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
P20146 UniProt NPD GO	PA2X_NOTSC	Probable phospholipase A2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.09	-	exc	1 *	Secreted protein				145
O48646 UniProt NPD GO	GPX6_ARATH	Probable phospholipid hydroperoxide glutathione peroxidase 6, mitochondrial precursor (EC 1.11.1.12) ...	0.09	-	mit	0	Mitochondrion (Potential)				232
Q2N2K2 UniProt NPD GO	PHYK2_SOYBN	Probable phytol kinase 2, chloroplast precursor (EC 2.7.-.-)	0.09	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				292
Q2N2K4 UniProt NPD GO	PHYK_MAIZE	Probable phytol kinase, chloroplast precursor (EC 2.7.-.-)	0.09	-	end	6 *	Plastid; chloroplast; chloroplast membrane; multi-pass membrane protein (Potential)				303
Q6B913 UniProt NPD GO	RRP3_GRATL	Probable plastid-specific 30S ribosomal protein 3 (PSRP-3)	0.09	-	cyt	0	Plastid; chloroplast				99
P57741 UniProt NPD GO	PFD3_ARATH	Probable prefoldin subunit 3	0.09	-	cyt	0					195
Q10329 UniProt NPD GO	PSA7_SCHPO	Probable proteasome subunit alpha type 7 (EC 3.4.25.1)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			259
Q9UQY2 UniProt NPD GO	PSB1_SCHPO	Probable proteasome subunit beta type 1 (EC 3.4.25.1)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [TAS]			225
P38658 UniProt NPD GO	ERP60_SCHMA	Probable protein disulfide-isomerase ER-60 precursor (EC 5.3.4.1) (ERP60)	0.09	-	gol	0	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				484
Q19537 UniProt NPD GO	RFA1_CAEEL	Probable replication factor A 73 kDa subunit (RP-A) (RF-A) (Replication factor-A protein 1)	0.09	-	cyt	0	Nucleus (By similarity)				655
Q41433 UniProt NPD GO	SPI6_SOLTU	Probable serine protease inhibitor 6 precursor (AM66)	0.09	-	exc	0	Vacuole (By similarity)				221
Q9VLV5 UniProt NPD GO	RUXE_DROME	Probable small nuclear ribonucleoprotein E (snRNP-E) (Sm protein E) (Sm-E) (SmE)	0.09	-	cyt	0	Nucleus (By similarity)				94
Q9VI10 UniProt NPD GO	SMD2_DROME	Probable small nuclear ribonucleoprotein Sm D2 (snRNP core protein D2) (Sm-D2)	0.09	-	nuc	0	Nucleus (By similarity)	small nuclear ribonucleoprotein complex [ISS]			119
P91918 UniProt NPD GO	RSMB_CAEEL	Probable small nuclear ribonucleoprotein-associated protein B (snRNP-B) (Sm protein B) (Sm-B) (SmB)	0.09	-	cyt	0	Nucleus (By similarity)				160
Q6A329 UniProt NPD GO	SUC6_ARATH	Probable sucrose transport protein SUC6 (Sucrose permease 6) (Sucrose-proton symporter 6)	0.09	-	end	12 *	Cell membrane; multi-pass membrane protein (Probable)				492
Q6FXN7 UniProt NPD GO	ETR1_CANGA	Probable trans-2-enoyl-CoA reductase, mitochondrial precursor (EC 1.3.1.38)	0.09	-	mit	0	Mitochondrion (By similarity)				385
Q9P6A5 UniProt NPD GO	SEC17_NEUCR	Probable vesicular-fusion protein sec17 homolog	0.09	-	cyt	0	Membrane; peripheral membrane protein (By similarity)				292
P24314 UniProt NPD GO	PCNA_CATRO	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.09	-	mit	0	Nucleus				268
O16852 UniProt NPD GO	PCNA_SARCR	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.09	-	cyt	0	Nucleus				260
P17917 UniProt NPD GO	PCNA_DROME	Proliferating cell nuclear antigen (PCNA) (Cyclin) (Mutagen-sensitive 209 protein)	0.09	-	cyt	0	Nucleus				260
Q16549 UniProt NPD GO	PCSK7_HUMAN	Proprotein convertase subtilisin/kexin type 7 precursor (EC 3.4.21.-) (Proprotein convertase PC7) (S ...	0.09	-	end	1 *	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...	integral to Golgi membrane [IDA]	604872		785
Q62849 UniProt NPD GO	PCSK7_RAT	Proprotein convertase subtilisin/kexin type 7 precursor (EC 3.4.21.-) (Proprotein convertase PC7) (S ...	0.09	-	end	1 *	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...				783
Q95L14 UniProt NPD GO	PTGES_BOVIN	Prostaglandin E synthase (EC 5.3.99.3)	0.09	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				153
Q8HZJ2 UniProt NPD GO	PTGES_HORSE	Prostaglandin E synthase (EC 5.3.99.3)	0.09	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				153
