Phasin - PFAM28P - GREMLIN Contacts

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Phasin - Poly(hydroxyalcanoate) granule associated protein (phasin)

PFAM:	PF05597	Sequences: QKQASQLAGAVKDSAQQIWLAGLGAFAKAQEEGGKLFEALVKEGEKLEKKTRKAAEEKVEEARGKVESMAGEVRAKAGGTWDKLEQVFEDRVARALNRLGVPTRKDIDALSARVDELTAKVEKLS	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	125 (120)
Sequences:	3329 (2068)
Seq/√Len:	188.7
META:	0.914

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
37_F	41_V	3.588	1.00
110_L	114_V	3.395	1.00
20_L	24_G	2.876	1.00
121_V	124_L	2.812	1.00
88_F	91_R	2.723	1.00
41_V	44_G	2.537	1.00
116_E	119_A	2.155	1.00
48_E	52_R	2.139	1.00
118_T	122_E	2.108	1.00
51_T	54_A	2.081	1.00
58_K	61_E	1.991	1.00
18_I	26_F	1.951	1.00
65_K	69_M	1.923	1.00
40_L	44_G	1.887	1.00
113_R	118_T	1.867	1.00
111_S	118_T	1.830	1.00
87_V	91_R	1.705	1.00
31_E	43_E	1.665	1.00
92_V	95_A	1.660	1.00
111_S	121_V	1.609	1.00
111_S	115_D	1.609	1.00
42_K	46_K	1.607	1.00
70_A	74_R	1.599	1.00
118_T	121_V	1.596	1.00
97_N	104_R	1.559	1.00
105_K	108_D	1.515	1.00
37_F	44_G	1.504	1.00
104_R	108_D	1.501	1.00
112_A	116_E	1.487	1.00
108_D	111_S	1.398	1.00
43_E	46_K	1.391	1.00
117_L	121_V	1.375	1.00
69_M	72_E	1.354	1.00
106_D	111_S	1.341	1.00
85_E	91_R	1.329	1.00
32_E	35_K	1.321	1.00
111_S	114_V	1.318	1.00
44_G	48_E	1.306	1.00
43_E	102_P	1.301	1.00
16_Q	48_E	1.282	1.00
59_V	63_R	1.279	1.00
116_E	120_K	1.279	1.00
19_W	23_L	1.250	1.00
33_G	37_F	1.244	1.00
19_W	25_A	1.232	1.00
18_I	21_A	1.183	1.00
6_Q	9_G	1.175	1.00
87_V	92_V	1.171	1.00
89_E	98_R	1.165	1.00
114_V	117_L	1.155	1.00
42_K	45_E	1.151	1.00
63_R	67_E	1.132	1.00
28_K	32_E	1.131	1.00
97_N	103_T	1.090	1.00
53_K	62_A	1.078	1.00
13_D	17_Q	1.075	1.00
26_F	30_Q	1.070	1.00
62_A	71_G	1.062	1.00
25_A	29_A	1.053	1.00
26_F	37_F	1.052	1.00
108_D	112_A	1.042	1.00
22_G	33_G	1.027	1.00
84_L	88_F	1.025	1.00
72_E	76_K	1.014	1.00
107_I	110_L	1.003	0.99
83_K	87_V	0.991	0.99
30_Q	43_E	0.983	0.99
76_K	80_T	0.976	0.99
5_S	9_G	0.976	0.99
110_L	117_L	0.971	0.99
71_G	74_R	0.955	0.99
45_E	49_K	0.950	0.99
20_L	27_A	0.941	0.99
26_F	33_G	0.927	0.99
55_A	61_E	0.914	0.99
91_R	99_L	0.914	0.99
28_K	31_E	0.908	0.99
24_G	44_G	0.897	0.99
19_W	33_G	0.893	0.99
89_E	94_R	0.884	0.99
53_K	57_E	0.873	0.99
37_F	81_W	0.854	0.98
14_S	26_F	0.845	0.98
16_Q	20_L	0.845	0.98
60_E	63_R	0.837	0.98
26_F	32_E	0.832	0.98
10_A	13_D	0.829	0.98
21_A	25_A	0.817	0.98
120_K	123_K	0.808	0.98
101_V	111_S	0.808	0.98
