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
P25233 UniProt NPD GO	NECD_MOUSE	Necdin	0.46	-	cyt	0	Cytoplasm. Mainly. Nucleus; nucleoplasm; nuclear matrix. Translocates to the nucleus where it is fou ...	centrosome [IDA] cytoplasm [IDA] nucleus [IDA]			325
P30990 UniProt NPD GO	NEUT_HUMAN	Neurotensin/neuromedin N precursor [Contains: Large neuromedin N (NmN-125); Neuromedin N (NmN) (NN); ...	0.46	-	exc	0	Secreted protein. Packaged within secretory vesicles	soluble fraction [TAS]	162650		170
Q14697 UniProt NPD GO	GANAB_HUMAN	Neutral alpha-glucosidase AB precursor (EC 3.2.1.84) (Glucosidase II subunit alpha)	0.46	-	end	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus (By similarity)		104160		944
Q8BHN3 UniProt NPD GO	GANAB_MOUSE	Neutral alpha-glucosidase AB precursor (EC 3.2.1.84) (Glucosidase II subunit alpha) (Alpha glucosida ...	0.46	-	end	1 *	Endoplasmic reticulum (By similarity). Golgi apparatus (By similarity)	alpha-glucosidase II complex [IPI] endoplasmic reticulum [TAS]			944
Q8TET4 UniProt NPD GO	GANC_HUMAN	Neutral alpha-glucosidase C (EC 3.2.1.20)	0.46	-	mit	0			104180		914
Q6T3U4 UniProt NPD GO	NPCL1_MOUSE	Niemann-Pick C1-like protein 1 precursor	0.46	-	end	13	Cell membrane; apical cell membrane; multi-pass membrane protein. Cell membrane; multi-pass membrane ...				1333
Q9UK39 UniProt NPD GO	NOCT_HUMAN	Nocturnin (CCR4 protein homolog)	0.46	-	mit	0		nucleus [TAS]	608468		431
P49011 UniProt NPD GO	NOGG_XENLA	Noggin precursor	0.46	-	nuc	0	Secreted protein				222
Q754H6 UniProt NPD GO	NCBP1_ASHGO	Nuclear cap-binding protein complex subunit 1	0.46	-	nuc	0	Nucleus (By similarity)				860
P34160 UniProt NPD GO	NCBP1_YEAST	Nuclear cap-binding protein complex subunit 1 (Protein GCR3) (Protein STO1) (Protein SUT1)	0.46	-	mit	0	Nucleus. Is able to exit the nucleus in an RNA-dependent manner	commitment complex [IPI] snRNA cap binding complex [IDA]			861
P25799 UniProt NPD GO	NFKB1_MOUSE	Nuclear factor NF-kappa-B p105 subunit (DNA-binding factor KBF1) (EBP-1) (NF-kappa-B1 p84/NF-kappa-B ...	0.46	+	nuc	0	Nucleus. Cytoplasm. Nuclear, but also found in the cytoplasm in an inactive form complexed to an inh ...	nucleus [IDA]		1VKX	971
P41828 UniProt NPD GO	NHR23_CAEEL	Nuclear hormone receptor family member nhr-23 (Steroid hormone receptor family member chr-3)	0.46	-	nuc	0	Nucleus (Probable)				588
O45666 UniProt NPD GO	NHR49_CAEEL	Nuclear hormone receptor family member nhr-49	0.46	-	nuc	0	Nucleus (Potential)				501
P51843 UniProt NPD GO	DAX1_HUMAN	Nuclear receptor 0B1 (Nuclear receptor DAX-1) (DSS-AHC critical region on the X chromosome protein 1 ...	0.46	-	mit	0	Nucleus		300473		470
Q06726 UniProt NPD GO	NR2F5_BRARE	Nuclear receptor Nr2f5 (Steroid receptor homolog SVP 46)	0.46	-	nuc	0	Nucleus (Potential)				403
Q6NU91 UniProt NPD GO	NOC4B_XENLA	Nucleolar complex protein 4 homolog B (NOC4 protein homolog B) (NOC4-like protein B) (Nucleolar comp ...	0.46	-	end	3	Nucleus; nuclear membrane; multi-pass membrane protein (By similarity). Nucleus; nucleolus (By simil ...				525
