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
P13045 UniProt NPD GO	GAL3_YEAST	Protein GAL3	0.17	-	nuc	0		cytoplasm [IDA]			520
Q5R991 UniProt NPD GO	K0241_PONPY	Protein KIAA0241 homolog	0.17	-	cyt	0	Membrane; single-pass membrane protein (Potential)				630
P53237 UniProt NPD GO	LST7_YEAST	Protein LST7 (Lethal with SEC thirteen protein 7)	0.17	-	cyt	0		vesicle coat [IDA]			242
P23060 UniProt NPD GO	MAK32_YEAST	Protein MAK32 (Maintenance of killer protein 32)	0.17	-	cyt	0					363
Q641F2 UniProt NPD GO	NDR1A_XENLA	Protein NDRG1-A (xNDRG1-A)	0.17	-	nuc	0					396
Q8BGQ4 UniProt NPD GO	POMT2_MOUSE	Protein O-mannosyl-transferase 2 (EC 2.4.1.109) (Dolichyl-phosphate-mannose--protein mannosyltransfe ...	0.17	-	end	10	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum membrane [ISS]			820
P79003 UniProt NPD GO	RER1_SACPS	Protein RER1 (Retention of ER proteins 1)	0.17	-	end	2	Golgi apparatus; Golgi membrane; multi-pass membrane protein				188
Q6B345 UniProt NPD GO	S10AB_RAT	Protein S100-A11 (S100 calcium-binding protein A11) (Calgizzarin)	0.17	-	nuc	0					98
P28783 UniProt NPD GO	S10A9_BOVIN	Protein S100-A9 (S100 calcium-binding protein A9) (Calgranulin-B) (Neutrophil cytosolic 23 kDa prote ...	0.17	-	nuc	0	Cytoplasm. Cytoskeleton. Loosely associated to the cytoskeleton				156
P50263 UniProt NPD GO	SIP18_YEAST	Protein SIP18	0.17	-	nuc	0		soluble fraction [IDA]			79
Q6WNK7 UniProt NPD GO	SUS1_YEAST	Protein SUS1	0.17	-	nuc	0	Nucleus. Located in the nucleoplasm and at the nuclear pores	nuclear pore [IDA] SAGA complex [IDA]			96
Q53HC9 UniProt NPD GO	TSSC1_HUMAN	Protein TSSC1 (Tumor-suppressing subchromosomal transferable fragment candidate gene 1 protein) (Tum ...	0.17	-	nuc	0			608998		387
P28089 UniProt NPD GO	WNT1_EVATR	Protein Wnt-1 (Fragment)	0.17	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				143
P28133 UniProt NPD GO	WNT3A_PLEJO	Protein Wnt-3a (Fragment)	0.17	-	nuc	0	Secreted protein; extracellular space; extracellular matrix				123
Q8R121 UniProt NPD GO	ZPI_MOUSE	Protein Z-dependent protease inhibitor precursor (PZ-dependent protease inhibitor) (PZI) (Serpin A10 ...	0.17	-	end	0	Secreted protein (By similarity)				448
Q8BXZ1 UniProt NPD GO	TXD10_MOUSE	Protein disulfide-isomerase TXNDC10 precursor (EC 5.3.4.1) (Thioredoxin domain-containing protein 10 ...	0.17	-	mit	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				456
O13782 UniProt NPD GO	PFTB_SCHPO	Protein farnesyltransferase subunit beta (EC 2.5.1.58) (CAAX farnesyltransferase subunit beta) (RAS ...	0.17	-	nuc	0					382
P04409 UniProt NPD GO	KPCA_BOVIN	Protein kinase C alpha type (EC 2.7.11.13) (PKC-alpha) (PKC-A)	0.17	-	cyt	0					671
P10102 UniProt NPD GO	KPCA_RABIT	Protein kinase C alpha type (EC 2.7.11.13) (PKC-alpha) (PKC-A)	0.17	-	cyt	0					671
P05696 UniProt NPD GO	KPCA_RAT	Protein kinase C alpha type (EC 2.7.11.13) (PKC-alpha) (PKC-A)	0.17	-	cyt	0				1DSY	671
P63318 UniProt NPD GO	KPCG_MOUSE	Protein kinase C gamma type (EC 2.7.11.13) (PKC-gamma)	0.17	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			697
P63319 UniProt NPD GO	KPCG_RAT	Protein kinase C gamma type (EC 2.7.11.13) (PKC-gamma)	0.17	-	cyt	0				1TBO	697
P10829 UniProt NPD GO	KPCG_RABIT	Protein kinase C gamma type (EC 2.7.11.13) (PKC-gamma) (PKC-delta)	0.17	-	cyt	0					697
Q01872 UniProt NPD GO	KRUP_LITFO	Protein krueppel (Fragment)	0.17	-	nuc	0	Nucleus (Probable)				46
Q01779 UniProt NPD GO	KRUP_MUSDO	Protein krueppel (Fragment)	0.17	-	nuc	0	Nucleus (Probable)				74
Q8TAX0 UniProt NPD GO	OSR1_HUMAN	Protein odd-skipped-related 1	0.17	-	nuc	0	Nucleus (Potential)		608891		266
Q8BU27 UniProt NPD GO	PP2CE_MOUSE	Protein phosphatase 2C isoform eta (EC 3.1.3.16) (PP2C-eta) (PP2CE) (Protein phosphatase 1M)	0.17	-	mit	0	Nucleus	nucleus [IDA]			406
