YCJO - ECOLI - GREMLIN Contacts

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YCJO - Inner membrane ABC transporter permease protein YcjO

UniProt:	P0AFR7	Sequences: MNRLFSGRSDMPFALLLLAPSLLLLGGLVAWPMVSNIEISFLRLPLNPNIESTFVGVSNYVRILSDPGFWHSLWMTVWYTALVVAGSTVLGLAVAMFFNREFRLRKTARSLVILSYVTPSISLVFAWKYMFNNGYGIVNYLGVDLLHLYEQAPLWFDNPGSSFVLVVLFAIWRYFPYAFISFLAILQTIDKSLYEAAEMDGANAWQRFRIVTLPAIMPVLATVVTLRTIWMFYMFADVYLLTTKVDILGVYLYKTAFAFNDLGKAAAISVVLFIIIFAVILLTRKRVNLNGNK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13912
Length:	293 (252)
Sequences:	69567 (44959)
Seq/√Len:	2832.1

ECOLI - YCJO POTH UGPA YDCU PSTC POTB YDCV MALG YCJP THIP PSTA CYSW UGPE MALF CYST POTI YNJC POTC MODB TAUC SSUC YEHY PHNE YEHW METI PROW YECS
BACSU - AMYD GANP YESP YTEP MDXF ARAP LPLB YURN GANQ MDXG YESQ LPLC ARAQ YURM AMYC YQGH YQGI YTCP SSUC YVGM YTLD OPUAB METP OPUCB TCYB YXEN OPUBD OPUBB TCYL OPUCD
HALSA - Q9HHQ7 Q9HP01 Q9HMT4 Q9HML6 Q9HP02 Q9HR05 Q9HPK3 Q9HS11 Q9HHQ6 Q9HNI9 Q9HS12
SULSO - Q97YY2 Q97UZ0 Q97YY3 Q97UF3 Q97ZC2 Q97UF4 Q97UY9 Q97ZC1 Q97ZT7 Q97VC0 Q97ZT6 Q97Z98

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
206_Q	210_I	4.041	1.00
74_W	78_W	3.201	1.00
183_L	187_Q	2.998	1.00
198_E	207_R	2.990	1.00
40_S	60_Y	2.746	1.00
72_S	251_Y	2.650	1.00
71_H	74_W	2.591	1.00
100_R	194_Y	2.591	1.00
203_N	206_Q	2.538	1.00
197_A	207_R	2.494	1.00
82_L	167_V	2.485	1.00
194_Y	212_T	2.479	1.00
185_I	219_V	2.459	1.00
86_G	171_I	2.418	1.00
246_D	254_K	2.407	1.00
58_S	61_V	2.378	1.00
61_V	65_S	2.366	1.00
70_W	74_W	2.345	1.00
84_V	224_V	2.320	1.00
204_A	207_R	2.260	1.00
182_F	220_L	2.225	1.00
205_W	209_R	2.221	1.00
58_S	62_R	2.182	1.00
102_F	105_R	2.113	1.00
202_A	206_Q	2.052	1.00
92_L	208_F	2.043	1.00
206_Q	209_R	2.043	1.00
261_D	264_K	2.039	1.00
178_A	223_V	1.956	1.00
99_N	187_Q	1.952	1.00
186_L	216_I	1.930	1.00
197_A	202_A	1.888	1.00
193_L	215_A	1.888	1.00
38_E	42_L	1.882	1.00
92_L	216_I	1.800	1.00
88_T	224_V	1.788	1.00
109_R	183_L	1.758	1.00
71_H	75_M	1.738	1.00
34_V	38_E	1.730	1.00
198_E	204_A	1.729	1.00
80_T	228_T	1.710	1.00
91_G	178_A	1.697	1.00
194_Y	207_R	1.687	1.00
281_L	285_K	1.685	1.00
62_R	264_K	1.638	1.00
78_W	82_L	1.633	1.00
92_L	182_F	1.627	1.00
83_V	231_M	1.627	1.00
98_F	179_F	1.582	1.00
94_V	179_F	1.581	1.00
194_Y	198_E	1.557	1.00
37_I	270_V	1.531	1.00
191_K	194_Y	1.477	1.00
19_A	23_L	1.476	1.00
242_T	245_V	1.462	1.00
101_E	105_R	1.452	1.00
251_Y	255_T	1.433	1.00
62_R	65_S	1.429	1.00
57_V	61_V	1.427	1.00
235_F	239_Y	1.423	1.00
79_Y	247_I	1.414	1.00
95_A	182_F	1.399	1.00
