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
Q9EPN1 UniProt NPD GO	NBEA_MOUSE	Protein neurobeachin (Lysosomal-trafficking regulator 2)	0.56	-	end	0	Cytoplasm. Membrane; peripheral membrane protein. Associated with pleomorphic tubulovesicular endome ...	cytosol [IDA] endomembrane system [IDA] Golgi trans face [IDA] plasma membrane [IDA] postsynaptic membrane [NAS]			2936
O18734 UniProt NPD GO	PP14A_PIG	Protein phosphatase 1 regulatory subunit 14A (Protein kinase C-potentiated inhibitor protein of 17 k ...	0.56	-	mit	0	Cytoplasm			1K5O	147
O97394 UniProt NPD GO	SDK_DROME	Protein sidekick precursor	0.56	-	mit	1	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [NAS]			2224
P11455 UniProt NPD GO	TERM_DROME	Protein terminus	0.56	-	nuc	0					428
O95486 UniProt NPD GO	SC24A_HUMAN	Protein transport protein Sec24A (SEC24-related protein A) (Fragment)	0.56	-	nuc	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity)	COPII vesicle coat [NAS]	607183		1078
P70600 UniProt NPD GO	FAK2_RAT	Protein tyrosine kinase 2 beta (EC 2.7.10.2) (Focal adhesion kinase 2) (FADK 2) (Proline-rich tyrosi ...	0.56	-	nuc	0	Cytoplasm. Cell membrane. Isoform 2: Cell membrane; cell-matrix junction; focal adhesion. Interactio ...				1009
Q14289 UniProt NPD GO	FAK2_HUMAN	Protein tyrosine kinase 2 beta (EC 2.7.10.2) (Focal adhesion kinase 2) (FADK 2) (Proline-rich tyrosi ...	0.56	-	nuc	0	Cytoplasm. Cell membrane. Interaction with Nephrocystin induces the membrane-association of the kina ...	cytoplasm [TAS]	601212	2FO6	1009
P79702 UniProt NPD GO	FOS_CYPCA	Proto-oncogene protein c-fos (Cellular oncogene fos)	0.56	+	nuc	0	Nucleus				347
P34580 UniProt NPD GO	YN21_CAEEL	Putative ATP-dependent RNA helicase T26G10.1 (EC 3.6.1.-)	0.56	+	end	0					489
Q9VW71 UniProt NPD GO	FAT2_DROME	Putative fat-like cadherin-related tumor suppressor homolog precursor	0.56	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [ISS]			4705
Q12103 UniProt NPD GO	YD109_YEAST	Putative lipase YDL109C (EC 3.1.-.-)	0.56	-	cyt	0					647
P40438 UniProt NPD GO	YIR3_YEAST	Putative membrane glycoprotein YIL173W precursor	0.56	-	end	1		endosome [IDA]			1549
Q9VXL0 UniProt NPD GO	OR13A_DROME	Putative odorant receptor 13a	0.56	-	end	7 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			418
Q08647 UniProt NPD GO	YO7T_YEAST	Putative pseudouridine synthase YOR243C (EC 5.4.99.-)	0.56	-	nuc	0		nucleus [IDA]			676
Q9N4D6 UniProt NPD GO	SEST_CAEEL	Putative sestrin	0.56	-	end	1 *	Nucleus (By similarity)				517
Q8N8Z3 UniProt NPD GO	CJ108_HUMAN	Putative uncharacterized protein C10orf108	0.56	-	nuc	0					221
P25593 UniProt NPD GO	YCG8_YEAST	Putative uncharacterized protein YCL068C	0.56	-	cyt	0					260
Q8BZ36 UniProt NPD GO	RINT1_MOUSE	RAD50-interacting protein 1 (RAD50 interactor 1) (Protein RINT-1)	0.56	-	nuc	0	Cytoplasm (Probable). The SNARE complex localizes to the endoplasmic reticulum (By similarity)	endoplasmic reticulum [ISS]			792
Q969K3 UniProt NPD GO	RNF34_HUMAN	RING finger protein 34 (RING finger protein RIFF) (FYVE-RING finger protein Momo) (Human RING finger ...	0.56	-	exc	0	Nucleus; nucleoplasm; nuclear speckle. Intracellular membrane; peripheral membrane protein		608299		372
O60104 UniProt NPD GO	MED7_SCHPO	RNA polymerase II mediator complex subunit 7	0.56	-	nuc	0	Nucleus (Probable)	mediator complex [IDA]			376
Q62835 UniProt NPD GO	RABE2_RAT	Rab GTPase-binding effector protein 2 (Rabaptin-5beta) (MP13 protein)	0.56	-	nuc	0	Cytoplasm (By similarity). Endosome; early endosome (By similarity)				554
Q5U1Z0 UniProt NPD GO	RBGPR_RAT	Rab3 GTPase-activating protein non-catalytic subunit (Rab3 GTPase-activating protein 150 kDa subunit ...	0.56	-	cyt	0	Cytoplasm. In neurons, it is enriched in the synaptic soluble fraction	soluble fraction [IDA]			1386
Q8VCC8 UniProt NPD GO	RPGF3_MOUSE	Rap guanine nucleotide exchange factor 3 (cAMP-regulated guanine nucleotide exchange factor I) (cAMP ...	0.56	-	nuc	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)				876
