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
O88736 UniProt NPD GO	DHB7_MOUSE	3-keto-steroid reductase (EC 1.1.1.270) (Estradiol 17-beta-dehydrogenase 7) (EC 1.1.1.62) (17-beta-H ...	0.06	-	end	1	Membrane; single-pass membrane protein	endoplasmic reticulum [IDA]			334
Q8LF48 UniProt NPD GO	THIK1_ARATH	3-ketoacyl-CoA thiolase 1, peroxisomal precursor (EC 2.3.1.16) (Beta-ketothiolase 1) (Acetyl-CoA acy ...	0.06	-	cyt	0	Peroxisome (By similarity)				443
P31176 UniProt NPD GO	FABH_PORUM	3-oxoacyl-[acyl-carrier-protein] synthase 3 (EC 2.3.1.41) (3-oxoacyl-[acyl-carrier-protein] synthase ...	0.06	-	end	0	Plastid; chloroplast				326
P34754 UniProt NPD GO	PHYB_ASPNG	3-phytase B precursor (EC 3.1.3.8) (Myo-inositol-hexaphosphate 3-phosphohydrolase B) (3 phytase B) ( ...	0.06	-	exc	0					479
P80853 UniProt NPD GO	CWP09_ARATH	30 kDa cell wall protein (Fragment)	0.06	-		0	Cell wall				15
P80852 UniProt NPD GO	CWP32_ARATH	31 kDa cell wall protein (Fragment)	0.06	-		0	Cell wall				14
Q09581 UniProt NPD GO	LEC3_CAEEL	32 kDa beta-galactoside-binding lectin lec-3 (32 kDa GBP)	0.06	-	cyt	0					297
P80850 UniProt NPD GO	CWP30_ARATH	33 kDa cell wall protein (Fragment)	0.06	-		0	Cell wall				14
P80823 UniProt NPD GO	CWP27_LYCES	35 kDa cell wall protein (Fragment)	0.06	-		0	Cell wall				15
Q2YDI0 UniProt NPD GO	RM11_BOVIN	39S ribosomal protein L11, mitochondrial precursor (L11mt) (MRP-L11)	0.06	-	nuc	0	Mitochondrion (By similarity)				192
Q9Y3B7 UniProt NPD GO	RM11_HUMAN	39S ribosomal protein L11, mitochondrial precursor (L11mt) (MRP-L11)	0.06	-	cyt	0	Mitochondrion	mitochondrial ribosome [NAS]			192
P31687 UniProt NPD GO	4CL2_SOYBN	4-coumarate--CoA ligase 2 (EC 6.2.1.12) (4CL 2) (4-coumaroyl-CoA synthase 2) (Clone 4CL16)	0.06	-	end	0					562
O42764 UniProt NPD GO	HPPD_MYCGR	4-hydroxyphenylpyruvate dioxygenase (EC 1.13.11.27) (4HPPD) (HPD) (HPPDase)	0.06	-	nuc	0					419
Q08752 UniProt NPD GO	PPID_HUMAN	40 kDa peptidyl-prolyl cis-trans isomerase (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-40) (CYP-40 ...	0.06	-	cyt	0	Cytoplasm		601753		369
O94017 UniProt NPD GO	RS16_CANAL	40S ribosomal protein S16	0.06	-	cyt	0					142
O60144 UniProt NPD GO	RS16_SCHPO	40S ribosomal protein S16	0.06	-	cyt	0					140
P40213 UniProt NPD GO	RS16_YEAST	40S ribosomal protein S16 (RP61R)	0.06	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [TAS]		1K5X	142
Q9CZX8 UniProt NPD GO	RS19_MOUSE	40S ribosomal protein S19	0.06	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [ISS] nucleolus [ISS]			144
P17074 UniProt NPD GO	RS19_RAT	40S ribosomal protein S19	0.06	-	cyt	0		cytosolic small ribosomal subunit (sensu Eu... [ISS] nucleolus [ISS]			144
O74892 UniProt NPD GO	RS2_SCHPO	40S ribosomal protein S2	0.06	+	mit	0					253
Q4KTC0 UniProt NPD GO	RS21_SUBDO	40S ribosomal protein S21	0.06	-	cyt	0					86
Q9HE74 UniProt NPD GO	RS23_NEUCR	40S ribosomal protein S23	0.06	-	mit	0					145
Q8SQM3 UniProt NPD GO	RS3_ENCCU	40S ribosomal protein S3	0.06	-	cyt	0					228
P52813 UniProt NPD GO	RS3A_ANOGA	40S ribosomal protein S3a (C3 protein)	0.06	-	nuc	0	Cytoplasm (By similarity)				268