Q9H8H0 UniProt NPD GO	NOL11_HUMAN	Nucleolar protein 11	0.46	-	cyt	0	Nucleus; nucleolus				719
Q01402 UniProt NPD GO	NDK2_SPIOL	Nucleoside diphosphate kinase 2, chloroplast precursor (EC 2.7.4.6) (Nucleoside diphosphate kinase I ...	0.46	-	mit	0	Plastid; chloroplast (Potential)				233
P82970 UniProt NPD GO	NSBP1_HUMAN	Nucleosome-binding protein 1	0.46	-	nuc	0	Nucleus	nucleus [NAS]	300385		282
Q17232 UniProt NPD GO	OAR_BOMMO	Octopamine receptor	0.46	-	end	7	Membrane; multi-pass membrane protein				479
P55814 UniProt NPD GO	OAZ_XENLA	Ornithine decarboxylase antizyme (ODC-Az)	0.46	-	mit	0					215
Q63504 UniProt NPD GO	NR1D2_RAT	Orphan nuclear receptor NR1D2 (Rev-erb-beta) (EAR4)	0.46	-	nuc	0	Nucleus (By similarity)				578
Q9Z1S7 UniProt NPD GO	OMD_RAT	Osteomodulin precursor (Osteoadherin) (OSAD) (Keratan sulfate proteoglycan osteomodulin) (KSPG osteo ...	0.46	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				423
P31096 UniProt NPD GO	OSTP_BOVIN	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1)	0.46	-	exc	0	Secreted protein	extracellular region [ISS]			278
O61267 UniProt NPD GO	LOK_DROME	Ovarian-specific serine/threonine-protein kinase Lok (EC 2.7.11.1) (Protein loki) (dMNK)	0.46	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Speckled subnuclear compartment	nucleus [IEP]			476
P20740 UniProt NPD GO	OVOS_CHICK	Ovostatin precursor (Ovomacroglobulin)	0.46	-	exc	0	Secreted protein				1473
Q4WX99 UniProt NPD GO	OXR1_ASPFU	Oxidation resistance protein 1	0.46	-	mit	0	Mitochondrion (By similarity)				324
Q4P6L3 UniProt NPD GO	AKR1_USTMA	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.46	-	end	5	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				844
O16785 UniProt NPD GO	PARV_CAEEL	Paralyzed arrest at two-fold protein 6 (Actopaxin homolog) (Parvin-like protein)	0.46	-	nuc	0	Cytoplasm. Localizes at body wall muscle attachments. Colocalizes with integrins and pat-4/ILK. Prob ...				375
Q6B4M5 UniProt NPD GO	PAR6A_RAT	Partitioning defective 6 homolog alpha (PAR-6 alpha) (PAR-6A) (PAR-6)	0.46	-	nuc	0	Cytoplasm (By similarity). Cell membrane (By similarity). Cell membrane; cell-cell junction; tight j ...				346
P30775 UniProt NPD GO	RF1M_YEAST	Peptide chain release factor 1, mitochondrial precursor (MRF-1)	0.46	-	nuc	0	Mitochondrion	mitochondrion [IDA]			413
P53728 UniProt NPD GO	CYP8_YEAST	Peptidyl-prolyl cis-trans isomerase CYP8 (EC 5.2.1.8) (PPIase) (Rotamase)	0.46	-	mit	2 *		vacuole (sensu Fungi) [IDA]			308
Q4R383 UniProt NPD GO	PIN1_MACFA	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1)	0.46	-	nuc	0	Nucleus (By similarity)				163
Q9QUR7 UniProt NPD GO	PIN1_MOUSE	Peptidyl-prolyl cis-trans isomerase NIMA-interacting 1 (EC 5.2.1.8) (Rotamase Pin1) (PPIase Pin1)	0.46	-	nuc	0	Nucleus (By similarity)				165
Q13356 UniProt NPD GO	PPIL2_HUMAN	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.46	-	nuc	0	Nucleus	nucleus [TAS]	607588	1ZKC	520
