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
O03068 UniProt NPD GO	ATPB_DENPU	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				486
O03074 UniProt NPD GO	ATPB_MICPL	ATP synthase subunit beta (EC 3.6.3.14) (ATPase subunit beta) (ATP synthase F1 sector subunit beta) ...	0.03	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				395
Q5ZLC5 UniProt NPD GO	ATPB_CHICK	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion				533
P00830 UniProt NPD GO	ATPB_YEAST	ATP synthase subunit beta, mitochondrial precursor (EC 3.6.3.14)	0.03	-	mit	0	Mitochondrion	proton-transporting ATP synthase, catalytic... [IMP] soluble fraction [IDA]			511
Q58DD9 UniProt NPD GO	ATPBB_BOVIN	ATP-binding domain 1 family member B	0.03	-	cyt	0					310
Q6PUR6 UniProt NPD GO	ATPBB_BRARE	ATP-binding domain 1 family member B	0.03	-	cyt	0					311
Q8M9Y9 UniProt NPD GO	CLPP_CHAGL	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	cyt	0	Plastid; chloroplast				201
P26567 UniProt NPD GO	CLPP_MAIZE	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	2	Plastid; chloroplast				216
Q6ENE9 UniProt NPD GO	CLPP_ORYNI	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	0	Plastid; chloroplast				216
P12209 UniProt NPD GO	CLPP_ORYSA	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	0	Plastid; chloroplast				216
Q85X43 UniProt NPD GO	CLPP_PINKO	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	1	Plastid; chloroplast				196
Q6L377 UniProt NPD GO	CLPP_SACHY	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	0	Plastid; chloroplast				216
Q6ENT9 UniProt NPD GO	CLPP_SACOF	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	0	Plastid; chloroplast				216
P24064 UniProt NPD GO	CLPP_WHEAT	ATP-dependent Clp protease proteolytic subunit (EC 3.4.21.92) (Endopeptidase Clp)	0.03	-	nuc	0	Plastid; chloroplast				216
Q08655 UniProt NPD GO	ASR1_LYCES	Abscisic stress ripening protein 1	0.03	-	cyt	0	Nucleus				115
Q8I948 UniProt NPD GO	ACN1_ACAGO	Acanthoscurrin-1 precursor	0.03	+	mit	1 *	Secreted protein	extracellular region [IDA]			156
Q9VVW1 UniProt NPD GO	A76A_DROME	Accessory gland protein Acp76A precursor	0.03	-	end	0	Secreted protein (Probable)				386
Q9VBL6 UniProt NPD GO	MS57A_DROME	Accessory gland-specific peptide 57Da precursor (Male accessory gland secretory protein 57Da)	0.03	-	exc	0	Secreted protein	extracellular region [NAS]			75
O78451 UniProt NPD GO	ILVH_GUITH	Acetolactate synthase small subunit (EC 2.2.1.6) (AHAS) (Acetohydroxy-acid synthase small subunit) ( ...	0.03	-	cyt	0	Plastid; chloroplast				169
O13440 UniProt NPD GO	ACSA_COPCI	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme)	0.03	-	nuc	0					661
Q9VP61 UniProt NPD GO	ACSA_DROME	Acetyl-coenzyme A synthetase (EC 6.2.1.1) (Acetate--CoA ligase) (Acyl-activating enzyme) (Acetyl-CoA ...	0.03	-	mit	0	Cytoplasm	cytoplasm [NAS]			670
P52910 UniProt NPD GO	ACS2_YEAST	Acetyl-coenzyme A synthetase 2 (EC 6.2.1.1) (Acetate--CoA ligase 2) (Acyl-activating enzyme 2)	0.03	-	nuc	0	Cytoplasm (Potential)	cytosol [IDA]			683
Q99NB1 UniProt NPD GO	ACS2L_MOUSE	Acetyl-coenzyme A synthetase 2-like, mitochondrial precursor (EC 6.2.1.1) (Acetate--CoA ligase 2) (A ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix				682
Q9NUB1 UniProt NPD GO	ACS2L_HUMAN	Acetyl-coenzyme A synthetase 2-like, mitochondrial precursor (EC 6.2.1.1) (Acetate--CoA ligase 2) (A ...	0.03	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				689
