Q9HR22 - HALSA - GREMLIN Contacts

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Q9HR22 - Ribose ABC transporter permease

UniProt:	Q9HR22	Sequences: MSQDTPRWRRAIARLVDASVKERLVISVAALVLAVAVGFVIVTLAGLAASCTTHPTIFGVRTPSCYDPFAVYSELFLGAIGHPEQVLFGTGTWTPLDFRVASLLRSTTLLVFTGLAVAVSFRAGMFNIGVQGQLLLGALAAALATVYAAPLVPGGVVGTLVLVPVGIVAGALAGGVWGAIPGALKAYADANEVITTIMLNFVAANLAYVAVSTWFTPADSSLVQTATIPAAARIPNVPFGFQPRDNFSLLGLLFAVALVVGVAYLLARTSFGYDLRTSGSQPEAAAYGGVKEKRTMVTSMGISGALGGISGAMLVLMVQGRWLSNLPQLGFDGITVSILAGNNPLGVGFAALLFGVLKSGSAAIGFGTNVPPALVDVLRGLIILFVAMPEFFRLLGGRLGVGGDVDA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	407 (310)
Sequences:	9861 (6698)
Seq/√Len:	380.4

ECOLI - XYLH LIVM YPHD YTFT LSRD LSRC YJFF ARAH ALSC MGLC RBSC LIVH
BACSU - YUFP YUFQ RBSC
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
111_V	255_A	4.195	1.00
171_A	305_A	4.156	1.00
140_A	173_A	3.371	1.00
175_G	301_G	3.137	1.00
175_G	305_A	3.091	1.00
187_Y	293_K	3.044	1.00
174_G	304_G	2.972	1.00
282_P	296_M	2.817	1.00
174_G	308_G	2.763	1.00
118_A	347_V	2.745	1.00
275_L	299_S	2.652	1.00
144_A	169_A	2.652	1.00
179_A	301_G	2.609	1.00
181_P	199_L	2.563	1.00
265_L	271_F	2.531	1.00
259_V	348_G	2.511	1.00
271_F	298_T	2.508	1.00
112_F	313_M	2.496	1.00
177_W	203_A	2.489	1.00
85_Q	360_G	2.321	1.00
115_L	262_V	2.274	1.00
283_E	286_A	2.193	1.00
294_R	298_T	2.148	1.00
107_T	355_G	2.145	1.00
231_A	234_I	2.142	1.00
253_L	257_A	2.133	1.00
115_L	258_L	2.101	1.00
291_K	294_R	2.090	1.00
263_A	267_A	2.087	1.00
261_G	265_L	2.008	1.00
92_T	95_P	1.972	1.00
84_E	88_F	1.893	1.00
119_V	262_V	1.883	1.00
122_R	276_R	1.882	1.00
107_T	352_L	1.872	1.00
179_A	297_V	1.858	1.00
125_M	300_M	1.852	1.00
199_L	203_A	1.823	1.00
192_E	300_M	1.799	1.00
121_F	337_S	1.795	1.00
183_A	187_Y	1.793	1.00
260_V	264_Y	1.787	1.00
332_D	379_R	1.772	1.00
278_S	295_T	1.762	1.00
78_G	81_G	1.753	1.00
113_T	333_G	1.743	1.00
125_M	192_E	1.732	1.00
332_D	358_K	1.724	1.00
114_G	347_V	1.720	1.00
141_A	170_G	1.699	1.00
198_M	384_L	1.689	1.00
181_P	196_T	1.679	1.00
186_A	293_K	1.651	1.00
99_R	359_S	1.625	1.00
111_V	351_A	1.603	1.00
274_D	295_T	1.599	1.00
144_A	148_A	1.593	1.00
271_F	275_L	1.565	1.00
167_I	312_A	1.562	1.00
112_F	310_S	1.556	1.00
125_M	296_M	1.543	1.00
270_S	274_D	1.537	1.00
340_A	346_G	1.527	1.00
116_A	306_L	1.520	1.00
226_A	229_P	1.517	1.00
182_G	297_V	1.514	1.00
123_A	299_S	1.509	1.00
230_A	233_R	1.491	1.00
