Sequence-based predictions GLA

^{by Benjamin Drexler and Fabian Grandke}

Secondary structure prediction

GLA sequence

PSIPRED

http://bioinf.cs.ucl.ac.uk/psipred/

Jpred3

http://www.compbio.dundee.ac.uk/www-jpred/index.html

EBI	Chain	Describtion	E-value
3hg5	B	Alpha-galactosidase A	0.0
3hg5	A	Alpha-galactosidase A	0.0
3hg4	B	Alpha-galactosidase A	0.0
3hg4	A	Alpha-galactosidase A	0.0
3hg2	B	Alpha-galactosidase A	0.0
3hg2	A	Alpha-galactosidase A	0.0
3gxt	B	Alpha-galactosidase A	0.0
3gxt	A	Alpha-galactosidase A	0.0
3gxp	B	Alpha-galactosidase A	0.0
3gxp	A	Alpha-galactosidase A	0.0
3gxn	B	Alpha-galactosidase A	0.0
3gxn	A	Alpha-galactosidase A	0.0
1r47	B	Alpha-galactosidase A	0.0
1r47	A	Alpha-galactosidase A	0.0
1r46	B	Alpha-galactosidase A	0.0
1r46	A	Alpha-galactosidase A	0.0
3hg3	B	Alpha-galactosidase A	0.0
3hg3	A	Alpha-galactosidase A	0.0
3lxc	B	Alpha-galactosidase A	0.0
3lxc	A	Alpha-galactosidase A	0.0
3lxb	B	Alpha-galactosidase A	0.0
3lxb	A	Alpha-galactosidase A	0.0
3lxa	B	Alpha-galactosidase A	0.0
3lxa	A	Alpha-galactosidase A	0.0
3lx9	B	Alpha-galactosidase A	0.0
3lx9	A	Alpha-galactosidase A	0.0
1ktc	A	alpha-N-acetylgalactosaminidase	e-113
1ktb	A	alpha-N-acetylgalactosaminidase	e-113
3igu	B	Alpha-N-acetylgalactosaminidase	e-100
3igu	A	Alpha-N-acetylgalactosaminidase	e-100
3h55	B	Alpha-N-acetylgalactosaminidase	e-100
3h55	A	Alpha-N-acetylgalactosaminidase	e-100
3h54	B	Alpha-N-acetylgalactosaminidase	e-100
3h54	A	Alpha-N-acetylgalactosaminidase	e-100
3h53	B	Alpha-N-acetylgalactosaminidase	e-100
3h53	A	Alpha-N-acetylgalactosaminidase	e-100

The lightblue colored protein is the protein that was used as query sequence.

Comparison with DSSP

http://swift.cmbi.ru.nl/servers/html/

Find a pdf version of this image here: File:GLA DSSP Comp.pdf

Prediction of disordered regions

DISOPRED

http://bioinf.cs.ucl.ac.uk/disopred/

POODLE

http://mbs.cbrc.jp/poodle/poodle.html

POODLE-S: Missing residues

POODLE-S: High B-Factor residues

IUPRED

http://iupred.enzim.hu/index.html

Short Disorder

Long Disorder

META-Disorder

http://www.predictprotein.org/

Hint: You will have to register. It is free of charge, but you can submit max. 3 sequences within the next 12 months!

https://www.rostlab.org/owiki/index.php/Metadisorder

PROFbval

https://rostlab.org/owiki/index.php/Profbval

NORSnet

https://www.rostlab.org/owiki/index.php/Norsnet

Ucon

https://www.rostlab.org/owiki/index.php/UCON

Prediction of transmembrane alpha-helices and signal peptides

Additional Proteins

• BACR_HALSA
• RET4_HUMAN
• INSL5_HUMAN
• LAMP1_HUMAN
• A4_HUMAN

Phobius and PolyPhobius

http://phobius.sbc.su.se/

OCTOPUS and SPOCTOPUS

http://octopus.cbr.su.se/index.php

TargetP

http://www.cbs.dtu.dk/services/TargetP/

Prediction of GO terms

GOPET

http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar

We used the default settings (GO aspect: molecular function, maximum number of predictions: 20, confidence threshold: 60, GOPET model 2007 june, version 2.0, GOPET database 2007). The results only contain GOids of the GO aspect "molecular function", since the other two GO aspects (cellular component and biological process) were not available.

