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
Q8VDK3 UniProt NPD GO	ELF5_MOUSE	ETS-related transcription factor Elf-5 (E74-like factor 5)	0.55	-	cyt	0					253
Q8R2G4 UniProt NPD GO	NAR3_MOUSE	Ecto-ADP-ribosyltransferase 3 precursor (EC 2.4.2.31) (NAD(P)(+)--arginine ADP-ribosyltransferase 3) ...	0.55	-	cyt	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				420
Q9UKM7 UniProt NPD GO	MA1B1_HUMAN	Endoplasmic reticulum mannosyl-oligosaccharide 1,2-alpha-mannosidase (EC 3.2.1.113) (ER alpha-1,2-ma ...	0.55	-	gol	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein	endoplasmic reticulum [TAS] integral to membrane [TAS] membrane fraction [TAS]	604346	1X9D	699
Q5NRQ1 UniProt NPD GO	EDN1_FELCA	Endothelin-1 precursor (ET-1) (Preproendothelin-1) (PPET1)	0.55	-	nuc	0	Secreted protein (By similarity)				202
P43064 UniProt NPD GO	EFG1_CANAL	Enhanced filamentous growth protein	0.55	-	nuc	0	Nucleus (Potential)				552
Q6SP97 UniProt NPD GO	ENKUR_MOUSE	Enkurin	0.55	-	nuc	0	Sperm acrosomal crescent and flagellar principal piece				255
Q9HGI6 UniProt NPD GO	ERF2_DEBHA	Eukaryotic peptide chain release factor GTP-binding subunit (ERF2) (Translation release factor 3) (P ...	0.55	-	nuc	0	Cytoplasm (Probable)				701
Q9HCK5 UniProt NPD GO	I2C4_HUMAN	Eukaryotic translation initiation factor 2C 4 (eIF2C 4) (eIF-2C 4) (Argonaute-4)	0.55	-	cyt	0			607356		861
Q3T122 UniProt NPD GO	IF37_BOVIN	Eukaryotic translation initiation factor 3 subunit 7 (eIF-3 zeta)	0.55	-	nuc	0					548
P25359 UniProt NPD GO	RRP43_YEAST	Exosome complex exonuclease RRP43 (EC 3.1.13.-) (Ribosomal RNA-processing protein 43)	0.55	-	nuc	0	Cytoplasm. Nucleus; nucleolus	cytoplasmic exosome (RNase complex) [IDA] nuclear exosome (RNase complex) [IDA]			394
Q8AY73 UniProt NPD GO	XPO2_ORENI	Exportin-2 (Exp2) (Importin-alpha re-exporter) (Chromosome segregation 1-like protein) (Cellular apo ...	0.55	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				971
Q5ZMR9 UniProt NPD GO	XPO4_CHICK	Exportin-4	0.55	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				1154
Q96ME1 UniProt NPD GO	FXL18_HUMAN	F-box/LRR-repeat protein 18 (F-box and leucine-rich repeat protein 18)	0.55	-	end	0		cytoplasm [ISS]	609084		805
Q9P7W4 UniProt NPD GO	POF10_SCHPO	F-box/WD repeat protein pof10 (Skp1-binding protein 2)	0.55	-	nuc	0	Cytoplasm	cytoplasm [IDA]			662
Q5KD17 UniProt NPD GO	POB3_CRYNE	FACT complex subunit POB3 (Facilitates chromatin transcription complex subunit POB3)	0.55	+	nuc	0	Nucleus (By similarity)				588
Q9W603 UniProt NPD GO	SPT16_XENLA	FACT complex subunit SPT16 (Facilitates chromatin transcription complex subunit spt16) (DNA unwindin ...	0.55	+	mit	0	Nucleus				1035
Q5AI48 UniProt NPD GO	YFAS1_CANAL	FAS1 domain-containing protein CaO19.3004 precursor	0.55	-	exc	0	Vacuole (By similarity)				410
