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
Q09141 UniProt NPD GO	CCL8_BOVIN	Small inducible cytokine A8 precursor (CCL8) (Monocyte chemotactic protein 2) (MCP-2) (Monocyte chem ...	0.16	-	exc	0	Secreted protein (By similarity)				99
P49873 UniProt NPD GO	CCL8_PIG	Small inducible cytokine A8 precursor (CCL8) (Monocyte chemotactic protein 2) (MCP-2) (Monocyte chem ...	0.16	-	exc	0	Secreted protein (By similarity)				99
P27048 UniProt NPD GO	RSMB_MOUSE	Small nuclear ribonucleoprotein-associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB)	0.16	-	nuc	0	Nucleus	cytoplasm [IDA] nucleus [IDA]			231
Q9TU66 UniProt NPD GO	RSMB_MONDO	Small nuclear ribonucleoprotein-associated protein B' (snRNP-B') (Sm protein B') (Sm-B') (SmB') (snR ...	0.16	-	nuc	0	Nucleus				240
Q9UBC9 UniProt NPD GO	SPRR3_HUMAN	Small proline-rich protein 3 (Cornifin beta) (Esophagin) (22 kDa pancornulin)	0.16	-	nuc	0	Cytoplasm	cornified envelope [TAS]	182271		169
Q8R1S9 UniProt NPD GO	S38A4_MOUSE	Sodium-coupled neutral amino acid transporter 4 (Na(+)-coupled neutral amino acid transporter 4) (Am ...	0.16	-	end	11	Cell membrane; multi-pass membrane protein	integral to membrane [TAS]			547
Q8WUM9 UniProt NPD GO	S20A1_HUMAN	Sodium-dependent phosphate transporter 1 (Solute carrier family 20 member 1) (Phosphate transporter ...	0.16	-	end	9 *	Membrane; multi-pass membrane protein		137570		679
P70414 UniProt NPD GO	NAC1_MOUSE	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.16	-	end	10 *	Cell membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [IDA]			970
Q01728 UniProt NPD GO	NAC1_RAT	Sodium/calcium exchanger 1 precursor (Na(+)/Ca(2+)-exchange protein 1)	0.16	-	end	10 *	Cell membrane; multi-pass membrane protein				971
P53794 UniProt NPD GO	SC5A3_HUMAN	Sodium/myo-inositol cotransporter (Na(+)/myo-inositol cotransporter)	0.16	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600444		718
P06685 UniProt NPD GO	AT1A1_RAT	Sodium/potassium-transporting ATPase alpha-1 chain precursor (EC 3.6.3.9) (Sodium pump 1) (Na+/K+ AT ...	0.16	-	end	10	Membrane; multi-pass membrane protein	sodium:potassium-exchanging ATPase complex [ISS]		1MO8	1023
P55014 UniProt NPD GO	S12A1_MOUSE	Solute carrier family 12 member 1 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2) ...	0.16	-	end	12	Membrane; multi-pass membrane protein				1095
P55016 UniProt NPD GO	S12A1_RAT	Solute carrier family 12 member 1 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 2) ...	0.16	-	end	11	Membrane; multi-pass membrane protein				1095
P55012 UniProt NPD GO	S12A2_MOUSE	Solute carrier family 12 member 2 (Bumetanide-sensitive sodium-(potassium)-chloride cotransporter 1) ...	0.16	-	end	12	Membrane; multi-pass membrane protein	apical plasma membrane [IDA] basolateral plasma membrane [IDA]			1205
Q9UP95 UniProt NPD GO	S12A4_HUMAN	Solute carrier family 12 member 4 (Electroneutral potassium-chloride cotransporter 1) (Erythroid K-C ...	0.16	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604119		1085
Q8IVM8 UniProt NPD GO	S22A9_HUMAN	Solute carrier family 22 member 9 (Organic anion transporter 4)	0.16	-	end	12 *	Membrane; multi-pass membrane protein (Potential)		607579		553
Q9BXS9 UniProt NPD GO	S26A6_HUMAN	Solute carrier family 26 member 6 (Pendrin-like protein 1) (Pendrin L1)	0.16	-	end	9	Membrane; multi-pass membrane protein				759
Q9H1N7 UniProt NPD GO	S35B3_HUMAN	Solute carrier family 35 member B3	0.16	+	end	10	Membrane; multi-pass membrane protein (Potential)				401
Q8CD26 UniProt NPD GO	SL35E_MOUSE	Solute carrier family 35 member E1	0.16	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				265
Q9JHI3 UniProt NPD GO	SO2B1_RAT	Solute carrier organic anion transporter family member 2B1 (Solute carrier family 21 member 9) (Orga ...	0.16	-	end	12 *	Membrane; multi-pass membrane protein				682
P12855 UniProt NPD GO	SOMA1_XENLA	Somatotropin A precursor (Growth hormone A) (GH-A)	0.16	-	cyt	0	Secreted protein				214
Q5R4U9 UniProt NPD GO	SORCN_PONPY	Sorcin	0.16	-	cyt	0	Cytoplasm (By similarity)				198
Q94743 UniProt NPD GO	SORCN_SCHJA	Sorcin	0.16	-	cyt	0					171
P30626 UniProt NPD GO	SORCN_HUMAN	Sorcin (22 kDa protein) (CP-22) (V19)	0.16	-	cyt	0	Cytoplasm	cytoplasm [TAS]	182520	1JUO	198
