NucPred on Proteomes

Authors: Andrea Krings, Amine Heddad, Markus Brameier and Bob MacCallum, Stockholm Bioinformatics Center, Stockholm University, Sweden.

NucPred - predictions for eukaryotic proteomes

Species:

Note: All filters/tests are combined with AND unless otherwise stated

Show only the proteins with links to database(s):
OMIM - human disease genes
PDB - protein 3D structure
( AND OR combination )

Annotation filters (can be slow! - Perl regexps allowed: e.g. nucleus|nucleolus)

UniProt ID (e.g. "PK3B_")
UniProt description (e.g. "kinase")
UniProt subcellular location
AND
UniProt GO component
AND
AND the
AND the

Only show proteins where the PredictNLS prediction is:

positive
negative

Only show proteins where the PSORT II predicted location

is is not

Click here: to filter by NucPred score

exclude all transmembrane proteins predicted by TMHMM
don't exclude lone N-terminal predicted transmembrane helices
(these could be signal peptides)

export all ACs and IDs as text file

Show proteins (ordered by NucPred score ) from to (currently 98716 matches)

You can bookmark/save your search criteria with this link. You can also start again with default settings.

UniProt accession	UniProt ID	UniProt description	NucPred score	Predict- NLS	PSORT II	TMHMM #helices	UniProt annotation for subcellular location	Uniprot GO cellular component	OMIM	PDB	sequence length
Q9UJ37 UniProt NPD GO	SIA7B_HUMAN	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.17	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				374
P50419 UniProt NPD GO	CAS3_RABIT	Alpha-S2B-casein precursor	0.17	-	exc	0	Secreted protein				182
O04931 UniProt NPD GO	AGLU_BETVU	Alpha-glucosidase precursor (EC 3.2.1.20) (Maltase)	0.17	-	mit	0					913
Q91W89 UniProt NPD GO	MA2C1_MOUSE	Alpha-mannosidase 2C1 (EC 3.2.1.24) (Alpha-D-mannoside mannohydrolase) (Mannosidase alpha class 2C m ...	0.17	-	nuc	0					1039
Q9NTJ4 UniProt NPD GO	MA2C1_HUMAN	Alpha-mannosidase 2C1 (EC 3.2.1.24) (Alpha-D-mannoside mannohydrolase) (Mannosidase alpha class 2C m ...	0.17	-	nuc	0			154580		1040
P79143 UniProt NPD GO	AMPN_CANFA	Aminopeptidase N (EC 3.4.11.2) (cAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.17	-	cyt	0	Membrane; single-pass type II membrane protein				191
Q91ZU1 UniProt NPD GO	ASB6_MOUSE	Ankyrin repeat and SOCS box protein 6 (ASB-6)	0.17	-	cyt	0	Cytoplasm				418
Q502K3 UniProt NPD GO	ANR52_BRARE	Ankyrin repeat domain-containing protein 52	0.17	-	nuc	0					1071
Q92040 UniProt NPD GO	ANX12_COLLI	Annexin A1 isoform p37 (Annexin I isoform p37) (Lipocortin I) (Calpactin II) (Chromobindin-9) (Phosp ...	0.17	-	cyt	0					343
Q40284 UniProt NPD GO	UFOG1_MANES	Anthocyanidin 3-O-glucosyltransferase (EC 2.4.1.115) (Flavonol 3-O-glucosyltransferase 1) (UDP-gluco ...	0.17	-	mit	0					449
O23917 UniProt NPD GO	HCBT2_DIACA	Anthranilate N-benzoyltransferase protein 2 (EC 2.3.1.144) (Anthranilate N-hydroxycinnamoyl/benzoylt ...	0.17	-	nuc	0					446
Q90343 UniProt NPD GO	NR13_COTJA	Anti-apoptotic protein NR13 (Apoptosis regulator Nr-13)	0.17	-	end	2	Cell membrane; multi-pass membrane protein				177
P07086 UniProt NPD GO	ALPS_LIMPO	Anti-lipopolysaccharide factor (anti-LPS) (LALF)	0.17	-	cyt	0					101
Q01747 UniProt NPD GO	LAPP_HAEOF	Anti-platelet protein precursor	0.17	-	exc	0	Secreted protein			1I8N	147
Q03519 UniProt NPD GO	TAP2_HUMAN	Antigen peptide transporter 2 (APT2) (Peptide transporter TAP2) (Peptide transporter PSF2) (Peptide ...	0.17	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...	cytosol [NAS] endoplasmic reticulum lumen [IMP] integral to membrane [NAS] TAP complex [NAS]	170261		686
Q8NK92 UniProt NPD GO	AORSN_ASPOR	Aorsin precursor (EC 3.4.21.-)	0.17	-	exc	0	Secreted protein; extracellular space	extracellular region [NAS]			652
Q9BBR8 UniProt NPD GO	CYF_LOTJA	Apocytochrome f precursor	0.17	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
Q85X29 UniProt NPD GO	CYF_PINKO	Apocytochrome f precursor	0.17	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				319
Q91827 UniProt NPD GO	AR1_XENLA	Apoptosis regulator R1 (XR1) (Fragment)	0.17	-	end	1	Membrane; single-pass membrane protein (Potential)				228
Q9EPB4 UniProt NPD GO	ASC_MOUSE	Apoptosis-associated speck-like protein containing a CARD (mASC) (PYD and CARD domain-containing pro ...	0.17	-	cyt	0	Cytoplasm (By similarity). Upstream of caspase activation, a redistribution from the cytoplasm to th ...	cytoplasm [ISS] cytosol [IDA] extracellular region [IDA]			193
