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
P11544 UniProt NPD GO	PALY_RHOTO	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.14	-	nuc	0	Cytoplasm (Probable)			1Y2M	716
P31425 UniProt NPD GO	PAL1_SOLTU	Phenylalanine ammonia-lyase 1 (EC 4.3.1.5)	0.14	-	nuc	0	Cytoplasm (Probable)				720
Q04004 UniProt NPD GO	PLP1_YEAST	Phosducin-like protein 1	0.14	-	nuc	0	Cytoplasm	cytoplasm [IPI]			230
P53844 UniProt NPD GO	PDR17_YEAST	Phosphatidylinositol transfer protein PDR17 (PITP) (Phosphatidylserine transport B pathway protein 2 ...	0.14	-	cyt	0	Cytoplasm	cytoplasm [IDA]			350
P53812 UniProt NPD GO	PIPNB_RAT	Phosphatidylinositol transfer protein beta isoform (PtdIns transfer protein beta) (PtdInsTP) (PI-TP- ...	0.14	-	cyt	0	Cytoplasm (By similarity). Golgi apparatus (By similarity)			2A1L	270
Q4R5E4 UniProt NPD GO	PGM1_MACFA	Phosphoglucomutase-1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.14	-	nuc	0	Cytoplasm (By similarity)				561
P37012 UniProt NPD GO	PGM2_YEAST	Phosphoglucomutase-2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.14	-	nuc	0	Cytoplasm				569
P08892 UniProt NPD GO	PGKD_TRYBB	Phosphoglycerate kinase A (EC 2.7.2.3) (PGK A allele 4)	0.14	-	cyt	0	Not known				508
O70250 UniProt NPD GO	PGAM2_MOUSE	Phosphoglycerate mutase 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme M ...	0.14	-	cyt	0					252
P16290 UniProt NPD GO	PGAM2_RAT	Phosphoglycerate mutase 2 (EC 5.4.2.1) (EC 5.4.2.4) (EC 3.1.3.13) (Phosphoglycerate mutase isozyme M ...	0.14	-	cyt	0					252
P49369 UniProt NPD GO	PA1_VESVU	Phospholipase A1 precursor (EC 3.1.1.32) (EC 3.1.1.4) (Allergen Ves v 1) (Ves v I)	0.14	-	nuc	0					336
Q8UUI0 UniProt NPD GO	PA23_LATCO	Phospholipase A2 PC1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.14	-	exc	1 *	Secreted protein (By similarity)				155
Q9PWI4 UniProt NPD GO	PLIGA_ELAQU	Phospholipase A2 inhibitor subunit gamma A precursor (PLI-gamma A)	0.14	-	exc	0	Secreted protein				202
P10116 UniProt NPD GO	PA22_LATCO	Phospholipase A2 isozyme 2 (EC 3.1.1.4) (Phospholipase A2 isozyme II) (PLA-II) (Phosphatidylcholine ...	0.14	-	nuc	0	Secreted protein				118
Q45Z30 UniProt NPD GO	PA21_TROCA	Phospholipase A2, acidic 1 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 1) (PLA-1)	0.14	-	exc	1 *	Secreted protein				151
Q45Z29 UniProt NPD GO	PA22_TROCA	Phospholipase A2, acidic 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 2) (PLA-2)	0.14	-	exc	1 *	Secreted protein				151
Q45Z28 UniProt NPD GO	PA23_TROCA	Phospholipase A2, acidic 3 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase 3) (PLA-3)	0.14	-	exc	1 *	Secreted protein				151
P00618 UniProt NPD GO	PA22_BUNMU	Phospholipase A2, beta bungarotoxin A2 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.14	-	exc	0	Secreted protein				145
P59018 UniProt NPD GO	PA25_BUNMU	Phospholipase A2, beta bungarotoxin A5 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.14	-	nuc	0	Secreted protein (By similarity)				137
Q85BP9 UniProt NPD GO	YCF4_ANTFO	Photosystem I assembly protein ycf4	0.14	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
P49526 UniProt NPD GO	YCF4_ODOSI	Photosystem I assembly protein ycf4	0.14	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				181
Q68RZ5 UniProt NPD GO	YCF4_PANGI	Photosystem I assembly protein ycf4	0.14	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				184
Q9SBN5 UniProt NPD GO	PSAN_VOLCA	Photosystem I reaction center subunit N, chloroplast precursor (PSI-N)	0.14	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; lumenal side (By similarity)				139
Q9ZT05 UniProt NPD GO	PSAK_MEDSA	Photosystem I reaction center subunit psaK, chloroplast precursor (Photosystem I subunit X) (PSI-K)	0.14	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (Probable)				129
Q9MUS1 UniProt NPD GO	PSBI_MESVI	Photosystem II reaction center I protein (PSII 4.8 kDa protein)	0.14	-	mit	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				38
