APPC - BACSU - GREMLIN Contacts

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APPC - Oligopeptide transport system permease protein AppC

UniProt:	P42063	Sequences: MSELQTTPSPEIRLKENISKKPETMTKIFWEKFSKNKLAILGAVILFIIIMSAVFAPLIAPYPQEQQSLLDKYKAPGLEHLMGTDKFGRDIFSRILYGARVSLLVGFASVVGSILIGTVLGALAGYFRGIVDAVIMRVVDIVLSIPDIFLLITLVTIFKPGVDKLILIFCLTGWTTTARLVRGEFLSLRSREYVLAAKTIGTKTHKIIFSHILPNALGPIIVSATLKVGSVILAESALSYLGFGIQPPIASWGNMLQDAQNFTVMIQAWWYPLFPGLFILMTVLCFNFVGDGLRDALDPKNIK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	303 (252)
Sequences:	28556 (18029)
Seq/√Len:	1135.7

ECOLI - DPPC OPPC GSID DDPC SAPC YEJE NIKC YEJB DPPB GSIC DDPB NIKB SAPB OPPB
BACSU - APPC DPPC OPPC OPPB DPPB APPB
HALSA - Q9HMW2 Q9HMI1 Q9HMX1 Q9HMI2 Q9HMX0 Q9HMW3
SULSO - Q97UH2 Q97YP2 Q97UG3 Q97VK7 Q97YP9 Q97VF6 Q97VK6 Q97VF8 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
185_F	212_I	2.747	1.00
132_D	182_R	2.629	1.00
202_T	206_K	2.430	1.00
188_L	193_Y	2.412	1.00
206_K	210_S	2.405	1.00
198_K	204_T	2.380	1.00
108_A	166_I	2.364	1.00
120_L	135_I	2.331	1.00
112_G	170_C	2.308	1.00
188_L	191_R	2.295	1.00
203_K	206_K	2.245	1.00
78_L	81_L	2.242	1.00
101_V	240_Y	2.222	1.00
205_H	209_F	2.200	1.00
254_N	258_D	2.087	1.00
192_E	195_L	2.071	1.00
68_S	71_D	2.047	1.00
194_V	207_I	2.013	1.00
194_V	212_I	2.011	1.00
94_R	255_M	1.960	1.00
122_A	185_F	1.938	1.00
225_T	290_G	1.920	1.00
123_L	127_F	1.920	1.00
90_D	93_S	1.891	1.00
127_F	131_V	1.887	1.00
127_F	204_T	1.875	1.00
115_L	119_V	1.828	1.00
177_T	227_K	1.808	1.00
63_P	66_Q	1.763	1.00
161_G	164_K	1.732	1.00
130_I	134_V	1.728	1.00
126_Y	204_T	1.719	1.00
193_Y	215_N	1.719	1.00
188_L	216_A	1.711	1.00
125_G	185_F	1.697	1.00
47_F	51_M	1.694	1.00
160_P	164_K	1.685	1.00
74_K	77_G	1.683	1.00
77_G	80_H	1.660	1.00
53_A	99_A	1.654	1.00
85_D	89_R	1.652	1.00
116_I	174_W	1.650	1.00
123_L	131_V	1.623	1.00
82_M	274_F	1.617	1.00
113_S	173_G	1.612	1.00
92_F	96_L	1.603	1.00
104_L	108_A	1.603	1.00
116_I	119_V	1.593	1.00
87_F	94_R	1.592	1.00
189_R	212_I	1.581	1.00
131_V	135_I	1.565	1.00
166_I	170_C	1.549	1.00
184_E	187_S	1.547	1.00
91_I	274_F	1.545	1.00
135_I	178_A	1.527	1.00
114_I	224_A	1.510	1.00
86_K	258_D	1.507	1.00
97_Y	100_R	1.503	1.00
139_V	178_A	1.502	1.00
126_Y	208_I	1.500	1.00
259_A	271_Y	1.489	1.00
39_A	292_G	1.473	1.00
89_R	93_S	1.453	1.00
117_G	177_T	1.444	1.00
187_S	191_R	1.436	1.00
256_L	275_P	1.419	1.00
110_V	224_A	1.412	1.00
42_G	285_C	1.388	1.00
55_F	58_L	1.377	1.00
121_G	125_G	1.366	1.00
71_D	74_K	1.347	1.00
