YDDE - ECOLI - GREMLIN Contacts

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YDDE - Uncharacterized isomerase YddE

UniProt:	P37757	Sequences: MKPQVYHVDAFTSQPFRGNSAGVVFPADNLSEAQMQLIARELGHSETAFLLHSDDSDVRIRYFTPTVEVPICGHATVAAHYVRAKVLGLGNCTIWQTSLAGKHRVTIEKHNDDYRISLEQGTPGFEPPLEGETRAAIINALHLTEDDILPGLPIQVATTGHSKVMIPLKPEVDIDALSPDLNALTAISKKIGCNGFFPFQIRPGKNETDGRMFSPAIGIVEDPVTGNANGPMGAWLVHHNVLPHDGNVLRVKGHQGRALGRDGMIEVTVTIRDNQPEKVTISGTAVILFHAEWAIEL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG11825
Length:	297 (260)
Sequences:	4093 (3020)
Seq/√Len:	187.3

ECOLI - YDDE
BACSU - YFHB
HALSA - Q9HHG6 Q9HS99

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
81_Y	287_I	3.600	1.00
250_R	268_T	3.556	1.00
31_S	34_Q	3.327	1.00
224_V	263_G	3.006	1.00
170_P	173_D	2.834	1.00
177_L	198_P	2.779	1.00
172_V	176_A	2.656	1.00
8_V	82_V	2.599	1.00
117_S	282_S	2.585	1.00
28_D	52_H	2.531	1.00
50_L	79_A	2.467	1.00
95_W	102_K	2.423	1.00
60_I	98_S	2.417	1.00
119_E	278_K	2.410	1.00
7_H	289_F	2.268	1.00
13_S	284_T	2.253	1.00
14_Q	17_R	2.245	1.00
181_L	220_V	2.187	1.00
59_R	97_T	2.177	1.00
115_R	266_E	2.066	1.00
233_G	267_V	1.949	1.00
268_T	280_T	1.945	1.00
53_S	59_R	1.936	1.00
93_T	106_T	1.926	1.00
4_Q	292_E	1.894	1.00
171_E	175_D	1.888	1.00
252_K	264_M	1.849	1.00
169_K	173_D	1.848	1.00
4_Q	290_H	1.832	1.00
93_T	104_R	1.826	1.00
254_H	262_D	1.784	1.00
210_G	229_N	1.777	1.00
180_D	183_A	1.748	1.00
57_D	97_T	1.735	1.00
9_D	41_E	1.716	1.00
25_F	50_L	1.712	1.00
38_I	293_W	1.710	1.00
48_A	79_A	1.702	1.00
12_T	17_R	1.668	1.00
252_K	266_E	1.651	1.00
254_H	258_A	1.642	1.00
224_V	265_I	1.621	1.00
70_P	99_L	1.620	1.00
120_Q	230_G	1.616	1.00
108_E	117_S	1.593	1.00
117_S	280_T	1.589	1.00
35_M	61_R	1.585	1.00
105_V	116_I	1.578	1.00
53_S	97_T	1.578	1.00
115_R	284_T	1.576	1.00
139_N	183_A	1.560	1.00
12_T	286_V	1.551	1.00
163_K	194_N	1.543	1.00
183_A	186_A	1.529	1.00
225_T	228_A	1.520	1.00
30_L	38_I	1.518	1.00
59_R	99_L	1.510	1.00
143_L	168_L	1.509	1.00
233_G	269_V	1.505	1.00
168_L	173_D	1.492	1.00
6_Y	82_V	1.487	1.00
229_N	253_G	1.478	1.00
5_V	289_F	1.462	1.00
254_H	264_M	1.460	1.00
39_A	47_T	1.448	1.00
270_T	280_T	1.427	1.00
30_L	34_Q	1.419	1.00
163_K	212_M	1.405	1.00
34_Q	38_I	1.395	1.00
32_E	35_M	1.389	1.00
167_P	199_F	1.379	1.00
105_V	118_L	1.362	1.00
71_I	227_N	1.354	1.00
60_I	79_A	1.349	1.00
168_L	174_I	1.339	1.00
175_D	258_A	1.329	1.00
6_Y	290_H	1.321	1.00
119_E	280_T	1.304	1.00
237_V	269_V	1.303	1.00
141_L	166_I	1.299	1.00
171_E	202_R	1.298	1.00