83_K	93_A	0.806	0.98
30_Q	33_G	0.797	0.97
51_T	55_A	0.791	0.97
40_L	48_E	0.786	0.97
31_E	34_G	0.781	0.97
67_E	74_R	0.776	0.97
104_R	107_I	0.774	0.97
35_K	84_L	0.767	0.97
67_E	70_A	0.763	0.97
88_F	92_V	0.757	0.97
95_A	102_P	0.756	0.97
77_A	81_W	0.747	0.96
107_I	111_S	0.747	0.96
56_E	60_E	0.741	0.96
9_G	13_D	0.741	0.96
115_D	119_A	0.741	0.96
65_K	70_A	0.738	0.96
88_F	101_V	0.730	0.96
58_K	63_R	0.728	0.96
115_D	118_T	0.718	0.95
57_E	60_E	0.718	0.95
7_L	12_K	0.711	0.95
119_A	123_K	0.699	0.95
20_L	45_E	0.697	0.95
7_L	10_A	0.692	0.94
27_A	33_G	0.689	0.94
93_A	97_N	0.689	0.94
33_G	100_G	0.687	0.94
87_V	95_A	0.681	0.94
48_E	57_E	0.677	0.94
19_W	26_F	0.666	0.93
12_K	16_Q	0.662	0.93
90_D	94_R	0.656	0.93
5_S	8_A	0.647	0.92
19_W	37_F	0.646	0.92
16_Q	45_E	0.638	0.92
8_A	11_V	0.637	0.91
31_E	68_S	0.634	0.91
96_L	101_V	0.629	0.91
17_Q	43_E	0.628	0.91
72_E	75_A	0.627	0.91
21_A	24_G	0.625	0.91
62_A	70_A	0.621	0.90
36_L	42_K	0.620	0.90
46_K	50_K	0.612	0.90
112_A	115_D	0.610	0.90
57_E	76_K	0.609	0.90
17_Q	89_E	0.607	0.89
63_R	80_T	0.591	0.88
64_G	68_S	0.590	0.88
35_K	77_A	0.583	0.87
66_V	71_G	0.582	0.87
86_Q	90_D	0.580	0.87
31_E	36_L	0.573	0.87
28_K	91_R	0.570	0.86
62_A	115_D	0.569	0.86
6_Q	111_S	0.566	0.86
61_E	64_G	0.563	0.86
82_D	87_V	0.563	0.86
24_G	27_A	0.561	0.85
37_F	47_L	0.558	0.85
66_V	69_M	0.554	0.85
24_G	41_V	0.554	0.85
45_E	48_E	0.552	0.84
57_E	63_R	0.551	0.84
54_A	57_E	0.547	0.84
101_V	107_I	0.546	0.84
23_L	30_Q	0.546	0.84
26_F	113_R	0.544	0.84
114_V	121_V	0.543	0.83
53_K	60_E	0.542	0.83
82_D	88_F	0.537	0.83
29_A	89_E	0.534	0.82
23_L	94_R	0.533	0.82
92_V	96_L	0.528	0.82
65_K	80_T	0.527	0.82
52_R	56_E	0.524	0.81
7_L	11_V	0.524	0.81
64_G	67_E	0.522	0.81
103_T	107_I	0.519	0.81
55_A	59_V	0.517	0.80
62_A	65_K	0.512	0.80
32_E	39_A	0.510	0.80
39_A	46_K	0.510	0.80
23_L	66_V	0.509	0.79
89_E	100_G	0.508	0.79
104_R	115_D	0.506	0.79
28_K	55_A	0.501	0.78
23_L	35_K	0.500	0.78
50_K	71_G	0.500	0.78

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
2yy0A	6	0.296	55.5	0.861	Contact Map
3qprA	8	0.008	45.4	0.869	Contact Map
2lemA	1	0.992	41.5	0.872	Contact Map
3c9iA	5	0.832	41.3	0.872	Contact Map
3r2pA	2	0.912	34.1	0.878	Contact Map
1dipA	2	0.272	34.1	0.878	Contact Map
2a01A	1	0.992	32.2	0.879	Contact Map
3ci9A	5	0.384	28.5	0.883	Contact Map
1jcdA	3	0.192	28.1	0.883	Contact Map
3s84A	2	0.68	27.7	0.883	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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