Difference between revisions of "Sequence-based predictions GLA"

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m (→‎Secondary structure prediction)
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==GOPET==
  
==GOPET==
 
http://genius.embnet.dkfz-heidelberg.de/menu/biounit/open-husar
  
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===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
  +
! GOid
  +
! Confidence
  +
! GO term
  +
|-
  +
|GO:0016798 || 98% || hydrolase activity acting on glycosyl bonds
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|-
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|GO:0004553 || 98% || hydrolase activity hydrolyzing O-glycosyl compounds
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|-
  +
|GO:0016787 || 97% || hydrolase activity
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|-
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|GO:0004557 || 96% || alpha-galactosidase activit
  +
|-
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|GO:0008456 || 89% || alpha-N-acetylgalactosaminidase activity
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|-
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|}
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  +
===BARC_HALSA===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
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! GOid
  +
! Confidence
  +
! GO term
  +
|-
  +
|GO:0005216 || 77%|| ion channel activity
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|-
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|GO:0008020 || 75%|| G-protein coupled photoreceptor activity
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|-
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|GO:0015078 || 60%|| hydrogen ion transmembrane transporter activity
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|-
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|-
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|}
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  +
===RET4_HUMAN===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
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! GOid
  +
! Confidence
  +
! GO term
  +
|-
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|GO:0005488 || 90% || binding
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|-
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|GO:0005501 || 81% || retinoid binding
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|-
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|GO:0008289 || 80% || lipid binding
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|-
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|GO:0019841 || 78% || retinol binding
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|-
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|GO:0005215 || 78% || transporter activity
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|-
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|GO:0016918 || 78% || retinal binding
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|-
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|GO:0005319 || 69% || lipid transporter activity
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|-
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|GO:0008035 || 60% || high-density lipoprotein particle binding
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|-
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|-
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|}
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===INSL5_HUMAN===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
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! GOid
  +
! Confidence
  +
! GO term
  +
|-
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|GO:0005179 || 80% || hormone activity
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|-
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|}
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  +
===LAMP1_HUMAN===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
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! GOid
  +
! Confidence
  +
! GO term
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|-
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|GO:0004812 || 60% || aminoacyl-tRNA ligase activity
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|-
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|GO:0005524 || 60% || ATP binding
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|-
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|}
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===A4_HUMAN===
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{|class="wikitable" border="1" style="text-align:center; border-spacing:0;"
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|-
  +
! GOid
  +
! Confidence
  +
! GO term
  +
|-
  +
|GO:0004866 || 87% || endopeptidase inhibitor activity
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|-
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|GO:0004867 || 86% || serine-type endopeptidase inhibitor activity
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|-
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|GO:0030568 || 83% || plasmin inhibitor activity
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|-
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|GO:0030304 || 83% || trypsin inhibitor activity
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|-
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|GO:0030414 || 82% || peptidase inhibitor activity
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|-
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|GO:0005488 || 79% || binding
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|-
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|GO:0005515 || 74% || protein binding
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|-
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|GO:0046872 || 73% || metal ion binding
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|-
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|GO:0003677 || 71% || DNA binding
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|-
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|GO:0008201 || 70% || heparin binding
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|-
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|GO:0008270 || 69% || zinc ion binding
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|-
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|GO:0005507 || 69% || copper ion binding
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|-
  +
|GO:0005506 || 67% || iron ion binding
  +
|-
  +
|}
   
 
==Pfam==
  
==Pfam==

Revision as of 17:40, 27 May 2011

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


Comparison with DSSP

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

Prediction of disordered regions

DISOPRED

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

POODLE

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

IUPRED

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

META-Disorder

http://www.predictprotein.org/

Prediction of transmembrane alpha-helices and signal peptides

Additional Proteins

TMHMM

Phobius and PolyPhobius

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

OCTOPUS and SPOCTOPUS

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

SignalP

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/

ProtFun 2.2

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

References

<references />

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