YAFV - ECOLI - GREMLIN Contacts

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YAFV - Hydrolase YafV

UniProt:	Q47679	Sequences: MPGLKITLLQQPLVWMDGPANLRHFDRQLEGITGRDVIVLPEMFTSGFAMEAAASSLAQDDVVNWMTAKAQQCNALIAGSVALQTESGSVNRFLLVEPGGTVHFYDKRHLFRMADEHLHYKAGNARVIVEWRGWRILPLVCYDLRFPVWSRNLNDYDLALYVANWPAPRSLHWQALLTARAIENQAYVAGCNRVGSDGNGCHYRGDSRVINPQGEIIATADAHQATRIDAELSMAALREYREKFPAWQDADEFRLW	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
EcoGene:	EG13334
Length:	256 (240)
Sequences:	13809 (9555)
Seq/√Len:	616.8

ECOLI - YAFV YBEM YOBB
BACSU - MTNU YHCX
HALSA - Q9HQZ3
SULSO - Q97WN8 Q97ZZ7 Q981B6

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
130_E	135_R	3.110	1.00
5_K	231_E	3.101	1.00
17_D	20_A	2.692	1.00
180_R	183_E	2.497	1.00
209_V	230_A	2.370	1.00
25_F	44_F	2.363	1.00
81_V	94_L	2.332	1.00
211_N	215_E	2.305	1.00
83_L	106_D	2.300	1.00
7_T	35_R	2.185	1.00
174_Q	219_T	2.161	1.00
139_L	150_S	2.155	1.00
92_R	106_D	2.143	1.00
7_T	229_D	2.140	1.00
26_D	65_W	2.002	1.00
157_D	238_R	1.971	1.00
33_T	229_D	1.964	1.00
220_A	228_I	1.936	1.00
8_L	191_C	1.900	1.00
175_A	178_T	1.897	1.00
30_E	72_Q	1.889	1.00
26_D	69_K	1.886	1.00
88_G	121_K	1.866	1.00
39_V	160_L	1.865	1.00
26_D	30_E	1.855	1.00
38_I	75_A	1.850	1.00
36_D	132_R	1.841	1.00
30_E	73_C	1.836	1.00
8_L	189_A	1.797	1.00
90_V	106_D	1.767	1.00
6_I	189_A	1.746	1.00
93_F	138_P	1.720	1.00
159_A	186_A	1.702	1.00
24_H	27_R	1.668	1.00
187_Y	212_P	1.665	1.00
68_A	72_Q	1.645	1.00
97_E	102_V	1.635	1.00
76_L	80_S	1.630	1.00
9_L	38_I	1.607	1.00
97_E	101_T	1.588	1.00
218_A	228_I	1.585	1.00
131_W	134_W	1.559	1.00
67_T	96_V	1.552	1.00
135_R	157_D	1.548	1.00
35_R	229_D	1.547	1.00
136_I	158_L	1.533	1.00
39_V	191_C	1.526	1.00
210_I	216_I	1.517	1.00
95_L	138_P	1.511	1.00
115_D	118_L	1.510	1.00
92_R	104_F	1.506	1.00
137_L	153_L	1.501	1.00
236_A	239_E	1.491	1.00
25_F	40_L	1.466	1.00
59_Q	63_V	1.463	1.00
29_L	38_I	1.454	1.00
28_Q	31_G	1.443	1.00
27_R	31_G	1.438	1.00
139_L	161_Y	1.414	1.00
189_A	209_V	1.410	1.00
177_L	190_G	1.408	1.00
76_L	95_L	1.407	1.00
98_P	132_R	1.402	1.00
187_Y	217_I	1.373	1.00
23_R	27_R	1.373	1.00
76_L	98_P	1.372	1.00
83_L	92_R	1.367	1.00
29_L	69_K	1.358	1.00
63_V	94_L	1.348	1.00
20_A	23_R	1.339	1.00
22_L	65_W	1.339	1.00
112_R	117_H	1.332	1.00
29_L	77_I	1.321	1.00
69_K	73_C	1.318	1.00