Q9BEF8 UniProt NPD GO	GHRL_CANFA	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.17	-	vac	0	Secreted protein				117
P39654 UniProt NPD GO	LX12L_MOUSE	Arachidonate 12-lipoxygenase, leukocyte-type (EC 1.13.11.31) (12-LOX)	0.17	-	cyt	0	Cytoplasm				662
Q32KX1 UniProt NPD GO	ARRD5_BOVIN	Arrestin domain-containing protein 5	0.17	-	mit	0					332
Q7M370 UniProt NPD GO	AAAD_RABIT	Arylacetamide deacetylase (EC 3.1.1.-) (AADAC) (50 kDa microsomal esterase/N-deacetylase)	0.17	-	cyt	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Microso ...	endoplasmic reticulum membrane [IDA]			398
P02706 UniProt NPD GO	ASGR1_RAT	Asialoglycoprotein receptor 1 (ASGPR 1) (ASGP-R 1) (Hepatic lectin 1) (RHL-1)	0.17	-	cyt	1 *	Membrane; single-pass type II membrane protein				283
Q91XE4 UniProt NPD GO	ACY3_MOUSE	Aspartoacylase-2 (EC 3.5.1.15) (Aminoacylase-3) (ACY-3) (Acylase III) (Hepatitis C virus core-bindin ...	0.17	-	cyt	0		apical plasma membrane [IDA] cytoplasm [IDA] membrane fraction [IDA]			318
Q6FJ38 UniProt NPD GO	ATG16_CANGA	Autophagy protein 16	0.17	-	cyt	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				108
Q75CI5 UniProt NPD GO	ATG10_ASHGO	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.17	-	cyt	0	Cytoplasm (By similarity)				170
Q6CBS9 UniProt NPD GO	ATG27_YARLI	Autophagy-related protein 27 precursor	0.17	-	nuc	1	Intracytoplasmic membrane; single-pass type I membrane protein (By similarity). Perivacuolar punctat ...				276
Q756G8 UniProt NPD GO	ATG7_ASHGO	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.17	-	nuc	0	Cytoplasm (By similarity)				625
Q6CXW3 UniProt NPD GO	ATG7_KLULA	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.17	-	cyt	0	Cytoplasm (By similarity)				603
Q52CS0 UniProt NPD GO	ATG7_MAGGR	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.17	-	cyt	0	Cytoplasm (By similarity)				718
P13088 UniProt NPD GO	AUX22_SOYBN	Auxin-induced protein AUX22	0.17	-	cyt	0	Nucleus (By similarity)				195
Q69VE0 UniProt NPD GO	IAA23_ORYSA	Auxin-responsive protein IAA23 (Indoleacetic acid-induced protein 23)	0.17	-	nuc	0	Nucleus (By similarity)				193
Q9N1E5 UniProt NPD GO	CD22_PANPA	B-cell receptor CD22 precursor (Siglec-2) (Fragment)	0.17	-	cyt	0	Membrane; single-pass type I membrane protein				332
Q96KE9 UniProt NPD GO	BTBD6_HUMAN	BTB/POZ domain-containing protein 6 (Lens BTB domain protein)	0.17	-	cyt	0					410
Q96P09 UniProt NPD GO	BIRC8_HUMAN	Baculoviral IAP repeat-containing protein 8 (Inhibitor of apoptosis-like protein 2) (IAP-like protei ...	0.17	-	cyt	0	Cytoplasm (Probable)			1XB1	236
P32847 UniProt NPD GO	B3AT_ONCMY	Band 3 anion exchange protein (Solute carrier family 4 member 1)	0.17	-	end	12	Membrane; multi-pass membrane protein				918
P04919 UniProt NPD GO	B3AT_MOUSE	Band 3 anion transport protein (Anion exchange protein 1) (AE 1) (Solute carrier family 4 member 1) ...	0.17	-	end	12	Membrane; multi-pass membrane protein				929
Q4R649 UniProt NPD GO	BBS5_MACFA	Bardet-Biedl syndrome 5 protein homolog	0.17	-	cyt	0	Localizes to basal bodies (By similarity)				341
Q9CZQ9 UniProt NPD GO	BBS5_MOUSE	Bardet-Biedl syndrome 5 protein homolog	0.17	-	cyt	0	Localizes to basal bodies				341
Q4W1I8 UniProt NPD GO	PER1_ZINEL	Basic peroxidase precursor 1 (EC 1.11.1.7) (ZePrx33.44) (ZePrx34.70)	0.17	-	mit	1 *	Secreted protein (By similarity)				321
Q09200 UniProt NPD GO	B4GN1_MOUSE	Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylc ...	0.17	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				533
Q7TNV9 UniProt NPD GO	BD14_MOUSE	Beta-defensin 14 precursor (Defensin, beta 14) (BD-14) (mBD-14)	0.17	-	mit	1 *	Secreted protein (By similarity)				67
P46164 UniProt NPD GO	BD06_BOVIN	Beta-defensin 6 (BNDB-6) (BNBD-6)	0.17	-	mit	0	Secreted protein				42
O97524 UniProt NPD GO	BGLR_FELCA	Beta-glucuronidase precursor (EC 3.2.1.31)	0.17	-	mit	1 *	Lysosome				651
P33687 UniProt NPD GO	LACB1_FELCA	Beta-lactoglobulin-1 (Beta-LG-1) (Beta-lactoglobulin I)	0.17	-	cyt	0					162
P54097 UniProt NPD GO	TECTB_CHICK	Beta-tectorin precursor	0.17	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...				329
P49079 UniProt NPD GO	AKH1_MAIZE	Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplast precursor (AK-HD 1) (AK-HSDH 1) [ ...	0.17	-	mit	0	Plastid; chloroplast				920
P51820 UniProt NPD GO	DRTS_SOYBN	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.17	-	cyt	0					530

