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
P12961 UniProt NPD GO	7B2_MOUSE	Neuroendocrine protein 7B2 precursor (Secretogranin-5) (Secretogranin V) (Secretory granule endocrin ...	0.53	-	mit	0	Neuroendocrine and endocrine secretory granules	secretory granule [ISS]			212
P08553 UniProt NPD GO	NFM_MOUSE	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.53	-	nuc	0		neurofilament [IDA]			848
P55860 UniProt NPD GO	NEUM_XENLA	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (B-50)	0.53	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Cytoplasmic surface of ...				214
O97969 UniProt NPD GO	NPY5R_PIG	Neuropeptide Y receptor type 5 (NPY5-R) (NPY-Y5 receptor) (Y5 receptor)	0.53	-	end	7 *	Membrane; multi-pass membrane protein				446
Q8BNJ6 UniProt NPD GO	NETO2_MOUSE	Neuropilin and tolloid-like protein 2 precursor (Brain-specific transmembrane protein containing 2 C ...	0.53	-	end	1	Isoform 1: Cell membrane; single-pass type I membrane protein (Potential). Isoform 2: Cell membrane; ...				525
P97546 UniProt NPD GO	NPTN_RAT	Neuroplastin precursor (Stromal cell-derived receptor 1) (SDR-1) (Glycoprotein 55/65) (gp55/65)	0.53	+	exc	1	Cell membrane; single-pass type I membrane protein (Potential)	integral to membrane of membrane fraction [TAS] postsynaptic membrane [TAS] presynaptic membrane [IDA]			281
O42777 UniProt NPD GO	TREB_EMENI	Neutral trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.53	-	cyt	0	Cytoplasm (By similarity)				748
Q96S42 UniProt NPD GO	NODAL_HUMAN	Nodal homolog precursor	0.53	-	mit	0	Secreted protein (By similarity)		601265		347
P35398 UniProt NPD GO	RORA_HUMAN	Nuclear receptor ROR-alpha (Nuclear receptor RZR-alpha)	0.53	-	nuc	0	Nucleus (Probable)		600825	1S0X	556
Q9UHY1 UniProt NPD GO	NRBP_HUMAN	Nuclear receptor-binding protein	0.53	-	nuc	0	Cytoplasm. Co-localizes with activated RAC3 to endomembranes and at the cell periphery in lamellipod ...	endomembrane system [IDA]	606010		535
Q4R8X0 UniProt NPD GO	NRBP_MACFA	Nuclear receptor-binding protein	0.53	-	nuc	0	Cytoplasm. Co-localizes with activated RAC3 to endomembranes and at the cell periphery in lamellipod ...	endomembrane system [ISS] perinuclear region [ISS]			535
Q5RBH9 UniProt NPD GO	NRBP_PONPY	Nuclear receptor-binding protein	0.53	-	nuc	0	Cytoplasm. Co-localizes with activated RAC3 to endomembranes and at the cell periphery in lamellipod ...	endomembrane system [ISS] perinuclear region [ISS]			535
Q99J45 UniProt NPD GO	NRBP_MOUSE	Nuclear receptor-binding protein (MLF1 adapter molecule) (HLS7-interacting protein kinase)	0.53	-	nuc	0	Cytoplasm. Co-localizes with activated RAC3 to endomembranes and at the cell periphery in lamellipod ...	perinuclear region [IDA]			535
Q8LCG7 UniProt NPD GO	NFYC2_ARATH	Nuclear transcription factor Y subunit C-2 (AtNF-YC-2) (Transcriptional activator HAP5B)	0.53	+	cyt	0	Nucleus (By similarity)				199
Q6FRV0 UniProt NPD GO	NOG1_CANGA	Nucleolar GTP-binding protein 1	0.53	-	nuc	0	Nucleus; nucleolus (By similarity)				645
O14236 UniProt NPD GO	NOG2_SCHPO	Nucleolar GTP-binding protein 2	0.53	-	nuc	0	Nucleus; nucleolus (By similarity)				537
P20397 UniProt NPD GO	NUCL_XENLA	Nucleolin (Protein C23)	0.53	+	nuc	0	Nucleus; nucleolus				650
O14310 UniProt NPD GO	NP106_SCHPO	Nucleoporin npp106 (Nuclear pore protein npp106)	0.53	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex	nuclear membrane [IDA]			933
Q7Z3B4 UniProt NPD GO	NUP54_HUMAN	Nucleoporin p54 (54 kDa nucleoporin)	0.53	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Biased toward ...	cytoplasm [TAS] nuclear pore [TAS] nucleoplasm [TAS]	607607		507
Q6P6T5 UniProt NPD GO	OCLN_RAT	Occludin	0.53	-	end	5	Membrane; multi-pass membrane protein	cytosol [IDA] tight junction [NAS]			523
Q8CEE6 UniProt NPD GO	PASK_MOUSE	PAS domain-containing serine/threonine-protein kinase (EC 2.7.11.1) (PAS-kinase) (PASKIN)	0.53	-	nuc	0	Cytoplasm (By similarity)				1383
Q95QU0 UniProt NPD GO	PCID_CAEEL	PCI domain-containing protein (CSN12-like protein)	0.53	-	cyt	0					413
Q9UKJ0 UniProt NPD GO	PILRB_HUMAN	Paired immunoglobulin-like type 2 receptor beta precursor (Activating receptor PILR-beta) (Cell surf ...	0.53	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]	605342		227
Q5AWJ3 UniProt NPD GO	PFA3_EMENI	Palmitoyltransferase pfa3 (EC 2.3.1.-) (Protein fatty acyltransferase 3)	0.53	-	end	4 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity)				516