P51021 UniProt NPD GO	PEX2_PODAN	Peroxisomal biogenesis factor 2 (Peroxin-2) (Peroxisomal protein CAR1)	0.46	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				554
Q6CPV1 UniProt NPD GO	PEX6_KLULA	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.46	-	cyt	0					1000
P50542 UniProt NPD GO	PEX5_HUMAN	Peroxisomal targeting signal 1 receptor (Peroxisome receptor 1) (Peroxisomal C-terminal targeting si ...	0.46	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...	peroxisomal membrane [TAS] peroxisome [TAS]	202370	1FCH	602
O46404 UniProt NPD GO	P55G_BOVIN	Phosphatidylinositol 3-kinase regulatory subunit gamma (PI3-kinase p85-subunit gamma) (PtdIns-3-kina ...	0.46	-	nuc	0					461
Q92569 UniProt NPD GO	P55G_HUMAN	Phosphatidylinositol 3-kinase regulatory subunit gamma (PI3-kinase p85-subunit gamma) (PtdIns-3-kina ...	0.46	-	nuc	0			606076		461
Q9SFB8 UniProt NPD GO	PI5K6_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 6 (EC 2.7.1.68) (AtPIP5K6) (1-phosphatidylinositol-4-phosp ...	0.46	-	nuc	0					715
Q7M6Y3 UniProt NPD GO	PICA_MOUSE	Phosphatidylinositol-binding clathrin assembly protein (Clathrin assembly lymphoid myeloid leukemia) ...	0.46	-	nuc	0	Cell membrane (By similarity). Clathrin-coated areas of the plasma membrane. Golgi apparatus (By sim ...	coated pit [IDA]			660
Q93100 UniProt NPD GO	KPBB_HUMAN	Phosphorylase b kinase regulatory subunit beta (Phosphorylase kinase subunit beta)	0.46	-	cyt	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		261750		1092
P34814 UniProt NPD GO	PYG_AGLNE	Phycobilisome rod-core linker polypeptide cpcG	0.46	-	nuc	0	Plastid; chloroplast				235
Q8LPB4 UniProt NPD GO	PSKR_DAUCA	Phytosulfokine receptor precursor (EC 2.7.11.1) (Phytosulfokine LRR receptor kinase)	0.46	-	nuc	2 *	Cell membrane; single-pass type I membrane protein (By similarity)				1021
Q9N2I2 UniProt NPD GO	IPSP_BOVIN	Plasma serine protease inhibitor precursor (PCI) (Protein C inhibitor) (Serpin A5)	0.46	+	end	0	Secreted protein				404
Q9CY58 UniProt NPD GO	PAIRB_MOUSE	Plasminogen activator inhibitor 1 RNA-binding protein (PAI1 RNA-binding protein 1) (PAI-RBP1) (SERPI ...	0.46	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Also found in perinuclear regions (By similarity ...				407
Q6AXS5 UniProt NPD GO	PAIRB_RAT	Plasminogen activator inhibitor 1 RNA-binding protein (PAI1 RNA-binding protein 1) (PAI-RBP1) (SERPI ...	0.46	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Also found in perinuclear regions (By similarity ...				407
P70683 UniProt NPD GO	PAFA_CAVPO	Platelet-activating factor acetylhydrolase precursor (EC 3.1.1.47) (PAF acetylhydrolase) (PAF 2-acyl ...	0.46	-	exc	0	Secreted protein; extracellular space				436
Q9R0M4 UniProt NPD GO	PODXL_MOUSE	Podocalyxin-like protein 1 precursor	0.46	-	exc	1	Membrane; single-pass type I membrane protein (Potential)	plasma membrane [IDA]			503

You are viewing entries 27801 to 27850 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.