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
P62136 UniProt NPD GO	PP1A_HUMAN	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.25	-	mit	0	Cytoplasm (By similarity)		176875		330
P62139 UniProt NPD GO	PP1A_RABIT	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.25	-	mit	0	Cytoplasm (By similarity)			1FJM	330
P62138 UniProt NPD GO	PP1A_RAT	Serine/threonine-protein phosphatase PP1-alpha catalytic subunit (EC 3.1.3.16) (PP-1A)	0.25	-	mit	0	Cytoplasm (By similarity)				330
Q20411 UniProt NPD GO	SRA11_CAEEL	Serpentine receptor class alpha-11 (Protein sra-11)	0.25	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				334
Q86WD7 UniProt NPD GO	SPA9_HUMAN	Serpin A9 precursor (Germinal center B-cell expressed transcript 1 protein)	0.25	-	end	0	Secreted protein (Potential)				417
P48594 UniProt NPD GO	SPB4_HUMAN	Serpin B4 (Squamous cell carcinoma antigen 2) (SCCA-2) (Leupin)	0.25	-	cyt	0	Cytoplasm. Seems to also be secreted in plasma by cancerous cells but at a low level	cytoplasm [NAS]	600518		390
O97018 UniProt NPD GO	SXL_CHRRU	Sex-lethal homolog	0.25	-	nuc	0	Nucleus (By similarity)				307
P80548 UniProt NPD GO	NXS1_MICNI	Short neurotoxin 1 (Neurotoxin alpha)	0.25	-	nuc	0	Secreted protein				60
P10455 UniProt NPD GO	NXSC_LATCO	Short neurotoxin C precursor	0.25	-	nuc	0	Secreted protein				83
Q9YGW8 UniProt NPD GO	NXS4_LATLA	Short neurotoxin VAN-29 precursor	0.25	-	nuc	0	Secreted protein				83
P49967 UniProt NPD GO	SR543_ARATH	Signal recognition particle 54 kDa protein 3 (SRP54)	0.25	-	cyt	0	Cytoplasm				495
P49970 UniProt NPD GO	SR543_HORVU	Signal recognition particle 54 kDa protein 3 (SRP54)	0.25	-	cyt	0	Cytoplasm				493
O88811 UniProt NPD GO	STAM2_MOUSE	Signal transducing adapter molecule 2 (STAM-2) (Hrs-binding protein)	0.25	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein			1UJ0	523
Q9UHE8 UniProt NPD GO	STEA1_HUMAN	Six transmembrane epithelial antigen of prostate 1	0.25	-	end	6	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] intercellular junction [TAS] plasma membrane [TAS]	604415		339
P35326 UniProt NPD GO	SPR2A_HUMAN	Small proline-rich protein 2A (SPR-2A) (2-1)	0.25	-	nuc	0	Cytoplasm	cornified envelope [NAS] cytoplasm [IDA]	182267		72
P22532 UniProt NPD GO	SPR2D_HUMAN	Small proline-rich protein 2D (SPR-2D) (Small proline-rich protein II) (SPR-II)	0.25	-	nuc	0	Cytoplasm	cornified envelope [NAS] cytoplasm [IDA]			72
P02719 UniProt NPD GO	SCNA_ELEEL	Sodium channel protein (Na(+) channel)	0.25	-	end	19	Membrane; multi-pass membrane protein				1820
P27922 UniProt NPD GO	SC6A3_BOVIN	Sodium-dependent dopamine transporter (DA transporter) (DAT)	0.25	-	end	12	Membrane; multi-pass membrane protein				693
P54710 UniProt NPD GO	ATNG_HUMAN	Sodium/potassium-transporting ATPase gamma chain (Sodium pump gamma chain) (Na+/K+ ATPase subunit ga ...	0.25	-	nuc	1 *	Membrane; single-pass type III membrane protein (Potential)	sodium:potassium-exchanging ATPase complex [NAS]	601814		66
Q6DNF7 UniProt NPD GO	GCY32_CAEEL	Soluble guanylate cyclase gcy-32 (EC 4.6.1.2)	0.25	-	cyt	0	Cytoplasm (By similarity)				684
P55017 UniProt NPD GO	S12A3_HUMAN	Solute carrier family 12 member 3 (Thiazide-sensitive sodium-chloride cotransporter) (Na-Cl symporte ...	0.25	-	end	11	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	600968		1021
P59158 UniProt NPD GO	S12A3_MOUSE	Solute carrier family 12 member 3 (Thiazide-sensitive sodium-chloride cotransporter) (Na-Cl symporte ...	0.25	-	end	10	Membrane; multi-pass membrane protein				1002
P55018 UniProt NPD GO	S12A3_RAT	Solute carrier family 12 member 3 (Thiazide-sensitive sodium-chloride cotransporter) (Na-Cl symporte ...	0.25	-	end	11	Membrane; multi-pass membrane protein				1002
Q9UKG4 UniProt NPD GO	S13A4_HUMAN	Solute carrier family 13 member 4 (Na(+)/sulfate cotransporter SUT-1)	0.25	-	end	12 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	604309		627
P45640 UniProt NPD GO	SOML_CYCLU	Somatolactin precursor (SL)	0.25	-	exc	0	Secreted protein				229
P30938 UniProt NPD GO	SSR5_RAT	Somatostatin receptor type 5 (SS5R)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				363