P54249 UniProt NPD GO	ACHA_ERICO	Acetylcholine receptor protein subunit alpha (Fragment)	0.03	-	cyt	0	Membrane; multi-pass membrane protein (By similarity)				84
P54250 UniProt NPD GO	ACHA_FELCA	Acetylcholine receptor protein subunit alpha (Fragment)	0.03	-	cyt	0	Membrane; multi-pass membrane protein (By similarity)				84
P54251 UniProt NPD GO	ACHA_HERIC	Acetylcholine receptor protein subunit alpha (Fragment)	0.03	-	cyt	0	Membrane; multi-pass membrane protein (By similarity)				84
P14143 UniProt NPD GO	ACHA_NAJNA	Acetylcholine receptor protein subunit alpha (Fragment)	0.03	-	cyt	0	Membrane; multi-pass membrane protein				104
P02710 UniProt NPD GO	ACHA_TORCA	Acetylcholine receptor protein subunit alpha precursor	0.03	-	end	5 *	Membrane; multi-pass membrane protein			3MRA	461
P05377 UniProt NPD GO	ACHAB_XENLA	Acetylcholine receptor protein subunit alpha-1-B precursor	0.03	-	end	4	Membrane; multi-pass membrane protein				457
P16005 UniProt NPD GO	ACHB_CHICK	Acetylcholine receptor protein subunit beta precursor (Fragment)	0.03	-	exc	0	Membrane; multi-pass membrane protein				118
Q9TLT0 UniProt NPD GO	ARGB_CYACA	Acetylglutamate kinase (EC 2.7.2.8) (NAG kinase) (AGK) (N-acetyl-L-glutamate 5-phosphotransferase)	0.03	-	nuc	0	Plastid; chloroplast				304
Q6BUP9 UniProt NPD GO	ARGD_DEBHA	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.03	-	nuc	0	Mitochondrion; mitochondrial matrix (By similarity)				466
P18544 UniProt NPD GO	ARGD_YEAST	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.03	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [NAS]			423
P54638 UniProt NPD GO	ARGE_DICDI	Acetylornithine deacetylase (EC 3.5.1.16) (Acetylornithinase) (AO) (N-acetylornithinase) (NAO)	0.03	-	cyt	0					448
P29021 UniProt NPD GO	CHIT_PETHY	Acidic endochitinase precursor (EC 3.2.1.14)	0.03	-	exc	1 *	Secreted protein. Extracellular fluid from leaves				254
O01615 UniProt NPD GO	AN322_CAEEL	Acidic leucine-rich nuclear phosphoprotein 32-related protein 2 (ANP32/acidic nuclear phosphoprotein ...	0.03	-	cyt	0					225
Q91XA9 UniProt NPD GO	CHIA_MOUSE	Acidic mammalian chitinase precursor (EC 3.2.1.14) (AMCase) (YNL)	0.03	-	vac	0	Secreted protein (Probable)	extracellular space [ISS]			473
P49608 UniProt NPD GO	ACOC_CUCMA	Aconitate hydratase, cytoplasmic (EC 4.2.1.3) (Citrate hydro-lyase) (Aconitase)	0.03	-	cyt	0	Cytoplasm				898
Q3C258 UniProt NPD GO	ACR1_ACTEQ	Acrorhagin-1 precursor (Acrorhagin I)	0.03	-	nuc	0	Secreted protein. Found in nematocyst				70
P26182 UniProt NPD GO	ACT_ACHBI	Actin	0.03	-	cyt	0	Cytoplasm				376
Q75D00 UniProt NPD GO	ACT_ASHGO	Actin	0.03	-	cyt	0	Cytoplasm				376
P60009 UniProt NPD GO	ACT_CANGA	Actin	0.03	-	cyt	0	Cytoplasm				375
P53498 UniProt NPD GO	ACT_CHLRE	Actin	0.03	-	cyt	0	Cytoplasm				377
P53502 UniProt NPD GO	ACT_FUCDI	Actin	0.03	-	cyt	0	Cytoplasm				375
Q39758 UniProt NPD GO	ACT_FUCVE	Actin	0.03	-	cyt	0	Cytoplasm				376
P51775 UniProt NPD GO	ACT_GIALA	Actin	0.03	-	cyt	0	Cytoplasm				375
O74258 UniProt NPD GO	ACT_PICAN	Actin	0.03	-	cyt	0	Cytoplasm				376
Q9P4D1 UniProt NPD GO	ACT_PICPA	Actin	0.03	-	cyt	0	Cytoplasm				376
P60011 UniProt NPD GO	ACT_SACBA	Actin	0.03	-	cyt	0	Cytoplasm				375

You are viewing entries 79001 to 79050 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.