256_V	260_V	1.480	1.00
79_A	82_H	1.451	1.00
290_V	295_T	1.421	1.00
233_R	236_N	1.415	1.00
172_L	175_G	1.412	1.00
264_Y	268_R	1.399	1.00
176_V	179_A	1.398	1.00
74_E	81_G	1.391	1.00
133_Q	177_W	1.385	1.00
226_A	231_A	1.383	1.00
118_A	342_N	1.381	1.00
257_A	261_G	1.364	1.00
139_L	207_A	1.350	1.00
278_S	292_E	1.343	1.00
120_S	303_S	1.339	1.00
113_T	134_L	1.336	1.00
258_L	306_L	1.336	1.00
342_N	347_V	1.327	1.00
282_P	286_A	1.316	1.00
171_A	309_I	1.314	1.00
176_V	180_I	1.310	1.00
286_A	293_K	1.307	1.00
112_F	258_L	1.292	1.00
131_Q	328_Q	1.289	1.00
136_L	177_W	1.287	1.00
111_V	348_G	1.280	1.00
345_L	349_F	1.278	1.00
144_A	166_G	1.277	1.00
304_G	308_G	1.277	1.00
91_G	94_T	1.273	1.00
164_P	168_V	1.248	1.00
298_T	301_G	1.247	1.00
117_V	333_G	1.236	1.00
83_P	86_V	1.227	1.00
199_L	202_V	1.223	1.00
170_G	312_A	1.218	1.00
183_A	297_V	1.218	1.00
143_L	210_A	1.217	1.00
179_A	183_A	1.209	1.00
275_L	295_T	1.199	1.00
153_P	165_V	1.199	1.00
132_G	200_N	1.193	1.00
136_L	203_A	1.190	1.00
89_G	92_T	1.189	1.00
277_T	285_A	1.183	1.00
185_K	192_E	1.177	1.00
374_L	377_V	1.172	1.00
111_V	259_V	1.172	1.00
321_R	325_N	1.167	1.00
119_V	299_S	1.156	1.00
274_D	290_V	1.154	1.00
74_E	78_G	1.137	1.00
226_A	230_A	1.132	1.00
251_G	313_M	1.127	1.00
250_L	253_L	1.125	1.00
185_K	300_M	1.123	1.00
187_Y	297_V	1.123	1.00
204_A	330_G	1.119	1.00
74_E	77_L	1.119	1.00
153_P	164_P	1.098	1.00
166_G	316_L	1.094	1.00
115_L	259_V	1.090	1.00
182_G	186_A	1.081	1.00
145_T	166_G	1.078	1.00
301_G	305_A	1.077	1.00
87_L	90_T	1.077	1.00
209_V	374_L	1.072	1.00
189_D	293_K	1.070	1.00
68_P	72_Y	1.062	1.00
102_S	247_F	1.058	1.00
190_A	195_T	1.053	1.00
322_W	325_N	1.051	1.00
143_L	147_Y	1.050	1.00
119_V	266_L	1.047	1.00
340_A	350_A	1.041	1.00
358_K	379_R	1.041	1.00
184_L	190_A	1.036	1.00
124_G	282_P	1.030	1.00
123_A	275_L	1.025	1.00
152_V	165_V	1.024	1.00
311_G	315_V	1.011	1.00
168_V	172_L	1.011	1.00
258_L	309_I	1.008	1.00
184_L	195_T	1.007	1.00
153_P	163_V	1.005	1.00
339_L	350_A	0.995	1.00
137_G	311_G	0.993	1.00
335_T	383_I	0.984	1.00
180_I	199_L	0.981	1.00
70_A	74_E	0.979	1.00
119_V	302_I	0.976	1.00
138_A	315_V	0.976	1.00
114_G	336_V	0.975	1.00
228_I	231_A	0.974	1.00
267_A	276_R	0.972	1.00
189_D	282_P	0.965	1.00
321_R	326_L	0.961	1.00
152_V	169_A	0.952	1.00
139_L	211_V	0.950	1.00
90_T	94_T	0.949	1.00
103_L	356_V	0.948	1.00
214_W	217_P	0.948	1.00
132_G	204_A	0.947	1.00
82_H	86_V	0.947	1.00
216_T	220_S	0.946	1.00
