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
P84007 UniProt NPD GO	PYF3_PENMO	Peptide tyrosine phenylalanine 3 (Pem-PYF3)	0.05	-		0	Secreted protein				9
Q8SXQ7 UniProt NPD GO	PGPLF_DROME	Peptidoglycan-recognition protein-LF (PGRP-like protein)	0.05	-	cyt	1 *	Membrane; multi-pass membrane protein (Potential)	integral to plasma membrane [NAS]		2F2L	369
Q9VYX7 UniProt NPD GO	PGPSA_DROME	Peptidoglycan-recognition protein-SA precursor (EC 3.4.17.13) (Protein semmelweis)	0.05	-	vac	1 *	Secreted protein. Secreted in hemolymph	extracellular region [IDA]		1SXR	203
O93826 UniProt NPD GO	PPIB_ARTBE	Peptidyl-prolyl cis-trans isomerase B precursor (EC 5.2.1.8) (PPIase B) (Rotamase B)	0.05	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				226
P87051 UniProt NPD GO	PPIL1_SCHPO	Peptidyl-prolyl cis-trans isomerase ppi1 (EC 5.2.1.8) (Cyclophilin ppi1)	0.05	-	cyt	0					155
Q41651 UniProt NPD GO	CYPB_VICFA	Peptidyl-prolyl cis-trans isomerase, chloroplast precursor (EC 5.2.1.8) (PPIase) (Rotamase) (Cycloph ...	0.05	-	mit	0	Plastid; chloroplast; chloroplast stroma				248
Q26287 UniProt NPD GO	PER_DROTE	Period circadian protein (Fragment)	0.05	-	nuc	0	Nucleus (By similarity). Cytoplasm; perinuclear region (By similarity). Nuclear at specific periods ...				88
Q25255 UniProt NPD GO	PE44_LUCCU	Peritrophin-44 precursor	0.05	-	exc	0					356
P37834 UniProt NPD GO	PER1_ORYSA	Peroxidase 1 precursor (EC 1.11.1.7)	0.05	-	exc	0	Secreted protein (By similarity)				326
Q96519 UniProt NPD GO	PER11_ARATH	Peroxidase 11 precursor (EC 1.11.1.7) (Atperox P11) (ATP23a/ATP23b)	0.05	-	mit	0	Secreted protein (By similarity)				336
Q9FJR1 UniProt NPD GO	PER65_ARATH	Peroxidase 65 precursor (EC 1.11.1.7) (Atperox P65) (ATP43)	0.05	-	exc	1 *	Secreted protein (By similarity)				334
P30044 UniProt NPD GO	PRDX5_HUMAN	Peroxiredoxin-5, mitochondrial precursor (EC 1.11.1.15) (Prx-V) (Peroxisomal antioxidant enzyme) (PL ...	0.05	-	cyt	0	Mitochondrion. Cytoplasm. Peroxisome	mitochondrion [IDA] peroxisome [IDA]	606583	1URM	214
P32573 UniProt NPD GO	SPS19_YEAST	Peroxisomal 2,4-dienoyl-CoA reductase SPS19 (EC 1.3.1.34) (Sporulation-specific protein SPX19)	0.05	-	pox	0	Peroxisome	peroxisomal matrix [IDA]			291
P22414 UniProt NPD GO	FOX2_CANTR	Peroxisomal hydratase-dehydrogenase-epimerase (HDE) (Multifunctional beta-oxidation protein) (MFP) [ ...	0.05	-	cyt	0	Peroxisome			2ET6	906
Q07066 UniProt NPD GO	PXMP2_RAT	Peroxisomal membrane protein 2 (22 kDa peroxisomal membrane protein)	0.05	-	mit	4 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	integral to peroxisomal membrane [TAS]			193
O59894 UniProt NPD GO	PEX7_PICPA	Peroxisomal targeting signal 2 receptor (PTS2 receptor) (Peroxin-7)	0.05	-	cyt	0	Peroxisome (By similarity). Cytoplasm (By similarity)				376
P55098 UniProt NPD GO	PEX2_MOUSE	Peroxisome assembly factor 1 (PAF-1) (Peroxin-2) (Peroxisomal membrane protein 3)	0.05	-	mit	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein				305
P10248 UniProt NPD GO	PALY_RHORB	Phenylalanine ammonia-lyase (EC 4.3.1.5)	0.05	-	nuc	0	Cytoplasm (Probable)				713
P15624 UniProt NPD GO	SYFB_YEAST	Phenylalanyl-tRNA synthetase beta chain (EC 6.1.1.20) (Phenylalanine--tRNA ligase beta chain) (PheRS ...	0.05	-	cyt	0	Cytoplasm	cytoplasm [TAS] phenylalanine-tRNA ligase complex [TAS]			594
P38221 UniProt NPD GO	CDS1_YEAST	Phosphatidate cytidylyltransferase (EC 2.7.7.41) (CDP-diglyceride synthetase) (CDP-diglyceride pyrop ...	0.05	-	end	6	Mitochondrion; mitochondrial membrane; multi-pass membrane protein. Endoplasmic reticulum; endoplasm ...				457
Q9D4B1 UniProt NPD GO	SMS2_MOUSE	Phosphatidylcholine:ceramide cholinephosphotransferase 2 (EC 2.7.-.-) (Sphingomyelin synthase 2)	0.05	-	end	6	Cell membrane; multi-pass membrane protein (By similarity). Golgi apparatus; Golgi membrane; multi-p ...	integral to Golgi membrane [ISS] integral to plasma membrane [ISS]			365
P70296 UniProt NPD GO	PEBP1_MOUSE	Phosphatidylethanolamine-binding protein 1 (PEBP-1) (HCNPpp) [Contains: Hippocampal cholinergic neur ...	0.05	+	cyt	0	Cytoplasm	cell surface [IDA]			186
P32449 UniProt NPD GO	AROG_YEAST	Phospho-2-dehydro-3-deoxyheptonate aldolase, tyrosine-inhibited (EC 2.5.1.54) (Phospho-2-keto-3-deox ...	0.05	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1OG0	370
