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
Q29131 UniProt NPD GO	MCR_TUPGB	Mineralocorticoid receptor (MR)	0.61	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic and nuclear in the absence of ligand ...				977
Q05930 UniProt NPD GO	MDM30_YEAST	Mitochondrial distribution and morphology protein 30	0.61	-	cyt	0	Cytoplasm. Mitochondrion	mitochondrion [IDA]			598
Q15388 UniProt NPD GO	TOM20_HUMAN	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.61	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)	mitochondrial outer membrane translocase co... [NAS]	601848		145
Q9DCC8 UniProt NPD GO	TOM20_MOUSE	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.61	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)	mitochondrial envelope [IDA] mitochondrion [IDA]			145
Q5RA31 UniProt NPD GO	TOM20_PONPY	Mitochondrial import receptor subunit TOM20 homolog (Mitochondrial 20 kDa outer membrane protein) (O ...	0.61	+	nuc	1 *	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (Potential)				145
Q99797 UniProt NPD GO	PMIP_HUMAN	Mitochondrial intermediate peptidase, mitochondrial precursor (EC 3.4.24.59) (MIP)	0.61	+	mit	0	Mitochondrion; mitochondrial matrix	mitochondrion [TAS]	602241		713
O21240 UniProt NPD GO	RT07_RECAM	Mitochondrial ribosomal protein S7	0.61	-	nuc	0	Mitochondrion				159
Q6QUV9 UniProt NPD GO	MPK13_ORYSA	Mitogen-activated protein kinase 13 (EC 2.7.11.24) (MAP kinase 13) (Benzothiadiazole-induced MAP kin ...	0.61	-	nuc	0					506
Q53N72 UniProt NPD GO	MPK15_ORYSA	Mitogen-activated protein kinase 15 (EC 2.7.11.24) (MAP kinase 15)	0.61	-	nuc	0					498
P07334 UniProt NPD GO	CDR1_SCHPO	Mitosis inducer protein kinase cdr1 (EC 2.7.11.1) (Protein kinase nim1)	0.61	-	mit	0		cytoplasm [IDA]			593
Q8TAX7 UniProt NPD GO	MUC7_HUMAN	Mucin-7 precursor (MUC-7) (Salivary mucin-7) (Apo-MG2)	0.61	-	exc	0	Secreted protein		600807		377
O89050 UniProt NPD GO	MKLN1_MOUSE	Muskelin	0.61	-	nuc	0	Cytoplasm				735
Q99PV3 UniProt NPD GO	MKLN1_RAT	Muskelin	0.61	-	nuc	0	Cytoplasm (By similarity)				735
Q8R015 UniProt NPD GO	MUT_MOUSE	Muted protein	0.61	-	nuc	0					185
P02686 UniProt NPD GO	MBP_HUMAN	Myelin basic protein (MBP) (Myelin A1 protein) (Myelin membrane encephalitogenic protein)	0.61	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin		159430	1YMM	304
Q8SPH9 UniProt NPD GO	MNDA_MACFA	Myeloid cell nuclear differentiation factor	0.61	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Uniformly distributed throughout the interphase ...				407
Q9NKV0 UniProt NPD GO	MLF_DROME	Myeloid leukemia factor (Myelodysplasia-myeloid leukemia factor) (dMLF)	0.61	-	nuc	0	Cytoplasm. Interacts with DRE-binding factor (DREF)	cytoplasm [IDA]			309
Q9QWV4 UniProt NPD GO	MLF1_MOUSE	Myeloid leukemia factor 1 (Myelodysplasia-myeloid leukemia factor 1) (Hematopoietic lineage switch 7 ...	0.61	-	nuc	0	Cytoplasm. Nucleus	centrosome [IDA] cytoplasm [IDA] nucleus [IDA]			267
