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
Q8N8S7 UniProt NPD GO	ENAH_HUMAN	Protein enabled homolog	0.77	-	nuc	0	Cytoplasm. Targeted to the leading edge of lamellipodia and filopodia by MRL family members. Colocal ...		609061		591
O54714 UniProt NPD GO	PIAS3_MOUSE	Protein inhibitor of activated STAT protein 3	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Mostly	nucleus [IDA]			628
O70260 UniProt NPD GO	PIAS3_RAT	Protein inhibitor of activated STAT protein 3 (Potassium channel-associated protein) (KChAP)	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Mostly (By similarity)				628
Q8C5D8 UniProt NPD GO	PIAS2_MOUSE	Protein inhibitor of activated STAT2 (Protein inhibitor of activated STAT x) (Msx-interacting zinc f ...	0.77	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes at least partially with promyelocytic leukemia nu ...				621
P10383 UniProt NPD GO	OTU_DROME	Protein ovarian tumor locus	0.77	-	nuc	0	Cytoplasm				853
Q923M0 UniProt NPD GO	PP16A_MOUSE	Protein phosphatase 1 regulatory subunit 16A (Myosin phosphatase targeting subunit 3)	0.77	-	nuc	0	Cell membrane; lipid-anchor (By similarity)	cytosol [TAS]			524
Q60ZN5 UniProt NPD GO	SDK_CAEBR	Protein sidekick homolog precursor (Neuronal IgCAM protein 4)	0.77	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				2322
P92189 UniProt NPD GO	STIL_DROME	Protein stand still	0.77	-	nuc	0	Nucleus. Associates with decondensed chromatin, including sites of active transcription	nuclear chromatin [IDA]			321
Q9P7V5 UniProt NPD GO	SEC72_SCHPO	Protein transport protein sec72	0.77	-	cyt	0					1822
P39736 UniProt NPD GO	BX42_DROME	Puff-specific protein Bx42	0.77	-	nuc	0	Nucleus	nuclear chromatin [NAS]			547
Q80VY9 UniProt NPD GO	DHX33_MOUSE	Putative ATP-dependent RNA helicase DHX33 (EC 3.6.1.-) (DEAH box protein 33)	0.77	-	mit	0	Nucleus; nucleolus (By similarity)				698
Q9FJ10 UniProt NPD GO	GAT23_ARATH	Putative GATA transcription factor 23	0.77	-	nuc	0	Nucleus (Probable)				139
Q9SL78 UniProt NPD GO	ATL2D_ARATH	Putative RING-H2 finger protein ATL2D precursor (RING-H2 finger protein ATL12)	0.77	-	mit	2 *					390
Q9VGC3 UniProt NPD GO	COG1_DROME	Putative conserved oligomeric Golgi complex component 1	0.77	-	nuc	0	Golgi apparatus (By similarity)	Golgi transport complex [ISS]			886
Q9SU64 UniProt NPD GO	CNG16_ARATH	Putative cyclic nucleotide-gated ion channel 16 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.77	+	mit	4	Cell membrane; multi-pass membrane protein (Potential)				705
Q9LEQ3 UniProt NPD GO	CNG18_ARATH	Putative cyclic nucleotide-gated ion channel 18 (Cyclic nucleotide-and calmodulin-regulated ion chan ...	0.77	+	end	7 *	Cell membrane; multi-pass membrane protein (Potential)				706
Q20875 UniProt NPD GO	DHX15_CAEEL	Putative pre-mRNA-splicing factor ATP-dependent RNA helicase F56D2.6 (EC 3.6.1.-)	0.77	-	nuc	0	Nucleus (By similarity)				739
Q09922 UniProt NPD GO	YAKB_SCHPO	Putative transcriptional regulatory protein C1F7.11c	0.77	-	nuc	0	Nucleus (Probable)				782