You are viewing entries 54051 to 54100 of 98716. You can see more proteins by changing the limits in the form at the top of this page, or click here for the next page of proteins .

If you find NucPred useful, please cite this paper:

NucPred - Predicting Nuclear Localization of Proteins. Brameier M, Krings A, Maccallum RM. Bioinformatics, 2007. PubMed id: 17332022

The authors also look forward to your comments and suggestions.

What does the NucPred score mean?

You have to decide on a NucPred score threshold. Sequences which score greater than or equal to this threshold are predicted to spend some time in the nucleus. Higher thresholds yield fewer predicted nuclear proteins, but these predictions are more accurate (you can have higher confidence in them). The table below gives more details of the performance of NucPred estimated using the sequences it was trained on (by cross-validation). Another benchmark is available in the Bioinformatics 2007 paper.

NucPred score threshold	Specificity	Sensitivity
see above	fraction of proteins predicted to be nuclear that actually are nuclear	fraction of true nuclear proteins that are predicted (coverage)
0.10	0.45	0.88
0.20	0.52	0.83
0.30	0.57	0.77
0.40	0.63	0.69
0.50	0.70	0.62
0.60	0.71	0.53
0.70	0.81	0.44
0.80	0.84	0.32
0.90	0.88	0.21
1.00	1.00	0.02

Sequences which score >= 0.8 with NucPred and which are predicted by PredictNLS to contain an NLS have been shown to be 93% correct with a coverage of 16%. (PredictNLS by itself is 87% correct with 26% coverage on the same data.)

Go back to the NucPred Home Page.