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
P51477 UniProt NPD GO	ARRS_XENLA	S-arrestin (Retinal S-antigen) (Rod photoreceptor arrestin)	0.11	-	cyt	0					396
Q12372 UniProt NPD GO	MMP1_YEAST	S-methylmethionine permease 1	0.11	-	end	12	Membrane; multi-pass membrane protein (Potential). Endoplasmic reticulum	plasma membrane [IMP]			583
Q9Z1W9 UniProt NPD GO	STK39_MOUSE	STE20/SPS1-related proline-alanine-rich protein kinase (EC 2.7.11.1) (Ste-20-related kinase) (Serine ...	0.11	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable). Nucleus when caspase-cleaved (Probable)	apical plasma membrane [IDA] basolateral plasma membrane [IDA] membrane fraction [IDA]			556
P02841 UniProt NPD GO	SGS7_DROME	Salivary glue protein Sgs-7 precursor	0.11	-	exc	1 *					74
P04191 UniProt NPD GO	AT2A1_RABIT	Sarcoplasmic/endoplasmic reticulum calcium ATPase 1 (EC 3.6.3.8) (Calcium pump 1) (SERCA1) (SR Ca(2+ ...	0.11	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. Sarcoplasmic ret ...			2C8L	1001
P18596 UniProt NPD GO	AT2A3_RAT	Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (EC 3.6.3.8) (Calcium pump 3) (SERCA3) (SR Ca(2+ ...	0.11	-	ves	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	endoplasmic reticulum membrane [IDA]			999
P04917 UniProt NPD GO	PGSG_RAT	Secretory granule proteoglycan core protein precursor (Chondroitin sulfate proteoglycan core protein ...	0.11	-	mit	1 *					179
Q90665 UniProt NPD GO	SEM4D_CHICK	Semaphorin-4D (Collapsin-4) (COLL-4) (Fragment)	0.11	-	cyt	0	Membrane; single-pass type I membrane protein (Probable)				295
P53616 UniProt NPD GO	SUN4_YEAST	Septation protein SUN4 precursor (Soluble cell wall protein 3)	0.11	-	exc	0	Cell wall	cell wall (sensu Fungi) [IDA] mitochondrial matrix [TAS]			420
O35423 UniProt NPD GO	SPYA_MOUSE	Serine--pyruvate aminotransferase, mitochondrial precursor (EC 2.6.1.51) (SPT) (Alanine--glyoxylate ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity). Peroxisome (By similarity)				413
Q8SVB5 UniProt NPD GO	PTPA_ENCCU	Serine/threonine-protein phosphatase 2A activator (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase ...	0.11	-	mit	0	Cytoplasm (By similarity)				247
P11493 UniProt NPD GO	PP2AB_PIG	Serine/threonine-protein phosphatase 2A catalytic subunit beta isoform (EC 3.1.3.16) (PP2A-beta) (Fr ...	0.11	-	cyt	0	Cytoplasm				293
O04951 UniProt NPD GO	PP2A5_ARATH	Serine/threonine-protein phosphatase PP2A-5 catalytic subunit (EC 3.1.3.16)	0.11	-	cyt	0	Cytoplasm (By similarity)				307
O88816 UniProt NPD GO	SNAT_MOUSE	Serotonin N-acetyltransferase (EC 2.3.1.87) (Aralkylamine N-acetyltransferase) (AA-NAT) (Serotonin a ...	0.11	-	cyt	0					205
P79819 UniProt NPD GO	TRFE_ORYLA	Serotransferrin precursor	0.11	-	exc	0	Secreted protein				690
O17846 UniProt NPD GO	SRA22_CAEEL	Serpentine receptor class alpha-22 (Protein sra-22)	0.11	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				339
Q95ZY4 UniProt NPD GO	SRB5_CAEEL	Serpentine receptor class beta-5 (Protein srb-5)	0.11	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				345
