LtrA - PFAM28P - GREMLIN Contacts

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LtrA - Bacterial low temperature requirement A protein (LtrA)

PFAM:	PF06772	Sequences: RVTPLELFFDLVFVFAVTQLTHLLAHDLTWGGLLRFLLLFFAVWWAWVGYTWLTNAFDPDDGPVRLLLLVQMAGVLVLALAIPEAFGDRGLVFALAYVVVRVGLVALYLRAARGDPALERRRAARRYAVGFLVAAVLWLAGAFLPGPARLALWAVALAIDLFAVPLLGRRRGWPVHPGHFAERYGLFVIIALGESIVAIGAGAAGLGLTAGLVAAAVLGLVLAAALWWLYFDVAAAAAERALRSARRGRLARDAYGYLHLPLVAGIVAVAAGLELALAHPGEPLPLAAALALAGGVALYLLGLAAFRRRLRGRLSRSRLVGAAALLALLPLALALPALALLALLAAVLVALAA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	353 (347)
Sequences:	8272 (6041)
Seq/√Len:	324.3
META:	0.731

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
144_L	152_L	3.755	1.00
84_E	89_R	3.542	1.00
94_A	142_A	3.152	1.00
182_E	186_L	3.140	1.00
101_R	160_D	2.995	1.00
27_D	32_G	2.888	1.00
73_A	220_L	2.824	1.00
27_D	35_R	2.610	1.00
230_Y	259_H	2.552	1.00
69_L	224_A	2.540	1.00
234_A	239_E	2.526	1.00
130_G	164_V	2.364	1.00
226_L	269_V	2.344	1.00
31_G	35_R	2.273	1.00
234_A	237_A	2.267	1.00
335_L	339_A	2.252	1.00
239_E	243_R	2.218	1.00
144_L	148_A	2.179	1.00
84_E	87_G	2.149	1.00
321_G	351_L	2.138	1.00
4_P	185_G	2.126	1.00
121_R	125_R	2.112	1.00
90_G	142_A	2.099	1.00
25_A	274_E	2.095	1.00
122_R	126_R	2.066	1.00
17_V	187_F	2.046	1.00
279_H	282_E	2.024	1.00
95_L	99_V	1.984	1.00
235_A	238_A	1.944	1.00
91_L	95_L	1.942	1.00
136_V	140_A	1.922	1.00
220_L	224_A	1.846	1.00
115_D	120_R	1.836	1.00
218_L	342_A	1.785	1.00
210_A	213_V	1.779	1.00
151_A	155_V	1.775	1.00
258_L	261_P	1.767	1.00
188_V	262_L	1.767	1.00
308_R	312_G	1.760	1.00
137_L	156_A	1.755	1.00
269_V	296_V	1.745	1.00
235_A	239_E	1.743	1.00
123_A	126_R	1.739	1.00
137_L	155_V	1.733	1.00
234_A	238_A	1.726	1.00
238_A	241_A	1.720	1.00
258_L	305_A	1.713	1.00
150_L	154_A	1.703	1.00
41_F	260_L	1.694	1.00
148_A	151_A	1.693	1.00
336_P	339_A	1.672	1.00
286_L	290_L	1.659	1.00
112_A	125_R	1.659	1.00
188_V	266_I	1.654	1.00
30_W	34_L	1.652	1.00
72_M	220_L	1.649	1.00
41_F	161_L	1.638	1.00
261_P	302_G	1.630	1.00
243_R	246_R	1.611	1.00
319_L	323_A	1.608	1.00
77_V	96_A	1.607	1.00
323_A	327_A	1.590	1.00
70_V	103_G	1.551	1.00
184_Y	256_G	1.535	1.00
317_S	320_V	1.532	1.00
73_A	217_V	1.529	1.00
65_R	228_W	1.529	1.00
122_R	125_R	1.526	1.00
254_A	306_F	1.526	1.00
74_G	99_V	1.524	1.00
318_R	321_G	1.523	1.00
22_H	26_H	1.518	1.00
24_L	36_F	1.518	1.00
134_A	159_I	1.516	1.00
78_L	96_A	1.516	1.00
20_L	39_L	1.501	1.00
147_P	151_A	1.500	1.00
265_G	302_G	1.500	1.00
188_V	263_V	1.469	1.00
242_L	245_A	1.464	1.00
9_F	71_Q	1.457	1.00
23_L	39_L	1.456	1.00
308_R	314_L	1.450	1.00
254_A	310_L	1.448	1.00
