PHA_synth_III_E - PFAM28P - GREMLIN Contacts

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PHA_synth_III_E - Poly(R)-hydroxyalkanoic acid synthase subunit (PHA_synth_III_E)

PFAM:	PF09712	Sequences: DWLELQRQYWDAWSDMMRQAMGAAPAANPWQEALQWWSALAPGSAPPAAKDAFERMLDQAKSYFKLMEQFAAAFAGKDASAAAAKDAWEQLQKWLEQLPQAFAGMFQGAAEQLYAEALQKFMGPWQSPLDNWQQMASSLSPAMPGDFLKLLELFNLWWDAQYEEEFGKLLKMPALGYTREHQERLQKLADAWLDYQQALAEYQALLYKAGQKAFERFQEKLAERAEKGEQIESLRELYDLWVDAAEEAYAELFLSEEFSKLYGELVNAQMRLRKAQQELVEDVLEALPMPTRSEMDELYKRIYELRREVRALK	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	313 (309)
Sequences:	1066 (895)
Seq/√Len:	50.9
META:	0.863

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
298_L	302_I	5.373	1.00
281_E	293_S	5.276	1.00
303_Y	307_R	5.085	1.00
305_L	309_V	4.982	1.00
231_I	237_L	3.250	1.00
260_K	264_E	3.175	1.00
68_E	72_A	3.132	1.00
176_G	179_R	2.894	1.00
309_V	312_L	2.853	1.00
302_I	305_L	2.683	1.00
132_W	136_A	2.581	1.00
50_K	54_E	2.544	1.00
35_Q	39_A	2.507	1.00
146_D	149_K	2.469	1.00
220_K	247_E	2.433	1.00
96_E	100_Q	2.429	1.00
97_Q	100_Q	2.406	1.00
4_E	8_Q	2.300	1.00
116_E	119_Q	2.246	1.00
11_D	15_D	2.106	1.00
116_E	120_K	2.099	1.00
232_E	236_E	2.063	1.00
92_Q	96_E	2.039	1.00
93_K	97_Q	1.985	1.00
219_E	223_E	1.966	1.00
26_A	29_P	1.844	0.99
4_E	7_R	1.819	0.99
99_P	102_F	1.777	0.99
295_M	298_L	1.757	0.99
36_W	41_A	1.752	0.99
94_W	98_L	1.741	0.99
176_G	180_E	1.738	0.99
96_E	99_P	1.729	0.99
263_G	267_N	1.728	0.99
36_W	40_L	1.727	0.99
100_Q	103_A	1.718	0.99
176_G	246_E	1.717	0.99
242_V	246_E	1.699	0.99
297_E	301_R	1.698	0.99
86_D	90_Q	1.697	0.99
299_Y	302_I	1.696	0.99
180_E	246_E	1.679	0.98
223_E	227_K	1.670	0.98
86_D	89_E	1.659	0.98
201_E	264_E	1.647	0.98
307_R	310_R	1.644	0.98
133_Q	139_L	1.644	0.98
61_K	65_K	1.640	0.98
99_P	103_A	1.635	0.98
80_S	83_A	1.633	0.98
254_L	262_Y	1.618	0.98
91_L	95_L	1.614	0.98
234_L	237_L	1.593	0.98
249_Y	290_P	1.570	0.98
37_W	42_P	1.567	0.98
124_P	127_S	1.559	0.97
295_M	299_Y	1.559	0.97
175_L	179_R	1.554	0.97
37_W	40_L	1.545	0.97
94_W	99_P	1.540	0.97
144_P	147_F	1.537	0.97
162_Y	190_D	1.536	0.97
220_K	224_R	1.521	0.97
7_R	11_D	1.512	0.97
134_Q	137_S	1.510	0.97
235_R	290_P	1.501	0.97
277_Q	288_P	1.498	0.97
180_E	281_E	1.497	0.97
15_D	19_Q	1.483	0.97
106_F	109_A	1.482	0.97
15_D	18_R	1.475	0.96
246_E	249_Y	1.470	0.96
220_K	240_L	1.469	0.96
