YHDW - BACSU - GREMLIN Contacts

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YHDW - Putative glycerophosphoryl diester phosphodiesterase YhdW

UniProt:	O07592	Sequences: MYIIAHRGASGYAPENTIAAFDLAVKMNADMIELDVQLTKDRQIVVIHDDRVDRTTNGSGFVKDFTLEELQKLDAGSWYGPAFQGERIPTLEAVLKRYHKKIGLLIELKGHPSQVGIEEEVGQLLGQFSFSINNIVQSFQFRSVQRFRELYPSIPTAVITRPNFGMLSRNQMKAFRSFANYVNIKHTRLNRLMIGSINKNGLNIFAWTVNNQKTAAKLQAMGVDGIVTDYPDFIIKDGKHENI	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_01
Length:	243 (228)
Sequences:	9370 (6926)
Seq/√Len:	458.7

ECOLI - GLPQ UGPQ
BACSU - YHDW GLPQ YQIK
HALSA - Q9HP18

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
198_N	224_D	2.851	1.00
19_A	86_E	2.737	1.00
96_K	128_F	2.631	1.00
23_L	26_K	2.605	1.00
92_E	124_L	2.477	1.00
22_D	97_R	2.454	1.00
21_F	34_L	2.401	1.00
11_G	230_Y	2.394	1.00
66_T	69_E	2.391	1.00
105_L	137_Q	2.294	1.00
67_L	71_Q	2.268	1.00
215_A	234_I	2.253	1.00
67_L	90_T	2.221	1.00
71_Q	93_A	2.159	1.00
18_I	89_P	2.084	1.00
12_Y	232_D	2.020	1.00
47_I	62_V	2.005	1.00
38_L	120_E	1.916	1.00
210_N	229_D	1.902	1.00
43_Q	67_L	1.899	1.00
92_E	127_Q	1.868	1.00
34_L	94_V	1.864	1.00
52_V	73_L	1.849	1.00
39_T	45_V	1.821	1.00
4_I	31_M	1.810	1.00
92_E	128_F	1.810	1.00
17_T	75_A	1.804	1.00
230_Y	233_F	1.793	1.00
157_A	181_Y	1.780	1.00
40_K	66_T	1.777	1.00
22_D	26_K	1.760	1.00
56_T	75_A	1.739	1.00
34_L	46_V	1.736	1.00
120_E	123_Q	1.724	1.00
31_M	103_G	1.721	1.00
61_F	64_D	1.720	1.00
13_A	23_L	1.714	1.00
25_V	102_I	1.709	1.00
58_G	73_L	1.681	1.00
205_F	225_G	1.657	1.00
211_N	214_T	1.651	1.00
52_V	65_F	1.632	1.00
43_Q	90_T	1.615	1.00
45_V	67_L	1.604	1.00
46_V	94_V	1.599	1.00
47_I	55_T	1.595	1.00
90_T	93_A	1.579	1.00
186_H	214_T	1.525	1.00
10_S	20_A	1.521	1.00
91_L	106_I	1.508	1.00
206_A	223_V	1.506	1.00
119_E	150_L	1.491	1.00
15_E	54_R	1.487	1.00
23_L	27_M	1.485	1.00
7_R	15_E	1.469	1.00
126_G	151_Y	1.466	1.00
39_T	43_Q	1.448	1.00
60_G	65_F	1.442	1.00
214_T	217_K	1.442	1.00
184_I	206_A	1.430	1.00
45_V	62_V	1.428	1.00
21_F	94_V	1.428	1.00
136_V	147_F	1.426	1.00
5_A	20_A	1.422	1.00
118_E	143_S	1.409	1.00
122_G	151_Y	1.404	1.00
146_R	150_L	1.383	1.00
53_D	59_S	1.375	1.00
137_Q	227_V	1.357	1.00
124_L	128_F	1.355	1.00
