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
P01023 UniProt NPD GO	A2MG_HUMAN	Alpha-2-macroglobulin precursor (Alpha-2-M)	0.36	-	exc	0		extracellular region [NAS]	103950	1BV8	1474
Q28838 UniProt NPD GO	ADA2A_BOVIN	Alpha-2A adrenergic receptor (Alpha-2A adrenoceptor) (Alpha-2A adrenoreceptor) (Alpha-2AAR) (Alpha-2 ...	0.36	-	end	7 *	Membrane; multi-pass membrane protein				452
P30545 UniProt NPD GO	ADA2B_MOUSE	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor)	0.36	-	end	7 *	Membrane; multi-pass membrane protein				450
P19328 UniProt NPD GO	ADA2B_RAT	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor)	0.36	-	end	7 *	Membrane; multi-pass membrane protein				453
O77723 UniProt NPD GO	ADA2B_ECHTE	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.36	-	end	6 *	Membrane; multi-pass membrane protein				384
Q9R2B6 UniProt NPD GO	SIA7D_MOUSE	Alpha-N-acetyl-neuraminyl-2,3-beta-galactosyl-1,3-N-acetyl-galactosaminide alpha-2,6-sialyltransfera ...	0.36	-	end	2 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				360
P60840 UniProt NPD GO	ENSA_MOUSE	Alpha-endosulfine (ARPP-19e)	0.36	-	nuc	0	Cytoplasm (By similarity)				121
P60841 UniProt NPD GO	ENSA_RAT	Alpha-endosulfine (ARPP-19e)	0.36	-	nuc	0	Cytoplasm				121
Q28789 UniProt NPD GO	FETA_PANTR	Alpha-fetoprotein precursor (Alpha-fetoglobulin) (Alpha-1-fetoprotein)	0.36	-	vac	0	Secreted protein				609
P53341 UniProt NPD GO	MAL12_YEAST	Alpha-glucosidase MAL12 (EC 3.2.1.20) (Maltase)	0.36	-	cyt	0					584
P07265 UniProt NPD GO	MAL62_YEAST	Alpha-glucosidase MAL62 (EC 3.2.1.20) (Maltase)	0.36	-	cyt	0					584
O75443 UniProt NPD GO	TECTA_HUMAN	Alpha-tectorin precursor	0.36	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...		603629		2155
Q9NP70 UniProt NPD GO	AMBN_HUMAN	Ameloblastin precursor	0.36	-	nuc	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [NAS]	601259		447
Q9Z0K9 UniProt NPD GO	AMEL_CAVPO	Amelogenin precursor	0.36	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				226
Q861X8 UniProt NPD GO	AMELY_PANTR	Amelogenin, Y isoform precursor (Fragment)	0.36	-	exc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				203
Q7TNS7 UniProt NPD GO	ACCN4_MOUSE	Amiloride-sensitive cation channel 4 (Acid-sensing ion channel 4)	0.36	-	nuc	0	Membrane; multi-pass membrane protein (By similarity)				539
P51172 UniProt NPD GO	SCNND_HUMAN	Amiloride-sensitive sodium channel subunit delta (Epithelial Na+ channel subunit delta) (Delta ENaC) ...	0.36	-	mit	1	Membrane; multi-pass membrane protein		601328		638
P53601 UniProt NPD GO	A4_MACFA	Amyloid beta A4 protein precursor (APP) (ABPP) (Alzheimer disease amyloid protein homolog) [Contains ...	0.36	-	end	1	Membrane; single-pass type I membrane protein (By similarity). Cell surface protein that rapidly bec ...				770
Q64438 UniProt NPD GO	ANG2_MOUSE	Angiogenin-2 precursor (Angiogenin-related protein)	0.36	-	exc	0					145
Q8WXI3 UniProt NPD GO	ASB10_HUMAN	Ankyrin repeat and SOCS box protein 10 (ASB-10)	0.36	-	cyt	0					429
Q15327 UniProt NPD GO	ANKR1_HUMAN	Ankyrin repeat domain-containing protein 1 (Cardiac ankyrin repeat protein) (Cytokine-inducible nucl ...	0.36	+	cyt	0	Nucleus	nucleus [TAS]	609599		319
Q99LW0 UniProt NPD GO	ANR10_MOUSE	Ankyrin repeat domain-containing protein 10	0.36	-	nuc	0					415
Q5ZLC8 UniProt NPD GO	ANR52_CHICK	Ankyrin repeat domain-containing protein 52	0.36	-	cyt	0					1073
P08133 UniProt NPD GO	ANXA6_HUMAN	Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein III) (Chromobindin-20) (67 kDa calelect ...	0.36	-	cyt	0	Stress fibers (By similarity)		114070	1M9I	672
Q9CZ52 UniProt NPD GO	ANTR1_MOUSE	Anthrax toxin receptor 1 precursor (Tumor endothelial marker 8)	0.36	-	nuc	1	Membrane; single-pass type I membrane protein (Probable)				562
Q25490 UniProt NPD GO	APLP_MANSE	Apolipophorins precursor [Contains: Apolipophorin-2 (Apolipophorin II) (apoLp-2); Apolipophorin-1 (A ...	0.36	-	nuc	0	Secreted protein				3305
