DPAL - ECOLI - GREMLIN Contacts

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DPAL - Diaminopropionate ammonia-lyase

UniProt:	P66899	Sequences: MSVFSLKIDIADNKFFNGETSPLFSQSQAKLARQFHQKIAGYRPTPLCALDDLANLFGVKKILVKDESKRFGLNAFKMLGGAYAIAQLLCEKYHLDIETLSFEHLKNAIGEKMTFATTTDGNHGRGVAWAAQQLGQNAVIYMPKGSAQERVDAILNLGAECIVTDMNYDDTVRLTMQHAQQHGWEVVQDTAWEGYTKIPTWIMQGYATLADEAVEQMREMGVTPTHVLLQAGVGAMAGGVLGYLVDVYSPQNLHSIIVEPDKADCIYRSGVKGDIVNVGGDMATIMAGLACGEPNPLGWEILRNCATQFISCQDSVAALGMRVLGNPYGNDPRIISGESGAVGLGVLAAVHYHPQRQSLMEKLALNKDAVVLVISTEGDTDVKHYREVVWEGKHAVAP	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13054
Length:	398 (313)
Sequences:	14461 (7702)
Seq/√Len:	435.3

ECOLI - DPAL ILVA SDHD TDCB TRPB CYSK CYSM DCYD
BACSU - ILVA SDHD TRPB THRC CYSM MCCA CYSK
HALSA - Q9HNH6 Q9HRU4 Q9HMQ7 TRPB Q9HNH0 Q9HQ70 Q9HRP3
SULSO - Q980P1 TRPB1 TRPB2 Q97ZL6 Q980F2 Q97ZT5

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
131_A	138_A	4.183	1.00
61_K	370_V	3.787	1.00
174_L	177_Q	3.356	1.00
213_A	372_L	3.293	1.00
49_A	61_K	3.156	1.00
316_V	349_A	3.043	1.00
141_Y	178_H	2.898	1.00
226_H	256_I	2.830	1.00
144_K	165_D	2.754	1.00
254_H	308_Q	2.690	1.00
177_Q	181_Q	2.690	1.00
148_Q	152_D	2.669	1.00
137_N	160_E	2.636	1.00
261_D	313_Q	2.554	1.00
139_V	160_E	2.513	1.00
87_Q	201_W	2.505	1.00
44_P	216_Q	2.461	1.00
44_P	215_E	2.413	1.00
89_L	92_K	2.350	1.00
227_V	244_L	2.323	1.00
267_Y	271_V	2.316	1.00
248_Y	253_L	2.225	1.00
241_L	305_C	2.161	1.00
248_Y	252_N	2.142	1.00
139_V	162_I	2.092	1.00
47_L	372_L	2.034	1.00
258_V	346_V	2.006	1.00
366_N	369_A	2.001	1.00
323_V	331_D	1.982	1.00
264_D	268_R	1.952	1.00
343_G	373_V	1.942	1.00
225_T	369_A	1.934	1.00
178_H	182_H	1.931	1.00
224_P	372_L	1.908	1.00
49_A	63_L	1.894	1.00
289_L	342_V	1.864	1.00
313_Q	316_V	1.863	1.00
49_A	54_A	1.856	1.00
114_T	139_V	1.851	1.00
63_L	370_V	1.841	1.00
210_A	240_V	1.810	1.00
256_I	308_Q	1.748	1.00
63_L	217_M	1.740	1.00
56_L	323_V	1.737	1.00
227_V	240_V	1.730	1.00
323_V	348_A	1.684	1.00
245_V	307_T	1.682	1.00
225_T	370_V	1.665	1.00
277_N	293_E	1.649	1.00
151_V	163_V	1.647	1.00
272_K	276_V	1.626	1.00
176_M	180_Q	1.619	1.00
268_R	271_V	1.613	1.00
324_L	336_S	1.609	1.00
228_L	258_V	1.601	1.00
237_A	306_A	1.588	1.00
226_H	369_A	1.580	1.00
152_D	155_L	1.517	1.00
89_L	136_Q	1.515	1.00
226_H	254_H	1.509	1.00
172_V	176_M	1.499	1.00
56_L	331_D	1.493	1.00
142_M	154_I	1.486	1.00
267_Y	311_S	1.433	1.00
210_A	243_Y	1.429	1.00
210_A	244_L	1.420	1.00
