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
P14712 UniProt NPD GO	PHYA_ARATH	Phytochrome A	0.45	-	mit	0					1122
P93528 UniProt NPD GO	PHYC_SORBI	Phytochrome C	0.45	-	mit	0					1135
Q9TJQ5 UniProt NPD GO	RK2_PROWI	Plastid 50S ribosomal protein L2	0.45	+	nuc	0	Plastid				273
P32767 UniProt NPD GO	PDR6_YEAST	Pleiotropic drug resistance regulatory protein 6	0.45	-	nuc	0		cytoplasm [IDA] nuclear pore [IDA]			1081
Q8T6B9 UniProt NPD GO	PUF68_DROME	Poly U-binding-splicing factor half pint (68 kDa poly U-binding-splicing factor) (Protein half pint) ...	0.45	-	nuc	0	Nucleus	nucleus [IDA]			637
P21187 UniProt NPD GO	PABP_DROME	Polyadenylate-binding protein (Poly(A)-binding protein) (PABP)	0.45	-	cyt	0		cytoplasm [IDA]			634
Q5AZX0 UniProt NPD GO	PFS2_EMENI	Polyadenylation factor subunit 2	0.45	-	nuc	0	Nucleus (By similarity)				567
Q7Z7M9 UniProt NPD GO	GALT5_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 5 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.45	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				940
O73606 UniProt NPD GO	KCNG2_CHICK	Potassium voltage-gated channel subfamily G member 2 (Voltage-gated potassium channel subunit Kv6.2) ...	0.45	-	end	5	Membrane; multi-pass membrane protein				518
Q920E3 UniProt NPD GO	KCNH5_MOUSE	Potassium voltage-gated channel subfamily H member 5 (Voltage-gated potassium channel subunit Kv10.2 ...	0.45	-	end	4	Membrane; multi-pass membrane protein				988
Q4WM95 UniProt NPD GO	FIP1_ASPFU	Pre-mRNA polyadenylation factor fip1	0.45	-	nuc	0	Nucleus (By similarity)				338
Q5BGP1 UniProt NPD GO	CWC22_EMENI	Pre-mRNA-splicing factor cwc22	0.45	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				545
Q6ZG25 UniProt NPD GO	SECY_ORYSA	Preprotein translocase secY subunit, chloroplast precursor (CpSecY)	0.45	-	end	8	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				556
Q9VCX3 UniProt NPD GO	RM45_DROME	Probable 39S ribosomal protein L45, mitochondrial precursor	0.45	-	cyt	0	Mitochondrion (By similarity)	mitochondrion [ISS]			361
Q9SJ12 UniProt NPD GO	ATP7_ARATH	Probable ATP synthase 24 kDa subunit, mitochondrial precursor (EC 3.6.3.14)	0.45	-	mit	0	Mitochondrion				240
Q61496 UniProt NPD GO	DDX4_MOUSE	Probable ATP-dependent RNA helicase DDX4 (EC 3.6.1.-) (DEAD box protein 4) (VASA homolog) (Mvh)	0.45	-	nuc	0	Cytoplasm. Cytoplasm; perinuclear region	cytoplasm [IDA] nucleus [IDA]			702
Q9P7X6 UniProt NPD GO	PSF1_SCHPO	Probable DNA replication complex GINS protein psf1	0.45	-	nuc	0	Nucleus (By similarity)				202
Q9R1K6 UniProt NPD GO	GPR34_MOUSE	Probable G-protein coupled receptor 34	0.45	-	end	7 *	Membrane; multi-pass membrane protein (By similarity)				375
Q5AD27 UniProt NPD GO	TAH18_CANAL	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.45	-	cyt	0					589
Q6BR77 UniProt NPD GO	TAH18_DEBHA	Probable NADPH reductase TAH18 (EC 1.-.-.-)	0.45	-	cyt	0					603
Q9LQ10 UniProt NPD GO	1A110_ARATH	Probable aminotransferase ACS10 (EC 2.6.1.-)	0.45	-	nuc	1 *					557
Q9Z100 UniProt NPD GO	CPXM_MOUSE	Probable carboxypeptidase X precursor (EC 3.4.17.-) (Metallocarboxypeptidase CPX-1)	0.45	+	vac	0	Secreted protein (Probable)	extracellular space [IDA]			722
Q8LET2 UniProt NPD GO	NUD11_ARATH	Probable coenzyme A diphosphatase NUDT11 (EC 3.6.1.-) (Nudix hydrolase 11) (AtNUDT11)	0.45	-	nuc	0	Peroxisome (Potential)				222
O74351 UniProt NPD GO	NFS1_SCHPO	Probable cysteine desulfurase, mitochondrial precursor (EC 2.8.1.7)	0.45	+	nuc	0	Mitochondrion (By similarity)				498
