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
P09116 UniProt NPD GO	CASB_RABIT	Beta-casein precursor	0.23	-	vac	0	Secreted protein				228
Q95JD2 UniProt NPD GO	D103A_PANTR	Beta-defensin 103A precursor (Defensin, beta 103A) (Defensin, beta 103) (Beta-defensin 3) (DEFB-3) ( ...	0.23	-	exc	1 *	Secreted protein (By similarity)				67
Q30KL1 UniProt NPD GO	DB116_PANTR	Beta-defensin 116 precursor (Defensin, beta 116)	0.23	-	nuc	0	Secreted protein (By similarity)				102
Q30KQ4 UniProt NPD GO	DB116_HUMAN	Beta-defensin 116 precursor (Defensin, beta 116) (Beta-defensin 16) (DEFB-16)	0.23	-	nuc	0	Secreted protein (By similarity)				102
P97580 UniProt NPD GO	MSMB_RAT	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.23	-	exc	0	Secreted protein. Sperm surface. Present in the secretions of the airways, the gastrointestinal and ...				113
Q96PL2 UniProt NPD GO	TECTB_HUMAN	Beta-tectorin precursor	0.23	-	end	0	Cell membrane; lipid-anchor; GPI-anchor; extracellular side (Probable). Found in the non-collagenous ...		602653		329
P53416 UniProt NPD GO	BBS_PHASS	Bibenzyl synthase (EC 2.3.1.-)	0.23	-	cyt	0					390
Q13057 UniProt NPD GO	COASY_HUMAN	Bifunctional coenzyme A synthase (CoA synthase) (NBP) (POV-2) [Includes: Phosphopantetheine adenylyl ...	0.23	-	end	0	Cytoplasm (By similarity)		609855		564
Q9DBL7 UniProt NPD GO	COASY_MOUSE	Bifunctional coenzyme A synthase (CoA synthase) [Includes: Phosphopantetheine adenylyltransferase (E ...	0.23	-	mit	0				2F6R	563
Q6GQK9 UniProt NPD GO	NDST1_XENLA	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 1 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.23	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				878
Q42783 UniProt NPD GO	BCCP_SOYBN	Biotin carboxyl carrier protein of acetyl-CoA carboxylase, chloroplast precursor (BCCP)	0.23	-	mit	0	Plastid; chloroplast				262
Q53S33 UniProt NPD GO	BOLA3_HUMAN	BolA-like protein 3	0.23	-	mit	0					107
P32247 UniProt NPD GO	BRS3_HUMAN	Bombesin receptor subtype-3 (BRS-3)	0.23	-	end	7 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [NAS]	300107		399
Q6H2Y3 UniProt NPD GO	BRS3_MACMU	Bombesin receptor subtype-3 (BRS-3)	0.23	-	end	7 *	Membrane; multi-pass membrane protein				398
P91896 UniProt NPD GO	BXF1_BOMMO	Bombyxin F-1 precursor (BBX-F1) [Contains: Bombyxin F-1 B chain; Bombyxin F-1 A chain]	0.23	-	exc	0	Secreted protein				95
Q9XI23 UniProt NPD GO	BORL2_ARATH	Boron transporter-like protein 2	0.23	-	end	10 *	Membrane; multi-pass membrane protein (By similarity)				683
P83284 UniProt NPD GO	IBB1_AMBAC	Bowman-birk type proteinase inhibitor (TaTI)	0.23	-	nuc	0					63
P56685 UniProt NPD GO	BUTH_ANDAU	Buthinin	0.23	-	nuc	0	Secreted protein				34
O88200 UniProt NPD GO	CLC11_MOUSE	C-type lectin domain family 11 member A precursor (Stem cell growth factor) (Lymphocyte secreted C-t ...	0.23	-	cyt	0	Cytoplasm (By similarity). Secreted protein (By similarity)	extracellular region [ISS]			328
P55206 UniProt NPD GO	ANFC_BOVIN	C-type natriuretic peptide precursor (SVSP15) [Contains: CNP-22; CNP-29; CNP-53]	0.23	-	exc	0	Secreted protein				126
P55207 UniProt NPD GO	ANFC_RAT	C-type natriuretic peptide precursor [Contains: CNP-22; CNP-29; CNP-53]	0.23	-	exc	0	Secreted protein				126
P27708 UniProt NPD GO	PYR1_HUMAN	CAD protein [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carb ...	0.23	-	nuc	0	Cytoplasm		114010		2225
P92937 UniProt NPD GO	CPK15_ARATH	CBL-interacting serine/threonine-protein kinase 15 (EC 2.7.11.1) (Serine/threonine-protein kinase AT ...	0.23	-	nuc	0					421
Q11206 UniProt NPD GO	SIA4C_HUMAN	CMP-N-acetylneuraminate-beta-galactosamide-alpha-2,3-sialyltransferase (EC 2.4.99.-) (Beta-galactosi ...	0.23	-	end	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein. Membrane-b ...		104240		333
Q08708 UniProt NPD GO	CM35A_HUMAN	CMRF35-A antigen precursor (CMRF-35) (CD300c antigen)	0.23	-	nuc	2 *	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS]	606786		224