37_K	40_I	1.345	1.00
149_F	153_T	1.333	1.00
137_R	140_D	1.326	1.00
196_A	200_I	1.306	1.00
182_R	186_L	1.303	1.00
120_L	178_A	1.303	1.00
75_A	79_E	1.303	1.00
130_I	133_A	1.297	1.00
188_L	194_V	1.285	1.00
121_G	181_V	1.284	1.00
124_A	135_I	1.274	1.00
222_V	294_R	1.273	1.00
122_A	208_I	1.269	1.00
117_G	181_V	1.265	1.00
125_G	189_R	1.262	1.00
82_M	92_F	1.260	1.00
95_I	278_F	1.258	1.00
269_W	273_L	1.245	1.00
293_L	296_A	1.244	1.00
170_C	174_W	1.239	1.00
101_V	104_L	1.238	1.00
188_L	212_I	1.226	1.00
40_I	44_V	1.218	1.00
180_L	223_S	1.211	1.00
154_L	168_I	1.208	1.00
49_I	280_L	1.208	1.00
294_R	298_D	1.206	1.00
163_D	167_L	1.195	1.00
197_A	211_H	1.186	1.00
51_M	55_F	1.184	1.00
77_G	81_L	1.179	1.00
221_I	297_L	1.178	1.00
160_P	163_D	1.169	1.00
89_R	94_R	1.156	1.00
185_F	216_A	1.150	1.00
105_V	235_E	1.143	1.00
86_K	262_F	1.138	1.00
197_A	207_I	1.135	1.00
122_A	213_L	1.121	1.00
197_A	202_T	1.120	1.00
142_V	175_T	1.108	1.00
292_G	296_A	1.104	1.00
128_R	189_R	1.097	1.00
118_T	181_V	1.095	1.00
195_L	198_K	1.092	1.00
133_A	137_R	1.078	1.00
89_R	97_Y	1.075	1.00
184_E	188_L	1.063	1.00
80_H	90_D	1.063	1.00
46_L	281_M	1.059	1.00
181_V	220_I	1.055	1.00
275_P	279_I	1.054	1.00
145_I	150_L	1.051	1.00
255_M	271_Y	1.048	1.00
119_V	122_A	1.047	1.00
44_V	48_I	1.047	1.00
168_I	172_T	1.046	1.00
206_K	209_F	1.045	1.00
174_W	178_A	1.038	1.00
181_V	185_F	1.033	1.00
259_A	272_P	1.026	1.00
82_M	95_I	1.025	1.00
151_L	168_I	1.024	1.00
138_V	142_V	1.020	1.00
228_V	286_F	1.016	1.00
100_R	104_L	1.005	1.00
84_T	90_D	1.000	1.00
91_I	271_Y	0.998	1.00
163_D	166_I	0.997	1.00
132_D	136_M	0.995	1.00
42_G	292_G	0.993	1.00
109_S	170_C	0.982	1.00
56_A	97_Y	0.980	1.00
76_P	79_E	0.980	1.00
41_L	44_V	0.979	1.00
200_I	211_H	0.978	1.00
197_A	200_I	0.974	1.00
49_I	282_T	0.972	1.00
181_V	216_A	0.971	1.00
257_Q	261_N	0.970	1.00
274_F	277_L	0.964	1.00
93_S	97_Y	0.964	1.00
198_K	207_I	0.964	1.00
98_G	255_M	0.962	1.00
136_M	178_A	0.961	1.00
91_I	255_M	0.958	1.00
60_A	93_S	0.955	1.00
44_V	47_F	0.952	1.00
131_V	134_V	0.952	1.00
109_S	113_S	0.951	1.00
128_R	190_S	0.947	1.00
94_R	271_Y	0.947	1.00
95_I	274_F	0.945	1.00
45_I	285_C	0.943	1.00
46_L	285_C	0.939	1.00
218_G	294_R	0.936	1.00
133_A	136_M	0.919	1.00
202_T	207_I	0.919	1.00
270_W	274_F	0.919	1.00
132_D	186_L	0.918	1.00
45_I	281_M	0.915	1.00
42_G	284_L	0.915	1.00
42_G	288_F	0.910	1.00
43_A	47_F	0.908	1.00
104_L	107_F	0.907	1.00
134_V	138_V	0.903	1.00
109_S	169_F	0.901	1.00
48_I	52_S	0.893	1.00
139_V	175_T	0.889	1.00
158_F	164_K	0.886	1.00