Q9N0A4 UniProt NPD GO	PGES2_MACFA	Prostaglandin E synthase 2 (EC 5.3.99.3) (Microsomal prostaglandin E synthase 2) (mPGES-2) [Contains ...	0.09	-	mit	0	Golgi apparatus; Golgi membrane; single-pass membrane protein (By similarity). Processed form: Cytop ...			1Z9H	377
P43117 UniProt NPD GO	PF2R_MOUSE	Prostaglandin F2-alpha receptor (Prostanoid FP receptor) (PGF receptor) (PGF2 alpha receptor)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				366
Q28905 UniProt NPD GO	PF2R_SHEEP	Prostaglandin F2-alpha receptor (Prostanoid FP receptor) (PGF receptor) (PGF2 alpha receptor)	0.09	-	end	6 *	Membrane; multi-pass membrane protein				362
P80508 UniProt NPD GO	PE2R_RABIT	Prostaglandin-E(2) 9-reductase (EC 1.1.1.189) (20-alpha-hydroxysteroid dehydrogenase) (EC 1.1.1.149) ...	0.09	-	cyt	0	Cytoplasm			1Q5M	323
P05980 UniProt NPD GO	PGFS1_BOVIN	Prostaglandin-F synthase 1 (EC 1.1.1.188) (PGF synthase 1) (PGF 1) (Prostaglandin-D2 11 reductase 1) ...	0.09	-	cyt	0	Cytoplasm				323
O02853 UniProt NPD GO	PTGDS_BOVIN	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.09	-	vac	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [IDA] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			191
Q9XS65 UniProt NPD GO	PTGDS_CANFA	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.09	-	exc	1 *	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [ISS] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			191
O22609 UniProt NPD GO	DEGP1_ARATH	Protease Do-like 1, chloroplast precursor (EC 3.4.21.-)	0.09	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				439
Q9U793 UniProt NPD GO	PSA2_TRYBB	Proteasome subunit alpha type 2 (EC 3.4.25.1) (20S proteasome subunit alpha-2)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				231
Q4R932 UniProt NPD GO	PSA4_MACFA	Proteasome subunit alpha type 4 (EC 3.4.25.1)	0.09	-	mit	0	Cytoplasm. Nucleus				261
P25789 UniProt NPD GO	PSA4_HUMAN	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome component C9) (Macropain subunit C9) (Mult ...	0.09	-	mit	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	176846		261
Q95005 UniProt NPD GO	PSA7_CAEEL	Proteasome subunit alpha type 7 (EC 3.4.25.1) (Proteasome subunit alpha 4)	0.09	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				253
Q9CWH6 UniProt NPD GO	PSA7L_MOUSE	Proteasome subunit alpha type 7-like (EC 3.4.25.1)	0.09	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
O64464 UniProt NPD GO	PSB1_ORYSA	Proteasome subunit beta type 1 (EC 3.4.25.1) (20S proteasome alpha subunit F) (20S proteasome subuni ...	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				221
P20618 UniProt NPD GO	PSB1_HUMAN	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome component C5) (Macropain subunit C5) (Multi ...	0.09	-	cyt	0	Cytoplasm. Nucleus	proteasome complex (sensu Eukaryota) [TAS]	602017		241
P91477 UniProt NPD GO	PSB2_CAEEL	Proteasome subunit beta type 2 (EC 3.4.25.1) (Proteasome subunit beta 4)	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				199
P15648 UniProt NPD GO	2C_DICDI	Protein 2C	0.09	-	nuc	0					98
Q6CIV8 UniProt NPD GO	AF9_KLULA	Protein AF-9 homolog	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				220
Q10319 UniProt NPD GO	AF9_SCHPO	Protein AF-9 homolog	0.09	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				217
Q9LZX1 UniProt NPD GO	Y5175_ARATH	Protein At5g01750	0.09	-	cyt	0				1ZXU	217
Q5U220 UniProt NPD GO	CJ057_RAT	Protein C10orf57 homolog	0.09	-	mit	3 *	Membrane; multi-pass membrane protein (Potential)				123
Q5RBQ2 UniProt NPD GO	CF072_PONPY	Protein C6orf72 homolog precursor	0.09	-	end	1	Membrane; single-pass type I membrane protein (Potential)				330
Q2T9N3 UniProt NPD GO	CI032_BOVIN	Protein C9orf32 homolog	0.09	-	cyt	0					222
Q96MD7 UniProt NPD GO	CI085_HUMAN	Protein C9orf85	0.09	-	nuc	0					179
Q9XF04 UniProt NPD GO	CLV3_ARATH	Protein CLAVATA3 precursor	0.09	-	exc	0	Secreted protein; extracellular space (Potential)				96
Q8WUE5 UniProt NPD GO	CX048_HUMAN	Protein CXorf48 (Tumor antigen BJ-HCC-20)	0.09	-	mit	0					264

You are viewing entries 66851 to 66900 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.