Q9HMW3 - HALSA - GREMLIN Contacts

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Q9HMW3 - Oligopeptide ABC permease

UniProt:	Q9HMW3	Sequences: MKWYIVKRVLWTFVVMWIALTLTFGLLVASPDTGQTKSVMSCSASGGDAQQCREQYRERQNLDKPITERYVNYVTNMATLNWGWSESRSQSVMAAISEAWPYTAQYAIPVLVVSTILGYGLGLYSAYKPYTKADYLGSFVGFFGISIPNFWFALVLIILLGTHFEFISTYYQSGIPINQGWASMANITQLLIPSFVLLTASLAWQMRYSRAQAIEQMNQEFVKVAKAKGASQWRLMIHHVFRMAAVPLTTSFVSSLLAIFWSGSVIIEQIFSIPGLGLMTFTAITEQDTTLVLATTMITVFLAIIGNLIEDVSYTILDPRIDYGDR	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	326 (301)
Sequences:	19142 (12317)
Seq/√Len:	710.0

ECOLI - YEJB DDPB DPPB NIKB GSIC OPPB SAPB YEJE DPPC SAPC NIKC GSID DDPC OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMW3 Q9HMX0 Q9HMI2 Q9HMW2 Q9HMI1 Q9HMX1
SULSO - Q97VF8 Q97YQ0 Q97UH1 Q97VK6 Q97UG4 Q97YP1 Q97VK7 Q97UG3 Q97YP2 Q97UH2 Q97YP9 Q97VF6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
28_V	69_R	3.229	1.00
64_K	72_N	3.214	1.00
64_K	68_E	3.201	1.00
75_T	79_T	2.753	1.00
71_V	75_T	2.747	1.00
213_A	240_V	2.630	1.00
58_E	63_D	2.622	1.00
50_Q	54_E	2.612	1.00
20_L	70_Y	2.600	1.00
109_P	194_S	2.431	1.00
226_K	232_Q	2.389	1.00
102_Y	273_I	2.383	1.00
234_R	238_H	2.345	1.00
33_T	57_R	2.298	1.00
278_L	282_T	2.286	1.00
21_T	70_Y	2.236	1.00
222_V	240_V	2.223	1.00
216_Q	221_F	2.199	1.00
67_T	71_V	2.083	1.00
216_Q	219_Q	2.074	1.00
3_W	7_K	2.047	1.00
253_V	310_E	2.036	1.00
95_A	279_M	2.022	1.00
91_S	94_A	2.019	1.00
121_L	137_G	2.013	1.00
231_S	234_R	1.982	1.00
53_R	57_R	1.936	1.00
217_M	240_V	1.916	1.00
88_R	95_A	1.906	1.00
19_A	300_V	1.900	1.00
167_I	188_T	1.896	1.00
233_W	237_I	1.894	1.00
49_A	52_C	1.889	1.00
52_C	55_Q	1.853	1.00
113_V	198_L	1.849	1.00
134_D	210_R	1.847	1.00
68_E	72_N	1.826	1.00
116_I	120_G	1.824	1.00
55_Q	59_R	1.803	1.00
54_E	57_R	1.772	1.00
167_I	191_L	1.756	1.00
161_G	169_T	1.753	1.00
90_Q	94_A	1.745	1.00
249_T	317_L	1.719	1.00
128_K	131_T	1.709	1.00
54_E	58_E	1.687	1.00
222_V	235_L	1.667	1.00
132_K	136_L	1.650	1.00
76_N	81_N	1.649	1.00
230_A	234_R	1.648	1.00
93_M	97_S	1.641	1.00
92_V	294_A	1.640	1.00
124_Y	128_K	1.636	1.00
172_Q	273_I	1.629	1.00
16_M	301_F	1.614	1.00
224_V	228_K	1.610	1.00
126_A	213_A	1.578	1.00
128_K	133_A	1.564	1.00
117_L	120_G	1.545	1.00
127_Y	236_M	1.543	1.00
133_A	137_G	1.538	1.00
72_N	75_T	1.536	1.00
313_S	316_I	1.523	1.00
158_I	163_H	1.510	1.00
