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
O43021 UniProt NPD GO	YGV7_SCHPO	Oxysterol-binding protein homolog C354.07c	0.24	-	cyt	0					399
P35454 UniProt NPD GO	NEU1_MOUSE	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.24	-	exc	0		extracellular region [IDA]			125
P01179 UniProt NPD GO	NEU1_RAT	Oxytocin-neurophysin 1 precursor (OT-NPI) [Contains: Oxytocin (Ocytocin); Neurophysin 1]	0.24	-	exc	0				1XY2	125
Q9ESG6 UniProt NPD GO	P2Y14_MOUSE	P2Y purinoceptor 14 (P2Y14) (UDP-glucose receptor) (G-protein coupled receptor 105)	0.24	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [ISS]			338
Q5ZI82 UniProt NPD GO	P2RY8_CHICK	P2Y purinoceptor 8 (P2Y8)	0.24	-	end	7 *	Membrane; multi-pass membrane protein				357
Q61908 UniProt NPD GO	MTCPA_MOUSE	P8 MTCP-1 protein (Mature T-cell proliferation-1 type A) (MTCP-1 type A) (P8MTCP1)	0.24	-	nuc	0	Mitochondrion				68
Q5FWP8 UniProt NPD GO	PCID2_XENLA	PCI domain-containing protein 2 (CSN12-like protein)	0.24	-	cyt	0					399
O14908 UniProt NPD GO	GIPC1_HUMAN	PDZ domain-containing protein GIPC1 (RGS19-interacting protein 1) (GAIP C-terminus-interacting prote ...	0.24	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein	cytosol [ISS] membrane [ISS] membrane fraction [IDA] soluble fraction [IDA]	605072		333
P15863 UniProt NPD GO	PAX1_HUMAN	Paired box protein Pax-1 (HUP48)	0.24	-	nuc	0	Nucleus		167411		440
O43316 UniProt NPD GO	PAX4_HUMAN	Paired box protein Pax-4	0.24	+	nuc	0	Nucleus		167413		350
Q750R7 UniProt NPD GO	ERFB_ASHGO	Palmitoyltransferase ERF2 (EC 2.3.1.-) (DHHC cysteine-rich domain-containing protein ERF2) (Ras prot ...	0.24	-	end	4	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				367
P01298 UniProt NPD GO	PAHO_HUMAN	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; Pancrea ...	0.24	-	exc	0	Secreted protein		167780	1TZ5	95
P00995 UniProt NPD GO	IPK1_HUMAN	Pancreatic secretory trypsin inhibitor precursor (Tumor-associated trypsin inhibitor) (TATI) (Serine ...	0.24	-	exc	0	Secreted protein		167790	1HPT	79
Q8BFY6 UniProt NPD GO	PEF1_MOUSE	Peflin (PEF protein with a long N-terminal hydrophobic domain) (Penta-EF hand domain-containing prot ...	0.24	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein in the presence of Ca(2+) (By similarity)				275
Q5U8Z7 UniProt NPD GO	PPID_AMAMU	Peptidyl-prolyl cis-trans isomerase D (EC 5.2.1.8) (PPIase D) (Rotamase D)	0.24	-	mit	0	Cytoplasm (By similarity)				371
O42281 UniProt NPD GO	RDS_CHICK	Peripherin (Retinal degeneration slow protein) (Photoreceptor outer segment membrane glycoprotein 1) ...	0.24	-	end	4 *	Membrane; multi-pass membrane protein				354
O17450 UniProt NPD GO	PE48_CHRBE	Peritrophin-48 precursor	0.24	-	exc	0					379
Q9LT91 UniProt NPD GO	PER66_ARATH	Peroxidase 66 precursor (EC 1.11.1.7) (Atperox P66) (ATP27a)	0.24	-	cyt	0	Secreted protein (By similarity)				322
P59121 UniProt NPD GO	PERE5_ARMRU	Peroxidase E5 (EC 1.11.1.7)	0.24	-	mit	0					306
Q01964 UniProt NPD GO	PEX2_PICPA	Peroxisomal biogenesis factor 2 (Peroxin-2) (Peroxisomal protein PER6)	0.24	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				461
P87200 UniProt NPD GO	PEX17_YARLI	Peroxisomal membrane protein PEX17 (Peroxin-17)	0.24	-	end	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein. Probably associated with the matrix f ...				671
Q6AYQ3 UniProt NPD GO	SYFM_RAT	Phenylalanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.20) (Phenylalanine--tRNA ligase) (Ph ...	0.24	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)				472
O70362 UniProt NPD GO	PHLD_MOUSE	Phosphatidylinositol-glycan-specific phospholipase D 1 precursor (EC 3.1.4.50) (PI-G PLD) (Glycoprot ...	0.24	-	exc	0	Secreted protein. Associated with the High-Density Lipoproteins (HDL) (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			837
Q9P931 UniProt NPD GO	PGM_EMENI	Phosphoglucomutase (EC 5.4.2.2) (Glucose phosphomutase) (PGM)	0.24	-	cyt	0	Cytoplasm (By similarity)				556
Q96G03 UniProt NPD GO	PGM2_HUMAN	Phosphoglucomutase-2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.24	-	cyt	0	Cytoplasm (By similarity)		172000		611
