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
Q43643 UniProt NPD GO	14332_SOLTU	14-3-3-like protein RA215	0.19	-	nuc	0					254
Q96291 UniProt NPD GO	BAS1_ARATH	2-cys peroxiredoxin BAS1, chloroplast precursor (EC 1.11.1.15)	0.19	-	mit	0	Plastid; chloroplast				266
P48391 UniProt NPD GO	2PS_GERHY	2-pyrone synthase (EC 2.3.1.-) (2-PS) (G2ps1)	0.19	-	cyt	0				1QLV	402
O42931 UniProt NPD GO	PRS7_SCHPO	26S protease regulatory subunit 7 homolog	0.19	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				438
P41836 UniProt NPD GO	PRS8_SCHPO	26S protease regulatory subunit 8 homolog (Protein let1)	0.19	-	nuc	0	Cytoplasm (Potential). Nucleus (Potential)				403
Q25544 UniProt NPD GO	PRS8_NAEFO	26S protease regulatory subunit 8 homolog (TAT-binding protein homolog)	0.19	-	mit	0	Cytoplasm (Potential). Nucleus (Potential)				414
Q6FPV6 UniProt NPD GO	RPN1_CANGA	26S proteasome regulatory subunit RPN1	0.19	-	end	0					983
Q8BKT8 UniProt NPD GO	S1769_MOUSE	26S proteasome-associated UCH37-interacting protein 1	0.19	-	cyt	0					248
Q99N85 UniProt NPD GO	RT18A_MOUSE	28S ribosomal protein S18a, mitochondrial precursor (MRP-S18-a) (Mrps18a) (MRP-S18-3)	0.19	-	mit	0	Mitochondrion				196
P27364 UniProt NPD GO	3BHS3_RAT	3 beta-hydroxysteroid dehydrogenase type 3 (3 beta-hydroxysteroid dehydrogenase type III) (3Beta-HSD ...	0.19	-	cyt	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
O46516 UniProt NPD GO	3BHS_HORSE	3 beta-hydroxysteroid dehydrogenase/delta 5-->4-isomerase (3Beta-HSD) [Includes: 3-beta-hydroxy-delt ...	0.19	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein. Mitochondrion; ...				372
P09110 UniProt NPD GO	THIK_HUMAN	3-ketoacyl-CoA thiolase, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase) (Acetyl-CoA acyltra ...	0.19	-	cyt	0	Peroxisome	peroxisome [NAS]	604054		424
O01949 UniProt NPD GO	ALL3_AEDAE	30 kDa salivary gland allergen Aed a 3 precursor	0.19	-	exc	0	Secreted protein (Potential)				253
P28163 UniProt NPD GO	SM30_STRPU	30 kDa spicule matrix protein precursor	0.19	-	end	0					290
P80808 UniProt NPD GO	CWP11_LYCES	35 kDa cell wall protein (Fragment)	0.19	-		0	Cell wall				10
P17649 UniProt NPD GO	GATA_YEAST	4-aminobutyrate aminotransferase (EC 2.6.1.19) (Gamma-amino-N-butyrate transaminase) (GABA transamin ...	0.19	-	cyt	0		intracellular [IC]			471
Q07254 UniProt NPD GO	RS10_XENLA	40S ribosomal protein S10	0.19	-	nuc	0	Cytoplasm				165
Q9SW09 UniProt NPD GO	RS10A_ARATH	40S ribosomal protein S10-1	0.19	-	cyt	0	Cytoplasm (By similarity)				177
P48150 UniProt NPD GO	RS14_CAEEL	40S ribosomal protein S14	0.19	-	cyt	0					152
P62265 UniProt NPD GO	RS14_CRIGR	40S ribosomal protein S14	0.19	+	nuc	0					150
P62263 UniProt NPD GO	RS14_HUMAN	40S ribosomal protein S14	0.19	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	130620		150
P62264 UniProt NPD GO	RS14_MOUSE	40S ribosomal protein S14	0.19	+	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [ISS]			150
Q9FY65 UniProt NPD GO	RS15C_ARATH	40S ribosomal protein S15-3	0.19	-	cyt	0	Cytoplasm				150
P46293 UniProt NPD GO	RS16_GOSHI	40S ribosomal protein S16	0.19	-	cyt	0	Cytoplasm				145
