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
Q5VK71 UniProt NPD GO	AKAP8_CANFA	A-kinase anchor protein 8 (A-kinase anchor protein 95 kDa) (AKAP 95)	0.91	+	nuc	0	Nucleus; nucleoplasm; nuclear matrix (By similarity). Associated with the nuclear matrix. Redistribu ...				698
Q9P2N4 UniProt NPD GO	ATS9_HUMAN	ADAMTS-9 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 9) ...	0.91	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [IDA]	605421		1935
Q68FF6 UniProt NPD GO	GIT1_MOUSE	ARF GTPase-activating protein GIT1 (G protein-coupled receptor kinase-interactor 1) (GRK-interacting ...	0.91	-	nuc	0	Cytoplasm (By similarity). Cycles between at least 3 distinct intracellular compartments, including ...				770
Q9Z272 UniProt NPD GO	GIT1_RAT	ARF GTPase-activating protein GIT1 (G protein-coupled receptor kinase-interactor 1) (GRK-interacting ...	0.91	-	nuc	0	Cytoplasm (By similarity). Cycles between at least 3 distinct intracellular compartments, including ...	focal adhesion [TAS]			770
Q8NFD5 UniProt NPD GO	ARI1B_HUMAN	AT-rich interactive domain-containing protein 1B (ARID domain-containing protein 1B) (Osa homolog 2) ...	0.91	-	nuc	0	Nucleus	SWI/SNF complex [IDA]			2236
Q9GZR7 UniProt NPD GO	DDX24_HUMAN	ATP-dependent RNA helicase DDX24 (EC 3.6.1.-) (DEAD box protein 24)	0.91	-	nuc	0			606181		859
Q6DRI7 UniProt NPD GO	DDX51_BRARE	ATP-dependent RNA helicase DDX51 (EC 3.6.1.-) (DEAD box protein 51)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				652
Q14562 UniProt NPD GO	DHX8_HUMAN	ATP-dependent RNA helicase DHX8 (EC 3.6.1.-) (DEAH box protein 8) (RNA helicase HRH1)	0.91	+	nuc	0	Nucleus	nucleus [TAS] spliceosome complex [TAS]	600396		1220
Q2UBZ5 UniProt NPD GO	SPB4_ASPOR	ATP-dependent rRNA helicase spb4 (EC 3.6.1.-)	0.91	-	nuc	0	Nucleus; nucleolus (By similarity)				638
O74764 UniProt NPD GO	SPB4_SCHPO	ATP-dependent rRNA helicase spb4 (EC 3.6.1.-)	0.91	+	nuc	0	Nucleus; nucleolus (By similarity)				606
P62297 UniProt NPD GO	ASPM_SHEEP	Abnormal spindle-like microcephaly-associated protein homolog (Fragment)	0.91	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). The nuclear-cytoplasmic distribution could be re ...				3374
Q62415 UniProt NPD GO	ASPP1_MOUSE	Apoptosis-stimulating of p53 protein 1 (Protein phosphatase 1 regulatory subunit 13B)	0.91	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Some fraction is nuclear	cytoplasm [ISS] nucleus [ISS]			1087
Q8CG79 UniProt NPD GO	ASPP2_MOUSE	Apoptosis-stimulating of p53 protein 2 (Tumor suppressor p53-binding protein 2) (p53BP2) (53BP2) (Fr ...	0.91	-	nuc	0	Cytoplasm; perinuclear region (By similarity). Predominantly. Nucleus (By similarity). Some small fr ...	cytoplasm [ISS]			1088
Q9XVN3 UniProt NPD GO	IASPP_CAEEL	Apoptotic enhancer 1 protein (Inhibitor member of the ASPP family) (Protein iASPP) (Ce-iASPP)	0.91	+	nuc	0	Nucleus				769
P05085 UniProt NPD GO	ARGR2_YEAST	Arginine metabolism regulation protein II	0.91	-	nuc	0	Nucleus	nucleus [IDA]			880
