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
P81371 UniProt NPD GO	LECS_VATMA	Seed lectin (VML) [Contains: Seed lectin alpha chain; Seed lectin gamma chain; Seed lectin beta chai ...	0.05	-	cyt	0					240
P17563 UniProt NPD GO	SBP1_MOUSE	Selenium-binding protein 1 (56 kDa selenium-binding protein) (SP56)	0.05	-	cyt	0	Cytoplasm				472
P37890 UniProt NPD GO	CBP1_ORYSA	Serine carboxypeptidase 1 precursor (EC 3.4.16.5) (Serine carboxypeptidase I) (Carboxypeptidase C)	0.05	-	pox	1 *		peroxisome [IEP]			510
P37291 UniProt NPD GO	GLYC_YEAST	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS]			469
Q96SA4 UniProt NPD GO	SERC2_HUMAN	Serine incorporator 2 (Tumor differentially expressed 2-like)	0.05	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				456
Q9QZI9 UniProt NPD GO	SERC3_MOUSE	Serine incorporator 3 (Tumor differentially expressed protein 1) (Membrane protein TMS-1) (Axotomy-i ...	0.05	-	end	11 *	Cell membrane; multi-pass membrane protein. Golgi apparatus; Golgi membrane; multi-pass membrane pro ...	Golgi apparatus [IDA] plasma membrane [IDA]			472
O15269 UniProt NPD GO	LCB1_HUMAN	Serine palmitoyltransferase 1 (EC 2.3.1.50) (Long chain base biosynthesis protein 1) (LCB 1) (Serine ...	0.05	-	nuc	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)		605712		473
P09036 UniProt NPD GO	ISK3_MOUSE	Serine protease inhibitor Kazal-type 3 precursor (Prostatic secretory glycoprotein) (P12)	0.05	-	exc	0	Secreted protein				80
Q9Y3F4 UniProt NPD GO	STRAP_HUMAN	Serine-threonine kinase receptor-associated protein (UNR-interacting protein) (WD-40 repeat protein ...	0.05	-	cyt	0			605986		350
Q9PU85 UniProt NPD GO	PIM3_COTJA	Serine/threonine-protein kinase Pim-3 (EC 2.7.11.1) (qpim)	0.05	-	nuc	0					323
P54613 UniProt NPD GO	2AAB_PIG	Serine/threonine-protein phosphatase 2A 65 kDa regulatory subunit A beta isoform (PP2A, subunit A, P ...	0.05	-	cyt	0		cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			602
Q74ZR2 UniProt NPD GO	PP4C_ASHGO	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				310
P60510 UniProt NPD GO	PP4C_HUMAN	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C) (Pp4) (Protein phospha ...	0.05	-	cyt	0	Cytoplasm. Nucleus. Centrosome	centrosome [NAS] nucleus [NAS]	602035		307
P97470 UniProt NPD GO	PP4C_MOUSE	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C) (Pp4) (Protein phospha ...	0.05	-	cyt	0	Cytoplasm. Nucleus. Centrosome	centrosome [NAS] nucleus [NAS]			307
P11084 UniProt NPD GO	PP4C_RABIT	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C) (Pp4) (Protein phospha ...	0.05	-	cyt	0	Cytoplasm. Nucleus. Centrosome				307
P48529 UniProt NPD GO	PPX1_ARATH	Serine/threonine-protein phosphatase PP-X isozyme 1 (EC 3.1.3.16)	0.05	-	cyt	0					305
Q921I1 UniProt NPD GO	TRFE_MOUSE	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal-binding globulin)	0.05	-	end	0	Secreted protein	endocytic vesicle [IDA] endosome [IDA]			697
P46564 UniProt NPD GO	SRV1_CAEEL	Serpentine receptor class V-1 (Protein srv-1) (Protein srg-12)	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				308
O18690 UniProt NPD GO	SRA21_CAEEL	Serpentine receptor class alpha-21 (Protein sra-21)	0.05	-	end	5 *	Membrane; multi-pass membrane protein (Potential)				339
Q95ZY1 UniProt NPD GO	SRB2_CAEEL	Serpentine receptor class beta-2 (Protein srb-2)	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				347
P46569 UniProt NPD GO	SRG11_CAEEL	Serpentine receptor class gamma-11 (Protein srg-11)	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				335
O45150 UniProt NPD GO	SRG30_CAEEL	Serpentine receptor class gamma-30 (Protein srg-30)	0.05	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				299
Q5BIR5 UniProt NPD GO	SPB8_BOVIN	Serpin B8	0.05	-	nuc	0	Cytoplasm (By similarity)				374
Q10482 UniProt NPD GO	STM1_SCHPO	Seven transmembrane protein 1	0.05	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				271
Q9BM97 UniProt NPD GO	JANA_DROER	Sex-regulated protein janus-A	0.05	-	mit	0					135
Q9BM96 UniProt NPD GO	JANA_DROOR	Sex-regulated protein janus-A	0.05	-	mit	0					135
P20613 UniProt NPD GO	SSP2_BOMMO	Sex-specific storage-protein 2 precursor (SP 2) (Arylphorin)	0.05	-	end	0	Secreted protein; extracellular space				704
O88876 UniProt NPD GO	DHRS3_MOUSE	Short-chain dehydrogenase/reductase 3 (EC 1.1.-.-) (Retinal short-chain dehydrogenase/reductase 1) ( ...	0.05	-	end	1 *	Membrane; multi-pass membrane protein (Potential)				302
