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
P33323 UniProt NPD GO	RE104_YEAST	Meiotic recombination protein REC104	0.44	-	nuc	0		condensed nuclear chromosome [IDA]			182
Q758Z4 UniProt NPD GO	MSC6_ASHGO	Meiotic sister-chromatid recombination protein 6, mitochondrial precursor	0.44	-	mit	0	Mitochondrion (By similarity)				717
Q5YCV9 UniProt NPD GO	TAU_HYLLA	Microtubule-associated protein tau	0.44	-	nuc	0	Cytoplasm; cytosol (By similarity). Cell membrane (By similarity). Mostly found in the axons of neur ...	axon [ISS] cytosol [ISS] growth cone [ISS] microtubule associated complex [ISS] plasma membrane [ISS] tubulin [ISS]			775
P82928 UniProt NPD GO	RT28_BOVIN	Mitochondrial 28S ribosomal protein S28 (S28mt) (MRP-S28) (MRP-S35)	0.44	-	nuc	0	Mitochondrion				189
Q63750 UniProt NPD GO	RM23_RAT	Mitochondrial 39S ribosomal protein L23 (L23mt) (MRP-L23) (L23 mitochondrial-related protein)	0.44	-	mit	0	Mitochondrion				146
Q04715 UniProt NPD GO	RM16_PETHY	Mitochondrial 60S ribosomal protein L16	0.44	-	mit	0	Mitochondrion				155
Q758X6 UniProt NPD GO	GEM1_ASHGO	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.44	+	cyt	1	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				661
Q6FIR8 UniProt NPD GO	GEM1_CANGA	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.44	+	cyt	0	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				649
Q5KEW5 UniProt NPD GO	GEM1_CRYNE	Mitochondrial Rho GTPase 1 (EC 3.6.5.-) (GTPase EF-hand protein of mitochondria 1)	0.44	-	mit	0	Mitochondrion; mitochondrial outer membrane; single-pass type IV membrane protein (By similarity)				686
P08466 UniProt NPD GO	NUC1_YEAST	Mitochondrial nuclease (EC 3.1.30.-)	0.44	-	nuc	1 *	Mitochondrion; mitochondrial inner membrane	mitochondrial inner membrane [IDA]			329
Q00859 UniProt NPD GO	MAPK_FUSSO	Mitogen-activated protein kinase (EC 2.7.11.24) (FsMAPK)	0.44	-	nuc	0	Nucleus (Potential)				355
Q39023 UniProt NPD GO	MPK3_ARATH	Mitogen-activated protein kinase 3 (EC 2.7.11.24) (MAP kinase 3) (AtMPK3)	0.44	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus in response to phosphorylation (Probable)				370
Q9UV50 UniProt NPD GO	HOG1_DEBHA	Mitogen-activated protein kinase HOG1 (EC 2.7.11.24) (MAP kinase HOG1)	0.44	-	cyt	0					387
Q40532 UniProt NPD GO	NTF4_TOBAC	Mitogen-activated protein kinase homolog NTF4 (EC 2.7.11.24) (P45)	0.44	-	cyt	0					393
Q8CF89 UniProt NPD GO	TAB1_MOUSE	Mitogen-activated protein kinase kinase kinase 7-interacting protein 1 (TGF-beta-activated kinase 1- ...	0.44	-	nuc	0					502
P40623 UniProt NPD GO	HMG1B_CHITE	Mobility group protein 1B	0.44	-	nuc	0	Nucleus				110
Q9I9P9 UniProt NPD GO	SMAD2_BRARE	Mothers against decapentaplegic homolog 2 (SMAD 2) (Mothers against DPP homolog 2) (Smad2)	0.44	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...				468
Q8NHP6 UniProt NPD GO	MSPD2_HUMAN	Motile sperm domain-containing protein 2	0.44	-	nuc	1					518
Q8BJG4 UniProt NPD GO	MOL2C_MOUSE	Mps one binder kinase activator-like 2C (Mob1 homolog 2C)	0.44	-	nuc	0					216
Q29435 UniProt NPD GO	MUC1_HYLLA	Mucin-1 precursor (MUC-1)	0.44	-	exc	2 *	Membrane; single-pass type I membrane protein				475
Q02817 UniProt NPD GO	MUC2_HUMAN	Mucin-2 precursor (Intestinal mucin-2)	0.44	-	nuc	0	Secreted protein		158370		5179
Q9M3B9 UniProt NPD GO	MDR14_ARATH	Multidrug resistance protein 14 (P-glycoprotein 20)	0.44	-	end	13	Membrane; multi-pass membrane protein (Potential)				1408
O70624 UniProt NPD GO	MYOC_MOUSE	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.44	-	mit	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...	extracellular space [IDA]			490
P56741 UniProt NPD GO	MYPC3_RAT	Myosin-binding protein C, cardiac-type (Cardiac MyBP-C) (C-protein, cardiac muscle isoform) (Fragmen ...	0.44	-	nuc	0					36
Q8TDC0 UniProt NPD GO	MYOZ3_HUMAN	Myozenin-3 (Calsarcin-3) (FATZ-related protein 3)	0.44	-	nuc	0	Localized at the Z-line of skeletal muscle (By similarity)				251
Q9R123 UniProt NPD GO	NAT6_MOUSE	N-acetyltransferase 6 (EC 2.3.1.-) (Fus-2 protein) (Fusion 2 protein)	0.44	-	nuc	0	Cytoplasm (By similarity)				314
Q9V3I8 UniProt NPD GO	OGG1_DROME	N-glycosylase/DNA lyase (dOgg1) [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic ...	0.44	-	mit	0	Nucleus. Cytoplasm. Nuclear and cytoplasmic in nurse cells and oocyte				343
