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
P87309 UniProt NPD GO	MDE2_SCHPO	Mei4-dependent protein 2	0.51	-	nuc	0					209
P39073 UniProt NPD GO	UME5_YEAST	Meiotic mRNA stability protein kinase UME5 (EC 2.7.11.23)	0.51	-	mit	0	Nucleus (Potential)	transcription factor complex [TAS]			541
Q9Y5K1 UniProt NPD GO	SPO11_HUMAN	Meiotic recombination protein SPO11	0.51	-	cyt	0	Nucleus (By similarity)		605114		396
P34808 UniProt NPD GO	MEI1_CAEEL	Meiotic spindle formation protein mei-1 (EC 3.6.4.3) (Katanin ATPase-containing subunit)	0.51	-	nuc	0	Localized to the spindle poles and condensed chromatin during female meiosis. This localization requ ...	nucleus [IDA] spindle pole [IDA]			472
Q3T0U1 UniProt NPD GO	MESD2_BOVIN	Mesoderm development candidate 2	0.51	+	exc	1 *					232
P70579 UniProt NPD GO	MGR8_RAT	Metabotropic glutamate receptor 8 precursor (mGluR8)	0.51	-	end	7	Membrane; multi-pass membrane protein	cell soma [IDA] integral to plasma membrane [IDA] neuron projection [IDA] postsynaptic membrane [TAS] presynaptic membrane [IDA]			908
P82927 UniProt NPD GO	RT32_BOVIN	Mitochondrial 28S ribosomal protein S32 (S32mt) (MRP-S32)	0.51	-	nuc	0	Mitochondrion				142
Q9Y291 UniProt NPD GO	RT33_HUMAN	Mitochondrial 28S ribosomal protein S33 (S33mt) (MRP-S33)	0.51	-	nuc	0	Mitochondrion	mitochondrial small ribosomal subunit [NAS]			106
P22353 UniProt NPD GO	RM08_YEAST	Mitochondrial 60S ribosomal protein L8 (YmL8)	0.51	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			237
P08977 UniProt NPD GO	RT13_MAIZE	Mitochondrial ribosomal protein S13	0.51	-	nuc	0	Mitochondrion				129
Q39026 UniProt NPD GO	MPK6_ARATH	Mitogen-activated protein kinase 6 (EC 2.7.11.24) (MAP kinase 6) (AtMPK6)	0.51	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (Probable)				395
Q07176 UniProt NPD GO	MMK1_MEDSA	Mitogen-activated protein kinase homolog MMK1 (EC 2.7.11.24) (MAP kinase MSK7) (MAP kinase ERK1)	0.51	-	cyt	0					387
P19467 UniProt NPD GO	MUC13_MOUSE	Mucin-13 precursor (Cell surface antigen 114/A10) (Lymphocyte antigen 64)	0.51	-	mit	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein (By similarity). Al ...				573
P08482 UniProt NPD GO	ACM1_RAT	Muscarinic acetylcholine receptor M1	0.51	-	end	7 *	Membrane; multi-pass membrane protein	synapse [TAS]			460
Q99KX1 UniProt NPD GO	MLF2_MOUSE	Myeloid leukemia factor 2 (Myelodysplasia-myeloid leukemia factor 2)	0.51	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
Q9NZM1 UniProt NPD GO	MYOF_HUMAN	Myoferlin (Fer-1-like protein 3)	0.51	+	nuc	1	Cell membrane; single-pass type II membrane protein (By similarity). Nucleus; nuclear membrane; sing ...	nuclear envelope [TAS] plasma membrane [TAS]	604603		2061
O95182 UniProt NPD GO	NDUA7_HUMAN	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.51	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side		602139		112
Q5R4H6 UniProt NPD GO	NRDC_PONPY	Nardilysin precursor (EC 3.4.24.61) (N-arginine dibasic convertase) (NRD convertase) (NRD-C)	0.51	-	mit	0					1152
Q90610 UniProt NPD GO	NEO1_CHICK	Neogenin (Fragment)	0.51	-	nuc	1	Membrane; single-pass type I membrane protein				1443
P34710 UniProt NPD GO	UNC6_CAEEL	Netrin unc-6 precursor (Uncoordinated protein 6)	0.51	-	nuc	1 *	Secreted protein; extracellular space; extracellular matrix; basement membrane. Epidermal basal lami ...	axon [IDA] cytoplasm [IDA]			612
Q90923 UniProt NPD GO	NET2_CHICK	Netrin-2 precursor (Fragment)	0.51	-	nuc	0	Secreted protein; extracellular space				581
Q26240 UniProt NPD GO	NOS_RHOPR	Nitric-oxide synthase, salivary gland (EC 1.14.13.39) (NOS)	0.51	-	cyt	0					1174
Q04948 UniProt NPD GO	IFE_BRALA	Non-neuronal cytoplasmic intermediate filament protein	0.51	-	nuc	0	Cytoplasm				464
P38861 UniProt NPD GO	NMD3_YEAST	Nonsense-mediated mRNA decay protein 3	0.51	-	cyt	0		cytosol [IDA] cytosolic large ribosomal subunit (sensu Eu... [IDA]			518
