124_N	128_D	1.279	1.00
17_F	21_T	1.271	1.00
116_G	120_A	1.269	1.00
57_D	60_M	1.267	1.00
61_T	64_F	1.263	1.00
49_I	52_K	1.256	1.00
99_K	170_A	1.255	1.00
75_F	87_N	1.254	1.00
84_Y	89_L	1.252	1.00
17_F	63_Y	1.251	1.00
12_A	287_I	1.242	1.00
89_L	274_L	1.238	1.00
138_G	187_A	1.232	1.00
194_R	198_I	1.226	1.00
241_V	286_T	1.219	1.00
182_S	186_I	1.211	1.00
58_P	61_T	1.209	1.00
192_I	235_Y	1.209	1.00
135_A	190_A	1.196	1.00
212_K	223_H	1.192	1.00
120_A	201_L	1.180	1.00
49_I	53_Y	1.179	1.00
115_A	190_A	1.178	1.00
295_V	299_V	1.173	1.00
262_L	274_L	1.173	1.00
126_K	129_Y	1.164	1.00
77_P	85_S	1.160	1.00
297_Y	301_D	1.140	1.00
35_F	46_M	1.139	1.00
20_I	66_Y	1.124	1.00
116_G	193_T	1.115	1.00
180_A	184_A	1.113	1.00
175_I	179_V	1.113	1.00
278_L	282_V	1.112	1.00
119_A	131_V	1.111	1.00
272_Y	276_L	1.105	1.00
169_G	173_F	1.091	1.00
141_I	146_V	1.090	1.00
117_V	220_I	1.079	1.00
193_T	232_V	1.076	1.00
88_D	92_S	1.075	1.00
48_N	51_A	1.073	1.00
80_K	269_N	1.071	1.00
197_M	228_A	1.064	1.00
169_G	172_K	1.060	1.00
99_K	174_M	1.056	1.00
193_T	197_M	1.055	1.00
54_H	65_S	1.053	1.00
230_L	297_Y	1.039	1.00
264_V	268_L	1.038	1.00
25_F	28_R	1.034	1.00
209_A	214_L	1.030	1.00
69_Q	72_H	1.030	1.00
36_T	46_M	1.024	1.00
209_A	219_I	1.024	1.00
104_A	182_S	1.023	1.00
21_T	25_F	1.006	1.00
199_E	203_S	1.002	1.00
114_S	117_V	0.998	1.00
18_I	22_I	0.993	1.00
209_A	223_H	0.992	1.00
89_L	92_S	0.992	1.00
134_L	138_G	0.986	1.00
147_A	180_A	0.977	1.00
196_S	199_E	0.960	1.00
14_P	17_F	0.958	1.00
91_A	95_P	0.956	1.00
289_F	293_V	0.953	1.00
171_L	175_I	0.945	1.00
79_F	265_N	0.942	1.00
265_N	269_N	0.940	1.00
17_F	67_L	0.937	1.00
218_R	221_L	0.933	1.00
150_L	176_L	0.931	1.00
104_A	108_A	0.922	1.00
37_G	41_L	0.913	1.00
77_P	83_D	0.912	1.00
93_S	262_L	0.906	1.00
132_M	190_A	0.902	1.00
210_R	219_I	0.902	1.00
88_D	91_A	0.901	1.00
240_F	289_F	0.897	1.00
113_V	193_T	0.895	1.00
117_V	225_L	0.895	1.00
216_M	219_I	0.888	1.00
104_A	181_L	0.888	1.00
16_L	287_I	0.888	1.00
128_D	198_I	0.884	1.00
120_A	198_I	0.883	1.00
196_S	200_V	0.881	1.00
143_S	250_I	0.879	1.00
186_I	190_A	0.879	1.00
174_M	178_M	0.870	1.00
86_V	274_L	0.870	1.00
51_A	57_D	0.867	1.00
44_E	48_N	0.866	1.00
265_N	268_L	0.859	1.00
28_R	59_I	0.857	1.00
99_K	102_A	0.854	1.00
129_Y	132_M	0.853	1.00
228_A	231_P	0.850	1.00
214_L	219_I	0.849	1.00
12_A	291_A	0.849	1.00
298_A	304_I	0.847	1.00
233_L	293_V	0.846	1.00
9_C	291_A	0.845	1.00
179_V	182_S	0.842	1.00
133_G	136_M	0.838	1.00
73_G	85_S	0.838	1.00
107_L	178_M	0.837	1.00
124_N	129_Y	0.836	1.00
37_G	49_I	0.836	1.00
109_V	114_S	0.834	1.00
112_G	116_G	0.832	1.00
38_E	41_L	0.829	1.00
193_T	228_A	0.829	1.00
