Q9HR23 - HALSA - GREMLIN Contacts

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Q9HR23 - Ribose ABC transporter permease

UniProt:	Q9HR23	Sequences: MRKPDRGTLMAALGGLAAVVVALGVVFPGSVAGELLGIASRPIMAEIALRLAVPITLAALGGIFAEKSGVINIGLEGLLIISSFTAVLVAWALGGTTSAALWTGFAGGVLASVLLAGLFAVVCIKYEADQIIAGLAVWLVALGLAPFASSVVFGGKNTTSINRFSEWTVPVLHDAFVNSGVGILSYVGHVLLRANPIVYLMFGAVAVSWYVLNHTAFGRWVEASGENPNALDTAGVNVHRVRYVSVLVSGLLSGMGGAALSVGHVGSFVGNGTTMIDGKGFIAIATYLFGNYNPLGTFGAAMLFSGLESLQIGIQQFTPYEVPSQLIQVIPYVTVVVVLVLVGRTRIPEAAGEYYESGDDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	361 (288)
Sequences:	27245 (17490)
Seq/√Len:	1030.6

ECOLI - LSRD XYLH YTFT YPHD LSRC LIVM YJFF MGLC ALSC ARAH RBSC LIVH
BACSU - YUFP YUFQ RBSC
HALSA - Q9HR23 Q9HR22
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
109_V	251_L	4.086	1.00
113_V	247_L	3.515	1.00
113_V	251_L	3.282	1.00
228_P	242_R	3.024	1.00
85_T	111_A	2.953	1.00
56_T	201_M	2.838	1.00
63_I	297_T	2.746	1.00
117_G	247_L	2.735	1.00
125_K	239_H	2.695	1.00
89_V	107_G	2.661	1.00
221_V	245_S	2.552	1.00
112_S	254_G	2.468	1.00
237_N	240_R	2.440	1.00
240_R	244_V	2.403	1.00
116_A	250_G	2.300	1.00
211_V	217_F	2.293	1.00
112_S	250_G	2.238	1.00
217_F	244_V	2.218	1.00
209_W	213_N	2.207	1.00
119_F	137_V	2.171	1.00
207_V	211_V	2.122	1.00
220_W	241_V	2.100	1.00
58_A	283_A	2.079	1.00
169_V	172_L	2.054	1.00
117_G	243_Y	2.044	1.00
109_V	255_M	2.041	1.00
86_A	108_G	2.036	1.00
210_Y	214_H	2.021	1.00
59_A	297_T	1.992	1.00
89_V	93_L	1.986	1.00
121_V	125_K	1.978	1.00
282_I	308_E	1.962	1.00
224_S	241_V	1.916	1.00
206_A	210_Y	1.902	1.00
52_A	305_S	1.897	1.00
100_A	103_T	1.855	1.00
64_F	208_S	1.846	1.00
102_W	106_A	1.843	1.00
223_A	231_L	1.790	1.00
105_F	258_A	1.773	1.00
65_A	249_S	1.773	1.00
120_A	243_Y	1.745	1.00
115_L	141_A	1.721	1.00
139_L	142_L	1.706	1.00
282_I	331_P	1.630	1.00
229_N	232_D	1.623	1.00
52_A	302_M	1.622	1.00
86_A	258_A	1.622	1.00
56_T	301_A	1.607	1.00
217_F	221_V	1.605	1.00
216_A	220_W	1.570	1.00
185_S	188_G	1.558	1.00
81_I	115_L	1.543	1.00
205_V	298_F	1.534	1.00
68_S	245_S	1.531	1.00
125_K	243_Y	1.530	1.00
57_L	259_A	1.530	1.00
137_V	141_A	1.523	1.00
88_L	148_A	1.503	1.00
67_K	222_E	1.502	1.00
109_V	258_A	1.494	1.00
88_L	92_A	1.490	1.00
