DAPF - BACSU - GREMLIN Contacts

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DAPF - Diaminopimelate epimerase

UniProt:	O32114	Sequences: MNSFRFTKMHGLGNSYIYVNQFEEQLPEEKLSEIAIQVSSVYTGIGSDGMILICPSDQAPVKMRIFNNDGSEGKNCGNGLRCVAKYAYEHKLVEETSFLIETLSGLVKAEVQVENGKVNVVTVDMGEPRLTKSELPMLDGGEEHTINETMAFGEVELTGTAVSMGNPHIVFPIADIEQAPLTTLGPVIEKDPRFPEGINVEFVETVNEQELHFRVWERGSGITQACGTGACAAAVASVLNGVSKRNQDITVHLAGGDLVINWKDNGHVMMTGPAETVCEGVYFL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	284 (261)
Sequences:	3870 (2672)
Seq/√Len:	165.4

ECOLI - DAPF
BACSU - DAPF

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
210_E	252_H	3.697	1.00
208_E	244_K	3.256	1.00
51_I	79_G	3.212	1.00
97_S	110_E	3.134	1.00
124_D	267_H	3.059	1.00
74_K	196_E	2.971	1.00
64_R	72_E	2.913	1.00
252_H	257_D	2.794	1.00
207_N	210_E	2.740	1.00
248_D	261_N	2.653	1.00
234_A	249_I	2.610	1.00
250_T	257_D	2.350	1.00
235_V	268_V	2.348	1.00
85_K	89_E	2.314	1.00
180_P	183_T	2.307	1.00
203_V	233_A	2.213	1.00
6_F	280_G	2.156	1.00
237_S	243_S	2.118	1.00
204_E	212_H	2.107	1.00
43_T	224_Q	2.104	1.00
38_V	282_Y	2.103	1.00
260_I	270_M	2.086	1.00
5_R	281_V	2.082	1.00
62_K	101_E	2.042	1.00
15_S	41_V	2.013	1.00
188_I	200_V	1.984	1.00
131_T	134_E	1.905	1.00
276_T	279_E	1.902	1.00
99_L	108_K	1.870	1.00
210_E	250_T	1.839	1.00
122_T	269_M	1.812	1.00
248_D	259_V	1.803	1.00
21_Q	54_C	1.794	1.00
172_P	237_S	1.787	1.00
10_H	275_E	1.773	1.00
110_E	122_T	1.772	1.00
129_R	134_E	1.736	1.00
159_G	169_I	1.697	1.00
56_S	101_E	1.692	1.00
160_T	236_A	1.685	1.00
12_L	225_A	1.685	1.00
212_H	252_H	1.683	1.00
234_A	251_V	1.670	1.00
39_S	47_S	1.644	1.00
211_L	233_A	1.638	1.00
122_T	271_T	1.637	1.00
127_E	266_G	1.618	1.00
203_V	211_L	1.606	1.00
59_A	106_L	1.573	1.00
5_R	279_E	1.558	1.00
211_L	251_V	1.557	1.00
190_K	197_G	1.557	1.00
189_E	197_G	1.556	1.00
90_H	279_E	1.547	1.00
151_A	154_E	1.545	1.00
201_E	229_G	1.521	1.00
61_V	87_A	1.518	1.00
19_V	50_M	1.496	1.00
175_D	178_Q	1.495	1.00
54_C	62_K	1.474	1.00
97_S	108_K	1.473	1.00
250_T	259_V	1.468	1.00
214_R	222_I	1.466	1.00
60_P	95_E	1.445	1.00
164_M	268_V	1.444	1.00
206_V	212_H	1.440	1.00
122_T	261_N	1.422	1.00
80_L	100_I	1.418	1.00
72_E	103_L	1.411	1.00
130_L	239_L	1.410	1.00
172_P	203_V	1.381	1.00
175_D	204_E	1.368	1.00
201_E	215_V	1.354	1.00
53_I	83_V	1.342	1.00
47_S	50_M	1.325	1.00
112_Q	122_T	1.322	1.00
149_T	156_E	1.316	1.00
11_G	82_C	1.315	1.00
54_C	64_R	1.308	1.00
125_M	231_C	1.292	1.00
172_P	242_V	1.285	1.00
211_L	237_S	1.275	1.00
