GANQ - BACSU - GREMLIN Contacts

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GANQ - Putative arabinogalactan oligomer transport system permease protein GanQ

UniProt:	O07011	Sequences: MLADMKVRRYIRLLFSYLLLAFMAVIIVYPLLWTAGASFNPGNSLISTSIIPKHPTFDHYKELFAGKESLQYVQWYVNSMKISLFTMAGSLLCVTFTAYAFSRFRFKGRKYALTLFLLLQMIPQFSALIALFVLAQILGMINSHWLLILLYIGGLIPMNTYLMKGYMDSIPMDLDESAKIDGASSTRIFFQIILPLSKPMAAVVAMNGFTGPLGDFVLSSTILRTPESYTLPVGLFNLVNDVMGASYTTFAAGALLISIPVAVIFIMLQKNFVSGLTAGGTKG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	283 (253)
Sequences:	69167 (45494)
Seq/√Len:	2860.2

ECOLI - YCJP MALG POTH UGPA UGPE YCJO PSTA YDCV POTI YDCU PSTC THIP POTC POTB CYST YNJC CYSW MALF MODB SSUC PHNE TAUC YEHY METI YEHW PROW YECS GLNP
BACSU - GANQ MDXG AMYC YESQ ARAQ YURM LPLC YTCP GANP AMYD ARAP YTEP MDXF LPLB YQGH YURN YESP YQGI YVGM YTLD SSUC OPUAB TCYB METP TCYL YXEN OPUCB OPUBB OPUCD OPUBD ARTQ
HALSA - Q9HML6 Q9HHQ6 Q9HP02 Q9HMT4 Q9HHQ7 Q9HP01 Q9HR05 Q9HPK3 Q9HS11 Q9HNI9 Q9HS12
SULSO - Q97UF3 Q97UY9 Q97YY3 Q97ZC1 Q97YY2 Q97VC0 Q97ZT7 Q97ZT6 Q97UZ0 Q97UF4 Q97ZC2 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
187_R	191_Q	4.087	1.00
77_V	81_K	3.223	1.00
179_K	188_I	3.013	1.00
164_K	168_D	3.001	1.00
38_S	60_Y	2.795	1.00
75_W	234_G	2.630	1.00
103_R	175_D	2.615	1.00
74_Q	77_V	2.614	1.00
184_S	187_R	2.557	1.00
178_A	188_I	2.553	1.00
175_D	193_I	2.499	1.00
85_F	148_I	2.493	1.00
89_G	152_I	2.439	1.00
166_Y	200_M	2.438	1.00
229_Y	237_N	2.424	1.00
58_D	61_K	2.423	1.00
61_K	65_A	2.381	1.00
73_V	77_V	2.371	1.00
87_M	205_A	2.306	1.00
185_S	188_I	2.276	1.00
186_T	190_F	2.268	1.00
58_D	62_E	2.257	1.00
163_M	201_A	2.256	1.00
246_S	249_T	2.146	1.00
106_F	109_R	2.083	1.00
187_R	190_F	2.057	1.00
95_T	189_F	2.044	1.00
183_A	187_R	2.019	1.00
159_N	204_V	1.987	1.00
102_S	168_D	1.956	1.00
167_M	197_S	1.949	1.00
174_L	196_L	1.907	1.00
178_A	183_A	1.871	1.00
32_L	36_G	1.835	1.00
91_L	205_A	1.812	1.00
95_T	197_S	1.808	1.00
113_L	164_K	1.794	1.00
36_G	40_N	1.787	1.00
74_Q	78_N	1.737	1.00
179_K	185_S	1.727	1.00
83_S	209_F	1.700	1.00
94_V	159_N	1.694	1.00
175_D	188_I	1.676	1.00
81_K	85_F	1.650	1.00
95_T	163_M	1.628	1.00
86_T	212_P	1.619	1.00
97_T	160_T	1.608	1.00
101_F	160_T	1.567	1.00
62_E	249_T	1.549	1.00
175_D	179_K	1.536	1.00
17_Y	21_A	1.493	1.00
216_F	220_S	1.476	1.00
105_R	109_R	1.467	1.00
234_G	238_L	1.456	1.00
108_G	111_Y	1.432	1.00
29_Y	33_W	1.427	1.00
172_M	175_D	1.426	1.00
62_E	65_A	1.422	1.00
35_A	255_L	1.419	1.00
57_F	61_K	1.415	1.00
159_N	208_G	1.408	1.00
67_K	71_Q	1.406	1.00
98_A	163_M	1.396	1.00
