Q9HMX0 - HALSA - GREMLIN Contacts

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Q9HMX0 - Dipeptide ABC transporter permease

UniProt:	Q9HMX0	Sequences: MNRPLYIAKRLLLGVPVLLFGLTLTFLILYLGPIDPVLAILGKDATPTAARNLEISLGIRYPNGSLVPLWVQYKNFLVNMVTFDFGTSWAIARDQPVAAMIVGRLPATIWLGFWSVLVALFVGIPVGLYAGLNSNSWSDYAASFGGIVWRAMPNFWLAVMLSGLLTAGGVLDGYGDFLIKTDVVGTSNALQHLFSGIDPFAGVPVLEFFWIPVPNLGPMAEAFKWILPAALVLGSSSMGNEVRIGRTAVLESLRSEYVDTAKAKGVSPRRIIVKHIGRNAVIPLLPVIMGEFYLLIGGSVLVEKVFSINGIGNLFIRAAFNSDIPVMMSLVFIFILMQILFNLLQDVLYTYIDPRITLSDTTE	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	363 (308)
Sequences:	16910 (10888)
Seq/√Len:	620.4

ECOLI - DDPB YEJB DPPB NIKB GSIC OPPB SAPB YEJE DPPC SAPC NIKC DDPC GSID OPPC
BACSU - APPB OPPB DPPB DPPC APPC OPPC
HALSA - Q9HMX0 Q9HMI2 Q9HMW3 Q9HMW2 Q9HMI1
SULSO - Q97YQ0 Q97VF8 Q97UH1 Q97UG4 Q97VK6 Q97YP1 Q97VK7 Q97UG3 Q97UH2 Q97YP2 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
67_V	71_V	3.582	1.00
30_Y	72_Q	3.401	1.00
67_V	75_N	3.387	1.00
78_V	82_T	2.996	1.00
74_K	78_V	2.863	1.00
22_L	73_Y	2.827	1.00
55_I	60_R	2.797	1.00
47_P	51_R	2.692	1.00
249_V	276_I	2.572	1.00
35_D	54_E	2.538	1.00
114_W	230_A	2.449	1.00
270_R	274_K	2.400	1.00
262_K	268_P	2.400	1.00
107_A	308_I	2.393	1.00
313_N	317_R	2.362	1.00
23_T	73_Y	2.334	1.00
258_V	276_I	2.286	1.00
60_R	67_V	2.277	1.00
70_W	74_K	2.226	1.00
21_G	335_I	2.125	1.00
5_L	9_K	2.063	1.00
100_M	314_L	2.053	1.00
50_A	54_E	2.031	1.00
96_P	99_A	2.031	1.00
289_M	345_Q	2.022	1.00
252_S	257_Y	1.962	1.00
267_S	270_R	1.930	1.00
253_L	276_I	1.920	1.00
49_A	52_N	1.901	1.00
118_V	234_G	1.878	1.00
52_N	56_S	1.870	1.00
285_L	352_I	1.868	1.00
269_R	273_V	1.853	1.00
93_R	100_M	1.809	1.00
126_V	142_A	1.795	1.00
171_L	224_K	1.788	1.00
95_Q	99_A	1.784	1.00
46_T	49_A	1.773	1.00
166_T	173_G	1.768	1.00
121_F	125_P	1.768	1.00
252_S	255_S	1.765	1.00
71_V	75_N	1.763	1.00
51_R	55_I	1.762	1.00
133_N	136_S	1.758	1.00
18_L	336_L	1.715	1.00
51_R	54_E	1.696	1.00
79_N	84_D	1.677	1.00
171_L	227_L	1.674	1.00
260_T	264_K	1.659	1.00
97_V	329_S	1.649	1.00
75_N	78_V	1.633	1.00
258_V	271_I	1.609	1.00
139_D	246_R	1.605	1.00
132_L	272_I	1.604	1.00
348_L	351_Y	1.603	1.00
137_W	141_A	1.594	1.00
286_P	349_Y	1.582	1.00
80_M	85_F	1.566	1.00
14_G	339_I	1.564	1.00
98_A	102_V	1.534	1.00
129_Y	138_S	1.505	1.00
315_F	330_L	1.504	1.00
19_L	73_Y	1.504	1.00
122_V	125_P	1.492	1.00
266_V	270_R	1.489	1.00