123_L	213_A	1.506	1.00
124_Y	133_A	1.490	1.00
280_T	295_T	1.480	1.00
250_T	314_Y	1.479	1.00
105_Q	172_Q	1.475	1.00
10_L	14_V	1.461	1.00
156_L	196_V	1.445	1.00
216_Q	244_A	1.443	1.00
90_Q	98_E	1.435	1.00
194_S	198_L	1.423	1.00
221_F	243_M	1.421	1.00
77_M	82_W	1.420	1.00
220_E	223_K	1.417	1.00
151_W	155_V	1.416	1.00
102_Y	172_Q	1.413	1.00
117_L	202_L	1.411	1.00
114_S	201_S	1.403	1.00
12_T	304_I	1.398	1.00
186_N	189_Q	1.387	1.00
216_Q	222_V	1.382	1.00
17_W	70_Y	1.380	1.00
56_Y	60_Q	1.378	1.00
64_K	67_T	1.366	1.00
68_E	71_V	1.364	1.00
72_N	76_N	1.360	1.00
17_W	21_T	1.360	1.00
228_K	239_H	1.336	1.00
159_L	163_H	1.332	1.00
65_P	68_E	1.322	1.00
283_A	291_L	1.317	1.00
115_T	252_F	1.312	1.00
61_N	64_K	1.310	1.00
198_L	202_L	1.301	1.00
130_Y	134_D	1.297	1.00
159_L	164_F	1.290	1.00
95_A	291_L	1.284	1.00
56_Y	59_R	1.281	1.00
279_M	291_L	1.278	1.00
122_G	126_A	1.267	1.00
118_G	209_S	1.261	1.00
6_V	10_L	1.255	1.00
118_G	205_Q	1.251	1.00
82_W	294_A	1.241	1.00
82_W	93_M	1.229	1.00
111_L	252_F	1.225	1.00
209_S	248_L	1.221	1.00
90_Q	95_A	1.220	1.00
127_Y	232_Q	1.219	1.00
246_V	314_Y	1.214	1.00
98_E	101_P	1.213	1.00
216_Q	240_V	1.209	1.00
210_R	214_I	1.195	1.00
122_G	209_S	1.195	1.00
36_T	53_R	1.188	1.00
105_Q	186_N	1.180	1.00
20_L	73_Y	1.179	1.00
33_T	36_T	1.179	1.00
84_W	91_S	1.178	1.00
205_Q	255_S	1.159	1.00
185_A	188_T	1.153	1.00
105_Q	109_P	1.152	1.00
102_Y	105_Q	1.151	1.00
126_A	217_M	1.146	1.00
208_Y	251_S	1.144	1.00
105_Q	190_L	1.136	1.00
144_G	203_A	1.136	1.00
147_I	152_F	1.136	1.00
295_T	299_T	1.135	1.00
55_Q	58_E	1.128	1.00
160_L	164_F	1.127	1.00
185_A	189_Q	1.123	1.00
137_G	206_M	1.120	1.00
187_I	191_L	1.105	1.00
281_F	285_T	1.097	1.00
12_T	308_L	1.092	1.00
21_T	25_G	1.090	1.00
312_V	316_I	1.088	1.00
125_S	137_G	1.084	1.00
172_Q	186_N	1.071	1.00
132_K	135_Y	1.068	1.00
36_T	39_V	1.064	1.00
5_I	312_V	1.062	1.00
121_L	206_M	1.062	1.00
306_G	310_E	1.059	1.00
155_V	159_L	1.059	1.00
126_A	214_I	1.047	1.00
257_L	306_G	1.033	1.00
61_N	72_N	1.031	1.00
149_N	267_I	1.029	1.00
97_S	101_P	1.025	1.00
196_V	200_A	1.023	1.00
25_G	28_V	1.023	1.00
94_A	98_E	1.022	1.00
95_A	98_E	1.021	1.00
85_S	288_D	1.018	1.00
9_V	308_L	1.015	1.00
16_M	304_I	1.009	1.00
156_L	192_I	1.009	1.00
17_W	74_V	1.007	1.00
51_Q	55_Q	1.006	1.00
258_A	303_A	0.994	1.00
76_N	79_T	0.987	1.00
141_G	206_M	0.985	1.00
28_V	66_I	0.985	1.00
