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
P26866 UniProt NPD GO	RT04_MARPO	Mitochondrial ribosomal protein S4	0.52	-	nuc	0	Mitochondrion				196
P43068 UniProt NPD GO	MKC1_CANAL	Mitogen-activated protein kinase MKC1 (EC 2.7.11.24) (MAP kinase MKC1)	0.52	-	cyt	0					501
Q00772 UniProt NPD GO	SLT2_YEAST	Mitogen-activated protein kinase SLT2/MPK1 (EC 2.7.11.24) (MAP kinase MPK1)	0.52	-	cyt	0		bud tip [IDA] cytoplasm [IDA] nucleus [IDA]			484
Q99JP0 UniProt NPD GO	M4K3_MOUSE	Mitogen-activated protein kinase kinase kinase kinase 3 (EC 2.7.11.1) (MAPK/ERK kinase kinase kinase ...	0.52	-	nuc	0					681
Q10189 UniProt NPD GO	SPO12_SCHPO	Mitosis-specific protein spo12	0.52	-	nuc	0					90
P80090 UniProt NPD GO	MPI3_LYMST	Molluscan insulin-related peptide 3 precursor (MIP III) [Contains: Molluscan insulin-related peptide ...	0.52	-	mit	1 *	Secretory granules				122
P70340 UniProt NPD GO	SMAD1_MOUSE	Mothers against decapentaplegic homolog 1 (SMAD 1) (Mothers against DPP homolog 1) (Mad-related prot ...	0.52	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS] transcription factor complex [IDA]			465
P97881 UniProt NPD GO	MUC13_RAT	Mucin-13 precursor	0.52	-	nuc	1	Cell membrane; single-pass type I membrane protein (Potential). Secreted protein (By similarity). Al ...				547
P60882 UniProt NPD GO	MEGF8_MOUSE	Multiple epidermal growth factor-like domains 8 (EGF-like domain-containing protein 4) (Multiple EGF ...	0.52	-	cyt	1	Membrane; single-pass type III membrane protein (Potential)				2330
P28698 UniProt NPD GO	MZF1_HUMAN	Myeloid zinc finger 1 (MZF-1) (Zinc finger protein 42) (Zinc finger and SCAN domain-containing prote ...	0.52	-	nuc	0	Nucleus		194550	2FI2	734
Q9XTA3 UniProt NPD GO	MYOC_BOVIN	Myocilin precursor (Trabecular meshwork-induced glucocorticoid response protein)	0.52	-	exc	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...				490
Q9Y217 UniProt NPD GO	MTMR6_HUMAN	Myotubularin-related protein 6 (EC 3.1.3.-)	0.52	-	nuc	0			603561		621
P52766 UniProt NPD GO	NUKC_LUPLU	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.52	-	nuc	0	Plastid; chloroplast				226
Q9M3M0 UniProt NPD GO	NUKC_SPIOL	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.52	-	nuc	0	Plastid; chloroplast				244
Q6L3D6 UniProt NPD GO	NUIC_SACHY	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.52	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q6ENP3 UniProt NPD GO	NUIC_SACOF	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.52	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q95MI5 UniProt NPD GO	NKG2A_PANTR	NKG2-A/NKG2-B type II integral membrane protein (NKG2-A/B-activating NK receptor) (NK cell receptor ...	0.52	-	nuc	1	Membrane; single-pass type II membrane protein				233
O95631 UniProt NPD GO	NET1_HUMAN	Netrin-1 precursor	0.52	-	nuc	1 *	Secreted protein; extracellular space (By similarity)		601614		604
P01165 UniProt NPD GO	7B2_PIG	Neuroendocrine protein 7B2 precursor (Secretogranin-5) (Secretogranin V) (Secretory granule endocrin ...	0.52	-	exc	0	Neuroendocrine and endocrine secretory granules	secretory granule [IDA]			207
Q8NC67 UniProt NPD GO	NETO2_HUMAN	Neuropilin and tolloid-like protein 2 precursor (Brain-specific transmembrane protein containing 2 C ...	0.52	-	end	1	Membrane; single-pass type I membrane protein (Potential)		607974		525
Q62809 UniProt NPD GO	NOGG_RAT	Noggin precursor (Fragment)	0.52	-	nuc	0	Secreted protein				144
Q6CC79 UniProt NPD GO	NHP6_YARLI	Nonhistone chromosomal protein 6	0.52	-	nuc	0	Nucleus (By similarity)				103
Q9TZ99 UniProt NPD GO	NH121_CAEEL	Nuclear hormone receptor family member nhr-121	0.52	-	nuc	0	Nucleus (Potential)				461
Q5ZIN1 UniProt NPD GO	NUDC_CHICK	Nuclear migration protein nudC (Nuclear distribution protein C homolog)	0.52	-	nuc	0	Cytoplasm (By similarity). In a filamentous pattern adjacent to the nucleus of migrating cerebellar ...				341
Q06725 UniProt NPD GO	NR2F1_BRARE	Nuclear receptor Nr2f1 (Steroid receptor homolog SVP 44)	0.52	-	nuc	0	Nucleus (Potential)				411
