PhnJ - PFAM28P - GREMLIN Contacts

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PhnJ - Phosphonate metabolism protein PhnJ

PFAM:	PF06007	Sequences: QGYNFAYLDEQTKRMIRRAILKAVAIPGYQVPFASREMPMPYGWGTGGLQVTASIIGPDDVLKVIDQGADDTTNAVSIRRFFARTAGVATTTDTAEATIIQTRHRIPETPLREGQILVYQVPIPEPLRFLEPRETETRKMHALAEYGLMHVKLYEDIARHGHIATSYDYPVMVNGRYVMDPSPIPKFDNPKLHMSPALQLFGAGREKRIYAVPPYTKVESLDFEDHPFEVERFDGKPCALCGATDSYLDEVITDDAGGRMFVCSDTDYCEKRRA	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	274 (272)
Sequences:	1406 (418)
Seq/√Len:	25.3
META:	0.73

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
168_D	180_D	4.757	1.00
179_M	212_V	4.168	1.00
194_M	217_K	4.070	1.00
175_G	217_K	3.769	1.00
189_N	220_S	3.697	1.00
24_V	198_L	3.651	1.00
119_Y	199_Q	3.574	1.00
51_V	55_I	3.455	1.00
193_H	217_K	3.434	1.00
20_I	209_I	3.061	1.00
102_T	199_Q	2.870	1.00
113_E	215_Y	2.857	1.00
99_I	118_V	2.824	1.00
240_L	273_R	2.776	0.99
109_T	271_K	2.740	0.99
171_V	179_M	2.721	0.99
102_T	201_F	2.696	0.99
20_I	51_V	2.650	0.99
192_L	199_Q	2.589	0.99
163_I	169_Y	2.502	0.99
93_D	271_K	2.494	0.99
263_C	269_C	2.471	0.99
5_F	87_G	2.461	0.99
56_I	62_L	2.431	0.99
119_Y	192_L	2.423	0.99
79_R	90_T	2.341	0.98
102_T	119_Y	2.336	0.98
113_E	196_P	2.284	0.98
56_I	86_A	2.251	0.98
172_M	178_V	2.186	0.97
196_P	215_Y	2.181	0.97
241_C	269_C	2.115	0.96
192_L	195_S	2.113	0.96
134_E	137_T	2.016	0.95
162_H	229_E	2.013	0.95
241_C	263_C	2.012	0.95
55_I	99_I	2.006	0.95
237_P	244_T	2.002	0.95
128_R	134_E	1.998	0.95
195_S	199_Q	1.971	0.95
40_M	49_L	1.918	0.94
95_A	109_T	1.908	0.94
53_A	82_F	1.881	0.93
253_T	256_A	1.880	0.93
243_A	246_S	1.809	0.92
240_L	270_E	1.796	0.91
193_H	219_E	1.786	0.91
24_V	116_I	1.783	0.91
81_F	85_T	1.778	0.91
4_N	10_E	1.726	0.90
123_I	129_F	1.726	0.90
83_A	90_T	1.691	0.89
243_A	272_R	1.671	0.88
20_I	24_V	1.659	0.88
157_I	226_H	1.652	0.88
71_D	270_E	1.646	0.87
136_E	139_K	1.635	0.87
61_V	89_A	1.622	0.87
56_I	99_I	1.617	0.86
219_E	222_D	1.566	0.85
138_R	208_R	1.536	0.83
34_A	49_L	1.531	0.83
125_E	137_T	1.504	0.82
52_T	62_L	1.500	0.82
134_E	138_R	1.472	0.81
117_L	199_Q	1.469	0.80
93_D	96_E	1.467	0.80
62_L	82_F	1.443	0.79
111_L	197_A	1.413	0.78
149_M	169_Y	1.391	0.77
117_L	195_S	1.390	0.77
71_D	77_S	1.378	0.76
94_T	267_D	1.374	0.76
130_L	148_L	1.363	0.75
119_Y	201_F	1.357	0.75
178_V	221_L	1.356	0.75
254_D	258_G	1.351	0.74
19_A	209_I	1.341	0.74
270_E	273_R	1.339	0.74
123_I	168_D	1.320	0.73
187_F	191_K	1.309	0.72
78_I	85_T	1.304	0.72
144_A	176_R	1.292	0.71
117_L	192_L	1.291	0.71
267_D	271_K	1.290	0.71
230_V	233_F	1.279	0.70
193_H	196_P	1.263	0.69