214_V	247_V	1.413	1.00
73_L	129_W	1.409	1.00
87_Q	91_E	1.407	1.00
240_V	374_I	1.404	1.00
228_L	350_V	1.403	1.00
38_K	83_Y	1.398	1.00
151_V	155_L	1.384	1.00
51_D	55_N	1.374	1.00
320_G	345_G	1.367	1.00
336_S	375_S	1.364	1.00
324_L	344_L	1.361	1.00
207_A	211_D	1.360	1.00
167_N	170_D	1.358	1.00
124_G	154_I	1.337	1.00
211_D	243_Y	1.337	1.00
30_K	33_R	1.328	1.00
270_G	309_F	1.325	1.00
286_M	317_A	1.324	1.00
241_L	255_S	1.317	1.00
86_A	134_L	1.316	1.00
191_A	296_P	1.306	1.00
85_I	115_F	1.299	1.00
262_K	314_D	1.298	1.00
217_M	224_P	1.295	1.00
248_Y	251_Q	1.288	1.00
310_I	346_V	1.283	1.00
37_Q	40_A	1.278	1.00
268_R	272_K	1.272	1.00
350_V	353_H	1.270	1.00
226_H	371_V	1.267	1.00
47_L	217_M	1.261	1.00
231_A	257_I	1.260	1.00
257_I	309_F	1.259	1.00
228_L	347_L	1.248	1.00
142_M	163_V	1.238	1.00
264_D	311_S	1.235	1.00
217_M	372_L	1.234	1.00
285_I	318_A	1.233	1.00
284_T	290_A	1.231	1.00
256_I	310_I	1.227	1.00
85_I	134_L	1.215	1.00
52_D	55_N	1.214	1.00
155_L	160_E	1.209	1.00
62_I	347_L	1.209	1.00
273_G	303_R	1.192	1.00
325_G	335_I	1.177	1.00
38_K	41_G	1.168	1.00
57_F	348_A	1.165	1.00
46_P	69_K	1.165	1.00
173_R	177_Q	1.163	1.00
47_L	213_A	1.162	1.00
141_Y	174_L	1.162	1.00
119_T	124_G	1.161	1.00
52_D	331_D	1.155	1.00
174_L	178_H	1.151	1.00
48_C	66_D	1.151	1.00
300_E	304_N	1.150	1.00
320_G	344_L	1.146	1.00
340_G	376_T	1.128	1.00
114_T	137_N	1.119	1.00
50_L	64_V	1.119	1.00
117_T	140_I	1.119	1.00
266_I	294_P	1.117	1.00
139_V	184_W	1.110	1.00
170_D	173_R	1.105	1.00
45_T	70_R	1.101	1.00
237_A	257_I	1.100	1.00
321_M	380_T	1.098	1.00
237_A	302_L	1.093	1.00
82_A	86_A	1.093	1.00
132_Q	138_A	1.087	1.00
151_V	161_C	1.087	1.00
209_L	374_I	1.084	1.00
64_V	375_S	1.075	1.00
213_A	224_P	1.075	1.00
322_R	326_N	1.069	1.00
127_V	138_A	1.056	1.00
244_L	253_L	1.056	1.00
206_Y	246_D	1.048	1.00
315_S	319_L	1.048	1.00
231_A	309_F	1.030	1.00
191_A	238_G	1.030	1.00
321_M	341_A	1.029	1.00
229_L	240_V	1.027	1.00
308_Q	353_H	1.026	1.00
267_Y	309_F	1.026	1.00
152_D	156_N	1.019	1.00
154_I	159_A	1.015	1.00
200_T	297_L	1.014	1.00
266_I	302_L	1.014	1.00
254_H	369_A	1.010	1.00
312_C	345_G	1.009	1.00
260_P	289_L	1.007	1.00
37_Q	41_G	1.005	1.00
319_L	323_V	0.997	1.00
217_M	370_V	0.996	1.00
209_L	236_M	0.994	1.00
289_L	339_S	0.992	1.00
177_Q	180_Q	0.981	1.00
316_V	319_L	0.981	1.00
129_W	133_Q	0.981	1.00
347_L	373_V	0.981	1.00
116_A	184_W	0.981	1.00
58_G	367_K	0.977	1.00
116_A	175_T	0.973	1.00
214_V	244_L	0.971	1.00