28_L	291_A	1.433	1.00
120_R	123_A	1.427	1.00
253_D	309_R	1.418	1.00
238_A	242_L	1.418	1.00
121_R	124_A	1.408	1.00
105_V	132_L	1.397	1.00
222_L	269_V	1.394	1.00
141_G	152_L	1.381	1.00
147_P	150_L	1.379	1.00
188_V	259_H	1.345	1.00
98_V	135_A	1.340	1.00
140_A	144_L	1.340	1.00
37_L	264_A	1.326	1.00
245_A	250_L	1.320	1.00
325_L	344_L	1.315	1.00
145_P	149_R	1.307	1.00
315_S	318_R	1.307	1.00
241_A	245_A	1.305	1.00
78_L	93_F	1.296	1.00
98_V	102_V	1.290	1.00
337_A	341_L	1.289	1.00
275_L	288_A	1.286	1.00
74_G	100_V	1.285	1.00
338_L	341_L	1.282	1.00
94_A	138_W	1.278	1.00
163_A	166_L	1.277	1.00
242_L	246_R	1.273	1.00
123_A	127_Y	1.267	1.00
336_P	340_L	1.266	1.00
57_F	120_R	1.260	1.00
327_A	330_P	1.256	1.00
12_V	72_M	1.253	1.00
38_L	150_L	1.245	1.00
311_R	315_S	1.244	1.00
41_F	157_L	1.234	1.00
15_F	200_G	1.229	1.00
46_A	100_V	1.227	1.00
316_R	319_L	1.216	1.00
94_A	141_G	1.215	1.00
165_P	168_G	1.211	1.00
102_V	106_A	1.208	1.00
132_L	136_V	1.203	1.00
42_A	138_W	1.201	1.00
77_V	92_V	1.201	1.00
20_L	36_F	1.195	1.00
40_F	264_A	1.191	1.00
293_A	297_A	1.191	1.00
272_G	292_L	1.187	1.00
94_A	98_V	1.183	1.00
151_A	154_A	1.178	1.00
241_A	246_R	1.172	1.00
226_L	299_Y	1.164	1.00
140_A	143_F	1.161	1.00
236_A	239_E	1.161	1.00
31_G	34_L	1.152	1.00
57_F	111_A	1.149	1.00
209_T	212_L	1.149	1.00
34_L	150_L	1.142	1.00
239_E	242_L	1.140	1.00
133_V	137_L	1.137	1.00
331_L	335_L	1.132	1.00
43_V	78_L	1.123	1.00
294_G	298_L	1.122	1.00
92_V	213_V	1.120	1.00
240_R	244_S	1.113	1.00
222_L	345_A	1.109	1.00
137_L	159_I	1.109	1.00
313_R	316_R	1.106	1.00
146_G	149_R	1.100	1.00
27_D	31_G	1.094	1.00
211_G	214_A	1.093	1.00
141_G	149_R	1.091	1.00
16_A	43_V	1.086	1.00
74_G	96_A	1.086	1.00
91_L	143_F	1.081	1.00
105_V	131_F	1.072	1.00
129_V	164_V	1.069	1.00
191_A	266_I	1.067	1.00
213_V	217_V	1.060	1.00
219_G	273_L	1.052	1.00
53_L	57_F	1.045	1.00
191_A	267_V	1.044	1.00
316_R	320_V	1.044	1.00
51_T	54_T	1.042	1.00
195_S	223_A	1.040	1.00
8_F	11_L	1.039	1.00
85_A	93_F	1.034	1.00
285_P	288_A	1.033	1.00
50_Y	64_V	1.032	1.00
65_R	232_D	1.029	1.00
302_G	306_F	1.028	1.00
321_G	324_A	1.025	1.00
101_R	105_V	1.023	1.00
128_A	132_L	1.021	1.00
322_A	326_L	1.020	1.00
311_R	314_L	1.018	1.00
40_F	44_W	1.017	1.00
57_F	64_V	1.013	1.00
234_A	241_A	1.011	1.00
340_L	343_L	1.001	1.00
144_L	149_R	0.990	1.00
56_A	108_Y	0.989	1.00
153_W	157_L	0.987	1.00
105_V	128_A	0.987	1.00
67_L	107_L	0.985	1.00
77_V	99_V	0.983	1.00
36_F	267_V	0.982	1.00
154_A	158_A	0.981	1.00
199_I	202_G	0.980	1.00
200_G	204_A	0.979	1.00
23_L	27_D	0.975	1.00
325_L	332_A	0.970	1.00
85_A	153_W	0.968	1.00
223_A	273_L	0.966	1.00
23_L	36_F	0.965	1.00
