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
P69414 UniProt NPD GO	PSAC_ORYSA	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6L3D9 UniProt NPD GO	PSAC_SACHY	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q6ENP6 UniProt NPD GO	PSAC_SACOF	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
P69415 UniProt NPD GO	PSAC_WHEAT	Photosystem I iron-sulfur center (Photosystem I subunit VII) (9 kDa polypeptide) (PSI-C) (PsaC)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein; stromal side (By ...				80
Q9S714 UniProt NPD GO	PSAE2_ARATH	Photosystem I reaction center subunit IV B, chloroplast precursor (PSI-E B)	0.07	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				145
P49107 UniProt NPD GO	PSAN_ARATH	Photosystem I reaction center subunit N, chloroplast precursor (PSI-N)	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				171
P31093 UniProt NPD GO	PSAN_HORVU	Photosystem I reaction center subunit N, chloroplast precursor (PSI-N)	0.07	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side				145
Q9SPM4 UniProt NPD GO	PSAG_TORRU	Photosystem I reaction center subunit V, chloroplast precursor (PSI-G)	0.07	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				112
Q6ENE8 UniProt NPD GO	PSBB_ORYNI	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.07	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P12157 UniProt NPD GO	PSBB_ORYSA	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.07	-	end	5 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P09447 UniProt NPD GO	PSBB_SECCE	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.07	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
P24065 UniProt NPD GO	PSBB_WHEAT	Photosystem II P680 chlorophyll A apoprotein (CP-47 protein)	0.07	-	end	6 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein				508
Q5SD22 UniProt NPD GO	PSBH_HUPLU	Photosystem II reaction center H protein (Photosystem II 10 kDa phosphoprotein) (PSII-H)	0.07	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				73
P23817 UniProt NPD GO	PH6B_CHRSP	Phycocyanin-645 beta chain (PC-645)	0.07	-	mit	0					177
O14832 UniProt NPD GO	PAHX_HUMAN	Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) ( ...	0.07	-	cyt	0	Peroxisome	peroxisome [TAS]	266500	2A1X	338
P55141 UniProt NPD GO	PHYA_PETCR	Phytochrome A	0.07	-	mit	0					1129
P28553 UniProt NPD GO	CRTI_SOYBN	Phytoene dehydrogenase, chloroplast precursor (EC 1.14.99.-) (Phytoene desaturase)	0.07	-	cyt	0	Plastid; chloroplast. Plastid; chromoplast				570
Q09919 UniProt NPD GO	FIP1_SCHPO	Plasma membrane iron permease	0.07	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				397
Q28369 UniProt NPD GO	RETBP_HORSE	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.07	-	mit	0	Secreted protein				201
P05121 UniProt NPD GO	PAI1_HUMAN	Plasminogen activator inhibitor 1 precursor (PAI-1) (Endothelial plasminogen activator inhibitor) (P ...	0.07	-	exc	0	Secreted protein	extracellular region [NAS]	173360	9PAI	402
P84036 UniProt NPD GO	VSPB_LACMU	Plasminogen-activating proteinase (EC 3.4.21.-) (LV-PA) (Fragments)	0.07	-	cyt	0	Secreted protein				216
P58140 UniProt NPD GO	RK16_ASTLO	Plastid 50S ribosomal protein L16	0.07	-	nuc	0	Plastid				133
P13797 UniProt NPD GO	PLST_HUMAN	Plastin-3 (T-plastin)	0.07	-	cyt	0	Cytoplasm		300131	1WJO	627
Q08857 UniProt NPD GO	CD36_MOUSE	Platelet glycoprotein 4 (Platelet glycoprotein IV) (GPIV) (GPIIIB) (CD36 antigen) (PAS IV) (PAS-4 pr ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein				471
Q07969 UniProt NPD GO	CD36_RAT	Platelet glycoprotein 4 (Platelet glycoprotein IV) (GPIV) (GPIIIB) (CD36 antigen) (PAS IV) (PAS-4 pr ...	0.07	-	end	2 *	Membrane; multi-pass membrane protein	integral to membrane [TAS] plasma membrane [IDA]			471
P14770 UniProt NPD GO	GPIX_HUMAN	Platelet glycoprotein IX precursor (GPIX) (CD42a antigen)	0.07	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	231200		177
Q61205 UniProt NPD GO	PA1B3_MOUSE	Platelet-activating factor acetylhydrolase IB subunit gamma (EC 3.1.1.47) (PAF acetylhydrolase 29 kD ...	0.07	-	cyt	0	Cytoplasm	cytoplasm [IDA]			232
