OPPC - BACSU - GREMLIN Contacts

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OPPC - Oligopeptide transport system permease protein OppC

UniProt:	P24139	Sequences: MQNIPKNMFEPAAANAGDAEKISKKSLSLWKDAMLRFRSNKLAMVGLIIIVLIILMAIFAPMFSRYDYSTTNLLNADKPPSKDHWFGTDDLGRDIFVRTWVGARISIFIGVAAAVLDLLIGVIWGSISGFRGGRTDEIMMRIADILWAVPSLLMVILLMVVLPKGLFTIIIAMTITGWINMARIVRGQVLQLKNQEYVLASQTLGAKTSRLLFKHIVPNAMGSILVTMTLTVPTAIFTEAFLSYLGLGVPAPLASWGTMASDGLPALTYYPWRLFFPAGFICITMFGFNVVGDGLRDALDPKLRK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	305 (252)
Sequences:	28582 (17851)
Seq/√Len:	1124.5

ECOLI - DPPC GSID DDPC OPPC SAPC NIKC YEJE YEJB NIKB GSIC DDPB DPPB SAPB OPPB
BACSU - OPPC APPC DPPC OPPB DPPB APPB
HALSA - Q9HMW2 Q9HMI1 Q9HMX1 Q9HMI2 Q9HMX0 Q9HMW3
SULSO - Q97UH2 Q97VK7 Q97UG3 Q97VF6 Q97YP2 Q97YP9 Q97VF8 Q97VK6 Q97UH1 Q97YP1 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
81_S	85_W	2.884	1.00
189_V	216_I	2.787	1.00
136_D	186_R	2.649	1.00
206_A	210_R	2.459	1.00
192_L	197_Y	2.439	1.00
202_Q	208_T	2.430	1.00
210_R	214_K	2.404	1.00
112_A	170_I	2.383	1.00
124_W	139_M	2.370	1.00
116_L	174_T	2.318	1.00
192_L	195_Q	2.306	1.00
82_K	85_W	2.294	1.00
105_I	244_Y	2.258	1.00
207_K	210_R	2.246	1.00
209_S	213_F	2.230	1.00
72_N	75_N	2.168	1.00
258_T	262_D	2.114	1.00
196_E	199_L	2.087	1.00
198_V	216_I	2.027	1.00
198_V	211_L	2.010	1.00
229_T	292_G	1.974	1.00
98_R	259_M	1.966	1.00
126_S	189_V	1.950	1.00
127_I	131_R	1.928	1.00
94_D	97_V	1.908	1.00
131_R	208_T	1.891	1.00
181_M	231_T	1.843	1.00
119_L	123_I	1.837	1.00
62_M	81_S	1.821	1.00
67_D	70_T	1.795	1.00
131_R	135_T	1.756	1.00
130_F	208_T	1.738	1.00
192_L	220_A	1.736	1.00
129_G	189_V	1.736	1.00
197_Y	219_N	1.729	1.00
134_R	138_I	1.726	1.00
57_A	103_A	1.706	1.00
51_V	55_L	1.706	1.00
89_D	93_R	1.691	1.00
120_I	178_W	1.643	1.00
117_D	177_G	1.636	1.00
96_F	100_W	1.636	1.00
86_F	276_F	1.634	1.00
193_K	216_I	1.628	1.00
120_I	123_I	1.620	1.00
127_I	135_T	1.617	1.00
91_L	98_R	1.615	1.00
108_F	112_A	1.570	1.00
95_I	276_F	1.569	1.00
188_Q	191_Q	1.563	1.00
135_T	139_M	1.548	1.00
143_A	182_A	1.532	1.00
170_I	174_T	1.528	1.00
130_F	212_L	1.524	1.00
263_G	273_R	1.522	1.00
118_L	228_M	1.520	1.00
101_V	104_R	1.514	1.00
139_M	182_A	1.505	1.00
93_R	97_V	1.488	1.00
90_D	262_D	1.480	1.00
43_A	294_G	1.479	1.00
75_N	78_K	1.449	1.00
191_Q	195_Q	1.439	1.00
121_G	181_M	1.422	1.00
125_G	129_G	1.419	1.00
260_A	277_P	1.410	1.00
114_A	228_M	1.402	1.00
59_F	62_M	1.391	1.00
46_G	287_G	1.363	1.00
125_G	185_V	1.351	1.00
141_R	144_D	1.351	1.00
