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
P06776 UniProt NPD GO	PDE2_YEAST	3',5'-cyclic-nucleotide phosphodiesterase 2 (EC 3.1.4.17) (PDEase 2) (High-affinity cAMP phosphodies ...	0.59	-	cyt	0		cytoplasm [IDA] nucleus [IDA]			526
P83565 UniProt NPD GO	RM40_RAT	39S ribosomal protein L40, mitochondrial (L40mt) (MRP-40) (Fragment)	0.59	+	nuc	0	Mitochondrion	mitochondrial ribosome [IDA]			29
Q9BHU1 UniProt NPD GO	RS26_OXYNO	40S ribosomal protein S26	0.59	-	nuc	0					125
P47903 UniProt NPD GO	RS27_CHLRE	40S ribosomal protein S27	0.59	-	nuc	0					86
O44012 UniProt NPD GO	RS6_LEIIN	40S ribosomal protein S6	0.59	-	nuc	0					249
Q9NE83 UniProt NPD GO	RS6_LEIMA	40S ribosomal protein S6	0.59	-	nuc	0					249
P11614 UniProt NPD GO	5HT1D_CANFA	5-hydroxytryptamine 1D receptor (5-HT-1D) (Serotonin receptor 1D)	0.59	-	end	7 *	Membrane; multi-pass membrane protein				377
Q08168 UniProt NPD GO	HRP_PLABE	58 kDa phosphoprotein (Heat shock-related protein) (HRP)	0.59	-	nuc	0	Cytoplasm				423
O74175 UniProt NPD GO	RL13_SCHPO	60S ribosomal protein L13	0.59	-	nuc	0					208
P30736 UniProt NPD GO	RL15_CHITE	60S ribosomal protein L15 (YL10)	0.59	-	nuc	0					203
Q3T025 UniProt NPD GO	RL17_BOVIN	60S ribosomal protein L17	0.59	-	nuc	0					183
Q5XTY7 UniProt NPD GO	RL17_FELCA	60S ribosomal protein L17	0.59	-	nuc	0					183
P18621 UniProt NPD GO	RL17_HUMAN	60S ribosomal protein L17 (L23)	0.59	-	nuc	0			603661		183
Q9CPR4 UniProt NPD GO	RL17_MOUSE	60S ribosomal protein L17 (L23)	0.59	-	nuc	0					183
P24049 UniProt NPD GO	RL17_RAT	60S ribosomal protein L17 (L23) (Amino acid starvation-induced protein) (ASI)	0.59	-	nuc	0					183
P35266 UniProt NPD GO	RL171_HORVU	60S ribosomal protein L17-1	0.59	-	nuc	0					170
Q39411 UniProt NPD GO	RL26_BRARA	60S ribosomal protein L26	0.59	-	nuc	0					146
Q42351 UniProt NPD GO	RL341_ARATH	60S ribosomal protein L34-1	0.59	-	mit	0					120
Q98TF7 UniProt NPD GO	RL35_CHICK	60S ribosomal protein L35	0.59	-	nuc	0					122
P42766 UniProt NPD GO	RL35_HUMAN	60S ribosomal protein L35	0.59	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS] nucleolus [TAS]			122
Q29361 UniProt NPD GO	RL35_PIG	60S ribosomal protein L35	0.59	-	nuc	0					122
P51402 UniProt NPD GO	RL37B_YEAST	60S ribosomal protein L37-B (L35) (YP55)	0.59	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			87
Q98TF5 UniProt NPD GO	RL39_CHICK	60S ribosomal protein L39	0.59	-	mit	0					51
P35296 UniProt NPD GO	RL40_ORYSA	60S ribosomal protein L40 (CEP52)	0.59	-	nuc	0					53
P47962 UniProt NPD GO	RL5_MOUSE	60S ribosomal protein L5	0.59	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)				296
P09895 UniProt NPD GO	RL5_RAT	60S ribosomal protein L5	0.59	-	mit	0	Cytoplasm (By similarity). Nucleus; nucleolus (By similarity)	ribosome [TAS]			296
P32100 UniProt NPD GO	RL7_DROME	60S ribosomal protein L7	0.59	-	cyt	0					252
O43572 UniProt NPD GO	AKA10_HUMAN	A kinase anchor protein 10, mitochondrial precursor (Protein kinase A-anchoring protein 10) (PRKA10) ...	0.59	-	nuc	0	Mitochondrion. Membrane. Cytoplasm. Predominantly mitochondrial but also membrane associated and cyt ...		604694		662
Q76LX8 UniProt NPD GO	ATS13_HUMAN	ADAMTS-13 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase with thrombospondin motifs 13 ...	0.59	-	exc	1 *	Secreted	cell surface [NAS] extracellular matrix (sensu Metazoa) [TAS]	604134		1427
Q9DBT5 UniProt NPD GO	AMPD2_MOUSE	AMP deaminase 2 (EC 3.5.4.6)	0.59	-	cyt	0					798