217_K	221_M	1.326	1.00
123_Q	127_Q	1.318	1.00
38_L	44_I	1.314	1.00
43_Q	92_E	1.310	1.00
92_E	96_K	1.291	1.00
18_I	97_R	1.287	1.00
42_R	120_E	1.281	1.00
65_F	69_E	1.271	1.00
119_E	123_Q	1.255	1.00
36_V	44_I	1.250	1.00
148_R	156_T	1.239	1.00
49_D	54_R	1.238	1.00
146_R	149_E	1.234	1.00
136_V	154_I	1.232	1.00
9_A	12_Y	1.228	1.00
216_A	220_A	1.227	1.00
70_L	88_I	1.215	1.00
39_T	70_L	1.214	1.00
148_R	180_N	1.200	1.00
9_A	23_L	1.179	1.00
122_G	147_F	1.177	1.00
125_L	136_V	1.172	1.00
65_F	70_L	1.168	1.00
58_G	65_F	1.166	1.00
118_E	146_R	1.154	1.00
39_T	67_L	1.149	1.00
191_R	195_G	1.143	1.00
197_I	204_I	1.136	1.00
194_I	204_I	1.129	1.00
203_N	224_D	1.127	1.00
137_Q	183_N	1.125	1.00
95_L	104_L	1.123	1.00
4_I	225_G	1.115	1.00
108_L	121_V	1.110	1.00
53_D	60_G	1.107	1.00
33_E	48_H	1.102	1.00
9_A	27_M	1.101	1.00
47_I	88_I	1.096	1.00
44_I	121_V	1.092	1.00
195_G	199_K	1.085	1.00
19_A	23_L	1.085	1.00
212_Q	216_A	1.081	1.00
69_E	72_K	1.076	1.00
95_L	125_L	1.075	1.00
25_V	97_R	1.074	1.00
74_D	85_G	1.072	1.00
18_I	22_D	1.057	1.00
21_F	32_I	1.053	1.00
124_L	127_Q	1.052	1.00
37_Q	50_D	1.046	1.00
209_V	215_A	1.039	1.00
105_L	205_F	1.014	1.00
5_A	10_S	1.013	1.00
4_I	105_L	1.009	1.00
144_V	156_T	0.994	1.00
71_Q	87_R	0.989	1.00
74_D	87_R	0.986	1.00
95_L	128_F	0.981	1.00
194_I	198_N	0.979	1.00
5_A	29_A	0.979	1.00
56_T	60_G	0.977	1.00
98_Y	104_L	0.975	1.00
51_R	61_F	0.972	1.00
52_V	58_G	0.971	1.00
131_S	151_Y	0.971	1.00
207_W	227_V	0.971	1.00
197_I	202_L	0.964	1.00
16_N	21_F	0.962	1.00
193_M	197_I	0.958	1.00
10_S	229_D	0.950	1.00
130_F	134_N	0.949	1.00
137_Q	157_A	0.947	1.00
44_I	120_E	0.947	1.00
105_L	227_V	0.945	1.00
36_V	106_I	0.944	1.00
130_F	133_N	0.940	1.00
9_A	232_D	0.939	1.00
36_V	91_L	0.937	1.00
44_I	124_L	0.934	1.00
21_F	46_V	0.928	1.00
108_L	143_S	0.926	1.00
12_Y	27_M	0.921	1.00
122_G	126_G	0.918	1.00
91_L	95_L	0.914	1.00
51_R	54_R	0.913	1.00
40_K	64_D	0.907	1.00
36_V	121_V	0.900	1.00
5_A	9_A	0.897	1.00
107_E	139_F	0.892	1.00
126_G	131_S	0.889	1.00
151_Y	154_I	0.889	1.00
119_E	146_R	0.886	1.00
183_N	205_F	0.884	1.00
65_F	73_L	0.884	1.00
16_N	89_P	0.879	1.00
53_D	57_N	0.878	1.00
3_I	235_I	0.868	1.00
215_A	226_I	0.865	1.00
181_Y	203_N	0.862	1.00