130_T	134_L	0.827	1.00
149_L	153_I	0.825	1.00
288_L	292_I	0.822	1.00
129_Y	133_G	0.817	1.00
78_S	271_D	0.815	1.00
86_V	262_L	0.814	1.00
207_R	210_R	0.811	1.00
44_E	47_A	0.810	1.00
116_G	197_M	0.807	1.00
9_C	13_I	0.804	1.00
102_A	106_F	0.797	1.00
91_A	94_F	0.791	1.00
241_V	289_F	0.788	1.00
154_F	176_L	0.788	1.00
263_F	266_G	0.786	1.00
114_S	118_I	0.784	1.00
292_I	296_L	0.783	1.00
20_I	280_I	0.782	1.00
172_K	176_L	0.782	1.00
284_A	288_L	0.782	1.00
127_W	130_T	0.780	1.00
100_L	251_E	0.777	1.00
90_V	277_S	0.776	1.00
67_L	70_L	0.774	1.00
70_L	280_I	0.768	1.00
64_F	67_L	0.766	1.00
152_M	156_I	0.764	1.00
262_L	278_L	0.764	1.00
221_L	224_A	0.762	1.00
219_I	224_A	0.762	1.00
97_S	101_G	0.761	1.00
68_K	71_A	0.760	1.00
41_L	46_M	0.758	1.00
139_V	187_A	0.754	1.00
209_A	212_K	0.749	1.00
295_V	298_A	0.748	1.00
75_F	90_V	0.746	1.00
115_A	186_I	0.742	1.00
109_V	189_I	0.736	1.00
175_I	178_M	0.736	1.00
56_N	59_I	0.735	1.00
103_A	256_L	0.735	1.00
32_G	270_R	0.735	1.00
25_F	59_I	0.733	1.00
43_P	46_M	0.732	1.00
14_P	18_I	0.730	1.00
28_R	272_Y	0.730	1.00
262_L	266_G	0.729	1.00
235_Y	239_A	0.728	1.00
63_Y	67_L	0.724	1.00
185_Y	188_S	0.722	1.00
7_R	10_L	0.721	1.00
297_Y	304_I	0.721	1.00
266_G	275_V	0.721	1.00
196_S	228_A	0.714	1.00
264_V	267_A	0.712	1.00
95_P	99_K	0.706	1.00
113_V	232_V	0.705	1.00
173_F	176_L	0.705	1.00
276_L	280_I	0.701	1.00
216_M	220_I	0.700	1.00
135_A	187_A	0.699	1.00
105_F	240_F	0.697	1.00
23_S	94_F	0.697	1.00
143_S	147_A	0.694	1.00
282_V	286_T	0.693	1.00
111_L	115_A	0.688	1.00
108_A	182_S	0.688	1.00
90_V	278_L	0.687	1.00
252_T	261_Q	0.686	1.00
128_D	132_M	0.686	1.00
110_I	113_V	0.683	1.00
207_R	211_A	0.681	1.00
146_V	183_L	0.681	1.00
111_L	182_S	0.680	1.00
276_L	279_T	0.675	1.00
100_L	178_M	0.675	1.00
277_S	281_L	0.671	1.00
147_A	253_I	0.670	1.00
119_A	128_D	0.670	1.00
79_F	273_S	0.668	1.00
90_V	281_L	0.668	1.00
172_K	175_I	0.668	1.00
73_G	77_P	0.667	1.00
247_S	250_I	0.665	1.00
121_L	221_L	0.663	1.00
103_A	171_L	0.662	1.00
171_L	174_M	0.662	1.00
66_Y	70_L	0.657	1.00
32_G	35_F	0.657	1.00
109_V	113_V	0.653	1.00
21_T	59_I	0.652	1.00
13_I	17_F	0.651	1.00
23_S	279_T	0.649	1.00
143_S	146_V	0.646	1.00
25_F	29_L	0.645	1.00
252_T	264_V	0.643	1.00
131_V	135_A	0.635	1.00
237_G	289_F	0.635	1.00
143_S	183_L	0.631	1.00
214_L	223_H	0.631	1.00
217_R	220_I	0.629	1.00
7_R	11_E	0.624	1.00
10_L	13_I	0.624	1.00
95_P	98_A	0.623	1.00
102_A	240_F	0.623	1.00
155_A	176_L	0.622	1.00
112_G	190_A	0.621	1.00
37_G	40_T	0.620	1.00
277_S	280_I	0.616	1.00
68_K	73_G	0.615	1.00
11_E	15_T	0.614	1.00
89_L	93_S	0.612	1.00
103_A	175_I	0.611	1.00
104_A	247_S	0.602	1.00
155_A	172_K	0.600	1.00
