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
P83750 UniProt NPD GO	ACTB_CYPCA	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60708 UniProt NPD GO	ACTB_HORSE	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60709 UniProt NPD GO	ACTB_HUMAN	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm	TIP60 histone acetyltransferase complex [IDA]	102630		375
Q711N9 UniProt NPD GO	ACTB_MESAU	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60710 UniProt NPD GO	ACTB_MOUSE	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm	cytosol [IDA] soluble fraction [IDA]			375
P68143 UniProt NPD GO	ACTB_OREMO	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
Q5R1X3 UniProt NPD GO	ACTB_PANTR	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P29751 UniProt NPD GO	ACTB_RABIT	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60711 UniProt NPD GO	ACTB_RAT	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
O42161 UniProt NPD GO	ACTB_SALSA	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60713 UniProt NPD GO	ACTB_SHEEP	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
Q91ZK5 UniProt NPD GO	ACTB_SIGHI	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
P60707 UniProt NPD GO	ACTB_TRIVU	Actin, cytoplasmic 1 (Beta-actin)	0.09	-	cyt	0	Cytoplasm				375
O93400 UniProt NPD GO	ACTB_XENLA	Actin, cytoplasmic 1 (Beta-actin) (Cytoplasmic beta actin)	0.09	-	cyt	0	Cytoplasm				375
P68142 UniProt NPD GO	ACT1_FUGRU	Actin, cytoplasmic 1 (Beta-actin-1)	0.09	-	cyt	0	Cytoplasm				375
Q7ZVI7 UniProt NPD GO	ACTB1_BRARE	Actin, cytoplasmic 1 (Beta-actin-1)	0.09	-	cyt	0	Cytoplasm				375
P53485 UniProt NPD GO	ACT2_FUGRU	Actin, cytoplasmic 2 (Beta-actin-2)	0.09	-	cyt	0	Cytoplasm				375
Q7ZVF9 UniProt NPD GO	ACTB2_BRARE	Actin, cytoplasmic 2 (Beta-actin-2)	0.09	-	cyt	0	Cytoplasm				375
P63256 UniProt NPD GO	ACTG_ANSAN	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm				375
P63258 UniProt NPD GO	ACTG_BOVIN	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm				375
P63261 UniProt NPD GO	ACTG_HUMAN	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm		102560		375
P63260 UniProt NPD GO	ACTG_MOUSE	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm	actin cytoskeleton [IDA] costamere [TAS]			375
P63259 UniProt NPD GO	ACTG_RAT	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm				375
P63257 UniProt NPD GO	ACTG_TRIVU	Actin, cytoplasmic 2 (Gamma-actin)	0.09	-	cyt	0	Cytoplasm				375
P53478 UniProt NPD GO	ACT5_CHICK	Actin, cytoplasmic type 5	0.09	-	cyt	0	Cytoplasm				376
P53505 UniProt NPD GO	ACT5_XENLA	Actin, cytoplasmic type 5	0.09	-	cyt	0	Cytoplasm				376
P53506 UniProt NPD GO	ACT8_XENLA	Actin, cytoplasmic type 8	0.09	-	cyt	0	Cytoplasm				376
P53463 UniProt NPD GO	ACTM_HELER	Actin, cytoskeletal (M)	0.09	-	cyt	0	Cytoplasm. Cytoskeleton				376
Q00214 UniProt NPD GO	ACTM_STYPL	Actin, muscle	0.09	-	cyt	0	Cytoplasm				379
