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
Q29RZ2 UniProt NPD GO	PPWD1_BOVIN	Peptidylprolyl isomerase domain and WD repeat-containing protein 1 (EC 5.2.1.8)	0.41	+	cyt	0					644
Q62009 UniProt NPD GO	POSTN_MOUSE	Periostin precursor (PN) (Osteoblast-specific factor 2) (OSF-2)	0.41	-	vac	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [IDA]			838
Q01603 UniProt NPD GO	PERO_DROME	Peroxidase precursor (EC 1.11.1.7) (DmPO)	0.41	-	mit	1 *	Secreted protein (Potential)				690
P02853 UniProt NPD GO	PHSB_PHAVU	Phaseolin, beta-type precursor	0.41	-	end	0	Protein body. Vacuole. Cotyledonary membrane-bound vacuolar protein bodies			2PHL	421
O77560 UniProt NPD GO	PHOS_CANFA	Phosducin (PHD) (33 kDa phototransducing protein)	0.41	-	nuc	0	Outer and inner segments of the rod cells (By similarity)				245
Q9H2J4 UniProt NPD GO	PDCL3_HUMAN	Phosducin-like protein 3 (Viral IAP-associated factor 1) (VIAF-1) (HTPHLP)	0.41	+	cyt	0	Cytoplasm	cytoplasm [IDA]			239
Q8BTI9 UniProt NPD GO	PK3CB_MOUSE	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit beta isoform (EC 2.7.1.153) (PI3-ki ...	0.41	-	cyt	0					1064
Q9JM80 UniProt NPD GO	PAG1_RAT	Phosphoprotein associated with glycosphingolipid-enriched microdomains 1 (Csk-binding protein) (Tran ...	0.41	-	exc	1 *	Cell membrane; single-pass type III membrane protein. Present in lipid rafts	integral to plasma membrane [TAS]			424
P33530 UniProt NPD GO	PHYA1_TOBAC	Phytochrome A1	0.41	-	mit	0					1124
P14713 UniProt NPD GO	PHYB_ARATH	Phytochrome B	0.41	-	cyt	0					1172
Q5PQT7 UniProt NPD GO	PHLA3_RAT	Pleckstrin homology-like domain family A member 3	0.41	-	nuc	0					125
Q8GU86 UniProt NPD GO	PDR5_ORYSA	Pleiotropic drug resistance protein 5	0.41	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1454
O43660 UniProt NPD GO	PLRG1_HUMAN	Pleiotropic regulator 1	0.41	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle	nucleus [TAS]	605961		514
Q58EG3 UniProt NPD GO	PVRL3_BRARE	Poliovirus receptor-related protein 3 precursor	0.41	-	nuc	1 *	Membrane; single-pass membrane protein (Potential)				574
Q9WVP6 UniProt NPD GO	PAPOB_MOUSE	Poly(A) polymerase beta (EC 2.7.7.19) (PAP beta) (Polynucleotide adenylyltransferase beta) (Testis-s ...	0.41	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			641
Q10295 UniProt NPD GO	PAP_SCHPO	Poly(A) polymerase pla1 (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase)	0.41	-	cyt	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IGI]			566
Q9UTN4 UniProt NPD GO	PFS2_SCHPO	Polyadenylation factor subunit 2	0.41	-	nuc	0	Nucleus	nucleolus [IDA] nucleus [IDA]			509
Q8NCW6 UniProt NPD GO	GLT11_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 11 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.41	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				608
Q8BGT9 UniProt NPD GO	GLT12_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 12 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.41	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				576
Q9H252 UniProt NPD GO	KCNH6_HUMAN	Potassium voltage-gated channel subfamily H member 6 (Voltage-gated potassium channel subunit Kv11.2 ...	0.41	-	end	4	Membrane; multi-pass membrane protein		608168		994
Q6BGR9 UniProt NPD GO	FIP1_DEBHA	Pre-mRNA polyadenylation factor FIP1	0.41	-	nuc	0	Nucleus (By similarity)				328
Q5A7Q3 UniProt NPD GO	PRP46_CANAL	Pre-mRNA-splicing factor PRP46 (Pre-mRNA-processing protein 46)	0.41	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				389
Q758S6 UniProt NPD GO	SN309_ASHGO	Pre-mRNA-splicing factor SNT309	0.41	-	cyt	0	Nucleus (By similarity)				197
