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
O74329 UniProt NPD GO	RS29_SCHPO	40S ribosomal protein S29	0.18	-	nuc	0					55
P55830 UniProt NPD GO	RS3A_DROME	40S ribosomal protein S3a (C3 protein)	0.18	-	nuc	0	Cytoplasm				267
Q5E988 UniProt NPD GO	RS5_BOVIN	40S ribosomal protein S5	0.18	-	nuc	0					203
P46782 UniProt NPD GO	RS5_HUMAN	40S ribosomal protein S5	0.18	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	603630		203
P97461 UniProt NPD GO	RS5_MOUSE	40S ribosomal protein S5	0.18	-	nuc	0					203
Q9XH45 UniProt NPD GO	RS7_BRAOL	40S ribosomal protein S7	0.18	-	cyt	0					191
P62085 UniProt NPD GO	RS7_DROYA	40S ribosomal protein S7	0.18	-	nuc	0					194
P49214 UniProt NPD GO	RS9_TOBAC	40S ribosomal protein S9 (S4) (Fragment)	0.18	-	mit	0					77
Q9ZSR8 UniProt NPD GO	RSSA_BRANA	40S ribosomal protein SA (p40) (Laminin receptor-like protein)	0.18	-	cyt	0	Cytoplasm				292
Q9Y478 UniProt NPD GO	AAKB1_HUMAN	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb)	0.18	-	nuc	0			602740		269
Q63147 UniProt NPD GO	HEM0_RAT	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.18	-	cyt	0	Mitochondrion; mitochondrial matrix				587
Q6XXX8 UniProt NPD GO	5HT1B_VULVU	5-hydroxytryptamine 1B receptor (5-HT-1B) (Serotonin receptor 1B) (5-HT1B) (5-HTR1B)	0.18	-	end	7 *	Membrane; multi-pass membrane protein				389
Q84U21 UniProt NPD GO	RK22_CHLRE	50S ribosomal protein L22, chloroplast precursor	0.18	-	mit	0	Plastid; chloroplast				175
Q27778 UniProt NPD GO	K6PF_SCHMA	6-phosphofructokinase (EC 2.7.1.11) (Phosphofructokinase) (Phosphohexokinase)	0.18	-	cyt	0					781
P93847 UniProt NPD GO	RL10_SOLME	60S ribosomal protein L10 (EQM)	0.18	-	nuc	0					219
Q08200 UniProt NPD GO	RL10_CHICK	60S ribosomal protein L10 (Jun-binding protein JIF-1) (Fragment)	0.18	-	mit	0					210
P38064 UniProt NPD GO	RM16_YEAST	60S ribosomal protein L16, mitochondrial precursor (YmL47)	0.18	-	cyt	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			232
Q08066 UniProt NPD GO	RL19_MAIZE	60S ribosomal protein L19 (Fragment)	0.18	-	nuc	0					62
P52819 UniProt NPD GO	RL22_CAEEL	60S ribosomal protein L22	0.18	-	nuc	0					130
Q12487 UniProt NPD GO	RM23_YEAST	60S ribosomal protein L23, mitochondrial precursor (YmL23)	0.18	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			163
Q9XSU7 UniProt NPD GO	RL27_CANFA	60S ribosomal protein L27	0.18	-	cyt	0					135
Q29333 UniProt NPD GO	RL27A_PIG	60S ribosomal protein L27a (Fragment)	0.18	+	nuc	0					53
P05747 UniProt NPD GO	RL29_YEAST	60S ribosomal protein L29 (YL43)	0.18	-	nuc	0		cytoplasm [IDA] cytosolic large ribosomal subunit (sensu Eu... [TAS]			58
O17307 UniProt NPD GO	RL37A_SCHMA	60S ribosomal protein L37a (Fragment)	0.18	-	nuc	0					91
Q8RXU5 UniProt NPD GO	R37A2_ARATH	60S ribosomal protein L37a-2	0.18	-	cyt	0					92
Q9HGL8 UniProt NPD GO	RL43A_SCHPO	60S ribosomal protein L43-A (L37A)	0.18	-	mit	0					94
P07823 UniProt NPD GO	GRP78_MESAU	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				654
P20029 UniProt NPD GO	GRP78_MOUSE	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [IDA]			655
Q91883 UniProt NPD GO	GRP78_XENLA	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				658
P11021 UniProt NPD GO	GRP78_HUMAN	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	cell surface [IEP] endoplasmic reticulum [TAS] endoplasmic reticulum lumen [TAS] ER-Golgi intermediate compartment [IDA] integral to endoplasmic reticulum membrane [IDA] nucleus [IDA] perinuclear region [IDA]	180300		654
P06761 UniProt NPD GO	GRP78_RAT	78 kDa glucose-regulated protein precursor (GRP 78) (Immunoglobulin heavy chain-binding protein) (Bi ...	0.18	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen	endoplasmic reticulum [TAS]			654