P57093 UniProt NPD GO	PAHX_RAT	Phytanoyl-CoA dioxygenase, peroxisomal precursor (EC 1.14.11.18) (Phytanoyl-CoA alpha-hydroxylase) ( ...	0.14	-	nuc	0	Peroxisome	peroxisome [IDA]			338
P49293 UniProt NPD GO	PSY_CUCME	Phytoene synthase, chloroplast precursor (EC 2.5.1.-) (MEL5)	0.14	-	cyt	0	Plastid; chloroplast				422
Q9CQ58 UniProt NPD GO	PRLC2_MOUSE	Placental prolactin-like protein C2 precursor (PRL-like protein C2) (PLP-C2) (Prolactin-like protein ...	0.14	-	exc	0	Secreted protein (By similarity)				241
Q920I0 UniProt NPD GO	PRLC2_RAT	Placental prolactin-like protein C2 precursor (PRL-like protein C2) (PLP-C2) (Prolactin-like protein ...	0.14	-	cyt	0	Secreted protein (By similarity)				241
Q8CGZ9 UniProt NPD GO	PRLPN_MOUSE	Placental prolactin-like protein N precursor (PRL-like protein N) (PLP-N)	0.14	-	vac	0	Secreted protein (By similarity)				251
P54211 UniProt NPD GO	PMA1_DUNBI	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.14	-	end	9	Cell membrane; multi-pass membrane protein				1131
Q00724 UniProt NPD GO	RETBP_MOUSE	Plasma retinol-binding protein precursor (PRBP) (RBP)	0.14	-	mit	0	Secreted protein				201
P12388 UniProt NPD GO	PAI2_MOUSE	Plasminogen activator inhibitor 2, macrophage (PAI-2)	0.14	-	cyt	0	Or: Cytoplasm. Or: Extracellular space				415
P24352 UniProt NPD GO	RR2_ASTLO	Plastid 30S ribosomal protein S2	0.14	-	cyt	0	Plastid				235
P24353 UniProt NPD GO	RR8_ASTLO	Plastid 30S ribosomal protein S8	0.14	-	cyt	0	Plastid				142
Q9TJQ7 UniProt NPD GO	RK19_PROWI	Plastid 50S ribosomal protein L19	0.14	-	cyt	0	Plastid				129
Q9GL76 UniProt NPD GO	PVRL1_PIG	Poliovirus receptor-related protein 1 precursor (Herpes virus entry mediator C) (HveC) (Nectin-1) (C ...	0.14	-	end	2 *	Membrane; single-pass type I membrane protein				515
Q92692 UniProt NPD GO	PVRL2_HUMAN	Poliovirus receptor-related protein 2 precursor (Herpes virus entry mediator B) (HveB) (Nectin-2) (C ...	0.14	-	end	1	Membrane; single-pass type I membrane protein	plasma membrane [TAS]	600798		538
O23969 UniProt NPD GO	SF21_HELAN	Pollen-specific protein SF21	0.14	-	nuc	0					352
Q2KIN5 UniProt NPD GO	HEM3_BOVIN	Porphobilinogen deaminase (EC 2.5.1.61) (Hydroxymethylbilane synthase) (HMBS)	0.14	-	cyt	0					361
O35111 UniProt NPD GO	KCNK3_MOUSE	Potassium channel subfamily K member 3 (Acid-sensitive potassium channel protein TASK-1) (TWIK-relat ...	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				409
P83112 UniProt NPD GO	KAX1A_PARTR	Potassium channel toxin alpha-KTx 1.10 (Parabutoxin-3) (PBTx3)	0.14	-	nuc	0	Secreted protein				37
P59944 UniProt NPD GO	KAX1D_LEIQH	Potassium channel toxin alpha-KTx 1.13 (Charybdotoxin c) (ChTx-c)	0.14	-	nuc	0	Secreted protein				37
P15383 UniProt NPD GO	KCNE1_RAT	Potassium voltage-gated channel subfamily E member 1 (IKs producing slow voltage-gated potassium cha ...	0.14	-	mit	1 *	Membrane; single-pass type I membrane protein				130
Q9UJ90 UniProt NPD GO	KCE1L_HUMAN	Potassium voltage-gated channel subfamily E member 1-like protein (AMME syndrome candidate gene 2 pr ...	0.14	-	nuc	1	Membrane; single-pass type I membrane protein	voltage-gated potassium channel complex [TAS]	300328		142
Q6FTK3 UniProt NPD GO	SN309_CANGA	Pre-mRNA-splicing factor SNT309	0.14	-	cyt	0	Nucleus (By similarity)				156
P83444 UniProt NPD GO	PAG59_SHEEP	Pregnancy-associated glycoprotein 59 (EC 3.4.23.-) (ovPAG-59) (Fragment)	0.14	-		0	Secreted protein				15
Q9GK16 UniProt NPD GO	PRND_BOVIN	Prion-like protein doppel precursor (PrPLP)	0.14	-	exc	2 *	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				178
P17640 UniProt NPD GO	MCH1_ONCTS	Pro-MCH 1 precursor [Contains: Neuropeptide-glutamic acid-valine (NEV) (Neuropeptide E-V); Melanin-c ...	0.14	-	exc	0					132
Q39891 UniProt NPD GO	LEU1_SOYBN	Probable 2-isopropylmalate synthase (EC 2.3.3.13) (Alpha-isopropylmalate synthase) (Alpha-IPM synthe ...	0.14	-	mit	0					565

You are viewing entries 58801 to 58850 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.