246_S	268_Y	1.260	0.69
140_M	169_Y	1.246	0.68
49_L	78_I	1.234	0.67
20_I	55_I	1.233	0.67
123_I	180_D	1.230	0.67
5_F	88_V	1.210	0.66
129_F	180_D	1.188	0.64
93_D	267_D	1.169	0.63
149_M	178_V	1.167	0.63
270_E	274_A	1.167	0.63
245_D	248_L	1.161	0.63
10_E	13_K	1.161	0.63
109_T	196_P	1.155	0.62
110_P	196_P	1.143	0.61
133_R	137_T	1.104	0.59
128_R	137_T	1.100	0.58
123_I	128_R	1.100	0.58
89_A	96_E	1.098	0.58
173_V	218_V	1.088	0.58
51_V	200_L	1.085	0.57
165_T	168_D	1.078	0.57
136_E	151_V	1.071	0.56
81_F	249_D	1.061	0.56
53_A	72_T	1.060	0.55
247_Y	266_T	1.054	0.55
92_T	270_E	1.049	0.55
166_S	231_E	1.033	0.54
73_T	77_S	1.029	0.53
95_A	271_K	1.026	0.53
186_K	230_V	1.020	0.53
61_V	98_T	1.016	0.52
35_S	42_Y	1.014	0.52
131_E	207_K	1.009	0.52
222_D	227_P	1.009	0.52
180_D	210_Y	1.008	0.52
156_D	163_I	1.005	0.52
129_F	168_D	1.005	0.52
33_F	44_W	1.001	0.51
6_A	86_A	0.975	0.49
29_Y	134_E	0.963	0.48
165_T	169_Y	0.962	0.48
196_P	199_Q	0.960	0.48
229_E	232_R	0.946	0.47
21_L	25_A	0.940	0.47
93_D	109_T	0.929	0.46
81_F	147_G	0.928	0.46
174_N	217_K	0.923	0.46
49_L	82_F	0.921	0.45
193_H	231_E	0.920	0.45
95_A	217_K	0.917	0.45
52_T	56_I	0.916	0.45
92_T	267_D	0.907	0.44
56_I	85_T	0.903	0.44
126_P	180_D	0.896	0.44
175_G	194_M	0.895	0.44
59_D	83_A	0.888	0.43
42_Y	53_A	0.886	0.43
175_G	219_E	0.884	0.43
14_R	138_R	0.882	0.43
5_F	59_D	0.874	0.42
6_A	85_T	0.871	0.42
57_G	168_D	0.868	0.42
106_I	192_L	0.858	0.41
98_T	114_G	0.856	0.41
207_K	212_V	0.856	0.41
15_M	72_T	0.855	0.41
208_R	262_V	0.853	0.41
152_K	165_T	0.851	0.40
49_L	53_A	0.845	0.40
150_H	224_E	0.844	0.40
194_M	215_Y	0.840	0.40
133_R	136_E	0.838	0.39
33_F	81_F	0.835	0.39
16_I	209_I	0.830	0.39
245_D	272_R	0.828	0.39
55_I	118_V	0.826	0.39
81_F	161_G	0.822	0.38
132_P	180_D	0.820	0.38
56_I	88_V	0.818	0.38
53_A	151_V	0.816	0.38
269_C	272_R	0.815	0.38
106_I	177_Y	0.811	0.38
114_G	195_S	0.809	0.37
124_P	153_L	0.808	0.37
203_A	206_E	0.806	0.37
140_M	148_L	0.804	0.37
145_E	220_S	0.803	0.37
151_V	186_K	0.797	0.37
42_Y	150_H	0.797	0.37
253_T	258_G	0.795	0.37
98_T	200_L	0.793	0.36
54_S	59_D	0.793	0.36
34_A	40_M	0.792	0.36
175_G	193_H	0.786	0.36
162_H	166_S	0.786	0.36
144_A	172_M	0.782	0.36
61_V	79_R	0.776	0.35
94_T	109_T	0.770	0.35
186_K	231_E	0.766	0.35
16_I	157_I	0.763	0.34
154_Y	264_S	0.761	0.34
44_W	218_V	0.758	0.34
264_S	269_C	0.757	0.34
117_L	256_A	0.757	0.34
20_I	26_I	0.749	0.33
25_A	147_G	0.745	0.33
15_M	19_A	0.744	0.33
123_I	149_M	0.744	0.33
156_D	166_S	0.741	0.33
37_E	181_P	0.734	0.32
262_V	267_D	0.732	0.32
83_A	86_A	0.732	0.32
173_V	179_M	0.731	0.32
42_Y	72_T	0.730	0.32
138_R	247_Y	0.724	0.32