P34092 UniProt NPD GO	MYOB_DICDI	Myosin IB heavy chain	0.61	-	nuc	0	Cytoplasm; cell cortex. Highest concentration just beneath the plasma membrane in the anterior pseud ...				1111
P37293 UniProt NPD GO	NAT2_YEAST	N-terminal acetyltransferase 2 (EC 2.3.1.88) (Amino-terminal, alpha-amino, acetyltransferase 2)	0.61	-	mit	1	Cytoplasm (Probable)	cytoplasm [IC] mitochondrion [IDA]			288
Q9NX02 UniProt NPD GO	NALP2_HUMAN	NACHT, LRR and PYD-containing protein 2 (PYRIN domain and NACHT domain-containing protein 1) (PYRIN- ...	0.61	-	cyt	0	Cytoplasm	cytoplasm [IDA]	609364		1062
Q9UBC1 UniProt NPD GO	IKBL_HUMAN	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.61	+	nuc	0			601022		381
Q861W0 UniProt NPD GO	IKBL_PANTR	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.61	+	nuc	0					380
Q9TSV7 UniProt NPD GO	IKBL_PIG	NF-kappa-B inhibitor-like protein 1 (Inhibitor of kappa B-like) (I-kappa-B-like) (IkappaBL) (Nuclear ...	0.61	+	nuc	0					380
Q95MI4 UniProt NPD GO	NKG2E_PANTR	NKG2-E type II integral membrane protein (NKG2-E-activating NK receptor) (NK cell receptor E)	0.61	-	nuc	1	Membrane; single-pass type II membrane protein				240
Q99271 UniProt NPD GO	NAH1_YEAST	Na(+)/H(+) antiporter	0.61	+	end	9 *	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			985
P19246 UniProt NPD GO	NFH_MOUSE	Neurofilament triplet H protein (200 kDa neurofilament protein) (Neurofilament heavy polypeptide) (N ...	0.61	-	nuc	0		mitochondrion [IDA] neurofilament [IDA]			1090
P79920 UniProt NPD GO	NDF4_XENLA	Neurogenic differentiation factor 4 (NeuroD4) (Atonal protein homolog 3) (Helix-loop-helix protein x ...	0.61	-	nuc	0	Nucleus (Potential)				315
Q99466 UniProt NPD GO	NOTC4_HUMAN	Neurogenic locus notch homolog protein 4 precursor (Notch 4) (hNotch4) [Contains: Notch 4 extracellu ...	0.61	-	end	0	Cell membrane; single-pass type I membrane protein. NICD: Nucleus. Following proteolytical processin ...	cell surface [IDA] integral to plasma membrane [TAS] nucleus [TAS]	164951		2003
Q9W0W6 UniProt NPD GO	NPLP1_DROME	Neuropeptide-like 1 precursor [Contains: MTYamide peptide; IPNamide peptide; NAP peptide; NPLP1-1; N ...	0.61	-	mit	0	Secreted protein	extracellular region [NAS]			309
Q14596 UniProt NPD GO	NBR1_HUMAN	Next to BRCA1 gene 1 protein (Neighbor of BRCA1 gene 1 protein) (Membrane component, chromosome 17, ...	0.61	-	nuc	0			166945	2CP8	966
Q03718 UniProt NPD GO	NSE5_YEAST	Non-structural maintenance of chromosome element 5 (Non-SMC element 5)	0.61	-	end	0	Nucleus	nucleus [IDA] Smc5-Smc6 complex [IPI]			556
P02316 UniProt NPD GO	HMGN1_BOVIN	Nonhistone chromosomal protein HMG-14 (High-mobility group nucleosome-binding domain-containing prot ...	0.61	-	nuc	0	Nucleus				100
Q9N1Q5 UniProt NPD GO	SP100_HYLLA	Nuclear autoantigen Sp-100 (Speckled 100 kDa) (Nuclear dot-associated Sp100 protein) (Fragment)	0.61	+	nuc	0	Nucleus (By similarity). Found in the nuclear body, a nucleoplasmic structure of punctate shape, whi ...				242