57_D	102_K	1.291	1.00
72_C	75_A	1.278	1.00
158_T	162_S	1.276	1.00
17_R	262_D	1.276	1.00
253_G	265_I	1.273	1.00
97_T	102_K	1.272	1.00
7_H	44_H	1.271	1.00
61_R	68_E	1.264	1.00
21_A	78_A	1.260	1.00
84_A	107_I	1.259	1.00
84_A	116_I	1.248	1.00
32_E	36_Q	1.246	1.00
197_F	229_N	1.233	1.00
114_Y	284_T	1.228	1.00
195_G	212_M	1.215	1.00
108_E	113_D	1.207	1.00
106_T	280_T	1.207	1.00
265_I	281_I	1.206	1.00
81_Y	85_K	1.203	1.00
22_G	42_L	1.182	1.00
266_E	282_S	1.181	1.00
5_V	42_L	1.174	1.00
24_V	293_W	1.163	1.00
250_R	266_E	1.155	1.00
208_T	232_M	1.144	1.00
135_A	139_N	1.143	1.00
171_E	209_D	1.143	1.00
168_L	198_P	1.139	1.00
36_Q	39_A	1.137	1.00
229_N	265_I	1.129	1.00
140_A	184_L	1.128	1.00
163_K	195_G	1.126	1.00
6_Y	25_F	1.123	1.00
215_P	219_I	1.123	1.00
29_N	51_L	1.111	1.00
45_S	223_P	1.110	1.00
137_I	164_V	1.108	1.00
209_D	258_A	1.103	1.00
214_S	219_I	1.099	1.00
92_C	107_I	1.087	1.00
67_V	217_I	1.084	1.00
115_R	282_S	1.077	1.00
36_Q	40_R	1.068	1.00
60_I	96_Q	1.062	1.00
165_M	231_P	1.055	1.00
33_A	37_L	1.051	1.00
174_I	200_Q	1.049	1.00
167_P	235_W	1.048	1.00
5_V	291_A	1.047	1.00
135_A	145_E	1.040	1.00
143_L	177_L	1.034	1.00
20_S	44_H	1.034	1.00
25_F	82_V	1.033	1.00
7_H	42_L	1.028	1.00
179_P	213_F	1.022	1.00
62_Y	75_A	1.014	1.00
172_V	175_D	1.013	1.00
138_I	145_E	1.012	1.00
210_G	253_G	1.012	1.00
104_R	119_E	1.004	0.99
46_E	225_T	1.001	0.99
23_V	82_V	0.999	0.99
21_A	72_C	0.994	0.99
212_M	228_A	0.991	0.99
70_P	163_K	0.990	0.99
136_A	139_N	0.988	0.99
15_P	288_L	0.986	0.99
80_H	96_Q	0.986	0.99
10_A	21_A	0.983	0.99
171_E	203_P	0.983	0.99
22_G	44_H	0.982	0.99
10_A	78_A	0.978	0.99
174_I	209_D	0.975	0.99
85_K	287_I	0.967	0.99
288_L	293_W	0.957	0.99
171_E	200_Q	0.951	0.99
140_A	183_A	0.948	0.99
46_E	223_P	0.946	0.99
214_S	218_G	0.945	0.99
137_I	166_I	0.944	0.99
50_L	83_R	0.943	0.99
165_M	232_M	0.942	0.99
269_V	279_V	0.940	0.99
199_F	235_W	0.935	0.99
259_L	262_D	0.920	0.99
210_G	232_M	0.916	0.99
51_L	59_R	0.915	0.99
56_S	102_K	0.910	0.99
46_E	75_A	0.904	0.99
270_T	276_P	0.903	0.99
108_E	115_R	0.894	0.99
235_W	239_H	0.885	0.99
8_V	23_V	0.880	0.99
53_S	56_S	0.877	0.99
123_P	161_H	0.867	0.98
48_A	60_I	0.866	0.98
225_T	255_Q	0.856	0.98
8_V	285_A	0.849	0.98
71_I	100_A	0.849	0.98
214_S	217_I	0.846	0.98
69_V	75_A	0.845	0.98
83_R	87_L	0.845	0.98
12_T	284_T	0.844	0.98
84_A	94_I	0.843	0.98
13_S	264_M	0.843	0.98
165_M	235_W	0.836	0.98
95_W	104_R	0.834	0.98
39_A	65_P	0.834	0.98
133_T	136_A	0.831	0.98
42_L	289_F	0.830	0.98
89_L	94_I	0.830	0.98