225_A	235_L	0.982	1.00
232_Q	235_L	0.974	1.00
14_V	17_W	0.971	1.00
110_V	198_L	0.968	1.00
32_D	287_Q	0.964	1.00
4_Y	315_T	0.959	1.00
94_A	97_S	0.958	1.00
18_I	22_L	0.955	1.00
191_L	195_F	0.952	1.00
128_K	232_Q	0.951	1.00
21_T	66_I	0.947	1.00
190_L	194_S	0.945	1.00
129_P	218_N	0.944	1.00
282_T	286_E	0.944	1.00
167_I	192_I	0.942	1.00
153_A	196_V	0.940	1.00
213_A	244_A	0.934	1.00
58_E	64_K	0.934	1.00
134_D	214_I	0.932	1.00
309_I	313_S	0.931	1.00
225_A	230_A	0.928	1.00
107_A	260_F	0.925	1.00
36_T	40_M	0.925	1.00
130_Y	135_Y	0.923	1.00
113_V	194_S	0.919	1.00
78_A	81_N	0.917	1.00
87_S	286_E	0.911	1.00
209_S	213_A	0.910	1.00
230_A	235_L	0.906	1.00
280_T	283_A	0.906	1.00
120_G	123_L	0.905	1.00
84_W	89_S	0.901	1.00
138_S	206_M	0.897	1.00
40_M	56_Y	0.897	1.00
37_K	53_R	0.896	1.00
36_T	41_S	0.895	1.00
99_A	279_M	0.895	1.00
70_Y	74_V	0.891	1.00
20_L	297_M	0.889	1.00
249_T	310_E	0.888	1.00
123_L	236_M	0.885	1.00
108_I	112_V	0.884	1.00
244_A	247_P	0.875	1.00
108_I	257_L	0.875	1.00
235_L	240_V	0.873	1.00
111_L	257_L	0.866	1.00
75_T	78_A	0.865	1.00
279_M	283_A	0.865	1.00
118_G	122_G	0.861	1.00
51_Q	54_E	0.860	1.00
315_T	321_I	0.860	1.00
28_V	289_T	0.860	1.00
105_Q	108_I	0.859	1.00
226_K	235_L	0.857	1.00
234_R	237_I	0.856	1.00
140_V	144_G	0.855	1.00
77_M	297_M	0.854	1.00
25_G	66_I	0.850	1.00
71_V	74_V	0.850	1.00
195_F	198_L	0.846	1.00
86_E	290_T	0.842	1.00
160_L	167_I	0.841	1.00
96_I	294_A	0.840	1.00
136_L	140_V	0.840	1.00
237_I	240_V	0.831	1.00
103_T	107_A	0.830	1.00
127_Y	237_I	0.823	1.00
305_I	309_I	0.821	1.00
50_Q	53_R	0.818	1.00
122_G	213_A	0.816	1.00
73_Y	77_M	0.815	1.00
110_V	197_L	0.814	1.00
120_G	124_Y	0.812	1.00
314_Y	321_I	0.812	1.00
172_Q	185_A	0.811	1.00
135_Y	138_S	0.807	1.00
202_L	206_M	0.806	1.00
119_Y	209_S	0.802	1.00
289_T	293_L	0.799	1.00
160_L	166_F	0.797	1.00
118_G	206_M	0.797	1.00
153_A	270_I	0.796	1.00
269_Q	278_L	0.795	1.00
109_P	273_I	0.789	1.00
121_L	202_L	0.787	1.00
23_T	296_T	0.786	1.00
264_S	267_I	0.784	1.00
13_F	17_W	0.777	1.00
110_V	114_S	0.774	1.00
225_A	239_H	0.774	1.00
129_P	214_I	0.772	1.00
152_F	199_T	0.771	1.00
119_Y	248_L	0.770	1.00
282_T	285_T	0.766	1.00
212_Q	216_Q	0.762	1.00
133_A	136_L	0.760	1.00
106_Y	194_S	0.760	1.00
312_V	315_T	0.757	1.00
212_Q	244_A	0.756	1.00
115_T	120_G	0.752	1.00
33_T	37_K	0.749	1.00
163_H	166_F	0.746	1.00