98_V	136_V	0.964	1.00
229_L	300_L	0.962	1.00
339_A	342_A	0.958	1.00
339_A	343_L	0.956	1.00
289_A	293_A	0.953	1.00
107_L	111_A	0.946	1.00
331_L	334_A	0.945	1.00
326_L	330_P	0.943	1.00
333_L	340_L	0.937	1.00
39_L	85_A	0.934	1.00
84_E	88_D	0.932	1.00
215_A	276_A	0.932	1.00
152_L	156_A	0.930	1.00
5_L	69_L	0.929	1.00
134_A	160_D	0.928	1.00
226_L	266_I	0.925	1.00
39_L	82_I	0.924	1.00
134_A	156_A	0.922	1.00
265_G	298_L	0.921	1.00
272_G	295_G	0.919	1.00
210_A	214_A	0.919	1.00
28_L	271_A	0.917	1.00
225_A	349_V	0.913	1.00
34_L	37_L	0.907	1.00
60_D	65_R	0.905	1.00
282_E	337_A	0.901	1.00
241_A	244_S	0.901	1.00
91_L	142_A	0.899	1.00
290_L	294_G	0.899	1.00
144_L	147_P	0.899	1.00
308_R	311_R	0.897	1.00
45_W	257_Y	0.896	1.00
341_L	345_A	0.896	1.00
129_V	133_V	0.892	1.00
198_A	274_E	0.892	1.00
81_A	92_V	0.890	1.00
74_G	103_G	0.886	1.00
221_V	349_V	0.886	1.00
284_L	289_A	0.886	1.00
7_L	14_V	0.885	1.00
332_A	340_L	0.885	1.00
35_R	150_L	0.884	1.00
34_L	154_A	0.883	1.00
15_F	18_T	0.879	1.00
146_G	151_A	0.879	1.00
97_Y	228_W	0.879	1.00
326_L	329_L	0.877	1.00
297_A	322_A	0.876	1.00
73_A	77_V	0.875	1.00
24_L	271_A	0.874	1.00
226_L	296_V	0.873	1.00
315_S	319_L	0.872	1.00
299_Y	303_L	0.871	1.00
29_T	32_G	0.870	1.00
6_E	179_H	0.869	1.00
61_D	110_R	0.869	1.00
38_L	153_W	0.868	1.00
320_V	324_A	0.865	1.00
304_A	322_A	0.863	1.00
302_G	305_A	0.862	1.00
134_A	164_V	0.859	1.00
67_L	103_G	0.854	1.00
298_L	302_G	0.848	1.00
48_V	256_G	0.846	1.00
321_G	347_V	0.845	1.00
150_L	157_L	0.844	1.00
125_R	129_V	0.844	1.00
91_L	139_L	0.843	1.00
92_V	95_L	0.842	1.00
33_L	37_L	0.841	1.00
258_L	309_R	0.840	1.00
200_G	207_G	0.840	1.00
333_L	336_P	0.840	1.00
48_V	51_T	0.840	1.00
165_P	170_R	0.835	1.00
310_L	315_S	0.834	1.00
314_L	317_S	0.829	1.00
175_V	248_G	0.821	1.00
335_L	340_L	0.821	1.00
192_L	223_A	0.819	1.00
35_R	86_F	0.817	1.00
234_A	240_R	0.816	1.00
308_R	313_R	0.816	1.00
62_G	66_L	0.815	1.00
66_L	70_V	0.815	1.00
200_G	206_L	0.809	1.00
313_R	317_S	0.809	1.00
196_I	223_A	0.808	1.00
25_A	275_L	0.808	1.00
204_A	207_G	0.807	1.00
291_A	295_G	0.805	1.00
318_R	330_P	0.800	1.00
24_L	33_L	0.798	1.00
330_P	334_A	0.797	1.00
105_V	109_L	0.793	1.00
42_A	93_F	0.790	1.00
43_V	82_I	0.789	1.00
221_V	345_A	0.788	1.00
139_L	143_F	0.788	1.00
98_V	142_A	0.788	1.00
333_L	342_A	0.785	1.00
237_A	241_A	0.778	1.00
335_L	338_L	0.777	1.00
129_V	132_L	0.775	1.00
15_F	196_I	0.774	1.00
324_A	328_L	0.769	1.00
70_V	99_V	0.768	1.00
14_V	186_L	0.767	1.00
287_A	291_A	0.766	1.00
328_L	332_A	0.766	1.00
22_H	25_A	0.765	1.00
199_I	207_G	0.763	1.00
199_I	223_A	0.762	1.00
195_S	198_A	0.761	0.99
101_R	104_L	0.759	0.99