8_V	287_I	0.829	0.98
34_Q	37_L	0.826	0.98
57_D	95_W	0.823	0.98
106_T	117_S	0.823	0.98
62_Y	72_C	0.820	0.98
71_I	103_H	0.819	0.98
215_P	218_G	0.819	0.98
98_S	118_L	0.816	0.98
207_E	244_H	0.810	0.98
9_D	16_F	0.807	0.98
48_A	75_A	0.805	0.98
269_V	276_P	0.804	0.98
10_A	62_Y	0.799	0.97
16_F	41_E	0.798	0.97
138_I	143_L	0.797	0.97
129_L	164_V	0.796	0.97
154_I	166_I	0.793	0.97
214_S	220_V	0.793	0.97
224_V	253_G	0.785	0.97
26_P	29_N	0.783	0.97
125_F	234_A	0.780	0.97
53_S	57_D	0.770	0.97
37_L	40_R	0.766	0.97
81_Y	285_A	0.764	0.97
175_D	209_D	0.764	0.97
35_M	63_F	0.763	0.97
208_T	253_G	0.762	0.97
136_A	183_A	0.760	0.97
82_V	86_V	0.758	0.96
50_L	87_L	0.758	0.96
164_V	193_C	0.758	0.96
171_E	258_A	0.755	0.96
197_F	212_M	0.753	0.96
162_S	194_N	0.753	0.96
29_N	32_E	0.752	0.96
207_E	251_V	0.752	0.96
182_N	185_T	0.752	0.96
140_A	196_F	0.748	0.96
206_N	254_H	0.748	0.96
268_T	282_S	0.747	0.96
167_P	239_H	0.741	0.96
174_I	177_L	0.737	0.96
117_S	268_T	0.732	0.96
24_V	42_L	0.730	0.96
62_Y	78_A	0.729	0.96
173_D	176_A	0.729	0.96
259_L	263_G	0.727	0.96
137_I	140_A	0.718	0.95
41_E	261_R	0.717	0.95
212_M	225_T	0.716	0.95
77_V	227_N	0.713	0.95
9_D	12_T	0.711	0.95
197_F	228_A	0.710	0.95
206_N	258_A	0.708	0.95
69_V	161_H	0.707	0.95
21_A	62_Y	0.706	0.95
6_Y	86_V	0.699	0.94
62_Y	96_Q	0.691	0.94
188_S	216_A	0.690	0.94
138_I	144_T	0.690	0.94
80_H	94_I	0.689	0.94
134_R	138_I	0.689	0.94
21_A	75_A	0.687	0.94
46_E	69_V	0.685	0.94
181_L	184_L	0.680	0.94
56_S	97_T	0.679	0.94
7_H	20_S	0.676	0.93
168_L	177_L	0.674	0.93
201_I	208_T	0.670	0.93
181_L	215_P	0.669	0.93
16_F	261_R	0.665	0.93
179_P	184_L	0.665	0.93
136_A	186_A	0.665	0.93
184_L	196_F	0.664	0.93
140_A	187_I	0.663	0.93
19_N	225_T	0.662	0.93
212_M	232_M	0.660	0.93
167_P	201_I	0.660	0.93
125_F	157_A	0.659	0.93
86_V	290_H	0.658	0.93
123_P	160_G	0.658	0.93
28_D	51_L	0.656	0.92
129_L	132_E	0.653	0.92
200_Q	209_D	0.650	0.92
4_Q	22_G	0.649	0.92
161_H	231_P	0.648	0.92
202_R	206_N	0.646	0.92
35_M	51_L	0.646	0.92
32_E	61_R	0.645	0.92
62_Y	69_V	0.645	0.92
197_F	232_M	0.644	0.92
75_A	78_A	0.643	0.92
6_Y	287_I	0.637	0.91
194_N	198_P	0.632	0.91
46_E	65_P	0.628	0.91
13_S	17_R	0.626	0.91
108_E	268_T	0.621	0.90
171_E	174_I	0.621	0.90
4_Q	291_A	0.621	0.90
17_R	37_L	0.620	0.90
4_Q	86_V	0.619	0.90
287_I	290_H	0.617	0.90
155_Q	239_H	0.616	0.90
19_N	226_G	0.613	0.90
232_M	236_L	0.613	0.90
199_F	236_L	0.610	0.89
165_M	197_F	0.610	0.89
5_V	288_L	0.610	0.89
113_D	284_T	0.606	0.89
70_P	161_H	0.604	0.89
24_V	47_T	0.603	0.89