271_V	308_Q	0.969	1.00
111_E	136_Q	0.966	1.00
264_D	267_Y	0.965	1.00
316_V	345_G	0.963	1.00
231_A	237_A	0.960	1.00
178_H	181_Q	0.958	1.00
261_D	311_S	0.954	1.00
297_L	300_E	0.952	1.00
137_N	184_W	0.951	1.00
31_L	34_Q	0.951	1.00
209_L	240_V	0.947	1.00
300_E	303_R	0.946	1.00
113_M	137_N	0.943	1.00
176_M	179_A	0.938	1.00
231_A	266_I	0.934	1.00
144_K	166_M	0.932	1.00
228_L	256_I	0.930	1.00
129_W	157_L	0.926	1.00
203_M	207_A	0.925	1.00
270_G	302_L	0.920	1.00
318_A	388_V	0.920	1.00
59_V	62_I	0.919	1.00
90_C	111_E	0.919	1.00
326_N	331_D	0.919	1.00
219_E	370_V	0.915	1.00
320_G	348_A	0.912	1.00
254_H	307_T	0.909	1.00
128_A	159_A	0.909	1.00
88_L	92_K	0.898	1.00
138_A	159_A	0.897	1.00
175_T	179_A	0.895	1.00
336_S	341_A	0.893	1.00
36_H	40_A	0.887	1.00
302_L	306_A	0.886	1.00
321_M	385_Y	0.884	1.00
228_L	346_V	0.883	1.00
43_R	72_G	0.881	1.00
266_I	309_F	0.877	1.00
54_A	61_K	0.874	1.00
160_E	182_H	0.874	1.00
350_V	354_P	0.872	1.00
35_F	39_I	0.870	1.00
213_A	240_V	0.867	1.00
383_K	387_E	0.866	1.00
81_G	126_G	0.866	1.00
90_C	112_K	0.864	1.00
33_R	37_Q	0.864	1.00
33_R	36_H	0.861	1.00
118_T	168_Y	0.861	1.00
173_R	176_M	0.854	1.00
166_M	170_D	0.850	1.00
340_G	375_S	0.850	1.00
293_E	296_P	0.849	1.00
203_M	297_L	0.849	1.00
162_I	174_L	0.848	1.00
47_L	63_L	0.848	1.00
84_A	202_I	0.847	1.00
211_D	215_E	0.846	1.00
66_D	375_S	0.842	1.00
139_V	178_H	0.840	1.00
324_L	375_S	0.839	1.00
349_A	352_Y	0.838	1.00
139_V	182_H	0.834	1.00
89_L	111_E	0.829	1.00
203_M	242_G	0.829	1.00
230_Q	376_T	0.827	1.00
258_V	310_I	0.826	1.00
61_K	368_D	0.826	1.00
42_Y	78_M	0.821	1.00
344_L	373_V	0.820	1.00
68_S	334_I	0.817	1.00
38_K	86_A	0.816	1.00
132_Q	157_L	0.816	1.00
209_L	213_A	0.815	1.00
164_T	174_L	0.813	1.00
78_M	129_W	0.811	1.00
351_H	354_P	0.810	1.00
345_G	349_A	0.807	1.00
268_R	276_V	0.806	1.00
346_V	350_V	0.801	1.00
317_A	342_V	0.801	1.00
127_V	140_I	0.797	1.00
64_V	324_L	0.796	1.00
318_A	338_E	0.796	1.00
262_K	282_M	0.795	1.00
113_M	183_G	0.795	1.00
36_H	215_E	0.794	1.00
262_K	283_A	0.794	1.00
52_D	332_P	0.792	1.00
188_Q	191_A	0.791	1.00
84_A	187_V	0.783	1.00
57_F	323_V	0.783	1.00
114_T	184_W	0.783	1.00
238_G	298_G	0.782	1.00
243_Y	247_V	0.780	1.00
30_K	34_Q	0.779	1.00
89_L	134_L	0.779	1.00
125_R	154_I	0.775	1.00
218_R	223_T	0.772	1.00
116_A	178_H	0.772	1.00
53_L	344_L	0.769	1.00
32_A	35_F	0.769	1.00
144_K	163_V	0.766	1.00
214_V	243_Y	0.764	1.00
384_H	387_E	0.762	1.00
203_M	301_I	0.762	1.00
148_Q	151_V	0.760	1.00
