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
Q5RFI8 UniProt NPD GO	PGM2_PONPY	Phosphoglucomutase-2 (EC 5.4.2.2) (Glucose phosphomutase 2) (PGM 2)	0.25	-	cyt	0	Cytoplasm (By similarity)				611
O00168 UniProt NPD GO	PLM_HUMAN	Phospholemman precursor (FXYD domain-containing ion transport regulator 1)	0.25	-	end	1 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	602359		92
P10117 UniProt NPD GO	PA2H_LATCO	Phospholipase A2 homolog 1 (Phospholipase A2 homolog I) (PLH-I)	0.25	-	nuc	0	Secreted protein				118
Q9P8P2 UniProt NPD GO	PLB1_CRYNV	Phospholipase B precursor (EC 3.1.1.5) (Lysophospholipase)	0.25	+	vac	0	Secreted protein				637
P93400 UniProt NPD GO	PLDA1_TOBAC	Phospholipase D alpha 1 (EC 3.1.4.4) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylcholine-hydr ...	0.25	-	cyt	0					808
Q43007 UniProt NPD GO	PLDA1_ORYSA	Phospholipase D alpha 1 precursor (EC 3.1.4.4) (PLD alpha 1) (Choline phosphatase 1) (Phosphatidylch ...	0.25	-	cyt	0					812
Q42805 UniProt NPD GO	PUR3_SOYBN	Phosphoribosylglycinamide formyltransferase, chloroplast precursor (EC 2.1.2.2) (GART) (GAR transfor ...	0.25	-	mit	0	Plastid; chloroplast				295
P26302 UniProt NPD GO	KPPR_WHEAT	Phosphoribulokinase, chloroplast precursor (EC 2.7.1.19) (Phosphopentokinase) (PRKase) (PRK)	0.25	-	mit	0	Plastid; chloroplast				404
P62719 UniProt NPD GO	YCF4_AEGCR	Photosystem I assembly protein ycf4	0.25	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
Q6L602 UniProt NPD GO	YCF4_AEGSP	Photosystem I assembly protein ycf4	0.25	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
P62720 UniProt NPD GO	YCF4_WHEAT	Photosystem I assembly protein ycf4	0.25	-	mit	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein (By similarity)				185
P34094 UniProt NPD GO	PHYB_SOLTU	Phytochrome B	0.25	-	cyt	0					1130
P81039 UniProt NPD GO	PACA_URAJA	Pituitary adenylate cyclase-activating polypeptide (PACAP)	0.25	-	nuc	0	Secreted protein				38
Q9XS47 UniProt NPD GO	PLGF_BOVIN	Placenta growth factor precursor (PlGF)	0.25	-	nuc	0	Secreted protein (By similarity)				149
P24545 UniProt NPD GO	PMA1_ZYGRO	Plasma membrane ATPase (EC 3.6.3.6) (Proton pump)	0.25	+	end	8	Cell membrane; multi-pass membrane protein				920
P09627 UniProt NPD GO	PMA1_SCHPO	Plasma membrane ATPase 1 (EC 3.6.3.6) (Proton pump 1)	0.25	+	end	9	Cell membrane; multi-pass membrane protein				919
P19657 UniProt NPD GO	PMA2_YEAST	Plasma membrane ATPase 2 (EC 3.6.3.6) (Proton pump 2)	0.25	+	end	10	Cell membrane; multi-pass membrane protein	plasma membrane [IDA]			947
P29524 UniProt NPD GO	PAI2_RAT	Plasminogen activator inhibitor 2 type A (PAI2A) (PAI-2)	0.25	-	cyt	0	Or: Cytoplasm (By similarity). Or: Extracellular space (By similarity)				416
P30062 UniProt NPD GO	RR19_EPIVI	Plastid 30S ribosomal protein S19	0.25	-	nuc	0	Plastid				94
Q2EEV8 UniProt NPD GO	RK2_HELSJ	Plastid ribosomal protein L2	0.25	-	nuc	0	Plastid				282
Q3SWT0 UniProt NPD GO	PECA1_RAT	Platelet endothelial cell adhesion molecule precursor (PECAM-1) (CD31 antigen)	0.25	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				678
P56400 UniProt NPD GO	GP1BB_MOUSE	Platelet glycoprotein Ib beta chain precursor (GP-Ib beta) (GPIbB) (GPIb-beta) (CD42c antigen)	0.25	-	end	1	Membrane; single-pass type I membrane protein				206
Q8IUK5 UniProt NPD GO	PXDC1_HUMAN	Plexin domain-containing protein 1 precursor (Tumor endothelial marker 7) (Tumor endothelial marker ...	0.25	-	end	1	Isoform 1: membrane; single-pass type I membrane protein (Potential). Isoform 2 and isoform 3: secre ...				500
Q7JGR2 UniProt NPD GO	PABP5_MACMU	Polyadenylate-binding protein 5 (Poly(A)-binding protein 5) (PABP 5)	0.25	-	nuc	0	Cytoplasm (By similarity)				382
Q7RY68 UniProt NPD GO	PFS2_NEUCR	Polyadenylation factor subunit 2	0.25	-	nuc	0	Nucleus (By similarity)				662
