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
P30706 UniProt NPD GO	PLSB_PEA	Glycerol-3-phosphate acyltransferase, chloroplast precursor (EC 2.3.1.15) (GPAT)	0.46	-	mit	0	Plastid; chloroplast; chloroplast stroma				457
Q91W43 UniProt NPD GO	GCSP_MOUSE	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.46	-	mit	0	Mitochondrion (By similarity)				1025
Q5RAF3 UniProt NPD GO	NMT1_PONPY	Glycylpeptide N-tetradecanoyltransferase 1 (EC 2.3.1.97) (Peptide N-myristoyltransferase 1) (Myristo ...	0.46	+	cyt	0	Cytoplasm (By similarity)				496
O14653 UniProt NPD GO	GOSR2_HUMAN	Golgi SNAP receptor complex member 2 (27 kDa Golgi SNARE protein) (Membrin)	0.46	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (Potential)		604027		212
O95390 UniProt NPD GO	GDF11_HUMAN	Growth/differentiation factor 11 precursor (GDF-11) (Bone morphogenetic protein 11)	0.46	-	mit	0	Secreted protein (Probable)		603936		407
Q9NR23 UniProt NPD GO	GDF3_HUMAN	Growth/differentiation factor 3 precursor (GDF-3)	0.46	-	exc	0	Secreted protein (Probable)		606522		364
Q7Z4P5 UniProt NPD GO	GDF7_HUMAN	Growth/differentiation factor 7 precursor (GDF-7)	0.46	+	mit	0	Secreted protein (By similarity)		604651		450
P38405 UniProt NPD GO	GNAL_HUMAN	Guanine nucleotide-binding protein G(olf) subunit alpha (Adenylate cyclase-stimulating G alpha prote ...	0.46	-	nuc	0			139312		381
P30675 UniProt NPD GO	GPA1_COPCO	Guanine nucleotide-binding protein subunit alpha	0.46	-	cyt	0					352
P25157 UniProt NPD GO	GNAL_DROME	Guanine nucleotide-binding protein subunit alpha homolog (Protein concertina)	0.46	-	cyt	0		heterotrimeric G-protein complex [NAS]			457
Q9N2J9 UniProt NPD GO	ENH2_HUMAN	HERV-H_3q26 provirus ancestral Env polyprotein precursor (Envelope polyprotein) (Env protein HERV-H/ ...	0.46	-	mit	2 *					563
P62689 UniProt NPD GO	GAK17_HUMAN	HERV-K_11q22.1 provirus ancestral Gag polyprotein (Gag polyprotein) [Contains: Matrix protein]	0.46	-	nuc	0					177
P18462 UniProt NPD GO	1A25_HUMAN	HLA class I histocompatibility antigen, A-25 alpha chain precursor (MHC class I antigen A*25) (A-10) ...	0.46	-	end	1	Membrane; single-pass type I membrane protein		142800		365
P04439 UniProt NPD GO	1A03_HUMAN	HLA class I histocompatibility antigen, A-3 alpha chain precursor (MHC class I antigen A*3)	0.46	-	end	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [NAS]	142800		365
P10314 UniProt NPD GO	1A32_HUMAN	HLA class I histocompatibility antigen, A-32 alpha chain precursor (MHC class I antigen A*32)	0.46	-	end	1 *	Membrane; single-pass type I membrane protein		142800		365
P54651 UniProt NPD GO	HSC90_DICDI	Heat shock cognate 90 kDa protein	0.46	-	nuc	0					700
P31543 UniProt NPD GO	CLP_TRYBB	Heat shock protein 100 (CLP protein)	0.46	-	cyt	0					868
P42730 UniProt NPD GO	HS101_ARATH	Heat shock protein 101	0.46	+	cyt	0					911
Q9CQN1 UniProt NPD GO	TRAP1_MOUSE	Heat shock protein 75 kDa, mitochondrial precursor (HSP 75) (Tumor necrosis factor type 1 receptor-a ...	0.46	-	mit	0	Mitochondrion (By similarity)	mitochondrion [IDA]			706
P51818 UniProt NPD GO	HSP83_ARATH	Heat shock protein 81-3 (HSP81-3) (HSP81.2)	0.46	+	cyt	0	Cytoplasm (Potential)				699
P27890 UniProt NPD GO	HSP83_LEIDO	Heat shock protein 83 (HSP 83) (HSP 90) (Fragment)	0.46	-	nuc	0	Cytoplasm (By similarity)				452
P09435 UniProt NPD GO	HSP73_YEAST	Heat shock protein SSA3	0.46	-	cyt	0	Cytoplasm	cytosol [IDA]			649
P15705 UniProt NPD GO	STI1_YEAST	Heat shock protein STI1	0.46	-	nuc	0	Cytoplasm	cytoplasm [IPI]			589
Q96RW7 UniProt NPD GO	HMCN1_HUMAN	Hemicentin-1 precursor (Fibulin-6) (FIBL-6)	0.46	-	nuc	0			608548		5635
Q7TQ32 UniProt NPD GO	RGMC_MOUSE	Hemojuvelin precursor (Hemochromatosis type 2 protein homolog) (RGM domain family member C)	0.46	-	exc	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	cell surface [IDA] extracellular space [IDA]			420
