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
Q9XET4 UniProt NPD GO	RS7_SECCE	40S ribosomal protein S7	0.17	-	cyt	0					192
P18080 UniProt NPD GO	HEM0_CHICK	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix				513
P40099 UniProt NPD GO	FTHC_YEAST	5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate synthetase) (Meth ...	0.17	-	mit	0		mitochondrion [IDA]			211
Q9N298 UniProt NPD GO	5HT1A_PANTR	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.17	-	end	7 *	Membrane; multi-pass membrane protein				422
P28564 UniProt NPD GO	5HT1B_RAT	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B)	0.17	-	end	7 *	Membrane; multi-pass membrane protein	plasma membrane [IDA]			386
P18599 UniProt NPD GO	5HT2A_CRIGR	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.17	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				471
P28223 UniProt NPD GO	5HT2A_HUMAN	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.17	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...	integral to plasma membrane [TAS]	182135		471
P50128 UniProt NPD GO	5HT2A_MACMU	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.17	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				471
P97288 UniProt NPD GO	5HT4R_MOUSE	5-hydroxytryptamine 4 receptor (5-HT-4) (Serotonin receptor 4) (5-HT4)	0.17	-	end	7 *	Membrane; multi-pass membrane protein				388
P52034 UniProt NPD GO	K6PF_DROME	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.17	-	cyt	0					788
O42938 UniProt NPD GO	K6PF_SCHPO	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase) (6PF-1-K)	0.17	-	mit	0	Cytoplasm (By similarity)				942
P48611 UniProt NPD GO	PTPS_DROME	6-pyruvoyl tetrahydrobiopterin synthase (EC 4.2.3.12) (PTPS) (PTP synthase) (Sepiapterin synthase A) ...	0.17	-	mit	0					168
Q9M5M7 UniProt NPD GO	RL10_EUPES	60S ribosomal protein L10	0.17	-	nuc	0					220
Q96L21 UniProt NPD GO	RL10L_HUMAN	60S ribosomal protein L10-like	0.17	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [NAS]			213
Q755D9 UniProt NPD GO	RL10A_ASHGO	60S ribosomal protein L10a	0.17	+	nuc	0					217
Q9UVJ4 UniProt NPD GO	RL10A_CANAL	60S ribosomal protein L10a	0.17	+	nuc	0					217
P23358 UniProt NPD GO	RL12_RAT	60S ribosomal protein L12	0.17	-	nuc	0					165
Q02753 UniProt NPD GO	RL21A_YEAST	60S ribosomal protein L21-A	0.17	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	160
Q8LD46 UniProt NPD GO	R23A1_ARATH	60S ribosomal protein L23a-1 (AtRPL23A-1)	0.17	-	nuc	0					154
Q9M3C3 UniProt NPD GO	R23A2_ARATH	60S ribosomal protein L23a-2	0.17	-	nuc	0					154
Q90YU1 UniProt NPD GO	RL17_ICTPU	60S ribosomal protein L27	0.17	-	cyt	0					135
O15883 UniProt NPD GO	RL27A_TRYBB	60S ribosomal protein L27a (L29)	0.17	-	nuc	0					145
Q9LMK0 UniProt NPD GO	R35A1_ARATH	60S ribosomal protein L35a-1	0.17	-	nuc	0					112
Q9FZH0 UniProt NPD GO	R35A2_ARATH	60S ribosomal protein L35a-2	0.17	-	nuc	0					111
Q9C912 UniProt NPD GO	R35A3_ARATH	60S ribosomal protein L35a-3	0.17	-	nuc	0					112
P51422 UniProt NPD GO	R35A4_ARATH	60S ribosomal protein L35a-4	0.17	-	nuc	0					111
P52866 UniProt NPD GO	RL36_DAUCA	60S ribosomal protein L36	0.17	-	nuc	0					106
Q3MIC0 UniProt NPD GO	RL37A_BOVIN	60S ribosomal protein L37a	0.17	-	nuc	0					91