P36952 UniProt NPD GO	SPB5_HUMAN	Serpin B5 precursor (Maspin) (Protease inhibitor 5)	0.11	-	mit	0	Secreted protein; extracellular space		154790	1XU8	375
P49064 UniProt NPD GO	ALBU_FELCA	Serum albumin precursor (Allergen Fel d 2)	0.11	-	exc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			608
P35543 UniProt NPD GO	SAA3_RABIT	Serum amyloid A-3 protein precursor	0.11	-	vac	0					122
Q61425 UniProt NPD GO	HCDH_MOUSE	Short chain 3-hydroxyacyl-CoA dehydrogenase, mitochondrial precursor (EC 1.1.1.35) (HCDH) (Medium an ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial inner membrane [IDA] mitochondrion [IDA]			314
P14534 UniProt NPD GO	NXS2_BUNFA	Short neurotoxin 2 (Toxin V-II-2) (Fasciatoxin)	0.11	-	nuc	0	Secreted protein				63
P43445 UniProt NPD GO	NXSH_BUNMU	Short neurotoxin homolog precursor	0.11	-	nuc	1 *	Secreted protein				83
Q9D9J8 UniProt NPD GO	SPLC3_MOUSE	Short palate, lung and nasal epithelium carcinoma-associated protein 3 homolog precursor	0.11	-	exc	0					232
P70665 UniProt NPD GO	SIAE_MOUSE	Sialate O-acetylesterase precursor (EC 3.1.1.53) (Sialic acid-specific 9-O-acetylesterase) (Yolk sac ...	0.11	-	nuc	0	Isoform 1: Lysosome. Isoform 2: cytoplasm				541
Q9BWM7 UniProt NPD GO	SFXN3_HUMAN	Sideroflexin-3	0.11	-	cyt	1	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				321
P58924 UniProt NPD GO	CXS3A_CONGE	Sigma-conotoxin GVIIIA precursor (Fragment)	0.11	-	nuc	0	Secreted protein				42
Q04969 UniProt NPD GO	SPC2_YEAST	Signal peptidase complex subunit SPC2 (Microsomal signal peptidase subunit 2)	0.11	-	end	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	signal peptidase complex [IDA]			178
P49964 UniProt NPD GO	SRP19_ORYSA	Signal recognition particle 19 kDa protein (SRP19)	0.11	-	nuc	0	Cytoplasm				136
P21262 UniProt NPD GO	SRP09_CANFA	Signal recognition particle 9 kDa protein (SRP9)	0.11	-	cyt	0	Cytoplasm				85
P10146 UniProt NPD GO	CCL1_MOUSE	Small inducible cytokine A1 precursor (CCL1) (T-cell activation protein TCA3) (TCA-3) (SIS-epsilon) ...	0.11	-	exc	0					92
Q8HYQ3 UniProt NPD GO	CCL3_MACMU	Small inducible cytokine A3 precursor (CCL3) (Macrophage inflammatory protein 1-alpha) (MIP-1-alpha) ...	0.11	-	exc	0	Secreted protein (By similarity)				92
Q91ZL1 UniProt NPD GO	CCL5_SIGHI	Small inducible cytokine A5 precursor (CCL5) (T-cell-specific RANTES protein)	0.11	-	vac	0	Secreted protein				91
Q9Z121 UniProt NPD GO	CCL8_MOUSE	Small inducible cytokine A8 precursor (CCL8) (Monocyte chemotactic protein 2) (MCP-2) (Monocyte chem ...	0.11	-	end	0	Secreted protein (By similarity)				97
Q7ZUG0 UniProt NPD GO	RUXE_BRARE	Small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.11	-	mit	0	Nucleus (By similarity)				92
Q28658 UniProt NPD GO	SPRR3_RABIT	Small proline-rich protein 3 (Cornifin beta)	0.11	-	nuc	0	Cytoplasm				231
Q9UPR5 UniProt NPD GO	NAC2_HUMAN	Sodium/calcium exchanger 2 precursor (Na(+)/Ca(2+)-exchange protein 2)	0.11	-	end	9	Membrane; multi-pass membrane protein		601901		921
