Sequence-based predictions GLA

From Bioinformatikpedia
Revision as of 16:04, 28 May 2011 by Grandke (talk | contribs) (→‎OCTOPUS and SPOCTOPUS)

by Benjamin Drexler and Fabian Grandke

Secondary structure prediction

GLA sequence

PSIPRED

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

GLA Psipred.png

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/

GLA DSSP Comp.png

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/

GLA Diso graph.png

POODLE

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

POODLE-S: Missing residues

GLA Poodle s missing.png


POODLE-S: High B-Factor residues

GLA Poodle s high b.png

IUPRED

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

Short Disorder

GLA Iupred Short.png

Long Disorder

GLA Iupred Long.png

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

GLA Meta disorder.png

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

TMHMM

GLA

BARC_HALSA

RET4_HUMAN

INSL5_HUMAN

LAMP1_HUMAN

A4_HUMAN

Phobius and PolyPhobius

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

GLA

Phobius

GLA Phob gla.png

SIGNAL 1 31

REGION 1 9 N-REGION.

REGION 10 22 H-REGION.

REGION 23 31 C-REGION.

TOPO_DOM 32 429 NON CYTOPLASMIC.


PolyPhobius

GLA Poly gla.png

SIGNAL 1 31

REGION 1 12 N-REGION.

REGION 13 26 H-REGION.

REGION 27 31 C-REGION.

TOPO_DOM 32 429 NON CYTOPLASMIC.

BARC_HALSA

Phobius

GLA Phob barc.png

TOPO_DOM 1 22 NON CYTOPLASMIC.

TRANSMEM 23 42

TOPO_DOM 43 53 CYTOPLASMIC.

TRANSMEM 54 76

TOPO_DOM 77 95 NON CYTOPLASMIC.

TRANSMEM 96 114

TOPO_DOM 115 120 CYTOPLASMIC.

TRANSMEM 121 142

TOPO_DOM 143 147 NON CYTOPLASMIC.

TRANSMEM 148 169

TOPO_DOM 170 189 CYTOPLASMIC.

TRANSMEM 190 212

TOPO_DOM 213 217 NON CYTOPLASMIC.

TRANSMEM 218 237

TOPO_DOM 238 262 CYTOPLASMIC.


PolyPhobius

GLA Poly barc.png

TOPO_DOM 1 21 NON CYTOPLASMIC.

TRANSMEM 22 43

TOPO_DOM 44 54 CYTOPLASMIC.

TRANSMEM 55 77

TOPO_DOM 78 94 NON CYTOPLASMIC.

TRANSMEM 95 114

TOPO_DOM 115 120 CYTOPLASMIC.

TRANSMEM 121 141

TOPO_DOM 142 147 NON CYTOPLASMIC.

TRANSMEM 148 166

TOPO_DOM 167 186 CYTOPLASMIC.

TRANSMEM 187 205

TOPO_DOM 206 215 NON CYTOPLASMIC.

TRANSMEM 216 237

TOPO_DOM 238 262 CYTOPLASMIC.

RET4_HUMAN

Phobius

GLA Phob ret4.png

SIGNAL 1 18

REGION 1 2 N-REGION.

REGION 3 13 H-REGION.

REGION 14 18 C-REGION.

TOPO_DOM 19 201 NON CYTOPLASMIC.


PolyPhobius

Poly ret4.png

SIGNAL 1 18

REGION 1 3 N-REGION.

REGION 4 13 H-REGION.

REGION 14 18 C-REGION.

TOPO_DOM 19 201 NON CYTOPLASMIC.

INSL5_HUMAN

Phobius

GLA Phob insl5.png

SIGNAL 1 22

REGION 1 5 N-REGION.

REGION 6 17 H-REGION.

REGION 18 22 C-REGION.

TOPO_DOM 23 135 NON CYTOPLASMIC.

PolyPhobius

Poly insl5.png

SIGNAL 1 22

REGION 1 4 N-REGION.

REGION 5 16 H-REGION.

REGION 17 22 C-REGION.

TOPO_DOM 23 135 NON CYTOPLASMIC.


LAMP1_HUMAN

Phobius

GLA Phob lamp1.png

SIGNAL 1 28

REGION 1 10 N-REGION.

REGION 11 22 H-REGION.

REGION 23 28 C-REGION.

TOPO_DOM 29 381 NON CYTOPLASMIC.

TRANSMEM 382 405

TOPO_DOM 406 417 CYTOPLASMIC.

PolyPhobius

GLA Poly lamp1.png

SIGNAL 1 28

REGION 1 9 N-REGION.

REGION 10 22 H-REGION.

REGION 23 28 C-REGION.

TOPO_DOM 29 381 NON CYTOPLASMIC.

TRANSMEM 382 405

TOPO_DOM 406 417 CYTOPLASMIC.


A4_HUMAN

Phobius

GLA Phob a4.png

SIGNAL 1 17

REGION 1 1 N-REGION.

REGION 2 12 H-REGION.

REGION 13 17 C-REGION.

TOPO_DOM 18 700 NON CYTOPLASMIC.

TRANSMEM 701 723

TOPO_DOM 724 770 CYTOPLASMIC.

PolyPhobius

GLA Poly a4.png

SIGNAL 1 17

REGION 1 3 N-REGION.

REGION 4 12 H-REGION.

REGION 13 17 C-REGION.

TOPO_DOM 18 700 NON CYTOPLASMIC.

TRANSMEM 701 723

TOPO_DOM 724 770 CYTOPLASMIC.

OCTOPUS and SPOCTOPUS

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

GLA

Octopus

GLA Octo gla.png

Spoctopus

GLA Spocto gla.png

BARC_HALSA

Octopus

GLA Octo bacr.png

Spoctopus

GLA Spocto bacr.png

RET4_HUMAN

Octopus

GLA Octo ret4.png

Spoctopus

GLA Spocto ret4.png

INSL5_HUMAN

Octopus

GLA Octo insl5.png

Spoctopus

GLA Spocto insl5.png

LAMP1_HUMAN

Octopus

GLA Octo lamp1.png

Spoctopus

GLA Spocto lamp1.png

A4_HUMAN

Octopus

Octo a4.png

Spoctopus

GLA Spocto a4.png

SignalP

GLA

BARC_HALSA

RET4_HUMAN

INSL5_HUMAN

LAMP1_HUMAN

A4_HUMAN

TargetP

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

GLA

BARC_HALSA

RET4_HUMAN

INSL5_HUMAN

LAMP1_HUMAN

A4_HUMAN

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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