DAPA - ECOLI - GREMLIN Contacts

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DAPA - 4-hydroxy-tetrahydrodipicolinate synthase

UniProt:	P0A6L2	Sequences: MFTGSIVAIVTPMDEKGNVCRASLKKLIDYHVASGTSAIVSVGTTGESATLNHDEHADVVMMTLDLADGRIPVIAGTGANATAEAISLTQRFNDSGIVGCLTVTPYYNRPSQEGLYQHFKAIAEHTDLPQILYNVPSRTGCDLLPETVGRLAKVKNIIGIKEATGNLTRVNQIKELVSDDFVLLSGDDASALDFMQLGGHGVISVTANVAARDMAQMCKLAAEGHFAEARVINQRLMPLHNKLFVEPNPIPVKWACKELGLVATDTLRLPMTPITDSGRETVRAALKHAGLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG10205
Length:	292 (285)
Sequences:	10351 (6869)
Seq/√Len:	406.9

ECOLI - DAPA YJHH YAGE NANA
BACSU - DAPA KDGD
HALSA - DAPAL
SULSO - Q97WF2 Q97UF0 Q97UI2 KDGA

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
225_H	228_E	3.884	1.00
29_D	66_L	3.363	1.00
14_D	18_N	3.240	1.00
116_Y	150_R	3.163	1.00
258_E	283_R	2.887	1.00
25_K	66_L	2.783	1.00
93_N	127_D	2.695	1.00
21_R	58_D	2.691	1.00
21_R	62_M	2.621	1.00
77_T	89_T	2.612	1.00
194_F	199_G	2.549	1.00
25_K	62_M	2.506	1.00
57_A	91_R	2.424	1.00
220_L	228_E	2.420	1.00
89_T	100_C	2.297	1.00
228_E	231_V	2.219	1.00
29_D	70_R	2.163	1.00
112_Q	147_T	2.086	1.00
195_M	221_A	2.063	1.00
82_T	118_H	2.055	1.00
6_I	38_A	2.053	1.00
124_E	154_V	2.010	1.00
112_Q	144_L	2.009	1.00
219_K	223_E	1.998	1.00
220_L	225_H	1.995	1.00
215_A	219_K	1.966	1.00
120_K	154_V	1.960	1.00
30_Y	34_S	1.959	1.00
37_S	219_K	1.922	1.00
142_D	169_R	1.919	1.00
149_G	176_L	1.892	1.00
283_R	287_K	1.885	1.00
58_D	61_M	1.881	1.00
29_D	33_A	1.867	1.00
120_K	124_E	1.848	1.00
113_E	117_Q	1.845	1.00
25_K	65_D	1.835	1.00
20_C	23_S	1.817	1.00
53_H	84_E	1.816	1.00
254_W	279_R	1.786	1.00
113_E	150_R	1.766	1.00
116_Y	120_K	1.741	1.00
61_M	65_D	1.725	1.00
28_I	63_T	1.724	1.00
213_D	235_R	1.722	1.00
131_I	159_G	1.713	1.00
7_V	207_A	1.702	1.00
55_E	268_R	1.681	1.00
34_S	212_R	1.675	1.00
24_L	63_T	1.666	1.00
64_L	73_V	1.663	1.00
58_D	62_M	1.653	1.00
123_A	154_V	1.634	1.00
117_Q	120_K	1.609	1.00
257_K	265_D	1.600	1.00
12_P	24_L	1.586	1.00
280_E	283_R	1.576	1.00
144_L	147_T	1.567	1.00
102_T	122_I	1.563	1.00
23_S	26_K	1.536	1.00
89_T	126_T	1.522	1.00
41_S	63_T	1.521	1.00
231_V	235_R	1.511	1.00
60_V	75_A	1.484	1.00
24_L	59_V	1.479	1.00
148_V	160_I	1.471	1.00
62_M	66_L	1.457	1.00
32_V	71_I	1.455	1.00
93_N	126_T	1.379	1.00
216_Q	228_E	1.374	1.00
85_A	122_I	1.368	1.00
216_Q	220_L	1.357	1.00
276_D	280_E	1.357	1.00
37_S	215_A	1.350	1.00
276_D	279_R	1.336	1.00
262_V	265_D	1.336	1.00
117_Q	121_A	1.325	1.00
6_I	40_V	1.312	1.00
93_N	128_L	1.311	1.00
10_V	256_C	1.304	1.00
174_K	183_L	1.304	1.00
131_I	203_I	1.296	1.00
53_H	87_S	1.288	1.00
280_E	284_A	1.287	1.00
91_R	94_D	1.285	1.00
47_E	253_K	1.285	1.00
79_A	85_A	1.273	1.00
257_K	262_V	1.271	1.00
5_S	36_T	1.264	1.00
