SAPC - ECOLI - GREMLIN Contacts

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SAPC - Peptide transport system permease protein SapC

UniProt:	P0AGH5	Sequences: MPYDSVYSEKRPPGTLRTAWRKFYSDASAMVGLYGCAGLAVLCIFGGWFAPYGIDQQFLGYQLLPPSWSRYGEVSFFLGTDDLGRDVLSRLLSGAAPTVGGAFVVTLAATICGLVLGTFAGATHGLRSAVLNHILDTLLAIPSLLLAIIVVAFAGPSLSHAMFAVWLALLPRMVRSIYSMVHDELEKEYVIAARLDGASTLNILWFAVMPNITAGLVTEITRALSMAILDIAALGFLDLGAQLPSPEWGAMLGDALELIYVAPWTVMLPGAAIMISVLLVNLLGDGVRRAIIAGVE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG20256
Length:	296 (253)
Sequences:	28856 (17943)
Seq/√Len:	1128.1

ECOLI - SAPC DPPC YEJE DDPC GSID OPPC NIKC YEJB DDPB GSIC DPPB NIKB SAPB OPPB
BACSU - DPPC APPC OPPC APPB OPPB DPPB
HALSA - Q9HMW2 Q9HMI1 Q9HMX1 Q9HMX0 Q9HMI2 Q9HMW3
SULSO - Q97UH2 Q97VK7 Q97UG3 Q97YP2 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
181_V	208_V	2.805	1.00
128_S	178_Y	2.686	1.00
184_E	189_Y	2.457	1.00
198_A	202_N	2.448	1.00
194_R	200_T	2.445	1.00
202_N	206_F	2.404	1.00
104_V	162_M	2.365	1.00
116_L	131_L	2.354	1.00
108_A	166_W	2.321	1.00
184_E	187_K	2.294	1.00
58_F	61_Y	2.280	1.00
97_P	236_F	2.258	1.00
199_S	202_N	2.247	1.00
201_L	205_W	2.208	1.00
188_E	191_I	2.116	1.00
250_A	254_D	2.107	1.00
190_V	208_V	2.033	1.00
190_V	203_I	2.025	1.00
118_T	181_V	1.988	1.00
221_T	284_G	1.982	1.00
90_R	251_M	1.957	1.00
123_T	127_R	1.924	1.00
119_F	123_T	1.901	1.00
123_T	200_T	1.895	1.00
53_G	56_Q	1.874	1.00
111_I	115_V	1.869	1.00
86_D	89_S	1.863	1.00
173_M	223_A	1.849	1.00
81_D	85_R	1.766	1.00
189_Y	211_N	1.753	1.00
64_L	67_S	1.749	1.00
184_E	212_I	1.741	1.00
37_A	41_V	1.730	1.00
121_G	181_V	1.729	1.00
126_L	130_V	1.726	1.00
122_A	200_T	1.724	1.00
43_C	95_A	1.710	1.00
78_L	268_L	1.696	1.00
88_L	92_L	1.657	1.00
112_C	170_L	1.641	1.00
109_A	169_L	1.609	1.00
119_F	127_R	1.601	1.00
185_L	208_V	1.596	1.00
100_G	104_V	1.595	1.00
112_C	115_V	1.594	1.00
76_F	86_D	1.591	1.00
83_L	90_R	1.589	1.00
127_R	131_L	1.584	1.00
162_M	166_W	1.565	1.00
87_V	268_L	1.554	1.00
29_A	286_G	1.547	1.00
131_L	174_V	1.546	1.00
93_S	96_A	1.529	1.00
180_M	183_D	1.528	1.00
135_L	174_V	1.506	1.00
82_D	254_D	1.502	1.00
110_T	220_I	1.495	1.00
255_A	265_T	1.489	1.00
85_R	89_S	1.489	1.00
122_A	204_L	1.484	1.00
72_G	77_F	1.464	1.00
106_T	220_I	1.451	1.00
113_G	173_M	1.449	1.00
117_G	121_G	1.440	1.00
183_D	187_K	1.438	1.00
252_L	269_P	1.418	1.00
133_H	136_D	1.395	1.00
45_F	48_W	1.395	1.00
32_G	279_L	1.388	1.00
117_G	177_I	1.367	1.00
126_L	129_A	1.344	1.00
116_L	174_V	1.338	1.00