90_A	104_G	1.488	1.00
57_L	256_G	1.484	1.00
79_L	260_L	1.467	1.00
290_G	296_G	1.458	1.00
58_A	79_L	1.438	1.00
60_L	208_S	1.435	1.00
64_F	245_S	1.426	1.00
244_V	247_L	1.392	1.00
70_V	242_R	1.389	1.00
220_W	236_V	1.387	1.00
171_V	174_D	1.377	1.00
44_M	309_S	1.375	1.00
228_P	232_D	1.369	1.00
70_V	246_V	1.363	1.00
236_V	241_V	1.358	1.00
293_N	296_G	1.356	1.00
61_G	252_L	1.353	1.00
80_I	145_A	1.332	1.00
70_V	130_Q	1.325	1.00
243_Y	247_L	1.323	1.00
99_A	103_T	1.313	1.00
124_I	239_H	1.312	1.00
32_A	310_L	1.308	1.00
170_P	174_D	1.298	1.00
78_L	115_L	1.275	1.00
103_T	106_A	1.259	1.00
224_S	238_V	1.255	1.00
110_L	113_V	1.254	1.00
104_G	108_G	1.241	1.00
62_G	283_A	1.240	1.00
192_L	195_N	1.239	1.00
220_W	231_L	1.237	1.00
56_T	298_F	1.229	1.00
75_L	253_S	1.218	1.00
121_V	243_Y	1.212	1.00
93_L	99_A	1.196	1.00
86_A	262_V	1.189	1.00
62_G	287_Y	1.189	1.00
122_V	133_A	1.189	1.00
231_L	236_V	1.185	1.00
232_D	239_H	1.177	1.00
59_A	286_T	1.174	1.00
85_T	89_V	1.170	1.00
247_L	251_L	1.160	1.00
67_K	292_Y	1.159	1.00
250_G	254_G	1.150	1.00
206_A	209_W	1.148	1.00
244_V	248_V	1.126	1.00
108_G	112_S	1.124	1.00
290_G	300_A	1.124	1.00
31_V	35_L	1.108	1.00
224_S	231_L	1.107	1.00
63_I	287_Y	1.101	1.00
309_S	312_I	1.099	1.00
221_V	241_V	1.097	1.00
59_A	287_Y	1.094	1.00
66_E	287_Y	1.093	1.00
94_G	100_A	1.092	1.00
326_L	329_V	1.091	1.00
77_G	142_L	1.089	1.00
84_F	145_A	1.082	1.00
46_E	50_R	1.082	1.00
119_F	133_A	1.081	1.00
113_V	254_G	1.077	1.00
213_N	222_E	1.075	1.00
308_E	331_P	1.073	1.00
108_G	258_A	1.073	1.00
199_Y	203_G	1.066	1.00
106_A	110_L	1.064	1.00
204_A	252_L	1.064	1.00
241_V	244_V	1.062	1.00
127_E	228_P	1.060	1.00
205_V	252_L	1.059	1.00
248_V	252_L	1.036	1.00
170_P	173_H	1.035	1.00
48_A	305_S	1.032	1.00
77_G	141_A	1.032	1.00
29_G	33_G	1.027	1.00
257_G	261_S	1.021	1.00
114_L	117_G	1.021	1.00
217_F	241_V	1.017	1.00
89_V	104_G	1.009	1.00
279_K	282_I	1.007	1.00
295_L	299_G	1.003	1.00
52_A	301_A	1.002	1.00
33_G	36_L	1.001	1.00
68_S	221_V	1.001	1.00
192_L	199_Y	0.996	1.00
203_G	207_V	0.995	1.00
36_L	40_S	0.992	1.00
60_L	204_A	0.982	1.00
76_E	280_G	0.981	1.00
54_P	256_G	0.980	1.00
201_M	205_V	0.976	1.00
209_W	214_H	0.975	1.00
84_F	149_S	0.973	1.00
99_A	102_W	0.971	1.00
121_V	126_Y	0.969	1.00