245_V	281_T	1.262	1.00
275_T	278_G	1.258	1.00
254_W	258_E	1.258	1.00
57_A	87_S	1.248	1.00
74_I	99_G	1.239	1.00
172_Q	176_L	1.234	1.00
212_R	216_Q	1.233	1.00
3_T	222_A	1.231	1.00
62_M	65_D	1.230	1.00
100_C	126_T	1.227	1.00
86_I	121_A	1.225	1.00
81_A	84_E	1.215	1.00
60_V	92_F	1.212	1.00
42_V	59_V	1.208	1.00
57_A	61_M	1.206	1.00
192_L	229_A	1.193	1.00
221_A	226_F	1.183	1.00
284_A	288_H	1.176	1.00
54_D	58_D	1.176	1.00
30_Y	261_L	1.170	1.00
53_H	91_R	1.167	1.00
32_V	70_R	1.165	1.00
90_Q	94_D	1.162	1.00
123_A	156_N	1.161	1.00
40_V	101_L	1.151	1.00
64_L	98_V	1.137	1.00
18_N	83_A	1.127	1.00
216_Q	219_K	1.122	1.00
28_I	67_A	1.121	1.00
7_V	31_H	1.120	1.00
61_M	91_R	1.115	1.00
227_A	230_R	1.112	1.00
22_A	25_K	1.112	1.00
226_F	230_R	1.110	1.00
28_I	66_L	1.106	1.00
121_A	124_E	1.095	1.00
14_D	20_C	1.094	1.00
254_W	283_R	1.091	1.00
146_E	176_L	1.085	1.00
121_A	269_L	1.083	1.00
218_C	222_A	1.082	1.00
67_A	73_V	1.077	1.00
150_R	153_K	1.076	1.00
77_T	92_F	1.075	1.00
254_W	257_K	1.074	1.00
13_M	51_L	1.064	1.00
57_A	94_D	1.061	1.00
23_S	263_A	1.058	1.00
121_A	125_H	1.057	1.00
255_A	286_L	1.056	1.00
182_V	200_H	1.049	1.00
74_I	131_I	1.046	1.00
21_R	25_K	1.040	1.00
100_C	128_L	1.026	1.00
113_E	275_T	1.025	1.00
284_A	287_K	1.023	1.00
274_I	282_V	1.006	1.00
90_Q	125_H	1.006	1.00
3_T	200_H	1.004	1.00
113_E	116_Y	1.002	1.00
7_V	36_T	0.999	1.00
78_G	103_V	0.998	1.00
15_E	266_T	0.998	1.00
86_I	90_Q	0.994	1.00
91_R	95_S	0.993	1.00
132_L	148_V	0.988	1.00
149_G	177_V	0.985	1.00
61_M	95_S	0.979	1.00
172_Q	241_N	0.975	1.00
75_A	97_I	0.972	1.00
274_I	278_G	0.971	1.00
25_K	29_D	0.970	1.00
53_H	88_L	0.962	1.00
228_E	232_I	0.961	1.00
5_S	215_A	0.955	1.00
152_A	181_F	0.947	1.00
64_L	97_I	0.941	1.00
281_T	284_A	0.939	1.00
86_I	125_H	0.936	1.00
279_R	283_R	0.933	1.00
116_Y	147_T	0.931	1.00
54_D	87_S	0.930	1.00
56_H	88_L	0.930	1.00
170_V	194_F	0.930	1.00
27_L	256_C	0.930	1.00
79_A	84_E	0.929	1.00
9_I	31_H	0.929	1.00
196_Q	226_F	0.924	1.00
257_K	279_R	0.923	1.00
230_R	234_Q	0.919	1.00
37_S	218_C	0.916	1.00
17_G	83_A	0.915	1.00
220_L	232_I	0.912	1.00
73_V	97_I	0.911	1.00
77_T	100_C	0.909	1.00
123_A	130_Q	0.909	1.00
278_G	281_T	0.908	1.00
134_N	142_D	0.906	1.00
23_S	262_V	0.906	1.00
206_T	240_H	0.902	1.00
13_M	268_R	0.900	1.00
115_L	141_C	0.900	1.00
100_C	130_Q	0.899	1.00
112_Q	150_R	0.898	1.00
41_S	59_V	0.896	1.00
210_A	239_L	0.896	1.00
28_I	62_M	0.893	1.00
145_P	176_L	0.892	1.00
64_L	95_S	0.883	1.00
238_P	288_H	0.880	1.00
87_S	91_R	0.878	1.00
242_K	285_A	0.877	1.00
104_T	141_C	0.872	1.00
151_L	157_I	0.869	1.00
17_G	269_L	0.868	1.00
195_M	218_C	0.863	1.00
117_Q	272_T	0.860	1.00
149_G	153_K	0.860	1.00
32_V	67_A	0.859	1.00
184_L	201_G	0.858	1.00
87_S	90_Q	0.858	1.00
