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
P41320 UniProt NPD GO	GLNA_SQUAC	Glutamine synthetase, mitochondrial precursor (EC 6.3.1.2) (Glutamate--ammonia ligase)	0.23	-	mit	0	Mitochondrion				403
Q43768 UniProt NPD GO	SYE_HORVU	Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate--tRNA ligase) (GluRS)	0.23	-	nuc	0					560
Q9QUH0 UniProt NPD GO	GLRX1_MOUSE	Glutaredoxin-1 (Thioltransferase-1) (TTase-1)	0.23	-	cyt	0	Cytoplasm				106
P46419 UniProt NPD GO	GSTM1_DERPT	Glutathione S-transferase (EC 2.5.1.18) (GST class-mu) (Major allergen Der p 8) (P dp 15)	0.23	-	cyt	0	Cytoplasm (By similarity)				219
Q9N1F5 UniProt NPD GO	GSTO1_PIG	Glutathione transferase omega-1 (EC 2.5.1.18) (GSTO 1-1) (Glutathione-dependent dehydroascorbate red ...	0.23	-	cyt	0	Cytoplasm				241
O49850 UniProt NPD GO	GCSP_FLAAN	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.23	-	mit	0	Mitochondrion				1034
P35573 UniProt NPD GO	GDE_HUMAN	Glycogen debranching enzyme (Glycogen debrancher) [Includes: 4-alpha-glucanotransferase (EC 2.4.1.25 ...	0.23	-	cyt	0		isoamylase complex [TAS]	232400		1532
P53534 UniProt NPD GO	PYGB_RAT	Glycogen phosphorylase, brain form (EC 2.4.1.1) (Fragment)	0.23	-	nuc	0					837
Q9ET01 UniProt NPD GO	PYGL_MOUSE	Glycogen phosphorylase, liver form (EC 2.4.1.1)	0.23	-	nuc	0					849
Q6FSD1 UniProt NPD GO	GPI11_CANGA	Glycosylphosphatidylinositol anchor biosynthesis protein 11	0.23	-	end	6 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				217
Q5ZLC9 UniProt NPD GO	GOGA7_CHICK	Golgin subfamily A member 7	0.23	-	cyt	0	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				137
P81014 UniProt NPD GO	GRN2_CYPCA	Granulin-2	0.23	-	mit	0	Secreted protein				57
Q28746 UniProt NPD GO	CSF3_SHEEP	Granulocyte colony-stimulating factor (G-CSF)	0.23	-	cyt	0	Secreted protein				174
O02837 UniProt NPD GO	CSF3_PIG	Granulocyte colony-stimulating factor precursor (G-CSF)	0.23	-	cyt	0	Secreted protein				195
P09919 UniProt NPD GO	CSF3_HUMAN	Granulocyte colony-stimulating factor precursor (G-CSF) (Pluripoietin) (Filgrastim) (Lenograstim)	0.23	-	exc	0	Secreted protein	extracellular space [TAS]	138970	2D9Q	207
P04187 UniProt NPD GO	GRAB_MOUSE	Granzyme B(G,H) precursor (EC 3.4.21.79) (Cytotoxic cell protease 1) (CCP1) (CTLA-1) (Fragmentin-2)	0.23	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of cytolytic T-lymphocytes and natural killer cells			2CP1	247
Q6PH57 UniProt NPD GO	GBB1_BRARE	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.23	-	cyt	0					340
O45040 UniProt NPD GO	GBB1_HOMAM	Guanine nucleotide-binding protein G(I)/G(S)/G(T) subunit beta 1 (Transducin beta chain 1)	0.23	-	cyt	0					340
Q9UT35 UniProt NPD GO	GDA1_SCHPO	Guanosine-diphosphatase (EC 3.6.1.42) (GDPase)	0.23	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [IDA]			556
Q8VBV8 UniProt NPD GO	GUC1B_MOUSE	Guanylyl cyclase-activating protein 2 (GCAP 2) (Guanylate cyclase activator 1B)	0.23	-	cyt	0	Membranes of outer segment (By similarity)				200
P51177 UniProt NPD GO	GUC1B_BOVIN	Guanylyl cyclase-activating protein 2 (GCAP 2) (Guanylate cyclase activator 1B) (Retinal guanylyl cy ...	0.23	-	cyt	0	Membranes of outer segment			1JBA	203
P01896 UniProt NPD GO	HA1Z_MOUSE	H-2 class I histocompatibility antigen, alpha chain (Clone PH-2D-2) (Fragment)	0.23	-	nuc	1					185
P10316 UniProt NPD GO	1A69_HUMAN	HLA class I histocompatibility antigen, A-69 alpha chain (MHC class I antigen A*69) (Aw-69) (A-28) ( ...	0.23	-	mit	0	Membrane; single-pass type I membrane protein		142800		273