192_A	196_D	1.322	1.00
178_Y	182_H	1.321	1.00
113_G	177_I	1.321	1.00
218_T	288_R	1.317	1.00
145_L	149_I	1.307	1.00
120_A	131_L	1.302	1.00
121_G	185_L	1.299	1.00
30_M	34_Y	1.295	1.00
91_L	272_A	1.288	1.00
97_P	100_G	1.280	1.00
159_S	163_F	1.260	1.00
263_P	267_M	1.253	1.00
184_E	190_V	1.251	1.00
118_T	204_L	1.251	1.00
39_L	274_M	1.245	1.00
150_V	164_A	1.237	1.00
184_E	208_V	1.232	1.00
78_L	88_L	1.230	1.00
41_V	45_F	1.230	1.00
166_W	170_L	1.228	1.00
176_S	219_E	1.228	1.00
287_V	290_A	1.221	1.00
61_Y	64_L	1.218	1.00
288_R	292_I	1.215	1.00
217_V	291_I	1.213	1.00
193_A	207_A	1.203	1.00
27_A	30_M	1.199	1.00
101_G	231_I	1.169	1.00
67_S	75_S	1.166	1.00
85_R	90_R	1.153	1.00
64_L	68_W	1.144	1.00
181_V	212_I	1.140	1.00
193_A	203_I	1.132	1.00
286_G	290_A	1.129	1.00
193_A	198_A	1.128	1.00
118_T	209_M	1.125	1.00
85_R	93_S	1.120	1.00
124_H	185_L	1.119	1.00
138_L	171_P	1.113	1.00
191_I	194_R	1.103	1.00
36_C	275_I	1.102	1.00
177_I	216_L	1.102	1.00
129_A	133_H	1.098	1.00
114_L	177_I	1.077	1.00
78_L	91_L	1.077	1.00
269_P	273_I	1.076	1.00
177_I	181_V	1.073	1.00
115_V	118_T	1.072	1.00
164_A	168_A	1.068	1.00
80_T	86_D	1.057	1.00
141_I	146_L	1.056	1.00
202_N	205_W	1.054	1.00
170_L	174_V	1.048	1.00
147_A	164_A	1.041	1.00
180_M	184_E	1.038	1.00
82_D	258_L	1.036	1.00
157_S	160_H	1.032	1.00
255_A	266_V	1.026	1.00
132_N	174_V	1.021	1.00
46_G	93_S	1.019	1.00
134_I	138_L	1.016	1.00
105_V	166_W	1.015	1.00
96_A	100_G	1.015	1.00
251_M	265_T	1.011	1.00
36_C	279_L	1.011	1.00
87_V	251_M	1.007	1.00
32_G	286_G	1.006	1.00
196_D	207_A	1.005	1.00
31_V	34_Y	1.002	1.00
159_S	162_M	1.001	1.00
128_S	132_N	0.995	1.00
34_Y	38_G	0.995	1.00
87_V	265_T	0.994	1.00
39_L	276_S	0.992	1.00
194_R	203_I	0.988	1.00
50_A	89_S	0.984	1.00
264_W	268_L	0.980	1.00
35_G	279_L	0.979	1.00
72_G	75_S	0.978	1.00
76_F	80_T	0.972	1.00
177_I	212_I	0.969	1.00
100_G	158_L	0.967	1.00
193_A	196_D	0.964	1.00
124_H	186_E	0.961	1.00
34_Y	37_A	0.960	1.00
105_V	109_A	0.953	1.00
214_A	288_R	0.946	1.00
32_G	278_L	0.946	1.00
268_L	271_A	0.938	1.00
91_L	268_L	0.938	1.00
127_R	130_V	0.935	1.00
253_G	257_E	0.935	1.00
89_S	93_S	0.934	1.00
52_Y	75_S	0.933	1.00
65_P	68_W	0.930	1.00
90_R	265_T	0.930	1.00
128_S	182_H	0.927	1.00
198_A	203_I	0.924	1.00
33_L	37_A	0.923	1.00
38_G	42_L	0.921	1.00
200_T	203_I	0.917	1.00
154_A	160_H	0.914	1.00
130_V	134_I	0.913	1.00
117_G	181_V	0.912	1.00
100_G	103_F	0.911	1.00
114_L	216_L	0.911	1.00
125_G	128_S	0.904	1.00
32_G	282_L	0.903	1.00
143_S	230_D	0.902	1.00
105_V	165_V	0.901	1.00