O02747 UniProt NPD GO	AHR_RABIT	Aryl hydrocarbon receptor (Ah receptor) (AhR)	0.91	-	nuc	0	Cytoplasm. Nucleus. First cytoplasmic, upon binding with ligand and interaction with a HSP90, it tra ...				847
Q61137 UniProt NPD GO	ASTN_MOUSE	Astrotactin-1 precursor (Neuronal migration protein GC14)	0.91	+	end	2	Membrane; multi-pass membrane protein (Potential)				1302
Q9Y2J2 UniProt NPD GO	E41L3_HUMAN	Band 4.1-like protein 3 (4.1B) (Differentially expressed in adenocarcinoma of the lung protein 1) (D ...	0.91	-	nuc	0		plasma membrane [NAS]	605331		1087
Q8BHX3 UniProt NPD GO	BOREA_MOUSE	Borealin (Cell division cycle-associated protein 8) (MESrg)	0.91	+	nuc	0	Nucleus; nucleolus. Cytoplasm. Localizes on chromosome arms and inner centromeres from prophase thro ...				289
Q7ZUF2 UniProt NPD GO	BRD9_BRARE	Bromodomain-containing protein 9	0.91	+	nuc	0					631
Q8WXK8 UniProt NPD GO	BPAEB_HUMAN	Bullous pemphigoid antigen 1, isoform 7 (Bullous pemphigoid antigen) (BPA) (Hemidesmosomal plaque pr ...	0.91	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	600088		3060
Q03701 UniProt NPD GO	CEBPZ_HUMAN	CCAAT/enhancer-binding protein zeta (CCAAT-box-binding transcription factor) (CCAAT-binding factor) ...	0.91	+	nuc	0	Nucleus	nucleus [TAS]			1054
P43069 UniProt NPD GO	CDC25_CANAL	Cell division control protein 25	0.91	-	nuc	0					1333
P49453 UniProt NPD GO	CENPC_SHEEP	Centromere protein C 1 (CENP-C) (Centromere autoantigen C) (Fragment)	0.91	-	nuc	0	Nucleus				402
P17106 UniProt NPD GO	CBF1_YEAST	Centromere-binding protein 1 (CBP-1) (Centromere-binding factor 1) (Centromere promoter factor 1)	0.91	+	nuc	0	Nucleus. Mitochondrion	kinetochore [TAS] mitochondrion [IDA] nucleus [IDA]			351
Q6P5D4 UniProt NPD GO	CP135_MOUSE	Centrosomal protein of 135 kDa (Cep135 protein) (Centrosomal protein 4)	0.91	-	nuc	0	Centrosome (By similarity)				1140
Q9D3R3 UniProt NPD GO	CEP72_MOUSE	Centrosomal protein of 72 kDa (Cep72 protein)	0.91	-	nuc	0	Centrosome (By similarity)				646
P38806 UniProt NPD GO	YNG2_YEAST	Chromatin modification-related protein YNG2 (ING1 homolog 2) (ESA1-associated factor 4)	0.91	+	nuc	0	Nucleus	H4/H2A histone acetyltransferase complex [IPI] nucleus [IDA]			282
P36012 UniProt NPD GO	CSE4_YEAST	Chromatin-associated protein CSE4	0.91	-	nuc	0	Nucleus	condensed nuclear chromosome, pericentric r... [IGI] kinetochore [IGI] nuclear nucleosome [IDA]		2FSC	229
Q9Y232 UniProt NPD GO	CDYL1_HUMAN	Chromodomain Y-like protein (CDY-like)	0.91	-	end	0	Nucleus (By similarity)		603778	2GTR	598
Q12873 UniProt NPD GO	CHD3_HUMAN	Chromodomain helicase-DNA-binding protein 3 (EC 3.6.1.-) (ATP-dependent helicase CHD3) (CHD-3) (Mi-2 ...	0.91	+	nuc	0	Nucleus		602120		2000
Q28107 UniProt NPD GO	FA5_BOVIN	Coagulation factor V precursor (Activated protein C cofactor) [Contains: Coagulation factor V heavy ...	0.91	+	nuc	0				1SDD	2211