104_L	107_T	1.399	1.00
31_W	35_S	1.399	1.00
178_A	227_R	1.392	1.00
99_N	183_L	1.389	1.00
213_L	220_L	1.387	1.00
56_G	59_N	1.383	1.00
35_S	39_I	1.365	1.00
186_L	212_T	1.348	1.00
222_T	226_L	1.347	1.00
68_G	71_H	1.335	1.00
87_S	227_R	1.323	1.00
182_F	223_V	1.306	1.00
89_V	93_A	1.289	1.00
100_R	191_K	1.283	1.00
191_K	195_E	1.268	1.00
235_F	253_Y	1.257	1.00
237_D	241_L	1.249	1.00
92_L	220_L	1.243	1.00
197_A	211_V	1.241	1.00
192_S	195_E	1.236	1.00
255_T	259_F	1.219	1.00
169_F	241_L	1.216	1.00
96_M	186_L	1.204	1.00
76_T	248_L	1.203	1.00
255_T	261_D	1.198	1.00
131_F	165_L	1.194	1.00
82_L	85_A	1.191	1.00
85_A	89_V	1.182	1.00
246_D	251_Y	1.175	1.00
107_T	110_S	1.164	1.00
189_I	215_A	1.162	1.00
23_L	27_G	1.155	1.00
13_F	17_L	1.152	1.00
12_P	16_L	1.135	1.00
203_N	207_R	1.129	1.00
166_V	238_V	1.124	1.00
217_M	221_A	1.113	1.00
88_T	220_L	1.113	1.00
75_M	78_W	1.112	1.00
14_A	18_L	1.103	1.00
285_K	288_N	1.091	1.00
36_N	270_V	1.086	1.00
182_F	219_V	1.079	1.00
60_Y	270_V	1.076	1.00
107_T	111_L	1.063	1.00
167_V	171_I	1.053	1.00
83_V	87_S	1.048	1.00
254_K	258_A	1.044	1.00
215_A	218_P	1.043	1.00
64_L	70_W	1.042	1.00
96_M	208_F	1.042	1.00
234_M	237_D	1.040	1.00
132_N	135_Y	1.038	1.00
181_S	223_V	1.036	1.00
282_L	286_R	1.035	1.00
16_L	20_P	1.029	1.00
82_L	86_G	1.028	1.00
99_N	186_L	1.026	1.00
86_G	167_V	1.020	1.00
194_Y	204_A	1.020	1.00
247_I	250_V	1.018	1.00
77_V	81_A	1.015	1.00
73_L	248_L	1.008	1.00
141_L	245_V	1.007	1.00
175_F	179_F	1.006	1.00
13_F	16_L	1.004	1.00
16_L	19_A	0.997	1.00
93_A	97_F	0.995	1.00
202_A	207_R	0.993	1.00
129_Y	133_N	0.992	1.00
251_Y	268_I	0.990	1.00
83_V	170_A	0.988	1.00
238_V	247_I	0.983	1.00
256_A	265_A	0.982	1.00
35_S	38_E	0.982	1.00
234_M	238_V	0.980	1.00
164_V	168_L	0.980	1.00
96_M	204_A	0.975	1.00
246_D	250_V	0.962	1.00
78_W	164_V	0.954	1.00
105_R	187_Q	0.952	1.00
207_R	210_I	0.941	1.00
15_L	19_A	0.928	1.00
170_A	231_M	0.924	1.00
137_I	164_V	0.923	1.00
85_A	224_V	0.921	1.00
69_F	268_I	0.913	1.00
127_W	241_L	0.912	1.00
59_N	263_G	0.908	1.00
78_W	81_A	0.908	1.00
239_Y	250_V	0.903	1.00
81_A	85_A	0.899	1.00
95_A	99_N	0.896	1.00
26_G	30_A	0.891	1.00
164_V	167_V	0.891	1.00
39_I	266_A	0.890	1.00
18_L	22_L	0.890	1.00
103_R	106_K	0.887	1.00
185_I	216_I	0.880	1.00
83_V	167_V	0.876	1.00
217_M	220_L	0.875	1.00
216_I	219_V	0.875	1.00
113_I	180_I	0.872	1.00
63_I	271_V	0.869	1.00
91_G	179_F	0.869	1.00
40_S	44_L	0.868	1.00
41_F	55_V	0.867	1.00
178_A	182_F	0.865	1.00
182_F	216_I	0.861	1.00
62_R	66_D	0.861	1.00
169_F	237_D	0.861	1.00
79_Y	170_A	0.860	1.00
39_I	42_L	0.858	1.00
