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
Q9LRZ5 UniProt NPD GO	PLDP1_ARATH	Phospholipase D p1 (EC 3.1.4.4) (AtPLDp1) (Phospholipase D1 PHOX and PX containing domain) (Phosphol ...	0.67	-	nuc	0					1096
O08684 UniProt NPD GO	PLD1_CRIGR	Phospholipase D1 (EC 3.1.4.4) (PLD 1) (Choline phosphatase 1) (Phosphatidylcholine-hydrolyzing phosp ...	0.67	-	cyt	0	Cytoplasm; perinuclear region (By similarity). Endoplasmic reticulum (By similarity). Golgi apparatu ...				1036
P46020 UniProt NPD GO	KPB1_HUMAN	Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform (Phosphorylase kinase alpha ...	0.67	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)		311870		1223
P18826 UniProt NPD GO	KPB1_MOUSE	Phosphorylase b kinase regulatory subunit alpha, skeletal muscle isoform (Phosphorylase kinase alpha ...	0.67	-	nuc	0	Cell membrane; lipid-anchor; cytoplasmic side (Potential)				1241
P97350 UniProt NPD GO	PKP1_MOUSE	Plakophilin-1	0.67	-	nuc	0	Nucleus (By similarity). Cell membrane; cell-cell junction; anchoring junction; desmosome (By simila ...	desmosome [ISS] nucleus [ISS]			728
P31393 UniProt NPD GO	PLST_CARAU	Plasticin	0.67	+	nuc	0					453
P24354 UniProt NPD GO	RR14_ASTLO	Plastid 30S ribosomal protein S14	0.67	+	nuc	0	Plastid				100
O60759 UniProt NPD GO	PSCBP_HUMAN	Pleckstrin homology Sec7 and coiled-coil domains-binding protein (Cytohesin-binding protein HE) (CYB ...	0.67	-	nuc	0	Cytoplasm. Membrane. May also be membrane-associated	cell cortex [IDA] cytoplasm [IDA]	604448		359
P63089 UniProt NPD GO	PTN_MOUSE	Pleiotrophin precursor (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding ...	0.67	-	nuc	1 *	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]			168
P63090 UniProt NPD GO	PTN_RAT	Pleiotrophin precursor (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding ...	0.67	-	nuc	1 *	Secreted protein				168
Q28527 UniProt NPD GO	KCNA4_MUSPF	Potassium voltage-gated channel subfamily A member 4 (Voltage-gated potassium channel subunit Kv1.4) ...	0.67	+	end	3	Membrane; multi-pass membrane protein				654
Q9JK96 UniProt NPD GO	KCNQ4_RAT	Potassium voltage-gated channel subfamily KQT member 4 (Voltage-gated potassium channel subunit Kv7. ...	0.67	-	nuc	0	Cell membrane; basal cell membrane; multi-pass membrane protein. Situated at the basal membrane of c ...				168
Q99633 UniProt NPD GO	PRP18_HUMAN	Pre-mRNA-splicing factor 18 (PRP18 homolog) (hPRP18)	0.67	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Colocalizes with spliceosomal snRNPs (By simi ...	nucleus [TAS] spliceosome complex [TAS]	604993		342
P49649 UniProt NPD GO	SECA_ODOSI	Preprotein translocase secA subunit	0.67	-	cyt	0	Plastid; chloroplast				888
Q8I0P7 UniProt NPD GO	PDE3_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-3 (EC 3.1.4.17)	0.67	-	nuc	0					578
Q9N2V9 UniProt NPD GO	PDE6_CAEEL	Probable 3',5'-cyclic phosphodiesterase pde-6 (EC 3.1.4.17)	0.67	-	nuc	0					760
P62521 UniProt NPD GO	CCDC8_RAT	Probable Coiled-coil domain-containing protein 8	0.67	-	nuc	0					643
P60704 UniProt NPD GO	ABEC3_CRILO	Probable DNA dC->dU-editing enzyme APOBEC3 (EC 3.5.4.-)	0.67	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				396
P91529 UniProt NPD GO	RPO3F_CAEEL	Probable DNA-directed RNA polymerase III subunit F (EC 2.7.7.6) (DNA-directed RNA polymerase III 39 ...	0.67	-	nuc	0	Nucleus (Potential)				296
Q9VCE6 UniProt NPD GO	MTA70_DROME	Probable N6-adenosine-methyltransferase MT-A70-like protein (EC 2.1.1.62)	0.67	-	nuc	0	Nucleus (Probable)	nucleus [ISS]			608
O22921 UniProt NPD GO	WRK25_ARATH	Probable WRKY transcription factor 25 (WRKY DNA-binding protein 25)	0.67	-	nuc	0	Nucleus (Probable)				393
