DDLA - ECOLI - GREMLIN Contacts

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DDLA - D-alanine--D-alanine ligase A

UniProt:	P0A6J8	Sequences: MEKLRVGIVFGGKSAEHEVSLQSAKNIVDAIDKSRFDVVLLGIDKQGQWHVSDASNYLLNADDPAHIALRPSATSLAQVPGKHEHQLIDAQNGQPLPTVDVIFPIVHGTLGEDGSLQGMLRVANLPFVGSDVLASAACMDKDVTKRLLRDAGLNIAPFITLTRANRHNISFAEVESKLGLPLFVKPANQGSSVGVSKVTSEEQYAIAVDLAFEFDHKVIVEQGIKGREIECAVLGNDNPQASTCGEIVLTSDFYAYDTKYIDEDGAKVVVPAAIAPEINDKIRAIAVQAYQTLGCAGMARVDVFLTPENEVVINEINTLPGFTNISMYPKLWQASGLGYTDLITRLIELALERHAADNALKTTM	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10213
Length:	364 (283)
Sequences:	14683 (7271)
Seq/√Len:	432.2

ECOLI - DDLA DDLB CARB ACCC PUR2
BACSU - DDL CARY CARB ACCC2 ACCC1 PUR2
HALSA - CARB Q9HPP8 Q9HQ67
SULSO - Q97VY6 CARB Q7LXR2

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
176_S	201_E	3.740	1.00
200_S	203_Q	3.393	1.00
118_G	136_A	3.248	1.00
284_A	288_Q	3.214	1.00
157_P	222_Q	3.110	1.00
172_A	205_A	3.090	1.00
148_L	289_A	3.020	1.00
118_G	122_V	2.902	1.00
275_A	278_I	2.880	1.00
180_L	201_E	2.688	1.00
150_D	292_T	2.673	1.00
92_N	96_L	2.474	1.00
199_T	225_K	2.451	1.00
237_D	296_A	2.426	1.00
276_P	280_D	2.351	1.00
61_A	77_A	2.338	1.00
285_I	311_V	2.318	1.00
278_I	281_K	2.227	1.00
306_T	310_E	2.133	1.00
174_V	177_K	2.098	1.00
280_D	284_A	2.096	1.00
197_K	223_G	2.061	1.00
287_V	291_Q	2.052	1.00
212_F	216_H	1.987	1.00
154_N	310_E	1.983	1.00
231_C	282_I	1.963	1.00
275_A	309_N	1.963	1.00
172_A	201_E	1.952	1.00
119_M	123_A	1.927	1.00
131_D	134_A	1.911	1.00
163_R	166_R	1.896	1.00
120_L	125_L	1.848	1.00
146_R	150_D	1.848	1.00
137_A	147_L	1.836	1.00
199_T	203_Q	1.832	1.00
143_V	146_R	1.826	1.00
278_I	305_L	1.776	1.00
131_D	296_A	1.771	1.00
201_E	205_A	1.756	1.00
159_I	177_K	1.748	1.00
235_G	241_A	1.742	1.00
154_N	285_I	1.735	1.00
136_A	143_V	1.697	1.00
173_E	177_K	1.665	1.00
225_K	307_P	1.664	1.00
89_D	92_N	1.638	1.00
137_A	143_V	1.608	1.00
148_L	313_I	1.603	1.00
233_V	290_Y	1.601	1.00
159_I	174_V	1.591	1.00
95_P	123_A	1.588	1.00
76_L	93_G	1.569	1.00
281_K	284_A	1.568	1.00
341_D	345_R	1.567	1.00
338_G	341_D	1.559	1.00
142_D	146_R	1.544	1.00
121_R	132_V	1.533	1.00
133_L	137_A	1.532	1.00
205_A	209_D	1.532	1.00
138_C	316_I	1.503	1.00
270_V	332_W	1.473	1.00
149_R	155_I	1.462	1.00
172_A	176_S	1.452	1.00
281_K	310_E	1.450	1.00
278_I	309_N	1.448	1.00
187_A	217_K	1.445	1.00
118_G	132_V	1.444	1.00
320_P	339_Y	1.441	1.00
206_I	210_L	1.437	1.00
234_L	346_L	1.436	1.00
288_Q	291_Q	1.433	1.00
175_E	180_L	1.432	1.00
234_L	298_M	1.432	1.00
234_L	342_L	1.420	1.00
54_A	74_T	1.416	1.00
233_V	286_A	1.412	1.00
94_Q	125_L	1.408	1.00
58_L	78_Q	1.402	1.00
344_T	348_E	1.400	1.00
280_D	283_R	1.399	1.00
188_N	215_D	1.393	1.00
241_A	287_V	1.390	1.00
243_T	283_R	1.389	1.00
174_V	178_L	1.388	1.00