150_S	154_G	0.969	1.00
148_A	151_V	0.966	1.00
196_P	199_Y	0.965	1.00
208_S	248_V	0.957	1.00
147_F	326_L	0.954	1.00
260_L	264_H	0.952	1.00
89_V	92_A	0.949	1.00
32_A	36_L	0.949	1.00
30_S	34_E	0.948	1.00
169_V	173_H	0.947	1.00
188_G	191_L	0.945	1.00
114_L	118_L	0.941	1.00
142_L	146_P	0.939	1.00
34_E	37_G	0.939	1.00
109_V	254_G	0.938	1.00
58_A	256_G	0.937	1.00
78_L	253_S	0.925	1.00
110_L	114_L	0.924	1.00
72_N	75_L	0.924	1.00
249_S	253_S	0.918	1.00
83_S	268_F	0.915	1.00
328_Q	331_P	0.914	1.00
286_T	301_A	0.910	1.00
310_L	314_I	0.909	1.00
83_S	261_S	0.907	1.00
152_V	156_K	0.906	1.00
26_V	29_G	0.904	1.00
239_H	243_Y	0.903	1.00
219_R	222_E	0.903	1.00
196_P	200_L	0.899	1.00
76_E	278_G	0.889	1.00
198_V	202_F	0.885	1.00
138_W	142_L	0.883	1.00
224_S	245_S	0.878	1.00
64_F	248_V	0.877	1.00
61_G	75_L	0.874	1.00
59_A	301_A	0.871	1.00
85_T	88_L	0.870	1.00
58_A	75_L	0.869	1.00
81_I	85_T	0.865	1.00
82_S	108_G	0.861	1.00
253_S	257_G	0.858	1.00
117_G	121_V	0.858	1.00
47_I	51_L	0.857	1.00
86_A	90_A	0.855	1.00
239_H	242_R	0.854	1.00
187_V	190_V	0.852	1.00
124_I	243_Y	0.850	1.00
185_S	189_H	0.848	1.00
286_T	300_A	0.845	1.00
53_V	198_V	0.844	1.00
202_F	206_A	0.843	1.00
293_N	297_T	0.843	1.00
87_V	268_F	0.841	1.00
240_R	243_Y	0.838	1.00
232_D	238_V	0.836	1.00
99_A	107_G	0.834	1.00
82_S	112_S	0.833	1.00
87_V	91_W	0.832	1.00
56_T	205_V	0.831	1.00
120_A	124_I	0.831	1.00
65_A	72_N	0.829	1.00
130_Q	246_V	0.828	1.00
304_F	331_P	0.827	1.00
197_I	259_A	0.827	1.00
103_T	107_G	0.817	1.00
33_G	40_S	0.813	1.00
238_V	242_R	0.812	1.00
62_G	75_L	0.810	1.00
251_L	255_M	0.808	1.00
60_L	297_T	0.808	1.00
64_F	212_L	0.807	1.00
82_S	257_G	0.796	1.00
61_G	253_S	0.796	1.00
183_I	187_V	0.796	1.00
68_S	224_S	0.795	1.00
251_L	254_G	0.795	1.00
191_L	199_Y	0.789	1.00
43_I	46_E	0.783	1.00
144_L	148_A	0.783	1.00
27_F	30_S	0.782	1.00
33_G	37_G	0.782	1.00
210_Y	213_N	0.781	1.00
51_L	55_I	0.780	1.00
152_V	155_G	0.777	1.00
94_G	99_A	0.776	1.00
77_G	138_W	0.773	1.00
122_V	126_Y	0.769	1.00
78_L	82_S	0.768	1.00
333_V	337_V	0.768	1.00
86_A	104_G	0.768	1.00
48_A	306_G	0.767	1.00
83_S	275_M	0.766	1.00
57_L	201_M	0.763	1.00
174_D	183_I	0.760	1.00
254_G	258_A	0.760	1.00
169_V	174_D	0.756	1.00
84_F	270_G	0.753	1.00
151_V	154_G	0.749	1.00