Q9NV58 UniProt NPD GO	RNF19_HUMAN	RING finger protein 19 (Dorfin) (Double ring-finger protein) (p38 protein)	0.77	+	mit	2	Expressed primarily in the XY body of pachytene spermatocytes and in the centrosome of somatic and g ...	centrosome [TAS]	607119		838
Q9JIT1 UniProt NPD GO	RNF32_MOUSE	RING finger protein 32 (Limb region protein 2)	0.77	-	mit	0	Cytoplasm (By similarity)				368
Q9P7H2 UniProt NPD GO	REXO3_SCHPO	RNA exonuclease 3 (EC 3.1.-.-)	0.77	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				540
Q6PAQ4 UniProt NPD GO	REXO4_MOUSE	RNA exonuclease 4 (EC 3.1.-.-) (Exonuclease XPMC2) (Prevents mitotic catastrophe 2 protein homolog)	0.77	+	nuc	0	Nucleus; nucleolus (By similarity)				432
Q9UJ41 UniProt NPD GO	RABX5_HUMAN	Rab5 GDP/GTP exchange factor (Rabaptin 5-associated exchange factor for Rab5) (Rabex-5)	0.77	-	nuc	0	Cytoplasm. Endosome; early endosome. Endosome; recycling endosome		609700	1TXU	708
P26043 UniProt NPD GO	RADI_MOUSE	Radixin (ESP10)	0.77	-	nuc	0	Highly concentrated in the undercoat of the cell-to-cell adherens junction and the cleavage furrow i ...	microvillus [IDA]		2D2Q	583
Q5TJE5 UniProt NPD GO	RGL2_CANFA	Ral guanine nucleotide dissociation stimulator-like 2 (RAS-associated protein RAB2L)	0.77	+	nuc	0					780
Q6ZTQ3 UniProt NPD GO	RASF6_HUMAN	Ras association domain-containing protein 6	0.77	-	nuc	0					369
Q5PQP2 UniProt NPD GO	RCAS1_RAT	Receptor-binding cancer antigen expressed on SiSo cells (Estrogen receptor-binding fragment-associat ...	0.77	-	mit	0	Golgi apparatus; Golgi membrane; single-pass type III membrane protein. Predominantly located in the ...				213
P23470 UniProt NPD GO	PTPRG_HUMAN	Receptor-type tyrosine-protein phosphatase gamma precursor (EC 3.1.3.48) (Protein-tyrosine phosphata ...	0.77	-	nuc	1 *	Membrane; single-pass type I membrane protein (Probable)	integral to plasma membrane [TAS]	176886		1445
Q9CQE5 UniProt NPD GO	RGS10_MOUSE	Regulator of G-protein signaling 10 (RGS10)	0.77	-	mit	0					181
P49809 UniProt NPD GO	EGL10_CAEEL	Regulator of G-protein signaling egl-10 (Egg-laying defective protein 10)	0.77	-	nuc	0		cytoplasm [IDA] neuron projection [IDA]			555
P22022 UniProt NPD GO	WETA_EMENI	Regulatory protein wetA	0.77	-	nuc	0					555
P16423 UniProt NPD GO	POLR_DROME	Retrovirus-related Pol polyprotein from type-2 retrotransposable element R2DM (Retrovirus-related Po ...	0.77	+	nuc	0					1057
O75676 UniProt NPD GO	KS6A4_HUMAN	Ribosomal protein S6 kinase alpha-4 (EC 2.7.11.1) (Nuclear mitogen-and stress-activated protein kina ...	0.77	-	cyt	0	Nucleus	nucleus [IDA]	603606		772
Q9P2E9 UniProt NPD GO	RRBP1_HUMAN	Ribosome-binding protein 1 (Ribosome receptor protein) (180 kDa ribosome receptor homolog) (ES/130-r ...	0.77	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type III membrane protein (By sim ...	endoplasmic reticulum [NAS] integral to endoplasmic reticulum membrane [NAS] ribosome [TAS]	601418		1410
Q8C310 UniProt NPD GO	ROBO4_MOUSE	Roundabout homolog 4 precursor	0.77	-	exc	0		external side of plasma membrane [IDA] integral to membrane [TAS]			1012
