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
Q9TTM9 UniProt NPD GO	ADA1D_PIG	Alpha-1D adrenergic receptor (Alpha 1D-adrenoceptor) (Alpha 1D-adrenoreceptor)	0.26	+	end	7	Membrane; multi-pass membrane protein				571
P23944 UniProt NPD GO	ADA1D_RAT	Alpha-1D adrenergic receptor (Alpha 1D-adrenoceptor) (Alpha 1D-adrenoreceptor) (Alpha-1A adrenergic ...	0.26	+	end	7	Membrane; multi-pass membrane protein				561
Q9SD76 UniProt NPD GO	PHSH_ARATH	Alpha-glucan phosphorylase, H isozyme (EC 2.4.1.1) (Starch phosphorylase H)	0.26	-	cyt	0	Cytoplasm (By similarity)				841
Q64255 UniProt NPD GO	SGCA_MESAU	Alpha-sarcoglycan precursor (Alpha-SG) (Adhalin) (50 kDa dystrophin-associated glycoprotein) (50DAG) ...	0.26	-	end	1	Sarcolemma; sarcolemmal membrane; single-pass type I membrane protein (By similarity)				387
Q9UV71 UniProt NPD GO	AOX2_CANAL	Alternative oxidase 2, mitochondrial precursor (EC 1.-.-.-)	0.26	-	mit	1	Mitochondrion (By similarity). Possibly in the inner surface of the inner mitochondrial membrane (By ...				365
Q00912 UniProt NPD GO	AOX_HANAN	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.26	-	vac	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side				342
Q9P429 UniProt NPD GO	AOX_VENIN	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.26	-	mit	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				361
P41390 UniProt NPD GO	PUR1_SCHPO	Amidophosphoribosyltransferase (EC 2.4.2.14) (Glutamine phosphoribosylpyrophosphate amidotransferase ...	0.26	-	cyt	0					533
O97742 UniProt NPD GO	SCNNB_RABIT	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.26	-	mit	1 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				641
P91885 UniProt NPD GO	AMPN_MANSE	Aminopeptidase N precursor (EC 3.4.11.2) (Microsomal aminopeptidase) (APN2)	0.26	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor				942
Q8WN64 UniProt NPD GO	ANGI_PAPHA	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.26	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q02858 UniProt NPD GO	TIE2_MOUSE	Angiopoietin-1 receptor precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor TIE-2) (mTIE2) (Ty ...	0.26	-	end	2 *	Membrane; single-pass type I membrane protein				1122
Q5RFN1 UniProt NPD GO	ACE2_PONPY	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.26	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				805
Q9P2R3 UniProt NPD GO	ANFY1_HUMAN	Ankyrin repeat and FYVE domain-containing protein 1 (Ankyrin repeats hooked to a zinc finger motif)	0.26	-	cyt	0	Cytoplasm. Endosome; endosomal membrane; peripheral membrane protein. Also associated with endosomal ...	endosome membrane [ISS]	607927		1169
Q8WXK4 UniProt NPD GO	ASB12_HUMAN	Ankyrin repeat and SOCS box protein 12 (ASB-12)	0.26	-	cyt	0					309
Q91ZT8 UniProt NPD GO	ASB9_MOUSE	Ankyrin repeat and SOCS box protein 9 (ASB-9)	0.26	-	cyt	0					290
Q8VE42 UniProt NPD GO	ANR49_MOUSE	Ankyrin repeat domain-containing protein 49 (Fetal globin-inducing factor) (Fetal globin-increasing ...	0.26	-	nuc	0					238
P27216 UniProt NPD GO	ANX13_HUMAN	Annexin A13 (Annexin XIII) (Annexin, intestine-specific) (ISA)	0.26	-	cyt	0	Cell membrane. Associated with the plasma membrane of undifferentiated, proliferating crypt epitheli ...	plasma membrane [NAS]	602573		315
Q29075 UniProt NPD GO	NKL_PIG	Antimicrobial peptide NK-lysin precursor (NKL) (Fragment)	0.26	-	nuc	0	Secreted protein			1NKL	129
P55056 UniProt NPD GO	APOC4_HUMAN	Apolipoprotein C-IV precursor (Apo-CIV) (ApoC-IV)	0.26	-	exc	0	Secreted protein		600745		127
Q9Z1R3 UniProt NPD GO	APOM_MOUSE	Apolipoprotein M (Apo-M) (ApoM)	0.26	-	nuc	0	Secreted protein (Potential)				190
Q24306 UniProt NPD GO	IAP1_DROME	Apoptosis 1 inhibitor (Inhibitor of apoptosis 1) (dIAP1) (Protein thread)	0.26	-	nuc	0				1SE0	438
Q91828 UniProt NPD GO	AR11_XENLA	Apoptosis regulator R11 (XR11)	0.26	-	nuc	1	Membrane; single-pass membrane protein (Potential)				204
P16469 UniProt NPD GO	LOX12_PIG	Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX)	0.26	-	nuc	0	Cytoplasm				662
P16050 UniProt NPD GO	LOX15_HUMAN	Arachidonate 15-lipoxygenase (EC 1.13.11.33) (Arachidonate omega-6 lipoxygenase) (15-LOX)	0.26	-	cyt	0	Cytoplasm		152392		661