34_L	104_L	0.862	1.00
89_P	94_V	0.861	1.00
57_N	60_G	0.859	1.00
196_S	200_N	0.858	1.00
105_L	135_I	0.857	1.00
228_T	234_I	0.853	1.00
13_A	19_A	0.851	1.00
22_D	98_Y	0.848	1.00
6_H	48_H	0.841	1.00
196_S	199_K	0.834	1.00
71_Q	90_T	0.832	1.00
195_G	198_N	0.830	1.00
45_V	70_L	0.820	1.00
8_G	21_F	0.816	1.00
209_V	218_L	0.813	1.00
137_Q	159_I	0.807	1.00
139_F	159_I	0.804	1.00
120_E	124_L	0.802	1.00
198_N	204_I	0.801	1.00
212_Q	236_K	0.798	1.00
181_Y	205_F	0.791	1.00
35_D	48_H	0.791	1.00
9_A	231_P	0.790	1.00
74_D	78_W	0.787	1.00
194_I	221_M	0.777	1.00
122_G	150_L	0.774	1.00
206_A	218_L	0.768	1.00
140_Q	143_S	0.767	1.00
107_E	138_S	0.767	1.00
29_A	231_P	0.766	1.00
57_N	61_F	0.762	1.00
38_L	42_R	0.751	1.00
219_Q	234_I	0.751	1.00
172_M	175_F	0.747	1.00
44_I	117_I	0.744	1.00
141_F	158_V	0.741	1.00
37_Q	63_K	0.738	1.00
210_N	228_T	0.737	1.00
70_L	73_L	0.735	1.00
215_A	233_F	0.734	1.00
38_L	117_I	0.728	1.00
76_G	79_Y	0.727	1.00
68_E	72_K	0.726	1.00
105_L	183_N	0.724	1.00
121_V	125_L	0.723	1.00
12_Y	23_L	0.722	1.00
43_Q	120_E	0.714	1.00
141_F	145_Q	0.708	1.00
155_P	180_N	0.707	1.00
212_Q	233_F	0.707	1.00
4_I	227_V	0.703	1.00
126_G	153_S	0.703	1.00
52_V	60_G	0.702	1.00
94_V	104_L	0.698	1.00
118_E	122_G	0.697	1.00
3_I	234_I	0.697	1.00
56_T	73_L	0.689	1.00
99_H	130_F	0.689	1.00
52_V	70_L	0.686	1.00
51_R	59_S	0.683	1.00
12_Y	230_Y	0.682	1.00
157_A	205_F	0.680	1.00
214_T	218_L	0.677	1.00
74_D	77_S	0.677	1.00
6_H	33_E	0.677	1.00
94_V	98_Y	0.676	1.00
47_I	56_T	0.675	1.00
131_S	134_N	0.670	1.00
93_A	96_K	0.666	1.00
157_A	183_N	0.662	1.00
37_Q	62_V	0.661	1.00
25_V	101_K	0.660	1.00
9_A	13_A	0.659	1.00
125_L	134_N	0.659	1.00
180_N	183_N	0.659	1.00
100_K	133_N	0.658	1.00
155_P	203_N	0.656	1.00
24_A	29_A	0.656	1.00
213_K	216_A	0.655	1.00
189_L	206_A	0.645	1.00
171_Q	174_A	0.637	0.99
125_L	131_S	0.636	0.99
75_A	89_P	0.636	0.99
218_L	221_M	0.634	0.99
185_K	188_R	0.633	0.99
161_R	185_K	0.632	0.99
147_F	156_T	0.632	0.99
95_L	124_L	0.629	0.99
191_R	221_M	0.628	0.99
45_V	90_T	0.625	0.99
34_L	106_I	0.618	0.99
3_I	29_A	0.617	0.99
32_I	102_I	0.614	0.99
27_M	235_I	0.613	0.99
27_M	232_D	0.613	0.99
145_Q	149_E	0.612	0.99
139_F	207_W	0.610	0.99
40_K	69_E	0.609	0.99
