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
O76038 UniProt NPD GO	SEGN_HUMAN	Secretagogin	0.21	-	cyt	0	Cytoplasm	cytoplasm [NAS]	609202		276
P05045 UniProt NPD GO	LEC1_DOLBI	Seed lectin subunit I precursor (SL) [Contains: Seed lectin subunit II]	0.21	-	exc	0				1LU2	275
P09918 UniProt NPD GO	LOX3_PEA	Seed lipoxygenase-3 (EC 1.13.11.12)	0.21	-	cyt	0	Cytoplasm				861
P34897 UniProt NPD GO	GLYM_HUMAN	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.21	-	mit	0	Mitochondrion	mitochondrion [TAS]	138450	2A7V	504
O54694 UniProt NPD GO	LCB2_CRIGR	Serine palmitoyltransferase 2 (EC 2.3.1.50) (Long chain base biosynthesis protein 2) (LCB 2) (Serine ...	0.21	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				560
P07759 UniProt NPD GO	SPA3K_MOUSE	Serine protease inhibitor A3K precursor (Contrapsin) (Serpin A3K)	0.21	-	end	0	Secreted protein				418
Q8BMY7 UniProt NPD GO	IPK2_MOUSE	Serine protease inhibitor Kazal-type 2 precursor	0.21	-	exc	0	Secreted protein (By similarity)				86
P05049 UniProt NPD GO	SNAK_DROME	Serine protease snake precursor (EC 3.4.21.-)	0.21	-	mit	0	Secreted protein	extracellular region [TAS]			435
P21549 UniProt NPD GO	SPYA_HUMAN	Serine--pyruvate aminotransferase (EC 2.6.1.51) (SPT) (Alanine--glyoxylate aminotransferase) (EC 2.6 ...	0.21	-	mit	0	Peroxisome. Except in some PH1 patients where AGT is found in the mitochondrial matrix	peroxisome [TAS]	259900	1J04	392
Q96Q40 UniProt NPD GO	AL2S7_HUMAN	Serine/threonine-protein kinase ALS2CR7 (EC 2.7.11.22) (Amyotrophic lateral sclerosis 2 chromosomal ...	0.21	-	mit	0					384
Q86SG6 UniProt NPD GO	NEK8_HUMAN	Serine/threonine-protein kinase Nek8 (EC 2.7.11.1) (Never in mitosis A-related kinase 8) (NimA-relat ...	0.21	-	cyt	0	Cytoplasm (By similarity). Predominantly (By similarity)		609799		692
Q7XKA8 UniProt NPD GO	SAPK5_ORYSA	Serine/threonine-protein kinase SAPK5 (EC 2.7.11.1) (Osmotic stress/abscisic acid-activated protein ...	0.21	-	cyt	0					370
Q9QZS5 UniProt NPD GO	SGK2_MOUSE	Serine/threonine-protein kinase Sgk2 (EC 2.7.11.1) (Serum/glucocorticoid-regulated kinase 2)	0.21	-	cyt	0					367
Q6DFJ6 UniProt NPD GO	TBK1_XENLA	Serine/threonine-protein kinase TBK1 (EC 2.7.11.1)	0.21	-	cyt	0	Cytoplasm (By similarity)				725
P48488 UniProt NPD GO	PP1_MEDVA	Serine/threonine-protein phosphatase PP1 (EC 3.1.3.16)	0.21	-	cyt	0					321
P23778 UniProt NPD GO	PP2A_BRANA	Serine/threonine-protein phosphatase PP2A catalytic subunit (EC 3.1.3.16) (Fragment)	0.21	-	cyt	0					309
O17820 UniProt NPD GO	SRG17_CAEEL	Serpentine receptor class gamma-17 (Protein srg-17)	0.21	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				320
P50453 UniProt NPD GO	SPB9_HUMAN	Serpin B9 (Cytoplasmic antiproteinase 3) (CAP-3) (CAP3) (Protease inhibitor 9)	0.21	-	cyt	0	Cytoplasm	cytoplasm [TAS] cytosol [TAS]	601799		376
O14018 UniProt NPD GO	SYSC_SCHPO	Seryl-tRNA synthetase, cytoplasmic (EC 6.1.1.11) (Serine--tRNA ligase) (SerRS)	0.21	-	cyt	0	Cytoplasm (By similarity)				450
P10457 UniProt NPD GO	NXS2_LATCO	Short neurotoxin II precursor	0.21	-	nuc	0	Secreted protein				83
O18881 UniProt NPD GO	SRP14_MACRA	Signal recognition particle 14 kDa protein (SRP14) (Fragment)	0.21	-	nuc	1 *	Cytoplasm				74
P53885 UniProt NPD GO	MDG1_YEAST	Signal transduction protein MDG1 (Multicopy suppressor of defective G-protein 1)	0.21	-	nuc	0	Cell membrane; peripheral membrane protein	plasma membrane [IDA]			366
O14087 UniProt NPD GO	RIM1_SCHPO	Single-stranded DNA-binding protein rim1, mitochondrial precursor (Mitochondrial ssDNA-binding prote ...	0.21	-	mit	0	Mitochondrion (By similarity)				150
P40090 UniProt NPD GO	SCC4_YEAST	Sister chromatid cohesion protein 4	0.21	-	cyt	0	Nucleus. Associates with chromatin	nuclear chromatin [IDA]			624
P29778 UniProt NPD GO	OV251_ONCVO	Small heat shock protein OV25-1	0.21	-	nuc	0					174
P13236 UniProt NPD GO	CCL4_HUMAN	Small inducible cytokine A4 precursor (CCL4) (Macrophage inflammatory protein 1-beta) (MIP-1-beta) ( ...	0.21	-	exc	1 *	Secreted protein	extracellular space [TAS]	182284	1JE4	92