210_L	213_E	1.385	1.00
76_L	97_P	1.378	1.00
120_L	127_F	1.377	1.00
231_C	283_R	1.356	1.00
89_D	93_G	1.355	1.00
57_Y	68_A	1.348	1.00
239_P	291_Q	1.334	1.00
91_Q	95_P	1.330	1.00
82_K	85_H	1.328	1.00
171_F	204_Y	1.295	1.00
276_P	279_N	1.290	1.00
147_L	292_T	1.286	1.00
198_V	207_A	1.284	1.00
157_P	177_K	1.279	1.00
102_I	120_L	1.277	1.00
226_G	307_P	1.260	1.00
138_C	293_L	1.241	1.00
182_L	220_V	1.239	1.00
149_R	157_P	1.238	1.00
229_I	305_L	1.235	1.00
144_T	148_L	1.234	1.00
337_L	342_L	1.234	1.00
281_K	285_I	1.232	1.00
298_M	319_L	1.224	1.00
121_R	127_F	1.216	1.00
208_V	218_V	1.200	1.00
128_V	344_T	1.197	1.00
126_P	237_D	1.196	1.00
145_K	155_I	1.189	1.00
196_S	210_L	1.185	1.00
77_A	81_G	1.174	1.00
342_L	345_R	1.169	1.00
94_Q	102_I	1.169	1.00
121_R	131_D	1.165	1.00
277_E	281_K	1.149	1.00
183_F	197_K	1.132	1.00
208_V	212_F	1.127	1.00
279_N	283_R	1.125	1.00
246_E	272_A	1.113	1.00
231_C	286_A	1.110	1.00
146_R	149_R	1.105	1.00
147_L	150_D	1.104	1.00
142_D	187_A	1.102	1.00
274_I	278_I	1.088	1.00
305_L	311_V	1.078	1.00
305_L	309_N	1.068	1.00
79_V	86_Q	1.066	1.00
285_I	288_Q	1.060	1.00
175_E	182_L	1.056	1.00
142_D	160_T	1.052	1.00
173_E	176_S	1.051	1.00
135_S	318_T	1.046	1.00
240_Q	291_Q	1.041	1.00
118_G	121_R	1.040	1.00
212_F	218_V	1.037	1.00
119_M	122_V	1.034	1.00
50_H	341_D	1.033	1.00
153_L	313_I	1.029	1.00
286_A	303_V	1.027	1.00
118_G	133_L	1.023	1.00
184_V	204_Y	1.023	1.00
227_R	246_E	1.017	1.00
180_L	204_Y	0.992	1.00
133_L	143_V	0.989	1.00
134_A	294_G	0.986	1.00
80_P	85_H	0.984	1.00
164_A	209_D	0.983	1.00
59_L	64_P	0.978	1.00
229_I	282_I	0.976	1.00
164_A	208_V	0.976	1.00
93_G	97_P	0.968	1.00
92_N	95_P	0.965	1.00
81_G	86_Q	0.964	1.00
143_V	147_L	0.959	1.00
184_V	218_V	0.956	1.00
145_K	221_E	0.955	1.00
254_Y	258_T	0.952	1.00
282_I	311_V	0.951	1.00
269_V	273_A	0.948	1.00
209_D	213_E	0.944	1.00
114_G	136_A	0.942	1.00
175_E	201_E	0.940	1.00
277_E	309_N	0.938	1.00
101_V	128_V	0.938	1.00
246_E	279_N	0.937	1.00
289_A	313_I	0.932	1.00
225_K	308_E	0.931	1.00
140_D	217_K	0.928	1.00
244_C	279_N	0.922	1.00
171_F	208_V	0.921	1.00
222_Q	310_E	0.909	1.00
235_G	291_Q	0.908	1.00
134_A	296_A	0.903	1.00
162_T	217_K	0.902	1.00
153_L	285_I	0.901	1.00
222_Q	312_V	0.900	1.00
126_P	296_A	0.899	1.00
161_L	171_F	0.899	1.00
184_V	198_V	0.899	1.00
82_K	86_Q	0.895	1.00
162_T	166_R	0.893	1.00
281_K	311_V	0.893	1.00
102_I	125_L	0.889	1.00
161_L	164_A	0.882	1.00
284_A	287_V	0.882	1.00
151_A	292_T	0.881	1.00
285_I	303_V	0.878	1.00
138_C	318_T	0.867	1.00
145_K	219_I	0.861	1.00
94_Q	120_L	0.860	1.00
140_D	187_A	0.858	1.00
91_Q	123_A	0.855	1.00
59_L	75_S	0.855	1.00
184_V	207_A	0.849	1.00
154_N	281_K	0.846	1.00
283_R	287_V	0.846	1.00
206_I	209_D	0.840	1.00
160_T	217_K	0.838	1.00
183_F	223_G	0.832	1.00
211_A	218_V	0.832	1.00
67_I	71_P	0.828	1.00
