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
P32755 UniProt NPD GO	HPPD_RAT	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (4-hydroxyphenylpyruvic acid oxida ...	0.11	-	cyt	0	Cytoplasm. Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein. Golgi ...	endoplasmic reticulum membrane [IDA] Golgi membrane [IDA]		1SQI	392
Q27203 UniProt NPD GO	HPPD_TETTH	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase) (4-hydroxyphenylpyruvic ...	0.11	-	cyt	0					404
Q9Y7L8 UniProt NPD GO	RS0A_SCHPO	40S ribosomal protein S0-A	0.11	-	cyt	0		small ribosomal subunit [TAS]			292
Q9P546 UniProt NPD GO	RS0B_SCHPO	40S ribosomal protein S0-B	0.11	-	mit	0		small ribosomal subunit [TAS]			287
Q9VB14 UniProt NPD GO	RS10A_DROME	40S ribosomal protein S10a	0.11	-	cyt	0	Cytoplasm (By similarity)				163
Q9M5M1 UniProt NPD GO	RS11_EUPES	40S ribosomal protein S11	0.11	-	cyt	0					159
P16181 UniProt NPD GO	RS11A_ARATH	40S ribosomal protein S11-1	0.11	-	nuc	0	Cytoplasm				160
Q8I7U0 UniProt NPD GO	RS13_PLUXY	40S ribosomal protein S13	0.11	-	mit	0					150
O14150 UniProt NPD GO	RS14_SCHPO	40S ribosomal protein S14	0.11	-	cyt	0					139
P06367 UniProt NPD GO	RS14A_YEAST	40S ribosomal protein S14-A (RP59A)	0.11	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS] small nucleolar ribonucleoprotein complex [IPI]		1K5X	136
Q90YQ8 UniProt NPD GO	RS15A_ICTPU	40S ribosomal protein S15a	0.11	-	cyt	0					129
P07280 UniProt NPD GO	RS19A_YEAST	40S ribosomal protein S19-A (S16A) (YS16) (RP55) (YP45)	0.11	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			143
P07281 UniProt NPD GO	RS19B_YEAST	40S ribosomal protein S19-B (S16B) (YS16) (RP55)	0.11	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			143
Q9CQR2 UniProt NPD GO	RS21_MOUSE	40S ribosomal protein S21	0.11	-	cyt	0		ribosome [ISS]			83
Q3E7Y3 UniProt NPD GO	RS22B_YEAST	40S ribosomal protein S22-B (S24) (YS22) (RP50) (YP58)	0.11	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]			129
Q9ZNS1 UniProt NPD GO	RS7_AVIMR	40S ribosomal protein S7	0.11	-	nuc	0					190
P48827 UniProt NPD GO	CHI4_TRIHA	42 kDa endochitinase precursor (EC 3.2.1.14)	0.11	-	vac	0	Secreted protein				423
Q8BGM7 UniProt NPD GO	AAKG3_MOUSE	5'-AMP-activated protein kinase subunit gamma-3 (AMPK gamma-3 chain) (AMPK gamma3)	0.11	-	end	0					489
Q5TFE4 UniProt NPD GO	NT5D1_HUMAN	5'-nucleotidase domain-containing protein 1	0.11	-	cyt	0					455
P22557 UniProt NPD GO	HEM0_HUMAN	5-aminolevulinate synthase, erythroid-specific, mitochondrial precursor (EC 2.3.1.37) (5-aminolevuli ...	0.11	-	mit	0	Mitochondrion; mitochondrial matrix		301300		587
O50008 UniProt NPD GO	METE_ARATH	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Vitamin-B12-ind ...	0.11	-	nuc	0	Cytoplasm (Potential)			1U22	765
Q75WB5 UniProt NPD GO	OPLA_BOVIN	5-oxoprolinase (EC 3.5.2.9) (5-oxo-L-prolinase) (Pyroglutamase) (5-OPase)	0.11	-	cyt	0					1288
O14841 UniProt NPD GO	OPLA_HUMAN	5-oxoprolinase (EC 3.5.2.9) (5-oxo-L-prolinase) (Pyroglutamase) (5-OPase)	0.11	-	cyt	0					1288
P97608 UniProt NPD GO	OPLA_RAT	5-oxoprolinase (EC 3.5.2.9) (5-oxo-L-prolinase) (Pyroglutamase) (5-OPase)	0.11	-	cyt	0					1288
P22798 UniProt NPD GO	RK15_SPIOL	50S ribosomal protein L15, chloroplast (CL15) (Fragments)	0.11	-	nuc	0	Plastid; chloroplast				91
P25864 UniProt NPD GO	RK9_ARATH	50S ribosomal protein L9, chloroplast precursor (CL9)	0.11	-	mit	0	Plastid; chloroplast				197