82_I	230_T	1.391	1.00
102_S	164_K	1.384	1.00
56_T	59_H	1.381	1.00
203_V	207_N	1.372	1.00
194_L	201_A	1.371	1.00
167_M	193_I	1.348	1.00
216_F	236_F	1.338	1.00
33_W	37_A	1.328	1.00
92_L	96_F	1.319	1.00
90_S	208_G	1.308	1.00
103_R	172_M	1.300	1.00
144_H	228_S	1.294	1.00
163_M	204_V	1.294	1.00
142_N	146_L	1.292	1.00
225_T	228_S	1.276	1.00
172_M	176_E	1.267	1.00
71_Q	74_Q	1.261	1.00
178_A	192_I	1.249	1.00
95_T	201_A	1.240	1.00
218_L	222_I	1.231	1.00
99_Y	167_M	1.219	1.00
266_I	270_K	1.214	1.00
238_L	246_S	1.208	1.00
226_P	229_Y	1.207	1.00
229_Y	234_G	1.202	1.00
79_S	231_L	1.192	1.00
173_D	176_E	1.179	1.00
150_L	222_I	1.175	1.00
88_A	92_L	1.172	1.00
111_Y	114_T	1.168	1.00
85_F	88_A	1.159	1.00
170_I	196_L	1.149	1.00
21_A	25_V	1.145	1.00
78_N	81_K	1.142	1.00
184_S	188_I	1.142	1.00
198_K	202_A	1.119	1.00
237_N	241_D	1.116	1.00
147_L	219_S	1.115	1.00
91_L	201_A	1.111	1.00
11_I	15_F	1.110	1.00
60_Y	255_L	1.104	1.00
44_S	54_H	1.104	1.00
12_R	16_S	1.096	1.00
34_T	255_L	1.094	1.00
62_E	66_G	1.088	1.00
111_Y	115_L	1.071	1.00
156_I	160_T	1.071	1.00
14_L	18_L	1.068	1.00
270_K	273_V	1.065	1.00
148_I	152_I	1.065	1.00
238_L	244_G	1.054	1.00
41_P	44_S	1.054	1.00
143_S	146_L	1.053	1.00
140_M	145_W	1.048	1.00
163_M	200_M	1.048	1.00
89_G	148_I	1.043	1.00
99_Y	189_F	1.042	1.00
230_T	233_V	1.032	1.00
215_D	218_L	1.032	1.00
85_F	89_G	1.027	1.00
66_G	71_Q	1.026	1.00
162_L	204_V	1.025	1.00
102_S	167_M	1.023	1.00
64_F	73_V	1.021	1.00
175_D	185_S	1.020	1.00
229_Y	233_V	1.019	1.00
196_L	199_P	1.010	1.00
80_M	84_L	1.007	1.00
86_T	90_S	1.001	1.00
11_I	14_L	1.001	1.00
96_F	100_A	0.997	1.00
219_S	230_T	0.994	1.00
86_T	151_Y	0.993	1.00
14_L	17_Y	0.987	1.00
33_W	36_G	0.982	1.00
99_Y	185_S	0.980	1.00
133_V	137_I	0.976	1.00
188_I	191_Q	0.973	1.00
183_A	188_I	0.971	1.00
109_R	168_D	0.961	1.00
76_Y	231_L	0.960	1.00
16_S	20_L	0.954	1.00
215_D	219_S	0.947	1.00
131_L	222_I	0.932	1.00
267_M	271_N	0.921	1.00
42_G	46_I	0.920	1.00
98_A	102_S	0.919	1.00
13_L	17_Y	0.918	1.00
81_K	84_L	0.918	1.00
151_Y	212_P	0.914	1.00
239_V	250_F	0.912	1.00
88_A	205_A	0.910	1.00
84_L	88_A	0.899	1.00
234_G	253_G	0.895	1.00
117_L	161_Y	0.895	1.00
76_Y	80_M	0.886	1.00
197_S	200_M	0.883	1.00
261_V	265_F	0.883	1.00
107_K	110_K	0.881	1.00
166_Y	197_S	0.879	1.00
37_A	251_A	0.878	1.00
89_G	92_L	0.876	1.00
24_A	28_V	0.876	1.00
159_N	163_M	0.875	1.00
198_K	201_A	0.871	1.00
189_F	194_L	0.866	1.00
94_V	160_T	0.864	1.00
38_S	42_G	0.861	1.00
131_L	150_L	0.861	1.00
40_N	44_S	0.860	1.00
163_M	197_S	0.859	1.00
90_S	94_V	0.857	1.00
37_A	40_N	0.856	1.00
