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
Q08388 UniProt NPD GO	PEMT_RAT	Phosphatidylethanolamine N-methyltransferase (EC 2.1.1.17) (PEAMT) (PEMT)	0.10	-	end	4 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential). Mito ...				198
Q00169 UniProt NPD GO	PIPNA_HUMAN	Phosphatidylinositol transfer protein alpha isoform (PtdIns transfer protein alpha) (PtdInsTP) (PI-T ...	0.10	-	cyt	0	Cytoplasm		600174	1UW5	269
P80108 UniProt NPD GO	PHLD1_HUMAN	Phosphatidylinositol-glycan-specific phospholipase D 1 precursor (EC 3.1.4.50) (PI-G PLD) (Glycoprot ...	0.10	-	vac	0	Secreted protein		602515		840
P80109 UniProt NPD GO	PHLD_BOVIN	Phosphatidylinositol-glycan-specific phospholipase D precursor (EC 3.1.4.50) (PI-G PLD) (Glycoprotei ...	0.10	-	end	0	Secreted protein. Associated with the High-Density Lipoproteins (HDL) (By similarity)				839
Q9BVG9 UniProt NPD GO	PTSS2_HUMAN	Phosphatidylserine synthase 2 (EC 2.7.8.-) (PtdSer synthase 2) (PSS-2) (Serine-exchange enzyme II)	0.10	-	end	7	Membrane; multi-pass membrane protein				487
P33182 UniProt NPD GO	PEPM_TETPY	Phosphoenolpyruvate phosphomutase precursor (EC 5.4.2.9) (Phosphoenolpyruvate mutase) (PEP mutase) ( ...	0.10	-	mit	0					300
O18719 UniProt NPD GO	PGM_ENTDI	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.10	-	mit	0	Cytoplasm (By similarity)				553
O15820 UniProt NPD GO	PGM_ENTHI	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.10	-	mit	0	Cytoplasm (By similarity)				553
P00949 UniProt NPD GO	PGM1_RABIT	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.10	-	nuc	0	Isoform 1: Cytoplasm. Isoform 2: Sarcoplasmic reticulum. Isoform 2 localizes to the junctional skele ...			3PMG	561
Q27685 UniProt NPD GO	PGKC_LEIME	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3) (Phosphoglycerate kinase C)	0.10	-	nuc	1	Glycosome				479
Q9DBJ1 UniProt NPD GO	PGAM1_MOUSE	Phosphoglycerate mutase 1 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme B ...	0.10	-	cyt	0					253
Q7M4I5 UniProt NPD GO	PA2_APIDO	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein (By similarity)				134
Q8JFB2 UniProt NPD GO	PA2I_LATSE	Phospholipase A2 GL16-1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (pkP5)	0.10	-	exc	1 *	Secreted protein (By similarity)				152
O57690 UniProt NPD GO	PLII_TRIFL	Phospholipase A2 inhibitor 1 precursor (Phospholipase A2 inhibitor I) (PLI-I)	0.10	-	exc	0	Secreted protein				200
P00595 UniProt NPD GO	PA21_HEMHA	Phospholipase A2 isozyme DE-1 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein				119
P00600 UniProt NPD GO	PA22_NAJME	Phospholipase A2 isozyme DE-II (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein				119
P04056 UniProt NPD GO	PA21B_PSEAU	Phospholipase A2 isozyme PA-11 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein				118
P20255 UniProt NPD GO	PA2A_PSEAU	Phospholipase A2 isozyme PA-12A (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein				118
Q9PRG0 UniProt NPD GO	PA23_AUSSU	Phospholipase A2 isozyme S1-11 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA1) ...	0.10	-	exc	0	Secreted protein (By similarity)				145
P14411 UniProt NPD GO	PA2X_BUNFA	Phospholipase A2 isozyme X, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.10	-	nuc	0	Secreted protein				118
P06596 UniProt NPD GO	PA21B_CANFA	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.10	-	exc	0	Secreted protein				146
Q9Z0Y2 UniProt NPD GO	PA21B_MOUSE	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.10	-	exc	0	Secreted protein	extracellular region [IDA]			146
Q10755 UniProt NPD GO	PA22_VIPAZ	Phospholipase A2, B chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (PLA2-I complex B chain ...	0.10	-	nuc	0	Secreted protein				122
O24296 UniProt NPD GO	GPX1_PEA	Phospholipid hydroperoxide glutathione peroxidase, chloroplast precursor (EC 1.11.1.12) (PHGPx)	0.10	-	nuc	0	Plastid; chloroplast; chloroplast stroma				236
Q6QBQ4 UniProt NPD GO	PLS3_RAT	Phospholipid scramblase 3 (PL scramblase 3) (Ca(2+)-dependent phospholipid scramblase 3)	0.10	-	cyt	0	Membrane; single-pass type II membrane protein (By similarity)				296
