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
Q9LTV6 UniProt NPD GO	DECR2_ARATH	Peroxisomal 2,4-dienoyl-CoA reductase (EC 1.3.1.34)	0.13	-	pox	0	Peroxisome (By similarity)				298
Q5RD76 UniProt NPD GO	NUD12_PONPY	Peroxisomal NADH pyrophosphatase NUDT12 (EC 3.6.1.22) (Nucleoside diphosphate-linked moiety X motif ...	0.13	-	cyt	0	Peroxisome (By similarity)				462
Q00940 UniProt NPD GO	PEX10_PICAN	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10) (Peroxisome assembly p ...	0.13	-	mit	0	Peroxisome; peroxisomal membrane; peripheral membrane protein				295
P45724 UniProt NPD GO	PAL2_ARATH	Phenylalanine ammonia-lyase 2 (EC 4.3.1.5)	0.13	-	cyt	0	Cytoplasm (Probable)				717
Q05659 UniProt NPD GO	BAR2_SCHCO	Pheromone B alpha 2 receptor (Fragment)	0.13	-	end	7 *	Membrane; multi-pass membrane protein				518
P31302 UniProt NPD GO	PRA1_USTMA	Pheromone receptor 1	0.13	-	end	7 *	Membrane; multi-pass membrane protein				357
Q92903 UniProt NPD GO	CDS1_HUMAN	Phosphatidate cytidylyltransferase 1 (EC 2.7.7.41) (CDP-diglyceride synthetase 1) (CDP-diglyceride p ...	0.13	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...		603548		461
P53808 UniProt NPD GO	PPCT_MOUSE	Phosphatidylcholine transfer protein (PC-TP) (StAR-related lipid transfer protein 2) (StARD2) (START ...	0.13	-	cyt	0	Cytoplasm				214
Q7TSN4 UniProt NPD GO	PIGW_RAT	Phosphatidylinositol-glycan biosynthesis class W protein (EC 2.3.-.-) (PIG-W)	0.13	-	end	13 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				502
P79023 UniProt NPD GO	AROG_CANAL	Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited (EC 2.5.1.54) (Phospho-2-keto-3-deox ...	0.13	-	nuc	0					370
P36871 UniProt NPD GO	PGM1_HUMAN	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.13	-	nuc	0	Isoform 1: Cytoplasm	cytoplasm [NAS]	171900		561
P38652 UniProt NPD GO	PGM1_RAT	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.13	-	nuc	0	Cytoplasm				561
Q5R979 UniProt NPD GO	PGM2L_PONPY	Phosphoglucomutase-2-like 1 (EC 5.4.2.2)	0.13	-	cyt	0					622
Q6PCE3 UniProt NPD GO	PGM2L_HUMAN	Phosphoglucomutase-2-like 1 (EC 5.4.2.2) (PMMLP)	0.13	-	cyt	0					622
Q8UUI2 UniProt NPD GO	PA24_LATLA	Phospholipase A2 PC16 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.13	-	exc	1 *	Secreted protein (By similarity)				145
P60045 UniProt NPD GO	PA23_NAJSG	Phospholipase A2 isoform 3 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.13	-	mit	0	Secreted protein			1ZM6	126
Q8QFW4 UniProt NPD GO	PA21B_BUNCE	Phospholipase A2, beta bungarotoxin A1 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.13	-	exc	0	Secreted protein (By similarity)				147
Q56JZ2 UniProt NPD GO	PA2GA_BOVIN	Phospholipase A2, membrane associated precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) ( ...	0.13	-	nuc	1 *	Membrane; peripheral membrane protein (By similarity)				144
Q92084 UniProt NPD GO	PA2A_NAJSP	Phospholipase A2, neutral A precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (NAJPLA-2A) ...	0.13	-	exc	0	Secreted protein				146
P55939 UniProt NPD GO	PLDA2_BRAOC	Phospholipase D alpha 2 precursor (EC 3.1.4.4) (PLD 2) (Choline phosphatase 2) (Phosphatidylcholine- ...	0.13	-	cyt	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				812
Q60HD6 UniProt NPD GO	PMM2_MACFA	Phosphomannomutase 2 (EC 5.4.2.8) (PMM 2)	0.13	-	cyt	0	Cytoplasm (By similarity)				246
P51258 UniProt NPD GO	YCF3_PORPU	Photosystem I assembly protein ycf3	0.13	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				173
P09362 UniProt NPD GO	YCF4_EUGGR	Photosystem I assembly protein ycf4	0.13	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				206
Q6EW42 UniProt NPD GO	YCF4_NYMAL	Photosystem I assembly protein ycf4	0.13	-	end	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q41387 UniProt NPD GO	PSBW_SPIOL	Photosystem II reaction center W protein, chloroplast precursor (PSII 6.1 kDa protein)	0.13	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				137
P48325 UniProt NPD GO	P2SAF_CYAPA	Photosystem II stability/assembly factor HCF136 precursor (Ycf48-like protein) (ORF333)	0.13	-	mit	0	Plastid; cyanelle; cyanelle thylakoid lumen (By similarity)				333