Q10425 UniProt NPD GO	IF39_SCHPO	Probable eukaryotic translation initiation factor 3 90 kDa subunit (eIF3 p90)	0.45	-	cyt	0		cytoplasm [IDA]			725
Q18406 UniProt NPD GO	EXOC5_CAEEL	Probable exocyst complex component 5 (Exocyst complex component Sec10)	0.45	-	mit	0					659
Q27484 UniProt NPD GO	H2B3_CAEEL	Probable histone H2B 3	0.45	-	nuc	0	Nucleus				122
P49868 UniProt NPD GO	HR3_GALME	Probable nuclear hormone receptor HR3 (GHR3)	0.45	-	nuc	0	Nucleus (Potential)				557
Q8I1F6 UniProt NPD GO	PRPA3_DROER	Probable phenoloxidase subunit A3 precursor (EC 1.14.18.1) (Tyrosinase A3) (PO A3)	0.45	-	cyt	0	Secreted protein (By similarity)	extracellular region [ISS]			683
O75110 UniProt NPD GO	ATP9A_HUMAN	Probable phospholipid-transporting ATPase IIA (EC 3.6.3.1) (ATPase class II type 9A) (ATPase IIA)	0.45	-	end	10	Membrane; multi-pass membrane protein (By similarity)		609126		1047
Q12609 UniProt NPD GO	STCF_EMENI	Probable sterigmatocystin biosynthesis P450 monooxygenase STCF (EC 1.14.-.-) (Cytochrome P450 60A2)	0.45	-	end	1					506
Q7RY78 UniProt NPD GO	SEN15_NEUCR	Probable tRNA-splicing endonuclease subunit sen-15 (tRNA-intron endonuclease sen-15)	0.45	-	nuc	0					223
P43551 UniProt NPD GO	YFF2_YEAST	Probable transcriptional regulatory protein YFL052W	0.45	-	mit	0	Nucleus (Probable)				465
Q8L7H3 UniProt NPD GO	XTH29_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 29 precursor (EC 2.4.1.207) (At-XTH29) (X ...	0.45	-	mit	0	Secreted protein; extracellular space; apoplast (Probable)				357
Q8WUM4 UniProt NPD GO	PDC6I_HUMAN	Programmed cell death 6-interacting protein (PDCD6-interacting protein) (ALG-2-interacting protein 1 ...	0.45	-	nuc	0	Cytoplasm; cytosol	cytosol [TAS]	608074		868
P01236 UniProt NPD GO	PRL_HUMAN	Prolactin precursor (PRL)	0.45	-	exc	0	Secreted protein		176760	1RW5	227
P51888 UniProt NPD GO	PRELP_HUMAN	Prolargin precursor (Proline-arginine-rich end leucine-rich repeat protein)	0.45	-	mit	0	Secreted protein; extracellular space; extracellular matrix	extracellular matrix (sensu Metazoa) [TAS]	601914		382
P27697 UniProt NPD GO	ABC1_YEAST	Protein ABC1, mitochondrial precursor	0.45	-	mit	0	Mitochondrion (Probable)	mitochondrion [IDA]			501
Q4WPM8 UniProt NPD GO	AF9_ASPFU	Protein AF-9 homolog	0.45	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				272
P55007 UniProt NPD GO	BART1_RAT	Protein BART-1 (Balloon angioplasty-responsive transcript 1)	0.45	-	nuc	0					235
Q9CWN7 UniProt NPD GO	CB029_MOUSE	Protein C2orf29 homolog	0.45	-	nuc	0					505
Q8IYR0 UniProt NPD GO	CF165_HUMAN	Protein C6orf165	0.45	-	mit	0					622
Q8CI78 UniProt NPD GO	CF096_MOUSE	Protein C6orf96 homolog	0.45	-	exc	0					450
Q9HBL7 UniProt NPD GO	CI046_HUMAN	Protein C9orf46	0.45	-	nuc	1	Membrane; multi-pass membrane protein (Potential)				147
Q9LV85 UniProt NPD GO	CPR5_ARATH	Protein CPR-5 (Protein constitutive expression of pathogenesis-related genes 5) (Protein constitutiv ...	0.45	+	end	4	Membrane; multi-pass membrane protein (Potential)				564
Q8L925 UniProt NPD GO	CRC_ARATH	Protein CRABS CLAW	0.45	-	nuc	0	Nucleus (By similarity)				181
Q8N2G8 UniProt NPD GO	LGP1_HUMAN	Protein D11Lgp1 homolog precursor	0.45	-	exc	0	Endoplasmic reticulum. Nucleus; nuclear envelope (By similarity)		608587		530
P38333 UniProt NPD GO	ENP1_YEAST	Protein ENP1	0.45	-	nuc	0	Nucleus	nucleolus [TAS] nucleus [IDA]			483
Q65WT0 UniProt NPD GO	G10B_ORYSA	Protein G10 homolog 2	0.45	-	nuc	0	Nucleus (Potential)				145
Q28BX9 UniProt NPD GO	K0528_XENTR	Protein KIAA0528 homolog	0.45	-	nuc	0					1014

You are viewing entries 28501 to 28550 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.