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
O57457 UniProt NPD GO	E41L4_BRARE	Band 4.1-like protein 4 (Protein Nbl4)	0.98	+	nuc	0					619
Q9HCS5 UniProt NPD GO	E41LA_HUMAN	Band 4.1-like protein 4A (Protein NBL4)	0.98	+	nuc	0					598
Q9NYF8 UniProt NPD GO	BCLF1_HUMAN	Bcl-2-associated transcription factor 1 (Btf)	0.98	-	mit	0	Cytoplasm. Nucleus	nucleus [NAS]			920
Q8K019 UniProt NPD GO	BCLF1_MOUSE	Bcl-2-associated transcription factor 1 (Btf)	0.98	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				919
Q9DEY9 UniProt NPD GO	BLM_XENLA	Bloom syndrome protein homolog (EC 3.6.1.-) (xBLM)	0.98	+	nuc	0	Nucleus (By similarity)				1364
P51587 UniProt NPD GO	BRCA2_HUMAN	Breast cancer type 2 susceptibility protein (Fanconi anemia group D1 protein)	0.98	+	nuc	0		extracellular space [TAS] nucleus [IDA] secretory granule [TAS]	114480	1N0W	3418
Q91YE5 UniProt NPD GO	BAZ2A_MOUSE	Bromodomain adjacent to zinc finger domain 2A (Transcription termination factor I-interacting protei ...	0.98	+	nuc	0	Nucleus; nucleolus. Colocalizes with the basal RNA polymerase I transcription factor UBF in the nucl ...	nucleolus organizer complex [ISS]			1850
Q9DE13 UniProt NPD GO	BAZ2B_CHICK	Bromodomain adjacent to zinc finger domain 2B (Extracellular matrix protein F22)	0.98	+	nuc	0					2130
P35817 UniProt NPD GO	BDF1_YEAST	Bromodomain-containing factor 1	0.98	+	nuc	0	Nucleus	nuclear chromatin [IDA] nucleus [IDA]			686
Q9NPI1 UniProt NPD GO	BRD7_HUMAN	Bromodomain-containing protein 7 (75 kDa bromodomain protein) (Protein CELTIX-1)	0.98	+	nuc	0	Isoform 2: Nucleus	nucleus [IDA]			651
Q91ZU6 UniProt NPD GO	BPA1_MOUSE	Bullous pemphigoid antigen 1, isoforms 1/2/3/4 (BPA) (Hemidesmosomal plaque protein) (Dystonia muscu ...	0.98	+	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS] hemidesmosome [IDA]			7389
O94833 UniProt NPD GO	BPAEA_HUMAN	Bullous pemphigoid antigen 1, isoforms 6/9/10 (Trabeculin-beta) (Bullous pemphigoid antigen) (BPA) ( ...	0.98	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	600088		5171
Q9WUF3 UniProt NPD GO	C8AP2_MOUSE	CASP8-associated protein 2 (FLICE-associated huge protein)	0.98	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	cytoplasm [ISS] nucleus [ISS]			1962
P43634 UniProt NPD GO	CHA4_YEAST	CHA4 activatory protein	0.98	+	nuc	0	Nucleus (Probable)	nucleus [IPI]			648
Q02100 UniProt NPD GO	SKO1_YEAST	CRE-binding bZIP protein SKO1	0.98	+	nuc	0	Nucleus	cytosol [IDA] nucleus [IDA]			647
Q8C5W0 UniProt NPD GO	CLMN_MOUSE	Calmin	0.98	-	nuc	1	Isoform 1, isoform 4: Membrane; single-pass type IV membrane protein (Potential). Isoforms 1 and iso ...	cytoplasm [IDA]			1052
P22204 UniProt NPD GO	DBF2_YEAST	Cell cycle protein kinase DBF2 (EC 2.7.11.1)	0.98	+	nuc	0		bud neck [IDA] spindle pole body [IDA]			572
Q10059 UniProt NPD GO	CDC12_SCHPO	Cell division control protein 12	0.98	-	nuc	0	Nucleus. Nuclear, and septum	contractile ring (sensu Fungi) [TAS]			1841
