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
Q09637 UniProt NPD GO	CYP9_CAEEL	Peptidyl-prolyl cis-trans isomerase 9 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-9)	0.65	-	nuc	0		intracellular [IDA]			309
Q03297 UniProt NPD GO	PER_DROWI	Period circadian protein (Fragment)	0.65	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				1093
Q9LE15 UniProt NPD GO	PER4_ARATH	Peroxidase 4 precursor (EC 1.11.1.7) (Atperox P4) (ATP46)	0.65	-	exc	0	Secreted protein (By similarity)				315
P28795 UniProt NPD GO	PEX3_YEAST	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal membrane protein PAS3)	0.65	-	mit	1 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	peroxisomal membrane [IDA]			441
P33760 UniProt NPD GO	PEX6_YEAST	Peroxisomal biogenesis factor 6 (Peroxin-6) (Peroxisome biosynthesis protein PAS8)	0.65	-	cyt	0		cytoplasm [IDA] peroxisome [IDA] soluble fraction [IDA]			1030
O02697 UniProt NPD GO	PK3CG_PIG	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (EC 2.7.1.153) (PI3-k ...	0.65	+	cyt	0				1E90	1102
P81831 UniProt NPD GO	CAPP1_CHLRE	Phosphoenolpyruvate carboxylase 1 (EC 4.1.1.31) (PEP carboxylase 1) (PEPCase 1) (PEPC 1)	0.65	-	cyt	0	Cytoplasm (By similarity)				974
Q5GM68 UniProt NPD GO	CAPP2_ARATH	Phosphoenolpyruvate carboxylase 2 (EC 4.1.1.31) (PEPCase 2) (PEPC 2) (AtPPC2)	0.65	-	nuc	0	Cytoplasm (By similarity)				963
Q09933 UniProt NPD GO	DIS1_SCHPO	Phosphoprotein p93	0.65	-	nuc	0	Spindle pole body. Spindle. Spindle pole body during metaphase and spindle microtubules during anaph ...				882
O75364 UniProt NPD GO	PITX3_HUMAN	Pituitary homeobox 3 (Homeobox protein PITX3)	0.65	+	nuc	0	Nucleus (By similarity)		602669		302
Q28161 UniProt NPD GO	PKP1_BOVIN	Plakophilin-1 (Band-6 protein) (B6P)	0.65	-	nuc	0	Nucleus (By similarity). Cell membrane; cell-cell junction; anchoring junction; desmosome (By simila ...	desmosome [ISS] nucleus [ISS]			727
Q5I0L6 UniProt NPD GO	PSCBP_RAT	Pleckstrin homology Sec7 and coiled-coil domain-binding protein	0.65	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). May also be membrane-associated (By similarity) ...				359
Q9UIW2 UniProt NPD GO	PLXA1_HUMAN	Plexin-A1 precursor (Semaphorin receptor NOV)	0.65	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)		601055		1896
Q51D88 UniProt NPD GO	PAP_ENTHI	Poly(A) polymerase (EC 2.7.7.19) (PAP) (Polynucleotide adenylyltransferase) (EhPAP)	0.65	-	cyt	0	Cytoplasm. Nucleus				522
Q8VE62 UniProt NPD GO	PAIP1_MOUSE	Polyadenylate-binding protein-interacting protein 1 (Poly(A)-binding protein-interacting protein 1) ...	0.65	-	nuc	0	Cytoplasm (Probable)				400
Q4GZT3 UniProt NPD GO	PKD2_BOVIN	Polycystin-2 (Polycystic kidney disease 2 protein homolog)	0.65	-	end	7	Membrane; multi-pass membrane protein (Potential)				970
Q63881 UniProt NPD GO	KCND2_RAT	Potassium voltage-gated channel subfamily D member 2 (Voltage-gated potassium channel subunit Kv4.2) ...	0.65	-	end	6 *	Cell membrane; multi-pass membrane protein. Interaction with DPP6, DLG4 or FREQ may increase cell su ...	integral to plasma membrane [IDA]		1S6C	630
O88943 UniProt NPD GO	KCNQ2_RAT	Potassium voltage-gated channel subfamily KQT member 2 (Voltage-gated potassium channel subunit Kv7. ...	0.65	-	nuc	5	Membrane; multi-pass membrane protein				852
Q6C186 UniProt NPD GO	CLF1_YARLI	Pre-mRNA-splicing factor CLF1	0.65	+	cyt	0	Nucleus (By similarity)				676
Q9HF03 UniProt NPD GO	CLF1_CRYNV	Pre-mRNA-splicing factor CLF1 (crooked-neck-like protein 1)	0.65	-	cyt	0	Nucleus (By similarity)				724
Q751P4 UniProt NPD GO	CWC22_ASHGO	Pre-mRNA-splicing factor CWC22	0.65	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				554
Q5KI78 UniProt NPD GO	ISY1_CRYNE	Pre-mRNA-splicing factor ISY1	0.65	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				348
Q4WEH7 UniProt NPD GO	PRP45_ASPFU	Pre-mRNA-splicing factor prp45 (Pre-mRNA-processing protein 45)	0.65	-	nuc	0	Nucleus (By similarity)				579