Q90YQ7 UniProt NPD GO	RS16_ICTPU	40S ribosomal protein S16	0.19	-	cyt	0					146
P08708 UniProt NPD GO	RS17_HUMAN	40S ribosomal protein S17	0.19	-	nuc	0		cytosolic small ribosomal subunit (sensu Eu... [IDA]	180472		134
Q9LF30 UniProt NPD GO	RS192_ARATH	40S ribosomal protein S19-2	0.19	-	nuc	0					143
O65751 UniProt NPD GO	RSSA_CICAR	40S ribosomal protein SA (p40)	0.19	-	nuc	0	Cytoplasm				300
Q5R801 UniProt NPD GO	AAKB1_PONPY	5'-AMP-activated protein kinase subunit beta-1 (AMPK beta-1 chain) (AMPKb)	0.19	-	nuc	0					269
P08680 UniProt NPD GO	HEM0_MOUSE	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.19	-	mit	0	Mitochondrion; mitochondrial matrix			1H7J	587
Q6XXX9 UniProt NPD GO	5HT1A_CANFA	5-hydroxytryptamine 1A receptor (5-HT-1A) (Serotonin receptor 1A) (5-HT1A)	0.19	-	end	7 *	Membrane; multi-pass membrane protein				423
P35363 UniProt NPD GO	5HT2A_MOUSE	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.19	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				471
Q5R4Q6 UniProt NPD GO	5HT2A_PONPY	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.19	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				471
P14842 UniProt NPD GO	5HT2A_RAT	5-hydroxytryptamine 2A receptor (5-HT-2A) (Serotonin receptor 2A) (5-HT-2)	0.19	-	end	7	Cell membrane; multi-pass membrane protein. Localizes to the post-synaptic thickening of axo-dendrit ...				471
P46224 UniProt NPD GO	CH60_PYRSA	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.19	-	mit	0	Plastid; chloroplast				585
Q09533 UniProt NPD GO	RL10_CAEEL	60S ribosomal protein L10 (QM protein homolog)	0.19	-	mit	0					214
Q10157 UniProt NPD GO	RL11_SCHPO	60S ribosomal protein L11	0.19	-	cyt	0					174
Q12672 UniProt NPD GO	RL21B_YEAST	60S ribosomal protein L21-B	0.19	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			160
P61356 UniProt NPD GO	RL27_BOVIN	60S ribosomal protein L27	0.19	-	cyt	0					135
P61357 UniProt NPD GO	RL27_CERNI	60S ribosomal protein L27	0.19	-	cyt	0					135
P61355 UniProt NPD GO	RL27_CHICK	60S ribosomal protein L27	0.19	-	cyt	0					135
P61353 UniProt NPD GO	RL27_HUMAN	60S ribosomal protein L27	0.19	-	cyt	0		ribosome [TAS]	607526		135
P61358 UniProt NPD GO	RL27_MOUSE	60S ribosomal protein L27	0.19	-	cyt	0					135
P61354 UniProt NPD GO	RL27_RAT	60S ribosomal protein L27	0.19	-	cyt	0					135
Q90YT0 UniProt NPD GO	RL37A_ICTPU	60S ribosomal protein L37a	0.19	-	nuc	0					91
O17570 UniProt NPD GO	RL38_CAEEL	60S ribosomal protein L38	0.19	-	nuc	0					70
Q9GLE5 UniProt NPD GO	MMP2_BOVIN	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.19	-	mit	0					661
Q5XIY4 UniProt NPD GO	ACN9_BRARE	ACN9 protein homolog, mitochondrial precursor	0.19	-	mit	0	Mitochondrion (Potential)				123
Q5VAN0 UniProt NPD GO	CD38_MACFA	ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (CD38 homolog ...	0.19	-	cyt	1 *	Membrane; single-pass type II membrane protein (By similarity)				301
Q4R4S4 UniProt NPD GO	ARL8B_MACFA	ADP-ribosylation factor-like protein 8B	0.19	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186

You are viewing entries 51451 to 51500 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.