ARAH - ECOLI - GREMLIN Contacts

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ARAH - L-arabinose transport system permease protein AraH

UniProt:	P0AE26	Sequences: MSSVSTSGSGAPKSSFSFGRIWDQYGMLVVFAVLFIACAIFVPNFATFINMKGLGLAISMSGMVACGMLFCLASGDFDLSVASVIACAGVTTAVVINLTESLWIGVAAGLLLGVLCGLVNGFVIAKLKINALITTLATMQIVRGLAYIISDGKAVGIEDESFFALGYANWFGLPAPIWLTVACLIIFGLLLNKTTFGRNTLAIGGNEEAARLAGVPVVRTKIIIFVLSGLVSAIAGIILASRMTSGQPMTSIGYELIVISACVLGGVSLKGGIGKISYVVAGILILGTVENAMNLLNISPFAQYVVRGLILLAAVIFDRYKQKAKRTV	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10059
Length:	328 (268)
Sequences:	31338 (19715)
Seq/√Len:	1204.3

ECOLI - ARAH YPHD XYLH ALSC YTFT RBSC MGLC LSRD LSRC YJFF LIVM LIVH
BACSU - RBSC YUFP YUFQ
HALSA - Q9HR22 Q9HR23
SULSO - Q97UZ8 Q97UZ9

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
110_L	230_L	3.941	1.00
114_V	226_V	3.600	1.00
114_V	230_L	3.099	1.00
91_T	112_L	3.001	1.00
118_L	226_V	2.962	1.00
207_E	221_K	2.857	1.00
95_V	108_A	2.756	1.00
200_T	224_I	2.555	1.00
69_L	279_V	2.554	1.00
216_P	219_R	2.515	1.00
62_G	180_T	2.509	1.00
126_K	218_V	2.462	1.00
219_R	223_I	2.359	1.00
117_G	229_G	2.347	1.00
188_G	192_N	2.345	1.00
190_L	196_F	2.315	1.00
113_G	233_A	2.302	1.00
189_L	193_K	2.268	1.00
118_L	222_I	2.261	1.00
120_N	138_T	2.217	1.00
257_I	290_E	2.200	1.00
199_N	220_T	2.178	1.00
122_F	126_K	2.152	1.00
196_F	223_I	2.122	1.00
186_I	190_L	2.090	1.00
101_S	104_I	2.069	1.00
64_V	258_V	1.999	1.00
86_A	146_A	1.968	1.00
92_T	109_G	1.965	1.00
110_L	234_I	1.960	1.00
103_W	107_A	1.895	1.00
113_G	229_G	1.831	1.00
92_T	237_I	1.819	1.00
203_I	220_T	1.784	1.00
58_I	287_G	1.773	1.00
106_V	237_I	1.766	1.00
185_I	189_L	1.756	1.00
65_A	279_V	1.742	1.00
71_C	228_S	1.709	1.00
70_F	187_F	1.696	1.00
121_G	222_I	1.689	1.00
202_A	210_A	1.683	1.00
140_Q	143_R	1.672	1.00
58_I	284_L	1.647	1.00
195_T	199_N	1.630	1.00
73_A	201_L	1.554	1.00
116_C	142_V	1.549	1.00
62_G	283_I	1.529	1.00
110_L	237_I	1.521	1.00
196_F	200_T	1.519	1.00
257_I	307_R	1.518	1.00
87_C	116_C	1.493	1.00
223_I	226_V	1.478	1.00
126_K	222_I	1.466	1.00
208_E	211_R	1.462	1.00
138_T	142_V	1.455	1.00
83_S	143_R	1.452	1.00
100_E	104_I	1.450	1.00
207_E	211_R	1.439	1.00
94_V	149_I	1.434	1.00
85_I	239_L	1.429	1.00
64_V	85_I	1.412	1.00
199_N	215_V	1.406	1.00
104_I	107_A	1.387	1.00
275_K	278_Y	1.382	1.00
184_L	280_V	1.379	1.00
265_G	278_Y	1.375	1.00
94_V	97_N	1.370	1.00
74_S	224_I	1.353	1.00
199_N	210_A	1.335	1.00
63_M	235_A	1.328	1.00
95_V	100_E	1.309	1.00
122_F	222_I	1.297	1.00
67_G	231_V	1.291	1.00
109_G	113_G	1.290	1.00
265_G	282_G	1.288	1.00
70_F	224_I	1.285	1.00
210_A	215_V	1.281	1.00
203_I	217_V	1.277	1.00