285_C	289_V	0.884	1.00
147_D	234_A	0.884	1.00
121_G	185_F	0.876	1.00
204_T	207_I	0.873	1.00
43_A	289_V	0.869	1.00
84_T	88_G	0.867	1.00
114_I	118_T	0.867	1.00
118_T	220_I	0.867	1.00
223_S	227_K	0.861	1.00
96_L	100_R	0.859	1.00
104_L	162_V	0.858	1.00
169_F	234_A	0.856	1.00
286_F	290_G	0.855	1.00
115_L	118_T	0.854	1.00
216_A	219_P	0.851	1.00
221_I	290_G	0.844	1.00
75_A	78_L	0.837	1.00
209_F	212_I	0.830	1.00
52_S	96_L	0.828	1.00
70_L	74_K	0.822	1.00
183_G	186_L	0.817	1.00
99_A	282_T	0.816	1.00
62_Y	93_S	0.816	1.00
94_R	97_Y	0.814	1.00
258_D	261_N	0.813	1.00
114_I	119_V	0.812	1.00
119_V	123_L	0.806	1.00
74_K	78_L	0.802	1.00
76_P	80_H	0.801	1.00
147_D	151_L	0.800	1.00
188_L	215_N	0.799	1.00
93_S	96_L	0.796	1.00
185_F	189_R	0.795	1.00
191_R	195_L	0.794	1.00
204_T	208_I	0.792	1.00
38_L	42_G	0.785	1.00
167_L	170_C	0.782	1.00
273_L	277_L	0.782	1.00
74_K	79_E	0.781	1.00
55_F	59_I	0.781	1.00
162_V	166_I	0.779	1.00
258_D	262_F	0.776	1.00
120_L	174_W	0.775	1.00
73_Y	78_L	0.775	1.00
58_L	269_W	0.775	1.00
255_M	275_P	0.774	1.00
125_G	186_L	0.771	1.00
109_S	231_V	0.769	1.00
54_V	58_L	0.768	1.00
195_L	199_T	0.767	1.00
62_Y	79_E	0.766	1.00
114_I	177_T	0.763	1.00
108_A	240_Y	0.760	1.00
61_P	93_S	0.756	1.00
39_A	43_A	0.754	1.00
108_A	111_V	0.753	1.00
107_F	111_V	0.752	1.00
164_K	167_L	0.751	1.00
39_A	288_F	0.747	1.00
279_I	283_V	0.743	1.00
129_G	133_A	0.742	1.00
112_G	166_I	0.742	1.00
295_D	301_N	0.735	1.00
143_L	175_T	0.735	1.00
257_Q	260_Q	0.735	1.00
274_F	278_F	0.733	1.00
159_K	164_K	0.730	1.00
52_S	99_A	0.730	1.00
202_T	211_H	0.728	1.00
207_I	212_I	0.727	1.00
124_A	132_D	0.722	1.00
76_P	270_W	0.719	1.00
73_Y	76_P	0.718	1.00
184_E	219_P	0.718	1.00
181_V	184_E	0.717	1.00
102_S	106_G	0.716	1.00
205_H	208_I	0.715	1.00
50_I	277_L	0.707	1.00
129_G	132_D	0.697	1.00
116_I	170_C	0.692	1.00
73_Y	268_A	0.690	1.00
96_L	99_A	0.689	1.00
184_E	216_A	0.686	1.00
85_D	268_A	0.685	1.00
41_L	45_I	0.685	1.00
289_V	293_L	0.683	1.00
281_M	285_C	0.680	1.00
294_R	301_N	0.680	1.00
128_R	132_D	0.680	1.00
225_T	286_F	0.676	1.00
273_L	276_G	0.675	1.00
69_L	73_Y	0.670	1.00
49_I	281_M	0.668	1.00
283_V	287_N	0.664	1.00
173_G	176_T	0.662	1.00
172_T	175_T	0.658	1.00
154_L	164_K	0.658	1.00
134_V	137_R	0.656	1.00
113_S	170_C	0.647	1.00
116_I	120_L	0.646	1.00
42_G	45_I	0.641	1.00
61_P	92_F	0.639	1.00
45_I	49_I	0.638	1.00
147_D	150_L	0.636	1.00
272_P	276_G	0.634	1.00
69_L	72_K	0.634	1.00
186_L	189_R	0.630	1.00
70_L	73_Y	0.630	1.00
95_I	275_P	0.626	1.00
235_E	239_S	0.626	1.00
