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
Q9UBY9 UniProt NPD GO	HSPB7_HUMAN	Heat-shock protein beta-7 (HspB7) (Cardiovascular heat shock protein) (cvHsp)	0.32	-	mit	0					170
P35385 UniProt NPD GO	HSPB7_MOUSE	Heat-shock protein beta-7 (HspB7) (Cardiovascular heat shock protein) (cvHsp) (Heat shock protein 25 ...	0.32	-	mit	0		cytoskeleton [TAS]			169
Q01580 UniProt NPD GO	HBEGF_PIG	Heparin-binding EGF-like growth factor precursor (HB-EGF) (HBEGF)	0.32	-	end	2 *	Precursor form: Cell membrane; single-pass type I membrane protein (By similarity). Mature form: Sec ...				208
P35584 UniProt NPD GO	HNF3G_MOUSE	Hepatocyte nuclear factor 3-gamma (HNF-3G) (Forkhead box protein A3)	0.32	+	nuc	0	Nucleus				353
P32183 UniProt NPD GO	HNF3G_RAT	Hepatocyte nuclear factor 3-gamma (HNF-3G) (Forkhead box protein A3)	0.32	+	nuc	0	Nucleus				354
P51989 UniProt NPD GO	RO21_XENLA	Heterogeneous nuclear ribonucleoprotein A2 homolog 1 (hnRNP A2(A))	0.32	-	cyt	0	Nucleus. Component of ribonucleosomes				346
P17268 UniProt NPD GO	H1_DROHY	Histone H1	0.32	-	nuc	0	Nucleus				249
Q24704 UniProt NPD GO	H11_DROVI	Histone H1.1	0.32	+	nuc	0	Nucleus				250
P04913 UniProt NPD GO	H2B1_SCHPO	Histone H2B-alpha (H2B.1)	0.32	-	nuc	0	Nucleus				125
O65819 UniProt NPD GO	H2B3_LYCES	Histone H2B.3 (LeH2B-3) (Fragment)	0.32	+	nuc	0	Nucleus (By similarity)				137
P81195 UniProt NPD GO	H31_STYLE	Histone H3-1 (Fragment)	0.32	-	nuc	0	Nucleus (By similarity)				114
P81197 UniProt NPD GO	H33_STYLE	Histone H3-3 (Fragment)	0.32	-	nuc	0	Nucleus (By similarity)				114
P59259 UniProt NPD GO	H4_ARATH	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q6PMI5 UniProt NPD GO	H4_CHEMJ	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q8T7J8 UniProt NPD GO	H4_EIMTE	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q6WZ83 UniProt NPD GO	H4_EUCGL	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q6LAF3 UniProt NPD GO	H4_FLATR	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
P62887 UniProt NPD GO	H4_LOLTE	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
P35057 UniProt NPD GO	H4_LYCES	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
P62787 UniProt NPD GO	H4_MAIZE	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
P82888 UniProt NPD GO	H4_OLILU	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
P62788 UniProt NPD GO	H4_PEA	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q76H85 UniProt NPD GO	H4_SILLA	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q6V9I2 UniProt NPD GO	H4_SOLCH	Histone H4	0.32	-	cyt	0	Nucleus (By similarity)				102
Q71V09 UniProt NPD GO	H4_CAPAN	Histone H4 (CaH4)	0.32	-	cyt	0	Nucleus (By similarity)				102
P62785 UniProt NPD GO	H41_WHEAT	Histone H4 variant TH011	0.32	-	cyt	0	Nucleus (By similarity)				102
P62786 UniProt NPD GO	H42_WHEAT	Histone H4 variant TH091	0.32	-	cyt	0	Nucleus (By similarity)				102
P80737 UniProt NPD GO	H41_BLEJA	Histone H4-1 (Fragment)	0.32	-	cyt	0	Nucleus (By similarity)				97