95_V	98_L	1.275	1.00
164_A	167_Y	1.269	1.00
62_G	280_V	1.260	1.00
81_V	232_S	1.248	1.00
125_A	218_V	1.239	1.00
168_A	171_F	1.238	1.00
222_I	226_V	1.234	1.00
68_M	262_C	1.231	1.00
76_D	131_A	1.229	1.00
107_A	111_L	1.229	1.00
76_D	221_K	1.226	1.00
54_L	288_T	1.226	1.00
50_N	291_N	1.225	1.00
192_N	201_L	1.222	1.00
215_V	220_T	1.218	1.00
105_G	109_G	1.216	1.00
63_M	238_I	1.213	1.00
66_C	187_F	1.210	1.00
54_L	287_G	1.194	1.00
203_I	210_A	1.193	1.00
167_Y	170_W	1.167	1.00
111_L	114_V	1.163	1.00
68_M	258_V	1.161	1.00
91_T	95_V	1.151	1.00
76_D	225_F	1.150	1.00
188_G	193_K	1.150	1.00
183_C	231_V	1.146	1.00
161_S	164_A	1.141	1.00
65_A	261_A	1.139	1.00
226_V	230_L	1.139	1.00
166_G	169_N	1.130	1.00
100_E	108_A	1.114	1.00
84_V	116_C	1.112	1.00
83_S	142_V	1.110	1.00
92_T	241_S	1.107	1.00
291_N	294_N	1.089	1.00
90_V	146_A	1.087	1.00
58_I	283_I	1.084	1.00
67_G	81_V	1.083	1.00
211_R	217_V	1.082	1.00
223_I	227_L	1.076	1.00
302_A	305_V	1.074	1.00
211_R	218_V	1.073	1.00
254_Y	257_I	1.071	1.00
187_F	227_L	1.068	1.00
220_T	223_I	1.056	1.00
290_E	307_R	1.056	1.00
109_G	237_I	1.055	1.00
163_F	166_G	1.055	1.00
143_R	147_Y	1.052	1.00
59_S	177_I	1.051	1.00
123_V	134_T	1.042	1.00
94_V	150_S	1.038	1.00
115_L	118_L	1.037	1.00
229_G	233_A	1.037	1.00
90_V	248_P	1.037	1.00
52_K	56_L	1.036	1.00
184_L	231_V	1.036	1.00
185_I	188_G	1.031	1.00
65_A	262_C	1.028	1.00
73_A	274_G	1.024	1.00
200_T	220_T	1.024	1.00
178_W	182_A	1.023	1.00
139_M	143_R	1.020	1.00
69_L	262_C	1.019	1.00
304_Y	307_R	1.018	1.00
182_A	186_I	1.015	1.00
114_V	233_A	1.009	1.00
261_A	282_G	0.997	1.00
125_A	135_T	0.991	1.00
122_F	127_L	0.991	1.00
227_L	231_V	0.988	1.00
107_A	110_L	0.980	1.00
261_A	283_I	0.972	1.00
87_C	91_T	0.967	1.00
120_N	134_T	0.959	1.00
196_F	220_T	0.958	1.00
292_A	296_L	0.954	1.00
83_S	139_M	0.949	1.00
188_G	277_S	0.937	1.00
277_S	281_A	0.936	1.00
64_V	235_A	0.933	1.00
72_L	262_C	0.932	1.00
236_G	240_A	0.928	1.00
175_A	178_W	0.928	1.00
123_V	127_L	0.926	1.00
128_K	207_E	0.926	1.00
124_I	134_T	0.922	1.00
90_V	150_S	0.921	1.00
219_R	222_I	0.918	1.00
228_S	232_S	0.918	1.00
65_A	283_I	0.912	1.00
82_A	255_E	0.910	1.00
198_R	201_L	0.903	1.00
57_A	61_S	0.900	1.00
160_E	163_F	0.897	1.00
49_I	52_K	0.897	1.00
74_S	200_T	0.896	1.00
69_L	274_G	0.895	1.00
148_I	302_A	0.890	1.00
73_A	192_N	0.890	1.00
180_T	184_L	0.888	1.00
78_D	81_V	0.883	1.00
209_A	213_A	0.880	1.00
60_M	235_A	0.877	1.00
88_A	113_G	0.876	1.00
95_V	105_G	0.874	1.00
88_A	109_G	0.872	1.00
293_M	306_V	0.872	1.00
286_L	307_R	0.872	1.00
218_V	221_K	0.866	1.00
181_V	185_I	0.865	1.00
191_L	200_T	0.864	1.00
111_L	115_L	0.863	1.00
68_M	81_V	0.863	1.00
