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
O80536 UniProt NPD GO	PIF3_ARATH	Phytochrome-interacting factor 3 (Phytochrome-associated protein 3) (Basic helix-loop-helix protein ...	0.95	+	nuc	0	Nucleus				524
P79122 UniProt NPD GO	PININ_BOVIN	Pinin	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Cell membrane; cell-cell junction (By similarity). Cell-cell ...				702
P10036 UniProt NPD GO	PIT1_BOVIN	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.95	+	nuc	0	Nucleus				291
Q9YGL7 UniProt NPD GO	PIT1_CHICK	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.95	+	nuc	0	Nucleus (By similarity)				363
Q05749 UniProt NPD GO	PIT1_MELGA	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.95	+	nuc	0	Nucleus				370
Q04788 UniProt NPD GO	PIT1_PIG	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.95	+	nuc	0	Nucleus				291
P79364 UniProt NPD GO	PIT1_SHEEP	Pituitary-specific positive transcription factor 1 (Pit-1) (Growth hormone factor 1) (GHF-1)	0.95	+	nuc	0	Nucleus				291
Q63312 UniProt NPD GO	PHLB1_RAT	Pleckstrin homology-like domain family B member 1 (Protein LL5-alpha) (Fragment)	0.95	+	nuc	0					831
Q80U70 UniProt NPD GO	JJAZ_MOUSE	Polycomb protein Suz12 (Suppressor of zeste 12 protein homolog)	0.95	+	nuc	0	Nucleus (Probable)				741
Q965H3 UniProt NPD GO	SOP2_CAEEL	Polycomb protein sop-2 (Suppressor of pal-1 protein 2)	0.95	-	nuc	0	Nucleus. Forms subnuclear bodies				735
P78364 UniProt NPD GO	PHC1_HUMAN	Polyhomeotic-like protein 1 (hPH1) (Early development regulatory protein 1)	0.95	-	nuc	0	Nucleus	nucleus [TAS]	602978		1004
Q6C8F5 UniProt NPD GO	CEF1_YARLI	Pre-mRNA-splicing factor CEF1	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				719
Q03654 UniProt NPD GO	CEF1_YEAST	Pre-mRNA-splicing factor CEF1 (PRP19-associated complex protein 85) (PRP nineteen-associated complex ...	0.95	+	nuc	0	Cytoplasm. Nucleus	spliceosome complex [IDA]			590
Q52B63 UniProt NPD GO	CWC22_MAGGR	Pre-mRNA-splicing factor CWC22	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				907
Q5KIP8 UniProt NPD GO	CWC25_CRYNE	Pre-mRNA-splicing factor CWC25	0.95	-	nuc	0	Nucleus (By similarity)				434
Q4P6I3 UniProt NPD GO	CWC25_USTMA	Pre-mRNA-splicing factor CWC25	0.95	+	nuc	0	Nucleus (By similarity)				520
Q4PI72 UniProt NPD GO	CWC26_USTMA	Pre-mRNA-splicing factor CWC26	0.95	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				339
Q6CC77 UniProt NPD GO	PRP45_YARLI	Pre-mRNA-splicing factor PRP45 (Pre-mRNA-processing protein 45)	0.95	+	nuc	0	Nucleus (By similarity)				568
P78794 UniProt NPD GO	CWC15_SCHPO	Pre-mRNA-splicing factor cwc15 (Complexed with cdc5 protein 15) (Cell cycle control protein cwf15)	0.95	-	nuc	0	Nucleus (Probable)				265
Q7SBU7 UniProt NPD GO	SPP2_NEUCR	Pre-mRNA-splicing factor spp-2	0.95	+	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				358
Q756J5 UniProt NPD GO	ESF1_ASHGO	Pre-rRNA-processing protein ESF1 (18S rRNA factor 1)	0.95	+	nuc	0	Nucleus; nucleolus (By similarity)				619
Q7Z3G6 UniProt NPD GO	PRIC2_HUMAN	Prickle-like protein 2	0.95	-	nuc	0	Nucleus; nuclear membrane (Potential)		608501		844
Q4TVV3 UniProt NPD GO	DDX46_BRARE	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.1.-) (DEAD box protein 46)	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...				1018
Q569Z5 UniProt NPD GO	DDX46_MOUSE	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.1.-) (DEAD box protein 46)	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle (By similarity). Nucleus; nucleoplasm; Cajal body (By similari ...				1032