P41042 UniProt NPD GO	RS4_DROME	40S ribosomal protein S4	0.06	-	mit	0					261
P49401 UniProt NPD GO	RS4_XENLA	40S ribosomal protein S4	0.06	-	mit	0					262
Q6PBC4 UniProt NPD GO	RS4_XENTR	40S ribosomal protein S4	0.06	-	mit	0					262
O80377 UniProt NPD GO	RSSA_DAUCA	40S ribosomal protein SA (p40)	0.06	-	cyt	0	Cytoplasm (By similarity)				297
P49348 UniProt NPD GO	APA2_KLULA	5',5'''-P-1,P-4-tetraphosphate phosphorylase 2 (EC 2.7.7.53) (Diadenosine 5',5'''-P1,P4-tetraphospha ...	0.06	-	nuc	0					331
O14092 UniProt NPD GO	HEM1_SCHPO	5-aminolevulinate synthase, mitochondrial precursor (EC 2.3.1.37) (5-aminolevulinic acid synthase) ( ...	0.06	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				558
P34969 UniProt NPD GO	5HT7R_HUMAN	5-hydroxytryptamine 7 receptor (5-HT-7) (Serotonin receptor 7) (5-HT-X) (5HT7)	0.06	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	182137		479
Q42662 UniProt NPD GO	METE_SOLSC	5-methyltetrahydropteroyltriglutamate--homocysteine methyltransferase (EC 2.1.1.14) (Vitamin-B12-ind ...	0.06	-	nuc	0	Cytoplasm (Potential)				764
P36212 UniProt NPD GO	RK123_ARATH	50S ribosomal protein L12-3, chloroplast precursor (CL12-C)	0.06	-	mit	0	Plastid; chloroplast				187
P80828 UniProt NPD GO	CWP04_ARATH	54 kDa cell wall protein (Fragment)	0.06	-		0	Cell wall				20
P31072 UniProt NPD GO	6PGD_TRYBB	6-phosphogluconate dehydrogenase, decarboxylating (EC 1.1.1.44)	0.06	-	cyt	0				1PGJ	479
O95336 UniProt NPD GO	6PGL_HUMAN	6-phosphogluconolactonase (EC 3.1.1.31) (6PGL)	0.06	-	mit	0			604951		258
Q37757 UniProt NPD GO	CH60_CYAPA	60 kDa chaperonin (Protein Cpn60) (groEL protein)	0.06	-	cyt	0	Plastid; cyanelle				541
P18687 UniProt NPD GO	CH60_CRIGR	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix				573
P63038 UniProt NPD GO	CH60_MOUSE	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			573
P63039 UniProt NPD GO	CH60_RAT	60 kDa heat shock protein, mitochondrial precursor (Hsp60) (60 kDa chaperonin) (CPN60) (Heat shock p ...	0.06	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				573
P29764 UniProt NPD GO	RLA0_CHERU	60S acidic ribosomal protein P0 (Light-induced 34 kDa protein)	0.06	-	cyt	0					321
P42038 UniProt NPD GO	RLA3_CLAHE	60S acidic ribosomal protein P2 (Allergen Cla h 3) (Cla h III)	0.06	-	exc	0					111
O82574 UniProt NPD GO	RL21_CYAPA	60S ribosomal protein L21	0.06	-	mit	0					161
Q9M9W1 UniProt NPD GO	RL222_ARATH	60S ribosomal protein L22-2	0.06	-	cyt	0					124
Q93140 UniProt NPD GO	RL23_BRUMA	60S ribosomal protein L23	0.06	-	cyt	0					140
Q9GNE2 UniProt NPD GO	RL23_AEDAE	60S ribosomal protein L23 (L17A)	0.06	-	cyt	0					140
P48159 UniProt NPD GO	RL23_DROME	60S ribosomal protein L23 (L17A)	0.06	-	cyt	0					140
P36526 UniProt NPD GO	RM27_YEAST	60S ribosomal protein L27, mitochondrial precursor (YmL27)	0.06	-	nuc	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			146
P39095 UniProt NPD GO	RL30_LEIMA	60S ribosomal protein L30	0.06	-	mit	0					104
P58375 UniProt NPD GO	RL30_SPOFR	60S ribosomal protein L30	0.06	-	mit	0					113

You are viewing entries 71351 to 71400 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.