51_M	292_A	0.859	1.00
89_G	240_A	0.859	1.00
85_I	251_S	0.855	1.00
203_I	224_I	0.853	1.00
62_G	184_L	0.850	1.00
85_I	254_Y	0.848	1.00
63_M	180_T	0.848	1.00
104_I	108_A	0.846	1.00
89_G	246_G	0.844	1.00
119_V	123_V	0.841	1.00
70_F	227_L	0.839	1.00
94_V	98_L	0.837	1.00
171_F	178_W	0.836	1.00
66_C	183_C	0.835	1.00
84_V	232_S	0.832	1.00
91_T	94_V	0.830	1.00
177_I	181_V	0.829	1.00
206_N	209_A	0.829	1.00
71_C	78_D	0.824	1.00
70_F	191_L	0.822	1.00
232_S	236_G	0.817	1.00
93_A	246_G	0.807	1.00
110_L	233_A	0.805	1.00
84_V	113_G	0.804	1.00
156_G	159_D	0.803	1.00
275_K	279_V	0.801	1.00
273_I	277_S	0.798	1.00
98_L	101_S	0.798	1.00
118_L	122_F	0.797	1.00
88_A	236_G	0.797	1.00
115_L	119_V	0.794	1.00
66_C	279_V	0.792	1.00
152_G	155_V	0.792	1.00
217_V	221_K	0.791	1.00
291_N	295_L	0.787	1.00
313_A	317_F	0.786	1.00
279_V	283_I	0.782	1.00
164_A	168_A	0.781	1.00
92_T	105_G	0.779	1.00
64_V	81_V	0.777	1.00
89_G	250_T	0.777	1.00
203_I	221_K	0.774	1.00
96_I	105_G	0.770	1.00
121_G	125_A	0.763	1.00
53_G	57_A	0.762	1.00
144_G	147_Y	0.759	1.00
218_V	222_I	0.759	1.00
207_E	217_V	0.757	1.00
190_L	193_K	0.750	1.00
167_Y	171_F	0.749	1.00
100_E	103_W	0.748	1.00
162_F	165_L	0.742	1.00
230_L	233_A	0.738	1.00
110_L	114_V	0.736	1.00
64_V	67_G	0.731	1.00
88_A	112_L	0.728	1.00
169_N	172_G	0.727	1.00
67_G	232_S	0.724	1.00
121_G	126_K	0.724	1.00
230_L	234_I	0.717	1.00
186_I	189_L	0.717	1.00
71_C	225_F	0.713	1.00
50_N	295_L	0.711	1.00
63_M	183_C	0.706	1.00
309_L	313_A	0.702	1.00
176_P	238_I	0.701	1.00
199_N	216_P	0.693	1.00
141_I	145_L	0.692	1.00
283_I	287_G	0.692	1.00
106_V	110_L	0.689	1.00
284_L	288_T	0.685	1.00
85_I	235_A	0.685	1.00
79_L	259_I	0.683	1.00
160_E	164_A	0.678	1.00
260_S	311_L	0.678	1.00
87_C	113_G	0.677	1.00
58_I	62_G	0.677	1.00
131_A	225_F	0.675	1.00
125_A	222_I	0.672	1.00
61_S	257_I	0.671	1.00
61_S	261_A	0.670	1.00
249_M	252_I	0.669	1.00
72_L	259_I	0.667	1.00
189_L	192_N	0.662	1.00
84_V	88_A	0.662	1.00
301_F	304_Y	0.661	1.00
59_S	180_T	0.659	1.00
87_C	142_V	0.658	1.00
54_L	291_N	0.656	1.00
55_G	59_S	0.652	1.00
113_G	117_G	0.650	1.00
143_R	255_E	0.646	1.00
170_W	178_W	0.645	1.00
184_L	188_G	0.642	1.00
84_V	229_G	0.636	1.00
217_V	220_T	0.636	1.00
187_F	231_V	0.636	1.00
102_L	241_S	0.635	1.00
173_L	176_P	0.635	1.00
233_A	237_I	0.635	1.00
307_R	311_L	0.633	1.00
187_F	191_L	0.628	1.00
117_G	226_V	0.628	1.00
300_P	303_Q	0.628	1.00
74_S	203_I	0.627	1.00
175_A	179_L	0.626	1.00
69_L	276_I	0.625	1.00
150_S	153_K	0.623	1.00
164_A	169_N	0.623	1.00
190_L	223_I	0.619	1.00
53_G	291_N	0.619	1.00
239_L	254_Y	0.619	1.00
227_L	230_L	0.617	1.00
76_D	207_E	0.617	1.00
69_L	73_A	0.615	1.00