112_F	255_A	0.945	1.00
297_V	301_G	0.938	1.00
381_L	385_F	0.937	1.00
263_A	268_R	0.935	1.00
260_V	263_A	0.934	1.00
107_T	351_A	0.934	1.00
63_P	66_Y	0.932	1.00
68_P	71_V	0.929	1.00
361_S	370_V	0.927	1.00
89_G	93_W	0.925	1.00
113_T	130_V	0.917	1.00
133_Q	307_G	0.912	1.00
186_A	297_V	0.912	1.00
278_S	299_S	0.912	1.00
178_G	304_G	0.911	1.00
183_A	188_A	0.911	1.00
135_L	207_A	0.906	1.00
142_A	321_R	0.906	1.00
133_Q	203_A	0.905	1.00
72_Y	75_L	0.903	1.00
262_V	306_L	0.900	1.00
314_L	329_L	0.899	1.00
129_G	181_P	0.898	1.00
232_A	235_P	0.891	1.00
229_P	232_A	0.891	1.00
226_A	234_I	0.887	1.00
63_P	67_D	0.886	1.00
244_R	247_F	0.884	1.00
140_A	169_A	0.883	1.00
175_G	308_G	0.879	1.00
303_S	307_G	0.879	1.00
172_L	176_V	0.879	1.00
123_A	300_M	0.879	1.00
360_G	364_I	0.876	1.00
254_F	309_I	0.876	1.00
100_V	104_L	0.865	1.00
298_T	302_I	0.861	1.00
296_M	299_S	0.861	1.00
193_V	197_I	0.860	1.00
144_A	147_Y	0.859	1.00
217_P	220_S	0.858	1.00
224_Q	227_T	0.857	1.00
254_F	313_M	0.856	1.00
75_L	78_G	0.854	1.00
271_F	295_T	0.854	1.00
141_A	312_A	0.853	1.00
255_A	259_V	0.851	1.00
181_P	195_T	0.850	1.00
305_A	308_G	0.846	1.00
314_L	318_V	0.846	1.00
308_G	312_A	0.839	1.00
65_C	69_F	0.837	1.00
136_L	206_L	0.836	1.00
118_A	337_S	0.835	1.00
305_A	309_I	0.834	1.00
262_V	302_I	0.834	1.00
72_Y	76_F	0.832	1.00
89_G	94_T	0.831	1.00
114_G	351_A	0.825	1.00
116_A	120_S	0.822	1.00
64_S	68_P	0.821	1.00
171_A	308_G	0.820	1.00
71_V	74_E	0.820	1.00
102_S	359_S	0.820	1.00
252_L	256_V	0.819	1.00
265_L	298_T	0.817	1.00
359_S	363_A	0.817	1.00
282_P	292_E	0.815	1.00
130_V	303_S	0.814	1.00
336_V	350_A	0.812	1.00
238_P	244_R	0.811	1.00
228_I	234_I	0.811	1.00
67_D	70_A	0.810	1.00
116_A	130_V	0.806	1.00
229_P	234_I	0.806	1.00
231_A	235_P	0.803	1.00
95_P	98_F	0.803	1.00
215_F	218_A	0.801	1.00
80_I	83_P	0.796	1.00
117_V	130_V	0.796	1.00
234_I	237_V	0.795	1.00
140_A	144_A	0.794	1.00
278_S	285_A	0.794	1.00
188_A	388_M	0.792	1.00
62_T	66_Y	0.790	1.00
98_F	101_A	0.790	1.00
126_F	191_N	0.783	1.00
307_G	311_G	0.783	1.00
119_V	265_L	0.782	1.00
134_L	310_S	0.780	1.00
232_A	236_N	0.780	1.00
227_T	230_A	0.779	1.00
70_A	79_A	0.775	1.00
322_W	326_L	0.772	1.00
337_S	347_V	0.768	1.00
70_A	73_S	0.762	1.00
131_Q	330_G	0.761	1.00
225_T	229_P	0.760	1.00
107_T	111_V	0.760	1.00
293_K	296_M	0.759	1.00
133_Q	137_G	0.757	1.00
295_T	298_T	0.757	1.00
128_I	331_F	0.755	1.00
79_A	83_P	0.755	1.00
75_L	79_A	0.754	1.00