Q8CH18 UniProt NPD GO	CCAR1_MOUSE	Cell division cycle and apoptosis regulator protein 1 (Cell cycle and apoptosis regulatory protein 1 ...	0.98	+	nuc	0	Cytoplasm; perinuclear region (By similarity)				1146
Q8BZ05 UniProt NPD GO	CEND1_MOUSE	Centaurin-delta 1 (Cnt-d1)	0.98	-	nuc	0	Cytoplasm (By similarity)				1703
Q8BXK8 UniProt NPD GO	CENG2_MOUSE	Centaurin-gamma 2 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.98	-	nuc	0	Cytoplasm (By similarity). Associates with the endocytic compartment (By similarity)				857
Q9UPQ3 UniProt NPD GO	CENG2_HUMAN	Centaurin-gamma 2 (ARF-GAP with GTP-binding protein-like, ankyrin repeat and pleckstrin homology dom ...	0.98	-	nuc	0	Cytoplasm. Associates with the endocytic compartment		608651		857
Q02224 UniProt NPD GO	CENPE_HUMAN	Centromeric protein E (CENP-E)	0.98	-	nuc	0	Kinetochore. Spindle. Associates with kinetochores during congression, relocates to the spindle midz ...	chromosome, pericentric region [IDA] nucleus [IMP]	117143	1T5C	2663
P46307 UniProt NPD GO	RR3_CHLEU	Chloroplast 30S ribosomal protein S3	0.98	+	nuc	0	Plastid; chloroplast				800
P13259 UniProt NPD GO	PCY1_YEAST	Choline-phosphate cytidylyltransferase (EC 2.7.7.15) (Phosphorylcholine transferase) (CTP:phosphocho ...	0.98	+	mit	0	Membrane. Most of its activity is membrane-associated	Golgi apparatus [TAS] nuclear envelope [IDA] nucleus [IDA]			424
Q5A6Q7 UniProt NPD GO	EAF7_CANAL	Chromatin modification-related protein EAF7	0.98	-	nuc	0	Nucleus (By similarity)				445
Q4IB96 UniProt NPD GO	VID21_GIBZE	Chromatin modification-related protein VID21	0.98	-	nuc	0	Nucleus (Probable)				1629
Q06488 UniProt NPD GO	RSC2_YEAST	Chromatin structure remodeling complex protein RSC2 (Remodel the structure of chromatin complex subu ...	0.98	-	nuc	0	Nucleus. Localizes to centromeric and flanking chromatin. Association with these loci is dependent o ...	RSC complex [IDA]			889
Q8TD26 UniProt NPD GO	CHD6_HUMAN	Chromodomain-helicase-DNA-binding protein 6 (EC 3.6.1.-) (ATP-dependent helicase CHD6) (CHD-6) (Radi ...	0.98	+	nuc	0	Nucleus (Probable)	nucleus [NAS]			2715
O95239 UniProt NPD GO	KIF4A_HUMAN	Chromosome-associated kinesin KIF4A (Chromokinesin)	0.98	+	nuc	0	Nucleus; nuclear matrix. Not present in the nucleolus. In early mitosis, associated with the mitotic ...	cytoplasm [TAS] spindle microtubule [TAS]	300521		1232
Q9P2M7 UniProt NPD GO	CING_HUMAN	Cingulin	0.98	-	nuc	0		tight junction [NAS]	609473		1197
P59242 UniProt NPD GO	CING_MOUSE	Cingulin	0.98	-	nuc	0		tight junction [NAS]			1191
O14578 UniProt NPD GO	CTRO_HUMAN	Citron Rho-interacting kinase (EC 2.7.11.1) (CRIK) (Rho-interacting, serine/threonine-protein kinase ...	0.98	-	nuc	0	Cytoplasm (By similarity)	intracellular [ISS]	605629		2027
