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
P39685 UniProt NPD GO	PO152_YEAST	Nucleoporin POM152 (Nuclear pore protein POM152) (Pore membrane protein POM152) (P150)	0.80	-	end	3	Nucleus; nuclear envelope; nuclear pore complex; central core structure; single-pass type II membran ...	mitochondrion [IDA] nuclear pore [IDA]			1337
O42101 UniProt NPD GO	NR5A2_CHICK	Orphan nuclear receptor NR5A2 (OR2.0) (FTF/LRH-1)	0.80	+	nuc	0	Nucleus (Probable)				501
Q9R1A7 UniProt NPD GO	PXR_RAT	Orphan nuclear receptor PXR (Pregnane X receptor)	0.80	+	cyt	0	Nucleus (By similarity)				431
P06308 UniProt NPD GO	OVUH_LYMST	Ovulation prohormone precursor [Contains: Beta-3-CDCP; Beta-2-CDCP; Beta-1-CDCP; Calfluxin; Alpha-CD ...	0.80	+	exc	1 *					259
Q12837 UniProt NPD GO	PO4F2_HUMAN	POU domain, class 4, transcription factor 2 (Brain-specific homeobox/POU domain protein 3B) (Brn-3B) ...	0.80	+	nuc	0	Nucleus		113725		410
Q63934 UniProt NPD GO	PO4F2_MOUSE	POU domain, class 4, transcription factor 2 (Brain-specific homeobox/POU domain protein 3B) (Brn-3B) ...	0.80	+	nuc	0	Nucleus				411
Q15319 UniProt NPD GO	PO4F3_HUMAN	POU domain, class 4, transcription factor 3 (Brain-specific homeobox/POU domain protein 3C) (Brn-3C) ...	0.80	+	nuc	0	Nucleus		602460		338
P16241 UniProt NPD GO	CF1A_DROME	POU-domain protein CF1A (Chorion factor 1A) (CF1-A) (Ventral veins lacking protein) (Drifter protein ...	0.80	+	nuc	0	Nucleus				427
Q96IZ0 UniProt NPD GO	PAWR_HUMAN	PRKC apoptosis WT1 regulator protein (Prostate apoptosis response 4 protein) (Par-4)	0.80	-	nuc	0	Cytoplasm. Nucleus. Mainly cytoplasmic in absence of apoptosis signal and in normal cells. Nuclear i ...	cytoplasm [NAS] nucleus [NAS]	601936		340
Q02548 UniProt NPD GO	PAX5_HUMAN	Paired box protein Pax-5 (B-cell-specific transcription factor) (BSAP)	0.80	-	nuc	0	Nucleus		167414	1MDM	391
Q02650 UniProt NPD GO	PAX5_MOUSE	Paired box protein Pax-5 (B-cell-specific transcription factor) (BSAP)	0.80	-	nuc	0	Nucleus	nucleus [IDA] transcription factor complex [TAS]			391
P47239 UniProt NPD GO	PAX7_MOUSE	Paired box protein Pax-7	0.80	+	nuc	0	Nucleus	transcription factor complex [TAS]			503
Q4WAQ9 UniProt NPD GO	PPIL4_ASPFU	Peptidyl-prolyl cis-trans isomerase-like 4 (EC 5.2.1.8) (PPIase) (Rotamase)	0.80	-	nuc	0	Nucleus (By similarity)				459
P15331 UniProt NPD GO	PERI_MOUSE	Peripherin	0.80	-	mit	0		axon [IDA]			475
Q8K2H1 UniProt NPD GO	PPHLN_MOUSE	Periphilin-1	0.80	-	nuc	0	Nucleus (By similarity)				381
O94227 UniProt NPD GO	PEX3_KLULA	Peroxisomal biogenesis factor 3 (Peroxin-3) (Peroxisomal membrane protein PAS3)	0.80	-	nuc	1 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				483
Q801X6 UniProt NPD GO	PHAR1_CHICK	Phosphatase and actin regulator 1	0.80	+	nuc	0	Cytoplasm (By similarity). Enriched at synapses (By similarity)				501
Q6AZN6 UniProt NPD GO	PK3C3_XENLA	Phosphatidylinositol 3-kinase catalytic subunit type 3 (EC 2.7.1.137) (PtdIns-3-kinase type 3) (PI3- ...	0.80	-	cyt	0					886
P59644 UniProt NPD GO	PI5PA_MOUSE	Phosphatidylinositol 4,5-bisphosphate 5-phosphatase A (EC 3.1.3.56)	0.80	-	nuc	0	Cytoplasm. Predominantly localized to membrane ruffles				1003
P53191 UniProt NPD GO	PIB2_YEAST	Phosphatidylinositol-3-phosphate-binding protein 2	0.80	-	nuc	0	Vacuole; vacuolar membrane; peripheral membrane protein	late endosome [TAS] mitochondrion [IDA]			635
Q8VD65 UniProt NPD GO	PI3R4_MOUSE	Phosphoinositide 3-kinase regulatory subunit 4 (EC 2.7.11.1) (PI3-kinase regulatory subunit 4)	0.80	-	nuc	0					1357
Q8TDX9 UniProt NPD GO	PK1L1_HUMAN	Polycystic kidney disease 1-like 1 protein (Polycystin-1L1)	0.80	-	end	12	Membrane; multi-pass membrane protein (Potential)	membrane [TAS]	609721		2849
Q924H2 UniProt NPD GO	PCQAP_MOUSE	Positive cofactor 2 glutamine/Q-rich-associated protein (PC2 glutamine/Q-rich-associated protein) (m ...	0.80	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				792
Q5RAA7 UniProt NPD GO	FIP1_PONPY	Pre-mRNA 3'-end-processing factor FIP1 (FIP1-like 1)	0.80	+	nuc	0	Nucleus (By similarity)				588
