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
P21576 UniProt NPD GO	VPS1_YEAST	Vacuolar sorting protein 1	0.69	-	nuc	0	Cytoplasm	cytoplasm [IDA] membrane fraction [IDA] mitochondrial outer membrane [IDA]			704
Q80Z96 UniProt NPD GO	VANG1_MOUSE	Vang-like protein 1 (Van Gogh-like protein 1) (Loop-tail protein 2)	0.69	-	end	4	Membrane; multi-pass membrane protein (Potential)				526
P84889 UniProt NPD GO	VANG2_RAT	Vang-like protein 2 (Van Gogh-like protein 2)	0.69	+	end	4	Membrane; multi-pass membrane protein (Potential)				521
Q91ZD4 UniProt NPD GO	VANG2_MOUSE	Vang-like protein 2 (Van Gogh-like protein 2) (Loop-tail-associated protein) (Loop-tail protein 1)	0.69	+	end	4	Membrane; multi-pass membrane protein (Potential)				521
Q9H322 UniProt NPD GO	VCX2_HUMAN	Variable charge X-linked protein 2 (VCX-B protein) (Variably charged protein X-B) (Variable charge p ...	0.69	-	nuc	0					139
Q9DDB0 UniProt NPD GO	VAX1B_XENLA	Ventral anterior homeobox 1b	0.69	+	nuc	0	Nucleus (By similarity)				287
Q9HBM0 UniProt NPD GO	VEZA_HUMAN	Vezatin	0.69	-	end	1	Membrane; single-pass type III membrane protein (Probable)				779
O95180 UniProt NPD GO	CAC1H_HUMAN	Voltage-dependent T-type calcium channel subunit alpha-1H (Voltage-gated calcium channel subunit alp ...	0.69	+	end	15	Membrane; multi-pass membrane protein	voltage-gated calcium channel complex [TAS]	607904		2353
Q9Y2I8 UniProt NPD GO	WDR37_HUMAN	WD repeat protein 37	0.69	+	mit	0					494
Q6X7J3 UniProt NPD GO	WOX11_ARATH	WUSCHEL-related homeobox 11	0.69	-	nuc	0	Nucleus (By similarity)				268
P78714 UniProt NPD GO	WC2_NEUCR	White collar 2 protein (WC2)	0.69	-	nuc	0	Nucleus				530
P70315 UniProt NPD GO	WASP_MOUSE	Wiskott-Aldrich syndrome protein homolog (WASp)	0.69	-	nuc	0		vesicle membrane [IDA]			520
Q7Z3T8 UniProt NPD GO	ZFY16_HUMAN	Zinc finger FYVE domain-containing protein 16 (Endofin) (Endosome-associated FYVE domain protein)	0.69	-	nuc	0	Cytoplasm. Endosome; early endosome. Localized to early endosomes. Membrane-associated, probably via ...	early endosome [IDA]	608880		1539
Q9UK12 UniProt NPD GO	ZN222_HUMAN	Zinc finger protein 222	0.69	-	nuc	0	Nucleus (Probable)				451
Q9NSD4 UniProt NPD GO	ZN275_HUMAN	Zinc finger protein 275	0.69	-	nuc	0	Nucleus (Probable)				458
Q06730 UniProt NPD GO	ZN33A_HUMAN	Zinc finger protein 33A (Zinc finger protein KOX31) (Zinc finger and ZAK-associated protein with KRA ...	0.69	-	nuc	0	Nucleus (Potential)	nucleus [NAS]	609480		810
Q9H7R0 UniProt NPD GO	ZN442_HUMAN	Zinc finger protein 442	0.69	-	nuc	0	Nucleus (Potential)				627
Q8NDQ6 UniProt NPD GO	ZN540_HUMAN	Zinc finger protein 540	0.69	-	nuc	0	Nucleus (Potential)				660
Q9NTW7 UniProt NPD GO	ZF64B_HUMAN	Zinc finger protein 64, isoforms 3 and 4 (Zinc finger protein 338)	0.69	-	nuc	0	Nucleus (Probable)				645
Q6AZW8 UniProt NPD GO	ZN660_HUMAN	Zinc finger protein 660	0.69	-	nuc	0	Nucleus (Probable)				331
Q8N859 UniProt NPD GO	ZN713_HUMAN	Zinc finger protein 713	0.69	-	nuc	0	Nucleus (Potential)				430
Q9XUB2 UniProt NPD GO	MEX5_CAEEL	Zinc finger protein mex-5	0.69	-	nuc	0	Nucleus (Potential)				468
Q6CII8 UniProt NPD GO	RNA14_KLULA	mRNA 3'-end processing protein RNA14	0.69	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Nucleus and/or cytoplasm (By similarity)				661
P53550 UniProt NPD GO	DCP2_YEAST	mRNA decapping enzyme 2 (EC 3.-.-.-) (Protein PSU1)	0.69	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...	cytoplasm [IDA] cytoplasmic mRNA processing body [IDA] nucleus [IDA]			970
