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
P23595 UniProt NPD GO	PP2A2_YEAST	Serine/threonine-protein phosphatase PP2A-2 catalytic subunit (EC 3.1.3.16)	0.19	-	cyt	0		protein phosphatase type 2A complex [TAS]			377
Q9Y6J8 UniProt NPD GO	STYL1_HUMAN	Serine/threonine/tyrosine-interacting-like protein 1 (Dual specificity protein phosphatase 24) (Map ...	0.19	-	cyt	0					313
Q5IS55 UniProt NPD GO	SNAT_PANTR	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.19	-	cyt	0					207
P80429 UniProt NPD GO	TRF2_SALSA	Serotransferrin II precursor (Siderophilin II) (STF II)	0.19	-	exc	0	Secreted protein				691
O62488 UniProt NPD GO	SRE27_CAEEL	Serpentine receptor class epsilon-27 (Protein sre-27)	0.19	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				364
Q6UXR4 UniProt NPD GO	SPA13_HUMAN	Serpin A13 precursor	0.19	-	end	0	Secreted protein (Potential)				307
P70124 UniProt NPD GO	SPB5_MOUSE	Serpin B5 precursor (Maspin) (Protease inhibitor 5)	0.19	-	nuc	0	Secreted protein; extracellular space				375
P07724 UniProt NPD GO	ALBU_MOUSE	Serum albumin precursor	0.19	-	exc	0	Secreted protein	cytoplasm [IDA] extracellular region [ISS] protein complex [ISS]			608
O17310 UniProt NPD GO	SXL_MUSDO	Sex-lethal homolog	0.19	-	nuc	0	Nucleus				324
P25675 UniProt NPD GO	NXS2_NAJHH	Short neurotoxin 2 (Toxin CM-10a)	0.19	-	nuc	0	Secreted protein				61
Q9JMH3 UniProt NPD GO	NEUR2_MOUSE	Sialidase-2 (EC 3.2.1.18) (Cytosolic sialidase) (N-acetyl-alpha-neuraminidase 2) (Murine thymic sial ...	0.19	-	cyt	0	Cytoplasm				379
P38724 UniProt NPD GO	ARN2_YEAST	Siderophore iron transporter ARN2 (Triacetylfusarinine C transporter 1) (Triacetylfusarinine C perme ...	0.19	-	end	14	Endosome; endosomal membrane; multi-pass membrane protein (By similarity)	cytoplasmic membrane-bound vesicle [TAS] endosome [TAS]			637
Q8TCT8 UniProt NPD GO	PSL2_HUMAN	Signal peptide peptidase-like 2A (EC 3.4.23.-) (Protein SPP-like 2A) (Protein SPPL2a) (Intramembrane ...	0.19	-	end	9 *	Membrane; multi-pass membrane protein (Probable)		608238		520
Q6IA17 UniProt NPD GO	SIGIR_HUMAN	Single Ig IL-1-related receptor (Single Ig IL-1R-related molecule) (Single immunoglobulin domain-con ...	0.19	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)	membrane [IMP]	605478		410
Q9JLZ8 UniProt NPD GO	SIGIR_MOUSE	Single Ig IL-1-related receptor (Single Ig IL-1R-related molecule) (Single immunoglobulin domain-con ...	0.19	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)	membrane [ISS]			409
Q6P5C5 UniProt NPD GO	SMUG1_MOUSE	Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-)	0.19	-	cyt	0	Nucleus (By similarity)	nucleolus [ISS]			279
Q9YGN6 UniProt NPD GO	SMUG1_XENLA	Single-strand selective monofunctional uracil DNA glycosylase (EC 3.2.2.-)	0.19	-	cyt	0	Nucleus (By similarity)			1OE6	281
P09381 UniProt NPD GO	SSBR_XENLA	Single-stranded DNA-binding protein R, mitochondrial precursor (Mt-SSB-R) (Mt-SSB 2)	0.19	-	mit	0	Mitochondrion				148
P09380 UniProt NPD GO	SSBS_XENLA	Single-stranded DNA-binding protein S, mitochondrial precursor (Mt-SSB-S) (Mt-SSB 1)	0.19	-	mit	0	Mitochondrion				146
P28042 UniProt NPD GO	SSB_RAT	Single-stranded DNA-binding protein, mitochondrial precursor (Mt-SSB) (MtSSB) (P16)	0.19	-	mit	0	Mitochondrion	mitochondrion [NAS]			151
P29779 UniProt NPD GO	OV252_ONCVO	Small heat shock protein OV25-2 (Fragment)	0.19	-	nuc	0					166
P52203 UniProt NPD GO	CCL2_CANFA	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.19	-	exc	0	Secreted protein				101
P42831 UniProt NPD GO	CCL2_PIG	Small inducible cytokine A2 precursor (CCL2) (Monocyte chemotactic protein 1) (MCP-1) (Monocyte chem ...	0.19	-	exc	0	Secreted protein				99
P16619 UniProt NPD GO	CCL3L_HUMAN	Small inducible cytokine A3-like 1 precursor (Tonsillar lymphocyte LD78 beta protein) (LD78-beta(1-7 ...	0.19	-	exc	0	Secreted protein	extracellular region [NAS]	601395		93
Q9JHH5 UniProt NPD GO	SCYBB_MOUSE	Small inducible cytokine B11 precursor (CXCL11) (Interferon-inducible T-cell alpha chemoattractant) ...	0.19	-	exc	1 *	Secreted protein				100
Q9TU67 UniProt NPD GO	RSMB_ERIEU	Small nuclear ribonucleoprotein-associated protein B' (snRNP-B') (Sm protein B') (Sm-B') (SmB') (snR ...	0.19	-	nuc	0	Nucleus				240