164_A	205_A	0.825	1.00
290_Y	293_L	0.820	1.00
121_R	133_L	0.820	1.00
222_Q	306_T	0.819	1.00
288_Q	292_T	0.817	1.00
301_V	316_I	0.817	1.00
115_S	136_A	0.812	1.00
243_T	287_V	0.810	1.00
248_V	272_A	0.806	1.00
242_S	245_G	0.806	1.00
184_V	220_V	0.792	1.00
243_T	335_S	0.790	1.00
142_D	219_I	0.789	1.00
293_L	316_I	0.788	1.00
204_Y	208_V	0.785	1.00
304_F	314_N	0.779	1.00
133_L	136_A	0.773	1.00
121_R	296_A	0.771	1.00
182_L	198_V	0.768	1.00
72_S	75_S	0.766	1.00
100_D	126_P	0.763	1.00
106_V	116_L	0.760	1.00
156_A	224_I	0.757	1.00
142_D	217_K	0.757	1.00
131_D	294_G	0.756	1.00
231_C	246_E	0.752	1.00
180_L	200_S	0.751	1.00
80_P	86_Q	0.751	1.00
178_L	182_L	0.742	1.00
345_R	348_E	0.741	1.00
152_G	288_Q	0.738	1.00
240_Q	345_R	0.737	1.00
176_S	180_L	0.733	1.00
172_A	175_E	0.732	1.00
179_G	222_Q	0.731	1.00
165_N	173_E	0.729	1.00
203_Q	206_I	0.729	1.00
69_L	75_S	0.729	1.00
195_V	257_D	0.724	1.00
161_L	208_V	0.721	1.00
61_A	81_G	0.720	1.00
164_A	172_A	0.719	1.00
183_F	195_V	0.717	1.00
253_F	260_Y	0.712	1.00
134_A	137_A	0.711	1.00
140_D	143_V	0.708	1.00
295_C	299_A	0.706	1.00
160_T	163_R	0.704	1.00
229_I	274_I	0.699	1.00
145_K	149_R	0.696	1.00
154_N	312_V	0.695	1.00
94_Q	99_V	0.693	1.00
54_A	73_A	0.692	1.00
239_P	287_V	0.691	1.00
286_A	290_Y	0.691	1.00
156_A	312_V	0.691	1.00
275_A	305_L	0.689	1.00
307_P	310_E	0.688	1.00
224_I	304_F	0.684	1.00
117_Q	132_V	0.683	1.00
196_S	207_A	0.682	1.00
290_Y	301_V	0.680	1.00
227_R	273_A	0.677	1.00
104_P	128_V	0.673	1.00
148_L	151_A	0.672	1.00
234_L	339_Y	0.670	1.00
289_A	292_T	0.669	1.00
203_Q	207_A	0.669	1.00
202_E	206_I	0.666	1.00
235_G	349_L	0.666	1.00
281_K	288_Q	0.664	1.00
245_G	332_W	0.663	1.00
171_F	220_V	0.662	1.00
120_L	123_A	0.661	1.00
99_V	102_I	0.657	0.99
340_T	344_T	0.653	0.99
277_E	280_D	0.652	0.99
284_A	291_Q	0.651	0.99
236_N	349_L	0.651	0.99
339_Y	343_I	0.650	0.99
157_P	312_V	0.650	0.99
290_Y	299_A	0.649	0.99
174_V	220_V	0.646	0.99
145_K	158_F	0.646	0.99
345_R	349_L	0.645	0.99
233_V	301_V	0.645	0.99
243_T	279_N	0.644	0.99
280_D	287_V	0.644	0.99
100_D	348_E	0.642	0.99
175_E	204_Y	0.642	0.99
60_N	63_D	0.641	0.99
270_V	328_Y	0.640	0.99
147_L	293_L	0.639	0.99
58_L	90_A	0.639	0.99
148_L	153_L	0.638	0.99
59_L	69_L	0.638	0.99
115_S	119_M	0.638	0.99
62_D	345_R	0.635	0.99
132_V	136_A	0.631	0.99
62_D	81_G	0.630	0.99
61_A	80_P	0.630	0.99
165_N	205_A	0.628	0.99
225_K	306_T	0.627	0.99
131_D	237_D	0.625	0.99
114_G	117_Q	0.625	0.99
91_Q	125_L	0.624	0.99
51_V	55_S	0.623	0.99
52_S	56_N	0.621	0.99
141_K	185_K	0.620	0.99
137_A	150_D	0.620	0.99
285_I	289_A	0.617	0.99
117_Q	121_R	0.617	0.99
171_F	175_E	0.616	0.99
113_D	139_M	0.615	0.99
207_A	211_A	0.615	0.99
59_L	62_D	0.614	0.99
230_E	254_Y	0.613	0.99
106_V	111_G	0.613	0.99
73_A	77_A	0.613	0.99
289_A	293_L	0.612	0.99