257_Y	279_N	1.489	1.00
138_S	142_A	1.488	1.00
129_Y	133_N	1.485	1.00
163_G	168_G	1.476	1.00
75_N	79_N	1.463	1.00
176_D	308_I	1.448	1.00
133_N	138_S	1.447	1.00
95_Q	103_G	1.440	1.00
131_G	249_V	1.438	1.00
12_L	16_P	1.435	1.00
156_W	160_M	1.434	1.00
19_L	23_T	1.423	1.00
161_L	232_V	1.423	1.00
230_A	234_G	1.412	1.00
252_S	280_A	1.407	1.00
264_K	275_H	1.407	1.00
318_A	326_V	1.399	1.00
122_V	238_M	1.398	1.00
119_A	237_S	1.392	1.00
252_S	258_V	1.384	1.00
164_L	168_G	1.379	1.00
22_L	76_F	1.379	1.00
37_V	50_A	1.368	1.00
53_L	57_L	1.365	1.00
128_L	249_V	1.359	1.00
314_L	326_V	1.350	1.00
256_E	259_D	1.345	1.00
68_P	71_V	1.343	1.00
234_G	238_M	1.340	1.00
221_E	225_W	1.338	1.00
53_L	56_S	1.334	1.00
71_V	74_K	1.331	1.00
100_M	326_V	1.324	1.00
8_A	12_L	1.311	1.00
110_W	176_D	1.276	1.00
35_D	38_L	1.268	1.00
123_G	245_G	1.264	1.00
87_T	96_P	1.256	1.00
282_I	349_Y	1.241	1.00
120_L	288_I	1.240	1.00
85_F	329_S	1.237	1.00
58_G	67_V	1.237	1.00
107_A	176_D	1.229	1.00
127_G	131_G	1.227	1.00
110_W	222_A	1.224	1.00
152_M	157_L	1.219	1.00
131_G	250_L	1.210	1.00
245_G	284_L	1.206	1.00
116_V	288_I	1.198	1.00
178_L	221_E	1.198	1.00
172_D	175_G	1.198	1.00
19_L	77_L	1.184	1.00
135_N	139_D	1.172	1.00
127_G	245_G	1.170	1.00
4_P	7_I	1.170	1.00
95_Q	100_M	1.169	1.00
103_G	106_P	1.167	1.00
18_L	339_I	1.166	1.00
160_M	164_L	1.166	1.00
58_G	75_N	1.158	1.00
23_T	27_L	1.158	1.00
85_F	98_A	1.153	1.00
14_G	343_L	1.148	1.00
38_L	50_A	1.145	1.00
67_V	70_W	1.140	1.00
246_R	250_L	1.135	1.00
161_L	228_P	1.132	1.00
223_F	227_L	1.130	1.00
41_L	53_L	1.130	1.00
7_I	347_V	1.127	1.00
88_S	323_D	1.124	1.00
330_L	334_F	1.123	1.00
149_W	239_G	1.120	1.00
123_G	241_E	1.119	1.00
110_W	114_W	1.103	1.00
316_I	320_F	1.093	1.00
252_S	276_I	1.092	1.00
142_A	242_V	1.091	1.00
107_A	110_W	1.089	1.00
347_V	351_Y	1.086	1.00
99_A	103_G	1.083	1.00
221_E	224_K	1.073	1.00
130_A	142_A	1.071	1.00
11_L	343_L	1.069	1.00
23_T	69_L	1.068	1.00
341_F	345_Q	1.064	1.00
34_I	322_S	1.064	1.00
100_M	103_G	1.057	1.00
244_I	287_V	1.050	1.00
131_G	253_L	1.050	1.00
22_L	332_F	1.046	1.00
118_V	230_A	1.039	1.00
317_R	321_N	1.037	1.00
102_V	106_P	1.033	1.00
171_L	228_P	1.029	1.00
30_Y	69_L	1.028	1.00
52_N	55_I	1.020	1.00
268_P	271_I	1.013	1.00
344_L	348_L	1.012	1.00
110_W	226_I	1.011	1.00
232_V	236_S	1.009	1.00
241_E	291_E	1.009	1.00
126_V	242_V	0.996	1.00
293_Y	338_Q	0.996	1.00
80_M	332_F	0.993	1.00
