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
O62389 UniProt NPD GO	NHR61_CAEEL	Nuclear hormone receptor family member nhr-61	0.25	+	cyt	0	Nucleus (Potential)				412
P60670 UniProt NPD GO	NPL4_MOUSE	Nuclear protein localization protein 4 homolog (Protein NPL4)	0.25	-	cyt	0	Cytoplasm (By similarity). Endoplasmic reticulum (By similarity). Nucleus (By similarity). Associate ...	endoplasmic reticulum [ISS] nuclear envelope-endoplasmic reticulum network [ISS]			607
Q9SLG0 UniProt NPD GO	NFYB1_ARATH	Nuclear transcription factor Y subunit B-1 (AtNF-YB-1) (Transcriptional activator HAP3A)	0.25	-	nuc	0	Nucleus (Probable)				141
O23310 UniProt NPD GO	NFYB3_ARATH	Nuclear transcription factor Y subunit B-3 (AtNF-YB-3) (Transcriptional activator HAP3C)	0.25	-	cyt	0	Nucleus (Probable)				161
O04027 UniProt NPD GO	NFYB4_ARATH	Nuclear transcription factor Y subunit B-4 (AtNF-YB-4) (Transcriptional activator HAP3D)	0.25	-	nuc	0	Nucleus (Probable)				139
Q6FRC6 UniProt NPD GO	NTF2_CANGA	Nuclear transport factor 2 (NTF-2)	0.25	-	cyt	0	Cytoplasm (By similarity)				125
Q6CQX4 UniProt NPD GO	NTF2_KLULA	Nuclear transport factor 2 (NTF-2)	0.25	-	cyt	0	Cytoplasm (By similarity)				125
P53011 UniProt NPD GO	SEH1_YEAST	Nucleoporin SEH1 (Nuclear pore protein SEH1) (SEC13 homolog 1)	0.25	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			349
P56597 UniProt NPD GO	NDK5_HUMAN	Nucleoside diphosphate kinase homolog 5 (NDK-H 5) (NDP kinase homolog 5) (nm23-H5) (Testis-specific ...	0.25	-	cyt	0			603575		212
Q99MH5 UniProt NPD GO	NDK5_MOUSE	Nucleoside diphosphate kinase homolog 5 (NDK-H 5) (NDP kinase homolog 5) (nm23-M5)	0.25	-	cyt	0					211
Q9VCZ3 UniProt NPD GO	OCTB1_DROME	Octopamine receptor beta-1R (DmOct-beta-1R) (DmOA2)	0.25	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			508
P21641 UniProt NPD GO	OLEO3_MAIZE	Oleosin Zm-II (Oleosin 18 kDa) (Lipid body-associated protein L2)	0.25	-	end	3 *	Surface of oil bodies. Oleosins exist at a monolayer lipid/water interface				187
Q8NH61 UniProt NPD GO	O51F1_HUMAN	Olfactory receptor 51F2	0.25	-	end	7 *	Membrane; multi-pass membrane protein				330
Q8NGI8 UniProt NPD GO	O5AN1_HUMAN	Olfactory receptor 5AN1 (Olfactory receptor OR11-244)	0.25	+	end	7 *	Membrane; multi-pass membrane protein				311
Q9UGF6 UniProt NPD GO	OR5V1_HUMAN	Olfactory receptor 5V1 (Hs6M1-21)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				321
Q9GLF6 UniProt NPD GO	OREX_CANFA	Orexin precursor (Hypocretin) (Hcrt) [Contains: Orexin-A (Hypocretin-1) (Hcrt1); Orexin-B (Hypocreti ...	0.25	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Associated with perikaryal rough ...				130
Q9R109 UniProt NPD GO	OAZ3_MOUSE	Ornithine decarboxylase antizyme 3 (ODC-Az 3) (AZ3) (OAZ-t)	0.25	-	nuc	0	Nucleus. Cytoplasm	cytoplasm [IDA] nucleus [IDA]			195
P78748 UniProt NPD GO	PYRF_SORMA	Orotidine 5'-phosphate decarboxylase (EC 4.1.1.23) (OMP decarboxylase) (OMPDCase) (OMPdecase) (Uridi ...	0.25	-	cyt	0					396
Q6TGW5 UniProt NPD GO	OSTF1_BRARE	Osteoclast-stimulating factor 1	0.25	-	nuc	0	Cytoplasm (By similarity)				214
Q02509 UniProt NPD GO	OC90_HUMAN	Otoconin 90 precursor (Oc90) (Phospholipase A2 homolog)	0.25	-	exc	0	Secreted protein (By similarity)		601658		493
Q9Y365 UniProt NPD GO	PCTL_HUMAN	PCTP-like protein (PCTP-L) (StAR-related lipid transfer protein 10) (StARD10) (START domain-containi ...	0.25	-	nuc	0					291
O15428 UniProt NPD GO	PINL_HUMAN	PIN1-like protein	0.25	-	nuc	0			602051		100
Q4I8B6 UniProt NPD GO	AKR1_GIBZE	Palmitoyltransferase AKR1 (EC 2.3.1.-) (Ankyrin repeat-containing protein AKR1)	0.25	-	end	6	Endosome; early endosome; early endosomal membrane; multi-pass membrane protein. Golgi apparatus; Go ...				702
Q4I1J3 UniProt NPD GO	PFA5_GIBZE	Palmitoyltransferase PFA5 (EC 2.3.1.-) (Protein fatty acyltransferase 5)	0.25	-	end	4	Membrane; multi-pass membrane protein (Potential)				507
P01299 UniProt NPD GO	PAHO_CANFA	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; Pancrea ...	0.25	-	exc	1 *	Secreted protein				93
