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
P34266 UniProt NPD GO	PGL2_CAEEL	P granule abnormality protein 2	0.61	-	cyt	0					532
Q01102 UniProt NPD GO	LYAM3_MOUSE	P-selectin precursor (Granule membrane protein 140) (GMP-140) (PADGEM) (Leukocyte-endothelial cell a ...	0.61	-	nuc	1	Membrane; single-pass type I membrane protein	membrane [IDA]			768
Q9C810 UniProt NPD GO	Y1342_ARATH	PHD finger protein At1g33420	0.61	-	nuc	0				1WEE	697
Q03052 UniProt NPD GO	PO3F1_HUMAN	POU domain, class 3, transcription factor 1 (Octamer-binding transcription factor 6) (Oct-6) (POU-do ...	0.61	+	cyt	0	Nucleus		602479		448
P20267 UniProt NPD GO	PO3F1_RAT	POU domain, class 3, transcription factor 1 (Octamer-binding transcription factor 6) (Oct-6) (POU-do ...	0.61	+	cyt	0	Nucleus	nucleus [TAS]			451
Q5TM49 UniProt NPD GO	PO5F1_MACMU	POU domain, class 5, transcription factor 1 (Octamer-binding transcription factor 3) (Oct-3)	0.61	+	cyt	0	Nucleus (By similarity)				360
O14813 UniProt NPD GO	PHX2A_HUMAN	Paired mesoderm homeobox protein 2A (Paired-like homeobox 2A) (Aristaless homeobox protein homolog) ...	0.61	+	nuc	0	Nucleus (By similarity)		602753		284
Q9BXP8 UniProt NPD GO	PAP2_HUMAN	Pappalysin-2 precursor (EC 3.4.24.-) (Pregnancy-associated plasma protein-A2) (PAPP-A2) (Pregnancy-a ...	0.61	-	nuc	0	Secreted protein (By similarity)	intracellular [NAS]			1791
P32871 UniProt NPD GO	PK3CA_BOVIN	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153) (PI3-k ...	0.61	-	nuc	0					1068
P42337 UniProt NPD GO	PK3CA_MOUSE	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit alpha isoform (EC 2.7.1.153) (PI3-k ...	0.61	-	nuc	0		lamellipodium [IDA] phosphoinositide 3-kinase complex [IPI]			1068
Q9JHG7 UniProt NPD GO	PK3CG_MOUSE	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit gamma isoform (EC 2.7.1.153) (PI3-k ...	0.61	+	cyt	0					1102
P56859 UniProt NPD GO	MET16_EMENI	Phosphoadenosine phosphosulfate reductase (EC 1.8.4.8) (PAPS reductase, thioredoxin dependent) (PAdo ...	0.61	-	cyt	0					293
Q9MAH0 UniProt NPD GO	CAPP1_ARATH	Phosphoenolpyruvate carboxylase 1 (EC 4.1.1.31) (PEPCase 1) (PEPC 1) (AtPPC1)	0.61	-	nuc	0	Cytoplasm (By similarity)				967
P16097 UniProt NPD GO	CAPP2_MESCR	Phosphoenolpyruvate carboxylase 2 (EC 4.1.1.31) (PEPCase 2) (PEPC 2)	0.61	-	cyt	0	Cytoplasm				960
P21782 UniProt NPD GO	PTN_BOVIN	Pleiotrophin precursor (PTN) (Heparin-binding growth-associated molecule) (HB-GAM) (Heparin-binding ...	0.61	-	nuc	1 *	Secreted protein				168
Q7Z3K3 UniProt NPD GO	POGZ_HUMAN	Pogo transposable element with ZNF domain	0.61	-	end	0	Nucleus (Probable)				1410
Q02280 UniProt NPD GO	KCNAE_DROME	Potassium voltage-gated channel protein eag (Ether-a-go-go protein)	0.61	+	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]			1174
Q05037 UniProt NPD GO	KCNA4_BOVIN	Potassium voltage-gated channel subfamily A member 4 (Voltage-gated potassium channel subunit Kv1.4) ...	0.61	-	end	3	Membrane; multi-pass membrane protein				660
P58126 UniProt NPD GO	KCNQ3_BOVIN	Potassium voltage-gated channel subfamily KQT member 3 (Voltage-gated potassium channel subunit Kv7. ...	0.61	-	end	5	Membrane; multi-pass membrane protein				866
Q6BU84 UniProt NPD GO	CWC22_DEBHA	Pre-mRNA-splicing factor CWC22	0.61	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				637
Q752B6 UniProt NPD GO	CWC23_ASHGO	Pre-mRNA-splicing factor CWC23	0.61	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				273
Q9W1U6 UniProt NPD GO	RL372_DROME	Probable 60S ribosomal protein L37-B	0.61	-	mit	0					89
