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
P21859 UniProt NPD GO	DIST_TRIFL	Disintegrin triflavin (RGD-containing peptide) (Platelet aggregation activation inhibitor)	0.50	-	nuc	0	Secreted protein			1J2L	70
Q6PKX4 UniProt NPD GO	DOK6_HUMAN	Docking protein 6 (Downstream of tyrosine kinase 6)	0.50	-	mit	0					331
Q8BFV3 UniProt NPD GO	DUS4_MOUSE	Dual specificity protein phosphatase 4 (EC 3.1.3.48) (EC 3.1.3.16)	0.50	-	nuc	0	Nucleus (By similarity)				398
P27619 UniProt NPD GO	DYN_DROME	Dynamin (EC 3.6.5.5) (dDyn) (Protein shibire)	0.50	-	nuc	0	Cytoplasm. Microtubule-associated	plasma membrane [IDA] synapse [IMP]			877
Q8WXU2 UniProt NPD GO	DYXC1_HUMAN	Dyslexia susceptibility 1 candidate gene 1 protein	0.50	-	nuc	0	Nucleus		608706		420
Q863A6 UniProt NPD GO	DYXC1_PANPA	Dyslexia susceptibility 1 candidate gene 1 protein homolog	0.50	-	nuc	0	Nucleus (By similarity)				420
Q863A7 UniProt NPD GO	DYXC1_PANTR	Dyslexia susceptibility 1 candidate gene 1 protein homolog	0.50	-	nuc	0	Nucleus (By similarity)				420
Q863A4 UniProt NPD GO	DYXC1_PONPY	Dyslexia susceptibility 1 candidate gene 1 protein homolog	0.50	-	nuc	0	Nucleus (By similarity)				420
Q14118 UniProt NPD GO	DAG1_HUMAN	Dystroglycan precursor (Dystrophin-associated glycoprotein 1) [Contains: Alpha-dystroglycan (Alpha-D ...	0.50	-	exc	1	Alpha-dystroglycan: Secreted protein; extracellular space. Beta-dystroglycan: Cell membrane; single- ...	actin cytoskeleton [TAS] extracellular matrix (sensu Metazoa) [TAS] integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [NAS]	128239	1EG4	895
P33148 UniProt NPD GO	CADHF_XENLA	EP-cadherin precursor (C-cadherin)	0.50	-	end	1	Membrane; single-pass type I membrane protein			1L3W	880
P28322 UniProt NPD GO	ETV4_MOUSE	ETS translocation variant 4 (Polyomavirus enhancer activator 3) (Protein PEA3)	0.50	-	nuc	0	Nucleus	nucleus [IC]			555
Q00869 UniProt NPD GO	ESYN_FUSEQ	Enniatin synthetase [Includes: N-methylcyclopeptide synthetase (EC 6.3.2.-); S-adenosyl-L-methionine ...	0.50	-	nuc	0					3131
Q9H201 UniProt NPD GO	EPN3_HUMAN	Epsin-3 (EPS-15-interacting protein 3)	0.50	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region. Concentrated in the perinuclear region and associated with ...		607264		632
Q9YHT3 UniProt NPD GO	ESR1_ANOCA	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.50	+	nuc	0	Nucleus				349
P54352 UniProt NPD GO	EAS_DROME	Ethanolamine kinase (EC 2.7.1.82) (EK) (Protein easily shocked)	0.50	-	cyt	0					517
O14681 UniProt NPD GO	EI24_HUMAN	Etoposide-induced protein 2.4 (p53-induced protein 8)	0.50	-	end	6			605170		359
Q63185 UniProt NPD GO	E2AK1_RAT	Eukaryotic translation initiation factor 2-alpha kinase 1 (EC 2.7.11.1) (Heme-regulated eukaryotic i ...	0.50	-	nuc	0		cytoplasm [ISS]			620
Q8CJF9 UniProt NPD GO	I2C3_MOUSE	Eukaryotic translation initiation factor 2C 3 (eIF2C 3) (eIF-2C 3) (Argonaute-3) (Piwi/argonaute fam ...	0.50	-	cyt	0					860
Q16610 UniProt NPD GO	ECM1_HUMAN	Extracellular matrix protein 1 precursor (Secretory component p85)	0.50	-	exc	1 *	Secreted protein; extracellular space	extracellular matrix (sensu Metazoa) [TAS]	602201		540
P28869 UniProt NPD GO	ERK1_CANAL	Extracellular signal-regulated kinase 1 (EC 2.7.11.24) (ERK1) (MAP kinase 1) (MAPK 1)	0.50	-	nuc	0					417
Q9NYY8 UniProt NPD GO	FAKD2_HUMAN	FAST kinase domains-containing protein 2	0.50	-	mit	0					710
O73747 UniProt NPD GO	FRG1_FUGRU	FRG1 protein	0.50	-	nuc	0	Nucleus; nucleoplasm; Cajal body (By similarity). Nucleus; nucleoplasm; nuclear speckle (By similari ...				255
Q9MZ06 UniProt NPD GO	FGFP1_BOVIN	Fibroblast growth factor-binding protein 1 precursor (FGF-binding protein 1) (FGF-BP1) (FGFBP-1) (FG ...	0.50	-	exc	0	Secreted protein; extracellular space (Probable). Extracellular and plasma membrane-associated (By s ...				234
Q06828 UniProt NPD GO	FMOD_HUMAN	Fibromodulin precursor (FM) (Collagen-binding 59 kDa protein) (Keratan sulfate proteoglycan fibromod ...	0.50	-	exc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	600245		376
P47927 UniProt NPD GO	AP2_ARATH	Floral homeotic protein APETALA2	0.50	-	nuc	0	Nucleus (Probable)				432