238_Y	246_E	1.468	0.96
85_K	88_W	1.464	0.96
63_Y	66_L	1.459	0.96
36_W	39_A	1.446	0.96
92_Q	99_P	1.442	0.96
95_L	99_P	1.441	0.96
38_S	41_A	1.424	0.96
72_A	76_G	1.416	0.95
84_A	88_W	1.412	0.95
238_Y	298_L	1.408	0.95
89_E	93_K	1.394	0.95
98_L	107_Q	1.380	0.95
79_A	85_K	1.377	0.95
198_A	268_A	1.368	0.95
293_S	298_L	1.347	0.94
212_K	215_E	1.344	0.94
81_A	84_A	1.331	0.94
209_A	252_L	1.319	0.93
99_P	104_G	1.317	0.93
8_Q	11_D	1.297	0.93
300_K	304_E	1.295	0.93
148_L	151_L	1.294	0.93
147_F	153_L	1.290	0.93
208_K	257_E	1.287	0.92
273_R	277_Q	1.277	0.92
51_D	55_R	1.275	0.92
121_F	125_W	1.256	0.92
30_W	34_L	1.255	0.92
153_L	156_L	1.250	0.91
117_A	123_G	1.235	0.91
98_L	108_G	1.235	0.91
256_E	260_K	1.226	0.91
215_E	219_E	1.216	0.90
212_K	251_E	1.209	0.90
132_W	138_S	1.208	0.90
55_R	63_Y	1.204	0.90
101_A	108_G	1.190	0.89
9_Y	12_A	1.190	0.89
281_E	292_R	1.185	0.89
266_V	270_M	1.176	0.89
233_S	236_E	1.167	0.88
3_L	6_Q	1.153	0.88
67_M	70_F	1.148	0.87
12_A	15_D	1.143	0.87
246_E	253_F	1.142	0.87
152_E	157_W	1.138	0.87
35_Q	38_S	1.134	0.87
216_R	219_E	1.132	0.87
180_E	293_S	1.123	0.86
135_M	140_S	1.112	0.86
25_P	28_N	1.110	0.86
91_L	94_W	1.109	0.86
40_L	43_G	1.101	0.85
87_A	90_Q	1.096	0.85
198_A	264_E	1.095	0.85
69_Q	72_A	1.090	0.84
118_L	123_G	1.088	0.84
214_F	217_F	1.080	0.84
249_Y	253_F	1.071	0.83
85_K	90_Q	1.070	0.83
152_E	155_N	1.068	0.83
116_E	122_M	1.063	0.83
132_W	135_M	1.062	0.83
24_A	29_P	1.055	0.83
175_L	284_L	1.052	0.82
32_E	35_Q	1.049	0.82
6_Q	9_Y	1.047	0.82
217_F	240_L	1.046	0.82
297_E	302_I	1.046	0.82
104_G	107_Q	1.041	0.82
100_Q	107_Q	1.038	0.81
238_Y	249_Y	1.038	0.81
301_R	306_R	1.037	0.81
95_L	102_F	1.035	0.81
145_G	153_L	1.034	0.81
92_Q	95_L	1.030	0.81
258_F	266_V	1.029	0.81
173_P	184_R	1.024	0.81
168_K	171_K	1.024	0.81
284_L	289_M	1.014	0.80
304_E	307_R	1.005	0.79
105_M	108_G	1.004	0.79
82_A	88_W	1.003	0.79
13_W	17_M	0.999	0.79
191_A	275_A	0.997	0.79
206_L	266_V	0.992	0.78
69_Q	73_A	0.986	0.78
245_A	276_Q	0.979	0.77
91_L	100_Q	0.968	0.77
249_Y	263_G	0.963	0.76
81_A	85_K	0.962	0.76
179_R	183_E	0.959	0.76
262_Y	265_L	0.958	0.76
226_E	229_E	0.956	0.76
212_K	216_R	0.955	0.76
217_F	295_M	0.954	0.76
129_L	134_Q	0.954	0.76
281_E	294_E	0.953	0.76
196_Q	239_D	0.949	0.75
290_P	301_R	0.948	0.75
170_L	183_E	0.939	0.74
298_L	306_R	0.937	0.74
173_P	202_Y	0.930	0.74
202_Y	272_L	0.927	0.74