44_T	107_Y	0.854	1.00
227_A	231_V	0.851	1.00
116_Y	154_V	0.849	1.00
191_A	202_V	0.846	1.00
196_Q	230_R	0.843	1.00
204_S	207_A	0.842	1.00
217_M	232_I	0.837	1.00
5_S	207_A	0.837	1.00
196_Q	221_A	0.837	1.00
277_S	280_E	0.832	1.00
90_Q	93_N	0.832	1.00
36_T	211_A	0.828	1.00
102_T	130_Q	0.825	1.00
123_A	157_I	0.819	1.00
82_T	86_I	0.818	1.00
9_I	39_I	0.806	1.00
42_V	75_A	0.806	1.00
154_V	157_I	0.804	1.00
258_E	287_K	0.801	1.00
60_V	97_I	0.801	1.00
210_A	236_L	0.796	1.00
60_V	95_S	0.794	1.00
5_S	202_V	0.790	1.00
285_A	288_H	0.788	1.00
20_C	262_V	0.785	1.00
265_D	279_R	0.783	1.00
277_S	281_T	0.782	1.00
145_P	169_R	0.775	1.00
185_S	194_F	0.773	1.00
22_A	26_K	0.769	1.00
26_K	261_L	0.764	1.00
224_G	227_A	0.763	1.00
92_F	97_I	0.762	1.00
17_G	266_T	0.761	1.00
34_S	211_A	0.760	1.00
24_L	28_I	0.756	1.00
258_E	279_R	0.753	1.00
104_T	143_L	0.749	1.00
145_P	172_Q	0.747	1.00
257_K	263_A	0.746	1.00
193_D	196_Q	0.745	1.00
145_P	149_G	0.745	1.00
265_D	273_P	0.744	1.00
54_D	57_A	0.742	1.00
9_I	24_L	0.739	1.00
83_A	87_S	0.739	1.00
28_I	39_I	0.738	1.00
72_P	98_V	0.738	1.00
38_A	74_I	0.737	1.00
67_A	70_R	0.737	1.00
14_D	266_T	0.736	1.00
85_A	102_T	0.735	1.00
135_V	139_T	0.733	1.00
210_A	213_D	0.731	1.00
32_V	66_L	0.726	1.00
96_G	128_L	0.726	1.00
143_L	148_V	0.725	1.00
233_N	237_M	0.723	1.00
51_L	59_V	0.715	1.00
5_S	218_C	0.715	1.00
133_Y	161_K	0.707	1.00
14_D	22_A	0.704	1.00
48_S	76_G	0.703	1.00
250_I	267_L	0.695	1.00
134_N	162_E	0.695	1.00
237_M	241_N	0.694	1.00
148_V	173_I	0.694	1.00
153_K	180_D	0.691	1.00
39_I	67_A	0.688	1.00
31_H	36_T	0.686	1.00
19_V	24_L	0.683	1.00
146_E	172_Q	0.682	1.00
170_V	183_L	0.682	1.00
213_D	216_Q	0.681	1.00
217_M	221_A	0.681	1.00
42_V	51_L	0.680	1.00
61_M	94_D	0.677	0.99
57_A	88_L	0.677	0.99
172_Q	175_E	0.677	0.99
216_Q	232_I	0.676	0.99
192_L	221_A	0.676	0.99
117_Q	269_L	0.672	0.99
132_L	143_L	0.671	0.99
177_V	200_H	0.671	0.99
57_A	92_F	0.670	0.99
111_S	250_I	0.667	0.99
212_R	259_L	0.666	0.99
112_Q	146_E	0.666	0.99
77_T	102_T	0.666	0.99
57_A	95_S	0.665	0.99
31_H	34_S	0.663	0.99
14_D	17_G	0.657	0.99
120_K	150_R	0.655	0.99
142_D	166_N	0.654	0.99
174_K	177_V	0.654	0.99
9_I	63_T	0.654	0.99
245_V	278_G	0.650	0.99
82_T	121_A	0.650	0.99
30_Y	259_L	0.649	0.99
60_V	64_L	0.645	0.99
256_C	259_L	0.644	0.99
53_H	57_A	0.644	0.99
19_V	59_V	0.642	0.99
44_T	133_Y	0.641	0.99
267_L	271_M	0.640	0.99
256_C	261_L	0.638	0.99
192_L	226_F	0.636	0.99
193_D	197_L	0.635	0.99
258_E	286_L	0.634	0.99
168_T	189_A	0.634	0.99
170_V	174_K	0.633	0.99
274_I	279_R	0.633	0.99
6_I	74_I	0.631	0.99
114_G	272_T	0.629	0.99
193_D	233_N	0.629	0.99
250_I	274_I	0.628	0.99
27_L	31_H	0.627	0.99
67_A	71_I	0.627	0.99
49_A	108_N	0.624	0.99
223_E	228_E	0.622	0.99
191_A	217_M	0.622	0.99