Q06712 UniProt NPD GO	PREG_NEUCR	Nuc-1 negative regulatory protein preg	0.51	-	mit	0					483
P27123 UniProt NPD GO	NASP_RABIT	Nuclear autoantigenic sperm protein (NASP)	0.51	-	nuc	0	Nucleus				680
P32493 UniProt NPD GO	NCA1_YEAST	Nuclear control of ATPase messenger RNA expression protein, mitochondrial precursor	0.51	-	nuc	0		mitochondrion [IDA]			518
O16966 UniProt NPD GO	NH106_CAEEL	Nuclear hormone receptor family member nhr-106	0.51	-	cyt	0	Nucleus (Potential)				382
O35685 UniProt NPD GO	NUDC_MOUSE	Nuclear migration protein nudC (Nuclear distribution protein C homolog) (Silica-induced gene 92 prot ...	0.51	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). A small proportion is nuclear, in a punctate pat ...			2CR0	332
Q63525 UniProt NPD GO	NUDC_RAT	Nuclear migration protein nudC (Nuclear distribution protein C homolog) (c15)	0.51	-	nuc	0	Cytoplasm. Nucleus (By similarity). A small proportion is nuclear, in a punctate pattern (By similar ...				332
Q9ZVL3 UniProt NPD GO	NFYC3_ARATH	Nuclear transcription factor Y subunit C-3 (AtNF-YC-3)	0.51	+	nuc	0	Nucleus (By similarity)				217
Q5RB52 UniProt NPD GO	NOL11_PONPY	Nucleolar protein 11	0.51	-	cyt	0	Nucleus; nucleolus (By similarity)				718
Q86SE8 UniProt NPD GO	NPM2_HUMAN	Nucleoplasmin-2	0.51	-	nuc	0	Nucleus (By similarity). Found in the oocyte nucleus before nuclear membrane breakdown, after which ...	cytoplasmic chromatin [IDA] nuclear chromatin [IDA] nucleus [IEP]	608073		214
Q5A360 UniProt NPD GO	SIL1_CANAL	Nucleotide exchange factor SIL1 precursor	0.51	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				414
Q25188 UniProt NPD GO	OAR_HELVI	Octopamine receptor	0.51	+	end	7	Membrane; multi-pass membrane protein				477
P18746 UniProt NPD GO	ZO26_XENLA	Oocyte zinc finger protein XLCOF26 (Fragment)	0.51	-	nuc	0	Nucleus (Potential)				196
O93479 UniProt NPD GO	ORC4_XENLA	Origin recognition complex subunit 4	0.51	-	mit	0	Nucleus				432
Q02803 UniProt NPD GO	OAZ_YEAST	Ornithine decarboxylase antizyme (ODC-Az)	0.51	-	nuc	0		cell [IC]			292
Q06416 UniProt NPD GO	PO5FL_HUMAN	POU domain, class 5, transcription factor 1-like protein 1 (Octamer-binding protein 3-like)	0.51	+	cyt	0	Nucleus (By similarity)	nucleus [TAS]			359
P51974 UniProt NPD GO	PAX8_RAT	Paired box protein Pax-8	0.51	-	nuc	0	Nucleus				458
Q9WVS6 UniProt NPD GO	PRKN2_MOUSE	Parkin (EC 6.3.2.-) (Ubiquitin E3 ligase PRKN)	0.51	-	nuc	0	Cytoplasm. Expressed in the endoplasmic reticulum, dendrites, some presynaptic terminals and in post ...	neuron projection [IDA]		1MG8	464
Q8VI36 UniProt NPD GO	PAXI_MOUSE	Paxillin	0.51	-	nuc	0		focal adhesion [IDA] lamellipodium [IDA]			591
Q9SI17 UniProt NPD GO	PER14_ARATH	Peroxidase 14 precursor (EC 1.11.1.7) (Atperox P14)	0.51	-	exc	0	Secreted protein (By similarity)				337
Q9QXY9 UniProt NPD GO	PEX3_MOUSE	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal assembly protein PEX3)	0.51	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				372
P35396 UniProt NPD GO	PPARB_MOUSE	Peroxisome proliferator-activated receptor delta (PPAR-delta) (PPAR-beta) (Nuclear hormone receptor ...	0.51	+	cyt	0	Nucleus				440
Q27452 UniProt NPD GO	PRP2_BOMMO	Phenoloxidase subunit 2 precursor (EC 1.14.18.1) (Tyrosinase 2) (PO 2)	0.51	-	cyt	0	Secreted protein	extracellular region [TAS]			693
Q8N4E4 UniProt NPD GO	PDCL2_HUMAN	Phosducin-like protein 2	0.51	-	nuc	0					250
Q02909 UniProt NPD GO	CAPP1_SOYBN	Phosphoenolpyruvate carboxylase, housekeeping isozyme (EC 4.1.1.31) (PEPCase) (PEPC 1)	0.51	-	nuc	0	Cytoplasm				967
P49085 UniProt NPD GO	PSY_MAIZE	Phytoene synthase, chloroplast precursor (EC 2.5.1.-)	0.51	-	mit	0	Plastid; chloroplast				410
P26262 UniProt NPD GO	KLKB1_MOUSE	Plasma kallikrein precursor (EC 3.4.21.34) (Plasma prekallikrein) (Kininogenin) (Fletcher factor) [C ...	0.51	-	nuc	1 *					638

You are viewing entries 24451 to 24500 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.