P40941 UniProt NPD GO	ADT2_ARATH	ADP,ATP carrier protein 2, mitochondrial precursor (ADP/ATP translocase 2) (Adenine nucleotide trans ...	0.18	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				385
Q41630 UniProt NPD GO	ADT2_WHEAT	ADP,ATP carrier protein 2, mitochondrial precursor (ADP/ATP translocase 2) (Adenine nucleotide trans ...	0.18	-	cyt	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				331
P31691 UniProt NPD GO	ADT_ORYSA	ADP,ATP carrier protein, mitochondrial precursor (ADP/ATP translocase) (Adenine nucleotide transloca ...	0.18	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				382
P27081 UniProt NPD GO	ADT2_SOLTU	ADP,ATP carrier protein, mitochondrial precursor (ADP/ATP translocase) (Adenine nucleotide transloca ...	0.18	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein				386
Q8VDL4 UniProt NPD GO	ADPGK_MOUSE	ADP-dependent glucokinase (EC 2.7.1.147) (ADPGK) (ADP-GK)	0.18	-	mit	0					496
Q9D0J4 UniProt NPD GO	ARL2_MOUSE	ADP-ribosylation factor-like protein 2	0.18	-	nuc	0				1KSJ	184
P56377 UniProt NPD GO	AP1S2_HUMAN	AP-1 complex subunit sigma-2 (Adapter-related protein complex 1 sigma-1B subunit) (Sigma-adaptin 1B) ...	0.18	-	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] membrane coat adaptor complex [TAS]	603532		157
Q9DB50 UniProt NPD GO	AP1S2_MOUSE	AP-1 complex subunit sigma-2 (Adapter-related protein complex 1 sigma-1B subunit) (Sigma-adaptin 1B) ...	0.18	-	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]			160
P84091 UniProt NPD GO	AP2M1_MOUSE	AP-2 complex subunit mu-1 (Adaptin mu-1) (AP-2 mu-2 chain) (Clathrin coat assembly protein AP50) (Cl ...	0.18	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane	mitochondrion [IDA] secretory granule [TAS]			435
P84092 UniProt NPD GO	AP2M1_RAT	AP-2 complex subunit mu-1 (Adaptin mu-1) (AP-2 mu-2 chain) (Clathrin coat assembly protein AP50) (Cl ...	0.18	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane			2BP5	435
Q96CW1 UniProt NPD GO	AP2M1_HUMAN	AP-2 complex subunit mu-1 (Adaptin mu-1) (AP-2 mu-2 chain) (Clathrin coat assembly protein AP50) (Cl ...	0.18	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane		601024	1H6E	435
Q02850 UniProt NPD GO	ATPF_ANTSP	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.18	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				182
P48085 UniProt NPD GO	ATPX_CYAPA	ATP synthase B' chain (EC 3.6.3.14) (Subunit II)	0.18	-	nuc	1 *	Plastid; cyanelle; cyanelle thylakoid membrane; single-pass membrane protein (By similarity)				164
P31399 UniProt NPD GO	ATP5H_RAT	ATP synthase D chain, mitochondrial (EC 3.6.3.14)	0.18	-	cyt	0		mitochondrion [TAS] proton-transporting ATP synthase complex (s... [IDA]			160
P32980 UniProt NPD GO	ATPD_TOBAC	ATP synthase delta chain, chloroplast precursor (EC 3.6.3.14)	0.18	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane				248
Q70XZ7 UniProt NPD GO	ATPE_AMBTC	ATP synthase epsilon chain (EC 3.6.3.14) (ATP synthase F1 sector epsilon subunit)	0.18	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				134
P49377 UniProt NPD GO	ATPG_KLULA	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.18	-	mit	0	Mitochondrion				289
Q06646 UniProt NPD GO	AT5G2_RAT	ATP synthase lipid-binding protein, mitochondrial precursor (EC 3.6.3.14) (ATP synthase proteolipid ...	0.18	-	nuc	2	Mitochondrion; mitochondrial membrane; multi-pass membrane protein				141
Q9ME79 UniProt NPD GO	ATP8_BOMMO	ATP synthase protein 8 (EC 3.6.3.14) (ATPase subunit 8) (A6L)	0.18	-	mit	1 *	Mitochondrion; mitochondrial membrane; single-pass membrane protein				53

You are viewing entries 52651 to 52700 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.