Q9XEC3 UniProt NPD GO	WRK42_ARATH	Probable WRKY transcription factor 42 (WRKY DNA-binding protein 42)	0.67	-	nuc	0	Nucleus (Potential)				528
Q9C983 UniProt NPD GO	WRK57_ARATH	Probable WRKY transcription factor 57 (WRKY DNA-binding protein 57)	0.67	-	nuc	0	Nucleus (Probable)				287
Q8NEL9 UniProt NPD GO	DDHD1_HUMAN	Probable phospholipase DDHD1 (EC 3.1.1.-) (DDHD domain protein 1) (Phosphatidic acid-preferring phos ...	0.67	-	nuc	0					900
Q8K2X1 UniProt NPD GO	AT10D_MOUSE	Probable phospholipid-transporting ATPase VD (EC 3.6.3.1) (ATPVD)	0.67	-	end	11	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			1416
Q99L28 UniProt NPD GO	RLP24_MOUSE	Probable ribosome biogenesis protein RLP24	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				163
Q6P6G7 UniProt NPD GO	RLP24_RAT	Probable ribosome biogenesis protein RLP24	0.67	+	nuc	0	Nucleus; nucleolus (By similarity)				163
Q9UHA3 UniProt NPD GO	RLP24_HUMAN	Probable ribosome biogenesis protein RLP24 (Ribosomal protein L24-like)	0.67	+	nuc	0	Nucleus; nucleolus				163
P43637 UniProt NPD GO	KGS9_YEAST	Probable serine/threonine-protein kinase YGL179C (EC 2.7.11.1)	0.67	-	nuc	0		cytoplasm [IDA]			560
Q85A69 UniProt NPD GO	CYSA_ANTFO	Probable sulfate/thiosulfate import ATP-binding protein cysA (EC 3.6.3.25) (Sulfate-transporting ATP ...	0.67	-	cyt	0	Plastid; chloroplast				381
P38737 UniProt NPD GO	ECM29_YEAST	Proteasome component ECM29 (Extracellular matrix protein 29)	0.67	-	vac	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] proteasome complex (sensu Eukaryota) [IDA]			1868
Q5VYK3 UniProt NPD GO	ECM29_HUMAN	Proteasome-associated protein ECM29 homolog (Ecm29)	0.67	-	nuc	0	Endoplasmic reticulum. Endoplasmic reticulum-Golgi intermediate compartment. Endosome. Centrosome. N ...	centrosome [IDA] cytoplasmic membrane-bound vesicle [IDA] early endosome [IDA] endoplasmic reticulum [IDA] ER to Golgi transport vesicle [IDA] late endosome [IDA] nucleus [IDA]			1845
Q6Q7P4 UniProt NPD GO	41_CANFA	Protein 4.1 (Band 4.1) (P4.1) (4.1R)	0.67	-	nuc	0	Cytoplasm. Nucleus				810
Q751A7 UniProt NPD GO	LIC4_ASHGO	Protein ATC1/LIC4	0.67	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				304
Q9Y324 UniProt NPD GO	CN111_HUMAN	Protein C14orf111	0.67	+	nuc	0					198
Q32PD0 UniProt NPD GO	CN111_BOVIN	Protein C14orf111 homolog	0.67	+	nuc	0					198
Q9CTH6 UniProt NPD GO	CN111_MOUSE	Protein C14orf111 homolog	0.67	+	nuc	0					198
Q5RFQ0 UniProt NPD GO	CN111_PONPY	Protein C14orf111 homolog	0.67	+	nuc	0					198
Q5XJK9 UniProt NPD GO	CC026_BRARE	Protein C3orf26 homolog	0.67	+	nuc	0					291
Q9CZT6 UniProt NPD GO	CC026_MOUSE	Protein C3orf26 homolog	0.67	-	nuc	0					276
Q6AYP6 UniProt NPD GO	CI138_RAT	Protein C9orf138 homolog	0.67	-	nuc	0					462
Q8IXQ3 UniProt NPD GO	CI040_HUMAN	Protein C9orf40	0.67	-	nuc	0					194
Q68FU5 UniProt NPD GO	CI085_RAT	Protein C9orf85 homolog	0.67	+	nuc	0					155
Q28FY7 UniProt NPD GO	DBF4_XENTR	Protein DBF4 homolog	0.67	-	nuc	0	Nucleus (By similarity)				663
Q6FWU4 UniProt NPD GO	DSE3_CANGA	Protein DSE3	0.67	-	nuc	0	Bud neck (By similarity)				438
Q96MK3 UniProt NPD GO	FA20A_HUMAN	Protein FAM20A precursor	0.67	-	exc	1 *	Secreted protein (Potential)				541
Q6GQN4 UniProt NPD GO	FA32A_BRARE	Protein FAM32A-like	0.67	-	nuc	0					109
P40956 UniProt NPD GO	GTS1_YEAST	Protein GTS1 (Protein LSR1)	0.67	+	nuc	0	Nucleus (Potential)	cytoplasm [IPI] nucleus [IDA]			396
Q08118 UniProt NPD GO	IRC10_YEAST	Protein IRC10 (Increased recombination centers protein 10)	0.67	-	nuc	0					586
Q8N6R0 UniProt NPD GO	K0859_HUMAN	Protein KIAA0859	0.67	+	mit	0					699

You are viewing entries 15401 to 15450 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.