32_I	98_Y	0.609	0.99
107_E	159_I	0.608	0.99
206_A	209_V	0.608	0.99
121_V	136_V	0.604	0.99
108_L	117_I	0.604	0.99
226_I	234_I	0.595	0.99
9_A	29_A	0.594	0.99
4_I	205_F	0.593	0.99
19_A	22_D	0.589	0.99
147_F	154_I	0.587	0.99
109_K	139_F	0.587	0.99
162_P	188_R	0.584	0.99
27_M	231_P	0.583	0.99
33_E	49_D	0.580	0.99
181_Y	184_I	0.580	0.99
17_T	20_A	0.578	0.99
37_Q	110_G	0.577	0.99
145_Q	176_R	0.577	0.99
135_I	181_Y	0.576	0.99
211_N	215_A	0.576	0.99
215_A	219_Q	0.575	0.99
142_R	145_Q	0.573	0.99
160_T	182_V	0.572	0.99
53_D	58_G	0.572	0.99
173_K	200_N	0.570	0.99
193_M	196_S	0.569	0.99
138_S	144_V	0.569	0.99
205_F	227_V	0.568	0.99
118_E	121_V	0.567	0.99
68_E	71_Q	0.564	0.99
103_G	155_P	0.564	0.99
55_T	75_A	0.563	0.99
91_L	124_L	0.559	0.99
168_S	171_Q	0.557	0.99
61_F	65_F	0.556	0.99
91_L	121_V	0.555	0.99
53_D	56_T	0.551	0.99
10_S	231_P	0.548	0.98
31_M	105_L	0.547	0.98
40_K	65_F	0.544	0.98
18_I	21_F	0.543	0.98
217_K	220_A	0.543	0.98
74_D	79_Y	0.541	0.98
169_R	172_M	0.539	0.98
56_T	59_S	0.539	0.98
144_V	148_R	0.538	0.98
33_E	109_K	0.538	0.98
14_P	55_T	0.538	0.98
169_R	196_S	0.537	0.98
3_I	231_P	0.534	0.98
99_H	133_N	0.534	0.98
31_M	135_I	0.532	0.98
31_M	137_Q	0.528	0.98
51_R	55_T	0.527	0.98
208_T	228_T	0.526	0.98
25_V	32_I	0.526	0.98
28_N	235_I	0.525	0.98
24_A	32_I	0.522	0.98
47_I	89_P	0.522	0.98
55_T	58_G	0.517	0.98
182_V	197_I	0.517	0.98
39_T	62_V	0.515	0.98
21_F	97_R	0.515	0.98
22_D	86_E	0.515	0.98
103_G	133_N	0.510	0.98
48_H	109_K	0.508	0.98
31_M	102_I	0.507	0.97
20_A	24_A	0.506	0.97
107_E	137_Q	0.503	0.97
33_E	107_E	0.503	0.97
233_F	236_K	0.503	0.97
125_L	130_F	0.502	0.97
29_A	102_I	0.502	0.97
170_N	173_K	0.500	0.97
189_L	221_M	0.500	0.97

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
4r7oA	4	0.9877	100	0.074	Contact Map
2pz0A	2	0.9835	100	0.092	Contact Map
2oogA	4	0.9877	100	0.103	Contact Map
2otdA	1	0.9712	100	0.111	Contact Map
1zccA	5	0.963	100	0.114	Contact Map
3l12A	2	0.9753	100	0.119	Contact Map
3qvqA	4	0.9835	100	0.12	Contact Map
3ks6A	1	0.9794	100	0.122	Contact Map
2o55A	1	0.9547	100	0.123	Contact Map
3ch0A	1	0.9671	100	0.124	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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