200_A	204_L	1.348	1.00
124_W	182_A	1.320	1.00
153_L	157_L	1.316	1.00
226_V	296_R	1.307	1.00
186_R	190_L	1.303	1.00
129_G	193_K	1.299	1.00
134_R	137_E	1.293	1.00
44_M	48_I	1.293	1.00
99_T	280_F	1.291	1.00
128_S	139_M	1.290	1.00
167_F	171_I	1.290	1.00
126_S	212_L	1.269	1.00
105_I	108_F	1.268	1.00
192_L	198_V	1.255	1.00
121_G	185_V	1.253	1.00
192_L	216_I	1.251	1.00
295_L	298_A	1.249	1.00
86_F	96_F	1.245	1.00
53_I	282_C	1.241	1.00
41_K	44_M	1.231	1.00
271_P	275_F	1.231	1.00
55_L	59_F	1.228	1.00
158_L	172_A	1.226	1.00
174_T	178_W	1.223	1.00
184_I	227_T	1.221	1.00
225_L	299_L	1.213	1.00
296_R	300_D	1.206	1.00
201_S	215_H	1.191	1.00
132_G	136_D	1.176	1.00
54_I	82_K	1.173	1.00
93_R	98_R	1.172	1.00
109_I	239_E	1.168	1.00
189_V	220_A	1.154	1.00
201_S	206_A	1.143	1.00
201_S	211_L	1.137	1.00
146_L	179_I	1.125	1.00
199_L	202_Q	1.124	1.00
50_I	283_I	1.124	1.00
93_R	101_V	1.115	1.00
137_E	141_R	1.111	1.00
81_S	84_H	1.107	1.00
126_S	217_V	1.099	1.00
185_V	224_I	1.093	1.00
294_G	298_A	1.092	1.00
122_V	185_V	1.086	1.00
123_I	126_S	1.075	1.00
185_V	189_V	1.074	1.00
188_Q	192_L	1.073	1.00
86_F	99_T	1.060	1.00
277_P	281_I	1.057	1.00
46_G	294_G	1.053	1.00
178_W	182_A	1.052	1.00
172_A	176_T	1.047	1.00
142_I	146_L	1.046	1.00
155_V	172_A	1.044	1.00
210_R	213_F	1.044	1.00
104_R	108_F	1.043	1.00
263_G	274_L	1.036	1.00
165_G	168_T	1.035	1.00
149_V	154_M	1.033	1.00
84_H	94_D	1.030	1.00
60_A	101_V	1.025	1.00
167_F	170_I	1.025	1.00
48_I	52_L	1.019	1.00
95_I	273_R	1.015	1.00
53_I	284_T	1.008	1.00
232_V	288_F	1.006	1.00
108_F	166_L	0.997	1.00
202_Q	211_L	0.996	1.00
204_L	215_H	0.995	1.00
113_A	174_T	0.994	1.00
136_D	140_M	0.992	1.00
88_T	94_D	0.985	1.00
45_V	48_I	0.983	1.00
185_V	220_A	0.982	1.00
259_M	273_R	0.981	1.00
95_I	259_M	0.980	1.00
140_M	182_A	0.978	1.00
272_W	276_F	0.977	1.00
50_I	287_G	0.976	1.00
64_S	97_V	0.967	1.00
46_G	286_F	0.965	1.00
49_I	287_G	0.962	1.00
201_S	204_L	0.955	1.00
48_I	51_V	0.954	1.00
47_L	51_V	0.950	1.00
276_F	279_G	0.949	1.00
136_D	190_L	0.947	1.00
113_A	117_D	0.946	1.00
138_I	142_I	0.945	1.00
52_L	56_M	0.945	1.00
206_A	211_L	0.942	1.00
97_V	101_V	0.941	1.00
98_R	273_R	0.937	1.00
151_S	238_T	0.935	1.00
78_K	81_S	0.934	1.00
102_G	259_M	0.926	1.00
125_G	189_V	0.924	1.00
137_E	140_M	0.918	1.00
222_G	296_R	0.918	1.00
99_T	276_F	0.916	1.00
208_T	211_L	0.914	1.00
108_F	111_V	0.905	1.00
46_G	290_V	0.904	1.00
113_A	173_M	0.898	1.00
143_A	179_I	0.889	1.00
49_I	283_I	0.889	1.00
162_L	168_T	0.889	1.00
288_F	292_G	0.883	1.00
122_V	224_I	0.881	1.00
