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
Q56S59 UniProt NPD GO	PHYLL_TOBAC	Phylloplanin precursor (T-phylloplanin)	0.01	-	exc	1 *	Secreted protein				150
P84566 UniProt NPD GO	PHYL1_PHYHY	Phylloseptin-1 (PS-1)	0.01	-		0	Secreted protein				19
P84567 UniProt NPD GO	PHYL2_PHYHY	Phylloseptin-2 (PS-2)	0.01	-		0	Secreted protein				18
P84568 UniProt NPD GO	PHYL3_PHYHY	Phylloseptin-3 (PS-3)	0.01	-		0	Secreted protein				19
P84569 UniProt NPD GO	PHYL4_PHYOR	Phylloseptin-4 (PS-4)	0.01	-		0	Secreted protein				20
P84570 UniProt NPD GO	PHYL5_PHYOR	Phylloseptin-5 (PS-5)	0.01	-		0	Secreted protein				19
P84571 UniProt NPD GO	PHYL6_PHYHY	Phylloseptin-6 (PS-6)	0.01	-		0	Secreted protein				17
P08615 UniProt NPD GO	TKN_PHYFU	Physalaemin	0.01	-		0	Secreted protein				11
Q9FRF9 UniProt NPD GO	PSK3_ORYSA	Phytosulfokines 3 precursor [Contains: Phytosulfokine-alpha (PSK-alpha) (Phytosulfokine-a); Phytosul ...	0.01	-	exc	0	Secreted protein (By similarity)				75
Q07932 UniProt NPD GO	MYR1_MYRPI	Pilosulin-1 precursor (Major allergen Myr p 1) (Myr p I) [Contains: Pilosulin-1; Pilosulin-1 65->112 ...	0.01	-	exc	0	Secreted protein				112
Q9LX49 UniProt NPD GO	PRN1_ARATH	Pirin 1 (AtPirin1)	0.01	-	mit	0	Nucleus (By similarity)				287
Q9D6H2 UniProt NPD GO	PP25_MOUSE	Placental protein 25 homolog (PP25)	0.01	-	cyt	0					143
Q7M290 UniProt NPD GO	PMA_AVESA	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump) (Fragments)	0.01	-	cyt	0	Cell membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			110
O61704 UniProt NPD GO	PSP1_PSEIC	Plasmatocyte-spreading peptide precursor	0.01	-	nuc	0				1B5N	141
P80010 UniProt NPD GO	PLMN_HORSE	Plasminogen (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Plasmin light chain B] (Fragment)	0.01	-	cyt	0	Secreted protein				338
Q9Y342 UniProt NPD GO	PLLP_HUMAN	Plasmolipin (Plasma membrane proteolipid)	0.01	-	end	4 *	Membrane; multi-pass membrane protein		600340		182
Q9DCU2 UniProt NPD GO	PLLP_MOUSE	Plasmolipin (Plasma membrane proteolipid)	0.01	-	end	4 *	Membrane; multi-pass membrane protein				182
P47987 UniProt NPD GO	PLLP_RAT	Plasmolipin (Plasma membrane proteolipid)	0.01	-	end	4 *	Membrane; multi-pass membrane protein	compact myelin [IDA] lipid raft [IDA]			182
P00294 UniProt NPD GO	PLAS_CAPBU	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00292 UniProt NPD GO	PLAS_CUCPE	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00293 UniProt NPD GO	PLAS_CUCSA	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
Q7SIB8 UniProt NPD GO	PLAS_DRYCA	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			1KDJ	102
P00290 UniProt NPD GO	PLAS_LACSA	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00295 UniProt NPD GO	PLAS_MERPE	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00298 UniProt NPD GO	PLAS_RUMOB	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00291 UniProt NPD GO	PLAS_SAMNI	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00297 UniProt NPD GO	PLAS_SOLCR	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P00296 UniProt NPD GO	PLAS_SOLTU	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P13133 UniProt NPD GO	PLAS_ULVAR	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				98
P56274 UniProt NPD GO	PLAS_ULVPE	Plastocyanin	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			1IUZ	98
P00288 UniProt NPD GO	PLAS_VICFA	Plastocyanin	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P84800 UniProt NPD GO	PLAS_THAOC	Plastocyanin (Fragments)	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				38
P35476 UniProt NPD GO	PLAS1_TOBAC	Plastocyanin A'/A''	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; lumenal side. Loo ...				99
P35477 UniProt NPD GO	PLAS2_TOBAC	Plastocyanin B'/B''	0.01	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; lumenal side. Loo ...				99
P11970 UniProt NPD GO	PLAS2_POPNI	Plastocyanin B, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				168
P26956 UniProt NPD GO	PLAS_SCEOB	Plastocyanin, chloroplast precursor	0.01	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				145
P07030 UniProt NPD GO	PLAS_SILPR	Plastocyanin, chloroplast precursor	0.01	-	vac	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			1BYP	165
P43030 UniProt NPD GO	SCYB7_PIG	Platelet basic protein precursor (PBP) (Small inducible cytokine B7) (CXCL7)	0.01	-	end	0	Secreted protein				119
P79106 UniProt NPD GO	PAFA2_BOVIN	Platelet-activating factor acetylhydrolase 2, cytoplasmic (EC 3.1.1.47) (Serine-dependent phospholip ...	0.01	-	cyt	0	Cytoplasm				392
P81941 UniProt NPD GO	PLE1_PSEAM	Pleurocidin precursor	0.01	-	cyt	0	Secreted protein			1Z64	68
Q90ZY0 UniProt NPD GO	PLE2_PSEAM	Pleurocidin precursor	0.01	-	mit	0	Secreted protein				68
Q90VW7 UniProt NPD GO	PLE3_PSEAM	Pleurocidin-like peptide WF3 precursor	0.01	-	exc	0	Secreted protein (By similarity)				61
Q90ZX8 UniProt NPD GO	PLE4_PSEAM	Pleurocidin-like peptide WF4 precursor	0.01	-	mit	0	Secreted protein (By similarity)				68
P84866 UniProt NPD GO	PLEUR_PLEOS	Pleurostatin (Fragment)	0.01	-		0					8
O81701 UniProt NPD GO	POLC4_ALNGL	Polcalcin Aln g 4 (Calcium-binding pollen allergen Aln g 4)	0.01	-	cyt	0					85
O64943 UniProt NPD GO	POLC2_JUNOX	Polcalcin Jun o 2 (Calcium-binding pollen allergen Jun o 2)	0.01	-	cyt	0					165
O81092 UniProt NPD GO	POLC3_OLEEU	Polcalcin Ole e 3 (Calcium-binding pollen allergen Ole e 3)	0.01	-	cyt	0					84
P43174 UniProt NPD GO	MPA5A_AMBPS	Pollen allergen Amb p 5a precursor (Amb p Va)	0.01	-	nuc	0					77
Q8LGR0 UniProt NPD GO	CHE1_CHEAL	Pollen allergen Che a 1 precursor	0.01	-	exc	1 *	Secreted protein (By similarity)				168
Q41183 UniProt NPD GO	MPAG2_DACGL	Pollen allergen Dac g 2 (Dac g II) (Fragment)	0.01	-	cyt	0	Secreted protein				36

You are viewing entries 90601 to 90650 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.