20_N	23_E	1.275	1.00
83_V	100_I	1.261	1.00
171_F	200_V	1.250	1.00
31_L	34_I	1.242	1.00
127_E	267_H	1.228	1.00
157_L	184_L	1.220	1.00
213_F	230_A	1.216	1.00
10_H	43_T	1.214	1.00
74_K	104_S	1.213	1.00
209_Q	244_K	1.206	1.00
88_Y	96_T	1.191	1.00
7_T	279_E	1.186	1.00
201_E	213_F	1.183	1.00
222_I	254_A	1.181	1.00
28_E	35_A	1.177	1.00
213_F	233_A	1.173	1.00
99_L	106_L	1.165	1.00
153_G	187_V	1.165	1.00
261_N	271_T	1.163	1.00
75_N	228_T	1.159	1.00
206_V	210_E	1.157	1.00
238_V	247_Q	1.157	1.00
68_N	220_S	1.149	1.00
76_C	226_C	1.145	1.00
45_I	278_C	1.140	1.00
40_S	44_G	1.135	1.00
89_E	276_T	1.113	1.00
177_E	212_H	1.113	1.00
35_A	50_M	1.112	1.00
233_A	251_V	1.105	1.00
225_A	253_L	1.093	1.00
17_I	38_V	1.091	1.00
112_Q	120_V	1.088	1.00
58_Q	101_E	1.087	1.00
263_K	267_H	1.084	1.00
84_A	109_A	1.084	1.00
190_K	216_W	1.084	1.00
13_G	224_Q	1.080	1.00
234_A	238_V	1.079	1.00
176_I	204_E	1.078	1.00
88_Y	111_V	1.066	0.99
53_I	87_A	1.065	0.99
61_V	93_V	1.060	0.99
100_I	109_A	1.058	0.99
13_G	43_T	1.058	0.99
160_T	240_N	1.057	0.99
85_K	274_A	1.056	0.99
235_V	262_W	1.055	0.99
33_E	36_I	1.045	0.99
59_A	101_E	1.042	0.99
56_S	59_A	1.039	0.99
66_F	72_E	1.032	0.99
128_P	262_W	1.031	0.99
12_L	253_L	1.030	0.99
162_V	236_A	1.028	0.99
149_T	158_T	1.026	0.99
93_V	98_F	1.021	0.99
22_F	55_P	1.019	0.99
238_V	262_W	1.019	0.99
167_P	218_R	1.016	0.99
17_I	47_S	1.007	0.99
231_C	268_V	1.006	0.99
102_T	105_G	1.001	0.99
181_L	202_F	0.999	0.99
40_S	43_T	0.992	0.99
120_V	271_T	0.990	0.99
137_M	161_A	0.988	0.99
90_H	276_T	0.983	0.99
247_Q	264_D	0.983	0.99
169_I	198_I	0.975	0.99
28_E	34_I	0.975	0.99
41_V	46_G	0.975	0.99
161_A	169_I	0.965	0.99
32_S	36_I	0.959	0.99
74_K	103_L	0.957	0.99
212_H	254_A	0.955	0.99
53_I	86_Y	0.952	0.99
7_T	276_T	0.949	0.99
31_L	52_L	0.944	0.99
111_V	121_V	0.944	0.99
17_I	278_C	0.940	0.99
15_S	46_G	0.933	0.99
42_Y	224_Q	0.931	0.99
18_Y	51_I	0.930	0.99
109_A	121_V	0.928	0.99
186_P	216_W	0.921	0.98
230_A	253_L	0.920	0.98
38_V	47_S	0.918	0.98
17_I	45_I	0.912	0.98
130_L	235_V	0.909	0.98
151_A	156_E	0.906	0.98
52_L	66_F	0.901	0.98
188_I	198_I	0.898	0.98
182_T	186_P	0.892	0.98
120_V	259_V	0.888	0.98
152_F	155_V	0.884	0.98
62_K	103_L	0.876	0.98
16_Y	47_S	0.874	0.98
21_Q	52_L	0.870	0.98
124_D	269_M	0.864	0.98
209_Q	248_D	0.861	0.98
244_K	247_Q	0.858	0.98
263_K	269_M	0.849	0.97
86_Y	90_H	0.846	0.97
4_F	281_V	0.846	0.97
226_C	229_G	0.841	0.97
80_L	109_A	0.836	0.97
150_M	159_G	0.834	0.97
244_K	248_D	0.833	0.97
75_N	107_V	0.830	0.97
189_E	216_W	0.826	0.97