80_I	84_E	0.753	1.00
136_L	140_A	0.749	1.00
274_D	285_A	0.744	1.00
78_G	82_H	0.742	1.00
213_T	216_T	0.738	1.00
70_A	81_G	0.737	1.00
76_F	80_I	0.736	1.00
346_G	350_A	0.726	1.00
76_F	79_A	0.726	1.00
135_L	204_A	0.724	1.00
134_L	314_L	0.724	1.00
88_F	364_I	0.718	1.00
228_I	233_R	0.718	1.00
117_V	120_S	0.717	1.00
101_A	246_N	0.714	1.00
337_S	342_N	0.713	1.00
392_F	396_G	0.710	1.00
137_G	173_A	0.708	1.00
67_D	71_V	0.704	1.00
361_S	378_L	0.703	1.00
292_E	296_M	0.702	0.99
121_F	126_F	0.702	0.99
114_G	337_S	0.702	0.99
122_R	266_L	0.700	0.99
320_G	323_L	0.695	0.99
277_T	284_A	0.692	0.99
212_S	215_F	0.692	0.99
109_L	310_S	0.691	0.99
128_I	334_I	0.686	0.99
271_F	302_I	0.686	0.99
103_L	355_G	0.683	0.99
113_T	116_A	0.681	0.99
343_N	346_G	0.674	0.99
171_A	312_A	0.672	0.99
136_L	173_A	0.671	0.99
184_L	188_A	0.669	0.99
117_V	303_S	0.669	0.99
124_G	296_M	0.664	0.99
135_L	326_L	0.662	0.99
212_S	216_T	0.658	0.99
141_A	145_T	0.657	0.99
346_G	349_F	0.655	0.99
137_G	170_G	0.654	0.99
139_L	210_A	0.653	0.99
319_Q	322_W	0.653	0.99
128_I	193_V	0.649	0.99
86_V	93_W	0.645	0.99
121_F	342_N	0.644	0.99
69_F	72_Y	0.643	0.99
230_A	234_I	0.642	0.99
301_G	304_G	0.640	0.99
166_G	170_G	0.639	0.99
169_A	173_A	0.636	0.99
71_V	75_L	0.636	0.99
130_V	307_G	0.635	0.99
77_L	80_I	0.633	0.99
338_I	341_G	0.631	0.99
293_K	297_V	0.630	0.99
340_A	348_G	0.630	0.99
167_I	171_A	0.627	0.99
78_G	83_P	0.626	0.99
165_V	168_V	0.626	0.99
211_V	215_F	0.623	0.99
123_A	296_M	0.620	0.99
376_D	379_R	0.619	0.99
148_A	152_V	0.617	0.99
227_T	232_A	0.616	0.99
183_A	186_A	0.616	0.99
224_Q	229_P	0.615	0.99
233_R	320_G	0.615	0.99
90_T	95_P	0.612	0.99
200_N	330_G	0.611	0.99
137_G	307_G	0.608	0.99
265_L	302_I	0.608	0.99
354_F	379_R	0.608	0.99
140_A	143_L	0.606	0.99
361_S	375_V	0.605	0.99
224_Q	230_A	0.604	0.98
120_S	299_S	0.604	0.98
70_A	77_L	0.604	0.98
131_Q	326_L	0.602	0.98
108_T	252_L	0.600	0.98
232_A	237_V	0.599	0.98
134_L	329_L	0.599	0.98
273_Y	276_R	0.598	0.98
78_G	86_V	0.598	0.98
108_T	255_A	0.598	0.98
229_P	233_R	0.590	0.98
103_L	359_S	0.590	0.98
164_P	167_I	0.590	0.98
148_A	153_P	0.588	0.98
119_V	271_F	0.587	0.98
62_T	65_C	0.587	0.98
211_V	214_W	0.587	0.98
336_V	351_A	0.586	0.98
82_H	356_V	0.586	0.98
331_F	335_T	0.582	0.98
230_A	236_N	0.581	0.98
142_A	146_V	0.580	0.98
74_E	82_H	0.579	0.98
250_L	254_F	0.577	0.98
231_A	236_N	0.576	0.98
227_T	231_A	0.576	0.98
200_N	204_A	0.576	0.98