Q9NX08 UniProt NPD GO	COMD8_HUMAN	COMM domain-containing protein 8	0.23	-	cyt	0					183
Q9VUL1 UniProt NPD GO	PYRG_DROME	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.23	-	cyt	0					627
Q03720 UniProt NPD GO	SLO_DROME	Calcium-activated potassium channel slowpoke (Maxi K channel) (MaxiK) (BK channel) (dSlo)	0.23	-	end	7	Membrane; multi-pass membrane protein (Probable)	plasma membrane [NAS]			1200
Q9NPA1 UniProt NPD GO	KCMB3_HUMAN	Calcium-activated potassium channel subunit beta 3 (Calcium-activated potassium channel, subfamily M ...	0.23	-	mit	2	Membrane; multi-pass membrane protein	membrane [NAS] voltage-gated potassium channel complex [IDA]	605222		279
Q9N1R0 UniProt NPD GO	CABP1_BOVIN	Calcium-binding protein 1 (CaBP1)	0.23	-	nuc	0					225
Q5ZM44 UniProt NPD GO	CHP1_CHICK	Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein)	0.23	-	nuc	0	Cytoplasm (By similarity)				194
Q5R7F0 UniProt NPD GO	CHP1_PONPY	Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein)	0.23	-	nuc	0	Cytoplasm (By similarity)				194
P61023 UniProt NPD GO	CHP1_RAT	Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein)	0.23	-	nuc	0	Cytoplasm			2CT9	194
Q99653 UniProt NPD GO	CHP1_HUMAN	Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein) (Calcineu ...	0.23	-	nuc	0	Cytoplasm (By similarity)		606988		194
P61022 UniProt NPD GO	CHP1_MOUSE	Calcium-binding protein p22 (Calcium-binding protein CHP) (Calcineurin homologous protein) (Sid 470) ...	0.23	-	nuc	0	Cytoplasm (By similarity)				194
P35564 UniProt NPD GO	CALX_MOUSE	Calnexin precursor	0.23	-	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. When bou ...	endoplasmic reticulum [IDA] integral to membrane [IDA]			591
Q08091 UniProt NPD GO	CNN1_MOUSE	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.23	-	nuc	0					297
Q08290 UniProt NPD GO	CNN1_RAT	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.23	-	nuc	0					297
Q7YRL2 UniProt NPD GO	CNN1_SHEEP	Calponin-1 (Calponin H1, smooth muscle) (Basic calponin)	0.23	-	nuc	0					297
Q99439 UniProt NPD GO	CNN2_HUMAN	Calponin-2 (Calponin H2, smooth muscle) (Neutral calponin)	0.23	-	nuc	0		cytoskeleton [TAS] intercellular junction [TAS]	602373	1WYN	308
Q5RFN6 UniProt NPD GO	CNN2_PONPY	Calponin-2 (Calponin H2, smooth muscle) (Neutral calponin)	0.23	-	nuc	0					308
Q9ERQ8 UniProt NPD GO	CAH7_MOUSE	Carbonic anhydrase 7 (EC 4.2.1.1) (Carbonic anhydrase VII) (Carbonate dehydratase VII) (CA-VII)	0.23	-	cyt	0	Cytoplasm (Probable)				264
P55261 UniProt NPD GO	CBPB1_CANFA	Carboxypeptidase B precursor (EC 3.4.17.2) (47 kDa zymogen granule membrane-associated protein) (ZAP ...	0.23	-	mit	0	Secreted protein (By similarity)				416
O75976 UniProt NPD GO	CBPD_HUMAN	Carboxypeptidase D precursor (EC 3.4.17.22) (Metallocarboxypeptidase D) (gp180)	0.23	-	end	1 *	Membrane; single-pass type I membrane protein (Potential)	membrane fraction [TAS]	603102		1380
P59287 UniProt NPD GO	CASS_RICCO	Casbene synthase, chloroplast precursor (EC 4.2.3.8)	0.23	-	cyt	0	Plastid; chloroplast				601
P55213 UniProt NPD GO	CASP3_RAT	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) (Yama protein) (CPP-3 ...	0.23	-	nuc	0	Cytoplasm	cytosol [IMP]			277
Q8MJC3 UniProt NPD GO	CASP3_RABIT	Caspase-3 precursor (EC 3.4.22.-) (CASP-3) (Apopain) (Cysteine protease CPP32) [Contains: Caspase-3 ...	0.23	-	nuc	0	Cytoplasm				277
P11934 UniProt NPD GO	CATA_PENJA	Catalase (EC 1.11.1.6)	0.23	-	end	1	Peroxisome			4CAT	670
P12365 UniProt NPD GO	CATA2_MAIZE	Catalase isozyme 2 (EC 1.11.1.6)	0.23	-	cyt	0	Or: Peroxisome. Or: Cytoplasm				491
O48560 UniProt NPD GO	CATA3_SOYBN	Catalase-3 (EC 1.11.1.6)	0.23	-	nuc	0	Peroxisome (By similarity). Glyoxysome (By similarity)				492

You are viewing entries 47151 to 47200 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.