P14678 UniProt NPD GO	RSMB_HUMAN	Small nuclear ribonucleoprotein-associated proteins B and B' (snRNP-B) (Sm protein B/B') (Sm-B/Sm-B' ...	0.19	-	nuc	0	Nucleus	small nuclear ribonucleoprotein complex [TAS] spliceosome complex [TAS]	182282	1D3B	240
O70557 UniProt NPD GO	SPR2F_MOUSE	Small proline-rich protein 2F	0.19	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			76
Q9JJP0 UniProt NPD GO	S20A1_RAT	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1) (Phosphate transporter ...	0.19	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [IDA]			681
Q6NV12 UniProt NPD GO	S20AB_BRARE	Sodium-dependent phosphate transporter 1-B (Solute carrier family 20 member 1-B)	0.19	-	end	9 *	Membrane; multi-pass membrane protein (Potential)				652
P23791 UniProt NPD GO	SL9A1_RABIT	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1) (Solute carrier family 9 member 1)	0.19	-	end	12 *	Membrane; multi-pass membrane protein				816
P18907 UniProt NPD GO	AT1A1_HORSE	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.19	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1021
Q9YH26 UniProt NPD GO	AT1A1_OREMO	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.19	-	end	8	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [ISS]			1023
O54701 UniProt NPD GO	NCKX2_RAT	Sodium/potassium/calcium exchanger 2 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 2) (Retinal cone ...	0.19	-	end	11 *	Membrane; multi-pass membrane protein				670
Q9UI40 UniProt NPD GO	NCKX2_HUMAN	Sodium/potassium/calcium exchanger 2 precursor (Na(+)/K(+)/Ca(2+)-exchange protein 2) (Retinal cone ...	0.19	-	end	11 *	Membrane; multi-pass membrane protein		609838		661
Q13621 UniProt NPD GO	S12A1_HUMAN	Solute carrier family 12 member 1 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2) ...	0.19	-	end	10	Membrane; multi-pass membrane protein	membrane fraction [TAS] plasma membrane [TAS]	601678		1099
P55015 UniProt NPD GO	S12A1_RABIT	Solute carrier family 12 member 1 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2) ...	0.19	-	end	12	Membrane; multi-pass membrane protein				1099
Q90592 UniProt NPD GO	GTR2_CHICK	Solute carrier family 2, facilitated glucose transporter member 2 (Glucose transporter type 2, liver ...	0.19	-	end	12 *	Membrane; multi-pass membrane protein				533
P70502 UniProt NPD GO	SO1A3_RAT	Solute carrier organic anion transporter family member 1A3 (Solute carrier family 21 member 4) (Sodi ...	0.19	-	end	9 *	Membrane; multi-pass membrane protein				670
O35913 UniProt NPD GO	SO1A4_RAT	Solute carrier organic anion transporter family member 1A4 (Solute carrier family 21 member 5) (Sodi ...	0.19	-	end	11 *	Membrane; multi-pass membrane protein				661
Q00910 UniProt NPD GO	SO2A1_RAT	Solute carrier organic anion transporter family member 2A1 (Solute carrier family 21 member 2) (Pros ...	0.19	-	end	11 *	Membrane; multi-pass membrane protein				643
P79838 UniProt NPD GO	SHH_PUNCO	Sonic hedgehog protein (SHH) (Fragments)	0.19	-	nuc	0	Sonic hedgehog protein C-product: Secreted protein; extracellular space (By similarity). Sonic hedge ...				121
Q9MZ28 UniProt NPD GO	SPG11_PANTR	Sperm-associated antigen 11 precursor (EP2 protein)	0.19	-	exc	0	Secreted protein				103
Q9NWM0 UniProt NPD GO	SMOX_HUMAN	Spermine oxidase (EC 1.5.3.-) (Polyamine oxidase 1) (PAO-1) (PAOh1)	0.19	-	cyt	0	Cytoplasm (By similarity)				555
Q9Z0L1 UniProt NPD GO	EDG6_MOUSE	Sphingosine 1-phosphate receptor Edg-6 (S1P receptor Edg-6) (Endothelial differentiation G-protein c ...	0.19	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			386
Q91X56 UniProt NPD GO	EDG8_MOUSE	Sphingosine 1-phosphate receptor Edg-8 (Endothelial differentiation sphingolipid G-protein-coupled r ...	0.19	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [TAS]			400
Q9JIA7 UniProt NPD GO	SPHK2_MOUSE	Sphingosine kinase 2 (EC 2.7.1.-) (SK 2) (SPK 2)	0.19	-	cyt	0		cytosol [IEP] membrane fraction [IEP]			617
Q5WR10 UniProt NPD GO	UAP56_CANFA	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q5ZHZ0 UniProt NPD GO	UAP56_CHICK	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428
Q5TM17 UniProt NPD GO	UAP56_MACMU	Spliceosome RNA helicase BAT1 (EC 3.6.1.-) (DEAD box protein UAP56) (56 kDa U2AF65-associated protei ...	0.19	-	cyt	0	Nucleus (By similarity)				428

You are viewing entries 52451 to 52500 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.