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/

GLA

Phobius

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

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

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

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

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

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

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

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

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

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

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

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

Spoctopus

BARC_HALSA

Octopus

Spoctopus

RET4_HUMAN

Octopus

Spoctopus

INSL5_HUMAN

Octopus

Spoctopus

LAMP1_HUMAN

Octopus

Spoctopus

A4_HUMAN

Octopus

Spoctopus

TargetP

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

Name	Length	mTP	SP	other	Loc	RC
GLA	429	0.041	0.860	0.141	S	2
BACR_HALSA	262	0.019	0.897	0.562	S	4
RET4_HUMAN	201	0.242	0.928	0.020	S	2
INSL5_HUMA	135	0.074	0.899	0.037	S	1
LAMP1_HUMA	417	0.043	0.953	0.017	S	1
A4_HUMAN	770	0.035	0.937	0.084	S	1

http://www.cbs.dtu.dk/services/TargetP-1.1/output.php

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

Pfam is a database composed of the protein domain families that is created by using Hidden Markov Models profiles(HMMs). Each protein domain family is represented by a multiple sequence alignment and a HMMs. One can search one protein sequence against Pfam and obtain all the possible domains that the query sequence might contain.

Pfam database includes two parts A and B where the protein domain families with different quality levels. In the 1.0 release of Pfam, the protein entries in Pfam-A and Pfam-B were from Swissprot (a few initial members of seed alignment in Pfam-A were from several sources: Swissprot, Prosite, ProDom etc.). In the current release of Pfam, the entries in Pfam-A and Pfam-B are from Pfamseq(UniProtKB) and ADDA respectively.

The Pfam-A contains the well characterized entries with annotation. It starts with the building of the seed alignment with a few selected representative sequence members under manually quality checking. Then the HMMs is applied automatically to make full alignment and try to detect all the possible members for each initial family. The families/domains in Pfam-A are in high quality level and could be used as a reliable annotation/classification evidence for the query sequence.

The Pfam-B is created based on the sequence alignment of the entries from ADDA by using HMMs. Those entries existing already in Pfam-A are excluded. There are no confirmed annotation and no manual quality checking for the families in Pfam-B, therefore there could be some errors (e.g. the members in one family could be just randomly aligned) and the overall quality is relative low. However, it still can be useful for the situation that one can not find domain evidence in Pfam-A for the query sequence.

We used the "sequence search" feature of Pfam to determine potential domains or domain families of the protein. Afterwards we checked out the corresponding page of the domain (family) for a GO annotation. The search was performed with the default settings (cut-off: use E-Value, threshold 1.0), but we also included Pfam-B in the search. Only one hit in Pfam-B was found which does not have any GO annotation and hence there was no gain in including Pfam-B. The classification in respect to the significance of a hit was done by the Pfam search algorithm. The results are listed in the tables below.

GLA

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Melibiase	Family	x	Molecular function	hydrolase activity, hydrolyzing O-glycosyl compounds	GO:0004553
Pfam-A	Melibiase	Family	x	Biological process	carbohydrate metabolic process	GO:0005975

BACR_HALSA

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Bacteriorhodopsin-like protein	Domain	x	Cellular component	membrane	GO:0016020
Pfam-A	Bacteriorhodopsin-like protein	Domain	x	Molecular function	ion channel activity	GO:0005216
Pfam-A	Bacteriorhodopsin-like protein	Domain	x	Biological process	ion transport	GO:0006811
Pfam-A	Domain of unknown function DUF21	Family		-	-	-

RET4_HUMAN

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Lipocalin / cytosolic fatty-acid binding protein family	Domain	x	Molecular function	binding	GO:0005488
Pfam-A	DspF/AvrF protein	Family		-	-	-
Pfam-B	PB008544	-	-	-	-	-

INSL5_HUMAN

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Insulin/IGF/Relaxin family	Domain	x	Cellular component	extracellular region	GO:0005576
Pfam-A	Insulin/IGF/Relaxin family	Domain	x	Molecular function	hormone activity	GO:0005179

LAMP1_HUMAN

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Lysosome-associated membrane glycoprotein	Family	x	Cellular component	membrane	GO:0016020
Pfam-A	Protein of unknown function DUF1180	Family		-	-	-

A4_HUMAN

Source	Description	Entry type	Significant	GO aspect	GO description	GO id
Pfam-A	Amyloid A4 N-terminal heparin-binding	Domain	x	Cellular component	integral to membrane	GO:0016021
Pfam-A	Amyloid A4 N-terminal heparin-binding	Domain	x	Molecular function	binding	GO:0005488
Pfam-A	Copper-binding of amyloid precursor, CuBD	Domain	x	-	-	-
Pfam-A	Kunitz/Bovine pancreatic trypsin inhibitor domain	Domain	x	Molecular function	serine-type endopeptidase inhibitor activity	GO:0004867
Pfam-A	E2 domain of amyloid precursor protein	Domain	x	-	-	-
Pfam-A	Beta-amyloid peptide	Family	x	Cellular component	integral to membrane	GO:0016021
Pfam-A	Beta-amyloid peptide	Family	x	Molecular function	binding	GO:0005488
Pfam-A	beta-amyloid precursor protein C-terminus	Family	x	-	-	-
Pfam-A	Exonuclease VII, large subunit	Family		-	-	-
Pfam-A	Transcriptional activator TraM	Family		-	-	-

ProtFun 2.2

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

References

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