Q01200 UniProt NPD GO	PRIA_LENED	Protein priA precursor	0.17	-	exc	1 *					258
Q9VZS3 UniProt NPD GO	SUI1_DROME	Protein translation factor SUI1 homolog	0.17	-	cyt	0					110
Q9HFC7 UniProt NPD GO	SC61B_YARLI	Protein transport protein SEC61 subunit beta	0.17	-	nuc	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein (By similarity)				91
P38166 UniProt NPD GO	SFT2_YEAST	Protein transport protein SFT2	0.17	-	end	4	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi membrane [IDA]			215
Q14761 UniProt NPD GO	PTCA_HUMAN	Protein tyrosine phosphatase receptor type C-associated protein (PTPRC-associated protein) (CD45-ass ...	0.17	-	exc	1 *		plasma membrane [IDA]	601577		206
O88806 UniProt NPD GO	PADI1_RAT	Protein-arginine deiminase type-1 (EC 3.5.3.15) (Protein-arginine deiminase type I) (Peptidylarginin ...	0.17	-	mit	0	Cytoplasm (By similarity)				662
Q9PTE6 UniProt NPD GO	TPS1_BRARE	Protein-tyrosine sulfotransferase 1 (EC 2.8.2.20) (Tyrosylprotein sulfotransferase-1) (TPST-1)	0.17	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				355
P16044 UniProt NPD GO	IBPI_TACTR	Proteinase inhibitor (BPI-type)	0.17	-	nuc	0	Secreted protein				61
P26824 UniProt NPD GO	PAR1_RAT	Proteinase-activated receptor 1 precursor (PAR-1) (Thrombin receptor)	0.17	-	end	7	Membrane; multi-pass membrane protein				432
Q5PXS1 UniProt NPD GO	LCK_AOTNA	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (p56-LCK) (Lymphocyte cell-specific protein ...	0.17	-	cyt	0	Cytoplasm (By similarity). Cell membrane; lipid-anchor; cytoplasmic side (By similarity). Present in ...	lipid raft [ISS] pericentriolar material [ISS] plasma membrane [ISS]			508
Q5DRD7 UniProt NPD GO	PCDBC_PANTR	Protocadherin beta 12 precursor (PCDH-beta12)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				795
Q9Y5E4 UniProt NPD GO	PCDB5_HUMAN	Protocadherin beta 5 precursor (PCDH-beta5)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)	integral to membrane [NAS]	606331		795
Q5DRC9 UniProt NPD GO	PCDB5_PANTR	Protocadherin beta 5 precursor (PCDH-beta5)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				795
Q9Y5G7 UniProt NPD GO	PCDG6_HUMAN	Protocadherin gamma A6 precursor (PCDH-gamma-A6)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)		606293		932
Q5DRB4 UniProt NPD GO	PCDG6_PANTR	Protocadherin gamma A6 precursor (PCDH-gamma-A6)	0.17	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				932
P21218 UniProt NPD GO	PORB_ARATH	Protochlorophyllide reductase B, chloroplast precursor (EC 1.3.1.33) (PCR B) (NADPH-protochlorophyll ...	0.17	-	mit	0	Plastid; chloroplast; chloroplast outer membrane. Plastid; chloroplast; chloroplast thylakoid membra ...				401
P50404 UniProt NPD GO	SFTPD_MOUSE	Pulmonary surfactant-associated protein D precursor (SP-D) (PSP-D)	0.17	-	nuc	0	Secreted protein; extracellular space	endocytic vesicle [ISS] extracellular region [ISS] lysosome [ISS]			374
P48777 UniProt NPD GO	UAPC_EMENI	Purine permease	0.17	-	end	12	Membrane; multi-pass membrane protein				580
Q9Y6J3 UniProt NPD GO	DAMS_HUMAN	Putative 10.3 kDa proline-rich protein DAMS	0.17	-	nuc	0					95
P53839 UniProt NPD GO	YN14_YEAST	Putative 2-hydroxyacid dehydrogenase YNL274C (EC 1.-.-.-)	0.17	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA] nucleus [IDA]			350
Q04907 UniProt NPD GO	RM32_CAEEL	Putative 39S ribosomal protein L32, mitochondrial precursor	0.17	-	nuc	0	Mitochondrion (By similarity)				168
Q9P7L3 UniProt NPD GO	RIB7_SCHPO	Putative 5-amino-6-(5-phosphoribosylamino)uracil reductase (EC 1.1.1.193) (HTP reductase)	0.17	-	nuc	0					268
Q9FKF2 UniProt NPD GO	ATH15_ARATH	Putative ABC2 homolog 15	0.17	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				953

You are viewing entries 54801 to 54850 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.