P26429 UniProt NPD GO	SC5A1_PIG	Sodium/glucose cotransporter 1 (Na(+)/glucose cotransporter 1) (High affinity sodium-glucose cotrans ...	0.11	-	end	13 *	Membrane; multi-pass membrane protein				605
Q92581 UniProt NPD GO	SL9A6_HUMAN	Sodium/hydrogen exchanger 6 (Na(+)/H(+) exchanger 6) (NHE-6) (Solute carrier family 9 member 6)	0.11	-	end	12 *	Mitochondrion; mitochondrial membrane; multi-pass membrane protein	endoplasmic reticulum membrane [ISS] integral to membrane [TAS] microsome [ISS] mitochondrion [TAS]	300231		669
Q8BZ00 UniProt NPD GO	SL9A9_MOUSE	Sodium/hydrogen exchanger 9 (Na(+)/H(+) exchanger 9) (NHE-9) (Solute carrier family 9 member 9)	0.11	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				644
Q62674 UniProt NPD GO	S28A1_RAT	Sodium/nucleoside cotransporter 1 (Na(+)/nucleoside cotransporter 1) (Sodium-coupled nucleoside tran ...	0.11	-	end	10	Membrane; multi-pass membrane protein				648
Q9I9C3 UniProt NPD GO	AT233_ANGAN	Sodium/potassium-transporting ATPase subunit beta-233 (Sodium/potassium-dependent ATPase beta-233 su ...	0.11	-	mit	1 *	Membrane; single-pass type II membrane protein	sodium:potassium-exchanging ATPase complex [NAS]			302
P30716 UniProt NPD GO	AT1B3_BUFMA	Sodium/potassium-transporting ATPase subunit beta-3 (Sodium/potassium-dependent ATPase beta-3 subuni ...	0.11	-	nuc	1 *	Membrane; single-pass type II membrane protein				279
Q63633 UniProt NPD GO	S12A5_RAT	Solute carrier family 12 member 5 (Electroneutral potassium-chloride cotransporter 2) (K-Cl cotransp ...	0.11	-	end	12	Membrane; multi-pass membrane protein	integral to membrane [ISS]			1116
Q91V14 UniProt NPD GO	S12A5_MOUSE	Solute carrier family 12 member 5 (Electroneutral potassium-chloride cotransporter 2) (K-Cl cotransp ...	0.11	-	end	12	Membrane; multi-pass membrane protein. Detected on dendrites, but not on axons of spinal cord neuron ...	integral to membrane [ISS] plasma membrane [IDA]			1115
Q924N4 UniProt NPD GO	S12A6_MOUSE	Solute carrier family 12 member 6 (Electroneutral potassium-chloride cotransporter 3) (K-Cl cotransp ...	0.11	-	end	10	Membrane; multi-pass membrane protein	axon [IDA] basolateral plasma membrane [IDA] integral to membrane [ISS]			1150
Q8AWB6 UniProt NPD GO	S35B1_CHICK	Solute carrier family 35 member B1 (Endoplasmic reticulum nucleotide sugar transporter 1)	0.11	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				325
Q99N01 UniProt NPD GO	SO4A1_RAT	Solute carrier organic anion transporter family member 4A1 (Solute carrier family 21 member 12) (Sod ...	0.11	-	end	11	Membrane; multi-pass membrane protein				723
P79697 UniProt NPD GO	SOML_CARAU	Somatolactin precursor (SL)	0.11	-	exc	0	Secreted protein				230
P42692 UniProt NPD GO	SLIB_CYPCA	Somatoliberin (Growth hormone-releasing factor) (GRF) (Growth hormone-releasing hormone) (GHRH)	0.11	-	nuc	0	Secreted protein				45

You are viewing entries 63501 to 63550 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.