264_L	282_G	0.614	1.00
67_G	71_C	0.614	1.00
54_L	58_I	0.614	1.00
84_V	142_V	0.611	1.00
93_A	155_V	0.610	1.00
290_E	303_Q	0.608	1.00
91_T	108_A	0.607	1.00
84_V	120_N	0.606	1.00
124_I	131_A	0.606	1.00
196_F	227_L	0.606	1.00
61_S	283_I	0.604	1.00
48_F	51_M	0.599	1.00
88_A	232_S	0.599	1.00
163_F	167_Y	0.592	1.00
128_K	218_V	0.590	1.00
56_L	177_I	0.588	1.00
140_Q	144_G	0.587	1.00
183_C	234_I	0.585	1.00
293_M	298_I	0.584	1.00
252_I	255_E	0.583	1.00
303_Q	307_R	0.583	1.00
95_V	112_L	0.580	1.00
70_F	190_L	0.579	1.00
84_V	117_G	0.575	1.00
56_L	242_R	0.571	1.00
60_M	239_L	0.571	1.00
66_C	184_L	0.567	1.00
143_R	252_I	0.567	1.00
221_K	224_I	0.564	1.00
257_I	304_Y	0.563	1.00
182_A	185_I	0.563	1.00
61_S	254_Y	0.561	1.00
158_E	161_S	0.561	1.00
261_A	279_V	0.561	1.00
262_C	279_V	0.559	1.00
136_L	140_Q	0.556	1.00
124_I	225_F	0.556	1.00
74_S	221_K	0.555	1.00
49_I	53_G	0.554	1.00
165_L	168_A	0.552	1.00
208_E	212_L	0.551	1.00
110_L	113_G	0.550	1.00
66_C	188_G	0.549	1.00
250_T	253_G	0.548	1.00
80_S	120_N	0.548	1.00
91_T	109_G	0.545	1.00
190_L	194_T	0.544	1.00
229_G	232_S	0.542	1.00
173_L	178_W	0.542	1.00
261_A	286_L	0.541	1.00
149_I	152_G	0.541	1.00
264_L	314_A	0.539	1.00
57_A	291_N	0.539	1.00
306_V	309_L	0.536	1.00
92_T	95_V	0.536	1.00
92_T	236_G	0.535	1.00
183_C	187_F	0.535	1.00
55_G	58_I	0.535	1.00
114_V	117_G	0.532	1.00
66_C	185_I	0.532	1.00
170_W	175_A	0.531	1.00
173_L	241_S	0.528	1.00
188_G	275_K	0.528	1.00
102_L	106_V	0.527	1.00
210_A	217_V	0.525	1.00
139_M	255_E	0.525	1.00
179_L	182_A	0.525	1.00
82_A	253_G	0.523	1.00
239_L	243_M	0.522	1.00
48_F	52_K	0.520	1.00
71_C	76_D	0.519	1.00
265_G	279_V	0.519	1.00
179_L	183_C	0.518	1.00
86_A	250_T	0.518	1.00
192_N	195_T	0.516	1.00
81_V	228_S	0.516	1.00
62_G	66_C	0.516	1.00
153_K	157_I	0.515	1.00
166_G	170_W	0.515	1.00
226_V	229_G	0.511	1.00
164_A	175_A	0.508	1.00
242_R	246_G	0.508	1.00
50_N	53_G	0.505	1.00
75_G	207_E	0.505	1.00
278_Y	282_G	0.504	1.00
135_T	139_M	0.504	1.00
87_C	112_L	0.503	1.00
201_L	204_G	0.503	1.00
100_E	105_G	0.503	1.00
253_G	257_I	0.503	1.00
78_D	228_S	0.502	1.00
61_S	65_A	0.501	1.00
53_G	56_L	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
4g1uA	2	0.814	97.5	0.873	Contact Map
2nq2A	2	0.8384	97.1	0.881	Contact Map
2qi9A	2	0.8811	97	0.882	Contact Map
2onkC	2	0.7226	39.8	0.944	Contact Map
3d31C	2	0.7317	37.4	0.945	Contact Map
1u7gA	3	0.5732	22.4	0.951	Contact Map
4cylA	1	0	10.8	0.957	Contact Map
2gfpA	2	0.5549	10.6	0.958	Contact Map
2m8rA	1	0.1372	8.2	0.96	Contact Map
3p5nA	2	0.3079	8.1	0.96	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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