Q5KDV1 UniProt NPD GO	CWC21_CRYNE	Pre-mRNA-splicing factor CWC21	0.80	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				205
Q5BDX1 UniProt NPD GO	CLF1_EMENI	Pre-mRNA-splicing factor clf1	0.80	+	nuc	0	Nucleus (By similarity)				602
Q9USV3 UniProt NPD GO	CWF7_SCHPO	Pre-mRNA-splicing factor cwf7 (Complexed with cdc5 protein 7) (Spliceosome-associated protein 27)	0.80	-	nuc	0	Nucleus (Probable)	spliceosome complex [IDA]			187
P25014 UniProt NPD GO	SECY_CYAPA	Preprotein translocase secY subunit	0.80	-	end	10 *	Plastid; cyanelle; cyanelle membrane; multi-pass membrane protein				492
Q22307 UniProt NPD GO	DHX9_CAEEL	Probable ATP-dependent RNA helicase A (EC 3.6.1.-) (Nuclear DNA helicase II) (NDH II)	0.80	+	nuc	0	Nucleus (By similarity)				1301
Q07886 UniProt NPD GO	DBP45_DROME	Probable ATP-dependent RNA helicase Dbp45A (EC 3.6.1.-) (DEAD box protein 45A)	0.80	+	nuc	0		nucleus [IC]			521
O46072 UniProt NPD GO	KZ_DROME	Probable ATP-dependent RNA helicase kurz (EC 3.6.1.-)	0.80	-	nuc	0					1192
Q8K451 UniProt NPD GO	GP156_RAT	Probable G-protein coupled receptor 156 (GABAB-related G-protein coupled receptor)	0.80	-	nuc	7 *	Membrane; multi-pass membrane protein				792
P38741 UniProt NPD GO	YHC4_YEAST	Probable RNA-binding protein YHL024W	0.80	-	nuc	0		cytoplasm [IDA]			713
Q9SUP6 UniProt NPD GO	WRK53_ARATH	Probable WRKY transcription factor 53 (WRKY DNA-binding protein 53)	0.80	-	nuc	0	Nucleus (Probable)				324
P53745 UniProt NPD GO	MNT4_YEAST	Probable alpha-1,3-mannosyltransferase MNT4 (EC 2.4.1.-)	0.80	-	mit	1 *	Membrane; single-pass type II membrane protein (Potential)				580
P50077 UniProt NPD GO	CCH1_YEAST	Probable calcium-channel protein	0.80	+	end	22	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			2039
O82226 UniProt NPD GO	CNGC6_ARATH	Probable cyclic nucleotide-gated ion channel 6 (AtCNGC6) (Cyclic nucleotide- and calmodulin-regulate ...	0.80	+	end	6	Cell membrane; multi-pass membrane protein (Potential)			1WGP	747
Q757M3 UniProt NPD GO	NUF2_ASHGO	Probable kinetochore protein NUF2	0.80	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				455
O80796 UniProt NPD GO	IM30_ARATH	Probable membrane-associated 30 kDa protein, chloroplast precursor	0.80	-	mit	0	Plastid; chloroplast; chloroplast inner membrane; peripheral membrane protein (By similarity). Plast ...	chloroplast envelope [IDA] plastid chromosome [IDA] thylakoid membrane (sensu Viridiplantae) [IDA]			330
Q8S0J7 UniProt NPD GO	IM30_ORYSA	Probable membrane-associated 30 kDa protein, chloroplast precursor	0.80	-	mit	0	Plastid; chloroplast; chloroplast inner membrane; peripheral membrane protein (By similarity). Plast ...				317
Q339W7 UniProt NPD GO	LHP1_ORYSA	Probable protein LIKE HETEROCHROMATIN PROTEIN1 (LHP1)	0.80	+	nuc	0					415
Q7XWP3 UniProt NPD GO	SEC1A_ORYSA	Probable protein transport Sec1a	0.80	-	nuc	0					665
Q9LUJ5 UniProt NPD GO	EBP2_ARATH	Probable rRNA-processing protein EBP2 homolog	0.80	-	nuc	0	Nucleus; nucleolus (By similarity)				293
Q9VSS2 UniProt NPD GO	SRP68_DROME	Probable signal recognition particle 68 kDa protein (SRP68)	0.80	-	nuc	0	Cytoplasm (By similarity)				604
Q23121 UniProt NPD GO	RSP1_CAEEL	Probable splicing factor, arginine/serine-rich 1 (RNA-binding protein srp-5) (CeSRp75)	0.80	+	nuc	0	Nucleus	nucleus [IDA]			312
Q04088 UniProt NPD GO	POF21_ARATH	Probable transcription factor PosF21 (AtbZIP59)	0.80	-	nuc	0	Nucleus				398
Q9LHS9 UniProt NPD GO	RBE_ARATH	Probable transcriptional regulator RABBIT EARS	0.80	-	nuc	0	Nucleus				226
Q9GKM0 UniProt NPD GO	PRM2_ERYPA	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.80	+	nuc	0	Nucleus (By similarity)				103
Q9GKM1 UniProt NPD GO	PRM2_SEMEN	Protamine-2 (Protamine-P2) (Sperm histone P2)	0.80	+	nuc	0	Nucleus (By similarity)				103
P02321 UniProt NPD GO	PRTY_THUTH	Protamine-Y1/Y2 (Thynnin-Y1/Y2)	0.80	+	nuc	0	Nucleus				34

You are viewing entries 9001 to 9050 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.