35_A	66_F	0.825	0.97
172_P	236_A	0.823	0.97
234_A	260_I	0.822	0.97
234_A	243_S	0.820	0.97
61_V	92_L	0.819	0.97
65_I	73_G	0.817	0.97
201_E	233_A	0.812	0.97
39_S	49_G	0.812	0.97
132_K	137_M	0.807	0.96
129_R	163_S	0.805	0.96
23_E	55_P	0.803	0.96
84_A	98_F	0.798	0.96
211_L	243_S	0.796	0.96
83_V	87_A	0.794	0.96
159_G	171_F	0.789	0.96
164_M	231_C	0.787	0.96
177_E	254_A	0.786	0.96
114_E	120_V	0.778	0.96
45_I	282_Y	0.778	0.96
84_A	111_V	0.778	0.96
259_V	271_T	0.776	0.96
128_P	164_M	0.775	0.96
166_N	201_E	0.771	0.95
7_T	86_Y	0.769	0.95
101_E	106_L	0.767	0.95
9_M	82_C	0.767	0.95
32_S	35_A	0.765	0.95
205_T	211_L	0.763	0.95
243_S	249_I	0.756	0.95
230_A	258_L	0.756	0.95
185_G	189_E	0.753	0.95
31_L	35_A	0.752	0.95
109_A	123_V	0.750	0.95
28_E	33_E	0.750	0.95
215_V	226_C	0.749	0.95
166_N	215_V	0.747	0.95
43_T	255_G	0.743	0.94
96_T	113_V	0.743	0.94
112_Q	271_T	0.741	0.94
170_V	236_A	0.734	0.94
19_V	38_V	0.733	0.94
11_G	225_A	0.725	0.94
181_L	185_G	0.724	0.94
104_S	107_V	0.723	0.94
79_G	84_A	0.723	0.94
80_L	123_V	0.722	0.94
28_E	31_L	0.721	0.93
37_Q	282_Y	0.718	0.93
132_K	139_D	0.712	0.93
161_A	198_I	0.711	0.93
139_D	193_R	0.711	0.93
22_F	92_L	0.710	0.93
261_N	269_M	0.709	0.93
20_N	92_L	0.701	0.92
98_F	109_A	0.699	0.92
163_S	166_N	0.695	0.92
16_Y	39_S	0.695	0.92
203_V	237_S	0.694	0.92
183_T	187_V	0.693	0.92
12_L	230_A	0.692	0.92
214_R	254_A	0.692	0.92
60_P	99_L	0.686	0.92
63_M	75_N	0.679	0.91
9_M	18_Y	0.677	0.91
10_H	277_V	0.676	0.91
152_F	187_V	0.675	0.91
247_Q	265_N	0.674	0.91
181_L	222_I	0.672	0.91
176_I	214_R	0.672	0.91
69_D	219_G	0.671	0.91
93_V	96_T	0.670	0.91
173_I	204_E	0.669	0.91
96_T	110_E	0.668	0.91
210_E	257_D	0.668	0.91
9_M	276_T	0.667	0.91
176_I	212_H	0.666	0.90
18_Y	39_S	0.664	0.90
169_I	188_I	0.664	0.90
74_K	166_N	0.664	0.90
216_W	220_S	0.663	0.90
169_I	200_V	0.663	0.90
33_E	37_Q	0.661	0.90
157_L	171_F	0.659	0.90
39_S	68_N	0.658	0.90
251_V	260_I	0.655	0.90
34_I	37_Q	0.655	0.90
150_M	191_D	0.653	0.90
258_L	270_M	0.651	0.89
173_I	179_A	0.648	0.89
56_S	60_P	0.647	0.89
237_S	242_V	0.627	0.88
189_E	220_S	0.622	0.87
247_Q	261_N	0.619	0.87
209_Q	247_Q	0.619	0.87
182_T	221_G	0.619	0.87
51_I	83_V	0.618	0.87
230_A	251_V	0.617	0.87
186_P	190_K	0.616	0.87
39_S	51_I	0.616	0.87
181_L	186_P	0.615	0.87
203_V	213_F	0.614	0.87
38_V	45_I	0.613	0.86
74_K	167_P	0.610	0.86
53_I	61_V	0.608	0.86
264_D	267_H	0.605	0.86
96_T	111_V	0.605	0.86
263_K	266_G	0.604	0.86
128_P	162_V	0.603	0.86
21_Q	26_L	0.603	0.86
136_P	161_A	0.603	0.86
108_K	124_D	0.602	0.85