Q2KIC0 UniProt NPD GO	CCD55_BOVIN	Coiled-coil domain-containing protein 55	0.91	-	nuc	0					559
Q9Y3X0 UniProt NPD GO	CCDC9_HUMAN	Coiled-coil domain-containing protein 9	0.91	-	nuc	0					531
P38432 UniProt NPD GO	P80C_HUMAN	Coilin (p80)	0.91	+	nuc	0	Nucleus. Nuclear coiled body located in the interchromatin space between the nucleolus and the nucle ...	nucleus [TAS]	600272		576
Q2QLB3 UniProt NPD GO	CTTB2_CALMO	Cortactin-binding protein 2 (CortBP2)	0.91	-	nuc	0					1663
P17544 UniProt NPD GO	ATF7_HUMAN	Cyclic AMP-dependent transcription factor ATF-7 (Activating transcription factor 7) (Transcription f ...	0.91	+	nuc	0	Nucleus		606371		494
Q8SQ19 UniProt NPD GO	CREB3_BOVIN	Cyclic AMP-responsive element-binding protein 3 (Luman protein)	0.91	+	nuc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				368
P83183 UniProt NPD GO	HSPC_ELECI	Cysteine-rich protamine	0.91	+	nuc	0	Nucleus				84
Q9ER72 UniProt NPD GO	SYC_MOUSE	Cysteinyl-tRNA synthetase (EC 6.1.1.16) (Cysteine--tRNA ligase) (CysRS)	0.91	+	cyt	0	Cytoplasm				831
Q6E3D5 UniProt NPD GO	CPB3_CAEBR	Cytoplasmic polyadenylation element-binding protein 3	0.91	-	nuc	0					753
Q2KNA0 UniProt NPD GO	CYTSA_CANFA	Cytospin-A	0.91	+	nuc	0					1117
Q9UKG1 UniProt NPD GO	DP13A_HUMAN	DCC-interacting protein 13 alpha (Dip13 alpha) (Adapter protein containing PH domain, PTB domain and ...	0.91	-	nuc	0	Endosome; early endosome; early endosomal membrane; peripheral membrane protein. Nucleus. Early endo ...	cytoplasm [IC] endosome membrane [IDA] nucleus [IDA]	604299		709
Q8K3H0 UniProt NPD GO	DP13A_MOUSE	DCC-interacting protein 13 alpha (Dip13 alpha) (Adapter protein containing PH domain, PTB domain and ...	0.91	-	nuc	0	Endosome; early endosome; early endosomal membrane; peripheral membrane protein (By similarity). Nuc ...	cytoplasm [ISS] endosome membrane [ISS] nucleus [ISS]			707
P35639 UniProt NPD GO	DDIT3_MOUSE	DNA damage-inducible transcript 3 (DDIT-3) (Growth arrest and DNA-damage-inducible protein GADD153) ...	0.91	+	nuc	0	Nucleus	nucleus [IC]			168
P13705 UniProt NPD GO	MSH3_MOUSE	DNA mismatch repair protein Msh3 (Repair-3 protein) (REP-1)	0.91	+	nuc	0					1091
P38086 UniProt NPD GO	RDH54_YEAST	DNA repair and recombination protein RDH54 (RAD homolog 54) (Recombination factor TID1) (Two-hybrid ...	0.91	-	nuc	0	Nucleus	nucleus [IC]			924
Q5KPG8 UniProt NPD GO	RAD5_CRYNE	DNA repair protein RAD5 (EC 3.6.1.-)	0.91	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1198
Q26454 UniProt NPD GO	MCM4_DROME	DNA replication licensing factor MCM4 (Protein disc proliferation abnormal)	0.91	-	nuc	0	Nucleus (By similarity)				866
Q6GL41 UniProt NPD GO	MCM4_XENTR	DNA replication licensing factor mcm4 (Minichromosome maintenance protein 4)	0.91	-	nuc	0	Nucleus. Associated with chromatin before the formation of nuclei and detaches from it as DNA replic ...	chromatin [ISS] MCM complex [ISS]			863

You are viewing entries 3601 to 3650 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.