OPPC - ECOLI - GREMLIN Contacts

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OPPC - Oligopeptide transport system permease protein OppC

UniProt:	P0AFH6	Sequences: MMLSKKNSETLENFSEKLEVEGRSLWQDARRRFMHNRAAVASLIVLVLIALFVILAPMLSQFAYDDTDWAMMSSAPDMESGHYFGTDSSGRDLLVRVAIGGRISLMVGVAAALVAVVVGTLYGSLSGYLGGKVDSVMMRLLEILNSFPFMFFVILLVTFFGQNILLIFVAIGMVSWLDMARIVRGQTLSLKRKEFIEAAQVGGVSTSGIVIRHIVPNVLGVVVVYASLLVPSMILFESFLSFLGLGTQEPLSSWGALLSDGANSMEVSPWLLLFPAGFLVVTLFCFNFIGDGLRDALDPKDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10676
Length:	302 (252)
Sequences:	28594 (17933)
Seq/√Len:	1129.7

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

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
187_T	214_I	2.812	1.00
134_D	184_R	2.687	1.00
190_L	195_F	2.443	1.00
204_V	208_G	2.433	1.00
208_G	212_R	2.431	1.00
200_Q	206_T	2.421	1.00
110_A	168_F	2.377	1.00
122_Y	137_M	2.374	1.00
114_V	172_G	2.349	1.00
190_L	193_K	2.319	1.00
103_I	242_F	2.294	1.00
205_S	208_G	2.280	1.00
207_S	211_I	2.212	1.00
194_E	197_E	2.138	1.00
68_D	71_M	2.116	1.00
196_I	214_I	2.032	1.00
196_I	209_I	2.026	1.00
124_S	187_T	1.979	1.00
227_S	290_G	1.964	1.00
129_L	133_V	1.922	1.00
125_L	129_L	1.921	1.00
129_L	206_T	1.915	1.00
92_D	95_V	1.895	1.00
117_V	121_L	1.861	1.00
179_M	229_L	1.818	1.00
63_A	66_D	1.798	1.00
190_L	218_V	1.747	1.00
247_T	260_D	1.744	1.00
195_F	217_N	1.741	1.00
127_G	187_T	1.739	1.00
47_V	51_L	1.731	1.00
87_D	91_R	1.726	1.00
132_K	136_V	1.726	1.00
128_Y	206_T	1.723	1.00
96_R	248_Q	1.711	1.00
53_V	101_G	1.700	1.00
118_V	176_W	1.659	1.00
118_V	121_L	1.647	1.00
94_L	98_A	1.640	1.00
115_A	175_S	1.638	1.00
89_S	96_R	1.636	1.00
84_F	274_F	1.630	1.00
125_L	133_V	1.615	1.00
191_K	214_I	1.614	1.00
106_M	110_A	1.602	1.00
82_H	92_D	1.601	1.00
133_V	137_M	1.581	1.00
186_Q	189_S	1.559	1.00
88_S	260_D	1.556	1.00
93_L	274_F	1.546	1.00
168_F	172_G	1.533	1.00
80_S	83_Y	1.533	1.00
75_A	79_E	1.531	1.00
137_M	180_A	1.531	1.00
261_G	271_L	1.527	1.00
141_L	180_A	1.526	1.00
128_Y	210_V	1.523	1.00
99_I	102_R	1.518	1.00
116_V	226_A	1.503	1.00
39_A	292_G	1.480	1.00
91_R	95_V	1.455	1.00
258_L	275_P	1.454	1.00
189_S	193_K	1.444	1.00
119_G	179_M	1.443	1.00
112_A	226_A	1.415	1.00
123_G	127_G	1.401	1.00
42_S	285_C	1.388	1.00
55_L	58_M	1.372	1.00
139_R	142_E	1.358	1.00
198_A	202_G	1.339	1.00
151_F	155_L	1.327	1.00
184_R	188_L	1.320	1.00
37_R	40_V	1.319	1.00
132_K	135_S	1.316	1.00
71_M	74_S	1.315	1.00
224_V	294_R	1.312	1.00
97_V	278_F	1.311	1.00
