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
O75190 UniProt NPD GO	DNJB6_HUMAN	DnaJ homolog subfamily B member 6 (Heat shock protein J2) (HSJ-2) (MSJ-1) (HHDJ1) (MRJ)	0.72	+	nuc	0					326
Q9QYI8 UniProt NPD GO	DNJB7_MOUSE	DnaJ homolog subfamily B member 7 (mDJ5)	0.72	+	nuc	0					312
P24785 UniProt NPD GO	MLE_DROME	Dosage compensation regulator (EC 3.6.1.-) (ATP-dependent RNA helicase mle) (Protein maleless) (Prot ...	0.72	+	mit	0	Nucleus. Mle is associated with hundreds of discrete sites along the length of the X chromosome in m ...	chromatin [IDA] dosage compensation complex (sensu Insecta) [TAS]			1293
P55266 UniProt NPD GO	DSRAD_RAT	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) (DRADA)	0.72	-	nuc	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)	nucleus [IDA]			1175
Q99MU3 UniProt NPD GO	DSRAD_MOUSE	Double-stranded RNA-specific adenosine deaminase (EC 3.5.4.-) (DRADA) (RNA adenosine deaminase 1)	0.72	-	nuc	0	Cytoplasm. Nucleus; nucleolus. Long forms starting at Met-1 are found predominantly in cytoplasm. Sh ...				1178
Q8HZK3 UniProt NPD GO	DUOX1_PIG	Dual oxidase 1 precursor (EC 1.6.3.1) (EC 1.11.1.-)	0.72	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Localizes to the a ...	apical plasma membrane [ISS]			1553
Q9NRD9 UniProt NPD GO	DUOX1_HUMAN	Dual oxidase 1 precursor (EC 1.6.3.1) (EC 1.11.1.-) (NADPH thyroid oxidase 1) (Thyroid oxidase 1) (L ...	0.72	-	end	6	Cell membrane; apical cell membrane; multi-pass membrane protein. Localizes to the apical membrane o ...	apical plasma membrane [NAS]	606758		1551
Q9ESD7 UniProt NPD GO	DYSF_MOUSE	Dysferlin (Dystrophy-associated fer-1-like protein) (Fer-1-like protein 1)	0.72	+	nuc	1	Sarcolemma; sarcolemmal membrane; single-pass type II membrane protein (By similarity)	sarcolemma [IDA]			2083
Q8N336 UniProt NPD GO	ELMD1_HUMAN	ELMO domain-containing protein 1	0.72	-	mit	0					334
P18146 UniProt NPD GO	EGR1_HUMAN	Early growth response protein 1 (EGR-1) (Krox-24 protein) (Transcription factor Zif268) (Nerve growt ...	0.72	-	nuc	0	Nucleus		128990		543
P51774 UniProt NPD GO	EGR2_RAT	Early growth response protein 2 (EGR-2) (Krox-20 protein)	0.72	-	nuc	0	Nucleus	nucleus [TAS]			470
O01639 UniProt NPD GO	E75_CHOFU	Ecdysone-inducible protein E75	0.72	-	nuc	0	Nucleus (By similarity)				690
P50239 UniProt NPD GO	E75_GALME	Ecdysone-inducible protein E75	0.72	-	nuc	0	Nucleus (Potential)				711
Q9H6S3 UniProt NPD GO	ES8L2_HUMAN	Epidermal growth factor receptor kinase substrate 8-like protein 2 (Epidermal growth factor receptor ...	0.72	+	nuc	0	Cytoplasm			1WXB	715
Q5RC07 UniProt NPD GO	ES8L2_PONPY	Epidermal growth factor receptor kinase substrate 8-like protein 2 (Epidermal growth factor receptor ...	0.72	+	nuc	0	Cytoplasm (By similarity)				716
Q8S3U9 UniProt NPD GO	EXOC2_ARATH	Exocyst complex component 2 (Exocyst complex component Sec5)	0.72	-	end	0					1090