94_G	251_M	0.897	1.00
129_A	132_N	0.890	1.00
35_G	275_I	0.889	1.00
279_L	283_L	0.877	1.00
135_L	171_P	0.864	1.00
280_V	284_G	0.864	1.00
165_V	230_D	0.864	1.00
33_L	283_L	0.864	1.00
217_V	284_G	0.864	1.00
68_W	75_S	0.863	1.00
125_G	129_A	0.849	1.00
52_Y	76_F	0.848	1.00
42_L	92_L	0.848	1.00
212_I	215_G	0.843	1.00
90_R	93_S	0.841	1.00
110_T	114_L	0.839	1.00
158_L	162_M	0.838	1.00
92_L	96_A	0.838	1.00
80_T	84_G	0.837	1.00
60_G	64_L	0.834	1.00
205_W	208_V	0.833	1.00
254_D	257_E	0.826	1.00
219_E	223_A	0.825	1.00
179_S	182_H	0.821	1.00
110_T	115_V	0.819	1.00
111_I	114_L	0.819	1.00
163_F	166_W	0.814	1.00
155_G	160_H	0.814	1.00
60_G	63_L	0.813	1.00
143_S	147_A	0.813	1.00
200_T	204_L	0.809	1.00
156_P	160_H	0.806	1.00
52_Y	89_S	0.805	1.00
181_V	185_L	0.804	1.00
29_A	282_L	0.803	1.00
115_V	119_F	0.800	1.00
95_A	276_S	0.796	1.00
187_K	191_I	0.795	1.00
160_H	163_F	0.790	1.00
68_W	77_F	0.789	1.00
51_P	89_S	0.788	1.00
89_S	92_L	0.788	1.00
103_F	107_L	0.787	1.00
29_A	33_L	0.785	1.00
150_V	160_H	0.785	1.00
116_L	170_L	0.784	1.00
105_V	227_A	0.783	1.00
191_I	195_L	0.782	1.00
267_M	271_A	0.779	1.00
48_W	263_P	0.777	1.00
62_Q	66_P	0.771	1.00
184_E	211_N	0.770	1.00
251_M	269_P	0.769	1.00
63_L	68_W	0.769	1.00
273_I	277_V	0.764	1.00
110_T	173_M	0.761	1.00
104_V	107_L	0.755	1.00
45_F	49_F	0.755	1.00
77_F	88_L	0.752	1.00
104_V	236_F	0.743	1.00
253_G	256_L	0.743	1.00
121_G	182_H	0.739	1.00
139_L	171_P	0.738	1.00
198_A	207_A	0.737	1.00
98_T	102_A	0.736	1.00
289_R	295_V	0.733	1.00
203_I	208_V	0.732	1.00
61_Y	76_F	0.728	1.00
42_L	95_A	0.719	1.00
108_A	162_M	0.717	1.00
258_L	261_V	0.716	1.00
120_A	128_S	0.716	1.00
180_M	215_G	0.715	1.00
28_S	32_G	0.712	1.00
177_I	180_M	0.711	1.00
254_D	258_L	0.708	1.00
268_L	272_A	0.707	1.00
40_A	271_A	0.705	1.00
92_L	95_A	0.705	1.00
277_V	281_N	0.702	1.00
63_L	66_P	0.698	1.00
169_L	172_R	0.694	1.00
275_I	279_L	0.691	1.00
201_L	204_L	0.690	1.00
39_L	275_I	0.688	1.00
221_T	280_V	0.687	1.00
112_C	166_W	0.685	1.00
168_A	171_P	0.680	1.00
81_D	262_A	0.679	1.00
59_L	62_Q	0.677	1.00
122_A	185_L	0.674	1.00
31_V	35_G	0.674	1.00
102_A	224_L	0.670	1.00
180_M	212_I	0.669	1.00
109_A	166_W	0.668	1.00
77_F	86_D	0.667	1.00
32_G	35_G	0.663	1.00
161_A	231_I	0.663	1.00
283_L	287_V	0.660	1.00
229_L	232_A	0.659	1.00
267_M	270_G	0.656	1.00
44_I	48_W	0.654	1.00
72_G	76_F	0.652	1.00
266_V	270_G	0.652	1.00
30_M	33_L	0.647	1.00
113_G	117_G	0.642	1.00
47_G	96_A	0.641	1.00
156_P	159_S	0.637	1.00
124_H	128_S	0.632	1.00
27_A	31_V	0.631	1.00
51_P	88_L	0.629	1.00
