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
P22389 UniProt NPD GO	EDN2_MOUSE	Endothelin-2 precursor (ET-2) (Preproendothelin-2) (PPET2) (Vasoactive intestinal contractor) (VIC)	0.76	-	exc	0	Secreted protein				175
Q99K30 UniProt NPD GO	ES8L2_MOUSE	Epidermal growth factor receptor kinase substrate 8-like protein 2 (Epidermal growth factor receptor ...	0.76	+	nuc	0	Cytoplasm (By similarity)				729
P80304 UniProt NPD GO	SPE_SEPOF	Epididymal sperm protein E	0.76	-	mit	0	Nucleus				51
P19785 UniProt NPD GO	ESR1_MOUSE	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.76	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] cytoplasm [IDA] membrane [ISS] nucleus [IDA]			599
Q29040 UniProt NPD GO	ESR1_PIG	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha)	0.76	+	nuc	0	Nucleus	chromatin remodeling complex [ISS] membrane [ISS]			595
Q91424 UniProt NPD GO	ESR1_CNEUN	Estrogen receptor (ER) (Estradiol receptor) (ER-alpha) (Fragment)	0.76	+	nuc	0	Nucleus				307
O08537 UniProt NPD GO	ESR2_MOUSE	Estrogen receptor beta (ER-beta)	0.76	+	nuc	0	Nucleus	nucleus [ISS]			530
Q9XSW2 UniProt NPD GO	ESR2_PIG	Estrogen receptor beta (ER-beta)	0.76	+	nuc	0	Nucleus	nucleus [ISS]			526
Q62986 UniProt NPD GO	ESR2_RAT	Estrogen receptor beta (ER-beta)	0.76	+	nuc	0	Nucleus	mitochondrion [IDA] nucleus [ISS]		1QKN	530
Q96A65 UniProt NPD GO	EXOC4_HUMAN	Exocyst complex component 4 (Exocyst complex component Sec8)	0.76	-	nuc	0			608185		974
Q9NVH0 UniProt NPD GO	EXDL2_HUMAN	Exonuclease 3'-5' domain-like-containing protein 2	0.76	-	nuc	0					496
P97464 UniProt NPD GO	EXT1_MOUSE	Exostosin-1 (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylgl ...	0.76	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	integral to endoplasmic reticulum membrane [IDA]			746
Q16394 UniProt NPD GO	EXT1_HUMAN	Exostosin-1 (EC 2.4.1.224) (EC 2.4.1.225) (Glucuronosyl-N-acetylglucosaminyl-proteoglycan/N-acetylgl ...	0.76	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein. Golgi a ...	endoplasmic reticulum [TAS] endoplasmic reticulum membrane [TAS] Golgi apparatus [TAS] integral to endoplasmic reticulum membrane [ISS] integral to membrane [TAS]	608177		746
O01705 UniProt NPD GO	EXT2_CAEEL	Exostosin-2 (EC 2.4.1.223) (EC 2.4.1.224) (Glucuronyl-galactosyl-proteoglycan/Glucuronosyl-N-acetylg ...	0.76	-	gol	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				814
P39014 UniProt NPD GO	MET30_YEAST	F-box protein MET30 (Methionine-requiring protein 30) (E3 ubiquitin ligase complex SCF(Met30) subuni ...	0.76	-	nuc	0	Cytoplasm. Nucleus	nuclear SCF ubiquitin ligase complex [IDA]			640
P47005 UniProt NPD GO	YJO9_YEAST	F-box protein YJL149W	0.76	-	nuc	0		SCF ubiquitin ligase complex [IPI]			663
Q9ESQ9 UniProt NPD GO	RFRP_RAT	FMRFamide-related peptides precursor [Contains: Neuropeptide NPSF (Neuropeptide RFRP-1); Neuropeptid ...	0.76	-	exc	0	Secreted protein				203
Q8VDC1 UniProt NPD GO	FYCO1_MOUSE	FYVE and coiled-coil domain-containing protein 1	0.76	-	nuc	0					1437
P53917 UniProt NPD GO	FAR11_YEAST	Factor arrest protein 11	0.76	-	nuc	0					953
Q9EQR6 UniProt NPD GO	FANCG_MOUSE	Fanconi anemia group G protein homolog (Protein FACG)	0.76	-	nuc	0	Nucleus				623
P22600 UniProt NPD GO	HEMH_BOVIN	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.76	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				416
P22830 UniProt NPD GO	HEMH_HUMAN	Ferrochelatase, mitochondrial precursor (EC 4.99.1.1) (Protoheme ferro-lyase) (Heme synthetase)	0.76	-	nuc	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side		177000	1HRK	423
P54633 UniProt NPD GO	TALA_DICDI	Filopodin (Talin homolog)	0.76	-	nuc	0	Cytoplasm. Rapidly assembles at the leading edge of cells in response to chemoattractant				2492
P35631 UniProt NPD GO	AP1_ARATH	Floral homeotic protein APETALA1 (Agamous-like MADS-box protein AGL7)	0.76	-	nuc	0	Nucleus				256
Q8X229 UniProt NPD GO	FCR3_CANAL	Fluconazole resistance protein 3	0.76	-	nuc	0	Nucleus (Probable)	nucleus [IC]			399