158_T	163_N	1.311	1.00
103_I	106_M	1.310	1.00
127_G	191_K	1.309	1.00
122_Y	180_A	1.302	1.00
84_F	94_L	1.296	1.00
165_L	169_V	1.294	1.00
119_G	183_V	1.292	1.00
123_G	183_V	1.292	1.00
126_S	137_M	1.287	1.00
190_L	196_I	1.282	1.00
124_S	210_V	1.275	1.00
156_L	170_A	1.268	1.00
269_P	273_L	1.267	1.00
231_P	283_L	1.258	1.00
293_L	296_A	1.254	1.00
182_I	225_Y	1.247	1.00
190_L	214_I	1.233	1.00
51_L	55_L	1.227	1.00
294_R	298_D	1.227	1.00
172_G	176_W	1.226	1.00
40_V	44_I	1.218	1.00
223_V	297_L	1.216	1.00
49_I	280_V	1.214	1.00
199_A	213_H	1.205	1.00
73_S	76_P	1.184	1.00
107_V	237_E	1.176	1.00
187_T	218_V	1.166	1.00
91_R	96_R	1.162	1.00
199_A	204_V	1.154	1.00
130_G	191_K	1.148	1.00
199_A	209_I	1.146	1.00
144_L	177_L	1.123	1.00
84_F	97_V	1.111	1.00
91_R	99_I	1.106	1.00
124_S	215_V	1.105	1.00
183_V	222_V	1.097	1.00
183_V	187_T	1.092	1.00
208_G	211_I	1.089	1.00
197_E	200_Q	1.088	1.00
135_S	139_R	1.085	1.00
292_G	296_A	1.084	1.00
121_L	124_S	1.070	1.00
46_L	281_V	1.064	1.00
275_P	279_L	1.059	1.00
120_T	183_V	1.059	1.00
140_L	144_L	1.056	1.00
186_Q	190_L	1.056	1.00
153_V	170_A	1.055	1.00
86_T	92_D	1.051	1.00
170_A	174_V	1.047	1.00
176_W	180_A	1.042	1.00
56_A	99_I	1.038	1.00
259_S	263_N	1.034	1.00
261_G	272_L	1.032	1.00
165_L	168_F	1.031	1.00
42_S	292_G	1.029	1.00
202_G	213_H	1.026	1.00
46_L	285_C	1.025	1.00
88_S	264_S	1.024	1.00
44_I	48_L	1.020	1.00
111_A	172_G	1.017	1.00
147_F	152_F	1.017	1.00
93_L	271_L	1.013	1.00
102_R	106_M	1.012	1.00
60_S	95_V	1.011	1.00
72_M	76_P	1.008	1.00
106_M	164_I	1.004	1.00
49_I	282_T	1.000	1.00
41_A	44_I	0.998	1.00
270_W	274_F	0.992	1.00
138_M	180_A	0.990	1.00
163_N	166_L	0.988	1.00
44_I	47_V	0.983	1.00
134_D	138_M	0.974	1.00
130_G	192_R	0.974	1.00
200_Q	209_I	0.973	1.00
97_V	274_F	0.967	1.00
111_A	115_A	0.961	1.00
45_V	285_C	0.956	1.00
199_A	202_G	0.954	1.00
183_V	218_V	0.951	1.00
82_H	86_T	0.943	1.00
159_F	163_N	0.942	1.00
95_V	99_I	0.942	1.00
96_R	271_L	0.942	1.00
230_V	286_F	0.942	1.00
134_D	188_L	0.941	1.00
149_F	236_F	0.939	1.00
248_Q	271_L	0.937	1.00
274_F	277_G	0.927	1.00
133_V	136_V	0.926	1.00
45_V	281_V	0.921	1.00
43_L	47_V	0.921	1.00
220_G	294_R	0.914	1.00
206_T	209_I	0.914	1.00
204_V	209_I	0.912	1.00
123_G	187_T	0.912	1.00
111_A	171_I	0.911	1.00
42_S	284_F	0.908	1.00
136_V	140_L	0.906	1.00
106_M	109_V	0.903	1.00
135_S	138_M	0.901	1.00
74_S	79_E	0.900	1.00
48_L	52_F	0.896	1.00
42_S	288_F	0.895	1.00
171_I	236_F	0.893	1.00
285_C	289_I	0.887	1.00
