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
Q02496 UniProt NPD GO	MUC1_MOUSE	Mucin-1 precursor (Polymorphic epithelial mucin) (PEMT) (Episialin)	0.62	-	exc	1	Cell membrane; apical cell membrane; single-pass type I membrane protein. Exclusively located in the ...				630
Q9UL63 UniProt NPD GO	MKLN1_HUMAN	Muskelin	0.62	-	nuc	0	Cytoplasm (By similarity)		605623		735
Q99MT2 UniProt NPD GO	MSH4_MOUSE	MutS protein homolog 4 (mMsh4)	0.62	-	mit	0		condensed chromosome [IDA] nucleus [IDA] synaptonemal complex [IDA]			958
Q9Z2D1 UniProt NPD GO	MTMR2_MOUSE	Myotubularin-related protein 2 (EC 3.1.3.-)	0.62	-	nuc	0		cytoplasm [IDA]			643
P15565 UniProt NPD GO	TRM1_YEAST	N(2),N(2)-dimethylguanosine tRNA methyltransferase, mitochondrial precursor (EC 2.1.1.32) (tRNA(guan ...	0.62	-	nuc	0	Mitochondrion. Nucleus. Cytoplasm. Found in nuclear/cytoplasmic compartments	mitochondrion [TAS] nuclear envelope [IDA] nuclear inner membrane [TAS]			570
O08760 UniProt NPD GO	OGG1_MOUSE	N-glycosylase/DNA lyase [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyri ...	0.62	-	mit	0	Nucleus (By similarity)	mitochondrion [IMP] nucleus [IMP]			345
Q8R2H1 UniProt NPD GO	IKBL_RAT	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.62	-	nuc	0					381
Q90478 UniProt NPD GO	L1CA1_BRARE	Neural cell adhesion molecule L1.1 (N-CAM L1.1) (Fragment)	0.62	-	nuc	1	Membrane; single-pass type I membrane protein				1197
Q61982 UniProt NPD GO	NOTC3_MOUSE	Neurogenic locus notch homolog protein 3 precursor (Notch 3) [Contains: Notch 3 extracellular trunca ...	0.62	+	mit	1	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	integral to plasma membrane [IC]			2318
Q9R172 UniProt NPD GO	NOTC3_RAT	Neurogenic locus notch homolog protein 3 precursor (Notch 3) [Contains: Notch 3 extracellular trunca ...	0.62	+	mit	1	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...				2319
Q99748 UniProt NPD GO	NRTN_HUMAN	Neurturin precursor	0.62	+	exc	0	Secreted protein		602018		197
P97463 UniProt NPD GO	NRTN_MOUSE	Neurturin precursor	0.62	+	mit	1 *	Secreted protein				195
Q9Z0J4 UniProt NPD GO	NOS1_MOUSE	Nitric-oxide synthase, brain (EC 1.14.13.39) (NOS type I) (Neuronal NOS) (N-NOS) (nNOS) (Constitutiv ...	0.62	-	nuc	0	Sarcolemma; sarcolemmal membrane; peripheral membrane protein. In skeletal muscle, it is localized b ...	synapse [IDA]			1429
Q9H9Q4 UniProt NPD GO	NHEJ1_HUMAN	Non-homologous end-joining factor 1 (Protein cernunnos) (XRCC4-like factor)	0.62	+	nuc	0	Nucleus				299
P22488 UniProt NPD GO	IFEA_HELAS	Non-neuronal cytoplasmic intermediate filament protein (IF)	0.62	-	nuc	0	Cytoplasm				575
Q5AM50 UniProt NPD GO	NMD4_CANAL	Nonsense-mediated decay protein 4	0.62	-	nuc	0	Cytoplasm (By similarity)				398
Q9ES39 UniProt NPD GO	NDE1_RAT	Nuclear distribution protein nudE homolog 1 (NudE) (rNudE)	0.62	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				344
Q6NRJ5 UniProt NPD GO	NDE1B_XENLA	Nuclear distribution protein nudE homolog 1-B	0.62	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				349
Q66H70 UniProt NPD GO	NFHEV_RAT	Nuclear factor from high endothelial venules (NF-HEV)	0.62	-	nuc	0	Nucleus (By similarity)				264
P49867 UniProt NPD GO	FTZF1_BOMMO	Nuclear hormone receptor FTZ-F1 (BmFTZ-F1)	0.62	+	mit	0	Nucleus (Potential)				534
Q63850 UniProt NPD GO	NUP62_MOUSE	Nuclear pore glycoprotein p62 (62 kDa nucleoporin)	0.62	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex. Central region of the nuclear pore, within the tran ...	cytoplasm [ISS] nuclear pore [ISS] nucleocytoplasmic shuttling complex [ISS]			526
Q8VY64 UniProt NPD GO	NFYA4_ARATH	Nuclear transcription factor Y subunit A-4 (AtNF-YA-4)	0.62	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			198
P15771 UniProt NPD GO	NUCL_CHICK	Nucleolin (Protein C23)	0.62	+	nuc	0	Nucleus; nucleolus				694
P32500 UniProt NPD GO	NDC1_YEAST	Nucleoporin NDC1 (Nuclear pore protein NDC1) (Nuclear division cycle protein 1)	0.62	-	end	6 *	Nucleus; nuclear envelope; nuclear pore complex; central core structure; multi-pass membrane protein ...	nuclear pore [IDA] spindle pole body [IDA]			655