208_F	213_L	0.857	1.00
209_R	213_L	0.853	1.00
127_W	169_F	0.852	1.00
87_S	91_G	0.849	1.00
95_A	179_F	0.844	1.00
73_L	77_V	0.841	1.00
255_T	268_I	0.839	1.00
98_F	109_R	0.838	1.00
86_G	89_V	0.838	1.00
106_K	109_R	0.832	1.00
251_Y	254_K	0.829	1.00
227_R	231_M	0.829	1.00
120_S	173_R	0.810	1.00
242_T	246_D	0.805	1.00
276_I	280_I	0.805	1.00
282_L	285_K	0.801	1.00
207_R	212_T	0.800	1.00
82_L	171_I	0.796	1.00
138_V	141_L	0.790	1.00
97_F	102_F	0.788	1.00
74_W	77_V	0.783	1.00
204_A	208_F	0.783	1.00
36_N	266_A	0.781	1.00
202_A	210_I	0.780	1.00
124_V	236_A	0.778	1.00
95_A	186_L	0.778	1.00
51_E	54_F	0.773	1.00
66_D	70_W	0.770	1.00
278_A	282_L	0.768	1.00
255_T	264_K	0.767	1.00
193_L	211_V	0.764	1.00
62_R	261_D	0.763	1.00
72_S	75_M	0.759	1.00
189_I	216_I	0.758	1.00
87_S	174_Y	0.757	1.00
137_I	140_Y	0.756	1.00
136_G	139_N	0.752	1.00
137_I	141_L	0.752	1.00
128_K	132_N	0.750	1.00
41_F	56_G	0.749	1.00
264_K	268_I	0.745	1.00
208_F	212_T	0.744	1.00
124_V	240_L	0.742	1.00
45_P	48_P	0.738	1.00
39_I	43_R	0.737	1.00
61_V	64_L	0.734	1.00
165_L	169_F	0.732	1.00
55_V	58_S	0.728	1.00
72_S	248_L	0.723	1.00
36_N	269_S	0.723	1.00
113_I	116_Y	0.723	1.00
87_S	178_A	0.723	1.00
94_V	175_F	0.722	1.00
31_W	34_V	0.721	1.00
88_T	182_F	0.721	1.00
80_T	84_V	0.719	1.00
166_V	242_T	0.715	1.00
98_F	108_A	0.713	1.00
84_V	228_T	0.712	1.00
252_L	268_I	0.711	1.00
217_M	286_R	0.708	1.00
20_P	23_L	0.704	1.00
91_G	182_F	0.704	1.00
76_T	249_G	0.704	1.00
283_T	286_R	0.703	1.00
67_P	71_H	0.703	1.00
98_F	183_L	0.703	1.00
182_F	186_L	0.702	1.00
191_K	198_E	0.698	1.00
43_R	54_F	0.698	1.00
70_W	73_L	0.696	1.00
234_M	247_I	0.693	1.00
17_L	21_S	0.691	1.00
220_L	223_V	0.691	1.00
84_V	88_T	0.690	1.00
25_L	29_V	0.690	1.00
17_L	20_P	0.690	1.00
266_A	269_S	0.688	1.00
123_L	172_W	0.686	1.00
165_L	241_L	0.679	1.00
87_S	231_M	0.679	1.00
120_S	236_A	0.678	1.00
54_F	58_S	0.677	1.00
248_L	272_L	0.674	1.00
174_Y	227_R	0.673	1.00
75_M	245_V	0.669	1.00
43_R	53_T	0.669	1.00
59_N	62_R	0.668	1.00
266_A	270_V	0.664	1.00
212_T	215_A	0.664	1.00
42_L	52_S	0.664	1.00
135_Y	138_V	0.659	1.00
57_V	60_Y	0.657	1.00
196_A	199_M	0.657	1.00
90_L	175_F	0.656	1.00
238_V	250_V	0.655	1.00
26_G	29_V	0.655	1.00
196_A	200_D	0.654	1.00
220_L	224_V	0.652	1.00
174_Y	230_W	0.650	1.00
79_Y	167_V	0.647	1.00
263_G	266_A	0.647	1.00
63_I	264_K	0.645	1.00
101_E	106_K	0.643	1.00
94_V	112_V	0.641	1.00
42_L	54_F	0.639	1.00
272_L	276_I	0.639	1.00
90_L	171_I	0.638	1.00
250_V	254_K	0.638	1.00
109_R	180_I	0.637	1.00
22_L	26_G	0.637	1.00
104_L	108_A	0.636	1.00
40_S	267_A	0.630	1.00