93_L	100_A	0.746	1.00
67_K	212_L	0.743	1.00
81_I	141_A	0.741	1.00
123_C	130_Q	0.737	1.00
208_S	252_L	0.737	1.00
211_V	214_H	0.736	1.00
309_S	313_G	0.731	1.00
337_V	341_L	0.727	1.00
228_P	238_V	0.727	1.00
66_E	284_I	0.727	1.00
123_C	246_V	0.725	1.00
106_A	109_V	0.725	1.00
78_L	141_A	0.720	1.00
142_L	280_G	0.720	1.00
118_L	122_V	0.719	1.00
205_V	209_W	0.719	1.00
82_S	111_A	0.718	1.00
184_L	187_V	0.718	1.00
57_L	204_A	0.716	1.00
79_L	256_G	0.713	1.00
297_T	301_A	0.712	1.00
140_V	144_L	0.711	1.00
212_L	221_V	0.710	1.00
100_A	104_G	0.710	1.00
116_A	247_L	0.708	1.00
79_L	279_K	0.708	1.00
58_A	61_G	0.703	1.00
112_S	116_A	0.702	1.00
70_V	228_P	0.701	1.00
27_F	31_V	0.698	1.00
220_W	237_N	0.692	1.00
32_A	37_G	0.691	1.00
122_V	128_A	0.691	1.00
79_L	276_I	0.690	1.00
52_A	56_T	0.689	1.00
78_L	112_S	0.686	1.00
224_S	242_R	0.685	1.00
85_T	107_G	0.683	1.00
109_V	113_V	0.681	1.00
64_F	211_V	0.681	1.00
151_V	155_G	0.672	1.00
209_W	295_L	0.671	1.00
278_G	282_I	0.670	1.00
55_I	286_T	0.670	1.00
90_A	262_V	0.668	1.00
42_P	45_A	0.668	1.00
60_L	205_V	0.666	1.00
242_R	245_S	0.666	1.00
301_A	305_S	0.665	1.00
208_S	212_L	0.663	1.00
207_V	210_Y	0.660	1.00
324_S	327_I	0.657	1.00
50_R	263_G	0.655	1.00
217_F	248_V	0.653	1.00
24_G	28_P	0.652	1.00
331_P	339_L	0.651	1.00
302_M	306_G	0.651	1.00
127_E	239_H	0.651	1.00
123_C	133_A	0.651	1.00
63_I	294_P	0.647	1.00
227_N	230_A	0.645	1.00
54_P	263_G	0.644	1.00
119_F	134_G	0.639	1.00
81_I	111_A	0.635	1.00
63_I	292_Y	0.634	1.00
55_I	279_K	0.633	1.00
74_G	119_F	0.631	1.00
55_I	282_I	0.631	1.00
168_T	172_L	0.630	1.00
149_S	152_V	0.627	1.00
168_T	171_V	0.627	1.00
138_W	280_G	0.623	1.00
200_L	204_A	0.623	1.00
153_F	156_K	0.620	1.00
75_L	249_S	0.620	1.00
105_F	109_V	0.618	1.00
68_S	242_R	0.616	1.00
26_V	30_S	0.615	1.00
139_L	143_G	0.614	1.00
81_I	112_S	0.611	1.00
287_Y	297_T	0.609	1.00
113_V	116_A	0.609	1.00
31_V	37_G	0.608	1.00
65_A	246_V	0.607	1.00
285_A	335_V	0.604	1.00
101_L	262_V	0.603	1.00
49_L	53_V	0.601	1.00
189_H	192_L	0.601	1.00
63_I	67_K	0.599	1.00
211_V	244_V	0.599	1.00
311_Q	322_V	0.598	1.00
32_A	35_L	0.598	1.00
47_I	309_S	0.598	1.00
325_Q	328_Q	0.597	1.00
247_L	250_G	0.596	1.00
238_V	241_V	0.596	1.00
248_V	251_L	0.591	1.00