P19658 UniProt NPD GO	EXO70_YEAST	Exocyst complex component EXO70 (Exocyst complex protein of 70 kDa)	0.72	-	nuc	0	Bud. Bud neck. Its polarization in the cell depends on EXO84	exocyst [IPI]		2B7M	623
Q9QZ11 UniProt NPD GO	EXO1_MOUSE	Exonuclease 1 (EC 3.1.-.-) (mExo1) (Exonuclease I)	0.72	-	nuc	0	Nucleus (By similarity). Colocalizes with PCNA to discrete nuclear foci in S-phase (By similarity)	nucleus [ISS]			837
Q02710 UniProt NPD GO	ECM23_YEAST	Extracellular matrix protein 23 (SRD1 homolog 2)	0.72	-	nuc	0					187
Q9Y3I1 UniProt NPD GO	FBX7_HUMAN	F-box only protein 7	0.72	-	nuc	0		ubiquitin ligase complex [TAS]	605648		522
Q6P5H6 UniProt NPD GO	FRMD5_MOUSE	FERM domain-containing protein 5	0.72	-	nuc	0					517
Q6TYB5 UniProt NPD GO	FEZ2_MOUSE	Fasciculation and elongation protein zeta 2 (Zygin-2) (Zygin II)	0.72	-	nuc	0					348
Q5RDS9 UniProt NPD GO	FGF13_PONPY	Fibroblast growth factor 13 (FGF-13)	0.72	+	nuc	0					245
Q92913 UniProt NPD GO	FGF13_HUMAN	Fibroblast growth factor 13 (FGF-13) (Fibroblast growth factor homologous factor 2) (FHF-2)	0.72	+	nuc	0			300070		245
P70377 UniProt NPD GO	FGF13_MOUSE	Fibroblast growth factor 13 (FGF-13) (Fibroblast growth factor homologous factor 2) (FHF-2)	0.72	+	nuc	0					245
O04116 UniProt NPD GO	FLL_PINRA	Floricaula/leafy-like protein (PRFLL)	0.72	-	nuc	0	Nucleus (Probable)				411
Q60987 UniProt NPD GO	FOXGB_MOUSE	Forkhead box protein G1B (Forkhead-related protein FKHL1) (Transcription factor BF-1) (Brain factor ...	0.72	-	nuc	0	Nucleus				481
P26016 UniProt NPD GO	FUR11_DROME	Furin-like protease 1, isoforms 1/1-X/2 precursor (EC 3.4.21.75) (Furin-1) (Kex2-like endoprotease 1 ...	0.72	-	mit	2	Golgi apparatus; Golgi membrane; multi-pass membrane protein	plasma membrane [IDA]			1269
O42575 UniProt NPD GO	CCNE3_XENLA	G1/S-specific cyclin-E3	0.72	+	mit	0	Nucleus (By similarity)				408
P97785 UniProt NPD GO	GFRA1_MOUSE	GDNF family receptor alpha-1 precursor (GFR-alpha-1) (GDNF receptor alpha) (GDNFR-alpha) (TGF-beta-r ...	0.72	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)	extrinsic to membrane [TAS]			468
P40036 UniProt NPD GO	GIP2_YEAST	GLC7-interacting protein 2	0.72	-	nuc	0		protein phosphatase type 1 complex [IPI]			548
Q80WJ1 UniProt NPD GO	GGN_MOUSE	Gametogenetin	0.72	-	nuc	0	Isoform 1: Cytoplasm; perinuclear region. Isoform 1 localizes along the nuclear membrane. Isoform 2: ...	cytoplasm [IDA] integral to membrane [NAS] nuclear envelope [NAS] nucleolus [IDA] perinuclear region [IDA]			673
P47805 UniProt NPD GO	G12_BRARE	Gastrulation-specific protein G12	0.72	-	nuc	0					152
O88513 UniProt NPD GO	GEMI_MOUSE	Geminin	0.72	-	nuc	0		nucleus [IDA]		1WLQ	206
Q9Y5Q8 UniProt NPD GO	TF3C5_HUMAN	General transcription factor 3C polypeptide 5 (Transcription factor IIIC-epsilon subunit) (TF3C-epsi ...	0.72	-	nuc	0	Nucleus	transcription factor TFIIIC complex [TAS]	604890		519