Q6CC39 UniProt NPD GO	PUS1_YARLI	tRNA pseudouridine synthase 1 (EC 5.4.99.-) (tRNA-uridine isomerase 1) (tRNA pseudouridylate synthas ...	0.69	-	nuc	0	Nucleus (By similarity)				528
P53065 UniProt NPD GO	TAD1_YEAST	tRNA-specific adenosine deaminase 1 (EC 3.5.4.-) (tRNA-specific adenosine-37 deaminase)	0.69	-	nuc	0		nucleus [IDA]			400
Q8CIZ8 UniProt NPD GO	VWF_MOUSE	von Willebrand factor precursor (vWF) [Contains: von Willebrand antigen 2 (von Willebrand antigen II ...	0.69	-	nuc	0	Secreted protein (By similarity). Localized to storage granules (By similarity)			1U0O	2813
O23878 UniProt NPD GO	13S1_FAGES	13S globulin seed storage protein 1 precursor (Legumin-like protein 1) [Contains: 13S globulin seed ...	0.68	-	mit	0					565
Q9CQL6 UniProt NPD GO	RM35_MOUSE	39S ribosomal protein L35, mitochondrial precursor (L35mt) (MRP-L35)	0.68	+	mit	0	Mitochondrion (By similarity)				188
Q9HD33 UniProt NPD GO	RM47_HUMAN	39S ribosomal protein L47, mitochondrial precursor (L47mt) (MRP-L47)	0.68	+	nuc	0	Mitochondrion				252
Q74ZK3 UniProt NPD GO	RS6_ASHGO	40S ribosomal protein S6	0.68	-	nuc	0					236
Q4N3P0 UniProt NPD GO	RS8_THEPA	40S ribosomal protein S8	0.68	+	nuc	0					188
Q25555 UniProt NPD GO	RS9_NAEFO	40S ribosomal protein S9	0.68	-	nuc	0					186
Q8L9A0 UniProt NPD GO	RM21_ARATH	50S ribosomal protein L21, mitochondrial precursor	0.68	+	mit	0	Mitochondrion (Probable)				270
O82712 UniProt NPD GO	RL15_QUESU	60S ribosomal protein L15	0.68	-	nuc	0					201
Q6FXY9 UniProt NPD GO	RL24_CANGA	60S ribosomal protein L24	0.68	-	nuc	0					155
O65743 UniProt NPD GO	RL24_CICAR	60S ribosomal protein L24	0.68	-	nuc	0	Cytoplasm				164
Q92354 UniProt NPD GO	RL24A_SCHPO	60S ribosomal protein L24-A	0.68	-	nuc	0					149
O74884 UniProt NPD GO	RL24B_SCHPO	60S ribosomal protein L24-B	0.68	-	nuc	0					149
P24000 UniProt NPD GO	RL24B_YEAST	60S ribosomal protein L24-B (L30B) (RP29) (YL21)	0.68	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			155
P25348 UniProt NPD GO	RM32_YEAST	60S ribosomal protein L32, mitochondrial precursor (YmL32)	0.68	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrial large ribosomal subunit [TAS]			183
Q8L805 UniProt NPD GO	RL35_WHEAT	60S ribosomal protein L35	0.68	-	nuc	0					124
P39032 UniProt NPD GO	RL36_RAT	60S ribosomal protein L36	0.68	-	nuc	0					104
P36531 UniProt NPD GO	RM36_YEAST	60S ribosomal protein L36, mitochondrial precursor (YmL36)	0.68	-	mit	0	Mitochondrion	mitochondrial large ribosomal subunit [IPI]			177
P62885 UniProt NPD GO	RL37_LEIDO	60S ribosomal protein L37	0.68	+	mit	0					82
P62886 UniProt NPD GO	RL37_LEIIN	60S ribosomal protein L37	0.68	+	mit	0					82
P14796 UniProt NPD GO	RL40_YEAST	60S ribosomal protein L40 (CEP52)	0.68	+	nuc	0					52
P24587 UniProt NPD GO	AKAP5_RAT	A-kinase anchor protein 5 (A-kinase anchor protein 150 kDa) (AKAP 150) (cAMP-dependent protein kinas ...	0.68	-	nuc	0					714
P40917 UniProt NPD GO	YAP4_YEAST	AP-1-like transcription factor YAP4 (Transcription activator CIN5) (Chromosome instability protein 5 ...	0.68	-	nuc	0	Cytoplasm. Nucleus	nucleus [IDA]			295
P53197 UniProt NPD GO	CDH1_YEAST	APC/C activator protein CDH1 (CDC20 homolog 1) (Homolog of CDC twenty 1)	0.68	-	nuc	0	Cytoplasm. Nucleus. Nuclear import and export are mediated by the importin PSE1 and the exportin MSN ...	anaphase-promoting complex [TAS] cytoplasm [IDA] nucleus [IDA]			566

You are viewing entries 14551 to 14600 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.