311_Q	330_I	0.590	1.00
86_A	89_V	0.589	1.00
195_N	198_V	0.589	1.00
89_V	100_A	0.586	1.00
29_G	32_A	0.585	1.00
135_L	138_W	0.584	1.00
286_T	297_T	0.582	1.00
230_A	234_A	0.582	1.00
187_V	191_L	0.580	1.00
209_W	293_N	0.578	1.00
223_A	230_A	0.573	1.00
335_V	339_L	0.572	1.00
183_I	188_G	0.572	1.00
55_I	301_A	0.568	1.00
61_G	65_A	0.566	1.00
277_D	280_G	0.565	1.00
184_L	188_G	0.564	1.00
109_V	112_S	0.564	1.00
250_G	253_S	0.563	1.00
222_E	292_Y	0.563	1.00
308_E	327_I	0.562	1.00
124_I	134_G	0.560	1.00
49_L	52_A	0.558	1.00
89_V	99_A	0.557	1.00
43_I	47_I	0.554	1.00
57_L	255_M	0.553	1.00
42_P	46_E	0.549	1.00
173_H	183_I	0.548	1.00
48_A	309_S	0.548	1.00
73_I	284_I	0.548	1.00
44_M	313_G	0.548	1.00
194_A	199_Y	0.548	1.00
168_T	173_H	0.546	1.00
222_E	225_G	0.546	1.00
183_I	190_V	0.546	1.00
339_L	342_V	0.545	1.00
147_F	151_V	0.545	1.00
86_A	257_G	0.542	1.00
260_L	279_K	0.542	1.00
168_T	174_D	0.541	1.00
305_S	309_S	0.541	1.00
37_G	40_S	0.538	1.00
29_G	306_G	0.537	1.00
137_V	140_V	0.531	1.00
185_S	191_L	0.531	1.00
203_G	206_A	0.526	1.00
281_F	285_A	0.525	1.00
34_E	38_I	0.523	1.00
150_S	153_F	0.522	1.00
89_V	94_G	0.520	1.00
56_T	60_L	0.520	1.00
53_V	57_L	0.519	1.00
53_V	201_M	0.518	1.00
31_V	34_E	0.517	1.00
184_L	191_L	0.517	1.00
200_L	255_M	0.516	1.00
78_L	116_A	0.513	1.00
88_L	91_W	0.513	1.00
331_P	335_V	0.512	1.00
60_L	209_W	0.512	1.00
200_L	203_G	0.510	1.00
60_L	206_A	0.510	1.00
47_I	50_R	0.505	1.00
65_A	70_V	0.505	1.00
211_V	215_T	0.504	1.00
35_L	38_I	0.504	1.00
289_F	300_A	0.504	1.00
283_A	287_Y	0.504	1.00
150_S	155_G	0.503	1.00
289_F	338_V	0.502	1.00
61_G	249_S	0.502	1.00
121_V	124_I	0.502	1.00
125_K	240_R	0.501	1.00
229_N	233_T	0.501	1.00
69_G	242_R	0.500	1.00
185_S	190_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
2nq2A	2	0.7867	96.5	0.895	Contact Map
4g1uA	2	0.7535	96	0.9	Contact Map
2qi9A	2	0.8116	95.9	0.9	Contact Map
2gfpA	2	0.5319	34.2	0.949	Contact Map
2m20A	2	0.1219	15.6	0.957	Contact Map
1u7gA	3	0.5346	14.4	0.957	Contact Map
4m64A	1	0.5679	11.5	0.959	Contact Map
3k3fA	3	0.8283	9.3	0.961	Contact Map
2rddB	1	0.0942	8.4	0.962	Contact Map
4pypA	1	0.5734	7.7	0.962	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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