Q12326 UniProt NPD GO	PMG3_YEAST	Phosphoglycerate mutase 3 (EC 5.4.2.1) (Phosphoglyceromutase 3) (PGAM 3) (MPGM 3) (BPG-dependent PGA ...	0.24	-	nuc	0					303
P70090 UniProt NPD GO	PA25_TRIGA	Phospholipase A2 isozyme 5 precursor (EC 3.1.1.4) (Phospholipase A2 isozyme V) (Phosphatidylcholine ...	0.24	-	exc	0	Secreted protein				138
P00594 UniProt NPD GO	PA21B_HORSE	Phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Group IB phospholipas ...	0.24	-	nuc	0	Secreted protein				132
Q43270 UniProt NPD GO	PLDA1_MAIZE	Phospholipase D alpha 1 (EC 3.1.4.4) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylcholine-hydr ...	0.24	-	cyt	0					812
Q2KIU2 UniProt NPD GO	PMVK_BOVIN	Phosphomevalonate kinase (EC 2.7.4.2) (PMKase)	0.24	-	cyt	0	Peroxisome (By similarity)				191
Q9MTP0 UniProt NPD GO	YCF3_OENHO	Photosystem I assembly protein ycf3	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				168
Q6ENH3 UniProt NPD GO	YCF3_ORYNI	Photosystem I assembly protein ycf3	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
P12203 UniProt NPD GO	YCF3_ORYSA	Photosystem I assembly protein ycf3	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
Q6ENW2 UniProt NPD GO	YCF3_SACOF	Photosystem I assembly protein ycf3	0.24	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
P46642 UniProt NPD GO	YCF4_MAIZE	Photosystem I assembly protein ycf4	0.24	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
Q6L389 UniProt NPD GO	YCF4_SACHY	Photosystem I assembly protein ycf4	0.24	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
Q6ENV3 UniProt NPD GO	YCF4_SACOF	Photosystem I assembly protein ycf4	0.24	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
Q9SSU8 UniProt NPD GO	PSY_DAUCA	Phytoene synthase, chloroplast precursor (EC 2.5.1.-)	0.24	-	mit	1	Plastid; chloroplast				398
Q95121 UniProt NPD GO	PEDF_BOVIN	Pigment epithelium-derived factor precursor (PEDF)	0.24	-	end	0	Secreted protein	extracellular region [IDA]			416
P97298 UniProt NPD GO	PEDF_MOUSE	Pigment epithelium-derived factor precursor (PEDF) (Stromal cell-derived factor 3) (SDF-3) (Caspin)	0.24	-	end	0	Secreted protein	extracellular region [IDA] extracellular space [IDA]			417
Q03211 UniProt NPD GO	PEXLP_TOBAC	Pistil-specific extensin-like protein precursor (PELP)	0.24	-	exc	0					426
P18509 UniProt NPD GO	PACA_HUMAN	Pituitary adenylate cyclase-activating polypeptide precursor (PACAP) [Contains: PACAP-related peptid ...	0.24	-	nuc	0	Secreted protein	soluble fraction [TAS]	102980	1GEA	176
O54830 UniProt NPD GO	PRLPE_MOUSE	Placental prolactin-like protein E precursor (PRL-like protein E) (PLP-E) (Placental prolactin-like ...	0.24	-	nuc	0	Secreted protein (By similarity)				266
Q07421 UniProt NPD GO	PMA1_AJECA	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.24	-	end	9	Cell membrane; multi-pass membrane protein				916
P22180 UniProt NPD GO	PMA1_LYCES	Plasma membrane ATPase 1 (EC 3.6.3.6) (Proton pump 1)	0.24	-	end	8	Cell membrane; multi-pass membrane protein				956
Q08436 UniProt NPD GO	PMA3_NICPL	Plasma membrane ATPase 3 (EC 3.6.3.6) (Proton pump 3)	0.24	-	end	8	Cell membrane; multi-pass membrane protein				956
Q01814 UniProt NPD GO	AT2B2_HUMAN	Plasma membrane calcium-transporting ATPase 2 (EC 3.6.3.8) (PMCA2) (Plasma membrane calcium pump iso ...	0.24	+	end	8	Cell membrane; multi-pass membrane protein	plasma membrane [TAS]	108733		1243
P11506 UniProt NPD GO	AT2B2_RAT	Plasma membrane calcium-transporting ATPase 2 (EC 3.6.3.8) (PMCA2) (Plasma membrane calcium pump iso ...	0.24	+	end	8	Cell membrane; multi-pass membrane protein	plasma membrane [TAS]			1243
Q64542 UniProt NPD GO	AT2B4_RAT	Plasma membrane calcium-transporting ATPase 4 (EC 3.6.3.8) (PMCA4) (Plasma membrane calcium pump iso ...	0.24	-	end	7	Cell membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			1203
P34772 UniProt NPD GO	RR19_ASTLO	Plastid 30S ribosomal protein S19	0.24	-	mit	0	Plastid				118

You are viewing entries 46601 to 46650 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.