88_T	92_G	0.878	1.00
225_L	292_G	0.874	1.00
118_L	122_V	0.869	1.00
173_M	238_T	0.865	1.00
119_L	122_V	0.865	1.00
135_T	138_I	0.864	1.00
287_G	291_V	0.856	1.00
74_L	78_K	0.854	1.00
132_G	193_K	0.850	1.00
227_T	231_T	0.847	1.00
56_M	100_W	0.844	1.00
166_L	170_I	0.842	1.00
220_A	223_S	0.841	1.00
98_R	101_V	0.841	1.00
100_W	104_R	0.837	1.00
47_L	291_V	0.837	1.00
171_I	174_T	0.823	1.00
66_Y	83_D	0.822	1.00
275_F	279_G	0.821	1.00
66_Y	97_V	0.818	1.00
118_L	123_I	0.814	1.00
74_L	77_D	0.812	1.00
189_V	193_K	0.811	1.00
103_A	284_T	0.810	1.00
187_G	190_L	0.807	1.00
97_V	100_W	0.805	1.00
208_T	212_L	0.804	1.00
192_L	219_N	0.803	1.00
213_F	216_I	0.803	1.00
123_I	127_I	0.802	1.00
151_S	155_V	0.802	1.00
118_L	181_M	0.800	1.00
163_P	168_T	0.800	1.00
111_V	115_V	0.799	1.00
259_M	277_P	0.792	1.00
113_A	235_A	0.787	1.00
112_A	244_Y	0.778	1.00
199_L	203_T	0.777	1.00
261_S	265_P	0.775	1.00
129_G	190_L	0.774	1.00
195_Q	199_L	0.774	1.00
158_L	168_T	0.770	1.00
43_A	290_V	0.768	1.00
65_R	97_V	0.766	1.00
124_W	178_W	0.764	1.00
43_A	47_L	0.764	1.00
106_S	110_G	0.763	1.00
297_D	303_L	0.763	1.00
147_W	179_I	0.760	1.00
59_F	63_F	0.758	1.00
128_S	136_D	0.758	1.00
168_T	171_I	0.755	1.00
77_D	80_P	0.753	1.00
281_I	285_M	0.752	1.00
132_G	137_E	0.747	1.00
206_A	215_H	0.744	1.00
262_D	265_P	0.742	1.00
42_L	46_G	0.740	1.00
116_L	170_I	0.739	1.00
261_S	264_L	0.739	1.00
76_A	80_P	0.738	1.00
112_A	115_V	0.737	1.00
188_Q	223_S	0.735	1.00
185_V	188_Q	0.732	1.00
275_F	278_A	0.718	1.00
56_M	103_A	0.718	1.00
62_M	271_P	0.713	1.00
211_L	216_I	0.712	1.00
296_R	303_L	0.708	1.00
100_W	103_A	0.707	1.00
291_V	295_L	0.706	1.00
120_I	174_T	0.705	1.00
209_S	212_L	0.705	1.00
283_I	287_G	0.700	1.00
276_F	280_F	0.699	1.00
58_I	62_M	0.699	1.00
89_D	270_Y	0.699	1.00
61_P	104_R	0.697	1.00
188_Q	220_A	0.691	1.00
177_G	180_N	0.690	1.00
229_T	288_F	0.687	1.00
45_V	49_I	0.686	1.00
53_I	283_I	0.682	1.00
41_K	45_V	0.680	1.00
54_I	279_G	0.673	1.00
285_M	289_N	0.669	1.00
117_D	174_T	0.667	1.00
46_G	49_I	0.664	1.00
176_T	179_I	0.660	1.00
120_I	124_W	0.659	1.00
130_F	193_K	0.659	1.00
121_G	125_G	0.657	1.00
274_L	278_A	0.654	1.00
77_D	270_Y	0.648	1.00
239_E	243_S	0.647	1.00
237_F	240_A	0.644	1.00
151_S	154_M	0.643	1.00
237_F	241_F	0.642	1.00
138_I	141_R	0.639	1.00
169_I	239_E	0.639	1.00
65_R	96_F	0.636	1.00
128_S	140_M	0.634	1.00
66_Y	269_Y	0.631	1.00
50_I	288_F	0.630	1.00
99_T	277_P	0.628	1.00
262_D	268_T	0.627	1.00
44_M	47_L	0.626	1.00
66_Y	84_H	0.626	1.00
114_A	231_T	0.625	1.00
139_M	143_A	0.625	1.00