GLA

GOid	Confidence	GO term
GO:0016798	98%	hydrolase activity acting on glycosyl bonds
GO:0004553	98%	hydrolase activity hydrolyzing O-glycosyl compounds
GO:0016787	97%	hydrolase activity
GO:0004557	96%	alpha-galactosidase activit
GO:0008456	89%	alpha-N-acetylgalactosaminidase activity

BARC_HALSA

GOid	Confidence	GO term
GO:0005216	77%	ion channel activity
GO:0008020	75%	G-protein coupled photoreceptor activity
GO:0015078	60%	hydrogen ion transmembrane transporter activity

RET4_HUMAN

GOid	Confidence	GO term
GO:0005488	90%	binding
GO:0005501	81%	retinoid binding
GO:0008289	80%	lipid binding
GO:0019841	78%	retinol binding
GO:0005215	78%	transporter activity
GO:0016918	78%	retinal binding
GO:0005319	69%	lipid transporter activity
GO:0008035	60%	high-density lipoprotein particle binding

INSL5_HUMAN

GOid	Confidence	GO term
GO:0005179	80%	hormone activity

LAMP1_HUMAN

GOid	Confidence	GO term
GO:0004812	60%	aminoacyl-tRNA ligase activity
GO:0005524	60%	ATP binding

A4_HUMAN

GOid	Confidence	GO term
GO:0004866	87%	endopeptidase inhibitor activity
GO:0004867	86%	serine-type endopeptidase inhibitor activity
GO:0030568	83%	plasmin inhibitor activity
GO:0030304	83%	trypsin inhibitor activity
GO:0030414	82%	peptidase inhibitor activity
GO:0005488	79%	binding
GO:0005515	74%	protein binding
GO:0046872	73%	metal ion binding
GO:0003677	71%	DNA binding
GO:0008201	70%	heparin binding
GO:0008270	69%	zinc ion binding
GO:0005507	69%	copper ion binding
GO:0005506	67%	iron ion binding

Pfam

http://pfam.sanger.ac.uk/

GLA

Domains:

• Melibiase (Pfam A)
  • Molecular function: hydrolase activity, hydrolyzing O-glycosyl compounds (GO:0004553)
  • Bilogical process: carbohydrate metabolic process (GO:0005975)

BACR_HALSA

Domains:

• Bacteriorhodopsin-like protein (Pfam A)
  • Cellular component: membrane (GO:0016020)
  • Molecular function: ion channel activity (GO:0005216)
  • Biological process: ion transport (GO:0006811)

• Domain of unknown function DUF21 (Pfam A, not significant)
  • No annotation

RET4_HUMAN

Domains:

•  Lipocalin / cytosolic fatty-acid binding protein family (Pfam A)
  • Molecular function: binding (GO:0005488)

• DspF/AvrF protein (Pfam A, not significant)
  • No annotation

• PB008544 (Pfam B)
  • No annotation

INSL5_HUMAN

Domains:

• Insulin/IGF/Relaxin family (Pfam A)
  • Cellular component: extracellular region (GO:0005576)
  • Molecular function: hormone activity (GO:0005179)

LAMP1_HUMAN

Domains:

• Lysosome-associated membrane glycoprotein (Pfam A)
  • Cellular component: membrane (GO:0016020)

• Protein of unknown function DUF1180 (Pfam A, not significant)
  • No annotation

A4_HUMAN

Domains:

• Amyloid A4 N-terminal heparin-binding (Pfam A)

• Copper-binding of amyloid precursor, CuBD

• Kunitz/Bovine pancreatic trypsin inhibitor domain

• E2 domain of amyloid precursor protein

• Beta-amyloid peptide (beta-APP)

• beta-amyloid precursor protein C-terminus

ProtFun 2.2

http://www.cbs.dtu.dk/services/ProtFun/

References

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