PhnG - PFAM28P - GREMLIN Contacts

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PhnG - Phosphonate metabolism protein PhnG

PFAM:	PF06754	Sequences: ARQRWMAVLARAPAAELAALLAALGLLPAYEVLRAPETGLVMVRGRIGGTGAPFNLGEATVTRAAVRLADGEVGHGYVLGRDKRKAELAALIDALLQDPARAAALEAAVLAPLAAAQAARRARRAAKAAATRVDFFTMVRG	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	141 (141)
Sequences:	3868 (2688)
Seq/√Len:	226.3
META:	0.785

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
59_A	79_L	3.852	1.00
4_R	114_A	3.104	1.00
16_E	116_A	2.988	1.00
31_E	67_R	2.932	1.00
32_V	87_E	2.734	1.00
78_V	85_K	2.665	1.00
14_A	82_D	2.665	1.00
65_A	75_H	2.466	1.00
72_E	98_D	2.457	1.00
6_M	89_A	2.368	1.00
122_A	126_A	2.358	1.00
43_V	59_A	2.215	1.00
18_A	84_R	2.203	1.00
8_V	110_L	2.161	1.00
13_P	16_E	2.130	1.00
5_W	96_L	2.100	1.00
7_A	11_R	2.091	1.00
44_R	55_N	2.015	1.00
76_G	89_A	1.826	1.00
42_M	58_E	1.685	1.00
41_V	61_V	1.677	1.00
44_R	53_P	1.652	1.00
32_V	66_V	1.638	1.00
84_R	87_E	1.630	1.00
11_R	117_Q	1.606	1.00
32_V	35_A	1.606	1.00
38_T	83_K	1.579	1.00
104_A	108_A	1.566	1.00
18_A	88_L	1.513	1.00
98_D	101_R	1.488	1.00
115_A	119_A	1.479	1.00
68_L	91_L	1.466	1.00
62_T	83_K	1.450	1.00
30_Y	91_L	1.422	1.00
29_A	69_A	1.418	1.00
114_A	118_A	1.386	1.00
8_V	114_A	1.375	1.00
65_A	73_V	1.368	1.00
64_A	86_A	1.323	1.00
102_A	106_E	1.321	1.00
14_A	18_A	1.302	1.00
92_I	109_V	1.289	1.00
123_R	127_K	1.266	1.00
31_E	69_A	1.260	1.00
21_L	27_L	1.259	1.00
70_D	98_D	1.252	1.00
21_L	92_I	1.245	1.00
47_I	52_A	1.243	1.00
117_Q	121_R	1.239	1.00
118_A	122_A	1.213	1.00
84_R	88_L	1.191	1.00
68_L	72_E	1.184	1.00
119_A	123_R	1.182	1.00
30_Y	87_E	1.162	1.00
16_E	19_A	1.158	1.00
16_E	113_L	1.151	1.00
116_A	120_R	1.148	1.00
18_A	22_A	1.146	1.00
78_V	86_A	1.136	1.00
21_L	88_L	1.112	1.00
6_M	76_G	1.111	1.00
82_D	85_K	1.099	1.00
33_L	73_V	1.085	1.00
96_L	106_E	1.083	1.00
103_A	107_A	1.069	1.00
106_E	111_A	1.062	1.00
34_R	65_A	1.060	1.00
8_V	117_Q	1.055	1.00
14_A	85_K	1.050	1.00
20_L	92_I	1.044	1.00
113_L	116_A	1.026	1.00
106_E	114_A	1.025	1.00
92_I	96_L	1.022	1.00
119_A	122_A	0.999	1.00
35_A	65_A	0.990	1.00
113_L	117_Q	0.981	1.00
85_K	89_A	0.980	1.00
35_A	83_K	0.971	1.00
61_V	77_Y	0.958	1.00
2_R	5_W	0.955	1.00
62_T	76_G	0.952	1.00
101_R	104_A	0.948	1.00
47_I	53_P	0.945	1.00
96_L	102_A	0.945	1.00
38_T	81_R	0.941	1.00
129_A	132_R	0.940	1.00
17_L	85_K	0.928	1.00
111_A	115_A	0.924	1.00
42_M	55_N	0.922	1.00
96_L	110_L	0.920	1.00
41_V	59_A	0.913	0.99
78_V	89_A	0.894	0.99
68_L	94_A	0.893	0.99
32_V	64_A	0.884	0.99
66_V	91_L	0.876	0.99
3_Q	7_A	0.866	0.99
2_R	93_D	0.859	0.99
67_R	73_V	0.858	0.99
109_V	112_P	0.858	0.99
107_A	111_A	0.857	0.99
105_L	112_P	0.848	0.99
15_A	19_A	0.843	0.99
1_A	4_R	0.820	0.99
12_A	113_L	0.816	0.99
74_G	93_D	0.815	0.99
14_A	88_L	0.807	0.99
55_N	58_E	0.792	0.99
124_R	127_K	0.786	0.98