O13434 UniProt NPD GO	PPCK_CANAL	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.05	-	cyt	0					553
Q6FRR0 UniProt NPD GO	PPCK_CANGA	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.05	-	cyt	0					544
O43112 UniProt NPD GO	PPCK_KLULA	Phosphoenolpyruvate carboxykinase [ATP] (EC 4.1.1.49)	0.05	-	nuc	0					543
P51058 UniProt NPD GO	PPCK_TRYCR	Phosphoenolpyruvate carboxykinase [ATP], glycosomal (EC 4.1.1.49)	0.05	-	cyt	0	Glycosome (By similarity)			1II2	472
P93804 UniProt NPD GO	PGMC1_MAIZE	Phosphoglucomutase, cytoplasmic 1 (EC 5.4.2.2) (Glucose phosphomutase 1) (PGM 1)	0.05	-	cyt	0	Cytoplasm				583
P41757 UniProt NPD GO	PGK_CANMA	Phosphoglycerate kinase (EC 2.7.2.3)	0.05	-	cyt	0	Cytoplasm				417
P83542 UniProt NPD GO	PA1_POLGA	Phospholipase A1 (EC 3.1.1.32) (Allergen Pol g 1) (Fragment)	0.05	-	nuc	0		extracellular region [NAS]			42
P81237 UniProt NPD GO	PA22_ACAAN	Phospholipase A2 (EC 3.1.1.4) (Acanthin II) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	nuc	0	Secreted protein				118
P51972 UniProt NPD GO	PA21_AGKPI	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (APP-D-49)	0.05	-	nuc	0	Secreted protein			1VAP	123
P81243 UniProt NPD GO	PA21B_BOTJA	Phospholipase A2 (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (BJ-PLA2)	0.05	-	cyt	0	Secreted protein				124
P20260 UniProt NPD GO	PA2C_PSEPO	Phospholipase A2 (EC 3.1.1.4) (Pseudexin C chain) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.05	-	nuc	0	Secreted protein				28
O42192 UniProt NPD GO	PA28_AGKHP	Phospholipase A2 A' (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	nuc	0	Secreted protein (By similarity)				122
Q8QG87 UniProt NPD GO	PA21_BOTIN	Phospholipase A2 BITP01A precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	mit	0	Secreted protein (By similarity)				138
P00623 UniProt NPD GO	PA2_CROAD	Phospholipase A2 alpha (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	nuc	0	Secreted protein				122
Q9I834 UniProt NPD GO	PA22_BOTMO	Phospholipase A2 homolog 2 (Myotoxin II) (MjTX-II) (M-VI)	0.05	-	nuc	0	Secreted protein				122
P00597 UniProt NPD GO	PA22_NAJKA	Phospholipase A2 isozyme 2 precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (NnkPLA-II) ...	0.05	-	mit	0	Secreted protein				146
Q9PUG9 UniProt NPD GO	PA215_AUSSU	Phospholipase A2 isozyme S12-65J precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (ASPLA ...	0.05	-	exc	0	Secreted protein (By similarity)				144
Q8WS88 UniProt NPD GO	PA2_ADACA	Phospholipase A2 precursor (EC 3.1.1.4) (AcPLA2) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	end	0	Secreted protein (By similarity). Found in nematocyst (By similarity)				156
P08873 UniProt NPD GO	PA20_NOTSC	Phospholipase A2 precursor (EC 3.1.1.4) (Notechis 11'2) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	exc	0	Secreted protein				145
P20249 UniProt NPD GO	PA22_AGKHA	Phospholipase A2, acidic (EC 3.1.1.4) (PA2-II) (Phosphatidylcholine 2-acylhydrolase)	0.05	-	cyt	0	Secreted protein				122
Q7SID6 UniProt NPD GO	PA2A_AGKAC	Phospholipase A2, acidic (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (PLA2)	0.05	-	cyt	0	Secreted protein			1IJL	123
Q92086 UniProt NPD GO	PA2C_NAJSP	Phospholipase A2, acidic C precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (NAJPLA-2C) ...	0.05	-	exc	0	Secreted protein (By similarity)				146
P82892 UniProt NPD GO	PA2B1_TRIST	Phospholipase A2, basic 1 (EC 3.1.1.4) (PA2-I) (PLA2-I) (Phosphatidylcholine 2-acylhydrolase) (Fragm ...	0.05	-		0	Secreted protein				16
Q8QFW3 UniProt NPD GO	PA22_BUNCE	Phospholipase A2, beta bungarotoxin A2 chain precursor (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydro ...	0.05	-	exc	1 *	Secreted protein (By similarity)				147
P59070 UniProt NPD GO	PA2V_AUSSU	Phospholipase A2, superbin d (EC 3.1.1.4) (Phosphatidylcholine 2-acylhydrolase) (Fragment)	0.05	-	nuc	0	Secreted protein				48
P07283 UniProt NPD GO	PMM_YEAST	Phosphomannomutase (EC 5.4.2.8) (PMM)	0.05	-	cyt	0	Cytoplasm	cytosol [IDA]			254
Q07463 UniProt NPD GO	PUR7_VIGAC	Phosphoribosylaminoimidazole-succinocarboxamide synthase, chloroplast precursor (EC 6.3.2.6) (SAICAR ...	0.05	-	mit	0	Plastid; chloroplast (Probable)				341

You are viewing entries 75151 to 75200 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.