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
Q6Q3F5 UniProt NPD GO	SIDT1_RAT	SID1 transmembrane family member 1 precursor	0.13	-	end	11	Membrane; multi-pass membrane protein (Potential)				831
Q9D174 UniProt NPD GO	S18L2_MOUSE	SS18-like protein 2	0.13	-	nuc	0					77
Q9UHA2 UniProt NPD GO	S18L2_HUMAN	SS18-like protein 2 (SYT homolog 2)	0.13	-	nuc	0			606473		77
Q64518 UniProt NPD GO	AT2A3_MOUSE	Sarcoplasmic/endoplasmic reticulum calcium ATPase 3 (EC 3.6.3.8) (Calcium pump 3) (SERCA3) (SR Ca(2+ ...	0.13	-	end	7	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Endoplasmic reticulum; endop ...	endoplasmic reticulum [IDA]			1038
P04459 UniProt NPD GO	KRSC_CHICK	Scale keratin (S-ker) (sKer)	0.13	-	nuc	0					154
Q02774 UniProt NPD GO	SHR3_YEAST	Secretory component protein SHR3	0.13	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to endoplasmic reticulum membrane [IDA]			210
Q64105 UniProt NPD GO	SPRE_MOUSE	Sepiapterin reductase (EC 1.1.1.153) (SPR)	0.13	-	mit	0	Cytoplasm			1SEP	261
P37292 UniProt NPD GO	GLYM_YEAST	Serine hydroxymethyltransferase, mitochondrial precursor (EC 2.1.2.1) (Serine methylase) (Glycine hy ...	0.13	-	mit	0	Mitochondrion	mitochondrion [IDA]			490
Q9R118 UniProt NPD GO	HTRA1_MOUSE	Serine protease HTRA1 precursor (EC 3.4.21.-)	0.13	-	exc	0	Secreted protein (By similarity)				480
Q63556 UniProt NPD GO	SPA3M_RAT	Serine protease inhibitor A3M precursor (Serine protease inhibitor 2.4) (SPI-2.4) (Fragment)	0.13	-	end	0	Secreted protein (By similarity)				412
Q60396 UniProt NPD GO	SPI24_APOSY	Serine proteinase inhibitor 2.4 precursor	0.13	-	end	0	Secreted protein (Probable)				418
P31029 UniProt NPD GO	SPYA_CALJA	Serine--pyruvate aminotransferase, mitochondrial precursor (EC 2.6.1.51) (SPT) (Alanine--glyoxylate ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix. Peroxisome				414
Q2QM47 UniProt NPD GO	BSL2_ORYSA	Serine/threonine protein phosphatase BSL2 homolog (EC 3.1.3.16) (BSU1-like protein 2 homolog)	0.13	-	nuc	0	Nucleus (By similarity)				1009
Q12126 UniProt NPD GO	CRK1_SCHPO	Serine/threonine-protein kinase crk1 (EC 2.7.11.23) (Mitotic catastrophe suppressor 6)	0.13	-	cyt	0					335
Q12706 UniProt NPD GO	PSK1_SCHPO	Serine/threonine-protein kinase psk1 (EC 2.7.11.22)	0.13	-	cyt	0					436
Q6FK00 UniProt NPD GO	PTPA2_CANGA	Serine/threonine-protein phosphatase 2A activator 2 (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomeras ...	0.13	-	nuc	0	Cytoplasm (By similarity)				358
P48463 UniProt NPD GO	PP2AA_CHICK	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.13	-	cyt	0	Cytoplasm	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P63330 UniProt NPD GO	PP2AA_MOUSE	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.13	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] plasma membrane [IDA] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
P63331 UniProt NPD GO	PP2AA_RAT	Serine/threonine-protein phosphatase 2A catalytic subunit alpha isoform (EC 3.1.3.16) (PP2A-alpha)	0.13	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS] membrane [ISS] microtubule cytoskeleton [ISS] mitochondrion [ISS] nucleus [ISS] protein phosphatase type 2A complex [ISS] soluble fraction [ISS]			309
Q8X178 UniProt NPD GO	PP2A2_ERYGR	Serine/threonine-protein phosphatase PP2A-2 catalytic subunit (EC 3.1.3.16)	0.13	-	cyt	0					328
P09571 UniProt NPD GO	TRFE_PIG	Serotransferrin (Transferrin) (Siderophilin) (Beta-1 metal-binding globulin)	0.13	-	nuc	0	Secreted protein			1H76	696
Q29443 UniProt NPD GO	TRFE_BOVIN	Serotransferrin precursor (Transferrin) (Siderophilin) (Beta-1-metal-binding globulin)	0.13	-	exc	0	Secreted protein				704
Q10936 UniProt NPD GO	SRA34_CAEEL	Serpentine receptor class alpha-34 (Protein sra-34)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				355
Q19474 UniProt NPD GO	SRD50_CAEEL	Serpentine receptor class delta-50 (Protein srd-50)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				337
P46572 UniProt NPD GO	SRG3_CAEEL	Serpentine receptor class gamma-3 (Protein srg-3)	0.13	-	end	7 *	Membrane; multi-pass membrane protein (Probable)				332