P06728 UniProt NPD GO	APOA4_MOUSE	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV)	0.36	-	nuc	0	Secreted protein				395
P09917 UniProt NPD GO	LOX5_HUMAN	Arachidonate 5-lipoxygenase (EC 1.13.11.34) (5-lipoxygenase) (5-LO)	0.36	-	cyt	0	Cytoplasm		152390		673
P12527 UniProt NPD GO	LOX5_RAT	Arachidonate 5-lipoxygenase (EC 1.13.11.34) (5-lipoxygenase) (5-LO)	0.36	-	cyt	0	Cytoplasm	nuclear envelope [TAS] sarcolemma [IDA]			672
P51464 UniProt NPD GO	ARLY_RANCA	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.36	-	cyt	0					467
P50293 UniProt NPD GO	ARY2_MESAU	Arylamine N-acetyltransferase 2 (EC 2.3.1.5) (Arylamide acetylase 2) (Arylamine N-acetyltransferase, ...	0.36	-	cyt	0	Cytoplasm				290
P32770 UniProt NPD GO	NRP1_YEAST	Asparagine-rich protein (Protein ARP)	0.36	-	nuc	0		cytoplasm [IDA]			719
Q9ER24 UniProt NPD GO	ATX10_RAT	Ataxin-10 (Spinocerebellar ataxia type 10 protein homolog) (Neuronal beta-catenin-like protein)	0.36	-	cyt	0					475
P18293 UniProt NPD GO	ANPRA_MOUSE	Atrial natriuretic peptide receptor A precursor (ANP-A) (ANPRA) (GC-A) (Guanylate cyclase) (EC 4.6.1 ...	0.36	-	nuc	0	Membrane; single-pass type I membrane protein				1057
P38182 UniProt NPD GO	ATG8_YEAST	Autophagy-related protein 8 precursor (Autophagy-related ubiquitin-like modifier ATG8) (Cytoplasm to ...	0.36	-	nuc	0	Membrane-associated through a lipid anchor. Found in Cvt vesicles, autophagosomes and vacuoles. This ...	autophagic vacuole [IDA] cytoplasm [IDA] cytosol [IDA] microtubule associated complex [IPI]			117
P11836 UniProt NPD GO	CD20_HUMAN	B-lymphocyte antigen CD20 (B-lymphocyte surface antigen B1) (Leu-16) (Bp35)	0.36	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	112210	1S8B	297
Q61D31 UniProt NPD GO	BAG1_CAEBR	BAG-family molecular chaperone regulator 1	0.36	-	nuc	0					209
O60125 UniProt NPD GO	BAG1A_SCHPO	BAG-family molecular chaperone regulator 1A (BAG-1A)	0.36	-	nuc	0					195
Q8HYZ0 UniProt NPD GO	BAMBI_SHEEP	BMP and activin membrane-bound inhibitor homolog precursor	0.36	-	mit	1	Membrane; single-pass type I membrane protein (Potential)				260
Q9NF14 UniProt NPD GO	BAT40_CAEEL	BTB and MATH domain-containing protein 40	0.36	-	nuc	0					402
P98170 UniProt NPD GO	BIRC4_HUMAN	Baculoviral IAP repeat-containing protein 4 (Inhibitor of apoptosis protein 3) (X-linked inhibitor o ...	0.36	-	nuc	0	Cytoplasm	cytoplasm [TAS] cytosol [TAS]	300079	1TFQ	497
P13917 UniProt NPD GO	7SB1_SOYBN	Basic 7S globulin precursor (Bg) (SBg7S) [Contains: Basic 7S globulin high kDa subunit; Basic 7S glo ...	0.36	-	nuc	0					427
Q9NVA1 UniProt NPD GO	BZFB_HUMAN	Basic FGF-repressed Zic-binding protein (bFZb)	0.36	-	mit	0	Cytoplasmic vesicle (By similarity). Cytoplasmic vesicular structures (By similarity)				299
Q9D1I2 UniProt NPD GO	BINCA_MOUSE	Bcl10-interacting CARD protein (BinCARD)	0.36	-	nuc	0	Nucleus (By similarity). Co-expression with BCL10 induced translocation from nucleus to cytosol (By ...				183
Q6UY87 UniProt NPD GO	VMD2_MACFA	Bestrophin-1 (Vitelliform macular dystrophy protein 2)	0.36	-	end	4 *	Cell membrane; multi-pass membrane protein (By similarity)				585
Q05714 UniProt NPD GO	CRBB2_CHICK	Beta crystallin B2 (Beta-crystallin Bp)	0.36	-	nuc	0					218
P05622 UniProt NPD GO	PGFRB_MOUSE	Beta platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-beta)	0.36	-	end	1	Membrane; single-pass type I membrane protein			1AYC	1098
Q09324 UniProt NPD GO	GCNT1_MOUSE	Beta-1,3-galactosyl-O-glycosyl-glycoprotein beta-1,6-N-acetylglucosaminyltransferase (EC 2.4.1.102) ...	0.36	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				428
Q9XSE4 UniProt NPD GO	CASB_TRIVU	Beta-casein precursor	0.36	-	exc	0	Secreted protein				285
P14772 UniProt NPD GO	BPT1_YEAST	Bile pigment transporter 1	0.36	-	end	14 *	Membrane; multi-pass membrane protein (Potential)	vacuolar membrane (sensu Fungi) [IDA]			1559

You are viewing entries 34751 to 34800 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.