26_D	72_Q	1.317	1.00
24_H	225_A	1.310	1.00
148_V	151_R	1.309	1.00
37_V	160_L	1.299	1.00
9_L	40_L	1.298	1.00
174_Q	178_T	1.293	1.00
103_H	127_V	1.292	1.00
136_I	160_L	1.282	1.00
211_N	217_I	1.280	1.00
239_E	243_K	1.275	1.00
85_T	90_V	1.270	1.00
93_F	162_V	1.267	1.00
70_A	77_I	1.265	1.00
196_S	202_H	1.263	1.00
76_L	131_W	1.242	1.00
14_V	20_A	1.237	1.00
9_L	227_R	1.237	1.00
139_L	149_W	1.235	1.00
30_E	69_K	1.228	1.00
81_V	104_F	1.224	1.00
32_I	227_R	1.220	1.00
206_D	219_T	1.217	1.00
78_A	93_F	1.214	1.00
55_S	58_A	1.213	1.00
65_W	68_A	1.209	1.00
78_A	160_L	1.204	1.00
66_M	79_G	1.202	1.00
78_A	95_L	1.202	1.00
64_N	67_T	1.197	1.00
74_N	98_P	1.189	1.00
221_D	224_Q	1.186	1.00
29_L	75_A	1.183	1.00
20_A	24_H	1.179	1.00
19_P	23_R	1.169	1.00
45_T	62_V	1.157	1.00
211_N	236_A	1.154	1.00
193_R	197_D	1.149	1.00
150_S	161_Y	1.147	1.00
24_H	28_Q	1.146	1.00
150_S	159_A	1.131	1.00
56_S	60_D	1.120	1.00
9_L	28_Q	1.114	1.00
158_L	189_A	1.113	1.00
175_A	182_I	1.113	1.00
11_Q	28_Q	1.108	1.00
78_A	138_P	1.104	1.00
94_L	104_F	1.104	1.00
26_D	68_A	1.103	1.00
90_V	121_K	1.091	1.00
177_L	210_I	1.084	1.00
22_L	26_D	1.084	1.00
105_Y	127_V	1.077	1.00
55_S	60_D	1.066	1.00
28_Q	227_R	1.053	1.00
35_R	38_I	1.050	1.00
142_Y	146_F	1.050	1.00
56_S	62_V	1.047	1.00
128_I	135_R	1.027	1.00
174_Q	208_R	1.026	1.00
14_V	17_D	1.024	1.00
83_L	104_F	1.020	1.00
19_P	61_D	1.019	1.00
63_V	96_V	1.019	1.00
76_L	79_G	1.014	1.00
170_S	206_D	1.009	1.00
156_Y	159_A	1.006	1.00
103_H	129_V	1.001	1.00
5_K	229_D	0.995	1.00
171_L	178_T	0.989	1.00
95_L	129_V	0.988	1.00
177_L	188_V	0.985	1.00
206_D	222_A	0.984	1.00
235_A	238_R	0.982	1.00
64_N	68_A	0.982	1.00
171_L	174_Q	0.978	1.00
181_A	188_V	0.976	1.00
238_R	242_E	0.970	1.00
55_S	59_Q	0.970	1.00
76_L	102_V	0.963	1.00
68_A	71_Q	0.954	1.00
10_Q	207_S	0.948	1.00
5_K	33_T	0.948	1.00
134_W	157_D	0.932	1.00
11_Q	25_F	0.931	1.00
70_A	100_G	0.928	1.00
23_R	65_W	0.926	1.00
65_W	69_K	0.916	1.00
69_K	72_Q	0.913	1.00
105_Y	143_D	0.911	1.00
56_S	59_Q	0.910	1.00
177_L	208_R	0.908	1.00
131_W	136_I	0.904	1.00
8_L	228_I	0.904	1.00
217_I	230_A	0.899	1.00
60_D	63_V	0.897	1.00
235_A	239_E	0.891	1.00
167_A	202_H	0.888	1.00
137_L	156_Y	0.886	1.00
128_I	156_Y	0.885	1.00
67_T	101_T	0.883	1.00
208_R	216_I	0.878	1.00
175_A	179_A	0.869	1.00
233_S	236_A	0.865	1.00