117_V	334_I	0.576	0.98
330_G	334_I	0.574	0.98
75_L	82_H	0.572	0.98
66_Y	70_A	0.570	0.98
170_G	308_G	0.568	0.98
64_S	67_D	0.567	0.98
127_N	303_S	0.567	0.98
229_P	235_P	0.567	0.98
134_L	326_L	0.565	0.98
204_A	208_Y	0.565	0.98
351_A	355_G	0.563	0.98
99_R	363_A	0.561	0.98
285_A	290_V	0.561	0.98
292_E	295_T	0.560	0.98
388_M	392_F	0.559	0.98
127_N	130_V	0.558	0.97
133_Q	304_G	0.558	0.97
227_T	233_R	0.557	0.97
286_A	292_E	0.557	0.97
373_A	376_D	0.556	0.97
91_G	95_P	0.555	0.97
336_V	347_V	0.555	0.97
226_A	236_N	0.555	0.97
393_R	396_G	0.554	0.97
86_V	90_T	0.554	0.97
178_G	181_P	0.552	0.97
68_P	75_L	0.552	0.97
327_P	330_G	0.552	0.97
338_I	353_L	0.552	0.97
124_G	338_I	0.550	0.97
120_S	125_M	0.550	0.97
319_Q	325_N	0.549	0.97
90_T	93_W	0.549	0.97
77_L	85_Q	0.548	0.97
88_F	92_T	0.547	0.97
206_L	209_V	0.545	0.97
73_S	78_G	0.544	0.97
110_L	336_V	0.543	0.97
104_L	107_T	0.542	0.97
254_F	258_L	0.542	0.97
120_S	127_N	0.541	0.97
226_A	232_A	0.540	0.97
137_G	174_G	0.539	0.97
224_Q	228_I	0.539	0.97
302_I	306_L	0.534	0.97
200_N	331_F	0.534	0.97
391_F	395_L	0.534	0.97
229_P	236_N	0.534	0.97
116_A	303_S	0.533	0.97
171_A	175_G	0.533	0.97
104_L	108_T	0.532	0.97
291_K	295_T	0.532	0.97
144_A	149_A	0.531	0.97
377_V	381_L	0.530	0.97
281_Q	284_A	0.530	0.97
180_I	184_L	0.530	0.97
77_L	81_G	0.528	0.97
101_A	252_L	0.527	0.96
123_A	338_I	0.526	0.96
87_L	92_T	0.524	0.96
238_P	245_D	0.519	0.96
246_N	253_L	0.519	0.96
106_S	362_A	0.518	0.96
149_A	153_P	0.518	0.96
102_S	105_R	0.517	0.96
83_P	87_L	0.516	0.96
226_A	233_R	0.516	0.96
116_A	333_G	0.514	0.96
192_E	296_M	0.513	0.96
70_A	82_H	0.512	0.96
249_L	252_L	0.512	0.96
87_L	93_W	0.510	0.96
379_R	382_I	0.509	0.96
64_S	72_Y	0.506	0.96
81_G	84_E	0.505	0.96
115_L	347_V	0.505	0.96
379_R	383_I	0.504	0.95
259_V	344_P	0.504	0.95
390_E	394_L	0.503	0.95
278_S	290_V	0.503	0.95
117_V	337_S	0.502	0.95
266_L	275_L	0.501	0.95
79_A	86_V	0.500	0.95

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	0.6732	96.3	0.916	Contact Map
2nq2A	2	0.7396	95	0.923	Contact Map
2qi9A	2	0.7273	93.7	0.928	Contact Map
4ezcA	3	0.7322	39	0.957	Contact Map
2gfpA	2	0.4619	37.7	0.957	Contact Map
2onkC	2	0.5921	36.8	0.957	Contact Map
2m20A	2	0.0958	26.4	0.96	Contact Map
2kluA	1	0.113	24.5	0.961	Contact Map
3d31C	2	0.5848	21.2	0.962	Contact Map
2l2tA	2	0.1081	20	0.963	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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