Q64294 UniProt NPD GO	PDPN_RAT	Podoplanin precursor (Glycoprotein 38) (Gp38) (OTS-8) (E11 antigen epitope) (T1A) (T1-alpha) (Type I ...	0.07	-	nuc	1	Membrane; single-pass type I membrane protein. Localized to actin-rich microvilli and plasma membran ...	filopodium [ISS] lamellipodium [ISS] plasma membrane [ISS] ruffle [ISS]			166
Q39419 UniProt NPD GO	POLC4_BETVE	Polcalcin Bet v 4 (Calcium-binding pollen allergen Bet v 4)	0.07	-	cyt	0				1H4B	85
Q84V36 UniProt NPD GO	POLC3_CHEAL	Polcalcin Che a 3 (Calcium-binding pollen allergen Che a 3)	0.07	-	cyt	0				1PMZ	86
P27760 UniProt NPD GO	MPA12_AMBAR	Pollen allergen Amb a 1.2 precursor (Antigen E) (Antigen Amb a I) (AaBA protein)	0.07	-	exc	0					398
Q9Y718 UniProt NPD GO	PGLR_PENDI	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.07	-	exc	0					367
Q05967 UniProt NPD GO	PGLR_TOBAC	Polygalacturonase precursor (EC 3.2.1.15) (PG) (Pectinase)	0.07	-	exc	0	Secreted protein				396
P19805 UniProt NPD GO	PGLR2_ASPTU	Polygalacturonase-2 precursor (EC 3.2.1.15) (Polygalacturonase II) (PG-II) (Pectinase-2)	0.07	-	mit	0					362
Q08303 UniProt NPD GO	PPOA_LYCES	Polyphenol oxidase A, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				630
Q08305 UniProt NPD GO	PPOC_LYCES	Polyphenol oxidase C, chloroplast precursor (EC 1.10.3.1) (PPO) (Catechol oxidase)	0.07	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen				626
Q5K2P8 UniProt NPD GO	POLS2_MOUSE	Polyserase-2 precursor (EC 3.4.21.-) (Polyserine protease 2) (Protease serine 36)	0.07	-	gol	0	Secreted protein; extracellular space; extracellular matrix. Not attached to membranes (By similarit ...				849
P13487 UniProt NPD GO	KAX11_LEIQH	Potassium channel toxin alpha-KTx 1.1 precursor (Charybdotoxin) (ChTX) (ChTX-Lq1) (ChTx-a)	0.07	-	exc	0	Secreted protein			2CRD	59
P0C173 UniProt NPD GO	KA161_MESTA	Potassium channel toxin alpha-KTx 16.1 (Tamulotoxin) (TmTX) (Alpha-KTx 1.8)	0.07	-	nuc	0	Secreted protein				36
P0C163 UniProt NPD GO	KAX2A_CENEL	Potassium channel toxin alpha-KTx 2.10 (Toxin Ce3)	0.07	-	nuc	0	Secreted protein				38
Q86QU5 UniProt NPD GO	KGX33_CENSC	Potassium channel toxin gamma-KTx 3.3 (Ergtoxin-like protein 2) (ErgTx2) (CsErg2) (CsErgTx2)	0.07	-	nuc	0	Secreted protein				43
Q86QV9 UniProt NPD GO	KGX4D_CENNO	Potassium channel toxin gamma-KTx 4.13 (Ergtoxin-like protein 3) (ErgTx3) (CnErg3) (CnErgTx3)	0.07	-	nuc	0	Secreted protein				43
Q86QT9 UniProt NPD GO	KGX44_CENEX	Potassium channel toxin gamma-KTx 4.4 (Ergtoxin-like protein 3) (ErgTx3) (CexErg3) (CexErgTx3)	0.07	-	nuc	0	Secreted protein				43
Q86QT8 UniProt NPD GO	KGX45_CENEX	Potassium channel toxin gamma-KTx 4.5 (Ergtoxin-like protein 4) (ErgTx4) (CexErg4) (CexErgTx4)	0.07	-	nuc	0	Secreted protein				43
Q86QU7 UniProt NPD GO	KGX47_CENLL	Potassium channel toxin gamma-KTx 4.7 (Ergtoxin-like protein 4) (ErgTx4) (CllErg4) (CllErgTx4)	0.07	-	nuc	0	Secreted protein				43
Q60409 UniProt NPD GO	KCNE1_CAVPO	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.07	-	nuc	1 *	Membrane; single-pass type I membrane protein				125
Q28705 UniProt NPD GO	KCNE1_RABIT	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.07	-	mit	1 *	Membrane; single-pass type I membrane protein				130
Q9QZ26 UniProt NPD GO	KCE1L_MOUSE	Potassium voltage-gated channel subfamily E member 1-like protein (MinK-like protein)	0.07	-	nuc	1	Membrane; single-pass type I membrane protein				143
P70057 UniProt NPD GO	KCNQ1_XENLA	Potassium voltage-gated channel subfamily KQT member 1 (Voltage-gated potassium channel subunit Kv7. ...	0.07	-	end	6	Membrane; multi-pass membrane protein				377
Q9BQ31 UniProt NPD GO	KCNS3_HUMAN	Potassium voltage-gated channel subfamily S member 3 (Voltage-gated potassium channel subunit Kv9.3) ...	0.07	-	end	3	Cell membrane; multi-pass membrane protein. Membrane; multi-pass membrane protein. May not reach the ...		603888		491

You are viewing entries 70701 to 70750 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.