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
P83587 UniProt NPD GO	PDHC_ORCLI	Pigment-dispersing hormone C (PDH C) (Light-adapting distal retinal pigment hormone C) (DRPH C)	0.00	-		0	Secreted protein				18
Q68Y23 UniProt NPD GO	MYR3_MYRBA	Pilosulin-3 precursor	0.00	-	end	0	Secreted protein				74
P0C023 UniProt NPD GO	MYR3B_MYRPI	Pilosulin-3b	0.00	-	cyt	0	Secreted protein				23
Q75C38 UniProt NPD GO	PMP3_ASHGO	Plasma membrane proteolipid 3	0.00	-	end	2 *	Cell membrane; multi-pass membrane protein (Potential)				55
Q4WYA5 UniProt NPD GO	PMP3_ASPFU	Plasma membrane proteolipid 3	0.00	-	end	1 *	Cell membrane; single-pass membrane protein (Potential)				57
Q2HAR0 UniProt NPD GO	PMP3_CHAGB	Plasma membrane proteolipid 3	0.00	-	nuc	1 *	Cell membrane; single-pass membrane protein (Potential)				53
Q5KL24 UniProt NPD GO	PMP3_CRYNE	Plasma membrane proteolipid 3	0.00	-	end	1 *	Cell membrane; multi-pass membrane protein (Potential)				57
Q6BVN0 UniProt NPD GO	PMP3_DEBHA	Plasma membrane proteolipid 3	0.00	-	end	2 *	Cell membrane; multi-pass membrane protein (Potential)				57
Q4HXT6 UniProt NPD GO	PMP3_GIBZE	Plasma membrane proteolipid 3	0.00	-	end	2 *	Cell membrane; multi-pass membrane protein (Potential)				67
Q871V2 UniProt NPD GO	PMP3_NEUCR	Plasma membrane proteolipid 3	0.00	-	end	1 *	Cell membrane; single-pass membrane protein (Potential)				57
Q9C1W4 UniProt NPD GO	PMP3_SCHPO	Plasma membrane proteolipid 3	0.00	-	end	1 *	Cell membrane; single-pass membrane protein (Potential)				50
P87284 UniProt NPD GO	PMP3_YEAST	Plasma membrane proteolipid 3	0.00	-	nuc	2 *	Cell membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			55
Q9P824 UniProt NPD GO	PMP3_CANAL	Plasma membrane proteolipid 3 homolog	0.00	-	end	2 *	Membrane; multi-pass membrane protein				55
P61641 UniProt NPD GO	RETBP_PANTR	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.00	-	exc	0	Secreted protein (By similarity)				201
P27485 UniProt NPD GO	RETBP_PIG	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.00	-	mit	0	Secreted protein			1AQB	201
P06912 UniProt NPD GO	RETBP_RABIT	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.00	-	mit	0	Secreted protein				201
P02753 UniProt NPD GO	RETBP_HUMAN	Plasma retinol-binding protein precursor (PRBP) (RBP) [Contains: Plasma retinol-binding protein(1-18 ...	0.00	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [TAS]	180250	1RBP	201
P14163 UniProt NPD GO	HAPP_PHYPO	Plasmodium-specific hydrophobic abundant protein precursor (HAP-P)	0.00	-	end	5 *	Membrane				187
P81707 UniProt NPD GO	PLP_BRANA	Plastidial lipid-associated protein (Fragment)	0.00	-		0					8
P00300 UniProt NPD GO	PLAS_CHLFU	Plastocyanin	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				98
P20422 UniProt NPD GO	PLAS_DAUCA	Plastocyanin	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				97
P07465 UniProt NPD GO	PLAS_ENTPR	Plastocyanin	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			7PCY	98
P84338 UniProt NPD GO	PLAS_GINBI	Plastocyanin	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				99
P17341 UniProt NPD GO	PLAS_PETCR	Plastocyanin A/B	0.00	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			1PLB	97
P42699 UniProt NPD GO	PLAS2_ARATH	Plastocyanin major isoform, chloroplast precursor (DNA-damage-repair/toleration protein DRT112)	0.00	-	mit	1	Plastid; chloroplast; chloroplast thylakoid lumen				167