125_A	128_A	0.785	0.98
87_E	91_L	0.783	0.98
116_A	119_A	0.777	0.98
4_R	106_E	0.774	0.98
12_A	117_Q	0.763	0.98
5_W	110_L	0.751	0.98
127_K	130_A	0.751	0.98
16_E	20_L	0.740	0.98
118_A	121_R	0.739	0.98
123_R	126_A	0.734	0.98
105_L	109_V	0.734	0.98
121_R	125_A	0.733	0.98
19_A	23_A	0.732	0.98
39_G	61_V	0.731	0.98
62_T	89_A	0.721	0.97
104_A	107_A	0.717	0.97
11_R	14_A	0.717	0.97
42_M	56_L	0.716	0.97
48_G	55_N	0.715	0.97
88_L	92_I	0.713	0.97
115_A	118_A	0.710	0.97
137_T	141_G	0.699	0.97
64_A	87_E	0.699	0.97
30_Y	68_L	0.698	0.97
60_T	81_R	0.696	0.97
125_A	129_A	0.689	0.97
85_K	88_L	0.675	0.96
135_F	138_M	0.674	0.96
12_A	17_L	0.672	0.96
9_L	92_I	0.671	0.96
103_A	106_E	0.668	0.96
8_V	11_R	0.660	0.96
14_A	84_R	0.654	0.95
36_P	64_A	0.653	0.95
65_A	77_Y	0.649	0.95
45_G	53_P	0.649	0.95
21_L	26_L	0.646	0.95
24_L	92_I	0.641	0.95
7_A	79_L	0.634	0.94
120_R	123_R	0.634	0.94
1_A	106_E	0.631	0.94
37_E	63_R	0.627	0.94
46_R	53_P	0.627	0.94
76_G	86_A	0.624	0.94
32_V	91_L	0.620	0.94
1_A	102_A	0.616	0.94
4_R	111_A	0.613	0.93
5_W	97_Q	0.608	0.93
71_G	81_R	0.607	0.93
111_A	114_A	0.607	0.93
21_L	25_G	0.605	0.93
21_L	91_L	0.605	0.93
35_A	87_E	0.603	0.93
117_Q	120_R	0.595	0.92
134_D	137_T	0.594	0.92
102_A	105_L	0.593	0.92
4_R	8_V	0.591	0.92
73_V	76_G	0.589	0.92
9_L	110_L	0.583	0.92
9_L	89_A	0.582	0.92
2_R	97_Q	0.578	0.91
34_R	39_G	0.575	0.91
20_L	109_V	0.565	0.90
23_A	105_L	0.563	0.90
27_L	101_R	0.557	0.90
40_L	59_A	0.556	0.90
34_R	37_E	0.554	0.89
13_P	116_A	0.548	0.89
113_L	120_R	0.546	0.89
17_L	82_D	0.544	0.89
4_R	7_A	0.544	0.89
106_E	110_L	0.538	0.88
49_G	60_T	0.537	0.88
6_M	10_A	0.536	0.88
29_A	122_A	0.534	0.88
26_L	115_A	0.533	0.88
68_L	98_D	0.532	0.88
138_M	141_G	0.532	0.88
24_L	28_P	0.527	0.87
22_A	27_L	0.527	0.87
67_R	71_G	0.526	0.87
13_P	120_R	0.526	0.87
10_A	89_A	0.526	0.87
95_L	101_R	0.523	0.87
26_L	104_A	0.523	0.87
19_A	122_A	0.523	0.87
45_G	55_N	0.522	0.87
62_T	86_A	0.521	0.86
86_A	89_A	0.521	0.86
104_A	111_A	0.521	0.86
137_T	140_R	0.519	0.86
17_L	21_L	0.518	0.86
31_E	123_R	0.518	0.86
134_D	140_R	0.516	0.86
64_A	89_A	0.516	0.86
109_V	113_L	0.512	0.86
108_A	123_R	0.510	0.85
93_D	97_Q	0.509	0.85
36_P	128_A	0.508	0.85
20_L	23_A	0.506	0.85
106_E	109_V	0.504	0.85
40_L	88_L	0.503	0.85
110_L	113_L	0.501	0.84
111_A	123_R	0.500	0.84

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
3amjB	1	0.2624	11	0.934	Contact Map
2ltrA	1	0.6596	9.2	0.937	Contact Map
2dk8A	1	0.3617	8.4	0.938	Contact Map
1di2A	1	0.4823	5.8	0.942	Contact Map
2jg5A	1	0.7872	4.8	0.944	Contact Map
1kyqA	2	0.3262	4.4	0.945	Contact Map
2wscK	1	0.4965	4.3	0.946	Contact Map
1jb0K	1	0.3262	4.3	0.946	Contact Map
3mf7A	3	0.7589	4	0.947	Contact Map
4xglA	1	0.3333	3.6	0.948	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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