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
P11638 UniProt NPD GO	QA1F_NEUCR	Quinic acid utilization activator	0.81	-	end	0	Nucleus				816
P42073 UniProt NPD GO	REF2_YEAST	RNA end formation protein 2	0.81	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI] nucleus [IDA]			533
Q9GZR2 UniProt NPD GO	REXO4_HUMAN	RNA exonuclease 4 (EC 3.1.-.-) (Exonuclease XPMC2) (hPMC2) (Prevents mitotic catastrophe 2 protein h ...	0.81	-	nuc	0	Nucleus; nucleolus	nucleus [NAS]	602930		422
P21329 UniProt NPD GO	RTJK_DROFU	RNA-directed DNA polymerase from mobile element jockey (EC 2.7.7.49) (Reverse transcriptase)	0.81	+	nuc	0					916
O35551 UniProt NPD GO	RABE1_MOUSE	Rab GTPase-binding effector protein 1 (Rabaptin-5) (Rabaptin-5alpha)	0.81	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity). Endosome; recycling endosome (B ...	endosome [IDA]			862
Q6NUV0 UniProt NPD GO	RB3GP_BRARE	Rab3 GTPase-activating protein catalytic subunit	0.81	-	nuc	0	Cytoplasm (Probable)				969
Q9PU45 UniProt NPD GO	RADI_CHICK	Radixin	0.81	-	nuc	0					583
P35241 UniProt NPD GO	RADI_HUMAN	Radixin	0.81	-	nuc	0	Highly concentrated in the undercoat of the cell-to-cell adherens junction and the cleavage furrow i ...		179410		583
Q8NFH8 UniProt NPD GO	REPS2_HUMAN	RalBP1-associated Eps domain-containing protein 2 (RalBP1-interacting protein 2) (Partner of RalBP1) ...	0.81	-	nuc	0	Cytoplasm		300317	1IQ3	660
P47736 UniProt NPD GO	RGP2_HUMAN	Rap1 GTPase-activating protein 1 (Rap1GAP)	0.81	-	nuc	0	Golgi apparatus; Golgi membrane; peripheral membrane protein		600278	1SRQ	663
Q67E01 UniProt NPD GO	RIPK5_XENLA	Receptor-interacting serine/threonine-protein kinase 5 (EC 2.7.11.1) (Dusty protein kinase) (Dusty P ...	0.81	+	nuc	0	Cytoplasm (Probable)				916
Q2KHW7 UniProt NPD GO	RGS10_BOVIN	Regulator of G-protein signaling 10 (RGS10)	0.81	-	mit	0					181
O08774 UniProt NPD GO	RGS12_RAT	Regulator of G-protein signaling 12 (RGS12)	0.81	-	nuc	0	Nucleus (By similarity)				1387
Q8WQC0 UniProt NPD GO	RGS7_CAEEL	Regulator of G-protein signaling rgs-7 (Regulator of G-protein signaling c2) (Protein C2-RGS)	0.81	-	nuc	0					819
Q90966 UniProt NPD GO	RARA_CHICK	Retinoic acid receptor alpha (RAR-alpha)	0.81	+	nuc	0	Nucleus				460
Q91X46 UniProt NPD GO	ARHG3_MOUSE	Rho guanine nucleotide exchange factor 3	0.81	-	nuc	0	Cytoplasm				524
Q5XI28 UniProt NPD GO	RAVR1_RAT	Ribonucleoprotein PTB-binding 1 (Protein raver-1)	0.81	-	nuc	0	Nucleus (By similarity). Cytoplasm (By similarity). Nuclear, in perinucleolar structures. Shuttles b ...				748
Q6NZC7 UniProt NPD GO	S23IP_MOUSE	SEC23-interacting protein	0.81	-	nuc	0					998
Q9Y566 UniProt NPD GO	SHAN1_HUMAN	SH3 and multiple ankyrin repeat domains protein 1 (Shank1) (Somatostatin receptor-interacting protei ...	0.81	-	nuc	0	Cytoplasm (By similarity). Postsynaptic density of neuronal cells (By similarity)	dendrite [NAS] intracellular [NAS] membrane fraction [IEP]	604999		2161
Q8R550 UniProt NPD GO	SH3K1_MOUSE	SH3-domain kinase-binding protein 1 (SH3-containing, expressed in tumorigenic astrocytes) (Regulator ...	0.81	-	nuc	0	Membrane; peripheral membrane protein (By similarity). Nucleus (By similarity)			1WI7	709
P43267 UniProt NPD GO	SOX15_MOUSE	SOX-15 protein	0.81	+	nuc	0	Nucleus (Potential)	cytoplasm [IDA]			231
O60248 UniProt NPD GO	SOX15_HUMAN	SOX-15 protein (SOX-20 protein) (SOX-12 protein)	0.81	+	nuc	0	Nucleus (Potential)	nucleus [NAS]	601297		233
Q9H3U7 UniProt NPD GO	SMOC2_HUMAN	SPARC-related modular calcium-binding protein 2 precursor (Secreted modular calcium-binding protein ...	0.81	-	exc	0	Secreted protein (Probable)		607223		446
Q6CKH1 UniProt NPD GO	SWC5_KLULA	SWR1-complex protein 5	0.81	-	nuc	0	Nucleus (By similarity)				315
O88453 UniProt NPD GO	SAFB1_RAT	Scaffold attachment factor B (Scaffold attachment factor B1) (SAF-B)	0.81	-	nuc	0	Nucleus	nucleus [IDA]			931
Q5XPK0 UniProt NPD GO	SCARL_ARATH	Scar-like domain-containing protein	0.81	+	nuc	0					2028