P16212 UniProt NPD GO	HLAE_PONPY	HLA class I histocompatibility antigen, alpha chain E precursor (MHC class I antigen E) (Fragment)	0.23	-	nuc	1	Membrane; single-pass type I membrane protein				359
P30511 UniProt NPD GO	HLAF_HUMAN	HLA class I histocompatibility antigen, alpha chain F precursor (HLA F antigen) (Leukocyte antigen F ...	0.23	-	end	1	Membrane; single-pass type I membrane protein		143110		362
P04440 UniProt NPD GO	HB2P_HUMAN	HLA class II histocompatibility antigen, DP(W4) beta chain precursor	0.23	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)				258
P37899 UniProt NPD GO	HSP70_PYRSA	Heat shock 70 kDa protein	0.23	-	cyt	0					649
O93866 UniProt NPD GO	HSP70_TRIRU	Heat shock 70 kDa protein	0.23	-	cyt	0					654
O43301 UniProt NPD GO	HS12A_HUMAN	Heat shock 70 kDa protein 12A	0.23	-	cyt	0					675
Q8K0U4 UniProt NPD GO	HS12A_MOUSE	Heat shock 70 kDa protein 12A	0.23	-	cyt	0					675
P11145 UniProt NPD GO	HSP74_TRYBB	Heat shock 70 kDa protein 4 (HSP70)	0.23	-	cyt	0					661
P12078 UniProt NPD GO	HSP73_PLAFA	Heat shock 70 kDa protein PPF203 (Fragment)	0.23	-	nuc	0					201
P08108 UniProt NPD GO	HSP70_ONCMY	Heat shock cognate 70 kDa protein (HSP70)	0.23	-	cyt	0					651
P19120 UniProt NPD GO	HSP7C_BOVIN	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.23	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...			3HSC	650
Q5NVM9 UniProt NPD GO	HSP7C_PONPY	Heat shock cognate 71 kDa protein (Heat shock 70 kDa protein 8)	0.23	-	cyt	0	Cytoplasm (By similarity). Translocates rapidly from the cytoplasm to the nuclei, and especially to ...				646
O43109 UniProt NPD GO	HSP90_PODAN	Heat shock protein 90 homolog (Suppressor of vegetative incompatibility MOD-E)	0.23	-	cyt	0					701
P06581 UniProt NPD GO	HSP16_CAEEL	Heat shock protein Hsp-16.41	0.23	-	nuc	0					143
P02513 UniProt NPD GO	HSP17_CAEEL	Heat shock protein Hsp16-48/Hsp16-49	0.23	-	nuc	0					143
Q707W3 UniProt NPD GO	HSP75_KLUDE	Heat shock protein SSB	0.23	-	cyt	0	Cytoplasm. Associated with translating ribosomes; may bind directly to the nascent polypeptide				612
Q5S1U1 UniProt NPD GO	HSPB1_PIG	Heat-shock protein beta-1 (HspB1) (Heat shock 27 kDa protein) (HSP 27)	0.23	-	nuc	0					207
Q9NFL5 UniProt NPD GO	HCYF_EURCA	Hemocyanin F chain (HcF)	0.23	-	cyt	0	Secreted protein; extracellular space	extracellular space [ISS]			628
Q9U572 UniProt NPD GO	CLOT_PENMO	Hemolymph clottable protein precursor	0.23	-	mit	0	Secreted protein. Secreted in hemolymph				1670
P04807 UniProt NPD GO	HXKB_YEAST	Hexokinase-2 (EC 2.7.1.1) (Hexokinase-B) (Hexokinase PII)	0.23	-	cyt	0		cytosol [IDA] nucleus [IDA]		1IG8	485
P35332 UniProt NPD GO	HPCL4_RAT	Hippocalcin-like protein 4 (Visinin-like protein 2) (VILIP-2) (Neural visinin-like protein 2) (NVL-2 ...	0.23	-	nuc	0					190
P07685 UniProt NPD GO	HIS2_NEUCR	Histidine biosynthesis trifunctional protein [Includes: Phosphoribosyl-AMP cyclohydrolase (EC 3.5.4. ...	0.23	-	cyt	0					870
Q9M5W4 UniProt NPD GO	H1_EUPES	Histone H1	0.23	-	nuc	0	Nucleus				229
P06893 UniProt NPD GO	H1B_XENLA	Histone H1B	0.23	+	nuc	0	Nucleus				219
Q8CGP5 UniProt NPD GO	H2A1F_MOUSE	Histone H2A type 1-F	0.23	-	nuc	0	Nucleus				129
Q64598 UniProt NPD GO	H2A1F_RAT	Histone H2A type 1-F	0.23	-	nuc	0	Nucleus				129
Q6FM31 UniProt NPD GO	H2A2_CANGA	Histone H2A.2	0.23	-	nuc	0	Nucleus				130

You are viewing entries 47401 to 47450 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.