P01301 UniProt NPD GO	PAHO_SHEEP	Pancreatic prohormone precursor (Pancreatic polypeptide) (PP) [Contains: Pancreatic hormone; Pancrea ...	0.25	-	nuc	0	Secreted protein				59
P04542 UniProt NPD GO	IPK1_CANFA	Pancreatic secretory trypsin inhibitor	0.25	-	nuc	0	Secreted protein				57
P00998 UniProt NPD GO	IPK1_PIG	Pancreatic secretory trypsin inhibitor	0.25	-	nuc	0	Secreted protein			1TGS	56
Q8CEG0 UniProt NPD GO	PANX3_MOUSE	Pannexin-3	0.25	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				392
Q94C59 UniProt NPD GO	PATL4_ARATH	Patellin-4	0.25	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Mainly membrane-associated. Cytoplasm (By sim ...				540
Q9SCU1 UniProt NPD GO	PATL6_ARATH	Patellin-6	0.25	-	cyt	0	Membrane; peripheral membrane protein (By similarity). Mainly membrane-associated. Cytoplasm (By sim ...				409
Q96576 UniProt NPD GO	PME3_LYCES	Pectinesterase-3 precursor (EC 3.1.1.11) (Pectin methylesterase 3) (PE 3)	0.25	-	gol	1 *					544
Q641Z8 UniProt NPD GO	PEF1_RAT	Peflin (PEF protein with a long N-terminal hydrophobic domain) (Penta-EF hand domain-containing prot ...	0.25	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein in the presence of Ca(2+) (By similarity)				283
P35763 UniProt NPD GO	PERF_RAT	Perforin-1 precursor (P1) (Lymphocyte pore-forming protein) (Cytolysin)	0.25	-	nuc	0	Integral membrane protein. Cytoplasmic granules of cytolytic T-lymphocytes	cytosol [TAS]			554
P91745 UniProt NPD GO	PE48A_LUCCU	Peritrophin-48 precursor	0.25	-	exc	0					375
O22959 UniProt NPD GO	PER19_ARATH	Peroxidase 19 precursor (EC 1.11.1.7) (Atperox P19) (ATP51)	0.25	-	exc	1 *	Secreted protein (By similarity)				346
O23044 UniProt NPD GO	PER3_ARATH	Peroxidase 3 precursor (EC 1.11.1.7) (Atperox P3) (Rare cold-inducible protein) (RCI3A) (ATPRC)	0.25	-	exc	1 *	Secreted protein (By similarity)				326
Q9LSY7 UniProt NPD GO	PER30_ARATH	Peroxidase 30 precursor (EC 1.11.1.7) (Atperox P30) (PRXR9) (ATP7a)	0.25	-	exc	1 *	Secreted protein (By similarity)				329
Q9SMU8 UniProt NPD GO	PER34_ARATH	Peroxidase 34 precursor (EC 1.11.1.7) (Atperox P34) (ATPCb)	0.25	-	exc	0	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				353
P15232 UniProt NPD GO	PER1B_ARMRU	Peroxidase C1B precursor (EC 1.11.1.7)	0.25	-	exc	1 *	Or: Secreted protein (Probable). Or: Vacuole (Probable). Carboxy-terminal extension appears to targe ...				351
O13289 UniProt NPD GO	CATA_CANAL	Peroxisomal catalase (EC 1.11.1.6)	0.25	-	cyt	0	Peroxisome (By similarity)				486
Q99144 UniProt NPD GO	PEX5_YARLI	Peroxisomal targeting signal receptor (Peroxisomal protein PAY32) (Peroxin-5) (PTS1 receptor)	0.25	-	cyt	0	Cytoplasm. Peroxisome; peroxisomal membrane; peripheral membrane protein. Its distribution appears t ...				598
Q9UUF0 UniProt NPD GO	PEX10_SCHPO	Peroxisome assembly protein 10 (Peroxin-10) (Peroxisome biogenesis factor 10)	0.25	-	end	0	Peroxisome; peroxisomal membrane; peripheral membrane protein (Potential)				306
Q9ET67 UniProt NPD GO	PEX12_CRILO	Peroxisome assembly protein 12 (Peroxin-12)	0.25	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				359
P37232 UniProt NPD GO	PPARA_XENLA	Peroxisome proliferator-activated receptor alpha (PPAR-alpha)	0.25	+	cyt	0	Nucleus				474
P45727 UniProt NPD GO	PALY_PERAE	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.25	-	nuc	0	Cytoplasm (Probable)				620
P45732 UniProt NPD GO	PALY_STYHU	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.25	-	nuc	0	Cytoplasm (Probable)				715
O95363 UniProt NPD GO	SYFM_HUMAN	Phenylalanyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.20) (Phenylalanine--tRNA ligase) (Ph ...	0.25	-	mit	0	Mitochondrion; mitochondrial matrix (Potential)	soluble fraction [TAS]			451
P56502 UniProt NPD GO	BAR3_SCHCO	Pheromone B alpha 3 receptor	0.25	-	end	6 *	Membrane; multi-pass membrane protein				625
O13010 UniProt NPD GO	PI52A_PIG	Phosphatidylinositol-4-phosphate 5-kinase type-2 alpha (EC 2.7.1.68) (Phosphatidylinositol-4-phospha ...	0.25	-	mit	0					406

You are viewing entries 45501 to 45550 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.