Q8GT95 UniProt NPD GO	PGIP1_ORYSA	Polygalacturonase inhibitor 1 precursor (Polygalacturonase-inhibiting protein) (Floral organ regulat ...	0.25	-	nuc	0					332
Q9Y2S7 UniProt NPD GO	PDIP2_HUMAN	Polymerase delta-interacting protein 2 (38 kDa DNA polymerase delta interaction protein) (p38)	0.25	-	mit	0	Nucleus (Probable)				368
Q9HET9 UniProt NPD GO	TPP1_SACMI	Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase) (DNA 3' phosphatase) (Three pr ...	0.25	+	nuc	0	Nucleus (Probable)				245
Q07537 UniProt NPD GO	GALT1_BOVIN	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.25	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				559
Q29121 UniProt NPD GO	GALT1_PIG	Polypeptide N-acetylgalactosaminyltransferase 1 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.25	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				559
Q8IUC8 UniProt NPD GO	GLT13_HUMAN	Polypeptide N-acetylgalactosaminyltransferase 13 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.25	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)		608369		556
Q6UE39 UniProt NPD GO	GLT13_RAT	Polypeptide N-acetylgalactosaminyltransferase 13 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltran ...	0.25	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				556
Q5RCW2 UniProt NPD GO	PNPT1_PONPY	Polyribonucleotide nucleotidyltransferase 1, mitochondrial precursor (EC 2.7.7.8) (PNPase 1)	0.25	-	mit	0	Mitochondrion (By similarity)				783
P84630 UniProt NPD GO	KA133_TITPA	Potassium channel toxin alpha-KTx13.3 (Toxin Tpa1)	0.25	-	nuc	0	Secreted protein				23
Q8H3P9 UniProt NPD GO	HAK7_ORYSA	Potassium transporter 7 (OsHAK7)	0.25	-	end	13 *	Membrane; multi-pass membrane protein (By similarity)				811
Q09470 UniProt NPD GO	KCNA1_HUMAN	Potassium voltage-gated channel subfamily A member 1 (Voltage-gated potassium channel subunit Kv1.1) ...	0.25	-	end	4	Membrane; multi-pass membrane protein	voltage-gated potassium channel complex [TAS]	176260		495
P17659 UniProt NPD GO	KCNA6_RAT	Potassium voltage-gated channel subfamily A member 6 (Voltage-gated potassium channel subunit Kv1.6) ...	0.25	-	end	5	Membrane; multi-pass membrane protein				530
Q9Y3B4 UniProt NPD GO	PM14_HUMAN	Pre-mRNA branch site protein p14 (SF3B 14 kDa subunit)	0.25	-	mit	0	Nucleus (Potential)		607835	2F9J	125
P59708 UniProt NPD GO	PM14_MOUSE	Pre-mRNA branch site protein p14 (SF3B 14 kDa subunit)	0.25	-	mit	0	Nucleus (Potential)				125
Q3SZE2 UniProt NPD GO	PFD1_BOVIN	Prefoldin subunit 1	0.25	-	cyt	0					122
O60925 UniProt NPD GO	PFD1_HUMAN	Prefoldin subunit 1	0.25	-	nuc	0			604897		122
Q5RAM7 UniProt NPD GO	PFD1_PONPY	Prefoldin subunit 1	0.25	-	nuc	0					122
Q5TZD1 UniProt NPD GO	PPC2B_BRARE	Presqualene diphosphate phosphatase B (EC 3.1.3.-) (Phosphatidic acid phosphatase type 2 domain-cont ...	0.25	-	end	3	Membrane; multi-pass membrane protein (Potential)				288
P05817 UniProt NPD GO	D11_DICDI	Prestalk D11 protein precursor	0.25	-	exc	0					282
Q18787 UniProt NPD GO	PRS7_CAEEL	Probable 26S protease regulatory subunit 7	0.25	-	cyt	0	Cytoplasm (Potential). Nucleus (Potential)				435
Q616T6 UniProt NPD GO	RM45_CAEBR	Probable 39S ribosomal protein L45, mitochondrial precursor	0.25	-	mit	0	Mitochondrion (By similarity)				361
Q694B5 UniProt NPD GO	ABC3C_GORGO	Probable DNA dC->dU-editing enzyme APOBEC-3C (EC 3.5.4.-)	0.25	-	cyt	0					190
Q8IZF7 UniProt NPD GO	GP111_HUMAN	Probable G-protein coupled receptor 111 (G-protein coupled receptor PGR20)	0.25	-	end	6	Membrane; multi-pass membrane protein	integral to membrane [TAS]			708
Q7TQP2 UniProt NPD GO	GP135_MOUSE	Probable G-protein coupled receptor 135	0.25	-	end	7	Membrane; multi-pass membrane protein				457
Q8TDT2 UniProt NPD GO	GP152_HUMAN	Probable G-protein coupled receptor 152 (G-protein coupled receptor PGR5)	0.25	-	end	7 *	Membrane; multi-pass membrane protein				470

You are viewing entries 45551 to 45600 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.