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
O74233 UniProt NPD GO	PGK_GLOMO	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm (By similarity)				416
P33161 UniProt NPD GO	PGK_PENCI	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm (By similarity)				417
P50313 UniProt NPD GO	PGK_TETTH	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	cyt	0					420
P24590 UniProt NPD GO	PGK_TRIVI	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm (By similarity)				417
P29407 UniProt NPD GO	PGK_YARLI	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	cyt	0	Cytoplasm (By similarity)				417
P00560 UniProt NPD GO	PGK_YEAST	Phosphoglycerate kinase (EC 2.7.2.3)	0.01	-	cyt	0	Cytoplasm	cytoplasm [IDA]		3PGK	415
O00871 UniProt NPD GO	PGK_TETPY	Phosphoglycerate kinase (EC 2.7.2.3) (Fragment)	0.01	-	cyt	0					375
P29405 UniProt NPD GO	PGK1_RHINI	Phosphoglycerate kinase 1 (EC 2.7.2.3)	0.01	-	cyt	0	Cytoplasm (By similarity)				417
P80659 UniProt NPD GO	PGKH_PHYPA	Phosphoglycerate kinase, chloroplast (EC 2.7.2.3) (Fragment)	0.01	-		0	Plastid; chloroplast				15
P36232 UniProt NPD GO	PGKH_CHLFU	Phosphoglycerate kinase, chloroplast (EC 2.7.2.3) (Period clock protein) (Fragment)	0.01	-	cyt	0	Plastid; chloroplast				36
P41758 UniProt NPD GO	PGKH_CHLRE	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3)	0.01	-	mit	0	Plastid; chloroplast				461
Q9SBN4 UniProt NPD GO	PGKH_VOLCA	Phosphoglycerate kinase, chloroplast precursor (EC 2.7.2.3)	0.01	-	mit	0	Plastid; chloroplast (By similarity)				462
P08966 UniProt NPD GO	PGKB_CRIFA	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3) (Phosphoglycerate kinase B)	0.01	-	cyt	0	Cytoplasm				417
P08893 UniProt NPD GO	PGKE_TRYBB	Phosphoglycerate kinase, cytosolic (EC 2.7.2.3) (Phosphoglycerate kinase B) (PGK B allele 4)	0.01	-	cyt	0	Cytoplasm				420
P08967 UniProt NPD GO	PGKC_CRIFA	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3) (Phosphoglycerate kinase C)	0.01	-	cyt	0	Glycosome				455
P50312 UniProt NPD GO	PGKC_LEIMA	Phosphoglycerate kinase, glycosomal (EC 2.7.2.3) (Phosphoglycerate kinase C) (gPGK)	0.01	-	nuc	1	Glycosome				479
P09041 UniProt NPD GO	PGK2_MOUSE	Phosphoglycerate kinase, testis specific (EC 2.7.2.3)	0.01	-	nuc	0	Cytoplasm (By similarity)				416
P81236 UniProt NPD GO	PA21B_ACAAN	Phospholipase A2 (EC 3.1.1.4) (Acanthin I) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	nuc	0	Secreted protein				119
P04362 UniProt NPD GO	PA2_HELHO	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.01	-	nuc	0	Secreted protein				39
P84736 UniProt NPD GO	PA2_TRIBL	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Trimorphin) (Fragment)	0.01	-	nuc	0	Secreted protein	extracellular space [IDA]			50
Q9I968 UniProt NPD GO	PA22_TRIMU	Phospholipase A2 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	end	0	Secreted protein (By similarity)				138
P00625 UniProt NPD GO	PA21B_TRIOK	Phospholipase A2 PLA2-01 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Phospholipase ...	0.01	-	end	0	Secreted protein				139
P84674 UniProt NPD GO	PA25_DABRP	Phospholipase A2 VRV-PL-V (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	nuc	0	Secreted protein				121
Q92152 UniProt NPD GO	PA23_TRIOK	Phospholipase A2 homolog PLA2-03 precursor	0.01	-	cyt	1 *	Secreted protein (By similarity)				137
Q8UVU7 UniProt NPD GO	PA2H_CERGO	Phospholipase A2 homolog Pgo-K49 precursor	0.01	-	exc	0	Secreted protein				137
Q8JFG1 UniProt NPD GO	PA2I_VIPAP	Phospholipase A2 inhibitor precursor (Vaspin A chain)	0.01	-	end	0	Secreted protein (By similarity)				138
P20476 UniProt NPD GO	PA21B_TRIGA	Phospholipase A2 isozyme 1 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme I) (Phosphatidylcholine ...	0.01	-	end	0	Secreted protein				138