Q8CDU6 UniProt NPD GO	HECD2_MOUSE	Probable E3 ubiquitin-protein ligase HECTD2 (HECT domain-containing protein 2)	0.65	-	cyt	0					774
O60291 UniProt NPD GO	MGRN1_HUMAN	Probable E3 ubiquitin-protein ligase MGRN1 (EC 6.3.2.-) (Mahogunin ring finger protein 1) (RING fing ...	0.65	-	nuc	0			607559		552
Q6XCF2 UniProt NPD GO	GPR34_GORGO	Probable G-protein coupled receptor 34	0.65	-	end	7	Membrane; multi-pass membrane protein (By similarity)				381
Q9UPC5 UniProt NPD GO	GPR34_HUMAN	Probable G-protein coupled receptor 34	0.65	-	end	7	Membrane; multi-pass membrane protein (By similarity)	integral to plasma membrane [TAS]	300241		381
Q3SAG9 UniProt NPD GO	GPR34_PANPA	Probable G-protein coupled receptor 34	0.65	-	end	7	Membrane; multi-pass membrane protein (By similarity)				381
P60019 UniProt NPD GO	GPR34_PANTR	Probable G-protein coupled receptor 34	0.65	-	end	7	Membrane; multi-pass membrane protein (By similarity)				381
Q9FLF7 UniProt NPD GO	MYST1_ARATH	Probable MYST-like histone acetyltransferase 1 (EC 2.3.1.48)	0.65	-	cyt	0	Nucleus (Probable)				445
Q6FRH1 UniProt NPD GO	TAH18_CANGA	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.65	-	nuc	0					621
Q9SUS1 UniProt NPD GO	WRK29_ARATH	Probable WRKY transcription factor 29 (WRKY DNA-binding protein 29)	0.65	-	nuc	0	Nucleus				304
Q93WV6 UniProt NPD GO	WRK68_ARATH	Probable WRKY transcription factor 68 (WRKY DNA-binding protein 68)	0.65	-	nuc	0	Nucleus (Probable)				277
Q75LD5 UniProt NPD GO	DMI1L_ORYSA	Probable ion channel DMI1-like, chloroplast precursor	0.65	-	end	2	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				893
Q8SQK7 UniProt NPD GO	NUF2_ENCCU	Probable kinetochore protein NUF2	0.65	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				439
O94385 UniProt NPD GO	PO152_SCHPO	Probable nucleoporin POM152-like	0.65	-	nuc	0	Nucleus; nuclear envelope; nuclear pore complex; central core structure; single-pass type II membran ...				1250
Q9GLW0 UniProt NPD GO	PRGR_CANFA	Progesterone receptor (PR)	0.65	+	nuc	0	Nucleus. Diverse nuclear localization patterns of PR observed in tumorous mammary and uterine tissue ...	nucleus [IDA]			939
O43555 UniProt NPD GO	GON2_HUMAN	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.65	-	exc	0	Secreted protein	soluble fraction [TAS]	602352		120
Q9QXU7 UniProt NPD GO	PROK2_MOUSE	Prokineticin-2 precursor (PK2) (Protein Bv8 homolog)	0.65	+	exc	0	Secreted protein	extracellular region [ISS]			128
P27918 UniProt NPD GO	PROP_HUMAN	Properdin precursor (Factor P)	0.65	-	exc	0	Secreted protein	extracellular space [TAS]	300383	1W0S	469
P41413 UniProt NPD GO	PCSK5_RAT	Proprotein convertase subtilisin/kexin type 5 precursor (EC 3.4.21.-) (Proprotein convertase PC5) (S ...	0.65	-	vac	1	PC5A is secreted through the regulated secretory pathway. PC5B is a type I membrane protein localize ...				1877
Q12500 UniProt NPD GO	AVL9_YEAST	Protein AVL9 (APL2 VPS1 synthetic lethal protein 9)	0.65	-	nuc	0	Cytoplasm	cytoplasm [IDA]			764
Q8BP27 UniProt NPD GO	CJ078_MOUSE	Protein C10orf78 homolog	0.65	-	nuc	0					319
Q9NSI2 UniProt NPD GO	CU070_HUMAN	Protein C21orf70	0.65	-	nuc	0					230
Q2T9Y1 UniProt NPD GO	CC026_BOVIN	Protein C3orf26 homolog	0.65	+	nuc	0					279
Q68EV5 UniProt NPD GO	CC026_XENLA	Protein C3orf26 homolog	0.65	+	nuc	0					277
P35401 UniProt NPD GO	CRAC_DICDI	Protein CRAC	0.65	-	nuc	0	Cytoplasm				697
Q8MJK1 UniProt NPD GO	PGEA1_BOVIN	Protein Chibby (PKD2 interactor, Golgi and endoplasmic reticulum associated 1) (PIGEA-14) (Cytosolic ...	0.65	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nuclear, in a punctate manner. Golgi apparatu ...				127
Q5VSL9 UniProt NPD GO	FA40A_HUMAN	Protein FAM40A	0.65	-	end	0					837
Q5KI47 UniProt NPD GO	GRC3_CRYNE	Protein GRC3	0.65	-	nuc	0	Nucleus (By similarity)				744

You are viewing entries 16501 to 16550 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.