63_L	256_L	0.854	1.00
59_H	248_T	0.853	1.00
220_S	233_V	0.846	1.00
234_G	237_N	0.846	1.00
86_T	148_I	0.846	1.00
110_K	113_L	0.845	1.00
90_S	155_L	0.845	1.00
81_K	144_H	0.837	1.00
39_F	55_P	0.836	1.00
190_F	194_L	0.831	1.00
72_Y	253_G	0.829	1.00
101_F	113_L	0.828	1.00
43_N	46_I	0.827	1.00
142_N	225_T	0.824	1.00
100_A	106_F	0.820	1.00
132_F	136_Q	0.819	1.00
208_G	212_P	0.815	1.00
39_F	56_T	0.813	1.00
188_I	193_I	0.812	1.00
98_A	167_M	0.807	1.00
136_Q	141_I	0.803	1.00
124_Q	154_G	0.802	1.00
236_F	240_N	0.799	1.00
34_T	251_A	0.797	1.00
64_F	67_K	0.794	1.00
77_V	80_M	0.792	1.00
82_I	151_Y	0.792	1.00
238_L	253_G	0.783	1.00
183_A	191_Q	0.782	1.00
174_L	192_I	0.781	1.00
98_A	160_T	0.779	1.00
263_V	267_M	0.776	1.00
85_F	152_I	0.774	1.00
90_S	159_N	0.770	1.00
75_W	78_N	0.768	1.00
185_S	189_F	0.765	1.00
128_L	221_T	0.760	1.00
238_L	249_T	0.750	1.00
249_T	253_G	0.749	1.00
29_Y	32_L	0.748	1.00
150_L	218_L	0.746	1.00
62_E	246_S	0.746	1.00
235_L	253_G	0.745	1.00
147_L	151_Y	0.743	1.00
83_S	87_M	0.742	1.00
189_F	193_I	0.742	1.00
142_N	145_W	0.741	1.00
170_I	197_S	0.732	1.00
51_I	54_H	0.731	1.00
128_L	217_V	0.727	1.00
198_K	271_N	0.726	1.00
87_M	209_F	0.725	1.00
37_A	41_P	0.722	1.00
75_W	231_L	0.718	1.00
231_L	257_I	0.717	1.00
79_S	232_P	0.716	1.00
101_F	112_A	0.716	1.00
61_K	64_F	0.715	1.00
257_I	261_V	0.715	1.00
163_M	167_M	0.714	1.00
73_V	76_Y	0.714	1.00
55_P	58_D	0.712	1.00
117_L	120_Q	0.711	1.00
215_D	230_T	0.708	1.00
91_L	163_M	0.706	1.00
124_Q	217_V	0.704	1.00
101_F	164_K	0.696	1.00
41_P	54_H	0.695	1.00
15_F	18_L	0.693	1.00
94_V	163_M	0.692	1.00
40_N	52_P	0.688	1.00
172_M	179_K	0.688	1.00
135_A	141_I	0.686	1.00
251_A	255_L	0.685	1.00
127_A	153_G	0.684	1.00
18_L	21_A	0.684	1.00
241_D	244_G	0.681	1.00
87_M	91_L	0.676	1.00
201_A	204_V	0.675	1.00
193_I	196_L	0.674	1.00
34_T	254_A	0.672	1.00
90_S	212_P	0.671	1.00
23_M	27_I	0.670	1.00
15_F	19_L	0.668	1.00
82_I	147_L	0.667	1.00
59_H	62_E	0.666	1.00
177_S	181_D	0.666	1.00
141_I	146_L	0.664	1.00
93_C	152_I	0.663	1.00
233_V	237_N	0.657	1.00
56_T	60_Y	0.657	1.00
97_T	156_I	0.656	1.00
138_L	141_I	0.646	1.00
20_L	24_A	0.645	1.00
82_I	148_I	0.644	1.00
19_L	23_M	0.642	1.00
200_M	204_V	0.641	1.00
78_N	228_S	0.640	1.00
177_S	180_I	0.640	1.00
41_P	53_K	0.632	1.00
140_M	143_S	0.631	1.00
57_F	60_Y	0.630	1.00
24_A	27_I	0.629	1.00
201_A	205_A	0.627	1.00
251_A	254_A	0.627	1.00
267_M	270_K	0.627	1.00
100_A	104_F	0.626	1.00
113_L	161_Y	0.624	1.00
141_I	144_H	0.624	1.00
97_T	116_F	0.622	1.00
162_L	200_M	0.621	1.00
108_G	112_A	0.618	1.00
44_S	53_K	0.617	1.00