Q5BJ56 UniProt NPD GO	FXR1_XENTR	Fragile X mental retardation syndrome-related protein 1 homolog (XtFxr1p)	0.76	-	nuc	0	Cytoplasm. Nucleus. Nuclear very early in embryonic development (at two hours post-fertilization), b ...				674
Q7ZTQ5 UniProt NPD GO	FXR1B_XENLA	Fragile X mental retardation syndrome-related protein 1 homolog-B (xFxr1p-B)	0.76	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				675
P50756 UniProt NPD GO	CCNE1_XENLA	G1/S-specific cyclin-E1	0.76	+	mit	0	Nucleus (By similarity)				408
Q91780 UniProt NPD GO	CCNE2_XENLA	G1/S-specific cyclin-E2 (Cyclin-E-1)	0.76	+	mit	0	Nucleus (By similarity)				408
Q5SSG4 UniProt NPD GO	GA2L2_MOUSE	GAS2-like protein 2 (Growth arrest-specific 2-like 2)	0.76	-	nuc	0					860
Q8LAU9 UniProt NPD GO	GATA1_ARATH	GATA transcription factor 1 (AtGATA-1)	0.76	-	nuc	0	Nucleus (Probable)				274
Q9FH57 UniProt NPD GO	GAT14_ARATH	GATA transcription factor 14	0.76	-	nuc	0	Nucleus (Probable)				339
Q9M350 UniProt NPD GO	GCP4_ARATH	Gamma-tubulin complex component 4 homolog	0.76	-	cyt	0	Centrosome (Potential)				745
Q9WUS4 UniProt NPD GO	CXA10_MOUSE	Gap junction alpha-10 protein (Connexin-57) (Cx57)	0.76	-	nuc	3 *	Membrane; multi-pass membrane protein				505
O73673 UniProt NPD GO	GCR_PAROL	Glucocorticoid receptor (GR)	0.76	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity). Cytoplasmic in the absence of ligand; nuclear af ...				807
Q9HCL2 UniProt NPD GO	PLSB_HUMAN	Glycerol-3-phosphate acyltransferase, mitochondrial precursor (EC 2.3.1.15) (GPAT)	0.76	-	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)		602395		828
P57695 UniProt NPD GO	GLRA1_BOVIN	Glycine receptor alpha-1 chain precursor (Glycine receptor 48 kDa subunit) (Strychnine-binding subun ...	0.76	-	end	3	Membrane; multi-pass membrane protein				457
Q5EY87 UniProt NPD GO	GRHL1_XENLA	Grainyhead-like protein 1 homolog (Transcription factor CP2-like 2)	0.76	-	nuc	0	Nucleus (By similarity)				609
O35793 UniProt NPD GO	GREM1_RAT	Gremlin-1 precursor (Cysteine knot superfamily 1, BMP antagonist 1) (Down-regulated in Mos-transform ...	0.76	-	exc	1 *	Secreted protein (Probable)				184
O88900 UniProt NPD GO	GRB14_RAT	Growth factor receptor-bound protein 14 (GRB14 adapter protein)	0.76	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				538
O60861 UniProt NPD GO	GAS7_HUMAN	Growth-arrest-specific protein 7 (GAS-7)	0.76	-	nuc	0	Cytoplasm (By similarity)		603127		412
P08539 UniProt NPD GO	GPA1_YEAST	Guanine nucleotide-binding protein alpha-1 subunit (GP1-alpha)	0.76	-	cyt	0		plasma membrane [IDA]		1SCG	471
Q14344 UniProt NPD GO	GNA13_HUMAN	Guanine nucleotide-binding protein alpha-13 subunit (G alpha-13)	0.76	-	mit	0	Membrane; lipid-anchor		604406		377
Q5ZJH9 UniProt NPD GO	DKC1_CHICK	H/ACA ribonucleoprotein complex subunit 4 (EC 5.4.99.-) (Dyskerin)	0.76	+	nuc	0	Nucleus; nucleolus (By similarity)				516
Q9UII4 UniProt NPD GO	HERC5_HUMAN	HECT domain and RCC1-like domain-containing protein 5 (Cyclin-E-binding protein 1)	0.76	+	mit	0	Cytoplasm; perinuclear region		608242		1024
Q92574 UniProt NPD GO	TSC1_HUMAN	Hamartin (Tuberous sclerosis 1 protein)	0.76	+	nuc	0	Cytoplasm. Membrane; peripheral membrane protein. At steady state found in association with membrane ...		607341		1164
Q5K8T2 UniProt NPD GO	SWR1_CRYNE	Helicase SWR1 (EC 3.6.1.-)	0.76	-	cyt	0	Nucleus (By similarity)				1246
P23899 UniProt NPD GO	HNF1B_RAT	Hepatocyte nuclear factor 1-beta (HNF-1beta) (HNF-1B) (Variant hepatic nuclear factor 1) (VHNF1)	0.76	+	nuc	0	Nucleus	nucleus [TAS]			557
P27889 UniProt NPD GO	HNF1B_MOUSE	Hepatocyte nuclear factor 1-beta (HNF-1beta) (HNF-1B) (Variant hepatic nuclear factor 1) (VHNF1) (Ho ...	0.76	+	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IPI]			558
P35680 UniProt NPD GO	HNF1B_HUMAN	Hepatocyte nuclear factor 1-beta (HNF-1beta) (HNF-1B) (Variant hepatic nuclear factor 1) (VHNF1) (Ho ...	0.76	+	nuc	0	Nucleus	nucleus [TAS]	604284		557

You are viewing entries 10801 to 10850 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.