130_E	133_G	0.864	1.00
25_F	79_G	0.863	1.00
63_V	67_T	0.856	1.00
32_I	35_R	0.855	1.00
79_G	96_V	0.854	1.00
181_A	210_I	0.853	1.00
59_Q	64_N	0.853	1.00
173_W	190_G	0.847	1.00
187_Y	237_L	0.843	1.00
151_R	184_N	0.843	1.00
7_T	227_R	0.840	1.00
218_A	230_A	0.827	1.00
194_V	224_Q	0.826	1.00
8_L	209_V	0.823	1.00
33_T	227_R	0.812	1.00
18_G	22_L	0.811	1.00
43_M	120_Y	0.811	1.00
134_W	158_L	0.809	1.00
6_I	232_L	0.807	1.00
216_I	219_T	0.807	1.00
85_T	106_D	0.801	1.00
4_L	134_W	0.799	1.00
36_D	98_P	0.799	1.00
19_P	65_W	0.798	1.00
108_R	149_W	0.795	1.00
50_M	54_A	0.791	1.00
11_Q	44_F	0.784	1.00
7_T	32_I	0.782	1.00
144_L	161_Y	0.775	1.00
27_R	30_E	0.769	1.00
234_M	238_R	0.768	1.00
76_L	97_E	0.765	1.00
236_A	240_Y	0.762	1.00
220_A	225_A	0.755	1.00
23_R	26_D	0.751	1.00
134_W	234_M	0.750	1.00
70_A	73_C	0.748	1.00
126_R	149_W	0.742	1.00
157_D	234_M	0.741	1.00
213_Q	240_Y	0.740	1.00
84_Q	89_S	0.739	1.00
98_P	101_T	0.736	1.00
24_H	224_Q	0.734	1.00
179_A	183_E	0.731	1.00
40_L	44_F	0.731	1.00
12_P	194_V	0.730	1.00
32_I	38_I	0.730	1.00
107_K	141_C	0.729	1.00
149_W	153_L	0.726	1.00
8_L	207_S	0.725	1.00
109_H	143_D	0.725	1.00
180_R	184_N	0.723	1.00
7_T	38_I	0.722	1.00
29_L	73_C	0.721	1.00
58_A	63_V	0.717	1.00
187_Y	236_A	0.714	1.00
4_L	133_G	0.710	1.00
29_L	40_L	0.710	1.00
11_Q	24_H	0.708	1.00
43_M	48_F	0.708	1.00
46_S	62_V	0.705	1.00
161_Y	188_V	0.704	1.00
172_H	176_L	0.704	1.00
208_R	219_T	0.693	1.00
171_L	175_A	0.693	1.00
25_F	66_M	0.689	1.00
32_I	75_A	0.688	1.00
4_L	232_L	0.687	1.00
77_I	80_S	0.685	1.00
91_N	107_K	0.685	1.00
36_D	133_G	0.684	1.00
76_L	132_R	0.680	1.00
10_Q	205_G	0.678	1.00
144_L	177_L	0.676	1.00
237_L	241_R	0.675	1.00
179_A	182_I	0.671	1.00
187_Y	232_L	0.671	1.00
97_E	132_R	0.671	1.00
60_D	64_N	0.669	1.00
109_H	146_F	0.667	1.00
66_M	77_I	0.665	1.00
173_W	177_L	0.662	1.00
25_F	29_L	0.661	1.00
37_V	78_A	0.661	1.00
108_R	126_R	0.661	1.00
139_L	153_L	0.657	1.00
17_D	21_N	0.653	1.00
50_M	53_A	0.653	1.00
61_D	64_N	0.649	1.00
95_L	136_I	0.647	1.00
57_L	84_Q	0.647	1.00
215_E	236_A	0.646	1.00
164_N	193_R	0.645	1.00
43_M	82_A	0.643	1.00
81_V	84_Q	0.642	1.00
67_T	71_Q	0.640	1.00
148_V	152_N	0.636	1.00
62_V	81_V	0.632	1.00
126_R	152_N	0.631	1.00
129_V	136_I	0.626	1.00
31_G	227_R	0.624	1.00
82_A	120_Y	0.624	1.00
35_R	75_A	0.622	1.00
61_D	65_W	0.621	1.00