P17405 UniProt NPD GO	ASM_HUMAN	Sphingomyelin phosphodiesterase precursor (EC 3.1.4.12) (Acid sphingomyelinase) (aSMase)	0.16	-	mit	1 *	Lysosome		607616		629
P48303 UniProt NPD GO	EDG1_RAT	Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate receptor 1) (S1P1)	0.16	-	end	7 *	Membrane; multi-pass membrane protein				383
O08530 UniProt NPD GO	EDG1_MOUSE	Sphingosine 1-phosphate receptor Edg-1 (Sphingosine 1-phosphate receptor 1) (S1P1) (Lysophospholipid ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein				382
P19837 UniProt NPD GO	SPD1_NEPCL	Spidroin 1 (Dragline silk fibroin 1) (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space				747
P46804 UniProt NPD GO	SPD2_NEPCL	Spidroin 2 (Dragline silk fibroin 2) (Fragment)	0.16	-	nuc	0	Secreted protein; extracellular space				627
P36596 UniProt NPD GO	FDFT_SCHPO	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.16	-	vac	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [IGI]			460
Q92459 UniProt NPD GO	FDFT_USTMA	Squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FPP:FPP far ...	0.16	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				572
O88908 UniProt NPD GO	SOAT2_MOUSE	Sterol O-acyltransferase 2 (EC 2.3.1.26) (Cholesterol acyltransferase 2) (Acyl coenzyme A:cholestero ...	0.16	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	membrane fraction [IDA]			525
P28343 UniProt NPD GO	THS1_VITVI	Stilbene synthase 1 (EC 2.3.1.95) (Resveratrol synthase 1) (Trihydroxystilbene synthase 1) (PSV25)	0.16	-	cyt	0	Cytoplasm				392
Q19200 UniProt NPD GO	STO1_CAEEL	Stomatin-1	0.16	-	nuc	1 *					330
Q22165 UniProt NPD GO	STO4_CAEEL	Stomatin-4	0.16	-	mit	1 *					281
P83093 UniProt NPD GO	STIM2_MOUSE	Stromal interaction molecule 2 (Fragment)	0.16	-	cyt	0	Cell membrane; single-pass type I membrane protein (Potential)				146
P08254 UniProt NPD GO	MMP3_HUMAN	Stromelysin-1 precursor (EC 3.4.24.17) (Matrix metalloproteinase-3) (MMP-3) (Transin-1) (SL-1)	0.16	-	exc	0		extracellular space [TAS]	185250	3USN	477
P25036 UniProt NPD GO	YSP3_YEAST	Subtilisin-like protease 3 precursor (EC 3.4.21.-) (Subtilisin-like protease III)	0.16	-	mit	0					478
Q01390 UniProt NPD GO	SUSY_PHAAU	Sucrose synthase (EC 2.4.1.13) (Sucrose-UDP glucosyltransferase)	0.16	-	cyt	0					805
Q41144 UniProt NPD GO	STC_RICCO	Sugar carrier protein C	0.16	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				523
Q9H2B4 UniProt NPD GO	S26A1_HUMAN	Sulfate anion transporter 1 (SAT-1) (Solute carrier family 26 member 1)	0.16	-	end	9	Membrane; multi-pass membrane protein (By similarity)	integral to membrane [TAS]			701
Q04807 UniProt NPD GO	SGP50_RAT	Sulfated 50 kDa glycoprotein precursor (SGP50) (Endothelial ligand FOR L-selectin) (Glycosylation-de ...	0.16	-	exc	0	Associated with the lumenal surface of the high endothelial venules of peripheral lymph nodes				146
O96347 UniProt NPD GO	SODM_CHAFE	Superoxide dismutase [Mn], mitochondrial precursor (EC 1.15.1.1)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix				224
Q9Y5Y6 UniProt NPD GO	ST14_HUMAN	Suppressor of tumorigenicity protein 14 (EC 3.4.21.-) (Serine protease 14) (Matriptase) (Membrane-ty ...	0.16	-	mit	1	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS] plasma membrane [TAS]	606797	2GV7	855
P06320 UniProt NPD GO	TVB7_MOUSE	T-cell receptor beta chain V region CTL-F3 precursor	0.16	-	exc	0					134
Q4ACW4 UniProt NPD GO	CD1D_PANTR	T-cell surface glycoprotein CD1d precursor (CD1d antigen)	0.16	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				335
P15813 UniProt NPD GO	CD1D_HUMAN	T-cell surface glycoprotein CD1d precursor (CD1d antigen) (R3G1)	0.16	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS]	188410	1ZT4	335
Q08339 UniProt NPD GO	CD4_ERYPA	T-cell surface glycoprotein CD4 (T-cell surface antigen T4/Leu-3) (Fragment)	0.16	-	cyt	1	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			397
P30433 UniProt NPD GO	CD8A_PONPY	T-cell surface glycoprotein CD8 alpha chain precursor (T-lymphocyte differentiation antigen T8/Leu-2 ...	0.16	-	end	2	Membrane; single-pass type I membrane protein	T cell receptor complex [ISS]			198
Q6BXF6 UniProt NPD GO	TCPD_DEBHA	T-complex protein 1 subunit delta (TCP-1-delta) (CCT-delta)	0.16	-	nuc	0	Cytoplasm (Potential)				533

You are viewing entries 56301 to 56350 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.