P23389 UniProt NPD GO	SCG1_BOVIN	Secretogranin-1 precursor (Secretogranin I) (SgI) (Chromogranin B) (CgB) [Contains: GAWK peptide; Pe ...	0.81	-	exc	0	Neuroendocrine and endocrine secretory granules. Found to be membrane bound inside the secretory ves ...				646
Q9P0V9 UniProt NPD GO	SEP10_HUMAN	Septin-10	0.81	-	nuc	0	Cytoplasm. Nucleus				517
Q91XS8 UniProt NPD GO	ST17B_RAT	Serine/threonine-protein kinase 17B (EC 2.7.11.1) (DAP kinase-related apoptosis-inducing protein kin ...	0.81	-	mit	0	Nucleus	actin cytoskeleton [IMP] nucleus [IEP]			371
Q6IP06 UniProt NPD GO	STK3_XENLA	Serine/threonine-protein kinase 3 (EC 2.7.11.1)	0.81	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)				493
Q6PA14 UniProt NPD GO	STK4_XENLA	Serine/threonine-protein kinase 4 (EC 2.7.11.1)	0.81	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm (By similarity)				485
O14427 UniProt NPD GO	CLA4_CANAL	Serine/threonine-protein kinase CLA4 (EC 2.7.11.1)	0.81	-	nuc	0					971
Q05512 UniProt NPD GO	MARK2_MOUSE	Serine/threonine-protein kinase MARK2 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 2) ( ...	0.81	-	nuc	0	Cell membrane; peripheral membrane protein (By similarity). Phosphorylated by PRKCZ in polarized epi ...	basal cortex [IDA] membrane [ISS] nucleus [IDA]			776
Q9H0K1 UniProt NPD GO	SN1L2_HUMAN	Serine/threonine-protein kinase SNF1-like kinase 2 (EC 2.7.11.1) (Qin-induced kinase)	0.81	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]	608973		926
P38903 UniProt NPD GO	2A5D_YEAST	Serine/threonine-protein phosphatase 2A 56 kDa regulatory subunit delta isoform (PP2A, B subunit, B' ...	0.81	-	nuc	0	Cytoplasm. Nucleus	bud neck [IDA] cytoplasm [IDA] nucleus [IDA] protein phosphatase type 2A complex [TAS] spindle pole body [IDA]			757
Q864Q3 UniProt NPD GO	SRY_DELLE	Sex-determining region Y protein (Testis-determining factor)	0.81	+	nuc	0	Nucleus				201
Q864P7 UniProt NPD GO	SRY_GRAGR	Sex-determining region Y protein (Testis-determining factor)	0.81	+	nuc	0	Nucleus				201
Q864P5 UniProt NPD GO	SRY_ORCOR	Sex-determining region Y protein (Testis-determining factor)	0.81	+	nuc	0	Nucleus				201
Q9UBN4 UniProt NPD GO	TRPC4_HUMAN	Short transient receptor potential channel 4 (TrpC4) (trp-related protein 4) (hTrp-4) (hTrp4)	0.81	-	end	8	Membrane; multi-pass membrane protein (Probable)		603651		977
P42224 UniProt NPD GO	STAT1_HUMAN	Signal transducer and activator of transcription 1-alpha/beta (Transcription factor ISGF-3 component ...	0.81	-	cyt	0	Cytoplasm. Nucleus. Translocated into the nucleus upon activation by IFN-alpha/beta	cytoplasm [TAS] nucleus [TAS]	209950	1YVL	750
P61635 UniProt NPD GO	STAT3_BOVIN	Signal transducer and activator of transcription 3	0.81	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated into the nucleus in response to pho ...				770
Q96FS4 UniProt NPD GO	SIPA1_HUMAN	Signal-induced proliferation-associated protein 1 (Sipa-1) (GTPase-activating protein Spa-1) (p130 S ...	0.81	-	nuc	0	Nucleus. Cytoplasm; perinuclear region. Mostly localized in the perinuclear membraneous region	nucleus [IC]	602180		1042
Q80TR4 UniProt NPD GO	SLIT1_MOUSE	Slit homolog 1 protein precursor (Slit-1)	0.81	-	nuc	0	Secreted protein (By similarity)	extracellular space [IDA]			1531
Q96FF9 UniProt NPD GO	CDCA5_HUMAN	Sororin (Cell division cycle-associated protein 5) (p35)	0.81	-	mit	0	Nucleus. Nuclear in interphase cells. During mitosis, it localizes throughout the cytoplasm	cytoplasm [ISS] nucleus [ISS]	609374		252
Q5MJ70 UniProt NPD GO	SPDYA_HUMAN	Speedy protein A (Speedy-1) (Spy1) (Rapid inducer of G2/M progression in oocytes A) (RINGO A) (hSpy/ ...	0.81	-	nuc	0	Nucleus	nucleus [IDA]			313
P15343 UniProt NPD GO	HSP3_HORSE	Sperm histone P2b (Protamine 2b) (ST2b)	0.81	+	nuc	0	Nucleus				58
Q9GLP9 UniProt NPD GO	HSP1_AEPRU	Sperm protamine P1	0.81	+	nuc	0	Nucleus				60
P35302 UniProt NPD GO	HSP1_ALOSE	Sperm protamine P1	0.81	+	mit	0	Nucleus				51
Q71V18 UniProt NPD GO	HSP1_ANTBE	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62
Q71V20 UniProt NPD GO	HSP1_ANTFL	Sperm protamine P1	0.81	+	nuc	0	Nucleus (By similarity)				62

You are viewing entries 8551 to 8600 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.