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
Q5NVL7 UniProt NPD GO	PPWD1_PONPY	Peptidylprolyl isomerase domain and WD repeat-containing protein 1 (EC 5.2.1.8)	0.40	+	cyt	0					646
P84117 UniProt NPD GO	PERI_PERAI	Perinerin	0.40	-	nuc	0					51
P40553 UniProt NPD GO	DOT5_YEAST	Peroxiredoxin DOT5 (EC 1.11.1.15) (Thioredoxin reductase) (Nuclear thiol peroxidase) (nTPx) (Disrupt ...	0.40	-	nuc	0	Nucleus	nucleus [IDA]		2A4V	215
P33289 UniProt NPD GO	PEX6_PICPA	Peroxisomal biogenesis factor 6 (Peroxin-6) (Peroxisome biosynthesis protein PAS5)	0.40	-	cyt	0	Cytoplasm. It may be associated with the cytoskeleton or it may be cytoplasmic				1165
Q6B8Z8 UniProt NPD GO	SYFB_GRATL	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.40	-	cyt	0	Plastid; chloroplast				697
Q00619 UniProt NPD GO	MAM2_SCHPO	Pheromone P-factor receptor	0.40	-	end	7 *	Membrane; multi-pass membrane protein				348
P06783 UniProt NPD GO	STE3_YEAST	Pheromone a factor receptor	0.40	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [IDA]			470
Q9QW08 UniProt NPD GO	PHOS_MOUSE	Phosducin (PHD) (33 kDa phototransducing protein) (Rod photoreceptor 1) (RPR-1)	0.40	-	cyt	0	Outer and inner segments of the rod cells	cytosol [TAS]			244
P42066 UniProt NPD GO	PEPCK_CUCSA	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49) (PEP carboxykinase) (Phosphoenolpyruvate carbo ...	0.40	-	cyt	0	Cytoplasm (Probable)				670
O73884 UniProt NPD GO	PHOP1_CHICK	Phosphoethanolamine/phosphocholine phosphatase (EC 3.1.3.75) (3X11A)	0.40	-	mit	0					268
Q9D1G2 UniProt NPD GO	PMVK_MOUSE	Phosphomevalonate kinase (EC 2.7.4.2) (PMKase)	0.40	-	pox	0	Peroxisome (By similarity)				191
P25764 UniProt NPD GO	PHYB_ORYSA	Phytochrome B	0.40	-	cyt	0					1171
Q9ZWI9 UniProt NPD GO	PHYC_ORYSA	Phytochrome C	0.40	-	pox	0					1137
Q8TC59 UniProt NPD GO	PIWL2_HUMAN	Piwi-like protein 2	0.40	-	cyt	0	Cytoplasm (By similarity)				973
Q8CDG1 UniProt NPD GO	PIWL2_MOUSE	Piwi-like protein 2	0.40	-	mit	0	Cytoplasm	cytoplasm [IDA]			971
Q63434 UniProt NPD GO	PLGF_RAT	Placenta growth factor precursor (PlGF)	0.40	-	exc	0	Secreted protein (By similarity)				158
P97290 UniProt NPD GO	IC1_MOUSE	Plasma protease C1 inhibitor precursor (C1 Inh) (C1Inh)	0.40	-	exc	0	Secreted protein				504
Q9TJR0 UniProt NPD GO	RR12_PROWI	Plastid 30S ribosomal protein S12	0.40	-	mit	0	Plastid				124
O08742 UniProt NPD GO	GPV_MOUSE	Platelet glycoprotein V precursor (GPV) (CD42D antigen)	0.40	-	end	1	Membrane; single-pass type I membrane protein				567
Q9WV52 UniProt NPD GO	PLEK2_MOUSE	Pleckstrin-2	0.40	-	cyt	0				1V3F	353
Q5Z9S8 UniProt NPD GO	PDR12_ORYSA	Pleiotropic drug resistance protein 12	0.40	-	end	13	Membrane; multi-pass membrane protein (By similarity)				1500
Q922V4 UniProt NPD GO	PLRG1_MOUSE	Pleiotropic regulator 1	0.40	-	cyt	0	Nucleus; nucleoplasm; nuclear speckle (By similarity)				513
Q9Y6F1 UniProt NPD GO	PARP3_HUMAN	Poly [ADP-ribose] polymerase 3 (EC 2.4.2.30) (PARP-3) (NAD(+) ADP-ribosyltransferase 3) (Poly[ADP-ri ...	0.40	-	nuc	0	Nucleus. Centrosome. Core component of the centrosome. Preferentially localized to the daughter cent ...		607726		533
P42731 UniProt NPD GO	PABP2_ARATH	Polyadenylate-binding protein 2 (Poly(A)-binding protein 2) (PABP 2)	0.40	-	nuc	0					629
P42841 UniProt NPD GO	PFS2_YEAST	Polyadenylation factor subunit 2	0.40	-	nuc	0	Nucleus	mRNA cleavage and polyadenylation specifici... [IPI]			465
Q03796 UniProt NPD GO	TPP1_YEAST	Polynucleotide 3'-phosphatase (EC 3.1.3.32) (2'(3')-polynucleotidase) (DNA 3' phosphatase) (Three pr ...	0.40	-	nuc	0	Nucleus (Probable)				238