104_A	108_I	0.746	1.00
117_L	121_L	0.743	1.00
301_F	305_I	0.741	1.00
96_I	295_T	0.740	1.00
85_S	90_Q	0.739	1.00
172_Q	190_L	0.738	1.00
269_Q	281_F	0.736	1.00
196_V	267_I	0.734	1.00
149_N	199_T	0.731	1.00
52_C	56_Y	0.729	1.00
75_T	80_L	0.725	1.00
74_V	77_M	0.725	1.00
160_L	192_I	0.723	1.00
191_L	194_S	0.723	1.00
293_L	296_T	0.721	1.00
201_S	204_W	0.720	1.00
21_T	67_T	0.719	1.00
315_T	322_D	0.717	1.00
101_P	104_A	0.716	1.00
123_L	241_F	0.716	1.00
114_S	198_L	0.713	1.00
74_V	78_A	0.711	1.00
215_E	219_Q	0.708	1.00
303_A	307_N	0.702	1.00
144_G	199_T	0.701	1.00
158_I	162_T	0.700	1.00
171_Y	189_Q	0.698	1.00
209_S	212_Q	0.696	1.00
279_M	295_T	0.691	1.00
232_Q	236_M	0.691	1.00
209_S	244_A	0.690	1.00
15_V	304_I	0.689	1.00
117_L	198_L	0.688	1.00
274_P	278_L	0.686	1.00
157_I	169_T	0.681	1.00
280_T	299_T	0.679	1.00
170_Y	272_S	0.678	1.00
209_S	241_F	0.677	1.00
24_F	28_V	0.674	1.00
14_V	18_I	0.671	1.00
145_I	203_A	0.671	1.00
92_V	291_L	0.667	1.00
187_I	190_L	0.665	1.00
225_A	228_K	0.665	1.00
101_P	105_Q	0.660	1.00
280_T	284_I	0.657	1.00
54_E	63_D	0.656	1.00
249_T	313_S	0.650	1.00
168_S	171_Y	0.647	1.00
36_T	57_R	0.645	1.00
136_L	139_F	0.644	1.00
137_G	141_G	0.644	1.00
57_R	63_D	0.644	1.00
38_S	41_S	0.643	1.00
141_G	203_A	0.643	1.00
109_P	187_I	0.642	1.00
283_A	292_V	0.641	1.00
23_T	27_L	0.640	1.00
23_T	28_V	0.639	1.00
198_L	201_S	0.638	1.00
9_V	13_F	0.637	1.00
100_W	104_A	0.637	1.00
139_F	143_F	0.636	1.00
299_T	303_A	0.636	1.00
37_K	41_S	0.630	1.00
95_A	99_A	0.629	1.00
66_I	69_R	0.628	1.00
97_S	100_W	0.627	1.00
292_V	296_T	0.625	1.00
223_K	226_K	0.624	1.00
92_V	279_M	0.623	1.00
99_A	278_L	0.623	1.00
258_A	302_L	0.623	1.00
10_L	312_V	0.622	1.00
281_F	284_I	0.622	1.00
109_P	191_L	0.621	1.00
294_A	298_I	0.619	1.00
147_I	151_W	0.619	1.00
188_T	191_L	0.618	1.00
265_V	281_F	0.616	1.00
25_G	29_A	0.615	1.00
269_Q	282_T	0.613	1.00
212_Q	215_E	0.611	1.00
156_L	195_F	0.611	1.00
8_R	311_D	0.609	1.00
107_A	257_L	0.608	1.00
125_S	134_D	0.607	1.00
27_L	292_V	0.605	1.00
20_L	74_V	0.604	1.00
149_N	152_F	0.601	1.00
68_E	75_T	0.600	1.00
310_E	314_Y	0.600	1.00
28_V	293_L	0.600	1.00
134_D	138_S	0.600	1.00
204_W	251_S	0.599	1.00
85_S	88_R	0.596	1.00
230_A	239_H	0.596	1.00
109_P	113_V	0.596	1.00
203_A	206_M	0.594	1.00
139_F	142_F	0.594	1.00
164_F	167_I	0.594	1.00
253_V	306_G	0.590	1.00
293_L	297_M	0.586	1.00