P06859 UniProt NPD GO	PA21B_TRIFL	Phospholipase A2 isozyme 1 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme I) (pgPLA 1a/pgPLA 2a) ( ...	0.01	-	vac	0	Secreted protein				138
P21792 UniProt NPD GO	PA23_MICNI	Phospholipase A2 isozyme 3 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.01	-	cyt	0	Secreted protein				28
P81480 UniProt NPD GO	PA23_TRIGA	Phospholipase A2 isozyme 3 (EC 3.1.1.4) (Phospholipase A2 isozyme III) (Phosphatidylcholine 2-acylhy ...	0.01	-	cyt	0	Secreted protein				122
P81479 UniProt NPD GO	PA24_TRIGA	Phospholipase A2 isozyme 4 (EC 3.1.1.4) (Phospholipase A2 isozyme IV) (Phosphatidylcholine 2-acylhyd ...	0.01	-	cyt	0	Secreted protein				122
P70088 UniProt NPD GO	PA26_TRIGA	Phospholipase A2 isozyme 6 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme VI) (Phosphatidylcholine ...	0.01	-	vac	0	Secreted protein				138
P20381 UniProt NPD GO	PA2J_TRIFL	Phospholipase A2 isozyme BP-I/BP-II precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Ba ...	0.01	-	exc	0	Secreted protein				138
P00603 UniProt NPD GO	PA22_NAJMO	Phospholipase A2 isozyme CM-II (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	cyt	0	Secreted protein				118
P24294 UniProt NPD GO	PA22_ERIMA	Phospholipase A2 isozyme PLA-2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	cyt	0	Secreted protein				121
P16354 UniProt NPD GO	PA23_HELSU	Phospholipase A2 isozymes PA3A/PA3B/PA5 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	cyt	0	Secreted protein				143
P00606 UniProt NPD GO	PA20_BUNMU	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	nuc	0	Secreted protein				145
P00624 UniProt NPD GO	PA2_CROAT	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	exc	0	Secreted protein			1PP2	138
Q10754 UniProt NPD GO	PA21B_VIPAZ	Phospholipase A2, A chain precursor (Phospholipase A2 inhibitor) (PLA2-I complex A chain) (Vaspin A ...	0.01	-	end	0	Secreted protein				138
P00626 UniProt NPD GO	PA2A_VIPAA	Phospholipase A2, ammodytoxin A precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	exc	1 *	Secreted protein				138
P11407 UniProt NPD GO	PA2C_VIPAA	Phospholipase A2, ammodytoxin C precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.01	-	exc	1 *	Secreted protein				138
P18997 UniProt NPD GO	PA22_AGKHP	Phospholipase A2, basic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.01	-	cyt	0	Secreted protein				32
P82894 UniProt NPD GO	PA23_TRIST	Phospholipase A2, basic 3 (EC 3.1.1.4) (PA2-III) (PLA2-III) (Phosphatidylcholine 2-acylhydrolase) (F ...	0.01	-	nuc	0	Secreted protein				28
P84474 UniProt NPD GO	PA2T2_BUNCA	Phospholipase A2, neurotoxin T2 A chain (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase T2 A) (Fra ...	0.01	-		0	Secreted protein				14
P24606 UniProt NPD GO	PA2S_HUMAN	Phospholipase A2, spermatozoa (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.01	-		0	Secreted protein				19
Q9UTJ2 UniProt NPD GO	PMM_SCHPO	Phosphomannomutase (EC 5.4.2.8) (PMM)	0.01	-	cyt	0	Cytoplasm (By similarity)				257
Q96CD2 UniProt NPD GO	COAC_HUMAN	Phosphopantothenoylcysteine decarboxylase (EC 4.1.1.36) (PPC-DC) (CoaC)	0.01	-	cyt	0			609854	1QZU	204
P52420 UniProt NPD GO	PUR2_ARATH	Phosphoribosylamine--glycine ligase, chloroplast precursor (EC 6.3.4.13) (GARS) (Glycinamide ribonuc ...	0.01	-	mit	0	Plastid; chloroplast				532
Q92210 UniProt NPD GO	PUR6_CANAL	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.01	-	cyt	0					568
P50504 UniProt NPD GO	PUR6_DEBOC	Phosphoribosylaminoimidazole carboxylase (EC 4.1.1.21) (AIR carboxylase) (AIRC)	0.01	-	cyt	0					557

You are viewing entries 90301 to 90350 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.