79_Y	166_V	0.630	1.00
219_V	223_V	0.630	1.00
12_P	15_L	0.628	1.00
253_Y	257_F	0.626	1.00
67_P	70_W	0.626	1.00
249_G	272_L	0.623	1.00
60_Y	267_A	0.622	1.00
56_G	60_Y	0.621	1.00
129_Y	132_N	0.619	1.00
68_G	251_Y	0.618	1.00
63_I	268_I	0.618	1.00
102_F	108_A	0.616	1.00
236_A	240_L	0.616	1.00
262_L	266_A	0.615	1.00
277_F	281_L	0.610	1.00
170_A	173_R	0.609	1.00
87_S	171_I	0.606	1.00
54_F	57_V	0.606	1.00
181_S	219_V	0.605	1.00
132_N	138_V	0.605	1.00
262_L	265_A	0.603	1.00
121_I	240_L	0.602	1.00
112_V	176_P	0.601	1.00
229_I	233_Y	0.599	1.00
21_S	25_L	0.598	1.00
76_T	232_F	0.591	1.00
15_L	18_L	0.587	1.00
78_W	141_L	0.586	1.00
116_Y	176_P	0.585	1.00
80_T	231_M	0.582	1.00
127_W	130_M	0.574	1.00
42_L	53_T	0.573	1.00
116_Y	177_Y	0.573	1.00
40_S	270_V	0.573	1.00
236_A	239_Y	0.571	1.00
88_T	92_L	0.571	1.00
103_R	107_T	0.569	1.00
207_R	211_V	0.565	1.00
264_K	267_A	0.564	1.00
94_V	97_F	0.563	1.00
203_N	209_R	0.562	1.00
30_A	34_V	0.562	1.00
189_I	194_Y	0.561	1.00
221_A	224_V	0.560	1.00
95_A	183_L	0.559	1.00
96_M	212_T	0.557	1.00
224_V	227_R	0.556	1.00
209_R	212_T	0.556	1.00
135_Y	140_Y	0.555	1.00
80_T	232_F	0.554	1.00
79_Y	83_V	0.552	1.00
170_A	234_M	0.551	1.00
166_V	170_A	0.548	1.00
131_F	138_V	0.547	1.00
130_M	138_V	0.547	1.00
44_L	52_S	0.545	1.00
230_W	233_Y	0.543	1.00
75_M	247_I	0.541	1.00
280_I	284_R	0.541	1.00
275_I	278_A	0.541	1.00
110_S	114_L	0.539	1.00
108_A	112_V	0.538	1.00
88_T	93_A	0.537	1.00
106_K	110_S	0.537	1.00
238_V	242_T	0.535	1.00
27_G	31_W	0.535	1.00
252_L	269_S	0.534	1.00
101_E	191_K	0.534	1.00
83_V	171_I	0.534	1.00
173_R	176_P	0.532	1.00
28_L	32_P	0.530	1.00
250_V	253_Y	0.529	1.00
84_V	89_V	0.529	1.00
68_G	246_D	0.528	1.00
78_W	167_V	0.528	1.00
141_L	164_V	0.526	1.00
19_A	22_L	0.521	1.00
124_V	128_K	0.517	1.00
120_S	124_V	0.512	1.00
84_V	231_M	0.511	1.00
231_M	234_M	0.510	1.00
111_L	115_S	0.510	1.00
118_T	122_S	0.507	1.00
115_S	176_P	0.507	1.00
195_E	198_E	0.506	1.00
101_E	104_L	0.505	1.00
69_F	251_Y	0.505	1.00
71_H	78_W	0.504	1.00
32_P	36_N	0.501	1.00
170_A	238_V	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	0.942	100	0.274	Contact Map
2onkC	2	0.8532	100	0.3	Contact Map
3d31C	2	0.843	100	0.312	Contact Map
3rlfF	1	0.9317	100	0.357	Contact Map
4tquN	1	0.8908	100	0.36	Contact Map
3rlfG	1	0.8976	100	0.369	Contact Map
4ymuD	2	0.727	99.9	0.517	Contact Map
3tuiA	2	0.7099	99.9	0.533	Contact Map
2a65A	2	0.7986	36.8	0.935	Contact Map
2m20A	2	0.1195	15.4	0.946	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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