233_L	236_S	0.626	1.00
165_L	235_E	0.623	1.00
236_S	254_N	0.620	1.00
57_P	100_R	0.619	1.00
233_L	237_A	0.618	1.00
126_Y	189_R	0.616	1.00
110_V	227_K	0.615	1.00
127_F	208_I	0.611	1.00
177_T	223_S	0.608	1.00
124_A	136_M	0.608	1.00
136_M	139_V	0.607	1.00
40_I	43_A	0.607	1.00
137_R	141_I	0.607	1.00
52_S	56_A	0.605	1.00
69_L	81_L	0.601	1.00
234_A	237_A	0.601	1.00
106_G	231_V	0.600	1.00
103_L	107_F	0.600	1.00
71_D	80_H	0.599	1.00
46_L	286_F	0.599	1.00
75_A	270_W	0.599	1.00
117_G	121_G	0.597	1.00
135_I	139_V	0.596	1.00
37_K	41_L	0.595	1.00
139_V	174_W	0.592	1.00
80_H	84_T	0.589	1.00
232_I	236_S	0.588	1.00
110_V	228_V	0.587	1.00
126_Y	209_F	0.587	1.00
176_T	227_K	0.586	1.00
177_T	181_V	0.585	1.00
153_T	157_I	0.584	1.00
255_M	258_D	0.584	1.00
53_A	276_G	0.584	1.00
62_Y	267_Q	0.584	1.00
231_V	234_A	0.582	1.00
111_V	115_L	0.581	1.00
99_A	103_L	0.580	1.00
288_F	292_G	0.576	1.00
125_G	132_D	0.576	1.00
202_T	205_H	0.576	1.00
128_R	186_L	0.576	1.00
222_V	225_T	0.568	1.00
142_V	174_W	0.566	1.00
150_L	172_T	0.566	1.00
255_M	259_A	0.562	1.00
236_S	257_Q	0.562	1.00
171_L	174_W	0.561	1.00
60_A	97_Y	0.556	1.00
72_K	76_P	0.555	1.00
114_I	220_I	0.553	1.00
291_D	294_R	0.549	1.00
49_I	53_A	0.549	1.00
62_Y	80_H	0.548	1.00
147_D	171_L	0.547	1.00
73_Y	271_Y	0.546	1.00
194_V	198_K	0.545	1.00
105_V	165_L	0.545	1.00
100_R	103_L	0.541	1.00
209_F	214_P	0.541	1.00
256_L	279_I	0.541	1.00
155_V	159_K	0.537	1.00
65_E	78_L	0.537	1.00
173_G	227_K	0.536	1.00
57_P	97_Y	0.535	1.00
167_L	171_L	0.534	1.00
108_A	163_D	0.532	1.00
236_S	258_D	0.528	1.00
120_L	123_L	0.528	1.00
176_T	223_S	0.525	1.00
94_R	98_G	0.525	1.00
270_W	273_L	0.524	1.00
217_L	221_I	0.519	1.00
203_K	207_I	0.519	1.00
38_L	41_L	0.519	1.00
124_A	182_R	0.518	1.00
110_V	114_I	0.516	1.00
56_A	59_I	0.515	1.00
81_L	92_F	0.514	1.00
68_S	72_K	0.513	1.00
46_L	289_V	0.513	1.00
50_I	54_V	0.512	1.00
67_Q	87_F	0.512	1.00
175_T	178_A	0.510	1.00
70_L	78_L	0.510	1.00
180_L	184_E	0.503	1.00
117_G	178_A	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	0.835	99.9	0.63	Contact Map
3d31C	2	0.7624	99.9	0.644	Contact Map
3tuiA	2	0.6667	99.9	0.659	Contact Map
3rlfF	1	0.9208	99.9	0.66	Contact Map
2onkC	2	0.7822	99.9	0.666	Contact Map
3rlfG	1	0.8416	99.9	0.682	Contact Map
4tquN	1	0.8614	99.8	0.685	Contact Map
4ymuD	2	0.6832	99.8	0.691	Contact Map
3j9pD	4	0.7756	65.7	0.94	Contact Map
2kogA	1	0.1881	54.6	0.944	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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