266_V	271_I	0.990	1.00
154_N	302_V	0.988	1.00
227_L	231_L	0.987	1.00
132_L	268_P	0.982	1.00
27_L	69_L	0.981	1.00
4_P	8_A	0.975	1.00
178_L	225_W	0.971	1.00
158_A	232_V	0.967	1.00
99_A	102_V	0.967	1.00
146_G	242_V	0.962	1.00
78_V	81_V	0.958	1.00
139_D	250_L	0.957	1.00
113_F	117_L	0.956	1.00
92_A	321_N	0.950	1.00
55_I	67_V	0.949	1.00
112_G	295_L	0.944	1.00
137_W	140_Y	0.944	1.00
41_L	45_A	0.943	1.00
177_F	225_W	0.940	1.00
27_L	30_Y	0.938	1.00
262_K	271_I	0.936	1.00
165_L	170_V	0.927	1.00
158_A	305_V	0.923	1.00
292_F	341_F	0.922	1.00
314_L	318_A	0.921	1.00
73_Y	77_L	0.921	1.00
30_Y	324_I	0.917	1.00
134_S	254_R	0.916	1.00
115_S	234_G	0.913	1.00
304_K	313_N	0.913	1.00
226_I	230_A	0.912	1.00
285_L	345_Q	0.906	1.00
20_F	24_L	0.899	1.00
87_T	94_D	0.897	1.00
104_R	314_L	0.892	1.00
128_L	272_I	0.891	1.00
125_P	128_L	0.887	1.00
245_G	249_V	0.886	1.00
135_N	140_Y	0.883	1.00
157_L	235_S	0.883	1.00
248_A	280_A	0.880	1.00
48_T	52_N	0.880	1.00
145_G	149_W	0.878	1.00
76_F	80_M	0.862	1.00
89_W	325_P	0.857	1.00
16_P	19_L	0.855	1.00
123_G	242_V	0.854	1.00
127_G	249_V	0.851	1.00
74_K	77_L	0.850	1.00
37_V	53_L	0.849	1.00
132_L	273_V	0.848	1.00
79_N	82_T	0.848	1.00
273_V	276_I	0.848	1.00
37_V	41_L	0.846	1.00
261_A	271_I	0.840	1.00
231_L	234_G	0.840	1.00
116_V	292_F	0.839	1.00
340_L	344_L	0.837	1.00
108_T	112_G	0.836	1.00
123_G	127_G	0.830	1.00
270_R	273_V	0.829	1.00
113_F	292_F	0.829	1.00
25_T	331_V	0.826	1.00
17_V	339_I	0.824	1.00
47_P	50_A	0.824	1.00
3_R	7_I	0.822	1.00
299_S	302_V	0.822	1.00
125_P	129_Y	0.822	1.00
101_I	330_L	0.820	1.00
78_V	83_F	0.820	1.00
141_A	145_G	0.819	1.00
165_L	171_L	0.819	1.00
261_A	266_V	0.818	1.00
336_L	340_L	0.813	1.00
271_I	276_I	0.813	1.00
315_F	318_A	0.812	1.00
350_T	356_I	0.812	1.00
6_Y	350_T	0.810	1.00
115_S	233_L	0.809	1.00
232_V	302_V	0.807	1.00
114_W	308_I	0.805	1.00
37_V	54_E	0.802	1.00
126_V	238_M	0.801	1.00
23_T	70_W	0.797	1.00
134_S	250_L	0.796	1.00
280_A	283_P	0.796	1.00
109_I	113_F	0.794	1.00
120_L	125_P	0.793	1.00
110_W	113_F	0.791	1.00
347_V	350_T	0.790	1.00
154_N	235_S	0.788	1.00
40_I	53_L	0.786	1.00
124_I	245_G	0.783	1.00
171_L	174_Y	0.782	1.00
143_S	242_V	0.782	1.00
106_P	109_I	0.779	1.00
293_Y	341_F	0.779	1.00
115_S	119_A	0.776	1.00
161_L	231_L	0.771	1.00
349_Y	356_I	0.770	1.00
138_S	141_A	0.767	1.00
140_Y	143_S	0.764	1.00
101_I	329_S	0.764	1.00
249_V	280_A	0.762	1.00
285_L	348_L	0.756	1.00
49_A	53_L	0.756	1.00
