PUUD - ECOLI - GREMLIN Contacts

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PUUD - Gamma-glutamyl-gamma-aminobutyrate hydrolase PuuD

UniProt:	P76038	Sequences: MENIMNNPVIGVVMCRNRLKGHATQTLQEKYLNAIIHAGGLPIALPHALAEPSLLEQLLPKLDGIYLPGSPSNVQPHLYGENGDEPDADPGRDLLSMAIINAALERRIPIFAICRGLQELVVATGGSLHRKLCEQPELLEHREDPELPVEQQYAPSHEVQVEEGGLLSALLPECSNFWVNSLHGQGAKVVSPRLRVEARSPDGLVEAVSVINHPFALGVQWHPEWNSSEYALSRILFEGFITACQHHIAEKQRL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13909
Length:	254 (222)
Sequences:	5995 (3990)
Seq/√Len:	267.8

ECOLI - PUUD PYRG
BACSU - PYRG
HALSA - PYRG
SULSO - PYRG

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
11_G	62_L	3.362	1.00
170_L	239_G	3.013	1.00
107_R	214_P	2.931	1.00
101_N	105_E	2.863	1.00
167_L	207_A	2.746	1.00
9_V	43_I	2.667	1.00
9_V	41_L	2.634	1.00
7_N	41_L	2.465	1.00
43_I	62_L	2.462	1.00
163_E	168_S	2.299	1.00
168_S	175_S	2.258	1.00
100_I	110_I	2.249	1.00
195_R	211_I	2.219	1.00
196_V	199_R	2.131	1.00
120_L	216_A	2.111	1.00
100_I	119_E	2.069	1.00
158_E	176_N	2.051	1.00
148_P	153_Y	2.043	1.00
98_A	101_N	1.999	1.00
148_P	151_Q	1.987	1.00
166_L	169_A	1.928	1.00
10_I	64_G	1.907	1.00
133_C	145_P	1.894	1.00
165_G	197_E	1.880	1.00
43_I	61_K	1.877	1.00
110_I	120_L	1.856	1.00
65_I	103_A	1.842	1.00
163_E	175_S	1.811	1.00
35_I	40_G	1.803	1.00
160_Q	176_N	1.765	1.00
215_F	239_G	1.761	1.00
156_S	178_W	1.760	1.00
158_E	178_W	1.705	1.00
194_L	208_V	1.657	1.00
38_A	245_Q	1.653	1.00
6_N	38_A	1.643	1.00
14_M	44_A	1.604	1.00
93_D	115_R	1.577	1.00
197_E	209_S	1.566	1.00
131_K	145_P	1.558	1.00
100_I	216_A	1.545	1.00
149_V	153_Y	1.543	1.00
7_N	39_G	1.524	1.00
67_L	100_I	1.510	1.00
207_A	221_W	1.506	1.00
143_E	146_E	1.505	1.00
124_T	194_L	1.501	1.00
151_Q	154_A	1.484	1.00
27_L	44_A	1.465	1.00
93_D	119_E	1.460	1.00
239_G	243_A	1.455	1.00
162_E	199_R	1.450	1.00
162_E	195_R	1.440	1.00
112_A	120_L	1.421	1.00
97_M	123_A	1.417	1.00
149_V	154_A	1.411	1.00
102_A	106_R	1.411	1.00
11_G	45_L	1.399	1.00
81_E	188_K	1.398	1.00
190_V	196_V	1.375	1.00
200_S	203_G	1.366	1.00
34_A	40_G	1.352	1.00
51_E	54_L	1.348	1.00
66_Y	113_I	1.346	1.00
30_K	34_A	1.342	1.00
100_I	123_A	1.342	1.00
167_L	197_E	1.341	1.00
60_P	106_R	1.336	1.00
124_T	128_L	1.320	1.00
64_G	244_C	1.319	1.00
148_P	154_A	1.313	1.00
198_A	207_A	1.312	1.00
129_H	188_K	1.312	1.00
62_L	65_I	1.307	1.00
166_L	217_L	1.300	1.00
164_G	168_S	1.287	1.00
210_V	213_H	1.285	1.00
57_Q	60_P	1.284	1.00
133_C	144_D	1.276	1.00
242_T	246_H	1.251	1.00
10_I	244_C	1.247	1.00
107_R	213_H	1.242	1.00
159_V	221_W	1.215	1.00
239_G	242_T	1.211	1.00
50_A	54_L	1.210	1.00
161_V	198_A	1.209	1.00
103_A	108_I	1.199	1.00
165_G	195_R	1.196	1.00
29_E	33_N	1.193	1.00
120_L	218_G	1.190	1.00
67_L	110_I	1.189	1.00
210_V	216_A	1.179	1.00
136_P	139_L	1.175	1.00
161_V	167_L	1.173	1.00
56_E	102_A	1.173	1.00
9_V	62_L	1.158	1.00
160_Q	175_S	1.157	1.00
186_G	204_L	1.130	1.00
119_E	122_V	1.130	1.00