218_V	221_V	0.884	1.00
141_L	177_L	0.880	1.00
62_F	95_V	0.868	1.00
52_F	98_A	0.860	1.00
120_T	222_V	0.860	1.00
286_F	290_G	0.858	1.00
116_V	120_T	0.857	1.00
225_Y	229_L	0.857	1.00
96_R	99_I	0.855	1.00
86_T	90_G	0.851	1.00
164_I	168_F	0.849	1.00
54_I	58_M	0.849	1.00
43_L	289_I	0.845	1.00
98_A	102_R	0.836	1.00
117_V	120_T	0.834	1.00
211_I	214_I	0.832	1.00
185_G	188_L	0.827	1.00
160_F	166_L	0.827	1.00
161_G	166_L	0.822	1.00
116_V	121_L	0.817	1.00
111_A	233_M	0.815	1.00
121_L	125_L	0.809	1.00
223_V	290_G	0.806	1.00
122_Y	176_W	0.805	1.00
273_L	277_G	0.804	1.00
127_G	188_L	0.803	1.00
101_G	282_T	0.803	1.00
58_M	269_P	0.798	1.00
206_T	210_V	0.797	1.00
260_D	263_N	0.796	1.00
95_V	98_A	0.794	1.00
187_T	191_K	0.793	1.00
169_V	172_G	0.792	1.00
131_G	135_S	0.791	1.00
149_F	153_V	0.791	1.00
76_P	79_E	0.790	1.00
259_S	262_A	0.789	1.00
166_L	169_V	0.784	1.00
193_K	197_E	0.784	1.00
110_A	242_F	0.783	1.00
52_F	101_G	0.779	1.00
38_A	42_S	0.778	1.00
116_V	179_M	0.778	1.00
131_G	134_D	0.775	1.00
190_L	217_N	0.771	1.00
110_A	113_L	0.768	1.00
197_E	201_V	0.768	1.00
295_D	301_D	0.767	1.00
83_Y	94_L	0.765	1.00
114_V	168_F	0.763	1.00
62_F	82_H	0.762	1.00
109_V	113_L	0.761	1.00
156_L	166_L	0.761	1.00
126_S	134_D	0.755	1.00
55_L	59_L	0.752	1.00
274_F	278_F	0.752	1.00
186_Q	221_V	0.751	1.00
104_S	108_G	0.751	1.00
204_V	213_H	0.746	1.00
260_D	264_S	0.744	1.00
100_G	248_Q	0.739	1.00
145_N	177_L	0.738	1.00
39_A	43_L	0.737	1.00
238_S	247_T	0.731	1.00
65_D	69_W	0.729	1.00
70_A	74_S	0.728	1.00
207_S	210_V	0.725	1.00
62_F	81_G	0.719	1.00
87_D	268_S	0.718	1.00
183_V	186_Q	0.718	1.00
118_V	172_G	0.717	1.00
281_V	285_C	0.716	1.00
209_I	214_I	0.713	1.00
61_Q	95_V	0.712	1.00
279_L	283_L	0.710	1.00
175_S	178_D	0.701	1.00
235_L	238_S	0.694	1.00
98_A	101_G	0.690	1.00
49_I	281_V	0.690	1.00
289_I	293_L	0.676	1.00
294_R	301_D	0.673	1.00
39_A	288_F	0.672	1.00
79_E	83_Y	0.671	1.00
231_P	286_F	0.671	1.00
50_A	277_G	0.665	1.00
167_I	237_E	0.664	1.00
42_S	45_V	0.663	1.00
272_L	276_A	0.660	1.00
149_F	152_F	0.659	1.00
83_Y	92_D	0.659	1.00
115_A	172_G	0.656	1.00
273_L	276_A	0.655	1.00
40_V	43_L	0.648	1.00
186_Q	218_V	0.647	1.00
130_G	134_D	0.646	1.00
136_V	139_R	0.644	1.00
227_S	286_F	0.644	1.00
283_L	287_N	0.642	1.00
119_G	123_G	0.641	1.00
41_A	45_V	0.641	1.00
69_W	72_M	0.639	1.00
118_V	122_Y	0.636	1.00
174_V	177_L	0.635	1.00
57_P	102_R	0.635	1.00
46_L	286_F	0.635	1.00
128_Y	191_K	0.633	1.00
236_F	239_F	0.631	1.00
68_D	82_H	0.625	1.00
70_A	73_S	0.621	1.00