97_E	103_H	0.620	1.00
159_A	188_V	0.618	1.00
151_R	247_W	0.615	1.00
85_T	88_G	0.606	1.00
111_F	142_Y	0.605	1.00
167_A	170_S	0.602	1.00
97_E	100_G	0.598	1.00
176_L	179_A	0.597	1.00
165_W	169_R	0.595	1.00
194_V	223_H	0.588	1.00
26_D	73_C	0.588	1.00
44_F	79_G	0.587	1.00
19_P	22_L	0.586	1.00
126_R	129_V	0.582	1.00
12_P	24_H	0.582	1.00
147_P	151_R	0.579	1.00
135_R	154_N	0.575	1.00
170_S	204_R	0.572	1.00
14_V	21_N	0.571	1.00
83_L	94_L	0.570	1.00
173_W	176_L	0.570	1.00
46_S	82_A	0.570	1.00
178_T	216_I	0.570	1.00
166_P	169_R	0.569	1.00
4_L	37_V	0.568	1.00
174_Q	206_D	0.567	1.00
18_G	62_V	0.566	1.00
62_V	65_W	0.561	1.00
14_V	24_H	0.560	1.00
91_N	141_C	0.559	1.00
51_E	54_A	0.559	1.00
22_L	69_K	0.556	1.00
45_T	66_M	0.554	1.00
164_N	203_Y	0.552	1.00
174_Q	216_I	0.551	1.00
137_L	159_A	0.550	1.00
28_Q	32_I	0.547	0.99
37_V	133_G	0.545	0.99
12_P	225_A	0.545	0.99
111_F	145_R	0.545	0.99
83_L	90_V	0.543	0.99
8_L	218_A	0.543	0.99
91_N	140_V	0.542	0.99
48_F	141_C	0.540	0.99
49_A	52_A	0.539	0.99
167_A	204_R	0.539	0.99
12_P	193_R	0.539	0.99
79_G	94_L	0.538	0.99
37_V	95_L	0.537	0.99
169_R	172_H	0.537	0.99
174_Q	210_I	0.536	0.99
193_R	203_Y	0.535	0.99
22_L	66_M	0.533	0.99
103_H	138_P	0.533	0.99
116_E	120_Y	0.532	0.99
244_F	247_W	0.532	0.99
116_E	119_H	0.530	0.99
196_S	200_G	0.530	0.99
234_M	237_L	0.526	0.99
42_E	141_C	0.525	0.99
25_F	69_K	0.519	0.99
126_R	153_L	0.518	0.99
192_N	207_S	0.518	0.99
76_L	133_G	0.518	0.99
145_R	176_L	0.518	0.99
18_G	56_S	0.514	0.99
93_F	140_V	0.512	0.99
22_L	45_T	0.512	0.99
49_A	53_A	0.511	0.99
178_T	210_I	0.511	0.99
43_M	46_S	0.508	0.99
127_V	154_N	0.508	0.99
111_F	141_C	0.508	0.99
145_R	165_W	0.507	0.99
105_Y	123_G	0.506	0.99
111_F	165_W	0.505	0.99
48_F	120_Y	0.505	0.99
70_A	101_T	0.502	0.99
153_L	156_Y	0.500	0.99

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
2e11A	2	0.9961	100	0.158	Contact Map
4izuA	2	0.9375	100	0.181	Contact Map
2vhhA	5	0.9961	100	0.193	Contact Map
3p8kA	2	0.9883	100	0.195	Contact Map
2w1vA	2	0.9883	100	0.196	Contact Map
3ivzA	2	0.9609	100	0.203	Contact Map
3wuyA	2	0.9492	100	0.211	Contact Map
1uf5A	4	0.9922	100	0.215	Contact Map
1emsA	3	0.9883	100	0.219	Contact Map
2dyuA	5	0.9766	100	0.224	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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