O35386 UniProt NPD GO	PAHX_MOUSE	Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) ( ...	0.13	-	nuc	0	Peroxisome	peroxisome [TAS]			338
Q9LZ76 UniProt NPD GO	PHYK1_ARATH	Phytol kinase 1, chloroplast precursor (EC 2.7.-.-) (Vitamin E pathway gene 5 protein)	0.13	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				304
O81277 UniProt NPD GO	PSK5_ORYSA	Phytosulfokines 5 precursor (Secretory protein SH27A) [Contains: Phytosulfokine-alpha (PSK-alpha) (P ...	0.13	-	gol	1 *	Secreted protein (By similarity)				102
P02777 UniProt NPD GO	PLF4_BOVIN	Platelet factor 4 (PF-4) (CXCL4)	0.13	-	nuc	0	Secreted protein	extracellular region [ISS]		1PLF	88
P48530 UniProt NPD GO	PTA1_XENLA	Pleiotrophic factor-alpha-1 precursor (PTF-alpha-1) (Midkine homolog)	0.13	-	nuc	0	Secreted protein (By similarity)				142
P41838 UniProt NPD GO	RAE1_SCHPO	Poly(A)+ RNA export protein	0.13	-	nuc	0	Nucleus. Nuclear periphery				352
Q9D6V8 UniProt NPD GO	PAIP2_MOUSE	Polyadenylate-binding protein-interacting protein 2 (Poly(A)-binding protein-interacting protein 2) ...	0.13	-	cyt	0	Cytoplasm (By similarity)				124
Q9FY19 UniProt NPD GO	PGLR2_JUNAS	Polygalacturonase precursor (PG) (EC 3.2.1.15) (Pectinase) (Major pollen allergen Jun a 2)	0.13	-	nuc	0	Secreted protein				507
P05117 UniProt NPD GO	PGLR_LYCES	Polygalacturonase-2 precursor (EC 3.2.1.15) (PG) (PG-2A) (PG-2B) (Pectinase)	0.13	-	exc	0	Secreted protein; extracellular space; apoplast. Cell wall. Associated to the cell wall				457
Q5K4E3 UniProt NPD GO	POLS2_HUMAN	Polyserase-2 precursor (EC 3.4.21.-) (Polyserine protease 2) (Protease serine 36)	0.13	-	mit	0	Secreted protein; extracellular space; extracellular matrix. Not attached to membranes	cytoplasm [IDA]			855
Q5HZB0 UniProt NPD GO	PORIM_RAT	Porimin precursor (Transmembrane protein 123)	0.13	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				194
O00180 UniProt NPD GO	KCNK1_HUMAN	Potassium channel subfamily K member 1 (Inward rectifying potassium channel protein TWIK-1) (Potassi ...	0.13	-	end	5 *	Membrane; multi-pass membrane protein (Potential)	voltage-gated potassium channel complex [TAS]	601745		336
P29186 UniProt NPD GO	TXBGK_BUNGR	Potassium channel toxin Bgk	0.13	-	nuc	0	Secreted protein. Found in nematocyst			1BGK	37
P58504 UniProt NPD GO	KA102_CENNO	Potassium channel toxin alpha-KTx 10.2 (Cobatoxin-2) (CoTx2)	0.13	-	nuc	0	Secreted protein				32
P59886 UniProt NPD GO	KAX38_BUTSI	Potassium channel toxin alpha-KTx 3.8 (Charybdotoxin-like peptide Bs 6) (Bs6)	0.13	-	nuc	0	Secreted protein				38
Q6XLL7 UniProt NPD GO	KAX68_OPICA	Potassium channel toxin alpha-KTx 6.8 precursor (OcKTx3)	0.13	-	exc	0	Secreted protein (By similarity)				61
Q00723 UniProt NPD GO	PRP38_YEAST	Pre-mRNA-splicing factor 38	0.13	-	nuc	0	Nucleus	U4/U6 x U5 tri-snRNP complex [IDA]			242
Q6CKE8 UniProt NPD GO	PRP46_KLULA	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.13	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				434
Q5A5N5 UniProt NPD GO	SLT11_CANAL	Pre-mRNA-splicing factor SLT11	0.13	-	nuc	0	Nucleus (By similarity)				303
P52166 UniProt NPD GO	PSN_CAEEL	Presenilin sel-12	0.13	-	end	9	Membrane; multi-pass membrane protein (Potential)	membrane [NAS]			444
Q5R5H4 UniProt NPD GO	PARL_PONPY	Presenilins-associated rhomboid-like protein, mitochondrial precursor (EC 3.4.21.105) (Mitochondrial ...	0.13	-	nuc	6	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity). Mitochondr ...				379
Q9D4F2 UniProt NPD GO	PPAC2_MOUSE	Presqualene diphosphate phosphatase (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-contai ...	0.13	-	end	2	Membrane; multi-pass membrane protein (Potential)				292
Q9UKY0 UniProt NPD GO	PRND_HUMAN	Prion-like protein doppel precursor (PrPLP) (Prion protein 2)	0.13	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)		604263	1LG4	176
P56943 UniProt NPD GO	MCH1_ONCKI	Pro-MCH 1 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.13	-	exc	1 *					132

You are viewing entries 60151 to 60200 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.