210_G	238_Y	0.925	0.73
148_L	154_F	0.924	0.73
18_R	22_G	0.922	0.73
145_G	148_L	0.921	0.73
300_K	303_Y	0.917	0.73
224_R	230_Q	0.915	0.73
87_A	95_L	0.914	0.72
198_A	261_L	0.913	0.72
258_F	284_L	0.913	0.72
112_Q	116_E	0.912	0.72
173_P	176_G	0.911	0.72
16_M	20_A	0.910	0.72
34_L	287_L	0.910	0.72
5_L	8_Q	0.910	0.72
91_L	102_F	0.905	0.72
276_Q	288_P	0.898	0.71
262_Y	281_E	0.896	0.71
168_K	173_P	0.895	0.71
31_Q	40_L	0.894	0.71
154_F	157_W	0.891	0.71
57_L	63_Y	0.890	0.70
56_M	63_Y	0.882	0.70
170_L	177_Y	0.874	0.69
188_L	279_L	0.873	0.69
162_Y	237_L	0.872	0.69
11_D	18_R	0.872	0.69
155_N	158_W	0.866	0.68
112_Q	115_A	0.865	0.68
203_Q	231_I	0.863	0.68
98_L	102_F	0.863	0.68
115_A	118_L	0.861	0.68
136_A	140_S	0.857	0.68
90_Q	96_E	0.857	0.68
263_G	270_M	0.856	0.67
304_E	311_A	0.854	0.67
179_R	246_E	0.853	0.67
244_A	248_A	0.850	0.67
183_E	187_K	0.850	0.67
53_F	60_A	0.849	0.67
100_Q	104_G	0.847	0.67
163_E	167_G	0.843	0.66
197_Q	201_E	0.839	0.66
144_P	148_L	0.837	0.66
184_R	278_E	0.834	0.65
183_E	246_E	0.831	0.65
10_W	17_M	0.828	0.65
23_A	27_A	0.827	0.65
259_S	263_G	0.824	0.64
233_S	237_L	0.824	0.64
82_A	85_K	0.823	0.64
302_I	309_V	0.817	0.64
38_S	42_P	0.815	0.64
294_E	299_Y	0.813	0.63
253_F	297_E	0.813	0.63
302_I	306_R	0.809	0.63
99_P	105_M	0.809	0.63
199_L	203_Q	0.807	0.63
102_F	159_D	0.800	0.62
231_I	242_V	0.798	0.62
301_R	307_R	0.796	0.62
171_K	190_D	0.795	0.62
11_D	14_S	0.793	0.61
140_S	144_P	0.792	0.61
294_E	298_L	0.791	0.61
178_T	182_Q	0.788	0.61
23_A	26_A	0.787	0.61
10_W	20_A	0.786	0.61
143_M	149_K	0.784	0.61
78_D	82_A	0.783	0.60
179_R	182_Q	0.782	0.60
240_L	273_R	0.781	0.60
238_Y	262_Y	0.779	0.60
90_Q	231_I	0.778	0.60
284_L	288_P	0.776	0.60
201_E	299_Y	0.775	0.60
97_Q	101_A	0.772	0.59
54_E	58_D	0.770	0.59
42_P	45_A	0.769	0.59
203_Q	206_L	0.769	0.59
8_Q	12_A	0.767	0.59
10_W	15_D	0.767	0.59
209_A	245_A	0.765	0.59
100_Q	109_A	0.762	0.58
246_E	250_A	0.759	0.58
9_Y	37_W	0.758	0.58
15_D	20_A	0.757	0.58
163_E	168_K	0.746	0.57
92_Q	97_Q	0.746	0.57
121_F	124_P	0.745	0.57
205_L	252_L	0.745	0.57
145_G	151_L	0.743	0.56
262_Y	297_E	0.742	0.56
126_Q	132_W	0.741	0.56
84_A	90_Q	0.740	0.56
67_M	74_F	0.738	0.56
101_A	106_F	0.731	0.55
221_L	225_A	0.730	0.55
106_F	111_E	0.730	0.55
15_D	21_M	0.729	0.55
236_E	239_D	0.728	0.55
199_L	295_M	0.720	0.54
176_G	249_Y	0.719	0.54
84_A	87_A	0.717	0.54