Q92736 UniProt NPD GO	RYR2_HUMAN	Ryanodine receptor 2 (Cardiac muscle-type ryanodine receptor) (RyR2) (RYR-2) (Cardiac muscle ryanodi ...	0.77	+	end	6	Membrane; multi-pass membrane protein (Probable)	plasma membrane [TAS]	604772		4967
P32943 UniProt NPD GO	CGS6_YEAST	S-phase entry cyclin-6	0.77	-	nuc	0					380
Q61120 UniProt NPD GO	SHC3_MOUSE	SHC-transforming protein 3 (SH2 domain protein C3) (Src homology 2 domain-containing-transforming pr ...	0.77	-	nuc	0					474
Q9Z104 UniProt NPD GO	HM20B_MOUSE	SWI/SNF-related matrix-associated actin-dependent regulator of chromatin subfamily E member 1-relate ...	0.77	+	nuc	0	Nucleus (By similarity). Localized to condensed chromosomes in mitosis in conjunction with BRCA2 (By ...	nucleus [NAS]		2CRJ	317
Q8BJS4 UniProt NPD GO	UN84B_MOUSE	Sad1/unc-84-like protein 2	0.77	-	mit	1	Nucleus; nuclear membrane; single-pass membrane protein (By similarity). Endosome; endosomal membran ...				699
P51142 UniProt NPD GO	DVL2_XENLA	Segment polarity protein dishevelled homolog DVL-2 (Dishevelled-2) (DSH homolog 2) (Xdsh)	0.77	+	nuc	0	Cytoplasm (Potential)			2F0A	736
P06601 UniProt NPD GO	PRD_DROME	Segmentation protein paired	0.77	+	nuc	0	Nucleus	nucleus [NAS]		1PDN	613
P49908 UniProt NPD GO	SEPP1_HUMAN	Selenoprotein P precursor (SeP)	0.77	-	exc	0	Secreted protein	extracellular region [NAS]	601484		381
Q7ZUQ3 UniProt NPD GO	STK3_BRARE	Serine/threonine-protein kinase 3 (EC 2.7.11.1)	0.77	-	nuc	0	Cytoplasm; the caspase-cleaved form cycles between nucleus and cytoplasm (By similarity)				492
Q5E9L6 UniProt NPD GO	STK4_BOVIN	Serine/threonine-protein kinase 4 (EC 2.7.11.1) (STE20-like kinase MST1) (MST-1) (Mammalian STE20-li ...	0.77	-	nuc	0	Cytoplasm. The caspase-cleaved form cycles between the nucleus and cytoplasm (By similarity)				487
Q2TA06 UniProt NPD GO	STK6_BOVIN	Serine/threonine-protein kinase 6 (EC 2.7.11.1) (Aurora-A)	0.77	-	nuc	0	Centrosome (By similarity). Spindle (By similarity). Localizes on centrosomes in interphase cells an ...				402
P87248 UniProt NPD GO	ATG1_COLLN	Serine/threonine-protein kinase ATG1 (EC 2.7.11.1) (Autophagy-related protein 1) (Colletotrichum lin ...	0.77	-	nuc	0	Cytoplasm (By similarity)				675
P53894 UniProt NPD GO	CBK1_YEAST	Serine/threonine-protein kinase CBK1 (EC 2.7.11.1) (Cell wall biosynthesis kinase)	0.77	-	nuc	0		bud neck [IDA] cytoplasm [IDA] mating projection tip [TAS] nucleus [IDA]			756
Q7KZI7 UniProt NPD GO	MARK2_HUMAN	Serine/threonine-protein kinase MARK2 (EC 2.7.11.1) (MAP/microtubule affinity-regulating kinase 2) ( ...	0.77	-	nuc	0	Cell membrane; peripheral membrane protein. Phosphorylated by PRKCZ in polarized epithelial cells, r ...	membrane [IMP]	600526		788
O35831 UniProt NPD GO	PCTK2_RAT	Serine/threonine-protein kinase PCTAIRE-2 (EC 2.7.11.22) (PCTAIRE-motif protein kinase 2)	0.77	-	mit	0					523

You are viewing entries 10551 to 10600 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.