P48837 UniProt NPD GO	NUP57_YEAST	Nucleoporin NUP57 (Nuclear pore protein NUP57)	0.52	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			541
Q9PUN1 UniProt NPD GO	OCLN_XENLA	Occludin	0.52	-	end	6 *	Membrane; multi-pass membrane protein				493
Q13516 UniProt NPD GO	OLIG2_HUMAN	Oligodendrocyte transcription factor 2 (Oligo2) (Basic helix-loop-helix protein class B 1) (Protein ...	0.52	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). The NLS contained in the bHLH domain could be ma ...		606386		323
Q9XYT4 UniProt NPD GO	ORCH_ORCCA	Orchestin precursor	0.52	-	exc	0	During the premolt period, localizes to microvilli-rich apical regions and to the subnuclear region. ...	basal part of cell [IDA] extracellular space [IDA] microvillus [IDA]			128
Q9XSY9 UniProt NPD GO	OSTP_SHEEP	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1)	0.52	-	exc	0	Secreted protein	extracellular region [ISS]			278
Q8N573 UniProt NPD GO	OXR1_HUMAN	Oxidation resistance protein 1	0.52	-	nuc	0	Mitochondrion		605609		758
Q62920 UniProt NPD GO	PDLI5_RAT	PDZ and LIM domain protein 5 (Enigma homolog) (Enigma-like PDZ and LIM domains protein)	0.52	-	nuc	0		cytosol [IDA] membrane fraction [IDA]			591
Q9BZV7 UniProt NPD GO	PO5FM_HUMAN	POU domain, class 5, transcription factor 1-like protein 2	0.52	+	cyt	0	Nucleus (By similarity)				359
Q9GZV8 UniProt NPD GO	PRD14_HUMAN	PR domain zinc finger protein 14 (PR domain-containing protein 14)	0.52	-	nuc	0	Nucleus (Potential)				571
Q03289 UniProt NPD GO	PFA5_YEAST	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.52	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				374
Q66H76 UniProt NPD GO	PAXI_RAT	Paxillin	0.52	-	nuc	0					586
Q43867 UniProt NPD GO	PME1_ARATH	Pectinesterase-1 precursor (EC 3.1.1.11) (Pectin methylesterase 1) (PE 1)	0.52	-	cyt	1 *					586
O08908 UniProt NPD GO	P85B_MOUSE	Phosphatidylinositol 3-kinase regulatory subunit beta (PI3-kinase p85-subunit beta) (PtdIns-3-kinase ...	0.52	-	nuc	0		phosphoinositide 3-kinase complex [NAS]			722
P42348 UniProt NPD GO	PI3K2_SOYBN	Phosphatidylinositol 3-kinase, nodule isoform (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K) ( ...	0.52	-	nuc	0					812
Q06705 UniProt NPD GO	CSR1_YEAST	Phosphatidylinositol transfer protein CSR1 (CHS5 SPA2 rescue protein 1) (SEC14 homolog protein 2)	0.52	-	cyt	0	Cytoplasm. Endosome	cytoplasm [IDA] cytosol [IDA] microsome [IDA] mitochondrion [IDA]			408
Q9LMN1 UniProt NPD GO	PI5KA_ARATH	Phosphatidylinositol-4-phosphate 5-kinase 10 (EC 2.7.1.68) (AtPIP5K10) (1-phosphatidylinositol-4-pho ...	0.52	-	nuc	0					427
Q2PC95 UniProt NPD GO	PIWIL_DUGJA	Piwi-like protein	0.52	-	nuc	0					818
P58135 UniProt NPD GO	RR9_ASTLO	Plastid 30S ribosomal protein S9	0.52	-	nuc	0	Plastid				128
Q6NSJ2 UniProt NPD GO	PHLB3_HUMAN	Pleckstrin homology-like domain family B member 3	0.52	-	nuc	0					279
Q6BEA0 UniProt NPD GO	PLXA4_BRARE	Plexin-A4 precursor	0.52	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				1903
Q9R152 UniProt NPD GO	PARP1_CRIGR	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.52	+	nuc	0	Nucleus				1012
P27008 UniProt NPD GO	PARP1_RAT	Poly [ADP-ribose] polymerase 1 (EC 2.4.2.30) (PARP-1) (ADPRT) (NAD(+) ADP-ribosyltransferase 1) (Pol ...	0.52	+	nuc	0		nucleus [NAS]			1013
P29341 UniProt NPD GO	PABP1_MOUSE	Polyadenylate-binding protein 1 (Poly(A)-binding protein 1) (PABP 1)	0.52	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Shuttles between the cytoplasm and the nucleus ( ...	cytoplasm [ISS]			636
P04147 UniProt NPD GO	PABP_YEAST	Polyadenylate-binding protein, cytoplasmic and nuclear (Poly(A)-binding protein) (PABP) (ARS consens ...	0.52	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] ribosome [IDA]		1IFW	576
Q5XI70 UniProt NPD GO	PCGF6_RAT	Polycomb group RING finger protein 6 (RING finger protein 134)	0.52	-	nuc	0	Nucleus (By similarity)				351

You are viewing entries 23851 to 23900 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.