O08889 UniProt NPD GO	HS2ST_CRILO	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-) (2-O-sulfotransferase) (2OST)	0.46	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				356
Q8R3H7 UniProt NPD GO	HS2ST_MOUSE	Heparan sulfate 2-O-sulfotransferase 1 (EC 2.8.2.-) (2-O-sulfotransferase) (2OST) (2-OST)	0.46	+	mit	0	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				356
P18900 UniProt NPD GO	COQ1_YEAST	Hexaprenyl pyrophosphate synthetase, mitochondrial precursor (EC 2.5.1.-) (HPS)	0.46	-	mit	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side	mitochondrion [IDA]			473
P12682 UniProt NPD GO	HMGB1_PIG	High mobility group protein B1 (High mobility group protein 1) (HMG-1)	0.46	-	nuc	0	Nucleus	condensed chromosome [ISS]			214
O54879 UniProt NPD GO	HMGB3_MOUSE	High mobility group protein B3 (High mobility group protein 4) (HMG-4) (High mobility group protein ...	0.46	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			199
Q9H3N8 UniProt NPD GO	HRH4_HUMAN	Histamine H4 receptor (HH4R) (GPRv53) (G-protein coupled receptor 105) (GPCR105) (SP9144) (AXOR35)	0.46	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [NAS]	606792		390
P10922 UniProt NPD GO	H10_MOUSE	Histone H1' (H1.0) (H1(0))	0.46	+	nuc	0	Nucleus				193
P08286 UniProt NPD GO	H110_CHICK	Histone H1.10 (Methylated DNA-binding protein 2-H1) (MDBP-2-H1)	0.46	+	nuc	0	Nucleus				219
P22492 UniProt NPD GO	H1T_HUMAN	Histone H1t (Testicular H1 histone)	0.46	-	nuc	0	Nucleus		142712		206
P35067 UniProt NPD GO	H2B_ACRFO	Histone H2B	0.46	+	nuc	0	Nucleus				125
Q6FWM8 UniProt NPD GO	H2B1_CANGA	Histone H2B.1	0.46	+	nuc	0	Nucleus (By similarity)				128
Q6FM30 UniProt NPD GO	H2B2_CANGA	Histone H2B.2	0.46	+	nuc	0	Nucleus (By similarity)				130
Q7XYZ0 UniProt NPD GO	H3_GRIJA	Histone H3	0.46	-	nuc	0	Nucleus (By similarity)				135
Q8SS77 UniProt NPD GO	H31_ENCCU	Histone H3.1	0.46	-	nuc	0	Nucleus (By similarity)				144
Q16695 UniProt NPD GO	H3T_HUMAN	Histone H3.4 (H3t) (H3/t) (H3/g)	0.46	-	mit	0	Nucleus	nucleosome [NAS]	602820		135
P53973 UniProt NPD GO	HDA1_YEAST	Histone deacetylase HDA1	0.46	-	nuc	0	Nucleus	histone deacetylase complex [IDA]			706
Q94517 UniProt NPD GO	HDAC1_DROME	Histone deacetylase Rpd3 (HD) (dRPD3)	0.46	-	nuc	0	Nucleus (Potential)	chromatin [IDA] cytoplasm [TAS] ESC/E(Z) complex [IDA] Myb complex [IDA] nucleus [TAS] NuRD complex [IPI] Sin3 complex [NAS]			521
O54864 UniProt NPD GO	SUV91_MOUSE	Histone-lysine N-methyltransferase, H3 lysine-9 specific 1 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.46	-	mit	0	Nucleus. Associates with centromeric constitutive heterochromatin	chromatin silencing complex [IDA] nuclear heterochromatin [TAS]			412
Q8SRR1 UniProt NPD GO	HD12_ENCCU	Homeobox protein HD-12 (EcHD-12)	0.46	-	nuc	0	Nucleus (Potential)				193
O42506 UniProt NPD GO	HXA9_FUGRU	Homeobox protein Hox-A9 (HoxA-9)	0.46	+	nuc	0	Nucleus				283
Q5EU41 UniProt NPD GO	HXD13_CARPS	Homeobox protein Hox-D13	0.46	+	nuc	0	Nucleus				333
P23397 UniProt NPD GO	HMEN_HELTR	Homeobox protein Ht-En (Fragment)	0.46	+	nuc	0	Nucleus (Probable)				98
Q9NSC5 UniProt NPD GO	HOME3_HUMAN	Homer protein homolog 3 (Homer-3)	0.46	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells (By similarity)		604800		361
Q9Z2X5 UniProt NPD GO	HOME3_RAT	Homer protein homolog 3 (Homer-3) (VASP/Ena-related gene up-regulated during seizure and LTP 3) (Ves ...	0.46	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells (By similarity)				358
P54310 UniProt NPD GO	LIPS_MOUSE	Hormone-sensitive lipase (EC 3.1.1.79) (HSL)	0.46	-	cyt	0					759

You are viewing entries 27651 to 27700 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.