Q9EQZ6 UniProt NPD GO	RPGF4_MOUSE	Rap guanine nucleotide exchange factor 4 (cAMP-regulated guanine nucleotide exchange factor II) (cAM ...	0.56	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein (By similarity)	cytosol [IDA]		2BYV	1011
Q5EBH1 UniProt NPD GO	RASF5_MOUSE	Ras association domain-containing family protein 5 (New ras effector 1) (Regulator for cell adhesion ...	0.56	-	nuc	0	Cytoplasm. Isoform 2 is mainly located in the perinuclear region of unstimulated primary T cells; up ...				413
Q62956 UniProt NPD GO	ERBB4_RAT	Receptor tyrosine-protein kinase erbB-4 precursor (EC 2.7.10.1)	0.56	-	nuc	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]			1308
P27864 UniProt NPD GO	RRP1_DROME	Recombination repair protein 1 (DNA-(apurinic or apyrimidinic site) lyase) (EC 4.2.99.18)	0.56	+	nuc	0	Nucleus				679
Q9JIR3 UniProt NPD GO	RIMS3_RAT	Regulating synaptic membrane exocytosis protein 3 (Nim3) (Rab-3-interacting molecule 3) (RIM 3) (RIM ...	0.56	-	nuc	0					307
P57771 UniProt NPD GO	RGS8_HUMAN	Regulator of G-protein signaling 8 (RGS8)	0.56	-	mit	0			607189		180
Q90416 UniProt NPD GO	RXRA_BRARE	Retinoic acid receptor RXR-alpha (Retinoid X receptor alpha)	0.56	+	nuc	0	Nucleus	nucleus [NAS]			441
P10978 UniProt NPD GO	POLX_TOBAC	Retrovirus-related Pol polyprotein from transposon TNT 1-94 [Includes: Protease (EC 3.4.23.-); Rever ...	0.56	-	nuc	0					1328
O94955 UniProt NPD GO	RHBT3_HUMAN	Rho-related BTB domain-containing protein 3	0.56	-	cyt	0			607353		611
O55004 UniProt NPD GO	RNAS4_RAT	Ribonuclease 4 precursor (EC 3.1.27.-) (RNase 4) (RL3)	0.56	-	exc	1 *	Secreted protein				147
Q8VD88 UniProt NPD GO	RNS1D_RAT	Ribonuclease pancreatic delta-type precursor (EC 3.1.27.5) (RNase 1 delta)	0.56	-	exc	0	Secreted protein (By similarity)				150
Q8VD92 UniProt NPD GO	RNS1D_RATEX	Ribonuclease pancreatic delta-type precursor (EC 3.1.27.5) (RNase 1 delta)	0.56	-	nuc	0	Secreted protein (By similarity)				150
Q6DKI1 UniProt NPD GO	RL7L_HUMAN	Ribosomal protein L7-like 1	0.56	+	cyt	0					246
Q8BSK8 UniProt NPD GO	KS6B1_MOUSE	Ribosomal protein S6 kinase beta-1 (EC 2.7.11.1) (Ribosomal protein S6 kinase I) (S6K) (p70-S6K)	0.56	+	mit	0	Cytoplasm. Synaptosome (By similarity). Also found in the soluble synaptosomal fractions (By similar ...				525
Q04225 UniProt NPD GO	RRB1_YEAST	Ribosome assembly protein RRB1	0.56	-	nuc	0	Nucleus	nucleolus [IDA]			511
Q93ZY2 UniProt NPD GO	ROGF1_ARATH	Rop guanine nucleotide exchange factor 1 (RopGEF1) (Kinase partner protein-like) (KPP-like)	0.56	-	nuc	0					548
Q5AGZ9 UniProt NPD GO	RUVB2_CANAL	RuvB-like helicase 2 (EC 3.6.1.-)	0.56	-	mit	0	Nucleus (By similarity)				498
P27011 UniProt NPD GO	SCRY3_OCTDO	S-crystallin 3 (OL3)	0.56	-	nuc	0					215
P55925 UniProt NPD GO	SFAS_SPESI	SF-assemblin	0.56	-	nuc	0					284
Q9QXK9 UniProt NPD GO	SH22A_MOUSE	SH2 domain protein 2A (Lck-associated adapter protein) (Lad) (Rlk/Itk-binding protein) (Ribp)	0.56	-	nuc	0	Cytoplasm. Cell membrane. Redistributed from cytoplasm to the plasma membrane in a T-cell activation ...				374
Q62255 UniProt NPD GO	SALL3_MOUSE	Sal-like protein 3 (Spalt-like protein 3) (MSal) (Fragment)	0.56	-	nuc	0	Nucleus (Probable)				1323
Q7YRN1 UniProt NPD GO	SFRP4_MACMU	Secreted frizzled-related protein 4 precursor (sFRP-4)	0.56	-	exc	0	Secreted protein (By similarity)				346
Q9JLS4 UniProt NPD GO	SFRP4_RAT	Secreted frizzled-related protein 4 precursor (sFRP-4) (Frizzled-related protein) (FRP) (DDC-4 prote ...	0.56	-	exc	0	Secreted protein (By similarity)				348
Q5T4F7 UniProt NPD GO	SFRP5_HUMAN	Secreted frizzled-related protein 5 precursor (sFRP-5) (Secreted apoptosis-related protein 3) (SARP- ...	0.56	-	exc	0	Secreted protein (By similarity)		604158		317
P47868 UniProt NPD GO	SCG3_RAT	Secretogranin-3 precursor (Secretogranin III) (SgIII) (1B1075)	0.56	-	nuc	0	Secreted protein. Neuroendocrine and endocrine secretory granules	cytoplasmic vesicle [TAS]			471
Q90607 UniProt NPD GO	SEM3A_CHICK	Semaphorin-3A precursor (Collapsin-1) (COLL-1)	0.56	+	cyt	0	Secreted protein (By similarity)				772
Q8C1B7 UniProt NPD GO	SEP11_MOUSE	Septin-11	0.56	-	cyt	0					430

You are viewing entries 21601 to 21650 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.