P91926 UniProt NPD GO	AP2A_DROME	AP-2 complex subunit alpha (Alpha-adaptin)	0.59	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...	coated vesicle [TAS] plasma membrane [IDA] synaptic vesicle [TAS]			940
Q9C0W7 UniProt NPD GO	AP2A_SCHPO	AP-2 complex subunit alpha (Alpha-adaptin) (Clathrin assembly protein large alpha chain) (Clathrin a ...	0.59	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...				878
P20447 UniProt NPD GO	DBP3_YEAST	ATP-dependent RNA helicase DBP3 (EC 3.6.1.-) (DEAD box protein 3) (Helicase CA3)	0.59	+	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			523
Q6FST5 UniProt NPD GO	DBP6_CANGA	ATP-dependent RNA helicase DBP6 (EC 3.6.1.-)	0.59	-	nuc	0	Nucleus; nucleolus (By similarity)				651
Q756G5 UniProt NPD GO	DBP8_ASHGO	ATP-dependent RNA helicase DBP8 (EC 3.6.1.-)	0.59	-	cyt	0	Nucleus; nucleolus (By similarity)				435
Q6FIL3 UniProt NPD GO	HAS1_CANGA	ATP-dependent RNA helicase HAS1 (EC 3.6.1.-)	0.59	+	nuc	0	Nucleus; nucleolus (By similarity)				494
Q8AVC1 UniProt NPD GO	AN32B_XENLA	Acidic leucine-rich nuclear phosphoprotein 32 family member B	0.59	-	nuc	0	Nucleus (By similarity)				239
P14605 UniProt NPD GO	CYAA_SCHPO	Adenylate cyclase (EC 4.6.1.1) (ATP pyrophosphate-lyase) (Adenylyl cyclase)	0.59	-	nuc	0					1692
Q96AP0 UniProt NPD GO	ACD_HUMAN	Adrenocortical dysplasia protein homolog (POT1 and TIN2-interacting protein)	0.59	-	mit	0	Nucleus (Potential)	nuclear telomere cap complex [IDA]	609377		544
P43651 UniProt NPD GO	AFLR_ASPPA	Aflatoxin biosynthesis regulatory protein	0.59	-	nuc	0	Nucleus (By similarity)				444
P24801 UniProt NPD GO	ANX2B_XENLA	Annexin A2-B (Annexin II type II) (Lipocortin II) (Calpactin I heavy chain)	0.59	-	nuc	0	Secreted protein; extracellular space; extracellular matrix; basement membrane. In the lamina beneat ...				339
P15268 UniProt NPD GO	MOSA_MAIZE	Autonomous transposable element EN-1 mosaic protein (Suppressor-mutator system protein) (SPM)	0.59	-	nuc	0					621
Q8LQ74 UniProt NPD GO	IAA6_ORYSA	Auxin-responsive protein IAA6 (Indoleacetic acid-induced protein 6)	0.59	-	nuc	0	Nucleus (By similarity)				335
Q12732 UniProt NPD GO	AVNA_ASPPA	Averantin oxidoreductase (EC 1.14.-.-) (Cytochrome P450 60A1)	0.59	-	nuc	1 *					495
Q9QUN3 UniProt NPD GO	BLNK_MOUSE	B-cell linker protein (Cytoplasmic adapter protein) (B-cell adapter containing SH2 domain protein) ( ...	0.59	-	nuc	0	Cytoplasm (By similarity). Membrane (By similarity). BCR activation results in the translocation to ...				457
P41182 UniProt NPD GO	BCL6_HUMAN	B-cell lymphoma 6 protein (BCL-6) (Zinc finger protein 51) (LAZ-3 protein) (BCL-5) (Zinc finger and ...	0.59	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]	109565	1R2B	706
O54940 UniProt NPD GO	BNIP2_MOUSE	BCL2/adenovirus E1B 19 kDa protein-interacting protein 2	0.59	-	cyt	0	Cytoplasm (By similarity). Cytoplasm; perinuclear region (By similarity). Localizes to the nuclear e ...	intracellular membrane-bound organelle [ISS] nuclear envelope [ISS]			326
Q99MP8 UniProt NPD GO	BRAP_MOUSE	BRCA1-associated protein (EC 6.3.2.-) (BRAP2) (Impedes mitogenic signal propagation) (IMP)	0.59	-	nuc	0	Cytoplasm (By similarity)				591
P41886 UniProt NPD GO	BAT41_CAEEL	BTB and MATH domain-containing protein 41	0.59	-	nuc	0					418
Q8BFX3 UniProt NPD GO	KCTD3_MOUSE	BTB/POZ domain-containing protein KCTD3	0.59	-	nuc	0					815

You are viewing entries 19401 to 19450 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.