128_P	140_S	0.714	0.53
40_L	46_P	0.714	0.53
6_Q	17_M	0.713	0.53
136_A	139_L	0.711	0.53
299_Y	303_Y	0.707	0.53
186_Q	258_F	0.702	0.52
32_E	46_P	0.701	0.52
58_D	70_F	0.701	0.52
282_D	285_E	0.700	0.52
85_K	89_E	0.700	0.52
174_A	249_Y	0.699	0.52
142_A	145_G	0.698	0.52
179_R	268_A	0.698	0.52
131_N	135_M	0.697	0.52
63_Y	68_E	0.694	0.51
150_L	154_F	0.693	0.51
216_R	251_E	0.691	0.51
120_K	123_G	0.689	0.51
131_N	140_S	0.689	0.51
233_S	265_L	0.688	0.51
133_Q	137_S	0.687	0.51
154_F	159_D	0.687	0.51
47_P	50_K	0.687	0.51
148_L	159_D	0.685	0.50
289_M	295_M	0.684	0.50
24_A	27_A	0.683	0.50
135_M	139_L	0.683	0.50
122_M	125_W	0.683	0.50
266_V	271_R	0.681	0.50
255_S	264_E	0.678	0.50
79_A	86_D	0.675	0.49
98_L	101_A	0.675	0.49
19_Q	22_G	0.674	0.49
198_A	201_E	0.673	0.49
253_F	262_Y	0.673	0.49
94_W	97_Q	0.672	0.49
183_E	252_L	0.669	0.49
284_L	307_R	0.667	0.49
85_K	105_M	0.665	0.48
250_A	254_L	0.664	0.48
58_D	75_A	0.662	0.48
35_Q	42_P	0.660	0.48
281_E	288_P	0.658	0.48
194_D	270_M	0.657	0.48
188_L	275_A	0.656	0.48
132_W	139_L	0.656	0.48
300_K	305_L	0.649	0.47
88_W	92_Q	0.647	0.47
14_S	18_R	0.645	0.46
296_D	305_L	0.644	0.46
242_V	250_A	0.641	0.46
128_P	133_Q	0.639	0.46
247_E	250_A	0.639	0.46
93_K	102_F	0.638	0.46
51_D	54_E	0.638	0.46
181_H	272_L	0.636	0.45
219_E	247_E	0.634	0.45
173_P	179_R	0.634	0.45
194_D	233_S	0.629	0.45
279_L	297_E	0.628	0.45
89_E	92_Q	0.628	0.45
87_A	92_Q	0.626	0.44
123_G	126_Q	0.619	0.44
58_D	61_K	0.616	0.43
176_G	183_E	0.614	0.43
169_L	272_L	0.614	0.43
28_N	32_E	0.614	0.43
12_A	23_A	0.614	0.43
263_G	266_V	0.613	0.43
284_L	299_Y	0.613	0.43
33_A	38_S	0.612	0.43
69_Q	75_A	0.609	0.43
35_Q	45_A	0.606	0.42
147_F	150_L	0.606	0.42
208_K	295_M	0.605	0.42
107_Q	110_A	0.604	0.42
128_P	131_N	0.603	0.42
5_L	14_S	0.601	0.42
25_P	29_P	0.600	0.42
144_P	154_F	0.599	0.42
31_Q	39_A	0.598	0.42
268_A	280_V	0.598	0.42
224_R	229_E	0.595	0.41
131_N	136_A	0.592	0.41
19_Q	26_A	0.591	0.41
31_Q	35_Q	0.588	0.41
3_L	17_M	0.588	0.41
103_A	109_A	0.585	0.40
182_Q	245_A	0.585	0.40
70_F	234_L	0.585	0.40
83_A	88_W	0.585	0.40
16_M	21_M	0.585	0.40
131_N	139_L	0.583	0.40
37_W	45_A	0.583	0.40
218_Q	237_L	0.582	0.40
89_E	223_E	0.581	0.40
188_L	222_A	0.581	0.40
78_D	81_A	0.580	0.40
105_M	111_E	0.578	0.40
17_M	20_A	0.577	0.39
213_A	262_Y	0.577	0.39
98_L	110_A	0.576	0.39
106_F	110_A	0.575	0.39
118_L	125_W	0.575	0.39