Q25472 UniProt NPD GO	ACT2_MOLOC	Actin, muscle-type (A2)	0.09	-	cyt	0	Cytoplasm				378
P24263 UniProt NPD GO	ACTD_PHYPO	Actin, spherule isoform	0.09	-	cyt	0	Cytoplasm				366
O18500 UniProt NPD GO	ACT2_SACKO	Actin-2	0.09	-	cyt	0	Cytoplasm				376
P41340 UniProt NPD GO	ACT3_LIMPO	Actin-3	0.09	-	cyt	0	Cytoplasm				376
P53458 UniProt NPD GO	ACT5_DIPDE	Actin-5 (Fragment)	0.09	-	cyt	0	Cytoplasm				371
Q07750 UniProt NPD GO	ADF1_CAEEL	Actin-depolymerizing factor 1 (Uncoordinated protein 60)	0.09	-	cyt	0		cytoplasm [IDA]			165
Q39251 UniProt NPD GO	ADF2_ARATH	Actin-depolymerizing factor 2 (ADF-2) (AtADF2)	0.09	-	cyt	0					137
Q99MR0 UniProt NPD GO	ACL6B_MOUSE	Actin-like protein 6B (53 kDa BRG1-associated factor B) (Actin-related protein Baf53b)	0.09	-	cyt	0	Nucleus (By similarity)	SWI/SNF complex [IDA]			426
O94805 UniProt NPD GO	ACL6B_HUMAN	Actin-like protein 6B (53 kDa BRG1-associated factor B) (Actin-related protein Baf53b) (ArpNalpha)	0.09	-	cyt	0	Nucleus	nucleus [IDA] SWI/SNF complex [ISS]			426
Q6C061 UniProt NPD GO	ARP4_YARLI	Actin-like protein ARP4	0.09	-	cyt	0	Nucleus (By similarity)				432
Q95126 UniProt NPD GO	AVR2B_BOVIN	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.09	-	end	1	Membrane; single-pass type I membrane protein				512
P27040 UniProt NPD GO	AVR2B_MOUSE	Activin receptor type 2B precursor (EC 2.7.11.30) (Activin receptor type IIB) (ACTR-IIB)	0.09	-	end	1	Membrane; single-pass type I membrane protein			1S4Y	536
P32887 UniProt NPD GO	ACP3_BRANA	Acyl carrier protein, chloroplast precursor (ACP) (Clones 34C02 and 10C04)	0.09	-	mit	0	Plastid; chloroplast				134
P32463 UniProt NPD GO	ACPM_YEAST	Acyl carrier protein, mitochondrial precursor (ACP) (NADH-ubiquinone oxidoreductase 9.6 kDa subunit) ...	0.09	-	mit	0	Mitochondrion	mitochondrion [IDA]			125
Q9D061 UniProt NPD GO	ACBD6_MOUSE	Acyl-CoA-binding domain-containing protein 6	0.09	-	cyt	0					282
Q66JD7 UniProt NPD GO	ACBD6_XENTR	Acyl-CoA-binding domain-containing protein 6	0.09	-	cyt	0					286
Q20507 UniProt NPD GO	ACBP3_CAEEL	Acyl-CoA-binding protein homolog 3 (ACBP-3)	0.09	-	cyt	0					116
Q96329 UniProt NPD GO	ACOX4_ARATH	Acyl-coenzyme A oxidase 4, peroxisomal (EC 1.3.3.6) (AOX 4) (Short-chain acyl-CoA oxidase) (SAOX) (A ...	0.09	-	mit	0	Glyoxysome. Peroxisome				436
P08790 UniProt NPD GO	ACOX5_CANTR	Acyl-coenzyme A oxidase 5 (EC 1.3.3.6) (Acyl-CoA oxidase 5) (PXP-5)	0.09	-	cyt	0	Peroxisome				661
P58137 UniProt NPD GO	ACOT8_MOUSE	Acyl-coenzyme A thioesterase 8 (EC 3.1.2.2) (Acyl-CoA thioesterase 8) (Peroxisomal acyl-coenzyme A t ...	0.09	-	pox	0	Peroxisome	mitochondrion [IDA] peroxisome [TAS]			320
Q5Z8K3 UniProt NPD GO	ADO1_ORYSA	Adagio-like protein 1	0.09	-	cyt	0	Nucleus (By similarity)				630

You are viewing entries 65651 to 65700 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.