Q7L014 UniProt NPD GO	DDX46_HUMAN	Probable ATP-dependent RNA helicase DDX46 (EC 3.6.1.-) (DEAD box protein 46) (PRP5 homolog)	0.95	+	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Nucleus; nucleoplasm; Cajal body. Present in Cajal bodies (CB ...				1032
O42861 UniProt NPD GO	YFC1_SCHPO	Probable ATP-dependent helicase C25A8.01c in chromosome I (EC 3.6.1.-)	0.95	-	nuc	0	Nucleus				922
O13768 UniProt NPD GO	ERCC3_SCHPO	Probable DNA repair helicase ercc3 (EC 3.6.1.-)	0.95	-	nuc	0	Nucleus				804
Q8C419 UniProt NPD GO	GP158_MOUSE	Probable G-protein coupled receptor 158 precursor	0.95	-	end	6	Membrane; multi-pass membrane protein				1200
Q8WZK0 UniProt NPD GO	YHRA_SCHPO	Probable RNA-binding protein C839.10	0.95	-	nuc	0	Nucleus				695
O94466 UniProt NPD GO	RGA7_SCHPO	Probable Rho-GTPase-activating protein 7	0.95	+	nuc	0					695
Q10164 UniProt NPD GO	RGA2_SCHPO	Probable Rho-type GTPase-activating protein 2	0.95	-	nuc	0	Nucleus				1275
O13802 UniProt NPD GO	EBP2_SCHPO	Probable rRNA-processing protein ebp2	0.95	-	nuc	0	Nucleus; nucleolus				333
P36003 UniProt NPD GO	KKR1_YEAST	Probable serine/threonine-protein kinase YKL171W (EC 2.7.11.1)	0.95	-	mit	0		cytoplasm [IDA]			928
Q23120 UniProt NPD GO	RSP2_CAEEL	Probable splicing factor, arginine/serine-rich 2 (RNA-binding protein srp-4) (CeSRp40)	0.95	+	nuc	0	Nucleus	nucleus [IDA]			281
O01159 UniProt NPD GO	RSP7_CAEEL	Probable splicing factor, arginine/serine-rich 7 (p54)	0.95	+	nuc	0	Nucleus (By similarity)				452
P38140 UniProt NPD GO	YB89_YEAST	Probable transcriptional regulatory protein YBR239C	0.95	+	nuc	0	Nucleus (Probable)	cytoplasm [IDA] nucleus [IDA]			529
Q5ACL9 UniProt NPD GO	BFR2_CANAL	Protein BFR2	0.95	-	nuc	0	Nucleus; nucleolus (By similarity)				512
Q06631 UniProt NPD GO	BFR2_YEAST	Protein BFR2 (Brefeldin A resistance protein 2)	0.95	-	nuc	0	Nucleus; nucleolus	nucleolus [IDA]			534
P41832 UniProt NPD GO	BNI1_YEAST	Protein BNI1 (Synthetic lethal 39)	0.95	+	nuc	0		actin cap [IDA] actin filament [IDA] bud neck [IDA] bud tip [IDA] incipient bud site [IDA] mating projection tip [IDA] polarisome [TAS]		1Y64	1953
Q13769 UniProt NPD GO	CV019_HUMAN	Protein C22orf19 (NF2/meningioma region protein pK1.3) (Placental protein 39.2)	0.95	-	nuc	0					683
Q08119 UniProt NPD GO	ESC8_YEAST	Protein ESC8 (Establishes silent chromatin protein 8)	0.95	+	nuc	0	Cytoplasm. Nucleus	nucleus [IPI]			714
Q8BGI4 UniProt NPD GO	FA13A_MOUSE	Protein FAM13A1 (Precm1 protein)	0.95	-	nuc	0					693
Q9Y4E1 UniProt NPD GO	FA21C_HUMAN	Protein FAM21C	0.95	-	nuc	0					1320
Q6A098 UniProt NPD GO	K0256_MOUSE	Protein KIAA0256	0.95	-	nuc	0					1086
Q6ZMT4 UniProt NPD GO	K1718_HUMAN	Protein KIAA1718	0.95	-	nuc	0					941
Q80WJ7 UniProt NPD GO	LYRIC_MOUSE	Protein LYRIC (Lysine-rich CEACAM1 co-isolated protein) (3D3/LYRIC) (Metastasis adhesion protein) (M ...	0.95	+	nuc	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...				579
P33420 UniProt NPD GO	NIP80_YEAST	Protein NIP80 (Protein NIP100)	0.95	-	nuc	0		dynactin complex [IDA]			868
O60035 UniProt NPD GO	PDC2_CANAL	Protein PDC2	0.95	-	nuc	0					836
Q5ZMK5 UniProt NPD GO	PTDSR_CHICK	Protein PTDSR	0.95	-	nuc	0	Nucleus (By similarity)				414
Q6PFM0 UniProt NPD GO	PTDSR_BRARE	Protein PTDSR (Phosphatidylserine receptor) (zfpsr)	0.95	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			403

You are viewing entries 2001 to 2050 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.