94_Q	97_P	0.611	0.99
127_F	132_V	0.609	0.99
325_I	330_K	0.608	0.99
116_L	120_L	0.607	0.99
51_V	56_N	0.606	0.99
161_L	166_R	0.606	0.99
197_K	225_K	0.605	0.99
91_Q	119_M	0.605	0.99
63_D	66_H	0.604	0.99
138_C	289_A	0.602	0.99
83_H	86_Q	0.602	0.99
61_A	64_P	0.602	0.99
194_G	211_A	0.600	0.99
235_G	290_Y	0.597	0.99
166_R	212_F	0.596	0.99
248_V	269_V	0.595	0.99
240_Q	332_W	0.594	0.99
162_T	212_F	0.594	0.99
59_L	63_D	0.594	0.99
57_Y	72_S	0.593	0.99
153_L	288_Q	0.593	0.99
147_L	151_A	0.592	0.99
187_A	219_I	0.591	0.99
204_Y	220_V	0.590	0.99
166_R	173_E	0.588	0.99
161_L	165_N	0.587	0.99
224_I	312_V	0.587	0.99
184_V	208_V	0.584	0.99
233_V	299_A	0.583	0.99
235_G	296_A	0.578	0.99
93_G	96_L	0.577	0.99
53_D	348_E	0.575	0.99
297_G	343_I	0.574	0.99
193_V	256_Y	0.573	0.99
207_A	210_L	0.573	0.99
164_A	212_F	0.568	0.99
247_I	254_Y	0.568	0.99
52_S	58_L	0.568	0.99
130_S	295_C	0.567	0.99
299_A	316_I	0.565	0.98
229_I	244_C	0.564	0.98
289_A	301_V	0.564	0.98
146_R	151_A	0.564	0.98
80_P	83_H	0.562	0.98
117_Q	135_S	0.561	0.98
164_A	171_F	0.558	0.98
112_E	190_G	0.558	0.98
156_A	222_Q	0.558	0.98
196_S	206_I	0.555	0.98
58_L	68_A	0.555	0.98
67_I	70_R	0.554	0.98
175_E	179_G	0.552	0.98
161_L	174_V	0.551	0.98
90_A	93_G	0.548	0.98
182_L	222_Q	0.547	0.98
229_I	272_A	0.547	0.98
188_N	216_H	0.546	0.98
59_L	66_H	0.544	0.98
255_A	258_T	0.544	0.98
103_F	343_I	0.539	0.98
198_V	204_Y	0.538	0.98
204_Y	207_A	0.537	0.98
103_F	128_V	0.537	0.98
60_N	86_Q	0.537	0.98
142_D	314_N	0.536	0.98
100_D	128_V	0.535	0.98
241_A	290_Y	0.535	0.98
234_L	328_Y	0.534	0.98
269_V	272_A	0.533	0.98
164_A	204_Y	0.533	0.98
226_G	308_E	0.531	0.98
248_V	273_A	0.530	0.98
98_T	123_A	0.529	0.98
78_Q	81_G	0.527	0.98
202_E	205_A	0.526	0.98
244_C	335_S	0.525	0.98
159_I	164_A	0.524	0.98
83_H	87_L	0.523	0.98
65_A	84_E	0.523	0.98
135_S	139_M	0.523	0.98
272_A	279_N	0.523	0.98
344_T	347_I	0.523	0.98
241_A	291_Q	0.522	0.97
196_S	211_A	0.519	0.97
109_T	189_Q	0.517	0.97
161_L	220_V	0.517	0.97
197_K	257_D	0.513	0.97
209_D	212_F	0.512	0.97
171_F	174_V	0.511	0.97
95_P	119_M	0.511	0.97
142_D	145_K	0.509	0.97
286_A	301_V	0.509	0.97
134_A	138_C	0.505	0.97
275_A	279_N	0.504	0.97
335_S	338_G	0.504	0.97
114_G	135_S	0.504	0.97
320_P	340_T	0.504	0.97
272_A	275_A	0.500	0.97
76_L	84_E	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
3i12A	2	0.9945	100	0.242	Contact Map
3lwbA	2	0.8709	100	0.249	Contact Map
3e5nA	2	0.9341	100	0.25	Contact Map
2fb9A	2	0.8819	100	0.252	Contact Map
3tqtA	2	0.9505	100	0.253	Contact Map
1ehiA	2	0.9753	100	0.268	Contact Map
4fu0A	2	0.9341	100	0.272	Contact Map
1e4eA	4	0.9258	100	0.272	Contact Map
2i87A	2	0.9313	100	0.273	Contact Map
3k3pA	2	0.8681	100	0.278	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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