88_Y	93_V	0.599	0.85
7_T	90_H	0.596	0.85
151_A	155_V	0.596	0.85
176_I	181_L	0.595	0.85
164_M	235_V	0.594	0.85
22_F	90_H	0.594	0.85
56_S	62_K	0.590	0.84
62_K	72_E	0.589	0.84
201_E	226_C	0.588	0.84
37_Q	275_E	0.588	0.84
80_L	83_V	0.583	0.84
14_N	48_D	0.580	0.83
102_T	107_V	0.579	0.83
224_Q	254_A	0.578	0.83
12_L	273_P	0.577	0.83
234_A	262_W	0.576	0.83
205_T	242_V	0.574	0.83
51_I	65_I	0.572	0.82
59_A	99_L	0.571	0.82
125_M	164_M	0.567	0.82
231_C	260_I	0.567	0.82
171_F	188_I	0.567	0.82
35_A	47_S	0.566	0.82
205_T	208_E	0.565	0.82
34_I	282_Y	0.565	0.82
16_Y	220_S	0.565	0.82
49_G	75_N	0.564	0.82
238_V	249_I	0.564	0.82
75_N	80_L	0.561	0.81
49_G	73_G	0.561	0.81
67_N	218_R	0.559	0.81
34_I	38_V	0.555	0.81
4_F	19_V	0.554	0.80
11_G	273_P	0.553	0.80
63_M	100_I	0.553	0.80
226_C	230_A	0.547	0.80
73_G	220_S	0.546	0.80
6_F	278_C	0.542	0.79
67_N	166_N	0.541	0.79
20_N	90_H	0.539	0.79
238_V	244_K	0.539	0.79
40_S	46_G	0.539	0.79
41_V	44_G	0.535	0.78
98_F	111_V	0.535	0.78
20_N	86_Y	0.533	0.78
201_E	222_I	0.532	0.78
154_E	157_L	0.529	0.77
51_I	63_M	0.528	0.77
186_P	189_E	0.527	0.77
135_L	161_A	0.526	0.77
20_N	24_E	0.525	0.77
138_L	193_R	0.524	0.77
162_V	170_V	0.524	0.77
100_I	107_V	0.523	0.77
128_P	235_V	0.522	0.76
171_F	184_L	0.521	0.76
79_G	86_Y	0.521	0.76
169_I	194_F	0.519	0.76
153_G	156_E	0.517	0.76
14_N	78_N	0.515	0.75
80_L	107_V	0.514	0.75
12_L	270_M	0.513	0.75
155_V	183_T	0.513	0.75
81_R	272_G	0.513	0.75
74_K	228_T	0.512	0.75
236_A	240_N	0.512	0.75
19_V	28_E	0.511	0.75
185_G	188_I	0.511	0.75
231_C	270_M	0.510	0.75
253_L	258_L	0.510	0.75
125_M	270_M	0.508	0.75
11_G	81_R	0.508	0.75
179_A	184_L	0.508	0.75
170_V	229_G	0.507	0.74
65_I	72_E	0.507	0.74
9_M	49_G	0.507	0.74
157_L	200_V	0.506	0.74
209_Q	250_T	0.505	0.74
58_Q	99_L	0.505	0.74
157_L	188_I	0.505	0.74
152_F	157_L	0.505	0.74
223_T	226_C	0.504	0.74
17_I	280_G	0.503	0.74
87_A	92_L	0.502	0.74
78_N	223_T	0.502	0.74
200_V	216_W	0.501	0.74
8_K	15_S	0.500	0.73
222_I	233_A	0.500	0.73

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
2otnA	2	1	100	0.29	Contact Map
3fveA	2	0.9049	100	0.322	Contact Map
3ejxA	5	0.9754	100	0.325	Contact Map
2gkeA	1	0.9542	100	0.333	Contact Map
3ednA	2	0.9472	100	0.44	Contact Map
1ym5A	2	0.9296	100	0.472	Contact Map
3g7kA	3	0.9894	100	0.477	Contact Map
1xubA	2	0.9155	100	0.486	Contact Map
1qyaA	2	0.9296	100	0.486	Contact Map
1u0kA	2	0.919	100	0.489	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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