Q8CDC0 UniProt NPD GO	SPB13_MOUSE	Serpin B13	0.13	-	nuc	0	Cytoplasm (By similarity)				389
P70564 UniProt NPD GO	SPB5_RAT	Serpin B5 precursor (Maspin) (Protease inhibitor 5)	0.13	-	nuc	0	Secreted protein; extracellular space				375
Q5XLE4 UniProt NPD GO	ALBU_EQUAS	Serum albumin precursor	0.13	-	nuc	0	Secreted protein	extracellular region [ISS] protein complex [ISS]			607
Q9WVK7 UniProt NPD GO	HCDH_RAT	Short chain 3-hydroxyacyl-CoA dehydrogenase, mitochondrial precursor (EC 1.1.1.35) (HCDH) (Medium an ...	0.13	-	mit	0	Mitochondrion; mitochondrial matrix				314
P01421 UniProt NPD GO	NXS4_NAJHA	Short neurotoxin 4 (Toxin CM-12) (Toxin V-NH-I2)	0.13	-	nuc	0	Secreted protein				61
Q5EA43 UniProt NPD GO	SFXN2_BOVIN	Sideroflexin-2	0.13	-	cyt	4	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				322
Q9JHY2 UniProt NPD GO	SFXN3_RAT	Sideroflexin-3	0.13	-	cyt	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)	mitochondrion [TAS]			321
Q4R512 UniProt NPD GO	SPCS2_MACFA	Signal peptidase complex subunit 2 (EC 3.4.-.-) (Microsomal signal peptidase 25 kDa subunit) (SPase ...	0.13	-	end	2	Membrane; multi-pass membrane protein (Potential)				226
P37106 UniProt NPD GO	SR541_ARATH	Signal recognition particle 54 kDa protein 1 (SRP54)	0.13	-	cyt	0	Cytoplasm				479
Q07490 UniProt NPD GO	CD24_RAT	Signal transducer CD24 precursor (Heat stable antigen) (HSA) (Nectadrin)	0.13	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [TAS]			76
Q9UGK3 UniProt NPD GO	STAP2_HUMAN	Signal-transducing adaptor protein 2 (STAP-2) (Breast tumor kinase substrate) (BRK substrate)	0.13	-	nuc	0	Cytoplasm		607881		403
P54622 UniProt NPD GO	SSB_DROME	Single-stranded DNA-binding protein, mitochondrial precursor (Mt-SSB) (MtSSB) (Dm mtSSB) (Protein lo ...	0.13	-	mit	0	Mitochondrion	mitochondrial chromosome [IDA] mitochondrion [IDA]			146
Q9CWR7 UniProt NPD GO	STEA1_MOUSE	Six transmembrane epithelial antigen of prostate 1	0.13	-	end	5	Membrane; multi-pass membrane protein (Potential)				339
Q8HYP4 UniProt NPD GO	CCL23_MACMU	Small inducible cytokine A23 precursor (CCL23)	0.13	-	exc	0	Secreted protein (By similarity)				120
Q9JKC0 UniProt NPD GO	CCL24_MOUSE	Small inducible cytokine A24 precursor (CCL24) (Eosinophil chemotactic protein 2) (Eotaxin-2)	0.13	-	exc	1 *	Secreted protein				119
Q64H35 UniProt NPD GO	CCL26_CANFA	Small inducible cytokine A26 precursor (CCL26) (Eotaxin-3)	0.13	-	nuc	1 *	Secreted protein (By similarity)				94
Q29288 UniProt NPD GO	CCL5_PIG	Small inducible cytokine A5 (CCL5) (T-cell-specific RANTES protein) (SIS-delta) (Fragment)	0.13	-	nuc	0	Secreted protein				50
O55038 UniProt NPD GO	SCYBD_MOUSE	Small inducible cytokine B13 precursor (CXCL13) (B lymphocyte chemoattractant) (CXC chemokine BLC)	0.13	-	exc	0	Secreted protein				109
O44437 UniProt NPD GO	SMD3_DROME	Small nuclear ribonucleoprotein SM D3 (snRNP core protein D3) (SM-D3)	0.13	+	cyt	0	Nucleus (By similarity)	small nuclear ribonucleoprotein complex [TAS]			151
Q05856 UniProt NPD GO	RSMB_DROME	Small nuclear ribonucleoprotein-associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB)	0.13	-	nuc	0	Nucleus				199
Q56A07 UniProt NPD GO	SCN2B_MOUSE	Sodium channel beta-2 subunit precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				215
P54900 UniProt NPD GO	SCN2B_RAT	Sodium channel beta-2 subunit precursor	0.13	-	end	1	Membrane; single-pass type I membrane protein	voltage-gated sodium channel complex [TAS]			215
Q969I6 UniProt NPD GO	S38A4_HUMAN	Sodium-coupled neutral amino acid transporter 4 (Na(+)-coupled neutral amino acid transporter 4) (Am ...	0.13	-	end	11	Cell membrane; multi-pass membrane protein		608065		547
P57103 UniProt NPD GO	NAC3_HUMAN	Sodium/calcium exchanger 3 precursor (Na(+)/Ca(2+)-exchange protein 3)	0.13	-	end	11 *	Membrane; multi-pass membrane protein		607991		927
P70549 UniProt NPD GO	NAC3_RAT	Sodium/calcium exchanger 3 precursor (Na(+)/Ca(2+)-exchange protein 3)	0.13	-	end	10 *	Membrane; multi-pass membrane protein				927

You are viewing entries 60401 to 60450 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.