48_T	51_R	0.755	1.00
122_V	126_V	0.754	1.00
45_A	50_A	0.753	1.00
268_P	272_I	0.747	1.00
238_M	242_V	0.744	1.00
149_W	235_S	0.743	1.00
119_A	234_G	0.734	1.00
122_V	234_G	0.732	1.00
77_L	81_V	0.725	1.00
37_V	57_L	0.725	1.00
304_K	317_R	0.725	1.00
6_Y	358_L	0.723	1.00
81_V	84_D	0.720	1.00
324_I	328_M	0.716	1.00
318_A	327_M	0.714	1.00
328_M	331_V	0.711	1.00
105_L	109_I	0.709	1.00
165_L	228_P	0.708	1.00
114_W	118_V	0.704	1.00
27_L	31_L	0.703	1.00
309_N	313_N	0.702	1.00
176_D	179_I	0.702	1.00
233_L	299_S	0.702	1.00
304_K	316_I	0.700	1.00
314_L	330_L	0.699	1.00
29_L	327_M	0.698	1.00
176_D	222_A	0.698	1.00
77_L	80_M	0.697	1.00
171_L	175_G	0.691	1.00
114_W	227_L	0.689	1.00
11_L	15_V	0.689	1.00
163_G	167_A	0.689	1.00
116_V	120_L	0.688	1.00
165_L	168_G	0.686	1.00
245_G	280_A	0.684	1.00
104_R	313_N	0.681	1.00
329_S	333_I	0.680	1.00
142_A	146_G	0.680	1.00
111_L	230_A	0.678	1.00
300_V	316_I	0.676	1.00
315_F	334_F	0.676	1.00
245_G	277_G	0.673	1.00
114_W	226_I	0.672	1.00
141_A	144_F	0.670	1.00
108_T	299_S	0.670	1.00
227_L	230_A	0.670	1.00
128_L	277_G	0.669	1.00
124_I	284_L	0.668	1.00
30_Y	328_M	0.666	1.00
257_Y	261_A	0.666	1.00
245_G	248_A	0.664	1.00
16_P	20_F	0.656	1.00
177_F	222_A	0.654	1.00
118_V	231_L	0.653	1.00
326_V	330_L	0.650	1.00
261_A	275_H	0.647	1.00
317_R	320_F	0.647	1.00
130_A	139_D	0.646	1.00
106_P	110_W	0.640	1.00
237_S	240_N	0.638	1.00
337_M	341_F	0.638	1.00
261_A	264_K	0.637	1.00
327_M	331_V	0.635	1.00
272_I	276_I	0.633	1.00
100_M	104_R	0.631	1.00
154_N	236_S	0.630	1.00
51_R	60_R	0.629	1.00
248_A	252_S	0.628	1.00
133_N	139_D	0.627	1.00
15_V	19_L	0.627	1.00
139_D	143_S	0.626	1.00
350_T	357_T	0.625	1.00
224_K	227_L	0.625	1.00
112_G	116_V	0.622	1.00
241_E	287_V	0.621	1.00
345_Q	349_Y	0.620	1.00
117_L	121_F	0.617	1.00
338_Q	342_N	0.616	1.00
170_V	175_G	0.616	1.00
156_W	159_V	0.615	1.00
282_I	356_I	0.614	1.00
10_R	346_D	0.613	1.00
177_F	180_K	0.613	1.00
162_S	173_G	0.613	1.00
177_F	221_E	0.611	1.00
128_L	273_V	0.611	1.00
144_F	148_V	0.605	1.00
335_I	339_I	0.603	1.00
136_S	140_Y	0.600	1.00
289_M	341_F	0.600	1.00
222_A	225_W	0.597	1.00
334_F	338_Q	0.596	1.00
69_L	72_Q	0.596	1.00
174_Y	307_S	0.595	1.00
175_G	178_L	0.592	1.00
22_L	77_L	0.591	1.00
93_R	326_V	0.591	1.00
176_D	226_I	0.591	1.00
240_N	287_V	0.590	1.00
14_G	18_L	0.589	1.00
293_Y	337_M	0.588	1.00
281_V	284_L	0.586	1.00
300_V	304_K	0.585	1.00
36_P	324_I	0.581	1.00