Q61660 UniProt NPD GO	FOXJ1_MOUSE	Forkhead box protein J1 (Forkhead-related protein FKHL13) (Hepatocyte nuclear factor 3 forkhead homo ...	0.50	-	nuc	0	Nucleus	nucleus [IDA]			421
Q6GLC9 UniProt NPD GO	FMR1_XENTR	Fragile X mental retardation protein 1 homolog (Protein FMR-1) (FMRP) (XtFmrp)	0.50	-	nuc	0	Cytoplasm. Nucleus. Nuclear very early in embryonic development (at two hours post-fertilization), b ...				590
Q9HD64 UniProt NPD GO	GAGD2_HUMAN	G antigen family D member 2 (Protein XAGE-1)	0.50	-	nuc	0			300289		160
P81274 UniProt NPD GO	GPSM2_HUMAN	G-protein signaling modulator 2 (Mosaic protein LGN)	0.50	-	nuc	0	Cytoplasm. Cytoplasm; cell cortex. Localizes in the cytoplasm in the interphase and at cell peripher ...				677
Q3U1Z5 UniProt NPD GO	GPSM3_MOUSE	G-protein signaling modulator 3	0.50	-	nuc	0	Cytoplasm (By similarity)				159
Q40671 UniProt NPD GO	CCNB2_ORYSA	G2/mitotic-specific cyclin-2 (B-like cyclin) (CycOs2)	0.50	-	cyt	0					419
P24870 UniProt NPD GO	CG23_YEAST	G2/mitotic-specific cyclin-3	0.50	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			427
O55007 UniProt NPD GO	GRIPE_RAT	GTPase-activating RapGAP domain-like 1 (GAP-related-interacting partner to E12) (GRIPE) (Tuberin-lik ...	0.50	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Translocated to the nucleus, when associated wit ...				747
Q6XQH0 UniProt NPD GO	G3ST2_MOUSE	Galactose 3-O-sulfotransferase 2 (EC 2.8.2.-) (Gal3ST-2) (Galbeta1-3GalNAc 3'-sulfotransferase 2) (B ...	0.50	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (Probable)				394
Q03077 UniProt NPD GO	GIL2_ENTHI	Galactose-inhibitable lectin 35 kDa subunit precursor	0.50	-	exc	0					288
O88741 UniProt NPD GO	GDAP1_MOUSE	Ganglioside-induced differentiation-associated protein 1 (GDAP1)	0.50	-	nuc	2	Cytoplasm				358
P48144 UniProt NPD GO	PACA_CLAMA	Glucagon family neuropeptides precursor [Contains: Growth hormone-releasing factor (GRF) (Growth hor ...	0.50	-	nuc	0	Secreted protein				195
P48508 UniProt NPD GO	GSH0_RAT	Glutamate--cysteine ligase regulatory subunit (EC 6.3.2.2) (Gamma-glutamylcysteine synthetase) (Gamm ...	0.50	-	nuc	0					274
Q08220 UniProt NPD GO	GSHB_YEAST	Glutathione synthetase (EC 6.3.2.3) (Glutathione synthase) (GSH synthetase) (GSH-S)	0.50	-	nuc	0		intracellular [TAS]		1M0W	491
P23378 UniProt NPD GO	GCSP_HUMAN	Glycine dehydrogenase [decarboxylating], mitochondrial precursor (EC 1.4.4.2) (Glycine decarboxylase ...	0.50	-	mit	0	Mitochondrion		605899		1020
Q06817 UniProt NPD GO	SYG2_YEAST	Glycyl-tRNA synthetase 2 (EC 6.1.1.14) (Glycine--tRNA ligase 2) (GlyRS 2) (GlyRS2)	0.50	-	nuc	0	Cytoplasm	cytoplasm [IDA]			618
Q9H4A6 UniProt NPD GO	GOLP3_HUMAN	Golgi phosphoprotein 3 (Coat-protein GPP34)	0.50	-	mit	0	Cytoplasm. Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane protein				298
Q9CRA5 UniProt NPD GO	GOLP3_MOUSE	Golgi phosphoprotein 3 (Coat-protein GPP34)	0.50	-	mit	0	Cytoplasm (By similarity). Golgi apparatus; Golgi stack; Golgi stack membrane; peripheral membrane p ...	Golgi apparatus [IDA]			298
Q9Z0J6 UniProt NPD GO	GDF15_RAT	Growth/differentiation factor 15 precursor (GDF-15)	0.50	-	nuc	1 *	Secreted protein (Probable)				303
P43029 UniProt NPD GO	GDF7_MOUSE	Growth/differentiation factor 7 precursor (GDF-7)	0.50	+	mit	0	Secreted protein (By similarity)	extracellular region [IDA]			461
Q05337 UniProt NPD GO	GNAF_DROME	Guanine nucleotide-binding protein G(f) subunit alpha	0.50	-	mit	0					399
Q05425 UniProt NPD GO	GPA1_NEUCR	Guanine nucleotide-binding protein alpha-1 subunit (GP1-alpha)	0.50	-	cyt	0					353
P87033 UniProt NPD GO	GPA2_USTMA	Guanine nucleotide-binding protein alpha-2 subunit	0.50	-	cyt	0					356
P61570 UniProt NPD GO	ENK17_HUMAN	HERV-K_11q22.1 provirus ancestral Env polyprotein precursor (Envelope polyprotein) [Contains: Surfac ...	0.50	-	end	2					661
P61582 UniProt NPD GO	NP12_HUMAN	HERV-K_1q22 provirus Np9 protein (HERV-K102 Np9 protein) (HERV-K(III) Np9 protein)	0.50	-	nuc	0	Nucleus (By similarity). When overexpressed (By similarity)				75

You are viewing entries 24951 to 25000 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.