31_Y	34_A	1.124	1.00
161_V	177_F	1.123	1.00
196_V	205_V	1.122	1.00
56_E	106_R	1.122	1.00
51_E	55_L	1.119	1.00
100_I	120_L	1.099	1.00
191_S	194_L	1.098	1.00
107_R	212_N	1.094	1.00
117_L	187_A	1.093	1.00
9_V	61_K	1.090	1.00
121_V	208_V	1.081	1.00
162_E	165_G	1.081	1.00
150_E	153_Y	1.079	1.00
121_V	147_L	1.075	1.00
238_E	242_T	1.071	1.00
121_V	187_A	1.067	1.00
117_L	208_V	1.066	1.00
165_G	209_S	1.065	1.00
104_L	124_T	1.062	1.00
65_I	108_I	1.047	1.00
162_E	190_V	1.045	1.00
140_E	143_E	1.040	1.00
121_V	191_S	1.034	1.00
6_N	245_Q	1.020	1.00
170_L	217_L	1.018	1.00
37_H	242_T	1.016	1.00
217_L	236_L	1.012	1.00
66_Y	240_F	1.009	1.00
102_A	105_E	1.008	1.00
55_L	98_A	1.004	1.00
124_T	210_V	1.004	1.00
148_P	152_Q	0.993	1.00
161_V	168_S	0.989	1.00
135_Q	140_E	0.986	1.00
111_F	240_F	0.985	1.00
52_P	98_A	0.984	1.00
240_F	244_C	0.983	1.00
31_Y	35_I	0.976	1.00
167_L	217_L	0.974	1.00
117_L	218_G	0.965	1.00
158_E	201_P	0.948	1.00
215_F	240_F	0.924	1.00
234_R	238_E	0.923	1.00
215_F	243_A	0.923	1.00
124_T	192_P	0.923	1.00
166_L	209_S	0.916	1.00
131_K	184_G	0.916	1.00
30_K	35_I	0.915	1.00
149_V	152_Q	0.914	1.00
226_N	234_R	0.908	1.00
121_V	194_L	0.904	1.00
115_R	139_L	0.891	1.00
92_R	96_S	0.890	1.00
40_G	241_I	0.878	1.00
199_R	203_G	0.869	1.00
200_S	204_L	0.861	1.00
18_R	46_P	0.855	1.00
137_E	146_E	0.853	1.00
127_S	188_K	0.848	1.00
150_E	154_A	0.847	1.00
65_I	99_I	0.847	1.00
197_E	207_A	0.844	1.00
59_L	103_A	0.842	1.00
93_D	139_L	0.834	0.99
64_G	240_F	0.829	0.99
121_V	126_G	0.826	0.99
242_T	245_Q	0.824	0.99
156_S	226_N	0.822	0.99
243_A	246_H	0.816	0.99
219_V	236_L	0.809	0.99
157_H	181_S	0.803	0.99
12_V	26_T	0.800	0.99
59_L	108_I	0.797	0.99
129_H	135_Q	0.793	0.99
159_V	198_A	0.791	0.99
13_V	68_P	0.791	0.99
110_I	216_A	0.782	0.99
33_N	36_I	0.781	0.99
101_N	127_S	0.774	0.99
160_Q	199_R	0.773	0.99
32_L	36_I	0.773	0.99
124_T	191_S	0.771	0.99
30_K	225_W	0.771	0.99
140_E	144_D	0.771	0.99
196_V	208_V	0.770	0.99
121_V	190_V	0.765	0.99
110_I	119_E	0.762	0.99
32_L	35_I	0.755	0.99
30_K	36_I	0.750	0.99
12_V	68_P	0.749	0.99
10_I	40_G	0.745	0.99
50_A	58_L	0.739	0.99
43_I	58_L	0.736	0.99
52_P	55_L	0.733	0.99
104_L	216_A	0.732	0.99
24_T	28_Q	0.731	0.99
170_L	215_F	0.728	0.99
187_A	208_V	0.727	0.99
159_V	179_V	0.723	0.99
131_K	134_E	0.719	0.98
160_Q	201_P	0.719	0.98
59_L	62_L	0.719	0.98
100_I	124_T	0.719	0.98
37_H	234_R	0.716	0.98
13_V	96_S	0.716	0.98
195_R	209_S	0.714	0.98
167_L	219_V	0.710	0.98
108_I	247_H	0.709	0.98
120_L	208_V	0.704	0.98
161_V	165_G	0.703	0.98
208_V	218_G	0.703	0.98
155_P	226_N	0.702	0.98
32_L	37_H	0.701	0.98
54_L	57_Q	0.701	0.98
187_A	205_V	0.700	0.98
81_E	130_R	0.699	0.98
20_K	44_A	0.697	0.98
207_A	219_V	0.695	0.98
168_S	172_P	0.692	0.98
29_E	91_G	0.691	0.98
103_A	110_I	0.681	0.98
79_Y	128_L	0.681	0.98
129_H	192_P	0.676	0.98
161_V	171_L	0.676	0.98
96_S	119_E	0.675	0.98
213_H	216_A	0.672	0.98
101_N	123_A	0.668	0.97
114_C	222_H	0.667	0.97