280_E	287_K	0.621	0.99
266_T	273_P	0.621	0.99
174_K	200_H	0.620	0.99
175_E	234_Q	0.618	0.99
84_E	87_S	0.614	0.99
178_S	181_F	0.613	0.99
40_V	74_I	0.612	0.99
127_D	156_N	0.611	0.99
41_S	73_V	0.607	0.99
171_N	175_E	0.602	0.99
52_N	83_A	0.601	0.99
247_P	251_P	0.600	0.99
152_A	177_V	0.599	0.99
42_V	56_H	0.594	0.99
8_A	205_V	0.593	0.99
171_N	197_L	0.591	0.99
166_N	169_R	0.587	0.99
13_M	55_E	0.586	0.99
29_D	32_V	0.586	0.99
281_T	285_A	0.585	0.99
146_E	149_G	0.583	0.98
8_A	188_D	0.578	0.98
147_T	150_R	0.572	0.98
220_L	223_E	0.571	0.98
246_E	278_G	0.571	0.98
5_S	31_H	0.569	0.98
158_I	182_V	0.568	0.98
8_A	204_S	0.567	0.98
133_Y	163_A	0.567	0.98
162_E	170_V	0.565	0.98
171_N	233_N	0.565	0.98
209_V	255_A	0.565	0.98
219_K	222_A	0.564	0.98
15_E	263_A	0.564	0.98
19_V	62_M	0.564	0.98
208_N	211_A	0.563	0.98
231_V	234_Q	0.561	0.98
131_I	158_I	0.561	0.98
69_G	98_V	0.561	0.98
111_S	114_G	0.560	0.98
195_M	222_A	0.559	0.98
192_L	233_N	0.557	0.98
152_A	178_S	0.557	0.98
267_L	272_T	0.557	0.98
104_T	119_F	0.555	0.98
21_R	66_L	0.555	0.98
76_G	101_L	0.554	0.98
97_I	128_L	0.553	0.98
109_R	137_S	0.550	0.98
171_N	193_D	0.548	0.98
149_G	178_S	0.547	0.98
111_S	246_E	0.547	0.98
177_V	180_D	0.545	0.98
175_E	238_P	0.544	0.98
263_A	266_T	0.542	0.98
74_I	101_L	0.541	0.98
254_W	267_L	0.541	0.98
192_L	196_Q	0.539	0.97
124_E	156_N	0.534	0.97
93_N	125_H	0.533	0.97
159_G	182_V	0.533	0.97
64_L	70_R	0.531	0.97
39_I	71_I	0.531	0.97
276_D	283_R	0.531	0.97
153_K	178_S	0.530	0.97
143_L	147_T	0.530	0.97
36_T	215_A	0.530	0.97
220_L	229_A	0.530	0.97
183_L	194_F	0.527	0.97
35_G	215_A	0.527	0.97
18_N	58_D	0.527	0.97
187_D	190_S	0.527	0.97
65_D	68_D	0.527	0.97
54_D	91_R	0.524	0.97
159_G	181_F	0.523	0.97
10_V	252_V	0.523	0.97
186_G	203_I	0.520	0.97
113_E	272_T	0.520	0.97
205_V	252_V	0.519	0.97
191_A	214_M	0.517	0.97
50_T	82_T	0.515	0.97
75_A	92_F	0.515	0.97
102_T	119_F	0.511	0.97
27_L	262_V	0.510	0.97
209_V	256_C	0.510	0.97
173_I	183_L	0.508	0.96
42_V	60_V	0.508	0.96
31_H	207_A	0.507	0.96
131_I	182_V	0.507	0.96
246_E	275_T	0.505	0.96
209_V	252_V	0.505	0.96
64_L	68_D	0.505	0.96
151_L	154_V	0.504	0.96
167_L	190_S	0.503	0.96
86_I	122_I	0.503	0.96
251_P	274_I	0.500	0.96
56_H	91_R	0.500	0.96

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
2ojpA	2	0.9932	100	0.03	Contact Map
3si9A	3	0.9966	100	0.031	Contact Map
3takA	2	0.9966	100	0.034	Contact Map
3qzeA	2	0.9932	100	0.035	Contact Map
3fluA	3	0.9966	100	0.035	Contact Map
3a5fA	3	0.9897	100	0.036	Contact Map
4pfmA	2	0.9966	100	0.036	Contact Map
1o5kA	3	0.9897	100	0.038	Contact Map
2ehhA	3	0.9932	100	0.038	Contact Map
4i7wA	3	0.9897	100	0.038	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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