16_I	33_F	0.719	0.32
61_V	247_Y	0.717	0.31
154_Y	169_Y	0.717	0.31
201_F	212_V	0.716	0.31
212_V	231_E	0.714	0.31
38_M	165_T	0.713	0.31
22_K	46_T	0.710	0.31
78_I	88_V	0.710	0.31
84_R	208_R	0.709	0.31
86_A	99_I	0.704	0.31
77_S	261_F	0.704	0.31
172_M	176_R	0.702	0.30
184_I	192_L	0.698	0.30
36_R	50_Q	0.698	0.30
42_Y	49_L	0.696	0.30
193_H	215_Y	0.695	0.30
125_E	128_R	0.695	0.30
156_D	169_Y	0.693	0.30
8_L	169_Y	0.692	0.30
119_Y	195_S	0.691	0.30
174_N	247_Y	0.683	0.29
114_G	215_Y	0.682	0.29
61_V	96_E	0.681	0.29
72_T	82_F	0.679	0.29
128_R	218_V	0.677	0.29
177_Y	268_Y	0.677	0.29
249_D	261_F	0.676	0.29
145_E	189_N	0.673	0.29
197_A	249_D	0.672	0.29
139_K	186_K	0.671	0.29
12_T	85_T	0.668	0.28
192_L	231_E	0.668	0.28
15_M	42_Y	0.668	0.28
133_R	267_D	0.668	0.28
171_V	218_V	0.667	0.28
254_D	259_R	0.666	0.28
123_I	247_Y	0.664	0.28
40_M	73_T	0.663	0.28
187_F	220_S	0.661	0.28
80_R	123_I	0.659	0.28
87_G	212_V	0.659	0.28
44_W	173_V	0.658	0.28
76_V	131_E	0.657	0.28
131_E	200_L	0.656	0.28
51_V	202_G	0.655	0.28
40_M	46_T	0.653	0.28
3_Y	7_Y	0.646	0.27
24_V	230_V	0.644	0.27
79_R	151_V	0.640	0.27
44_W	125_E	0.639	0.27
80_R	151_V	0.636	0.27
148_L	151_V	0.635	0.26
243_A	269_C	0.632	0.26
44_W	128_R	0.630	0.26
7_Y	86_A	0.630	0.26
56_I	240_L	0.629	0.26
130_L	212_V	0.628	0.26
102_T	208_R	0.628	0.26
55_I	207_K	0.626	0.26
102_T	156_D	0.623	0.26
4_N	12_T	0.623	0.26
89_A	251_V	0.622	0.26
77_S	148_L	0.621	0.26
51_V	79_R	0.619	0.26
99_I	111_L	0.619	0.26
97_A	115_Q	0.617	0.25
212_V	250_E	0.616	0.25
233_F	246_S	0.613	0.25
41_P	208_R	0.613	0.25
55_I	59_D	0.611	0.25
187_F	190_P	0.611	0.25
179_M	207_K	0.609	0.25
241_C	246_S	0.608	0.25
123_I	132_P	0.607	0.25
222_D	226_H	0.606	0.25
44_W	179_M	0.606	0.25
44_W	171_V	0.605	0.25
255_D	258_G	0.604	0.25
145_E	160_H	0.603	0.25
118_V	273_R	0.603	0.25
41_P	49_L	0.598	0.24
186_K	229_E	0.594	0.24
132_P	191_K	0.594	0.24
81_F	149_M	0.594	0.24
7_Y	125_E	0.593	0.24
100_I	111_L	0.591	0.24
262_V	266_T	0.591	0.24
163_I	226_H	0.590	0.24
12_T	15_M	0.590	0.24
174_N	266_T	0.589	0.24
94_T	112_R	0.587	0.24
69_A	182_S	0.587	0.24
20_I	200_L	0.584	0.24
51_V	209_I	0.583	0.24
41_P	143_L	0.583	0.24
155_E	190_P	0.582	0.24
71_D	240_L	0.582	0.24
73_T	247_Y	0.581	0.24
138_R	181_P	0.579	0.23
158_A	186_K	0.579	0.23
168_D	178_V	0.578	0.23
34_A	145_E	0.577	0.23
99_I	261_F	0.573	0.23
132_P	168_D	0.571	0.23
81_F	160_H	0.570	0.23
78_I	220_S	0.570	0.23
80_R	176_R	0.569	0.23
15_M	53_A	0.568	0.23
263_C	272_R	0.568	0.23
251_V	260_M	0.567	0.23
16_I	112_R	0.566	0.23
106_I	191_K	0.565	0.23
139_K	145_E	0.564	0.23
39_P	43_G	0.563	0.23
154_Y	220_S	0.563	0.23