Q9NXR1 UniProt NPD GO	NDE1_HUMAN	Nuclear distribution protein nudE homolog 1 (NudE)	0.61	-	nuc	0	Concentrates at the plus ends of microtubules coincident with kinetochores in metaphase and anaphase ...		609449		346
Q9CZA6 UniProt NPD GO	NDE1_MOUSE	Nuclear distribution protein nudE homolog 1 (NudE) (mNudE)	0.61	-	nuc	0	Cytoplasm. Centrosome. Spindle. Localizes to the interphase centrosome and to the mitotic spindle. C ...	centrosome [IDA] spindle [IDA]			344
Q28CJ6 UniProt NPD GO	NDEL1_XENTR	Nuclear distribution protein nudE-like 1	0.61	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				346
Q6DK98 UniProt NPD GO	NDL1A_XENLA	Nuclear distribution protein nudE-like 1-A	0.61	-	nuc	0	Cytoplasm (By similarity). Centrosome (By similarity). Spindle (By similarity). Localizes to the int ...				345
Q90932 UniProt NPD GO	NFIX_CHICK	Nuclear factor 1 X-type (Nuclear factor 1/X) (NF1-X) (NFI-X) (NF-I/X) (CCAAT-box-binding transcripti ...	0.61	-	nuc	0	Nucleus				431
P41829 UniProt NPD GO	NHR6_CAEEL	Nuclear hormone receptor family member nhr-6 (Cnr8)	0.61	-	nuc	0	Nucleus (Probable)				619
O18141 UniProt NPD GO	NHR79_CAEEL	Nuclear hormone receptor family member nhr-79	0.61	-	nuc	0	Nucleus (Potential)				463
Q9QYK3 UniProt NPD GO	NRBF2_RAT	Nuclear receptor-binding factor 2 (NRBF-2)	0.61	-	nuc	0	Nucleus. Cytoplasm				287
Q9SIT9 UniProt NPD GO	NFYB7_ARATH	Nuclear transcription factor Y subunit B-7 (AtNF-YB-7)	0.61	-	nuc	0	Nucleus (Probable)				215
P80303 UniProt NPD GO	NUCB2_HUMAN	Nucleobindin-2 precursor (DNA-binding protein NEFA) (Gastric cancer antigen Zg4)	0.61	-	exc	1 *	Membrane; peripheral membrane protein. Cytoplasm. Secreted protein	cytosol [TAS] ER-Golgi intermediate compartment [IDA] extracellular space [TAS] plasma membrane [TAS]	608020		420
P47054 UniProt NPD GO	NU192_YEAST	Nucleoporin NUP192 (Nuclear pore protein NUP192)	0.61	-	end	0	Nucleus; nuclear envelope; nuclear pore complex; multi-pass membrane protein (Potential). Cytoplasmi ...	nuclear pore [TAS]			1683
Q9P7M8 UniProt NPD GO	NU184_SCHPO	Nucleoporin nup184 (Nuclear pore protein nup184)	0.61	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex				1564
P24068 UniProt NPD GO	OCS1_MAIZE	Ocs element-binding factor 1 (OCSBF-1)	0.61	+	nuc	0	Nucleus				151
P46873 UniProt NPD GO	OSM3_CAEEL	Osmotic avoidance abnormal protein 3 (Kinesin-like protein osm-3)	0.61	-	nuc	0					699
P10451 UniProt NPD GO	OSTP_HUMAN	Osteopontin precursor (Bone sialoprotein-1) (Secreted phosphoprotein 1) (SPP-1) (Urinary stone prote ...	0.61	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS] extracellular region [TAS]	166490		314
Q5AEM5 UniProt NPD GO	OXR1_CANAL	Oxidation resistance protein 1	0.61	+	nuc	0	Mitochondrion (By similarity)				345

You are viewing entries 18601 to 18650 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.