136_S	141_A	0.581	1.00
101_I	311_I	0.580	1.00
133_N	268_P	0.579	1.00
26_F	30_Y	0.576	1.00
14_G	340_L	0.576	1.00
102_V	105_L	0.572	1.00
343_L	347_V	0.571	1.00
267_S	271_I	0.570	1.00
136_S	139_D	0.569	1.00
166_T	169_G	0.569	1.00
71_V	78_V	0.568	1.00
26_F	69_L	0.566	1.00
152_M	156_W	0.564	1.00
110_W	308_I	0.563	1.00
146_G	239_G	0.560	1.00
150_R	239_G	0.559	1.00
131_G	139_D	0.557	1.00
241_E	245_G	0.555	1.00
273_V	278_R	0.553	1.00
154_N	157_L	0.552	1.00
37_V	40_I	0.551	1.00
266_V	275_H	0.549	1.00
54_E	60_R	0.548	1.00
293_Y	297_G	0.546	0.99
112_G	292_F	0.545	0.99
10_R	13_L	0.543	0.99
234_G	237_S	0.542	0.99
119_A	241_E	0.541	0.99
319_A	327_M	0.541	0.99
240_N	244_I	0.540	0.99
41_L	49_A	0.539	0.99
133_N	273_V	0.539	0.99
121_F	124_I	0.539	0.99
128_L	132_L	0.539	0.99
109_I	296_I	0.538	0.99
339_I	342_N	0.538	0.99
349_Y	353_D	0.538	0.99
26_F	72_Q	0.537	0.99
42_G	45_A	0.534	0.99
56_S	94_D	0.534	0.99
291_E	294_L	0.534	0.99
281_V	285_L	0.533	0.99
37_V	45_A	0.533	0.99
354_P	357_T	0.530	0.99
273_V	277_G	0.529	0.99
241_E	284_L	0.527	0.99
25_T	30_Y	0.526	0.99
120_L	124_I	0.524	0.99
258_V	262_K	0.524	0.99
244_I	248_A	0.524	0.99
112_G	299_S	0.524	0.99
301_L	305_V	0.523	0.99
293_Y	345_Q	0.521	0.99
251_E	255_S	0.520	0.99
147_I	151_A	0.520	0.99
240_N	291_E	0.519	0.99
45_A	49_A	0.518	0.99
231_L	235_S	0.516	0.99
256_E	260_T	0.516	0.99
239_G	242_V	0.516	0.99
297_G	300_V	0.514	0.99
114_W	234_G	0.514	0.99
228_P	232_V	0.513	0.99
348_L	352_I	0.513	0.99
325_P	328_M	0.512	0.99
146_G	149_W	0.512	0.99
130_A	246_R	0.510	0.99
132_L	253_L	0.510	0.99
6_Y	343_L	0.510	0.99
38_L	42_G	0.509	0.99
20_F	23_T	0.509	0.99
178_L	222_A	0.507	0.99
233_L	302_V	0.507	0.99
97_V	326_V	0.506	0.99
255_S	260_T	0.506	0.99
111_L	308_I	0.506	0.99
326_V	329_S	0.504	0.99
237_S	291_E	0.503	0.99
342_N	345_Q	0.502	0.99
156_W	305_V	0.501	0.99
13_L	17_V	0.501	0.99
300_V	315_F	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	0.5758	99.9	0.716	Contact Map
4tquM	1	0.7466	99.9	0.732	Contact Map
3rlfF	1	0.7383	99.9	0.732	Contact Map
2onkC	2	0.6639	99.8	0.742	Contact Map
3d31C	2	0.6777	99.8	0.745	Contact Map
4ymuD	2	0.5785	99.8	0.746	Contact Map
3rlfG	1	0.7713	99.8	0.757	Contact Map
4tquN	1	0.7163	99.8	0.76	Contact Map
4lz6A	1	0.2369	13.4	0.965	Contact Map
1q16C	2	0.3388	10.6	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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