176_L	180_A	0.600	1.00
119_A	132_M	0.598	1.00
187_A	190_A	0.598	1.00
193_T	196_S	0.598	1.00
125_T	128_D	0.595	1.00
248_M	252_T	0.593	1.00
263_F	282_V	0.592	1.00
45_V	49_I	0.592	1.00
203_S	207_R	0.592	1.00
94_F	98_A	0.590	1.00
130_T	133_G	0.588	1.00
98_A	102_A	0.587	1.00
188_S	235_Y	0.587	1.00
176_L	179_V	0.586	1.00
67_L	71_A	0.586	1.00
286_T	290_N	0.585	1.00
103_A	106_F	0.584	1.00
15_T	287_I	0.584	1.00
196_S	231_P	0.583	1.00
275_V	279_T	0.582	1.00
94_F	285_L	0.581	1.00
35_F	50_E	0.580	1.00
41_L	45_V	0.578	1.00
35_F	49_I	0.578	1.00
147_A	151_V	0.577	1.00
70_L	73_G	0.574	1.00
19_L	285_L	0.574	1.00
180_A	250_I	0.572	1.00
188_S	242_G	0.570	1.00
133_G	137_T	0.569	1.00
101_G	247_S	0.567	1.00
273_S	277_S	0.567	1.00
31_P	34_P	0.566	1.00
184_A	187_A	0.563	1.00
138_G	183_L	0.562	1.00
132_M	135_A	0.560	1.00
257_P	261_Q	0.559	1.00
193_T	225_L	0.559	1.00
200_V	227_P	0.556	1.00
106_F	110_I	0.555	1.00
61_T	68_K	0.554	1.00
195_G	198_I	0.553	1.00
12_A	288_L	0.553	1.00
27_M	31_P	0.550	1.00
206_I	210_R	0.549	1.00
8_R	294_D	0.549	1.00
23_S	27_M	0.547	1.00
188_S	239_A	0.545	1.00
239_A	242_G	0.543	1.00
185_Y	242_G	0.543	1.00
192_I	196_S	0.543	1.00
27_M	30_A	0.542	1.00
42_P	46_M	0.542	1.00
248_M	264_V	0.541	1.00
197_M	201_L	0.538	1.00
120_A	128_D	0.538	1.00
143_S	184_A	0.538	1.00
13_I	18_I	0.535	1.00
229_L	233_L	0.535	1.00
249_V	252_T	0.533	1.00
189_I	193_T	0.533	1.00
252_T	265_N	0.531	1.00
233_L	296_L	0.531	1.00
11_E	27_M	0.530	1.00
12_A	15_T	0.527	1.00
185_Y	239_A	0.527	1.00
50_E	56_N	0.527	1.00
197_M	225_L	0.526	1.00
181_L	250_I	0.525	1.00
141_I	145_V	0.521	1.00
122_K	220_I	0.518	1.00
11_E	14_P	0.516	1.00
229_L	232_V	0.516	1.00
70_L	74_D	0.516	1.00
182_S	185_Y	0.515	1.00
121_L	201_L	0.514	1.00
125_T	130_T	0.513	1.00
145_V	148_P	0.512	1.00
93_S	261_Q	0.510	1.00
189_I	235_Y	0.510	1.00
214_L	217_R	0.509	1.00
230_L	304_I	0.506	1.00
21_T	60_M	0.505	1.00
183_L	186_I	0.505	1.00
215_P	219_I	0.504	1.00
52_K	83_D	0.504	1.00
188_S	192_I	0.504	1.00
122_K	128_D	0.502	1.00
74_D	85_S	0.502	1.00
101_G	105_F	0.501	1.00
15_T	288_L	0.501	1.00
125_T	129_Y	0.500	1.00
16_L	288_L	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	0.683	99.9	0.645	Contact Map
4tquM	1	0.8497	99.9	0.655	Contact Map
3rlfF	1	0.8562	99.8	0.679	Contact Map
4ymuD	2	0.6863	99.8	0.69	Contact Map
2onkC	2	0.8137	99.8	0.691	Contact Map
3d31C	2	0.8039	99.8	0.703	Contact Map
4tquN	1	0.8399	99.7	0.72	Contact Map
3rlfG	1	0.8856	99.7	0.729	Contact Map
3j5pB	3	0.2157	7.2	0.961	Contact Map
3dh4A	3	0.2451	4.1	0.966	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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