Q9SWE5 UniProt NPD GO	HAL3A_ARATH	Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (Halotolerance protein Hal3a) (AtHal3a) (PPC ...	0.10	-	nuc	0				1MVN	209
P15567 UniProt NPD GO	PUR6_SCHPO	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.10	-	cyt	0					552
Q9UUB4 UniProt NPD GO	PUR7_SCHPO	Phosphoribosylaminoimidazole-succinocarboxamide synthase (EC 6.3.2.6) (SAICAR synthetase)	0.10	-	cyt	0					299
Q60866 UniProt NPD GO	PTER_MOUSE	Phosphotriesterase-related protein (Parathion hydrolase-related protein)	0.10	-	cyt	0					349
P49481 UniProt NPD GO	PSAD_ODOSI	Photosystem I reaction center subunit II (Photosystem I 16 kDa polypeptide) (PSI-D)	0.10	-	cyt	0	Plastid; chloroplast				139
P48114 UniProt NPD GO	PSAE_CYAPA	Photosystem I reaction center subunit IV (PSI-E)	0.10	-	mit	0	Plastid; cyanelle; cyanelle thylakoid membrane; peripheral membrane protein; stromal side (By simila ...				70
P51347 UniProt NPD GO	PSBW_PORPU	Photosystem II reaction center W protein	0.10	-	cyt	0	Plastid; chloroplast				115
P41586 UniProt NPD GO	PACR_HUMAN	Pituitary adenylate cyclase-activating polypeptide type I receptor precursor (PACAP type I receptor) ...	0.10	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	102981		468
Q5RFI5 UniProt NPD GO	FUCO2_PONPY	Plasma alpha-L-fucosidase precursor (EC 3.2.1.51) (Alpha-L-fucosidase 2) (Alpha-L-fucoside fucohydro ...	0.10	-	exc	0	Secreted protein (Probable)				465
P81824 UniProt NPD GO	VSP1_BOTJA	Platelet-aggregating proteinase PA-BJ (EC 3.4.21.-)	0.10	-	mit	0	Secreted protein			1CXJ	232
Q5BIP2 UniProt NPD GO	PGFRL_BOVIN	Platelet-derived growth factor receptor-like protein precursor	0.10	-	cyt	0	Secreted protein (Probable)				375
Q2PFX1 UniProt NPD GO	PGFRL_MACFA	Platelet-derived growth factor receptor-like protein precursor	0.10	-	vac	0	Secreted protein (Probable)				375
Q6PE55 UniProt NPD GO	PGFRL_MOUSE	Platelet-derived growth factor receptor-like protein precursor	0.10	-	cyt	0	Secreted protein (Probable)				375
Q9QZC7 UniProt NPD GO	PKHB2_MOUSE	Pleckstrin homology domain-containing family B member 2 (Evectin-2)	0.10	-	ves	0	Membrane; peripheral membrane protein (Potential)				221
Q8VWY7 UniProt NPD GO	POLC2_TOBAC	Polcalcin Nic t 2 (Calcium-binding pollen allergen Nic t 2)	0.10	-	cyt	0					86
Q12447 UniProt NPD GO	PAA1_YEAST	Polyamine N-acetyltransferase 1 (EC 2.3.1.-) (Arylalkylamine N-acetyltransferase homolog) (scAANAT)	0.10	-	cyt	0	Cytoplasm	cytoplasm [IDA]			191
P35336 UniProt NPD GO	PGLR_ACTCH	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.10	-	mit	1 *	Secreted protein				467
O42824 UniProt NPD GO	PGLR_PENJA	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.10	-	exc	0					371
Q07181 UniProt NPD GO	PGLR_GIBFU	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase) (FmPG)	0.10	-	mit	0				1HG8	373
P26213 UniProt NPD GO	PGLR1_ASPNG	Polygalacturonase-1 precursor (EC 3.2.1.15) (Polygalacturonase I) (PG-I) (Pectinase 1)	0.10	-	exc	0				1NHC	368
Q91Z31 UniProt NPD GO	PTBP2_MOUSE	Polypyrimidine tract-binding protein 2 (Brain-enriched polypyrimidine tract-binding protein) (Brain- ...	0.10	-	cyt	0	Nucleus	spliceosome complex [IDA]			531
Q66H20 UniProt NPD GO	PTBP2_RAT	Polypyrimidine tract-binding protein 2 (Neural polypyrimidine tract-binding protein) (PTB-like prote ...	0.10	-	cyt	0	Nucleus (By similarity)				531
Q86QV0 UniProt NPD GO	KGX15_CENLL	Potassium channel toxin gamma-KTx 1.5 (Ergtoxin-like protein 1) (ErgTx1) (CllErg1) (CllErgTx1)	0.10	-	nuc	0	Secreted protein				42
Q86QU3 UniProt NPD GO	KGX4A_CENSC	Potassium channel toxin gamma-KTx 4.10 (Ergtoxin-like protein 4) (ErgTx4) (CsErg4) (CsErgTx4)	0.10	-	nuc	0	Secreted protein				43
Q86QU8 UniProt NPD GO	KGX46_CENLL	Potassium channel toxin gamma-KTx 4.6 (Ergtoxin-like protein 3) (ErgTx3) (CllErg3) (CllErgTx3)	0.10	-	nuc	0	Secreted protein				43

You are viewing entries 64951 to 65000 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.