O09106 UniProt NPD GO	HDAC1_MOUSE	Histone deacetylase 1 (HD1)	0.32	-	cyt	0	Nucleus	cytoplasm [TAS] heterochromatin [IDA] nucleus [TAS] NuRD complex [IPI]			482
Q9H5I1 UniProt NPD GO	SUV92_HUMAN	Histone-lysine N-methyltransferase, H3 lysine-9 specific 2 (EC 2.1.1.43) (Histone H3-K9 methyltransf ...	0.32	-	nuc	0	Nucleus (By similarity). Associates with constitutive heterochromatin (By similarity)	chromatin [IDA]	606503		410
Q9Y875 UniProt NPD GO	MET2_EMENI	Homoserine O-acetyltransferase (EC 2.3.1.31) (Homoserine O-trans-acetylase)	0.32	-	nuc	0					489
P43571 UniProt NPD GO	YFC5_YEAST	Hypothetical 117.8 kDa protein in STE2-FRS2 intergenic region	0.32	-	end	8	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA]			1029
P53305 UniProt NPD GO	YG4L_YEAST	Hypothetical 12.4 kDa protein in NAB1A-GPI1 intergenic region	0.32	+	nuc	0		mitochondrial small ribosomal subunit [IDA]			110
P47132 UniProt NPD GO	YJ57_YEAST	Hypothetical 13.1 kDa protein in STE18-GRR1 intergenic region	0.32	-	gol	0					116
P40542 UniProt NPD GO	YIC5_YEAST	Hypothetical 14.1 kDa protein in IRR1-TIM44 intergenic region	0.32	-	nuc	0					124
P40083 UniProt NPD GO	YEW7_YEAST	Hypothetical 16.6 kDa protein in GDI1-COX15 intergenic region	0.32	-	nuc	0					148
P40500 UniProt NPD GO	YII9_YEAST	Hypothetical 23.9 kDa protein in SGA1-KTR7 intergenic region	0.32	-	end	2	Membrane; multi-pass membrane protein (Potential)				205
P43557 UniProt NPD GO	YFE6_YEAST	Hypothetical 24.0 kDa protein in EMP47-SEC53 intergenic region	0.32	-	nuc	1		mitochondrion [IDA]			207
O19913 UniProt NPD GO	YCF44_CYACA	Hypothetical 45.3 kDa protein ycf44	0.32	-	end	4 *	Plastid; chloroplast				396
P48332 UniProt NPD GO	YCXB_CYAPA	Hypothetical 9.4 kDa protein in trpG-ccsA intergenic region (ORF77)	0.32	-	mit	0	Plastid; cyanelle				77
P25380 UniProt NPD GO	YCE8_YEAST	Hypothetical SPS2-like 52.0 kDa protein in APA1/DTP-PDI1 intergenic region	0.32	-	exc	1 *					463
P93299 UniProt NPD GO	M430_ARATH	Hypothetical mitochondrial protein AtMg00430/AtMg01150 (ORF106a/ORF106g)	0.32	-	nuc	0	Mitochondrion (Potential)				106
P93305 UniProt NPD GO	M500_ARATH	Hypothetical mitochondrial protein AtMg00500 (ORF141)	0.32	-	mit	0	Mitochondrion (Potential)				141
P92510 UniProt NPD GO	M680_ARATH	Hypothetical mitochondrial protein AtMg00680 (ORF122c)	0.32	-	nuc	1 *	Mitochondrion (Potential)				122
O04656 UniProt NPD GO	Y5714_ARATH	Hypothetical protein At5g27140	0.32	+	end	2					435
Q10939 UniProt NPD GO	YWS3_CAEEL	Hypothetical protein B0310.3	0.32	-	nuc	1					264
Q11077 UniProt NPD GO	YWV3_CAEEL	Hypothetical protein B0403.3 precursor	0.32	-	nuc	0	Secreted protein (Potential)				270
O74447 UniProt NPD GO	YCG2_SCHPO	Hypothetical protein C16C4.02c in chromosome III	0.32	-	cyt	0					548
Q10363 UniProt NPD GO	YDBC_SCHPO	Hypothetical protein C22E12.12 in chromosome I	0.32	-	nuc	0					96
Q09797 UniProt NPD GO	YAA3_SCHPO	Hypothetical protein C22G7.03 in chromosome I	0.32	+	mit	0					236

You are viewing entries 38551 to 38600 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.