131_R	212_L	0.623	1.00
140_M	143_A	0.622	1.00
180_N	231_T	0.620	1.00
72_N	76_A	0.617	1.00
181_M	227_T	0.617	1.00
79_P	272_W	0.617	1.00
49_I	53_I	0.616	1.00
84_H	88_T	0.616	1.00
57_A	278_A	0.616	1.00
190_L	193_K	0.615	1.00
110_G	235_A	0.612	1.00
115_V	119_L	0.605	1.00
238_T	241_F	0.604	1.00
107_I	111_V	0.603	1.00
181_M	185_V	0.600	1.00
141_R	145_I	0.597	1.00
114_A	232_V	0.596	1.00
160_V	164_K	0.591	1.00
69_S	73_L	0.590	1.00
206_A	209_S	0.590	1.00
73_L	76_A	0.589	1.00
143_A	178_W	0.588	1.00
157_L	161_V	0.588	1.00
259_M	262_D	0.586	1.00
154_M	176_T	0.584	1.00
146_L	178_W	0.582	1.00
112_A	167_F	0.582	1.00
240_A	258_T	0.581	1.00
236_I	240_A	0.574	1.00
103_A	107_I	0.574	1.00
235_A	238_T	0.573	1.00
168_T	172_A	0.573	1.00
118_L	224_I	0.571	1.00
76_A	79_P	0.571	1.00
129_G	136_D	0.571	1.00
56_M	60_A	0.571	1.00
130_F	213_F	0.564	1.00
177_G	231_T	0.560	1.00
260_A	281_I	0.560	1.00
226_V	229_T	0.560	1.00
61_P	101_V	0.558	1.00
213_F	218_P	0.558	1.00
60_A	63_F	0.557	1.00
290_V	294_G	0.556	1.00
259_M	263_G	0.556	1.00
198_V	202_Q	0.554	1.00
73_L	77_D	0.551	1.00
240_A	261_S	0.551	1.00
175_I	178_W	0.550	1.00
151_S	175_I	0.549	1.00
80_P	272_W	0.547	1.00
64_S	101_V	0.547	1.00
128_S	186_R	0.542	1.00
171_I	175_I	0.538	1.00
78_K	88_T	0.538	1.00
104_R	107_I	0.537	1.00
98_R	102_G	0.534	1.00
179_I	182_A	0.534	1.00
207_K	211_L	0.533	1.00
77_D	273_R	0.532	1.00
159_M	163_P	0.531	1.00
124_W	127_I	0.531	1.00
115_V	118_L	0.530	1.00
293_D	296_R	0.530	1.00
121_G	182_A	0.530	1.00
184_I	188_Q	0.528	1.00
109_I	169_I	0.524	1.00
180_N	227_T	0.523	1.00
50_I	291_V	0.523	1.00
114_A	118_L	0.522	1.00
85_W	96_F	0.521	1.00
174_T	177_G	0.521	1.00
46_G	50_I	0.517	1.00
221_M	225_L	0.517	1.00
144_D	147_W	0.515	1.00
110_G	232_V	0.514	1.00
272_W	275_F	0.513	1.00
240_A	262_D	0.512	1.00
53_I	57_A	0.507	1.00
155_V	159_M	0.505	1.00
133_G	136_D	0.504	1.00
109_I	170_I	0.504	1.00
140_M	144_D	0.503	1.00
231_T	235_A	0.502	1.00
42_L	290_V	0.501	1.00
122_V	126_S	0.501	1.00
155_V	241_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	0.8295	99.9	0.632	Contact Map
3d31C	2	0.7607	99.9	0.649	Contact Map
3tuiA	2	0.6656	99.9	0.657	Contact Map
3rlfF	1	0.9082	99.9	0.661	Contact Map
2onkC	2	0.777	99.9	0.666	Contact Map
3rlfG	1	0.8361	99.9	0.683	Contact Map
4tquN	1	0.8525	99.8	0.683	Contact Map
4ymuD	2	0.6852	99.8	0.689	Contact Map
3j9pD	4	0.777	45.7	0.946	Contact Map
2kogA	1	0.2	21.6	0.955	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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