246_V	321_I	0.586	1.00
204_W	255_S	0.585	1.00
314_Y	318_D	0.585	1.00
151_W	154_L	0.584	1.00
115_T	205_Q	0.581	1.00
302_L	306_G	0.578	1.00
116_I	119_Y	0.573	1.00
221_F	225_A	0.573	1.00
251_S	255_S	0.572	1.00
131_T	134_D	0.571	1.00
265_V	269_Q	0.569	1.00
205_Q	251_S	0.568	1.00
319_P	322_D	0.565	1.00
4_Y	308_L	0.564	1.00
39_V	56_Y	0.564	1.00
255_S	259_I	0.563	1.00
245_A	249_T	0.562	1.00
131_T	135_Y	0.561	1.00
187_I	194_S	0.560	1.00
205_Q	209_S	0.558	1.00
57_R	62_L	0.557	1.00
236_M	240_V	0.555	1.00
88_R	291_L	0.552	1.00
258_A	306_G	0.551	1.00
291_L	295_T	0.550	1.00
161_G	192_I	0.550	1.00
245_A	248_L	0.550	1.00
128_K	134_D	0.549	1.00
205_Q	248_L	0.549	1.00
125_S	138_S	0.547	1.00
111_L	115_T	0.547	1.00
27_L	30_S	0.547	1.00
7_K	11_W	0.545	1.00
105_Q	273_I	0.543	1.00
149_N	200_A	0.542	1.00
113_V	195_F	0.542	1.00
112_V	116_I	0.538	1.00
34_G	289_T	0.535	1.00
109_P	112_V	0.535	1.00
109_P	190_L	0.535	1.00
127_Y	217_M	0.534	1.00
192_I	196_V	0.534	1.00
204_W	208_Y	0.533	1.00
168_S	189_Q	0.533	1.00
300_V	304_I	0.532	1.00
37_K	40_M	0.531	1.00
59_R	89_S	0.529	1.00
7_K	10_L	0.528	1.00
208_Y	212_Q	0.526	1.00
107_A	264_S	0.525	1.00
308_L	312_V	0.523	1.00
80_L	84_W	0.522	1.00
237_I	242_R	0.522	1.00
149_N	153_A	0.521	1.00
304_I	307_N	0.521	1.00
231_S	235_L	0.521	1.00
223_K	227_A	0.520	1.00
123_L	237_I	0.519	1.00
233_W	236_M	0.519	1.00
96_I	276_L	0.519	1.00
70_Y	73_Y	0.517	1.00
161_G	165_E	0.516	1.00
23_T	30_S	0.515	1.00
66_I	70_Y	0.514	1.00
107_A	111_L	0.512	1.00
125_S	210_R	0.511	1.00
106_Y	268_E	0.508	0.99
290_T	293_L	0.507	0.99
222_V	226_K	0.507	0.99
230_A	233_W	0.506	0.99
197_L	264_S	0.506	0.99
141_G	144_G	0.506	0.99
11_W	14_V	0.506	0.99
135_Y	139_F	0.505	0.99
200_A	203_A	0.504	0.99
103_T	268_E	0.504	0.99
8_R	11_W	0.503	0.99
237_I	241_F	0.501	0.99
131_T	136_L	0.500	0.99

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
3tuiA	2	0.6411	99.9	0.661	Contact Map
4tquM	1	0.8252	99.9	0.682	Contact Map
3rlfF	1	0.8374	99.9	0.686	Contact Map
4ymuD	2	0.6442	99.8	0.695	Contact Map
2onkC	2	0.7454	99.8	0.703	Contact Map
3d31C	2	0.7577	99.8	0.707	Contact Map
4tquN	1	0.7853	99.7	0.726	Contact Map
3rlfG	1	0.8067	99.7	0.736	Contact Map
1q16C	2	0.3681	13.3	0.959	Contact Map
2yevC	1	0.0951	4.9	0.967	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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