60_Y	252_A	0.616	1.00
105_R	110_K	0.616	1.00
67_K	74_Q	0.616	1.00
133_V	136_Q	0.615	1.00
265_F	269_Q	0.607	1.00
63_L	249_T	0.606	1.00
116_F	157_P	0.602	1.00
155_L	211_G	0.600	1.00
79_S	213_L	0.600	1.00
232_P	257_I	0.597	1.00
107_K	111_Y	0.596	1.00
125_F	221_T	0.593	1.00
106_F	112_A	0.591	1.00
217_V	220_S	0.591	1.00
98_A	164_K	0.590	1.00
120_Q	157_P	0.589	1.00
134_L	141_I	0.587	1.00
83_S	213_L	0.587	1.00
155_L	208_G	0.587	1.00
268_L	271_N	0.582	1.00
83_S	212_P	0.582	1.00
124_Q	128_L	0.582	1.00
38_S	252_A	0.582	1.00
28_V	32_L	0.581	1.00
217_V	221_T	0.578	1.00
188_I	192_I	0.577	1.00
262_A	266_I	0.577	1.00
63_L	253_G	0.575	1.00
40_N	54_H	0.574	1.00
90_S	152_I	0.573	1.00
131_L	134_L	0.572	1.00
219_S	233_V	0.569	1.00
248_T	251_A	0.566	1.00
190_F	193_I	0.566	1.00
82_I	144_H	0.566	1.00
120_Q	158_M	0.565	1.00
38_S	255_L	0.563	1.00
247_Y	251_A	0.562	1.00
71_Q	234_G	0.562	1.00
110_K	114_T	0.561	1.00
210_T	214_G	0.560	1.00
52_P	55_P	0.560	1.00
114_T	118_L	0.559	1.00
112_A	116_F	0.556	1.00
82_I	86_T	0.555	1.00
212_P	215_D	0.555	1.00
41_P	45_L	0.555	1.00
266_I	269_Q	0.555	1.00
105_R	172_M	0.553	1.00
54_H	58_D	0.552	1.00
211_G	214_G	0.552	1.00
202_A	205_A	0.550	1.00
104_F	185_S	0.549	1.00
184_S	190_F	0.549	1.00
86_T	152_I	0.549	1.00
91_L	95_T	0.548	1.00
17_Y	20_L	0.548	1.00
119_L	157_P	0.548	1.00
25_V	29_Y	0.547	1.00
205_A	208_G	0.546	1.00
40_N	53_K	0.542	1.00
37_A	42_G	0.540	1.00
93_C	156_I	0.540	1.00
99_Y	193_I	0.540	1.00
66_G	73_V	0.538	1.00
247_Y	250_F	0.538	1.00
151_Y	215_D	0.537	1.00
67_K	73_V	0.535	1.00
263_V	266_I	0.535	1.00
97_T	100_A	0.533	1.00
91_L	96_F	0.528	1.00
13_L	16_S	0.528	1.00
87_M	212_P	0.526	1.00
170_I	175_D	0.526	1.00
233_V	236_F	0.525	1.00
176_E	179_K	0.525	1.00
39_F	57_F	0.521	1.00
94_V	156_I	0.515	1.00
41_P	56_T	0.515	1.00
204_V	208_G	0.514	1.00
42_G	52_P	0.514	1.00
61_K	66_G	0.513	1.00
151_Y	219_S	0.512	1.00
245_A	249_T	0.512	1.00
78_N	230_T	0.508	1.00
249_T	252_A	0.508	1.00
95_T	194_L	0.504	1.00
264_I	268_L	0.503	1.00
35_A	39_F	0.503	1.00
113_L	168_D	0.502	1.00
72_Y	234_G	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
3rlfG	1	0.9541	100	0.251	Contact Map
4tquN	1	0.9399	100	0.265	Contact Map
2onkC	2	0.8551	100	0.31	Contact Map
4tquM	1	0.9046	100	0.328	Contact Map
3d31C	2	0.8375	100	0.332	Contact Map
3rlfF	1	0.9258	100	0.388	Contact Map
4ymuD	2	0.7527	99.9	0.483	Contact Map
3tuiA	2	0.735	99.9	0.524	Contact Map
2a65A	2	0.8375	10.9	0.947	Contact Map
4xp4A	1	0.8693	8.1	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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