P43209 UniProt NPD GO	RL37A_BRARA	60S ribosomal protein L37a	0.17	-	cyt	0					92
P32046 UniProt NPD GO	RL37A_CHICK	60S ribosomal protein L37a	0.17	-	nuc	0					91
P61513 UniProt NPD GO	RL37A_HUMAN	60S ribosomal protein L37a	0.17	-	nuc	0					91
P61514 UniProt NPD GO	RL37A_MOUSE	60S ribosomal protein L37a	0.17	-	nuc	0					91
P61515 UniProt NPD GO	RL37A_RAT	60S ribosomal protein L37a	0.17	-	nuc	0					91
Q7SZB4 UniProt NPD GO	RL37A_XENLA	60S ribosomal protein L37a	0.17	-	cyt	0					91
Q6FSN6 UniProt NPD GO	RL7_CANGA	60S ribosomal protein L7	0.17	-	nuc	0					244
Q90YW1 UniProt NPD GO	RL8_ICTPU	60S ribosomal protein L8	0.17	-	mit	0	Cytoplasm				256
P46286 UniProt NPD GO	RL81_ARATH	60S ribosomal protein L8-1 (60S ribosomal protein L2) (Protein EMBRYO DEFECTIVE 229)	0.17	-	mit	0	Cytoplasm				258
Q75C78 UniProt NPD GO	GRP78_ASHGO	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.17	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				674
Q6FW50 UniProt NPD GO	GRP78_CANGA	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.17	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				667
Q9HG01 UniProt NPD GO	GRP78_PICAN	78 kDa glucose-regulated protein homolog precursor (GRP 78) (Immunoglobulin heavy chain-binding prot ...	0.17	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)	endoplasmic reticulum lumen [ISS]			665
O55074 UniProt NPD GO	AKAP7_MOUSE	A-kinase anchor protein 7 (Protein kinase A-anchoring protein 7) (A-kinase anchor protein 18) (A-kin ...	0.17	-	nuc	0	Membrane; lipid-anchor	nucleus [IDA]			80
P31962 UniProt NPD GO	MFA1_USTMA	A1-specific pheromone (Mating factor A1)	0.17	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				40
O77633 UniProt NPD GO	ADA10_PIG	ADAM 10 (EC 3.4.24.81) (A disintegrin and metalloproteinase domain 10) (Mammalian disintegrin-metall ...	0.17	-	nuc	0	Membrane; single-pass type I membrane protein (By similarity)				75
Q9JI76 UniProt NPD GO	ADA21_MOUSE	ADAM 21 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 21) (ADAM 31)	0.17	-	end	1	Membrane; single-pass type I membrane protein				729
Q03419 UniProt NPD GO	IZH1_YEAST	ADIPOR-like receptor IZH1 (Implicated in zinc homeostasis protein 1)	0.17	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [IDA] membrane [TAS]			316
P18239 UniProt NPD GO	ADT2_YEAST	ADP,ATP carrier protein 2 (ADP/ATP translocase 2) (Adenine nucleotide translocator 2) (ANT 2)	0.17	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA]			318
Q9BRR6 UniProt NPD GO	ADPGK_HUMAN	ADP-dependent glucokinase (EC 2.7.1.147) (ADPGK) (ADP-GK) (RbBP-35)	0.17	-	mit	0					497
P26991 UniProt NPD GO	ARF_GIALA	ADP-ribosylation factor	0.17	+	mit	0					190
P36992 UniProt NPD GO	AMBP_PLEPL	AMBP protein precursor [Contains: Alpha-1-microglobulin; Inter-alpha-trypsin inhibitor light chain ( ...	0.17	-	exc	0	Secreted protein (By similarity)				355
Q96PC3 UniProt NPD GO	AP1S3_HUMAN	AP-1 complex subunit sigma-3 (Adapter-related protein complex 1 sigma-1C subunit) (Sigma-adaptin 1C) ...	0.17	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles located at the Golgi compl ...	AP-1 adaptor complex [ISS] Golgi trans face [ISS]			154

You are viewing entries 53951 to 54000 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.