310_I	349_A	0.758	1.00
269_S	276_V	0.755	1.00
240_V	255_S	0.755	1.00
169_D	173_R	0.750	1.00
288_G	339_S	0.747	1.00
168_Y	171_T	0.747	1.00
213_A	374_I	0.746	1.00
155_L	163_V	0.744	1.00
168_Y	172_V	0.741	1.00
88_L	185_E	0.739	1.00
116_A	179_A	0.736	1.00
237_A	255_S	0.734	1.00
242_G	246_D	0.731	1.00
81_G	130_A	0.727	1.00
214_V	248_Y	0.723	1.00
85_I	130_A	0.721	1.00
113_M	178_H	0.721	1.00
299_W	303_R	0.719	1.00
84_A	201_W	0.719	1.00
214_V	218_R	0.716	1.00
325_G	385_Y	0.715	1.00
50_L	332_P	0.714	1.00
314_D	317_A	0.714	1.00
42_Y	70_R	0.714	1.00
322_R	389_V	0.710	1.00
354_P	369_A	0.710	1.00
86_A	90_C	0.710	1.00
211_D	247_V	0.709	1.00
66_D	334_I	0.708	1.00
92_K	185_E	0.707	1.00
111_E	134_L	0.702	1.00
141_Y	164_T	0.701	1.00
34_Q	37_Q	0.697	1.00
227_V	255_S	0.697	1.00
175_T	186_V	0.694	1.00
60_K	368_D	0.693	1.00
115_F	136_Q	0.693	1.00
127_V	187_V	0.692	1.00
265_C	269_S	0.692	1.00
313_Q	349_A	0.692	1.00
36_H	211_D	0.692	1.00
275_I	299_W	0.691	1.00
56_L	348_A	0.691	1.00
200_T	204_Q	0.691	1.00
57_F	347_L	0.690	1.00
83_Y	86_A	0.687	1.00
229_L	237_A	0.686	1.00
269_S	294_P	0.681	1.00
348_A	352_Y	0.674	1.00
275_I	296_P	0.673	1.00
224_P	253_L	0.673	1.00
178_H	184_W	0.670	1.00
146_S	287_A	0.668	1.00
168_Y	189_D	0.664	1.00
115_F	131_A	0.663	1.00
36_H	39_I	0.661	1.00
301_I	305_C	0.656	1.00
33_R	211_D	0.654	0.99
33_R	247_V	0.652	0.99
172_V	188_Q	0.649	0.99
92_K	113_M	0.648	0.99
204_Q	207_A	0.643	0.99
123_H	206_Y	0.642	0.99
83_Y	87_Q	0.641	0.99
202_I	206_Y	0.635	0.99
42_Y	82_A	0.634	0.99
148_Q	155_L	0.633	0.99
150_R	287_A	0.633	0.99
84_A	87_Q	0.631	0.99
153_A	156_N	0.631	0.99
54_A	59_V	0.630	0.99
269_S	272_K	0.630	0.99
336_S	340_G	0.629	0.99
62_I	373_V	0.628	0.99
223_T	253_L	0.626	0.99
215_E	247_V	0.625	0.99
259_E	265_C	0.623	0.99
384_H	388_V	0.621	0.99
120_D	288_G	0.620	0.99
179_A	186_V	0.619	0.99
310_I	353_H	0.614	0.99
383_K	386_R	0.611	0.99
50_L	53_L	0.610	0.99
125_R	153_A	0.608	0.99
240_V	244_L	0.608	0.99
349_A	353_H	0.607	0.99
179_A	184_W	0.606	0.99
226_H	350_V	0.604	0.99
298_G	309_F	0.603	0.99
51_D	54_A	0.602	0.99
117_T	127_V	0.601	0.99
296_P	300_E	0.601	0.99
256_I	350_V	0.601	0.99
35_F	40_A	0.599	0.99
245_V	255_S	0.597	0.99
344_L	375_S	0.596	0.99
230_Q	343_G	0.595	0.99
204_Q	242_G	0.594	0.99
162_I	178_H	0.593	0.99
258_V	342_V	0.593	0.99
34_Q	38_K	0.592	0.99
347_L	351_H	0.589	0.99
256_I	346_V	0.588	0.99
276_V	279_G	0.587	0.99
60_K	369_A	0.587	0.99
83_Y	204_Q	0.586	0.99
54_A	62_I	0.586	0.99
