PHA_gran_rgn - PFAM28P - GREMLIN Contacts

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PHA_gran_rgn - Putative polyhydroxyalkanoic acid system protein (PHA_gran_rgn)

PFAM:	PF09650	Sequences: IDISIPHSLGKEEARRRAEKGAEKLAEKFGLEETWEGDTLRFSRSGVSGTIDVTDDEVRLEVDLPFLLAAFKGKIESEIRKELDKLL	Download Alignment We filter this alignment to remove sites that have many gaps before running GREMLIN. Date: 2015_10
Length:	87 (83)
Sequences:	10903 (6947)
Seq/√Len:	762.5
META:	0.956

GREMLIN Results:

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

Residue pairs sorted by coevolution strength:

i	j	Sco	Prob
36_E	41_R	2.576	1.00
54_T	57_E	2.496	1.00
4_S	57_E	2.407	1.00
76_E	80_R	2.299	1.00
15_R	19_E	2.227	1.00
10_G	13_E	2.096	1.00
2_D	61_E	1.947	1.00
11_K	55_D	1.947	1.00
39_T	52_D	1.928	1.00
39_T	50_T	1.909	1.00
2_D	59_R	1.824	1.00
13_E	17_R	1.755	1.00
13_E	16_R	1.724	1.00
72_K	76_E	1.687	1.00
11_K	38_D	1.655	1.00
67_L	70_A	1.644	1.00
4_S	59_R	1.612	1.00
26_A	33_E	1.593	1.00
42_F	49_G	1.496	1.00
5_I	84_D	1.481	1.00
19_E	23_E	1.411	1.00
78_E	81_K	1.408	1.00
74_K	77_S	1.397	1.00
41_R	50_T	1.348	1.00
50_T	61_E	1.328	1.00
80_R	84_D	1.325	1.00
54_T	59_R	1.308	1.00
24_K	28_K	1.285	1.00
34_T	41_R	1.282	1.00
19_E	33_E	1.254	1.00
24_K	27_E	1.249	1.00
77_S	81_K	1.234	1.00
9_L	17_R	1.213	1.00
16_R	20_K	1.165	1.00
15_R	38_D	1.151	1.00
48_S	63_D	1.120	1.00
36_E	39_T	1.113	1.00
73_G	76_E	1.113	1.00
78_E	82_E	1.103	1.00
21_G	25_L	1.072	1.00
43_S	48_S	1.064	1.00
44_R	65_P	1.036	1.00
74_K	78_E	1.004	1.00
69_A	72_K	0.989	1.00
52_D	59_R	0.972	1.00
10_G	14_A	0.961	1.00
11_K	15_R	0.940	1.00
23_E	33_E	0.939	1.00
10_G	56_D	0.907	1.00
12_E	16_R	0.889	1.00
66_F	70_A	0.873	1.00
63_D	66_F	0.871	1.00
30_G	44_R	0.866	1.00
5_I	80_R	0.857	1.00
23_E	26_A	0.853	1.00
10_G	55_D	0.849	1.00
70_A	74_K	0.849	1.00
52_D	61_E	0.846	1.00
73_G	77_S	0.845	1.00
71_F	74_K	0.840	1.00
12_E	55_D	0.827	1.00
15_R	53_V	0.827	1.00
32_E	43_S	0.827	1.00
6_P	57_E	0.819	1.00
19_E	35_W	0.812	1.00
20_K	24_K	0.809	1.00
21_G	24_K	0.807	1.00
15_R	35_W	0.798	1.00
44_R	47_V	0.793	1.00
28_K	82_E	0.786	1.00
9_L	13_E	0.781	1.00
64_L	75_I	0.781	1.00
16_R	19_E	0.780	1.00
77_S	80_R	0.780	1.00
43_S	46_G	0.776	1.00
23_E	27_E	0.770	1.00
33_E	40_L	0.757	1.00
50_T	63_D	0.756	1.00
14_A	53_V	0.750	1.00
66_F	69_A	0.747	1.00
20_K	23_E	0.746	1.00
70_A	73_G	0.723	1.00
47_V	62_V	0.722	1.00
22_A	33_E	0.721	1.00
75_I	78_E	0.698	1.00
3_I	60_L	0.690	1.00
34_T	43_S	0.688	1.00
30_G	45_S	0.680	1.00
22_A	25_L	0.673	1.00
35_W	40_L	0.661	1.00
6_P	56_D	0.657	1.00
18_A	21_G	0.651	1.00
41_R	48_S	0.643	1.00
18_A	40_L	0.642	1.00
74_K	82_E	0.640	1.00
80_R	83_L	0.633	1.00
8_S	56_D	0.632	1.00
11_K	54_T	0.622	1.00
40_L	44_R	0.620	1.00
18_A	51_I	0.615	1.00
75_I	79_I	0.613	1.00
18_A	22_A	0.609	1.00
10_G	16_R	0.608	1.00
5_I	83_L	0.599	1.00
67_L	71_F	0.599	1.00
65_P	68_L	0.598	1.00
33_E	44_R	0.591	1.00
25_L	29_F	0.588	1.00
17_R	65_P	0.583	1.00
9_L	14_A	0.582	1.00
46_G	65_P	0.575	1.00
68_L	71_F	0.571	1.00
67_L	72_K	0.559	1.00
64_L	68_L	0.556	1.00
49_G	62_V	0.549	1.00
47_V	65_P	0.533	1.00
25_L	58_V	0.533	1.00
26_A	31_L	0.529	1.00
31_L	45_S	0.523	1.00
37_G	52_D	0.521	1.00
45_S	70_A	0.507	1.00
46_G	66_F	0.502	1.00
17_R	20_K	0.500	1.00
49_G	60_L	0.500	1.00

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
3lnoA	1	0.8506	27.8	0.851	Contact Map
2gjhA	2	0.6092	23.2	0.857	Contact Map
3cq1A	2	0.8046	21.3	0.859	Contact Map
3udcA	3	0.8736	18.1	0.864	Contact Map
2jpiA	1	0.954	15.5	0.867	Contact Map
3ux2A	2	0.8621	15.2	0.868	Contact Map
2mblA	1	0.6552	14.8	0.869	Contact Map
2mobA	1	0.7126	14.3	0.87	Contact Map
1usuB	1	0.8966	14.2	0.87	Contact Map
1uwdA	1	0.8161	13.8	0.87	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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