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
P31326 UniProt NPD GO	OTC_RANCA	Ornithine carbamoyltransferase, mitochondrial precursor (EC 2.1.3.3) (OTCase) (Ornithine transcarbam ...	0.37	-	mit	0	Mitochondrion; mitochondrial matrix				350
Q9HFU8 UniProt NPD GO	OAZ_SCHOT	Ornithine decarboxylase antizyme (ODC-Az)	0.37	-	cyt	0					224
Q91379 UniProt NPD GO	NR2E1_CHICK	Orphan nuclear receptor NR2E1 (Nuclear receptor TLX) (Tailless homolog) (Tll)	0.37	-	nuc	0	Nucleus (By similarity)				385
Q6INU3 UniProt NPD GO	PDLI7_XENLA	PDZ and LIM domain protein 7	0.37	-	nuc	0					421
Q8NHV9 UniProt NPD GO	PEPP1_HUMAN	Paired-like homeobox protein PEPP-1 (Ovary-, testis- and epididymis-expressed gene protein)	0.37	-	nuc	0	Nucleus	nucleus [IDA]	300446		184
Q8K4K6 UniProt NPD GO	PANK1_MOUSE	Pantothenate kinase 1 (EC 2.7.1.33) (Pantothenic acid kinase 1) (mPank1) (mPank)	0.37	-	mit	0					548
P15743 UniProt NPD GO	PTHY_CHICK	Parathyroid hormone precursor (PTH)	0.37	-	exc	0	Secreted protein				119
P41767 UniProt NPD GO	RF1M_KLULA	Peptide chain release factor 1, mitochondrial precursor (MRF-1)	0.37	-	mit	0	Mitochondrion				396
Q9GN97 UniProt NPD GO	PGPLD_DROME	Peptidoglycan-recognition protein-LD	0.37	-	nuc	1		integral to plasma membrane [NAS]			282
Q9VV96 UniProt NPD GO	PGSB2_DROME	Peptidoglycan-recognition protein-SB2 precursor (EC 3.5.1.28)	0.37	-	exc	0	Secreted protein (Potential)	extracellular region [IDA]			182
O74448 UniProt NPD GO	PIN1_SCHPO	Peptidyl-prolyl cis-trans isomerase pin1 (EC 5.2.1.8)	0.37	-	nuc	0	Nucleus				175
P0C1J8 UniProt NPD GO	PIN1_RHIOR	Peptidyl-prolyl cis-trans isomerase pin1 (EC 5.2.1.8) (PPIase pin1) (Parvulin pin1)	0.37	-	nuc	0	Nucleus (By similarity)				150
P14222 UniProt NPD GO	PERF_HUMAN	Perforin-1 precursor (P1) (Lymphocyte pore-forming protein) (PFP) (Cytolysin)	0.37	-	vac	0	Integral membrane protein. Cytoplasmic granules of cytolytic T-lymphocytes		603553		555
Q15063 UniProt NPD GO	POSTN_HUMAN	Periostin precursor (PN) (Osteoblast-specific factor 2) (OSF-2)	0.37	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [ISS]	608777		836
P40855 UniProt NPD GO	PEX19_HUMAN	Peroxisomal biogenesis factor 19 (Peroxin-19) (Peroxisomal farnesylated protein) (33 kDa housekeepin ...	0.37	-	nuc	0	Cytoplasm. Mainly. Peroxisome; peroxisomal membrane; lipid-anchor; cytoplasmic side. Some fraction m ...	cytoplasm [ISS] integral to membrane [TAS] peroxisome [ISS]	600279		299
O62807 UniProt NPD GO	PPARG_PIG	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.37	+	cyt	0	Nucleus				504
O19052 UniProt NPD GO	PPARG_RABIT	Peroxisome proliferator-activated receptor gamma (PPAR-gamma)	0.37	+	cyt	0	Nucleus				475
O44249 UniProt NPD GO	PRP1_MANSE	Phenoloxidase subunit 1 (EC 1.14.18.1) (proPO-P1)	0.37	-	nuc	0	Secreted protein	extracellular region [IDA]			684
O93967 UniProt NPD GO	PALY_AMAMU	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.37	-	nuc	0	Cytoplasm (Probable)				740
Q5F356 UniProt NPD GO	PI52A_CHICK	Phosphatidylinositol-4-phosphate 5-kinase type-2 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.37	-	mit	0					405
Q2QTC2 UniProt NPD GO	PWD_ORYSA	Phosphoglucan, water dikinase, chloroplast precursor (EC 2.7.9.5)	0.37	-	mit	0	Plastid; chloroplast. Starch granules during starch mobilization in darkness (By similarity)				1206
P36886 UniProt NPD GO	PSAK_HORVU	Photosystem I reaction center subunit psaK, chloroplast precursor (Photosystem I subunit X) (PSI-K) ...	0.37	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				131
Q39557 UniProt NPD GO	PHY2_CERPU	Phytochrome 2	0.37	-	mit	0					1121
P08196 UniProt NPD GO	PSY1_LYCES	Phytoene synthase 1, chloroplast precursor (EC 2.5.1.-) (Fruit ripening-specific protein pTOM5)	0.37	-	cyt	0	Plastid; chloroplast				412
P16613 UniProt NPD GO	PACA_SHEEP	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.37	-	nuc	0	Secreted protein				176