O18938 UniProt NPD GO	SOMA_BUBBU	Somatotropin precursor (Growth hormone)	0.25	-	exc	1 *	Secreted protein				217
P45655 UniProt NPD GO	SOMA_CORAU	Somatotropin precursor (Growth hormone)	0.25	-	vac	0	Secreted protein				210
Q9DGG5 UniProt NPD GO	SOMA_ONCMA	Somatotropin precursor (Growth hormone)	0.25	-	mit	0	Secreted protein				210
Q95230 UniProt NPD GO	SP17_PAPHA	Sperm surface protein Sp17 (Sperm autoantigenic protein 17)	0.25	+	nuc	0	Membrane; peripheral membrane protein (Potential)				163
Q99K82 UniProt NPD GO	SMOX_MOUSE	Spermine oxidase (EC 1.5.3.-) (Polyamine oxidase 1) (PAO-1) (PAOh1)	0.25	-	cyt	0	Cytoplasm. Isoform 2: Cytoplasm. Nucleus				555
Q8R1R3 UniProt NPD GO	STAR7_MOUSE	StAR-related lipid transfer protein 7 (StARD7) (START domain-containing protein 7)	0.25	-	cyt	0					295
Q863B3 UniProt NPD GO	SND1_BOVIN	Staphylococcal nuclease domain-containing protein 1 (p100 co-activator) (100 kDa coactivator)	0.25	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). In IL-4 stimulated cells colocalizes with STAT6 ...				910
Q9DE06 UniProt NPD GO	STAR_SALFO	Steroidogenic acute regulatory protein, mitochondrial precursor (StAR) (StARD1)	0.25	-	mit	0	Mitochondrion (By similarity)				287
Q60457 UniProt NPD GO	SOAT1_CRIGR	Sterol O-acyltransferase 1 (EC 2.3.1.26) (Cholesterol acyltransferase 1) (Acyl coenzyme A:cholestero ...	0.25	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				546
P83515 UniProt NPD GO	SCAL2_STRCA	Struthiocalcin-2 (SCA-2)	0.25	-	cyt	0	Eggshell matrix				142
O70531 UniProt NPD GO	S26A2_RAT	Sulfate transporter (Diastrophic dysplasia protein homolog) (Solute carrier family 26 member 2)	0.25	+	end	9	Membrane; multi-pass membrane protein				739
P36077 UniProt NPD GO	SRX1_YEAST	Sulfiredoxin (EC 1.8.98.2) (Sulphiredoxin)	0.25	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			127
Q9WUW8 UniProt NPD GO	ST1C2_RAT	Sulfotransferase 1C2 (EC 2.8.2.-) (Sulfotransferase K1) (rSULT1C2)	0.25	-	cyt	0	Lysosome				296
Q9I919 UniProt NPD GO	GPR85_BRARE	Super conserved receptor expressed in brain 2	0.25	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				371
O35717 UniProt NPD GO	SOCS2_MOUSE	Suppressor of cytokine signaling 2 (SOCS-2) (Cytokine-inducible SH2 protein 2) (CIS-2)	0.25	-	nuc	0		cytoplasm [ISS]			198
Q02563 UniProt NPD GO	SV2A_RAT	Synaptic vesicle glycoprotein 2A (Synaptic vesicle protein 2A) (Synaptic vesicle protein 2)	0.25	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...	integral to membrane [IDA] synaptic vesicle membrane [IDA]			742
Q9JIS5 UniProt NPD GO	SV2A_MOUSE	Synaptic vesicle glycoprotein 2A (Synaptic vesicle protein 2A) (Synaptic vesicle protein 2) (Calcium ...	0.25	-	end	12	Synaptic vesicle; synaptic vesicle membrane; multi-pass membrane protein. Enriched in chromaffin gra ...	synaptic vesicle [IDA]			742
P36975 UniProt NPD GO	SNP25_DROME	Synaptosomal-associated protein 25 (SNAP-25) (Synaptosomal-associated 25 kDa protein)	0.25	-	nuc	0	Complexed with macromolecular elements of the nerve terminal	plasma membrane [NAS]			212
O00186 UniProt NPD GO	STXB3_HUMAN	Syntaxin-binding protein 3 (UNC-18 homolog 3) (UNC-18C) (UNC-18-3) (Platelet Sec1 protein) (PSP)	0.25	-	nuc	0	Cytoplasm; cytosol. In platelets, predominantly cytosolic. Membane. Low amounts membrane-associated		608339		592
Q61003 UniProt NPD GO	CD6_MOUSE	T-cell differentiation antigen CD6 precursor	0.25	-	exc	1	Membrane; single-pass type I membrane protein				665
Q8R183 UniProt NPD GO	TIMD2_MOUSE	T-cell immunoglobulin and mucin domain-containing protein 2 precursor (TIMD-2) (T cell membrane prot ...	0.25	-	end	1	Membrane; single-pass type I membrane protein (Potential)				305
P04214 UniProt NPD GO	TVB6_MOUSE	T-cell receptor beta chain V region E1 precursor	0.25	-	exc	0				1KJ2	136
O04450 UniProt NPD GO	TCPE_ARATH	T-complex protein 1 subunit epsilon (TCP-1-epsilon) (CCT-epsilon)	0.25	-	cyt	0	Cytoplasm (By similarity)				535
Q9XGN1 UniProt NPD GO	TTG1_ARATH	TRANSPARENT TESTA GLABRA 1 protein (TTG1 protein)	0.25	-	nuc	0	Cytoplasm				341

You are viewing entries 45751 to 45800 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.