P06409 UniProt NPD GO	NUKC_TOBAC	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.44	-	nuc	0	Plastid; chloroplast				247
P26304 UniProt NPD GO	NUKC_WHEAT	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.44	-	nuc	0	Plastid; chloroplast				245
Q7YJT0 UniProt NPD GO	NUIC_CALFE	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.44	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q9BBP0 UniProt NPD GO	NUIC_LOTJA	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.44	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				161
Q9M3I7 UniProt NPD GO	NUIC_SPIOL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.44	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				170
P06700 UniProt NPD GO	SIR2_YEAST	NAD-dependent histone deacetylase SIR2 (EC 3.5.1.-) (Regulatory protein SIR2) (Silent information re ...	0.44	-	nuc	0	Nucleus; nucleolus. Associated with nucleolar chromatin. Preferentially bound to the spacer regions ...	nuclear telomere cap complex [IDA] nuclear telomeric heterochromatin [IDA] nucleolus [IDA] RENT complex [IDA]			562
Q9CQJ8 UniProt NPD GO	NDUB9_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 9 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.44	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			178
Q02379 UniProt NPD GO	NIPM_BOVIN	NADH-ubiquinone oxidoreductase 15 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-15 kDa) (CI-15 k ...	0.44	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side				105
O43181 UniProt NPD GO	NUYM_HUMAN	NADH-ubiquinone oxidoreductase 18 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (C ...	0.44	-	mit	0	Mitochondrion; mitochondrial inner membrane; matrix side	membrane fraction [TAS]	602694		175
P56181 UniProt NPD GO	NUOM_HUMAN	NADH-ubiquinone oxidoreductase 9 kDa subunit, mitochondrial precursor (EC 1.6.5.3) (EC 1.6.99.3) (Co ...	0.44	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side		602184		108
P42580 UniProt NPD GO	NKX12_MOUSE	NK1 transcription factor-related protein 2 (Homeobox protein SAX-1) (NKX-1.1)	0.44	+	nuc	0	Nucleus (Probable)				305
Q07444 UniProt NPD GO	NKG2E_HUMAN	NKG2-E type II integral membrane protein (NKG2-E-activating NK receptor) (NK cell receptor E)	0.44	-	nuc	1	Membrane; single-pass type II membrane protein		602892		240
P60322 UniProt NPD GO	NANO2_MOUSE	Nanos homolog 2	0.44	-	nuc	0					136
Q8BHG1 UniProt NPD GO	NRDC_MOUSE	Nardilysin precursor (EC 3.4.24.61) (N-arginine dibasic convertase) (NRD convertase) (NRD-C)	0.44	-	mit	0					1161
Q07310 UniProt NPD GO	NRX3A_RAT	Neurexin-3-alpha precursor (Neurexin III-alpha)	0.44	-	end	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein. Some isoforms seem ...				1578
Q9GLR1 UniProt NPD GO	NEC1_BOVIN	Neuroendocrine convertase 1 precursor (EC 3.4.21.93) (NEC 1) (PC1) (Prohormone convertase 1) (Propro ...	0.44	+	mit	0	Secretory vesicle. Localized in the secretion granules (By similarity)				753
P05408 UniProt NPD GO	7B2_HUMAN	Neuroendocrine protein 7B2 precursor (Secretogranin-5) (Secretogranin V) (Secretory granule endocrin ...	0.44	-	mit	0	Neuroendocrine and endocrine secretory granules	secretory granule [ISS]	173120		212
Q6S9D9 UniProt NPD GO	NEUM_FELCA	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43)	0.44	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Cytoplasmic surface of ...				242
Q98987 UniProt NPD GO	NEUM_SERCA	Neuromodulin (Axonal membrane protein GAP-43) (Growth-associated protein 43) (Fragment)	0.44	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity). Cytoplasmic surface of ...				241
Q9QWJ9 UniProt NPD GO	NRP1_RAT	Neuropilin-1 precursor (Vascular endothelial cell growth factor 165 receptor)	0.44	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [NAS]			922
Q99784 UniProt NPD GO	NOE1_HUMAN	Noelin precursor (Neuronal olfactomedin-related ER localized protein) (Olfactomedin-1)	0.44	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)		605366		485
Q7S045 UniProt NPD GO	NHP6_NEUCR	Nonhistone chromosomal protein 6	0.44	-	nuc	0	Nucleus (By similarity)				103
O16963 UniProt NPD GO	NH130_CAEEL	Nuclear hormone receptor family member nhr-130	0.44	-	cyt	0	Nucleus (Potential)				440

You are viewing entries 29101 to 29150 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.