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
O18373 UniProt NPD GO	SPS1_DROME	Selenide, water dikinase (EC 2.7.9.3) (Selenophosphate synthetase) (Selenium donor protein) (Protein ...	0.02	-	cyt	0					398
P63300 UniProt NPD GO	SEPW1_MOUSE	Selenoprotein W	0.02	-	cyt	0	Cytoplasm	cytoplasm [TAS] plasma membrane [TAS]			87
Q95KL4 UniProt NPD GO	SEPW1_PIG	Selenoprotein W	0.02	-	cyt	0	Cytoplasm	cytoplasm [ISS] plasma membrane [ISS]			86
P63301 UniProt NPD GO	SEPW1_RAT	Selenoprotein W	0.02	-	cyt	0	Cytoplasm	cytoplasm [ISS] plasma membrane [ISS]			87
P80964 UniProt NPD GO	PB1_PIG	Seminal plasma protein pB1 precursor (pAIF-1) (DQH protein)	0.02	-	mit	0	Secreted protein				130
P27626 UniProt NPD GO	DIN1_RAPSA	Senescence-associated protein DIN1	0.02	-	mit	0					183
P83567 UniProt NPD GO	SOVO_SEPOF	SepOvotropin	0.02	-		0	Secreted protein				13
Q39218 UniProt NPD GO	SAT3_ARATH	Serine acetyltransferase 3, mitochondrial precursor (EC 2.3.1.30) (AtSAT-3) (SAT-m) (AtSERAT2;2)	0.02	-	mit	0	Mitochondrion				376
Q8W2B8 UniProt NPD GO	SAT4_ARATH	Serine acetyltransferase 4 (EC 2.3.1.30) (AtSAT-4) (AtSERAT3;2)	0.02	-	cyt	0	Cytoplasm				355
P34898 UniProt NPD GO	GLYC_NEUCR	Serine hydroxymethyltransferase, cytosolic (EC 2.1.2.1) (Serine methylase) (Glycine hydroxymethyltra ...	0.02	-	cyt	0	Cytoplasm				480
P34899 UniProt NPD GO	GLYM_PEA	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.02	-	mit	0	Mitochondrion				518
Q3MHV9 UniProt NPD GO	SERC1_BOVIN	Serine incorporator 1 (Tumor differentially expressed protein 2)	0.02	-	end	9 *	Cell membrane; multi-pass membrane protein (By similarity)				453
Q9NRX5 UniProt NPD GO	SERC1_HUMAN	Serine incorporator 1 (Tumor differentially expressed protein 2) (Tumor differentially expressed 1 p ...	0.02	-	end	11 *	Cell membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] plasma membrane [ISS]			453
Q9QZI8 UniProt NPD GO	SERC1_MOUSE	Serine incorporator 1 (Tumor differentially expressed protein 2) (Tumor differentially expressed 1 p ...	0.02	-	end	11 *	Cell membrane; multi-pass membrane protein	endoplasmic reticulum membrane [ISS] plasma membrane [ISS]			453
Q58CW5 UniProt NPD GO	SERC2_BOVIN	Serine incorporator 2 (Tumor differentially expressed 2-like)	0.02	-	end	11 *	Membrane; multi-pass membrane protein (Potential)				452
P83290 UniProt NPD GO	SPAZ_ARTOL	Serine protease (EC 3.4.21.-) (Aoz) (Fragment)	0.02	-		0					20
Q17004 UniProt NPD GO	SP24D_ANOGA	Serine protease SP24D precursor (EC 3.4.21.-) (AGSP24D)	0.02	-	end	2 *					269
O46163 UniProt NPD GO	SGP3_SCHGR	Serine protease inhibitor 3 precursor (Serine protease inhibitor III) (Protease inhibitor SGPI-3)	0.02	-	exc	1 *	Secreted protein				63
O60575 UniProt NPD GO	ISK4_HUMAN	Serine protease inhibitor Kazal-type 4 precursor (Peptide PEC-60 homolog)	0.02	-	mit	0	Secreted protein (By similarity)				86
Q9QZX7 UniProt NPD GO	SRR_MOUSE	Serine racemase (EC 5.1.1.-)	0.02	-	nuc	0					339
P84187 UniProt NPD GO	SGAT_MAIZE	Serine--glyoxylate aminotransferase (EC 2.6.1.45) (SGAT) (Alanine--glyoxylate aminotransferase) (EC ...	0.02	-	cyt	0	Peroxisome				136
P51817 UniProt NPD GO	PRKX_HUMAN	Serine/threonine-protein kinase PRKX (EC 2.7.11.1) (Protein kinase PKX1)	0.02	-	cyt	0			300083		358
Q6FM81 UniProt NPD GO	PP4C_CANGA	Serine/threonine-protein phosphatase 4 catalytic subunit (EC 3.1.3.16) (PP4C)	0.02	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				309
O00743 UniProt NPD GO	PPP6_HUMAN	Serine/threonine-protein phosphatase 6 (EC 3.1.3.16) (PP6)	0.02	-	cyt	0	Cytoplasm (By similarity)		300141		305
Q9CQR6 UniProt NPD GO	PPP6_MOUSE	Serine/threonine-protein phosphatase 6 (EC 3.1.3.16) (PP6)	0.02	-	cyt	0	Cytoplasm (By similarity)				305
Q64620 UniProt NPD GO	PPP6_RAT	Serine/threonine-protein phosphatase 6 (EC 3.1.3.16) (PP6) (Protein phosphatase V) (PP-V)	0.02	-	cyt	0	Cytoplasm (By similarity)				305