Q9HAT2 UniProt NPD GO	SIAE_HUMAN	Sialate O-acetylesterase precursor (EC 3.1.1.53) (Sialic acid-specific 9-O-acetylesterase) (H-Lse)	0.05	-	vac	0	Lysosome (Probable)		610079		523
Q9NR45 UniProt NPD GO	SIAS_HUMAN	Sialic acid synthase (N-acetylneuraminate synthase) (EC 2.5.1.56) (N-acetylneuraminic acid synthase) ...	0.05	-	nuc	0		cytoplasm [NAS]	605202	1WVO	359
Q925N2 UniProt NPD GO	SFXN2_MOUSE	Sideroflexin-2	0.05	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrial inner membrane [IDA]			322
Q5F383 UniProt NPD GO	PSL1_CHICK	Signal peptide peptidase-like 2B (EC 3.4.23.-) (Protein SPP-like 2B) (Protein SPPL2b)	0.05	-	end	9	Membrane; multi-pass membrane protein (Probable)				596
Q8TCT6 UniProt NPD GO	PSL4_HUMAN	Signal peptide peptidase-like 3 (EC 3.4.23.-) (SPP-like 3 protein) (Intramembrane protease 2) (IMP2) ...	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Probable)		608240		385
Q9CUS9 UniProt NPD GO	PSL4_MOUSE	Signal peptide peptidase-like 3 (EC 3.4.23.-) (SPP-like 3 protein) (Intramembrane protease 2) (IMP2) ...	0.05	-	end	9 *	Membrane; multi-pass membrane protein (Probable)				384
O22265 UniProt NPD GO	SR43C_ARATH	Signal recognition particle 43 kDa protein, chloroplast precursor (CpSRP43) (Chromo protein SRP43)	0.05	-	mit	0	Plastid; chloroplast; chloroplast stroma	thylakoid membrane (sensu Viridiplantae) [IDA]		1X3Q	373
P17437 UniProt NPD GO	XP2_XENLA	Skin secretory protein xP2 precursor (Protein APEG)	0.05	-	exc	0	Secreted protein				439
P54661 UniProt NPD GO	SMLA_DICDI	Small aggregate formation protein	0.05	-	nuc	0	Cytoplasm				284
Q16663 UniProt NPD GO	CCL15_HUMAN	Small inducible cytokine A15 precursor (CCL15) (Macrophage inflammatory protein 5) (MIP-5) (Chemokin ...	0.05	-	exc	1 *	Secreted protein	extracellular space [TAS]	601393	2HCC	113
Q95N01 UniProt NPD GO	CCL17_CANFA	Small inducible cytokine A17 precursor (CCL17) (Thymus and activation-regulated chemokine) (CC chemo ...	0.05	-	exc	0	Secreted protein				99
P50230 UniProt NPD GO	CCL4_RAT	Small inducible cytokine A4 precursor (CCL4) (Macrophage inflammatory protein 1-beta) (MIP-1-beta)	0.05	-	exc	0	Secreted protein				92
P46632 UniProt NPD GO	CCL4_RABIT	Small inducible cytokine A4 precursor (CCL4) (Macrophage inflammatory protein 1-beta) (MIP-1-beta) ( ...	0.05	-	exc	0	Secreted protein				92
Q8MIN2 UniProt NPD GO	SCYB6_HORSE	Small inducible cytokine B6 precursor (CXCL6) (Granulocyte chemotactic protein 2) (GCP-2)	0.05	-	exc	0	Secreted protein (By similarity)				113
P48065 UniProt NPD GO	S6A12_HUMAN	Sodium- and chloride-dependent betaine transporter (Na+/Cl-betaine/GABA transporter) (BGT-1)	0.05	-	end	12 *	Membrane; multi-pass membrane protein	integral to membrane [TAS]	603080		614
Q9XT77 UniProt NPD GO	SC5A6_RABIT	Sodium-dependent multivitamin transporter (Na(+)-dependent multivitamin transporter)	0.05	-	end	13 *	Membrane; multi-pass membrane protein				636
Q06496 UniProt NPD GO	NPT2A_RAT	Sodium-dependent phosphate transport protein 2A (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotran ...	0.05	-	end	11	Membrane; multi-pass membrane protein				637
Q06495 UniProt NPD GO	NPT2A_HUMAN	Sodium-dependent phosphate transport protein 2A (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotran ...	0.05	-	end	9	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182309		639
Q28620 UniProt NPD GO	NPT2A_RABIT	Sodium-dependent phosphate transport protein 2A (Sodium/phosphate cotransporter 2A) (Na(+)/Pi cotran ...	0.05	-	end	9	Membrane; multi-pass membrane protein				642
Q9DBP0 UniProt NPD GO	NPT2B_MOUSE	Sodium-dependent phosphate transport protein 2B (Sodium/phosphate cotransporter 2B) (Na(+)/Pi cotran ...	0.05	-	end	9	Membrane; multi-pass membrane protein	apical plasma membrane [IDA]			697
Q68KI4 UniProt NPD GO	NHX1_ARATH	Sodium/hydrogen exchanger 1 (Na(+)/H(+) exchanger 1) (NHE-1)	0.05	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein. Tonoplast. Endoplasmic reticulum; endoplasm ...				538
Q62773 UniProt NPD GO	S28A2_RAT	Sodium/nucleoside cotransporter 2 (Na(+)/nucleoside cotransporter 2) (Sodium-coupled nucleoside tran ...	0.05	-	end	12	Membrane; multi-pass membrane protein				659

You are viewing entries 75651 to 75700 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.