O35936 UniProt NPD GO	LX15B_MOUSE	Arachidonate 15-lipoxygenase type II (EC 1.13.11.33) (15-LOX-2) (8S-lipoxygenase) (8S-LOX)	0.26	-	cyt	0	Cytoplasm (By similarity)	intracellular [ISS]			677
Q9CX83 UniProt NPD GO	ARMX1_MOUSE	Armadillo repeat-containing X-linked protein 1	0.26	-	mit	1 *					456
P38707 UniProt NPD GO	SYNC_YEAST	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.26	-	cyt	0	Cytoplasm	cytoplasm [TAS]			554
P32329 UniProt NPD GO	YPS1_YEAST	Aspartic proteinase 3 precursor (EC 3.4.23.41) (Yapsin-1)	0.26	-	exc	0	Endoplasmic reticulum; endoplasmic reticulum membrane; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]		1YPS	569
Q9M391 UniProt NPD GO	ATX3H_ARATH	Ataxin-3 homolog (EC 3.4.22.-) (Machado-Joseph disease-like protein) (MJD1a-like)	0.26	-	cyt	0	Nucleus (By similarity)				280
Q5Z749 UniProt NPD GO	IAA21_ORYSA	Auxin-responsive protein IAA21 (Indoleacetic acid-induced protein 21)	0.26	-	cyt	0	Nucleus (By similarity)				266
Q9ZSY8 UniProt NPD GO	IAA27_ARATH	Auxin-responsive protein IAA27 (Indoleacetic acid-induced protein 27) (Auxin-induced protein 27) (Ph ...	0.26	-	nuc	0	Nucleus (By similarity)				305
Q61125 UniProt NPD GO	BKRB1_MOUSE	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.26	-	end	7 *	Membrane; multi-pass membrane protein				334
P50615 UniProt NPD GO	BTG3_MOUSE	BTG3 protein (Tob5 protein) (Abundant in neuroepithelium area protein)	0.26	-	nuc	0					252
P19171 UniProt NPD GO	CHIB_ARATH	Basic endochitinase B precursor (EC 3.2.1.14) (Pathogenesis-related protein 3) (PR-3) (AtChiB)	0.26	-	cyt	0	Vacuole. Vacuolar and protoplast				335
P26453 UniProt NPD GO	BASI_RAT	Basigin precursor (OX-47 antigen) (Glycoprotein CE9) (CD147 antigen)	0.26	+	end	1 *	Cell membrane; single-pass type I membrane protein (By similarity). Colocalizes with SLC16A1 and SLC ...				388
Q8VXX9 UniProt NPD GO	BETL1_ARATH	Bet1-like protein At4g14600	0.26	-	cyt	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				137
Q80WN9 UniProt NPD GO	B4GT2_CRIGR	Beta-1,4-galactosyltransferase 2 (EC 2.4.1.-) (Beta-1,4-GalTase 2) (Beta4Gal-T2) (b4Gal-T2) (UDP-gal ...	0.26	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				369
Q91YI4 UniProt NPD GO	ARRB2_MOUSE	Beta-arrestin-2 (Arrestin, beta 2)	0.26	-	mit	0	Cytoplasm. Nucleus	intracellular [IDA]			410
Q5IAA9 UniProt NPD GO	D107A_PANTR	Beta-defensin 107A precursor (Defensin, beta 107A) (Defensin, beta 107) (Beta-defensin 7) (DEFB-7) ( ...	0.26	-	mit	1 *	Secreted protein (By similarity)				66
Q30KQ6 UniProt NPD GO	DB114_HUMAN	Beta-defensin 114 precursor (Defensin, beta 114) (Beta-defensin 14) (DEFB-14)	0.26	-	mit	1 *	Secreted protein (By similarity)				69
Q9BEE3 UniProt NPD GO	DB126_MACFA	Beta-defensin 126 precursor (Defensin, beta 126) (Epididymal secretory protein 13.2) (ESP13.2)	0.26	-	nuc	1 *	Secreted protein	extracellular region [NAS]			123
Q56UD0 UniProt NPD GO	INV6_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 6 precursor (EC 3.2.1.26) (Sucrose hydrolase 6) (Invert ...	0.26	-	mit	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				596
P13613 UniProt NPD GO	LACB1_EQUAS	Beta-lactoglobulin-1 (Beta-LG-1) (Beta-lactoglobulin I, major monomeric)	0.26	-	cyt	0	Secreted protein				162
Q27128 UniProt NPD GO	PAPSS_URECA	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase (PAPS synthetase) (PAPSS) (Sulfurylase ...	0.26	-	cyt	0		intracellular [ISS]			610
Q8MIR4 UniProt NPD GO	COASY_PIG	Bifunctional coenzyme A synthase (CoA synthase) (NBP) (POV-2) [Includes: Phosphopantetheine adenylyl ...	0.26	-	mit	0	Cytoplasm (By similarity)				562
Q23695 UniProt NPD GO	DRTS_CRIFA	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.26	-	nuc	0					515
Q5U4X8 UniProt NPD GO	NDST1_XENTR	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.26	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				878
Q9CWG9 UniProt NPD GO	BL1S2_MOUSE	Biogenesis of lysosome-related organelles complex-1 subunit 2 (BLOC subunit 2)	0.26	-	nuc	0	Centrosome. Localizes to the centrosomes in a microtubule-dependent manner (By similarity)	cytosol [IDA]			143
P21815 UniProt NPD GO	SIAL_HUMAN	Bone sialoprotein-2 precursor (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin- ...	0.26	-	exc	0	Secreted protein		147563		317

You are viewing entries 43951 to 44000 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.