96_E	103_A	0.574	0.39
182_Q	186_Q	0.572	0.39
4_E	17_M	0.572	0.39
272_L	276_Q	0.570	0.39
65_K	72_A	0.570	0.39
151_L	154_F	0.570	0.39
195_Y	269_Q	0.569	0.39
100_Q	105_M	0.569	0.39
268_A	290_P	0.569	0.39
3_L	7_R	0.569	0.39
296_D	302_I	0.569	0.39
122_M	294_E	0.563	0.38
192_W	272_L	0.563	0.38
93_K	99_P	0.562	0.38
277_Q	281_E	0.562	0.38
228_G	312_L	0.561	0.38
3_L	14_S	0.560	0.38
261_L	265_L	0.559	0.38
24_A	28_N	0.558	0.38
128_P	139_L	0.558	0.38
65_K	68_E	0.557	0.38
119_Q	123_G	0.557	0.38
197_Q	202_Y	0.557	0.38
188_L	192_W	0.556	0.37
92_Q	102_F	0.555	0.37
27_A	32_E	0.554	0.37
90_Q	99_P	0.552	0.37
245_A	292_R	0.552	0.37
206_L	251_E	0.551	0.37
103_A	107_Q	0.550	0.37
55_R	70_F	0.549	0.37
65_K	69_Q	0.548	0.37
130_D	140_S	0.548	0.37
26_A	37_W	0.548	0.37
12_A	20_A	0.547	0.37
55_R	58_D	0.547	0.37
14_S	45_A	0.546	0.36
201_E	268_A	0.546	0.36
209_A	269_Q	0.545	0.36
23_A	28_N	0.545	0.36
32_E	36_W	0.545	0.36
236_E	273_R	0.544	0.36
195_Y	274_K	0.544	0.36
16_M	23_A	0.540	0.36
78_D	85_K	0.537	0.36
210_G	246_E	0.536	0.36
98_L	105_M	0.531	0.35
83_A	87_A	0.530	0.35
42_P	64_F	0.530	0.35
245_A	249_Y	0.530	0.35
95_L	101_A	0.528	0.35
78_D	89_E	0.526	0.35
194_D	237_L	0.525	0.34
150_L	157_W	0.524	0.34
131_N	137_S	0.523	0.34
172_M	206_L	0.522	0.34
14_S	25_P	0.520	0.34
82_A	86_D	0.519	0.34
90_Q	93_K	0.519	0.34
190_D	193_L	0.518	0.34
154_F	158_W	0.517	0.34
235_R	239_D	0.517	0.34
249_Y	291_T	0.516	0.34
290_P	294_E	0.516	0.34
97_Q	103_A	0.515	0.34
153_L	157_W	0.514	0.33
60_A	67_M	0.514	0.33
29_P	36_W	0.513	0.33
46_P	49_A	0.511	0.33
269_Q	276_Q	0.510	0.33
153_L	159_D	0.510	0.33
262_Y	276_Q	0.508	0.33
296_D	300_K	0.508	0.33
22_G	25_P	0.508	0.33
262_Y	272_L	0.508	0.33
40_L	45_A	0.507	0.33
209_A	213_A	0.506	0.33
159_D	164_E	0.500	0.32
168_K	197_Q	0.500	0.32
234_L	267_N	0.500	0.32

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
3tweA	2	0.0671	50.5	0.945	Contact Map
2e87A	1	0.4633	49.5	0.945	Contact Map
1dipA	2	0.1086	37.5	0.949	Contact Map
3zqeA	1	0.4601	35.8	0.95	Contact Map
2d4yA	1	0.3642	31.1	0.951	Contact Map
4y66B	1	0.4058	29	0.952	Contact Map
2yy0A	6	0.1182	28.6	0.952	Contact Map
4dznA	3	0.0671	23.7	0.954	Contact Map
1deqA	1	0.1981	21.6	0.955	Contact Map
4j2cA	1	0.3131	20.6	0.955	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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