112_A	229_L	0.620	1.00
179_M	183_V	0.618	1.00
188_L	191_K	0.616	1.00
71_M	82_H	0.615	1.00
113_L	117_V	0.614	1.00
129_L	210_V	0.614	1.00
152_F	174_V	0.613	1.00
97_V	275_P	0.612	1.00
60_S	99_I	0.612	1.00
68_D	72_M	0.611	1.00
45_V	49_I	0.607	1.00
237_E	241_S	0.607	1.00
112_A	230_V	0.606	1.00
137_M	141_L	0.605	1.00
37_R	41_A	0.605	1.00
224_V	227_S	0.605	1.00
74_S	81_G	0.603	1.00
138_M	141_L	0.599	1.00
179_M	225_Y	0.599	1.00
53_V	276_A	0.596	1.00
108_G	233_M	0.595	1.00
127_G	134_D	0.594	1.00
204_V	207_S	0.594	1.00
178_D	229_L	0.594	1.00
105_L	109_V	0.593	1.00
126_S	138_M	0.592	1.00
130_G	188_L	0.592	1.00
52_F	56_A	0.590	1.00
141_L	176_W	0.590	1.00
144_L	176_W	0.588	1.00
233_M	236_F	0.585	1.00
139_R	143_I	0.584	1.00
110_A	165_L	0.581	1.00
128_Y	211_I	0.578	1.00
238_S	259_S	0.577	1.00
56_A	59_L	0.576	1.00
102_R	105_L	0.574	1.00
235_L	239_F	0.574	1.00
173_M	176_W	0.573	1.00
61_Q	94_L	0.568	1.00
234_I	238_S	0.567	1.00
155_L	159_F	0.565	1.00
62_F	267_V	0.564	1.00
264_S	271_L	0.564	1.00
101_G	105_L	0.562	1.00
57_P	99_I	0.559	1.00
166_L	170_A	0.559	1.00
211_I	216_P	0.557	1.00
66_D	70_A	0.554	1.00
116_V	222_V	0.553	1.00
72_M	75_A	0.551	1.00
112_A	116_V	0.548	1.00
96_R	100_G	0.546	1.00
205_S	209_I	0.543	1.00
126_S	184_R	0.541	1.00
76_P	81_G	0.540	1.00
288_F	292_G	0.540	1.00
108_G	230_V	0.540	1.00
196_I	200_Q	0.536	1.00
142_E	145_N	0.529	1.00
119_G	180_A	0.529	1.00
229_L	233_M	0.527	1.00
219_L	223_V	0.525	1.00
175_S	229_L	0.525	1.00
172_G	175_S	0.525	1.00
182_I	186_Q	0.524	1.00
291_D	294_R	0.523	1.00
258_L	279_L	0.519	1.00
157_V	161_G	0.518	1.00
122_Y	125_L	0.518	1.00
76_P	80_S	0.518	1.00
107_V	167_I	0.515	1.00
38_A	41_A	0.515	1.00
270_W	273_L	0.515	1.00
238_S	260_D	0.514	1.00
138_M	142_E	0.512	1.00
46_L	289_I	0.511	1.00
192_R	197_E	0.510	1.00
49_I	53_V	0.508	1.00
169_V	173_M	0.507	1.00
38_A	288_F	0.506	1.00
50_A	53_V	0.504	1.00
277_G	280_V	0.501	1.00
149_F	173_M	0.501	1.00
107_V	168_F	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	0.8377	99.9	0.62	Contact Map
3d31C	2	0.7616	99.9	0.643	Contact Map
3tuiA	2	0.6689	99.9	0.656	Contact Map
2onkC	2	0.7848	99.9	0.66	Contact Map
3rlfF	1	0.9139	99.9	0.679	Contact Map
4tquN	1	0.8742	99.8	0.68	Contact Map
3rlfG	1	0.8411	99.8	0.686	Contact Map
4ymuD	2	0.6921	99.8	0.689	Contact Map
3j9pD	4	0.7351	47.1	0.945	Contact Map
2kogA	1	0.1887	35.2	0.949	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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