130_V	133_H	0.629	1.00
143_S	146_L	0.626	1.00
229_L	233_A	0.625	1.00
231_I	235_G	0.625	1.00
36_C	280_V	0.625	1.00
288_R	295_V	0.625	1.00
107_L	111_I	0.620	1.00
173_M	177_I	0.619	1.00
182_H	185_L	0.619	1.00
91_L	269_P	0.618	1.00
112_C	116_L	0.616	1.00
106_T	223_A	0.613	1.00
173_M	219_E	0.609	1.00
146_L	168_A	0.603	1.00
232_A	250_A	0.601	1.00
99_V	103_F	0.601	1.00
230_D	233_A	0.600	1.00
120_A	132_N	0.600	1.00
102_A	227_A	0.599	1.00
123_T	204_L	0.598	1.00
132_N	135_L	0.595	1.00
124_H	182_H	0.591	1.00
135_L	170_L	0.590	1.00
198_A	201_L	0.589	1.00
172_R	223_A	0.587	1.00
131_L	135_L	0.586	1.00
35_G	39_L	0.584	1.00
43_C	270_G	0.583	1.00
251_M	254_D	0.583	1.00
58_F	76_F	0.582	1.00
133_H	137_T	0.581	1.00
96_A	99_V	0.580	1.00
58_F	62_Q	0.577	1.00
138_L	170_L	0.575	1.00
228_I	232_A	0.575	1.00
64_L	80_T	0.573	1.00
52_Y	261_V	0.572	1.00
104_V	159_S	0.566	1.00
95_A	99_V	0.566	1.00
251_M	255_A	0.566	1.00
167_L	170_L	0.565	1.00
42_L	46_G	0.564	1.00
218_T	221_T	0.563	1.00
169_L	223_A	0.560	1.00
232_A	253_G	0.558	1.00
149_I	153_F	0.557	1.00
160_H	164_A	0.557	1.00
143_S	167_L	0.556	1.00
113_G	174_V	0.553	1.00
50_A	93_S	0.552	1.00
227_A	230_D	0.550	1.00
122_A	205_W	0.548	1.00
252_L	273_I	0.547	1.00
282_L	286_G	0.547	1.00
106_T	110_T	0.546	1.00
66_P	264_W	0.543	1.00
110_T	216_L	0.542	1.00
120_A	178_Y	0.541	1.00
190_V	194_R	0.540	1.00
116_L	119_F	0.539	1.00
285_D	288_R	0.538	1.00
224_L	280_V	0.535	1.00
63_L	262_A	0.533	1.00
28_S	282_L	0.532	1.00
163_F	167_L	0.531	1.00
205_W	210_P	0.531	1.00
101_G	161_A	0.529	1.00
54_I	93_S	0.529	1.00
166_W	169_L	0.529	1.00
136_D	139_L	0.528	1.00
47_G	93_S	0.528	1.00
121_G	128_S	0.527	1.00
62_Q	65_P	0.527	1.00
258_L	265_T	0.527	1.00
36_C	283_L	0.526	1.00
90_R	94_G	0.525	1.00
151_V	155_G	0.521	1.00
232_A	254_D	0.521	1.00
171_P	174_V	0.514	1.00
199_S	203_I	0.512	1.00
57_Q	83_L	0.509	1.00
264_W	267_M	0.508	1.00
176_S	180_M	0.507	1.00
213_T	217_V	0.504	1.00
56_Q	68_W	0.504	1.00
40_A	43_C	0.501	1.00
132_N	136_D	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	0.8547	99.9	0.607	Contact Map
3d31C	2	0.7838	99.9	0.63	Contact Map
3tuiA	2	0.6824	99.9	0.631	Contact Map
2onkC	2	0.8007	99.9	0.644	Contact Map
3rlfF	1	0.8919	99.9	0.655	Contact Map
4tquN	1	0.8986	99.8	0.665	Contact Map
3rlfG	1	0.8581	99.8	0.669	Contact Map
4ymuD	2	0.7061	99.8	0.673	Contact Map
3j9pD	4	0.7635	40.7	0.945	Contact Map
4ry2A	2	0.9662	26.4	0.95	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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