66_D	69_K	0.585	0.99
165_D	170_D	0.585	0.99
227_V	253_L	0.581	0.99
118_T	186_V	0.580	0.99
316_V	351_H	0.576	0.99
53_L	56_L	0.575	0.99
85_I	127_V	0.571	0.99
84_A	188_Q	0.570	0.99
275_I	278_V	0.570	0.99
213_A	227_V	0.570	0.99
227_V	372_L	0.570	0.99
141_Y	162_I	0.569	0.99
115_F	138_A	0.566	0.99
226_H	354_P	0.565	0.99
142_M	151_V	0.564	0.99
257_I	306_A	0.564	0.99
112_K	137_N	0.564	0.99
170_D	174_L	0.564	0.99
274_D	299_W	0.562	0.98
118_T	175_T	0.561	0.98
263_A	266_I	0.559	0.98
225_T	368_D	0.558	0.98
153_A	331_D	0.558	0.98
64_V	336_S	0.558	0.98
118_T	172_V	0.557	0.98
53_L	57_F	0.556	0.98
53_L	323_V	0.553	0.98
68_S	375_S	0.552	0.98
245_V	305_C	0.552	0.98
321_M	338_E	0.551	0.98
137_N	182_H	0.551	0.98
317_A	341_A	0.547	0.98
126_G	130_A	0.544	0.98
65_K	212_E	0.543	0.98
67_E	376_T	0.542	0.98
172_V	175_T	0.542	0.98
312_C	346_V	0.541	0.98
84_A	92_K	0.540	0.98
73_L	78_M	0.539	0.98
269_S	273_G	0.538	0.98
116_A	141_Y	0.538	0.98
111_E	185_E	0.535	0.98
149_E	382_V	0.535	0.98
335_I	378_G	0.533	0.98
269_S	299_W	0.531	0.98
55_N	58_G	0.531	0.98
84_A	185_E	0.531	0.98
60_K	367_K	0.530	0.98
123_H	187_V	0.529	0.98
275_I	279_G	0.529	0.98
207_A	243_Y	0.528	0.98
315_S	318_A	0.528	0.98
64_V	344_L	0.524	0.98
87_Q	90_C	0.524	0.98
214_V	217_M	0.523	0.98
245_V	304_N	0.522	0.98
85_I	187_V	0.522	0.98
146_S	151_V	0.521	0.98
78_M	133_Q	0.521	0.98
59_V	371_V	0.520	0.97
319_L	348_A	0.520	0.97
38_K	87_Q	0.519	0.97
33_R	40_A	0.519	0.97
39_I	82_A	0.519	0.97
227_V	374_I	0.518	0.97
171_T	175_T	0.518	0.97
47_L	216_Q	0.517	0.97
43_R	70_R	0.515	0.97
124_G	140_I	0.514	0.97
146_S	163_V	0.512	0.97
160_E	163_V	0.510	0.97
36_H	41_G	0.510	0.97
54_A	57_F	0.510	0.97
259_E	267_Y	0.510	0.97
112_K	183_G	0.509	0.97
258_V	312_C	0.509	0.97
155_L	161_C	0.507	0.97
386_R	389_V	0.507	0.97
57_F	351_H	0.506	0.97
286_M	289_L	0.505	0.97
31_L	204_Q	0.502	0.97
224_P	248_Y	0.501	0.97
89_L	185_E	0.501	0.97
243_Y	246_D	0.500	0.97

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
4d9iA	2	0.9623	100	0.242	Contact Map
1tdjA	2	0.8367	100	0.284	Contact Map
2gn0A	2	0.8241	100	0.287	Contact Map
1v71A	2	0.7965	100	0.29	Contact Map
3ss7X	1	0.9397	100	0.298	Contact Map
3l6bA	2	0.8065	100	0.303	Contact Map
1ve5A	3	0.7714	100	0.309	Contact Map
2rkbA	2	0.794	100	0.319	Contact Map
4h27A	1	0.7915	100	0.33	Contact Map
3iauA	1	0.8593	100	0.336	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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