Q9NPB6 UniProt NPD GO	PAR6A_HUMAN	Partitioning defective 6 homolog alpha (PAR-6 alpha) (PAR-6A) (PAR-6) (PAR6C) (Tax interaction prote ...	0.53	-	nuc	0	Cytoplasm. Cell membrane. Colocalizes with GTP-bound CDC42 or RAC1 at membrane ruffles and with PARD ...	nucleus [ISS] tight junction [ISS]	607484	1WMH	346
P49024 UniProt NPD GO	PAXI_CHICK	Paxillin	0.53	-	nuc	0					559
Q12639 UniProt NPD GO	PLYA_MYCPO	Pectin lyase precursor (EC 4.2.2.10)	0.53	-	exc	0	Secreted protein (Potential)				299
O75570 UniProt NPD GO	RF1M_HUMAN	Peptide chain release factor 1, mitochondrial precursor (MRF-1)	0.53	-	mit	0	Mitochondrion	mitochondrion [TAS]	604601		445
Q9TL36 UniProt NPD GO	FTSI_NEPOL	Peptidoglycan synthetase ftsI homolog (EC 2.4.1.129) (Peptidoglycan glycosyltransferase)	0.53	+	nuc	1 *	Membrane; single-pass membrane protein (Potential)				709
P51346 UniProt NPD GO	SYFB_PORPU	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.53	-	nuc	0	Plastid; chloroplast				720
P23726 UniProt NPD GO	P85B_BOVIN	Phosphatidylinositol 3-kinase regulatory subunit beta (PI3-kinase p85-subunit beta) (PtdIns-3-kinase ...	0.53	-	nuc	0		phosphoinositide 3-kinase complex [ISS]			724
Q63788 UniProt NPD GO	P85B_RAT	Phosphatidylinositol 3-kinase regulatory subunit beta (PI3-kinase p85-subunit beta) (PtdIns-3-kinase ...	0.53	-	nuc	0		phosphoinositide 3-kinase complex [ISS]			722
Q6ZY51 UniProt NPD GO	PWD_ARATH	Phosphoglucan, water dikinase, chloroplast precursor (EC 2.7.9.5)	0.53	-	mit	0	Plastid; chloroplast. Starch granules during starch mobilization in darkness				1196
Q9GV36 UniProt NPD GO	PRSN_PIEBR	Pierisin (EC 2.4.2.-) (NAD--DNA ADP-ribosyltransferase) (Pierisin-2) (Pierisin-B)	0.53	-	nuc	0					850
P05154 UniProt NPD GO	IPSP_HUMAN	Plasma serine protease inhibitor precursor (PCI) (Protein C inhibitor) (Serpin A5) (Plasminogen acti ...	0.53	-	end	0	Secreted protein	extracellular region [NAS]	601841	2PAI	406
Q01177 UniProt NPD GO	PLMN_RAT	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Angiostati ...	0.53	-	nuc	0	Secreted protein				812
P06868 UniProt NPD GO	PLMN_BOVIN	Plasminogen precursor (EC 3.4.21.7) [Contains: Plasmin heavy chain A; Activation peptide; Plasmin he ...	0.53	-	exc	0	Secreted protein				812
Q95229 UniProt NPD GO	PDGFB_SHEEP	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.53	-	exc	0					241
P01127 UniProt NPD GO	PDGFB_HUMAN	Platelet-derived growth factor B chain precursor (PDGF B-chain) (Platelet-derived growth factor beta ...	0.53	-	exc	0		extracellular region [NAS]	190040	1PDG	241
P53632 UniProt NPD GO	PAP2_YEAST	Poly(A) RNA polymerase protein 2 (EC 2.7.7.-) (DNA polymerase sigma) (DNA polymerase kappa) (Topoiso ...	0.53	-	nuc	0	Nucleus	nucleus [IDA] TRAMP complex [IDA]			584
Q9EPH8 UniProt NPD GO	PABP1_RAT	Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)	0.53	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the cytoplasm and the nucleus ( ...	cytoplasm [ISS]			636
Q8ST83 UniProt NPD GO	PHO_DROME	Polycomb protein PHO (Protein pleiohomeotic) (Transcription factor YY1 homolog)	0.53	-	nuc	0	Nucleus	nuclear chromatin [IDA]			520
Q86SR1 UniProt NPD GO	GLT10_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 10 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.53	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		608043		603
O88703 UniProt NPD GO	HCN2_MOUSE	Potassium/sodium hyperpolarization-activated cyclic nucleotide-gated channel 2 (Brain cyclic nucleot ...	0.53	-	end	3	Membrane; multi-pass membrane protein			1Q5O	863
Q5AGC1 UniProt NPD GO	FIP1_CANAL	Pre-mRNA polyadenylation factor FIP1	0.53	-	nuc	0	Nucleus (By similarity)				326
Q5BAJ7 UniProt NPD GO	FIP1_EMENI	Pre-mRNA polyadenylation factor fip1	0.53	-	nuc	0	Nucleus (By similarity)				338
Q6BP48 UniProt NPD GO	CWC15_DEBHA	Pre-mRNA-splicing factor CWC15	0.53	-	nuc	0	Nucleus (Probable)				226
Q4PGU6 UniProt NPD GO	SLT11_USTMA	Pre-mRNA-splicing factor SLT11	0.53	-	nuc	0	Nucleus (By similarity)				324
Q06364 UniProt NPD GO	PSD3_DAUCA	Probable 26S proteasome non-ATPase regulatory subunit 3 (26S proteasome subunit S3) (Nuclear antigen ...	0.53	-	nuc	0	Nucleus				489
O42897 UniProt NPD GO	RPN3_SCHPO	Probable 26S proteasome regulatory subunit rpn3	0.53	-	cyt	0		nucleus [TAS]			497

You are viewing entries 23251 to 23300 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.