Q8C102 UniProt NPD GO	GALT5_MOUSE	Polypeptide N-acetylgalactosaminyltransferase 5 (EC 2.4.1.41) (Protein-UDP acetylgalactosaminyltrans ...	0.40	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				930
Q9ERS1 UniProt NPD GO	KCNKC_RAT	Potassium channel subfamily K member 12 (Tandem pore domain halothane-inhibited potassium channel 2) ...	0.40	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				430
O18965 UniProt NPD GO	KCNH1_BOVIN	Potassium voltage-gated channel subfamily H member 1 (Voltage-gated potassium channel subunit Kv10.1 ...	0.40	-	end	4	Membrane; multi-pass membrane protein				987
Q07930 UniProt NPD GO	PML1_YEAST	Pre-mRNA leakage protein 1	0.40	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]			204
Q4IF44 UniProt NPD GO	FIP1_GIBZE	Pre-mRNA polyadenylation factor FIP1	0.40	-	nuc	0	Nucleus (By similarity)				328
Q5KBF5 UniProt NPD GO	CWC2_CRYNE	Pre-mRNA-splicing factor CWC2	0.40	-	nuc	0	Nucleus (By similarity)				342
Q12046 UniProt NPD GO	CWC2_YEAST	Pre-mRNA-splicing factor CWC2 (Complexed with CEF1 protein 2) (PRP19-associated complex protein 40) ...	0.40	-	nuc	0	Nucleus	spliceosome complex [IDA]			339
Q69ZQ2 UniProt NPD GO	ISY1_MOUSE	Pre-mRNA-splicing factor ISY1 homolog	0.40	-	mit	0	Nucleus (Potential)			1X4T	285
Q753D4 UniProt NPD GO	RSE1_ASHGO	Pre-mRNA-splicing factor RSE1	0.40	+	cyt	0	Nucleus (By similarity)				1288
Q13046 UniProt NPD GO	PSG7_HUMAN	Pregnancy-specific beta-1-glycoprotein 7 precursor (PSBG-7)	0.40	-	nuc	0	Secreted protein (Potential)		176396		419
Q9C7A8 UniProt NPD GO	PSF2_ARATH	Probable DNA replication complex GINS protein PSF2	0.40	-	cyt	0	Nucleus (By similarity)				210
Q9VQY9 UniProt NPD GO	PSF2_DROME	Probable DNA replication complex GINS protein PSF2	0.40	-	nuc	0	Nucleus (By similarity)	nucleus [ISS]			203
Q01521 UniProt NPD GO	RPOP_PODAN	Probable DNA-directed RNA polymerase (EC 2.7.7.6)	0.40	-	mit	0					948
P22372 UniProt NPD GO	RPOP_CLAPU	Probable DNA-directed RNA polymerase (EC 2.7.7.6) (ORF2)	0.40	-	cyt	1					936
Q8IZF3 UniProt NPD GO	GP115_HUMAN	Probable G-protein coupled receptor 115 (G-protein coupled receptor PGR18)	0.40	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [TAS]			752
Q99MT7 UniProt NPD GO	GPR87_MOUSE	Probable G-protein coupled receptor 87	0.40	-	end	7 *	Membrane; multi-pass membrane protein				358
Q9FFS3 UniProt NPD GO	WRK24_ARATH	Probable WRKY transcription factor 24 (WRKY DNA-binding protein 24)	0.40	-	nuc	0	Nucleus (Probable)				179
Q8GY11 UniProt NPD GO	WRK43_ARATH	Probable WRKY transcription factor 43 (WRKY DNA-binding protein 43)	0.40	-	nuc	0	Nucleus (Probable)				109
Q9FYA2 UniProt NPD GO	WRK75_ARATH	Probable WRKY transcription factor 75 (WRKY DNA-binding protein 75)	0.40	-	nuc	0	Nucleus (Probable)				145
Q9V4U7 UniProt NPD GO	C6A14_DROME	Probable cytochrome P450 6a14 (EC 1.14.-.-) (CYPVIA14)	0.40	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				509
Q75CQ8 UniProt NPD GO	FRE8_ASHGO	Probable ferric reductase transmembrane component (EC 1.16.1.7) (Ferric-chelate reductase 8)	0.40	-	end	5 *	Membrane; multi-pass membrane protein				686
Q9VT52 UniProt NPD GO	INSL3_DROME	Probable insulin-like peptide 3 precursor (Insulin-related peptide) (DILP3) [Contains: Probable insu ...	0.40	-	exc	1 *	Secreted protein (Potential)	extracellular region [ISS]			120
Q5ALU2 UniProt NPD GO	SPC24_CANAL	Probable kinetochore protein SPC24	0.40	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				252
Q4X0I7 UniProt NPD GO	SPC24_ASPFU	Probable kinetochore protein spc24	0.40	-	nuc	0	Nucleus (By similarity). Associated with kinetochores (By similarity)				200

You are viewing entries 32051 to 32100 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.