O70558 UniProt NPD GO	SPR2G_MOUSE	Small proline-rich protein 2G	0.21	-	nuc	0	Cytoplasm (By similarity)	cornified envelope [NAS]			76
O09116 UniProt NPD GO	SPRR3_MOUSE	Small proline-rich protein 3 (Cornifin beta)	0.21	-	nuc	0	Cytoplasm				238
Q8NBS3 UniProt NPD GO	S4A11_HUMAN	Sodium bicarbonate transporter-like protein 11 (Bicarbonate transporter-related protein 1) (Solute c ...	0.21	-	end	11	Membrane; multi-pass membrane protein		610206		891
Q61609 UniProt NPD GO	S20A1_MOUSE	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1) (Phosphate transporter ...	0.21	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				681
Q92123 UniProt NPD GO	AT1A1_XENLA	Sodium/potassium-transporting ATPase alpha-1 chain (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ ATPase 1)	0.21	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1025
P50997 UniProt NPD GO	AT1A1_CANFA	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.21	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]			1021
P92006 UniProt NPD GO	GCY34_CAEEL	Soluble guanylate cyclase gcy-34 (EC 4.6.1.2)	0.21	-	cyt	0	Cytoplasm (By similarity)				686
Q5DWW9 UniProt NPD GO	SSY23_ORYSA	Soluble starch synthase 2-3, chloroplast precursor (EC 2.4.1.21) (Soluble starch synthase II-3) (Sta ...	0.21	-	mit	0	Plastid; amyloplast. Granule-bound and soluble				810
Q91Y63 UniProt NPD GO	S13A3_MOUSE	Solute carrier family 13 member 3 (Sodium-dependent high-affinity dicarboxylate transporter 2) (Na(+ ...	0.21	-	end	11 *	Membrane; multi-pass membrane protein	membrane fraction [IDA]			600
P19357 UniProt NPD GO	GTR4_RAT	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.21	-	end	11 *	Intracytoplasmic membrane; perinuclear region; multi-pass membrane protein (By similarity). Localize ...	endosome [IDA] membrane [IDA]			509
P14142 UniProt NPD GO	GTR4_MOUSE	Solute carrier family 2, facilitated glucose transporter member 4 (Glucose transporter type 4, insul ...	0.21	-	end	11 *	Intracytoplasmic membrane; perinuclear region; multi-pass membrane protein (By similarity). Localize ...	cytoplasmic vesicle membrane [IDA] endosome [IDA] integral to membrane of membrane fraction [IDA] integral to plasma membrane [IDA] microsome [IDA] perinuclear region [IDA] plasma membrane [IDA]			509
P21919 UniProt NPD GO	SOML_GADMO	Somatolactin precursor (SL)	0.21	-	exc	0	Secreted protein				235
Q6E211 UniProt NPD GO	SOML_ORYLA	Somatolactin precursor (SL)	0.21	-	end	0	Secreted protein				230
Q9YGH3 UniProt NPD GO	SMS1B_CARAU	Somatostatin IB precursor [Contains: [Pro12]-somatostatin-24; [Pro2]-somatostatin-14]	0.21	-	exc	0	Secreted protein				111
P01171 UniProt NPD GO	SMS1_ICTPU	Somatostatin-1 precursor (Somatostatin I) [Contains: Somatostatin-14 (SS-14)]	0.21	-	exc	0	Secreted protein				114
P20332 UniProt NPD GO	SOMA2_ONCMY	Somatotropin 2 precursor (Growth hormone 2)	0.21	-	vac	0	Secreted protein				210
O13188 UniProt NPD GO	SOMA_CORLV	Somatotropin precursor (Growth hormone)	0.21	-	vac	0	Secreted protein				210
Q9W6R8 UniProt NPD GO	SOMA_HETFO	Somatotropin precursor (Growth hormone)	0.21	-	end	0	Secreted protein				200
Q9VS60 UniProt NPD GO	SMSR1_DROME	Sphingomyelin synthase-related 1	0.21	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			600
Q15428 UniProt NPD GO	SF3A2_HUMAN	Splicing factor 3A subunit 2 (Spliceosome-associated protein 62) (SAP 62) (SF3a66)	0.21	-	nuc	0	Nucleus (By similarity)	small nuclear ribonucleoprotein complex [TAS] spliceosome complex [IDA]	600796		464
Q06350 UniProt NPD GO	CHI2_YEAST	Sporulation-specific chitinase 2 precursor (EC 3.2.1.14)	0.21	-	mit	1 *	Secreted protein (Potential)	cytoplasm [IDA]			511
P59096 UniProt NPD GO	STAR6_MOUSE	StAR-related lipid transfer protein 6 (StARD6) (START domain-containing protein 6)	0.21	-	nuc	0					233
Q09005 UniProt NPD GO	STM1B_XENLA	Stathmin-1-B (Stathmin clone XO20) (Fragment)	0.21	-	nuc	0	Cytoplasm				71
Q7KV14 UniProt NPD GO	STEL3_DROME	Stellate protein CG33238	0.21	-	nuc	0		cytoplasm [ISS] nucleus [ISS] protein kinase CK2 complex [ISS]			171

You are viewing entries 50051 to 50100 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.