Q99M76 UniProt NPD GO	STAG3_RAT	Cohesin subunit SA-3 (Stromal antigen 3) (Stromalin 3) (SCC3 homolog 3)	0.98	-	mit	0	Nucleus (By similarity). Associates with chromatin. In prophase I stage of meiosis, it is found alon ...	nucleus [TAS] synaptonemal complex [TAS]			1256
Q2M243 UniProt NPD GO	CCD27_HUMAN	Coiled-coil domain-containing protein 27	0.98	-	nuc	0					656
Q6PG04 UniProt NPD GO	CCD82_MOUSE	Coiled-coil domain-containing protein 82	0.98	+	nuc	0					518
O94679 UniProt NPD GO	CND1_SCHPO	Condensin complex subunit 1 (p128) (XCAP-D2 homolog)	0.98	-	end	0	Nucleus. Cytoplasm. In interphase cells, the majority of the condensin complex is found in the cytop ...	condensin complex [IDA] cytoplasm [IDA] nucleus [IDA]			1158
Q6CPQ8 UniProt NPD GO	MUS81_KLULA	Crossover junction endonuclease MUS81 (EC 3.1.22.-)	0.98	+	nuc	0	Nucleus (By similarity)				614
O76039 UniProt NPD GO	CDKL5_HUMAN	Cyclin-dependent kinase-like 5 (EC 2.7.11.22) (Serine/threonine-protein kinase 9)	0.98	-	nuc	0			312750		1030
Q24K09 UniProt NPD GO	DNMT1_BOVIN	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Dnmt1)	0.98	+	nuc	0	Nucleus (By similarity)				1611
P13864 UniProt NPD GO	DNMT1_MOUSE	DNA (cytosine-5)-methyltransferase 1 (EC 2.1.1.37) (Dnmt1) (DNA methyltransferase MmuI) (DNA MTase M ...	0.98	-	nuc	0	Nucleus. Cytoplasm. It is nucleoplasmic through most of the cell cycle and associates with replicati ...	heterochromatin [IDA] nucleus [IDA] replication fork [IDA]			1620
Q03468 UniProt NPD GO	ERCC6_HUMAN	DNA excision repair protein ERCC-6 (EC 3.6.1.-) (ATP-dependent helicase ERCC6) (Cockayne syndrome pr ...	0.98	+	nuc	0	Nucleus (Probable)		609413		1493
P28040 UniProt NPD GO	DPOA_SCHPO	DNA polymerase alpha catalytic subunit (EC 2.7.7.7) (DNA polymerase I)	0.98	+	nuc	0	Nucleus	alpha DNA polymerase:primase complex [TAS]			1405
O75417 UniProt NPD GO	DPOLQ_HUMAN	DNA polymerase theta (EC 2.7.7.7) (DNA polymerase eta)	0.98	-	exc	0		nucleoplasm [TAS]	604419		1762
P07271 UniProt NPD GO	PIF1_YEAST	DNA repair and recombination protein PIF1, mitochondrial precursor (EC 3.6.1.-) (ATP-dependent helic ...	0.98	-	mit	0	Mitochondrion	mitochondrion [IDA] nucleus [IC]			857
P06777 UniProt NPD GO	RAD1_YEAST	DNA repair protein RAD1	0.98	-	nuc	0	Nucleus	nucleotide-excision repair factor 1 complex [IPI] nucleus [IDA]			1100
P33301 UniProt NPD GO	XRS2_YEAST	DNA repair protein XRS2	0.98	-	nuc	0		Mre11 complex [IPI] nucleus [IDA]			854
Q4WVM1 UniProt NPD GO	RAD5_ASPFU	DNA repair protein rad5 (EC 3.6.1.-)	0.98	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				1245
P36607 UniProt NPD GO	RAD5_SCHPO	DNA repair protein rad5 (EC 3.6.1.-)	0.98	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			1133
P38859 UniProt NPD GO	DNA2_YEAST	DNA replication ATP-dependent helicase DNA2 (EC 3.6.1.-)	0.98	-	nuc	0		nuclear chromosome, telomeric region [IDA] nucleus [TAS]			1522

You are viewing entries 551 to 600 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.