269_V	277_E	0.602	0.89
141_L	198_P	0.602	0.89
208_T	258_A	0.601	0.89
224_V	229_N	0.601	0.89
90_G	93_T	0.600	0.89
129_L	133_T	0.598	0.88
146_D	169_K	0.597	0.88
20_S	45_S	0.597	0.88
141_L	196_F	0.596	0.88
64_T	219_I	0.596	0.88
237_V	251_V	0.592	0.88
21_A	285_A	0.590	0.88
21_A	60_I	0.589	0.88
143_L	173_D	0.588	0.88
40_R	66_T	0.588	0.88
43_G	261_R	0.588	0.88
126_E	155_Q	0.586	0.87
212_M	231_P	0.586	0.87
10_A	75_A	0.579	0.87
26_P	30_L	0.578	0.87
197_F	210_G	0.578	0.87
120_Q	159_T	0.578	0.87
31_S	35_M	0.575	0.86
40_R	260_G	0.573	0.86
200_Q	203_P	0.572	0.86
104_R	107_I	0.572	0.86
81_Y	116_I	0.572	0.86
25_F	29_N	0.571	0.86
66_T	218_G	0.570	0.86
162_S	231_P	0.568	0.86
74_H	226_G	0.566	0.86
207_E	254_H	0.566	0.86
158_T	161_H	0.562	0.85
251_V	267_V	0.562	0.85
134_R	145_E	0.561	0.85
233_G	281_I	0.561	0.85
122_T	279_V	0.559	0.85
157_A	165_M	0.558	0.85
66_T	219_I	0.556	0.85
98_S	101_G	0.554	0.84
118_L	230_G	0.553	0.84
206_N	264_M	0.551	0.84
185_T	216_A	0.551	0.84
27_A	51_L	0.550	0.84
83_R	94_I	0.548	0.84
163_K	228_A	0.543	0.83
194_N	227_N	0.541	0.83
202_R	209_D	0.540	0.83
123_P	230_G	0.540	0.83
199_F	202_R	0.540	0.83
141_L	177_L	0.539	0.83
42_L	288_L	0.539	0.83
4_Q	26_P	0.538	0.83
24_V	38_I	0.537	0.83
166_I	196_F	0.532	0.82
185_T	220_V	0.530	0.82
155_Q	159_T	0.530	0.82
123_P	231_P	0.529	0.82
157_A	160_G	0.529	0.82
15_P	286_V	0.528	0.82
82_V	85_K	0.525	0.81
161_H	227_N	0.524	0.81
9_D	14_Q	0.523	0.81
75_A	222_D	0.522	0.81
157_A	231_P	0.522	0.81
22_G	72_C	0.522	0.81
32_E	99_L	0.522	0.81
64_T	69_V	0.521	0.81
167_P	174_I	0.518	0.80
223_P	263_G	0.518	0.80
171_E	254_H	0.518	0.80
154_I	164_V	0.517	0.80
267_V	281_I	0.517	0.80
72_C	225_T	0.516	0.80
48_A	72_C	0.510	0.79
8_V	81_Y	0.509	0.79
100_A	103_H	0.508	0.79
10_A	72_C	0.508	0.79
45_S	65_P	0.507	0.79
62_Y	71_I	0.507	0.79
10_A	224_V	0.506	0.79
202_R	207_E	0.504	0.78
80_H	105_V	0.503	0.78
52_H	58_V	0.502	0.78
54_D	97_T	0.502	0.78
72_C	76_T	0.501	0.78
258_A	262_D	0.500	0.78

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
1qyaA	2	0.9933	100	0.245	Contact Map
1ym5A	2	0.9529	100	0.252	Contact Map
3ednA	2	0.9832	100	0.263	Contact Map
1xubA	2	0.9293	100	0.273	Contact Map
1s7jA	1	0.8754	100	0.29	Contact Map
1u0kA	2	0.9428	100	0.292	Contact Map
4dunA	2	0.8687	100	0.311	Contact Map
4jbdA	2	0.8754	100	0.399	Contact Map
3ejxA	5	0.9091	100	0.423	Contact Map
4juuA	2	0.9024	100	0.428	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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