Q8NB91 UniProt NPD GO	FANCB_HUMAN	Fanconi anemia group B protein (Protein FACB) (Fanconi anemia-associated polypeptide of 95 kDa) (FAA ...	0.55	-	nuc	0	Nucleus		300515		859
P17634 UniProt NPD GO	FIBG_XENLA	Fibrinogen gamma chain precursor	0.55	-	exc	0	Secreted protein				438
Q920R4 UniProt NPD GO	GASP1_RAT	G-protein coupled receptor-associated sorting protein 1 (GASP-1) (Per1-interacting protein)	0.55	-	nuc	0	Cytoplasm				1346
P47794 UniProt NPD GO	CCN1E_BRARE	G1/S-specific cyclin-E	0.55	-	nuc	0	Nucleus (By similarity)				410
Q92521 UniProt NPD GO	PIGB_HUMAN	GPI mannosyltransferase 3 (EC 2.4.1.-) (GPI mannosyltransferase III) (GPI-MT-III) (Phosphatidylinosi ...	0.55	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein		604122		554
Q14444 UniProt NPD GO	GP137_HUMAN	GPI-anchored protein p137 (p137GPI) (Membrane component chromosome 11 surface marker 1)	0.55	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (Probable)	integral to plasma membrane [TAS]	601178		649
Q5R541 UniProt NPD GO	GEM_PONPY	GTP-binding protein GEM	0.55	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side (By similarity)				296
P55040 UniProt NPD GO	GEM_HUMAN	GTP-binding protein GEM (GTP-binding mitogen-induced T-cell protein) (RAS-like protein KIR)	0.55	-	nuc	0	Cell membrane; peripheral membrane protein; cytoplasmic side		600164		296
P02890 UniProt NPD GO	BAB1_BABBO	Gene BABR protein 1	0.55	-	nuc	0					191
Q9Z1Z0 UniProt NPD GO	VDP_MOUSE	General vesicular transport factor p115 (Transcytosis-associated protein) (TAP) (Vesicle docking pro ...	0.55	-	nuc	0	Cytoplasm; cytosol (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By ...				959
P41542 UniProt NPD GO	VDP_RAT	General vesicular transport factor p115 (Transcytosis-associated protein) (TAP) (Vesicle docking pro ...	0.55	-	nuc	0	Cytoplasm; cytosol. Golgi apparatus; Golgi membrane; peripheral membrane protein. Recycles between t ...				959
Q01812 UniProt NPD GO	GRIK4_RAT	Glutamate receptor, ionotropic kainate 4 precursor (Glutamate receptor KA-1) (KA1)	0.55	-	end	4	Membrane; multi-pass membrane protein	ionotropic glutamate receptor complex [TAS]			956
Q8MJ26 UniProt NPD GO	GYS1_MACMU	Glycogen [starch] synthase, muscle (EC 2.4.1.11)	0.55	-	cyt	0					737
Q8NBJ4 UniProt NPD GO	GP73_HUMAN	Golgi phosphoprotein 2 (Golgi membrane protein GP73)	0.55	-	nuc	1 *	Golgi apparatus; cis-Golgi network; cis-Golgi network membrane; single-pass type II membrane protein ...	Golgi apparatus [TAS] integral to plasma membrane [TAS]	606804		401
Q921M4 UniProt NPD GO	GOGA2_MOUSE	Golgin subfamily A member 2 (Cis-Golgi matrix protein GM130)	0.55	-	nuc	0	Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein	Golgi apparatus [IDA] Golgi cis-face [IDA]			888
Q9Z217 UniProt NPD GO	GDF11_RAT	Growth/differentiation factor 11 precursor (GDF-11) (Bone morphogenetic protein 11) (Fragment)	0.55	-	nuc	0	Secreted protein (Probable)				345
O15975 UniProt NPD GO	GNAQ_PATYE	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.55	-	cyt	0					353