25_Q	29_E	0.665	0.97
111_F	219_V	0.665	0.97
65_I	110_I	0.665	0.97
45_L	62_L	0.646	0.97
104_L	210_V	0.646	0.97
104_L	123_A	0.645	0.97
35_I	66_Y	0.644	0.97
189_V	205_V	0.643	0.97
210_V	214_P	0.643	0.97
193_R	211_I	0.643	0.97
55_L	59_L	0.640	0.97
67_L	120_L	0.640	0.97
194_L	210_V	0.638	0.97
55_L	102_A	0.637	0.97
38_A	234_R	0.637	0.97
33_N	228_S	0.636	0.97
68_P	92_R	0.634	0.97
34_A	37_H	0.632	0.97
97_M	101_N	0.632	0.97
235_I	238_E	0.629	0.96
31_Y	36_I	0.628	0.96
121_V	127_S	0.628	0.96
99_I	102_A	0.625	0.96
66_Y	96_S	0.625	0.96
123_A	127_S	0.623	0.96
164_G	169_A	0.618	0.96
29_E	32_L	0.616	0.96
113_I	219_V	0.616	0.96
50_A	55_L	0.615	0.96
93_D	122_V	0.614	0.96
94_L	98_A	0.609	0.96
55_L	58_L	0.608	0.96
13_V	99_I	0.607	0.96
94_L	97_M	0.605	0.96
133_C	140_E	0.602	0.95
135_Q	143_E	0.600	0.95
190_V	208_V	0.598	0.95
26_T	69_G	0.598	0.95
13_V	47_H	0.595	0.95
166_L	215_F	0.594	0.95
20_K	27_L	0.592	0.95
113_I	237_F	0.590	0.95
159_V	167_L	0.589	0.95
17_N	20_K	0.588	0.95
34_A	237_F	0.585	0.95
94_L	126_G	0.584	0.95
9_V	63_D	0.581	0.94
38_A	241_I	0.580	0.94
59_L	102_A	0.580	0.94
115_R	119_E	0.579	0.94
162_E	168_S	0.578	0.94
51_E	56_E	0.577	0.94
181_S	206_E	0.572	0.94
132_L	145_P	0.571	0.94
167_L	198_A	0.568	0.94
15_C	25_Q	0.566	0.94
180_N	226_N	0.565	0.94
34_A	227_S	0.564	0.94
182_L	225_W	0.562	0.93
69_G	222_H	0.562	0.93
12_V	27_L	0.561	0.93
111_F	217_L	0.560	0.93
31_Y	37_H	0.560	0.93
127_S	189_V	0.559	0.93
160_Q	203_G	0.559	0.93
228_S	232_L	0.558	0.93
166_L	170_L	0.556	0.93
132_L	144_D	0.556	0.93
12_V	32_L	0.555	0.93
63_D	247_H	0.551	0.93
244_C	247_H	0.545	0.92
157_H	200_S	0.544	0.92
30_K	33_N	0.540	0.92
159_V	177_F	0.539	0.92
189_V	192_P	0.536	0.92
174_C	232_L	0.535	0.92
56_E	60_P	0.534	0.92
171_L	177_F	0.531	0.91
69_G	114_C	0.530	0.91
81_E	93_D	0.529	0.91
102_A	108_I	0.528	0.91
33_N	37_H	0.528	0.91
21_G	26_T	0.525	0.91
50_A	98_A	0.524	0.91
190_V	205_V	0.524	0.91
59_L	106_R	0.522	0.91
11_G	43_I	0.521	0.91
132_L	204_L	0.521	0.91
14_M	25_Q	0.521	0.91
97_M	119_E	0.519	0.90
159_V	207_A	0.517	0.90
52_P	101_N	0.516	0.90
131_K	144_D	0.516	0.90
54_L	98_A	0.513	0.90
37_H	238_E	0.512	0.90
36_I	233_S	0.511	0.90
57_Q	61_K	0.508	0.90
227_S	233_S	0.505	0.89
23_A	29_E	0.504	0.89
34_A	241_I	0.502	0.89
164_G	195_R	0.502	0.89
161_V	175_S	0.501	0.89
8_P	244_C	0.501	0.89
170_L	235_I	0.501	0.89
20_K	46_P	0.500	0.89
95_L	182_L	0.500	0.89

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
3fijA	4	0.8661	100	0.38	Contact Map
4l8fC	3	0.9213	100	0.447	Contact Map
4zdjA	4	0.878	100	0.455	Contact Map
1l9xA	1	0.9055	100	0.458	Contact Map
1s1mA	4	0.8819	100	0.465	Contact Map
3nvaA	2	0.8701	100	0.478	Contact Map
1vcoA	4	0.8661	100	0.482	Contact Map
2v4uA	1	0.8858	100	0.501	Contact Map
2w7tA	1	0.8819	100	0.505	Contact Map
3uowA	2	0.8386	100	0.526	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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