271_A	275_L	0.757	0.99
278_A	281_G	0.756	0.99
343_L	347_V	0.755	0.99
164_V	167_L	0.754	0.99
113_R	116_P	0.751	0.99
126_R	171_R	0.751	0.99
102_V	132_L	0.745	0.99
94_A	153_W	0.742	0.99
320_V	323_A	0.741	0.99
23_L	35_R	0.740	0.99
236_A	241_A	0.738	0.99
196_I	220_L	0.737	0.99
262_L	306_F	0.735	0.99
6_E	10_D	0.734	0.99
133_V	136_V	0.733	0.99
288_A	292_L	0.730	0.99
330_P	333_L	0.726	0.99
138_W	156_A	0.726	0.99
4_P	8_F	0.726	0.99
120_R	124_A	0.726	0.99
336_P	344_L	0.725	0.99
332_A	335_L	0.723	0.99
152_L	155_V	0.720	0.99
341_L	346_A	0.720	0.99
18_T	197_V	0.719	0.99
126_R	167_L	0.718	0.99
237_A	240_R	0.714	0.99
293_A	344_L	0.714	0.99
222_L	225_A	0.714	0.99
328_L	331_L	0.713	0.99
228_W	231_F	0.713	0.99
190_I	274_E	0.712	0.99
22_H	274_E	0.711	0.99
309_R	312_G	0.710	0.99
310_L	313_R	0.710	0.99
109_L	128_A	0.709	0.99
142_A	145_P	0.706	0.99
218_L	221_V	0.705	0.99
265_G	269_V	0.704	0.99
58_D	64_V	0.704	0.99
149_R	160_D	0.703	0.99
217_V	221_V	0.700	0.99
37_L	260_L	0.699	0.99
332_A	343_L	0.698	0.99
325_L	329_L	0.698	0.99
141_G	144_L	0.698	0.99
336_P	341_L	0.698	0.99
91_L	94_A	0.695	0.99
19_Q	22_H	0.689	0.99
240_R	243_R	0.688	0.99
340_L	348_L	0.688	0.99
7_L	11_L	0.686	0.99
278_A	282_E	0.684	0.99
341_L	344_L	0.684	0.99
67_L	110_R	0.683	0.99
332_A	336_P	0.683	0.99
24_L	28_L	0.682	0.99
46_A	75_V	0.682	0.99
28_L	287_A	0.679	0.99
92_V	96_A	0.678	0.99
50_Y	54_T	0.676	0.99
334_A	338_L	0.671	0.99
133_V	164_V	0.669	0.99
26_H	30_W	0.668	0.99
89_R	208_L	0.667	0.99
191_A	263_V	0.666	0.99
44_W	260_L	0.665	0.99
24_L	268_A	0.665	0.99
161_L	260_L	0.665	0.99
244_S	247_R	0.664	0.99
288_A	291_A	0.661	0.99
338_L	342_A	0.660	0.99
324_A	330_P	0.659	0.99
140_A	152_L	0.659	0.99
286_L	289_A	0.658	0.99
336_P	345_A	0.658	0.99
297_A	301_L	0.656	0.99
115_D	174_P	0.655	0.98
49_G	104_L	0.654	0.98
90_G	94_A	0.654	0.98
290_L	293_A	0.654	0.98
315_S	321_G	0.654	0.98
105_V	108_Y	0.651	0.98
304_A	314_L	0.649	0.98
262_L	302_G	0.648	0.98
17_V	191_A	0.648	0.98
25_A	271_A	0.647	0.98
14_V	197_V	0.646	0.98
229_L	303_L	0.645	0.98
303_L	307_R	0.641	0.98
59_P	68_L	0.640	0.98
236_A	240_R	0.640	0.98
206_L	209_T	0.638	0.98
293_A	329_L	0.637	0.98
32_G	35_R	0.636	0.98
290_L	329_L	0.633	0.98
71_Q	100_V	0.631	0.98
76_L	200_G	0.628	0.98
5_L	68_L	0.627	0.98
344_L	348_L	0.627	0.98
284_L	337_A	0.626	0.98
15_F	20_L	0.622	0.98
228_W	232_D	0.618	0.98
17_V	22_H	0.618	0.98
293_A	296_V	0.616	0.98
334_A	343_L	0.616	0.98
7_L	10_D	0.614	0.98
279_H	285_P	0.612	0.98
235_A	242_L	0.611	0.98
293_A	332_A	0.611	0.98
55_N	179_H	0.606	0.98
55_N	175_V	0.605	0.97
334_A	339_A	0.605	0.97
325_L	330_P	0.603	0.97