P27751 UniProt NPD GO	RK32_ASTLO	Plastid 50S ribosomal protein L32	0.37	-	nuc	0	Plastid				49
Q9ZWQ8 UniProt NPD GO	PAP_CITUN	Plastid-lipid-associated protein, chloroplast precursor (CitPAP)	0.37	-	mit	0	Plastid; chloroplast (Potential)				323
Q9D659 UniProt NPD GO	GI24_MOUSE	Platelet receptor Gi24 precursor	0.37	-	end	1	Membrane; single-pass type I membrane protein (Potential)				309
Q9ULL4 UniProt NPD GO	PLXB3_HUMAN	Plexin-B3 precursor	0.37	-	end	0	Membrane; single-pass type I membrane protein		300214		1909
Q8N4A0 UniProt NPD GO	GALT4_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 4 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.37	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Probable)	Golgi apparatus [TAS]	603565		578
Q9JIS4 UniProt NPD GO	KCNKA_RAT	Potassium channel subfamily K member 10 (Outward rectifying potassium channel protein TREK-2) (TREK- ...	0.37	-	end	6	Membrane; multi-pass membrane protein (Potential)				538
Q9HB15 UniProt NPD GO	KCNKC_HUMAN	Potassium channel subfamily K member 12 (Tandem pore domain halothane-inhibited potassium channel 2) ...	0.37	-	end	6 *	Membrane; multi-pass membrane protein (Potential)		607366		430
P22001 UniProt NPD GO	KCNA3_HUMAN	Potassium voltage-gated channel subfamily A member 3 (Voltage-gated potassium channel subunit Kv1.3) ...	0.37	-	end	5	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176263		523
P19156 UniProt NPD GO	ATP4A_PIG	Potassium-transporting ATPase alpha chain 1 (EC 3.6.3.10) (Proton pump) (Gastric H+/K+ ATPase subuni ...	0.37	-	end	8	Membrane; multi-pass membrane protein			1IWF	1033
Q6FXX1 UniProt NPD GO	CWC24_CANGA	Pre-mRNA-splicing factor CWC24	0.37	-	nuc	0	Nucleus (By similarity)				226
Q7RUX3 UniProt NPD GO	SLT11_NEUCR	Pre-mRNA-splicing factor slt-11	0.37	-	nuc	0	Nucleus (By similarity)				392
P17959 UniProt NPD GO	RS9_TRYBB	Probable 40S ribosomal protein S9	0.37	-	nuc	0					190
P40024 UniProt NPD GO	YEM6_YEAST	Probable ATP-dependent transporter YER036C	0.37	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			610
O74946 UniProt NPD GO	DPOA2_SCHPO	Probable DNA polymerase subunit alpha B	0.37	-	nuc	0	Nucleus	alpha DNA polymerase:primase complex [TAS]			574
O62193 UniProt NPD GO	PSF2_CAEEL	Probable DNA replication complex GINS protein PSF2	0.37	-	cyt	0	Nucleus (By similarity)				180
Q9NYM4 UniProt NPD GO	GPR83_HUMAN	Probable G-protein coupled receptor 83 precursor (G-protein coupled receptor 72)	0.37	+	end	7	Membrane; multi-pass membrane protein		605569		423
P30731 UniProt NPD GO	GPR83_MOUSE	Probable G-protein coupled receptor 83 precursor (Glucocorticoid-induced receptor)	0.37	-	end	7	Membrane; multi-pass membrane protein				423
Q9SRM0 UniProt NPD GO	ATL3D_ARATH	Probable RING-H2 finger protein ATL3D	0.37	-	nuc	1 *					158
P34567 UniProt NPD GO	TF2H2_CAEEL	Probable TFIIH basal transcription factor complex p44 subunit (General transcription factor IIH poly ...	0.37	-	cyt	0	Nucleus (By similarity)				376
Q9XWV3 UniProt NPD GO	ARPC3_CAEEL	Probable actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC)	0.37	-	nuc	0					183
Q9VWR2 UniProt NPD GO	CP308_DROME	Probable cytochrome P450 308a1 (EC 1.14.-.-) (CYPCCCVIIIA1)	0.37	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				490
Q9V4U9 UniProt NPD GO	C6A13_DROME	Probable cytochrome P450 6a13 (EC 1.14.-.-) (CYPVIA13)	0.37	-	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				493
Q9C8K0 UniProt NPD GO	DRL5_ARATH	Probable disease resistance protein At1g51480	0.37	-	mit	0					854
Q8RXS5 UniProt NPD GO	DRL40_ARATH	Probable disease resistance protein At5g63020 (pNd11)	0.37	-	cyt	0					888
Q17632 UniProt NPD GO	RRP44_CAEEL	Probable exosome complex exonuclease RRP44 (EC 3.1.13.-) (Ribosomal RNA-processing protein 44) (DIS3 ...	0.37	-	cyt	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				1029

You are viewing entries 34401 to 34450 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.