59_D	247_Y	0.563	0.23
167_Y	181_P	0.562	0.23
239_A	258_G	0.562	0.23
85_T	202_G	0.562	0.23
235_G	253_T	0.561	0.23
54_S	233_F	0.561	0.23
158_A	246_S	0.560	0.22
232_R	235_G	0.560	0.22
129_F	132_P	0.560	0.22
149_M	208_R	0.559	0.22
199_Q	212_V	0.557	0.22
184_I	212_V	0.557	0.22
125_E	139_K	0.556	0.22
49_L	180_D	0.556	0.22
102_T	262_V	0.556	0.22
152_K	156_D	0.554	0.22
35_S	150_H	0.553	0.22
129_F	148_L	0.552	0.22
137_T	171_V	0.551	0.22
54_S	89_A	0.551	0.22
133_R	157_I	0.550	0.22
78_I	82_F	0.550	0.22
49_L	201_F	0.548	0.22
38_M	235_G	0.546	0.22
124_P	134_E	0.544	0.22
172_M	180_D	0.543	0.22
11_Q	151_V	0.543	0.22
34_A	136_E	0.543	0.22
87_G	190_P	0.542	0.22
69_A	77_S	0.541	0.22
158_A	194_M	0.540	0.21
150_H	186_K	0.539	0.21
245_D	268_Y	0.539	0.21
22_K	26_I	0.539	0.21
70_D	203_A	0.538	0.21
238_C	241_C	0.536	0.21
77_S	80_R	0.534	0.21
143_L	167_Y	0.533	0.21
100_I	171_V	0.532	0.21
77_S	209_I	0.532	0.21
69_A	78_I	0.530	0.21
33_F	266_T	0.530	0.21
144_A	229_E	0.530	0.21
115_Q	257_G	0.528	0.21
243_A	248_L	0.528	0.21
57_G	124_P	0.528	0.21
243_A	274_A	0.527	0.21
62_L	90_T	0.527	0.21
239_A	262_V	0.524	0.21
6_A	160_H	0.524	0.21
2_G	96_E	0.523	0.21
9_D	17_R	0.522	0.21
44_W	137_T	0.522	0.21
174_N	177_Y	0.522	0.21
79_R	154_Y	0.522	0.21
160_H	164_A	0.522	0.21
140_M	154_Y	0.521	0.21
169_Y	230_V	0.520	0.20
143_L	266_T	0.520	0.20
140_M	207_K	0.519	0.20
178_V	219_E	0.517	0.20
85_T	94_T	0.517	0.20
250_E	261_F	0.517	0.20
136_E	149_M	0.516	0.20
149_M	154_Y	0.516	0.20
95_A	112_R	0.516	0.20
51_V	118_V	0.515	0.20
91_T	115_Q	0.515	0.20
111_L	119_Y	0.513	0.20
148_L	220_S	0.513	0.20
126_P	168_D	0.512	0.20
152_K	180_D	0.511	0.20
128_R	167_Y	0.511	0.20
136_E	264_S	0.510	0.20
163_I	227_P	0.509	0.20
7_Y	22_K	0.508	0.20
95_A	110_P	0.508	0.20
118_V	234_D	0.508	0.20
19_A	23_A	0.507	0.20
45_G	48_G	0.506	0.20
230_V	235_G	0.506	0.20
89_A	255_D	0.505	0.20
162_H	165_T	0.505	0.20
71_D	126_P	0.505	0.20
33_F	171_V	0.504	0.20
148_L	169_Y	0.504	0.20
9_D	36_R	0.504	0.20
20_I	166_S	0.504	0.20
33_F	36_R	0.502	0.20
49_L	143_L	0.501	0.20
5_F	234_D	0.500	0.20

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
3efoB	1	0.3102	69.6	0.973	Contact Map
3eh2A	1	0.3942	54.5	0.975	Contact Map
2fsuA	2	0.562	37.5	0.978	Contact Map
2fqhA	1	0.1642	27	0.979	Contact Map
3eh1A	1	0.354	20.4	0.98	Contact Map
1vd4A	1	0.1825	19.1	0.981	Contact Map
2yrcA	1	0.1533	12.1	0.982	Contact Map
2epxA	1	0.1569	12.1	0.982	Contact Map
3n2bA	2	0.4015	11.3	0.983	Contact Map
1m2oA	2	0.3029	11.1	0.983	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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