P14790 UniProt NPD GO	68MP_BOVIN	6.8 kDa mitochondrial proteolipid	0.11	-	cyt	0	Mitochondrion				60
P49464 UniProt NPD GO	CH60_ODOSI	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.11	-	nuc	0	Plastid; chloroplast				528
Q5ZL72 UniProt NPD GO	CH60_CHICK	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.11	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				573
Q29214 UniProt NPD GO	RLA0_PIG	60S acidic ribosomal protein P0 (L10E) (Fragment)	0.11	-	cyt	0					93
Q9FE58 UniProt NPD GO	RL223_ARATH	60S ribosomal protein L22-3	0.11	-	nuc	0					124
P48158 UniProt NPD GO	RL23_CAEEL	60S ribosomal protein L23	0.11	-	cyt	0					140
P02406 UniProt NPD GO	RL28_YEAST	60S ribosomal protein L28 (L27A) (L29) (YL24) (RP62)	0.11	+	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS] nucleus [IMP]		1K5Y	148
O48558 UniProt NPD GO	RL30_MAIZE	60S ribosomal protein L30	0.11	-	nuc	0					112
P49153 UniProt NPD GO	RL30_TRYBB	60S ribosomal protein L30	0.11	-	mit	0					105
P35679 UniProt NPD GO	RL4A_SCHPO	60S ribosomal protein L4-A (L2)	0.11	-	cyt	0					363
Q751L1 UniProt NPD GO	RL43_ASHGO	60S ribosomal protein L43	0.11	-	nuc	0					92
Q4PSL7 UniProt NPD GO	RL82_ARATH	60S ribosomal protein L8-2	0.11	-	mit	0					260
P17076 UniProt NPD GO	RL8A_YEAST	60S ribosomal protein L8-A (L7A-2) (L4-2) (YL5) (RP6) (Maintenance of killer protein 7)	0.11	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1K5Y	255
P31334 UniProt NPD GO	RM09_YEAST	60S ribosomal protein L9, mitochondrial precursor (YmL9)	0.11	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [TAS]			269
Q90611 UniProt NPD GO	MMP2_CHICK	72 kDa type IV collagenase precursor (EC 3.4.24.24) (72 kDa gelatinase) (Matrix metalloproteinase-2) ...	0.11	-	cyt	0					663
P12794 UniProt NPD GO	GRP78_PLAFA	78 kDa glucose-regulated protein homolog (GRP 78) (Antigenic heat shock protein 70) (HSP70-2) (Fragm ...	0.11	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				279
Q9VCY8 UniProt NPD GO	ADRL_DROME	ADIPOR-like receptor CG5315	0.11	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			444
Q75F81 UniProt NPD GO	IZH3_ASHGO	ADIPOR-like receptor IZH3	0.11	-	end	7	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				419
Q64244 UniProt NPD GO	CD38_RAT	ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (CD38 homolog ...	0.11	-	nuc	1 *	Membrane; single-pass type II membrane protein	nucleus [IDA]			303
P40946 UniProt NPD GO	ARF3_DROME	ADP-ribosylation factor 3	0.11	-	cyt	0					174
P51645 UniProt NPD GO	ARF6_XENLA	ADP-ribosylation factor 6	0.11	-	cyt	0					174
Q6NZW8 UniProt NPD GO	ARL8B_BRARE	ADP-ribosylation factor-like protein 8B	0.11	-	cyt	0	Endosome; late endosome (By similarity). Lysosome (By similarity). Alternatively, may localize with ...				186
Q5R5A1 UniProt NPD GO	ADT2_PONPY	ADP/ATP translocase 2 (Adenine nucleotide translocator 2) (ANT 2) (ADP,ATP carrier protein 2) (Solut ...	0.11	-	cyt	2	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein (By similarity)				297
P54672 UniProt NPD GO	AP2M_DICDI	AP-2 complex subunit mu (Clathrin coat assembly protein AP50) (Clathrin coat-associated protein AP50 ...	0.11	-	cyt	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane				439

You are viewing entries 62201 to 62250 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.