P38410 UniProt NPD GO	GNAQ_XENLA	Guanine nucleotide-binding protein G(q) subunit alpha (Guanine nucleotide-binding protein alpha-q)	0.55	-	cyt	0					353
P18852 UniProt NPD GO	GBG_YEAST	Guanine nucleotide-binding protein subunit gamma	0.55	-	nuc	0	Membrane; lipid-anchor	cytoplasm [IDA] heterotrimeric G-protein complex [IDA] plasma membrane [IDA]		1SCG	110
P31539 UniProt NPD GO	HS104_YEAST	Heat shock protein 104	0.55	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			908
Q2TBI4 UniProt NPD GO	TRAP1_BOVIN	Heat shock protein 75 kDa, mitochondrial precursor (HSP 75) (Tumor necrosis factor type 1 receptor-a ...	0.55	-	mit	0	Mitochondrion (By similarity)				703
P33126 UniProt NPD GO	HSP81_ORYSA	Heat shock protein 81-1 (HSP81-1) (Heat shock protein 82)	0.55	-	cyt	0	Cytoplasm (Potential)	cytoplasm [IEP]			699
P51819 UniProt NPD GO	HSP83_IPONI	Heat shock protein 83	0.55	+	cyt	0	Cytoplasm (Potential)				703
Q8J2M3 UniProt NPD GO	HSP82_ASHGO	Heat shock protein HSP82	0.55	-	cyt	0	Cytoplasm (By similarity)				704
Q02575 UniProt NPD GO	HEN1_HUMAN	Helix-loop-helix protein 1 (HEN1) (Nescient helix loop helix 1) (NSCL-1)	0.55	+	nuc	0			162360		133
Q9NQG7 UniProt NPD GO	HPS4_HUMAN	Hermansky-Pudlak syndrome 4 protein (Light-ear protein homolog)	0.55	-	nuc	0		cytoplasm [IDA] lysosome [IDA] melanosome [IDA] membrane fraction [IDA] platelet dense granule [IDA]	606682		708
O60506 UniProt NPD GO	HNRPQ_HUMAN	Heterogeneous nuclear ribonucleoprotein Q (hnRNP Q) (hnRNP-Q) (Synaptotagmin-binding, cytoplasmic RN ...	0.55	-	cyt	0	Nucleus (By similarity). Isoform 1, isoform 2, isoform 3: Nucleus; nucleoplasm (By similarity). Isof ...	nucleus [TAS] ribonucleoprotein complex [TAS]			623
Q7TMK9 UniProt NPD GO	HNRPQ_MOUSE	Heterogeneous nuclear ribonucleoprotein Q (hnRNP Q) (hnRNP-Q) (Synaptotagmin-binding, cytoplasmic RN ...	0.55	-	cyt	0	Nucleus. Cytoplasm. Isoforms 1 and 2 are expressed predominantly in the nucleoplasm (By similarity). ...	cytoplasm [IDA]			623
Q7TP47 UniProt NPD GO	HNRPQ_RAT	Heterogeneous nuclear ribonucleoprotein Q (hnRNP Q) (hnRNP-Q) (Synaptotagmin-binding, cytoplasmic RN ...	0.55	-	cyt	0	Nucleus; nucleoplasm (By similarity). Cytoplasm (By similarity). Expressed predominantly in the nucl ...				533
Q3ZBV4 UniProt NPD GO	HMGN3_BOVIN	High mobility group nucleosome-binding domain-containing protein 3	0.55	-	nuc	0	Nucleus (By similarity)				100
Q5ZIR5 UniProt NPD GO	HMGN3_CHICK	High mobility group nucleosome-binding domain-containing protein 3	0.55	-	nuc	0	Nucleus (By similarity)				98
Q1XDD9 UniProt NPD GO	SYH_PORYE	Histidyl-tRNA synthetase (EC 6.1.1.21) (Histidine--tRNA ligase) (HisRS)	0.55	-	nuc	0	Plastid; chloroplast				430
P21897 UniProt NPD GO	H2B_CHITH	Histone H2B	0.55	+	nuc	0	Nucleus				124

You are viewing entries 21951 to 22000 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.