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
P84281 UniProt NPD GO	PA3A_RANPA	Palustrin-3a	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			48
P84262 UniProt NPD GO	PA3B_RANPA	Palustrin-3b	0.00	-	cyt	0	Secreted protein	extracellular region [IDA]			48
P83239 UniProt NPD GO	PAN1_PANIM	Pandinin-1	0.00	-	cyt	0	Secreted protein				44
P83240 UniProt NPD GO	PAN2_PANIM	Pandinin-2	0.00	-	mit	0	Secreted protein				24
O24035 UniProt NPD GO	PANC_LOTJA	Pantoate--beta-alanine ligase precursor (EC 6.3.2.1) (Pantothenate synthetase) (Pantoate-activating ...	0.00	-	cyt	0	Cytoplasm (Potential)				307
Q66JT7 UniProt NPD GO	COQ2_MOUSE	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.00	-	mit	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				374
Q499N4 UniProt NPD GO	COQ2_RAT	Para-hydroxybenzoate--polyprenyltransferase, mitochondrial precursor (EC 2.5.1.-) (PHB:polyprenyltra ...	0.00	-	end	5	Mitochondrion; mitochondrial membrane; multi-pass membrane protein (By similarity)				374
P81865 UniProt NPD GO	PAP1_PARPV	Pardaxin P-1	0.00	-	mit	0	Secreted protein				33
P23067 UniProt NPD GO	PAP2_PARPV	Pardaxin P-2	0.00	-	mit	0	Secreted protein				33
P81866 UniProt NPD GO	PAP3_PARPV	Pardaxin P-3	0.00	-	mit	0	Secreted protein				33
P81861 UniProt NPD GO	PAP4_PARMA	Pardaxin P-4	0.00	-	mit	0	Secreted protein			1XC0	33
P81863 UniProt NPD GO	PAP1_PARMA	Pardaxin-1 (Pardaxin I) (PXI) (Fragment)	0.00	-		0	Secreted protein				10
P35491 UniProt NPD GO	PRVM_SCYCA	Parvalbumin (Fragment)	0.00	-	cyt	0					50
P02628 UniProt NPD GO	PRVA_ESOLU	Parvalbumin alpha	0.00	-	cyt	0				3PAT	108
P02629 UniProt NPD GO	PRVA_LATCH	Parvalbumin alpha	0.00	-	cyt	0					111
P30563 UniProt NPD GO	PRVA_TRISE	Parvalbumin alpha	0.00	-	cyt	0				5PAL	109
P09227 UniProt NPD GO	PRVA_CYPCA	Parvalbumin alpha (A1)	0.00	-	cyt	0					108
P18087 UniProt NPD GO	PRVA_RANCA	Parvalbumin alpha (PA 4.97)	0.00	-	cyt	0					110
P02616 UniProt NPD GO	PRVB_AMPME	Parvalbumin beta	0.00	-	cyt	0					108
P02618 UniProt NPD GO	PRVB_CYPCA	Parvalbumin beta	0.00	-	cyt	0				5CPV	108
P02619 UniProt NPD GO	PRVB_ESOLU	Parvalbumin beta	0.00	-	cyt	0				4PAL	107
P56503 UniProt NPD GO	PRVB_MERBI	Parvalbumin beta	0.00	-	cyt	0				1BU3	108
P02620 UniProt NPD GO	PRVB_MERME	Parvalbumin beta	0.00	-	cyt	0					108
P02621 UniProt NPD GO	PRVB_MERMR	Parvalbumin beta	0.00	-	cyt	0				1A75	108
P02617 UniProt NPD GO	PRVB_RANES	Parvalbumin beta	0.00	-	cyt	0					108
P02622 UniProt NPD GO	PRVB_GADCA	Parvalbumin beta (Allergen Gad c 1) (Gad c I) (Allergen M)	0.00	-	cyt	0					113
Q90YK9 UniProt NPD GO	PRVB_GADMO	Parvalbumin beta (Allergen Gad m 1)	0.00	-	cyt	0					108
P59747 UniProt NPD GO	PRVB_SCOJP	Parvalbumin beta (Allergen Sco j 1)	0.00	-	cyt	0					108
Q90YK7 UniProt NPD GO	PRVB_THECH	Parvalbumin beta (Allergen The c 1)	0.00	-	cyt	0					108
P84536 UniProt NPD GO	PRVB_RANTE	Parvalbumin beta (Fragment)	0.00	-		0	Cytoplasm. In muscle and nervous system. Secreted protein. In cutaneous mucus				12
P05941 UniProt NPD GO	PRVB_OPSTA	Parvalbumin beta (Parvalbumin IIIF)	0.00	-	cyt	0					109
P05939 UniProt NPD GO	PRVB_LEUCE	Parvalbumin beta (V)	0.00	-	cyt	0					106
Q91482 UniProt NPD GO	PRVB1_SALSA	Parvalbumin beta 1 (Major allergen Sal s 1)	0.00	-	cyt	0					109
Q91483 UniProt NPD GO	PRVB2_SALSA	Parvalbumin beta 2 (Major allergen Sal s 1)	0.00	-	cyt	0					107
Q9I8V0 UniProt NPD GO	PRV2_BRARE	Parvalbumin-2 (Parvalbumin beta)	0.00	-	cyt	0					108
Q804W2 UniProt NPD GO	PRV7_BRARE	Parvalbumin-7 (Parvalbumin alpha) (Parvalbumin-4a)	0.00	-	cyt	0					108
P16273 UniProt NPD GO	PRPX_HORVU	Pathogen-related protein	0.00	-	cyt	0					235
Q05736 UniProt NPD GO	PR1_ASPOF	Pathogenesis-related protein 1 (AOPR1)	0.00	-	cyt	0	Cytoplasm				158
P27538 UniProt NPD GO	PR2_PETCR	Pathogenesis-related protein 2	0.00	-	cyt	0					158
P25986 UniProt NPD GO	PR2_PHAVU	Pathogenesis-related protein 2 (PvPR2)	0.00	-	cyt	0					155
P28493 UniProt NPD GO	PR5_ARATH	Pathogenesis-related protein 5 precursor (PR-5)	0.00	-	mit	1 *	Secreted protein; extracellular space; apoplast. Accumulates in the apoplast before secretion				239
P19417 UniProt NPD GO	PR11_PETCR	Pathogenesis-related protein A (PR1-1)	0.00	-	cyt	0					155
P19418 UniProt NPD GO	PR13_PETCR	Pathogenesis-related protein B (PR1-3)	0.00	-	cyt	0					155
P17642 UniProt NPD GO	PRS2_SOLTU	Pathogenesis-related protein STH-2	0.00	-	cyt	0					155
P17641 UniProt NPD GO	PRS1_SOLTU	Pathogenesis-related protein STH-21	0.00	-	cyt	0					155
Q00205 UniProt NPD GO	PLYB_ASPNG	Pectin lyase B precursor (EC 4.2.2.10) (PLB)	0.00	-	vac	1 *				1QCX	378
P80577 UniProt NPD GO	PEDB_HYDAT	Pedibin	0.00	-	nuc	0					21
Q8N0N8 UniProt NPD GO	KA2_MESMA	Peptide BmKa2 precursor (Acidic venom peptide Ka2)	0.00	-	exc	1 *	Secreted protein				74
P82695 UniProt NPD GO	PH2_PERAM	Peptide hormone 2 (Pea-VEAacid 2)	0.00	-		0					15
P82696 UniProt NPD GO	PH3_PERAM	Peptide hormone 3 (Pea-VEAacid 1)	0.00	-		0					17

You are viewing entries 96251 to 96300 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.