225_A	348_L	0.602	0.97
252_R	256_G	0.602	0.97
98_V	139_L	0.601	0.97
255_Y	306_F	0.600	0.97
72_M	79_A	0.596	0.97
90_G	149_R	0.588	0.97
334_A	341_L	0.587	0.97
2_V	51_T	0.587	0.97
46_A	49_G	0.585	0.97
3_T	60_D	0.585	0.97
30_W	33_L	0.584	0.97
61_D	64_V	0.584	0.97
141_G	145_P	0.580	0.97
338_L	345_A	0.576	0.97
289_A	333_L	0.574	0.97
57_F	115_D	0.574	0.97
163_A	167_L	0.573	0.97
93_F	153_W	0.572	0.96
156_A	160_D	0.570	0.96
168_G	171_R	0.569	0.96
131_F	135_A	0.568	0.96
337_A	340_L	0.566	0.96
61_D	65_R	0.566	0.96
38_L	141_G	0.566	0.96
38_L	42_A	0.565	0.96
238_A	306_F	0.565	0.96
345_A	349_V	0.564	0.96
321_G	325_L	0.564	0.96
145_P	148_A	0.563	0.96
328_L	340_L	0.557	0.96
27_D	30_W	0.555	0.96
52_W	56_A	0.554	0.96
76_L	196_I	0.553	0.96
134_A	137_L	0.552	0.96
304_A	319_L	0.552	0.96
317_S	322_A	0.551	0.96
283_P	288_A	0.550	0.96
285_P	289_A	0.550	0.96
316_R	321_G	0.550	0.96
15_F	19_Q	0.548	0.96
175_V	251_A	0.547	0.95
199_I	206_L	0.546	0.95
148_A	152_L	0.545	0.95
111_A	124_A	0.544	0.95
99_V	103_G	0.542	0.95
342_A	345_A	0.541	0.95
342_A	346_A	0.539	0.95
106_A	110_R	0.539	0.95
71_Q	107_L	0.539	0.95
226_L	348_L	0.538	0.95
303_L	306_F	0.538	0.95
314_L	321_G	0.536	0.95
291_A	294_G	0.536	0.95
64_V	107_L	0.535	0.95
155_V	159_I	0.534	0.95
46_A	101_R	0.534	0.95
335_L	343_L	0.533	0.95
312_G	319_L	0.532	0.95
166_L	169_R	0.531	0.95
340_L	351_L	0.529	0.95
246_R	249_R	0.528	0.95
104_L	131_F	0.527	0.94
98_V	104_L	0.526	0.94
112_A	128_A	0.524	0.94
339_A	346_A	0.523	0.94
49_G	131_F	0.522	0.94
307_R	315_S	0.522	0.94
322_A	325_L	0.520	0.94
167_L	171_R	0.519	0.94
317_S	321_G	0.519	0.94
15_F	76_L	0.519	0.94
311_R	317_S	0.518	0.94
307_R	313_R	0.516	0.94
105_V	135_A	0.515	0.94
324_A	327_A	0.514	0.94
308_R	318_R	0.513	0.94
313_R	325_L	0.511	0.94
216_A	274_E	0.508	0.93
327_A	331_L	0.508	0.93
304_A	315_S	0.508	0.93
312_G	317_S	0.507	0.93
345_A	351_L	0.507	0.93
181_A	235_A	0.507	0.93
112_A	117_A	0.505	0.93
14_V	194_E	0.505	0.93
289_A	332_A	0.505	0.93
337_A	348_L	0.504	0.93
59_P	62_G	0.504	0.93
187_F	191_A	0.504	0.93
108_Y	120_R	0.502	0.93
45_W	48_V	0.501	0.93
215_A	277_L	0.500	0.93

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
4m64A	1	0.8385	10.6	0.962	Contact Map
2cfqA	1	0.8442	9.8	0.963	Contact Map
4w6vA	1	0.3314	9.5	0.963	Contact Map
3wdoA	1	0.3173	6.9	0.965	Contact Map
2gfpA	2	0.8159	6.7	0.966	Contact Map
4tphA	2	0.3059	5	0.968	Contact Map
2htgA	1	0.0765	4.8	0.968	Contact Map
4xnjA	1	0.3173	4.6	0.968	Contact Map
3m73A	3	0.762	3.7	0.97	Contact Map
4q65A	1	0.2975	3.1	0.971	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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