P39705 UniProt NPD GO	NUP60_YEAST	Nucleoporin NUP60 (Nuclear pore protein NUP60)	0.62	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex; nucleoplasmic side. Nuclear basket	nuclear pore [TAS]			539
Q28269 UniProt NPD GO	OCLN_CANFA	Occludin	0.62	-	end	5	Membrane; multi-pass membrane protein				521
Q38899 UniProt NPD GO	ORC2_ARATH	Origin recognition complex subunit 2	0.62	-	cyt	0	Nucleus				363
Q9BZW0 UniProt NPD GO	PO5FN_HUMAN	POU domain, class 5, transcription factor 1-like protein 3	0.62	+	cyt	0	Nucleus (By similarity)				286
Q4WZL8 UniProt NPD GO	PFA3_ASPFU	Palmitoyltransferase pfa3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.62	-	mit	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				548
Q8WUA2 UniProt NPD GO	PPIL4_HUMAN	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-like protei ...	0.62	+	nuc	0	Nucleus (Probable)				492
O70589 UniProt NPD GO	CSKP_MOUSE	Peripheral plasma membrane protein CASK (EC 2.7.11.1) (Calcium/calmodulin-dependent serine protein k ...	0.62	-	nuc	0	Cytoplasm (By similarity)	basolateral plasma membrane [IDA] cytosol [IDA] synapse [IDA] synaptosome [IDA]		1Y74	924
O14936 UniProt NPD GO	CSKP_HUMAN	Peripheral plasma membrane protein CASK (EC 2.7.11.1) (hCASK) (Calcium/calmodulin-dependent serine p ...	0.62	-	nuc	0	Cytoplasm (Potential)	actin cytoskeleton [TAS] plasma membrane [TAS]	300172	1ZL8	926
Q93V93 UniProt NPD GO	PER44_ARATH	Peroxidase 44 precursor (EC 1.11.1.7) (Atperox P44) (ATP35)	0.62	-	exc	0	Secreted protein (By similarity)				310
O13764 UniProt NPD GO	PEX6_SCHPO	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.62	-	cyt	0					948
P35056 UniProt NPD GO	PEX5_YEAST	Peroxisomal targeting signal receptor (Peroxisomal protein PAS10) (Peroxin-5) (PTS1 receptor)	0.62	-	nuc	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...	cytosol [IDA] peroxisome [IDA]			612
Q01961 UniProt NPD GO	PEX12_PICPA	Peroxisome assembly protein 12 (Peroxin-12) (Peroxisome assembly protein PAS10)	0.62	-	nuc	2	Peroxisome; peroxisomal membrane; multi-pass membrane protein				409
P78741 UniProt NPD GO	BBR1_SCHCO	Pheromone B beta 1 receptor	0.62	-	end	7 *	Membrane; multi-pass membrane protein				541
P17442 UniProt NPD GO	PHO81_YEAST	Phosphate system positive regulatory protein PHO81 (CDK inhibitor PHO81)	0.62	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			1178
P42336 UniProt NPD GO	PK3CA_HUMAN	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153) (PI3-k ...	0.62	-	nuc	0			604370		1068
P51063 UniProt NPD GO	CAPP_PICAB	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.62	-	nuc	0	Cytoplasm (By similarity)				963
P51059 UniProt NPD GO	CAPP2_MAIZE	Phosphoenolpyruvate carboxylase 2 (EC 4.1.1.31) (PEPCase 2) (PEPC 2)	0.62	-	nuc	0	Cytoplasm (By similarity)				967
O35160 UniProt NPD GO	PITX3_MOUSE	Pituitary homeobox 3 (Homeobox protein PITX3)	0.62	+	nuc	0	Nucleus				302
Q2Q5Y8 UniProt NPD GO	PIWI2_SCHMD	Piwi-like protein 2 (SMEDWI-2)	0.62	+	nuc	0					833
Q9JII2 UniProt NPD GO	PRLPL_MOUSE	Placental prolactin-like protein L precursor (PRL-like protein L) (PLP-L)	0.62	-	exc	0	Secreted protein (By similarity)				230
O15031 UniProt NPD GO	PLXB2_HUMAN	Plexin-B2 precursor (MM1)	0.62	+	end	0	Membrane; single-pass type I membrane protein		604293		1838
Q8BZH4 UniProt NPD GO	POGZ_MOUSE	Pogo transposable element with ZNF domain	0.62	-	nuc	0	Nucleus (Probable)				1409
P23798 UniProt NPD GO	PCGF2_MOUSE	Polycomb group RING finger protein 2 (DNA-binding protein Mel-18) (RING finger protein 110) (Zinc fi ...	0.62	-	nuc	0	Nucleus	nuclear body [IDA] nucleus [IDA]			342
Q8BG81 UniProt NPD GO	PDIP3_MOUSE	Polymerase delta-interacting protein 3	0.62	-	nuc	0	Nucleus (Probable)				420
Q6BYU0 UniProt NPD GO	CWC24_DEBHA	Pre-mRNA-splicing factor CWC24	0.62	-	nuc	0	Nucleus (By similarity)				232
Q753C4 UniProt NPD GO	SPP2_ASHGO	Pre-mRNA-splicing factor SPP2	0.62	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				207

You are viewing entries 18051 to 18100 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.