P11490 UniProt NPD GO	PLAS1_ARATH	Plastocyanin minor isoform, chloroplast precursor	0.00	-	mit	1	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				171
O22646 UniProt NPD GO	PLAS_FRIAG	Plastocyanin, chloroplast precursor	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				166
P17340 UniProt NPD GO	PLAS_LYCES	Plastocyanin, chloroplast precursor	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				170
P16002 UniProt NPD GO	PLAS_PEA	Plastocyanin, chloroplast precursor	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...				168
P00289 UniProt NPD GO	PLAS_SPIOL	Plastocyanin, chloroplast precursor	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; lumenal side			2PCF	168
P18068 UniProt NPD GO	PLAS_CHLRE	Plastocyanin, chloroplast precursor (PC6-2)	0.00	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein. Lumenal side. Loo ...			2PLT	145
Q9Z126 UniProt NPD GO	PLF4_MOUSE	Platelet factor 4 precursor (PF-4) (CXCL4)	0.00	-	cyt	0	Secreted protein	extracellular region [ISS]			105
P20034 UniProt NPD GO	PDGFB_PIG	Platelet-derived growth factor B chain (PDGF B-chain) (Platelet-derived growth factor beta polypepti ...	0.00	-		0					15
P36987 UniProt NPD GO	TXP13_PLETR	Plectoxin-13 (Plectoxin XIII) (PLT-XIII) (PLTXIII) (Fragment)	0.00	-	cyt	0	Secreted protein				24
P22103 UniProt NPD GO	PNEU_HUMAN	Pneumadin (PNM)	0.00	-		0					10
P21996 UniProt NPD GO	PNEU_RAT	Pneumadin (PNM)	0.00	-		0					10
P69196 UniProt NPD GO	POLC1_BRANA	Polcalcin Bra n 1 (Calcium-binding pollen allergen Bra n 1)	0.00	-	cyt	0					79
P69197 UniProt NPD GO	POLC1_BRARA	Polcalcin Bra r 1 (Calcium-binding pollen allergen Bra r 1)	0.00	-	cyt	0					79
P10414 UniProt NPD GO	MPAT5_AMBTR	Pollen allergen Amb t 5 precursor (Amb t V) (Allergen Ra5G)	0.00	-	nuc	0				3BBG	73
P22285 UniProt NPD GO	MPA92_POAPR	Pollen allergen KBG 41 precursor (Pollen allergen Poa p 9) (Poa p IX)	0.00	-	mit	1 *					333
P14947 UniProt NPD GO	MPAL2_LOLPR	Pollen allergen Lol p 2-A (Lol p II-A)	0.00	-	cyt	0	Secreted protein				97
O24172 UniProt NPD GO	ALL6_OLEEU	Pollen allergen Ole e 6	0.00	-	nuc	0				1SS3	50
Q40962 UniProt NPD GO	MPA5A_PHLPR	Pollen allergen Phl p 5a (Phl p Va) (Fragment)	0.00	-	cyt	0	Secreted protein (Potential)				286
Q40963 UniProt NPD GO	MPA5B_PHLPR	Pollen allergen Phl p 5b precursor (Phl p Vb) (Fragment)	0.00	+	mit	0				1L3P	284
P83181 UniProt NPD GO	POA1_SALKA	Pollen allergen Sal k 1 (Fragments)	0.00	-	cyt	0					42
P0C1R0 UniProt NPD GO	PROTO_POLPI	Polybia-CP (Polybia chemotactic peptide)	0.00	-		0	Secreted protein				12
P84388 UniProt NPD GO	PLYB1_POLPI	Polybine-1 (Polybine-I)	0.00	-		0	Secreted protein	extracellular region [IDA]			14
P84389 UniProt NPD GO	PLYB2_POLPI	Polybine-2 (Polybine-II)	0.00	-		0	Secreted protein	extracellular region [IDA]			14
P35337 UniProt NPD GO	PGLR_BRANA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.00	-	vac	0	Secreted protein				397
Q29244 UniProt NPD GO	PIGR_PIG	Polymeric-immunoglobulin receptor (Poly-Ig receptor) (PIGR) (Fragment)	0.00	-	cyt	0	Cell membrane; single-pass type I membrane protein. Processed form: Secreted protein				102

You are viewing entries 97051 to 97100 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.