Q9NUL7 UniProt NPD GO	DDX28_HUMAN	Probable ATP-dependent RNA helicase DDX28 (EC 3.6.1.-) (Mitochondrial DEAD box protein 28)	0.61	-	mit	0	Nucleus. Mitochondrion. Transported between these two compartments. Nuclear localization depends on ...		607618		540
P17844 UniProt NPD GO	DDX5_HUMAN	Probable ATP-dependent RNA helicase DDX5 (EC 3.6.1.-) (DEAD box protein 5) (RNA helicase p68)	0.61	+	nuc	0	Nucleus	nucleus [NAS]	180630		614
Q9P5N0 UniProt NPD GO	YH85_SCHPO	Probable ATP-dependent permease C359.05	0.61	-	end	13 *	Membrane; multi-pass membrane protein				1465
Q7ZUL9 UniProt NPD GO	MGRN1_BRARE	Probable E3 ubiquitin-protein ligase MGRN1 (EC 6.3.2.-) (Mahogunin ring finger protein 1)	0.61	-	nuc	0					529
Q7TT36 UniProt NPD GO	GP125_MOUSE	Probable G-protein coupled receptor 125 precursor	0.61	-	end	7	Membrane; multi-pass membrane protein (Potential)				1310
Q8BL07 UniProt NPD GO	GP150_MOUSE	Probable G-protein coupled receptor 150 (G-protein coupled receptor PGR11)	0.61	-	end	5	Membrane; multi-pass membrane protein				427
Q9U2C4 UniProt NPD GO	GALT9_CAEEL	Probable N-acetylgalactosaminyltransferase 9 (EC 2.4.1.-) (Protein-UDP acetylgalactosaminyltransfera ...	0.61	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				579
Q9VX09 UniProt NPD GO	ARP8_DROME	Probable actin-related protein 8	0.61	-	mit	0		actin filament [NAS]			607
Q9FKZ1 UniProt NPD GO	DRL42_ARATH	Probable disease resistance protein At5g66900	0.61	-	cyt	0					809
Q09831 UniProt NPD GO	KAD5_SCHPO	Probable serine/threonine-protein kinase C4G8.05 (EC 2.7.11.1)	0.61	+	nuc	0					566
Q09524 UniProt NPD GO	YQN3_CAEEL	Probable tRNA pseudouridine synthase E02H1.3 (EC 5.4.99.-) (tRNA-uridine isomerase) (tRNA pseudourid ...	0.61	-	mit	0					402
Q8TFH7 UniProt NPD GO	SEN2_SCHPO	Probable tRNA-splicing endonuclease subunit sen2 (EC 3.1.27.9) (tRNA-intron endonuclease sen2)	0.61	-	cyt	1 *					380
O60139 UniProt NPD GO	UBP4_SCHPO	Probable ubiquitin carboxyl-terminal hydrolase 4 (EC 3.1.2.15) (Ubiquitin thioesterase 4) (Ubiquitin ...	0.61	-	nuc	0					438
Q757T0 UniProt NPD GO	HUL4_ASHGO	Probable ubiquitin-protein ligase HUL4 (EC 6.3.2.-) (HECT ubiquitin ligase 4)	0.61	-	mit	0	Nucleus (Probable)				839
Q9CXS4 UniProt NPD GO	PRR6_MOUSE	Proline-rich protein 6	0.61	-	nuc	0	Nucleus. Enriched at the nuclear periphery and around the nucleolus (By similarity)				252
Q86XK3 UniProt NPD GO	CJ078_HUMAN	Protein C10orf78	0.61	-	nuc	0					307
Q9BT56 UniProt NPD GO	CL039_HUMAN	Protein C12orf39 precursor [Contains: Putative amidated peptide NWTPQAMLYLKGAQ]	0.61	-	exc	1 *	Secreted protein (Potential)				116
Q32PB5 UniProt NPD GO	CC022_BOVIN	Protein C3orf22 homolog	0.61	-	nuc	0					134
Q66JZ4 UniProt NPD GO	CC023_MOUSE	Protein C3orf23 homolog	0.61	-	mit	0					499
Q4R7D3 UniProt NPD GO	CI138_MACFA	Protein C9orf138 homolog	0.61	-	nuc	0					474
P21705 UniProt NPD GO	DAL82_YEAST	Protein DAL82	0.61	-	nuc	0		nucleus [IDA]			255
Q66L44 UniProt NPD GO	DOS_MOUSE	Protein Dos (Downstream of Stk11 protein) (Fragment)	0.61	-	nuc	0					552
Q8IZP2 UniProt NPD GO	F10A4_HUMAN	Protein FAM10A4	0.61	-	nuc	0	Cytoplasm (Probable)				240
Q8NFC6 UniProt NPD GO	FA44A_HUMAN	Protein FAM44A	0.61	-	nuc	0					502
P41818 UniProt NPD GO	GLC8_YEAST	Protein GLC8	0.61	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			229
Q6FW56 UniProt NPD GO	GRC3_CANGA	Protein GRC3	0.61	-	nuc	0	Nucleus (By similarity)				630
P26798 UniProt NPD GO	INO2_YEAST	Protein INO2	0.61	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			304
Q9UPV7 UniProt NPD GO	K1045_HUMAN	Protein KIAA1045	0.61	-	nuc	0				1WIL	400

You are viewing entries 18651 to 18700 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.