P46506 UniProt NPD GO	SRB11_CAEEL	Serpentine receptor class beta-11 (Protein srb-11)	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				346
O02241 UniProt NPD GO	SRB17_CAEEL	Serpentine receptor class beta-17 (Protein srb-17)	0.02	-	end	6 *	Membrane; multi-pass membrane protein (Probable)				308
P54141 UniProt NPD GO	SRB6_CAEEL	Serpentine receptor class beta-6 (Protein srb-6)	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				337
P91210 UniProt NPD GO	SRD25_CAEEL	Serpentine receptor class delta-25 (Protein srd-25)	0.02	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				318
Q17760 UniProt NPD GO	SRD7_CAEEL	Serpentine receptor class delta-7 (Protein srd-7)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Potential)				318
P46568 UniProt NPD GO	SRG10_CAEEL	Serpentine receptor class gamma-10 (Protein srg-10)	0.02	-	end	8 *	Membrane; multi-pass membrane protein (Probable)				324
Q9DG83 UniProt NPD GO	VSP6_TRIMU	Serpentokallikrein-1 precursor (EC 3.4.21.-)	0.02	-	exc	0	Secreted protein				260
Q5R899 UniProt NPD GO	SPB6_PONPY	Serpin B6	0.02	-	cyt	0	Cytoplasm (By similarity)				376
P83517 UniProt NPD GO	ALBU_NEOFS	Serum albumin (Fragments)	0.02	-	nuc	0	Secreted protein				101
P22000 UniProt NPD GO	SAA2_RABIT	Serum amyloid A-2 protein precursor	0.02	-	exc	0					122
P52430 UniProt NPD GO	PON1_MOUSE	Serum paraoxonase/arylesterase 1 (EC 3.1.1.2) (EC 3.1.8.1) (PON 1) (Serum aryldialkylphosphatase 1) ...	0.02	-	mit	0	Secreted protein; extracellular space			1V04	354
P55159 UniProt NPD GO	PON1_RAT	Serum paraoxonase/arylesterase 1 (EC 3.1.1.2) (EC 3.1.8.1) (PON 1) (Serum aryldialkylphosphatase 1) ...	0.02	-	mit	0	Secreted protein; extracellular space			1V04	354
Q15165 UniProt NPD GO	PON2_HUMAN	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.02	-	cyt	0	Membrane; peripheral membrane protein		602447		354
Q91090 UniProt NPD GO	PON2_MELGA	Serum paraoxonase/arylesterase 2 (EC 3.1.1.2) (EC 3.1.8.1) (PON 2) (Serum aryldialkylphosphatase 2) ...	0.02	-	mit	0	Membrane; peripheral membrane protein (By similarity)				354
Q62087 UniProt NPD GO	PON3_MOUSE	Serum paraoxonase/lactonase 3 (EC 3.1.1.-)	0.02	-	end	0	Secreted protein; extracellular space (By similarity)				354
P54365 UniProt NPD GO	JANB_DROPS	Sex-regulated protein janus-B	0.02	-	nuc	0					140
P08471 UniProt NPD GO	SXIG_VOLCA	Sexual inducer glycoprotein precursor	0.02	-	exc	1 *					208
Q9NRA2 UniProt NPD GO	S17A5_HUMAN	Sialin (Solute carrier family 17 member 5) (Sodium/sialic acid cotransporter) (AST) (Membrane glycop ...	0.02	-	end	10 *	Lysosome; lysosomal membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [TAS] lysosomal membrane [TAS] membrane fraction [TAS]	604369		495
Q9MZD1 UniProt NPD GO	S17A5_SHEEP	Sialin (Solute carrier family 17 member 5) (Sodium/sialic acid cotransporter) (Membrane glycoprotein ...	0.02	-	end	11 *	Lysosome; lysosomal membrane; multi-pass membrane protein (Potential)				495
Q5E9M8 UniProt NPD GO	SFXN1_BOVIN	Sideroflexin-1	0.02	-	cyt	3	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				321
Q9H9B4 UniProt NPD GO	SFXN1_HUMAN	Sideroflexin-1 (Tricarboxylate carrier protein) (TCC)	0.02	-	cyt	3	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				321
Q08299 UniProt NPD GO	ENB1_YEAST	Siderophore iron transporter ENB1 (Siderophore iron transporter ARN4) (Enterobactin permease)	0.02	-	end	11	Endosome; endosomal membrane; multi-pass membrane protein (By similarity)	cytoplasmic membrane-bound vesicle [TAS] endosome [TAS]			606
Q12133 UniProt NPD GO	SPC3_YEAST	Signal peptidase complex subunit SPC3 (Microsomal signal peptidase subunit 3)	0.02	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	signal peptidase complex [IDA]			184
P02885 UniProt NPD GO	SILU_RHIPU	Sillucin	0.02	-	nuc	0	Secreted protein				30

You are viewing entries 85701 to 85750 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.