Q6FMB1 UniProt NPD GO	SPP2_CANGA	Pre-mRNA-splicing factor SPP2	0.41	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				169
Q04503 UniProt NPD GO	DP87_DICDI	Prespore protein DP87 precursor	0.41	-	exc	0	Stored in prespore vacuoles until it is discharged into the interspace of spores during spore format ...				555
Q8TEA8 UniProt NPD GO	DTD1_HUMAN	Probable D-tyrosyl-tRNA(Tyr) deacylase (EC 3.1.-.-)	0.41	-	nuc	0	Cytoplasm (Potential)				209
Q626F4 UniProt NPD GO	PSF1_CAEBR	Probable DNA replication complex GINS protein PSF1	0.41	-	nuc	0	Nucleus (By similarity)				201
Q96P69 UniProt NPD GO	GPR78_HUMAN	Probable G-protein coupled receptor 78	0.41	-	end	6 *	Membrane; multi-pass membrane protein		606921		363
Q9H1C0 UniProt NPD GO	GPR92_HUMAN	Probable G-protein coupled receptor 92	0.41	+	end	7 *	Membrane; multi-pass membrane protein		606926		372
Q5JK52 UniProt NPD GO	NADK1_ORYSA	Probable NAD kinase 1 (EC 2.7.1.23)	0.41	-	nuc	0					532
O94613 UniProt NPD GO	TAH18_SCHPO	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.41	-	nuc	0					558
P53927 UniProt NPD GO	YNL0_YEAST	Probable RNA-binding protein YNL110C	0.41	-	nuc	0		nucleolus [IDA] nucleus [IDA]			220
Q9M8M6 UniProt NPD GO	WRK66_ARATH	Probable WRKY transcription factor 66 (WRKY DNA-binding protein 66)	0.41	-	nuc	0	Nucleus (Probable)				235
Q6ES10 UniProt NPD GO	HAT1_ORYSA	Probable acetyltransferase type B catalytic subunit (EC 2.3.1.48) (HAT B)	0.41	+	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity)				466
P51485 UniProt NPD GO	ARRB_CAEEL	Probable beta-arrestin	0.41	-	nuc	0					435
Q9C9H5 UniProt NPD GO	GUN9_ARATH	Probable family 9 endoglucanase At1g71380 precursor (EC 3.2.1.4)	0.41	-	exc	0	Cell wall	cell wall (sensu Magnoliophyta) [IDA]			484
Q59PT6 UniProt NPD GO	SPC25_CANAL	Probable kinetochore protein SPC25	0.41	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				239
Q2UF95 UniProt NPD GO	SPC24_ASPOR	Probable kinetochore protein spc24	0.41	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				200
Q5AZQ6 UniProt NPD GO	SPC24_EMENI	Probable kinetochore protein spc24	0.41	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				200
Q92350 UniProt NPD GO	YDH5_SCHPO	Probable nudix hydrolase C6G9.05 (EC 3.6.1.-)	0.41	-	nuc	0					285
Q9NEW6 UniProt NPD GO	RSP3_CAEEL	Probable splicing factor, arginine/serine-rich 3 (CeSF2) (CeSF2/ASF)	0.41	+	nuc	0	Nucleus (By similarity)				258
Q96WV1 UniProt NPD GO	TRMB_SCHPO	Probable tRNA (guanine-N(7)-)-methyltransferase (EC 2.1.1.33) (tRNA(m7G46)-methyltransferase)	0.41	-	nuc	0					273
Q9TLQ4 UniProt NPD GO	YCF27_CYACA	Probable transcriptional regulator ycf27 (OmpR-like protein)	0.41	-	nuc	0	Plastid; chloroplast				249
Q15113 UniProt NPD GO	PCOC1_HUMAN	Procollagen C-endopeptidase enhancer 1 precursor (Procollagen COOH-terminal proteinase enhancer 1) ( ...	0.41	-	exc	0	Secreted protein		600270	1UAP	449
Q7ZZV3 UniProt NPD GO	PRL_ANGJA	Prolactin precursor (PRL)	0.41	-	exc	0	Secreted protein				209
P21993 UniProt NPD GO	PRL_ONCMY	Prolactin precursor (PRL)	0.41	-	exc	0	Secreted protein				210
P69130 UniProt NPD GO	PRL1_ONCKE	Prolactin-1 precursor (Prolactin I) (PRL-I)	0.41	-	exc	0	Secreted protein				211
P69131 UniProt NPD GO	PRL1_ONCTS	Prolactin-1 precursor (Prolactin I) (PRL-I)	0.41	-	exc	0	Secreted protein				211
Q91364 UniProt NPD GO	PRL2_ONCTS	Prolactin-2 precursor (Prolactin II) (PRL-II)	0.41	-	exc	0	Secreted protein				210
Q9NQ31 UniProt NPD GO	BCA3_HUMAN	Proline-rich protein BCA3 (Breast cancer-associated gene 3 protein) (PKA-interacting protein) (AKIP1 ...	0.41	+	nuc	0	Nucleus. Locates to punctate spots		609191		210

You are viewing entries 31301 to 31350 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.