Q5TDP6 UniProt NPD GO	GLUD1_HUMAN	Glutamate--ammonia ligase domain-containing protein 1 (Lengsin) (Lens glutamine synthase-like)	0.72	-	nuc	0					509
Q60780 UniProt NPD GO	GAS7_MOUSE	Growth-arrest-specific protein 7 (GAS-7)	0.72	-	nuc	0	Cytoplasm	actin filament [IDA] ruffle [IDA]			421
Q9WV93 UniProt NPD GO	HEY1_MOUSE	Hairy/enhancer-of-split related with YRPW motif 1 (Hairy and enhancer of split-related protein 1) (H ...	0.72	+	nuc	0	Nucleus (By similarity)	nucleus [IDA]			299
Q9Y5J3 UniProt NPD GO	HEY1_HUMAN	Hairy/enhancer-of-split related with YRPW motif 1 (Hairy and enhancer of split-related protein 1) (H ...	0.72	+	nuc	0	Nucleus (By similarity)		602953		304
P41152 UniProt NPD GO	HSF30_LYCPE	Heat shock factor protein HSF30 (Heat shock transcription factor 30) (HSTF 30) (Heat stress transcri ...	0.72	+	cyt	0	Nucleus				351
Q96UX5 UniProt NPD GO	HSP78_CANAL	Heat shock protein 78, mitochondrial precursor	0.72	-	mit	0	Mitochondrion; mitochondrial matrix				812
Q9JJ50 UniProt NPD GO	HGS_RAT	Hepatocyte growth factor-regulated tyrosine kinase substrate (SNAP-25-interacting protein Hrs-2)	0.72	-	nuc	0	Cytoplasm. Endosome; early endosome; early endosomal membrane; peripheral membrane protein. Endosome ...	cytosol [IDA] membrane [IDA] secretory granule [IDA]			776
Q91474 UniProt NPD GO	HNF1_SALSA	Hepatocyte nuclear factor 1 (HNF-1) (SHNF1)	0.72	-	nuc	0	Nucleus (By similarity)				559
P22361 UniProt NPD GO	HNF1A_MOUSE	Hepatocyte nuclear factor 1-alpha (HNF-1A) (Liver-specific transcription factor LF-B1) (LFB1)	0.72	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [IPI]		1LFB	628
Q99MH3 UniProt NPD GO	HEPC_RAT	Hepcidin precursor	0.72	-	exc	1 *	Secreted protein				84
P05205 UniProt NPD GO	HP1_DROME	Heterochromatin protein 1 (HP1) (Nonhistone chromosomal protein C1A9 antigen)	0.72	+	nuc	0	Nucleus	centric heterochromatin [NAS] nuclear heterochromatin [IDA] polytene chromosome chromocenter [IDA] polytene chromosome puff [IDA] polytene chromosome, telomeric region [IDA]		1Q3L	206
P04196 UniProt NPD GO	HRG_HUMAN	Histidine-rich glycoprotein precursor (Histidine-proline-rich glycoprotein) (HPRG)	0.72	-	exc	0	Secreted protein	extracellular region [NAS]	142640		525
Q4X0W8 UniProt NPD GO	HAT1_ASPFU	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.72	+	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				570
Q4I6A4 UniProt NPD GO	HAT1_GIBZE	Histone acetyltransferase type B catalytic subunit (EC 2.3.1.48)	0.72	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				478
O17323 UniProt NPD GO	HDA4_CAEEL	Histone deacetylase 4 (Histone deacetylase 7) (CeHDA-7)	0.72	-	nuc	0	Nucleus (Probable)				816

You are viewing entries 12751 to 12800 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.