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
P21462 UniProt NPD GO	FPR1_HUMAN	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein	endosome [TAS] integral to membrane [TAS] plasma membrane [TAS]	136537		350
P79176 UniProt NPD GO	FPR1_GORGO	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				346
P79241 UniProt NPD GO	FPR1_PANTR	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				346
P79235 UniProt NPD GO	FPR1_PONPY	fMet-Leu-Phe receptor (fMLP receptor) (N-formyl peptide receptor) (FPR) (N-formylpeptide chemoattrac ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				346
Q8WW01 UniProt NPD GO	SEN15_HUMAN	tRNA-splicing endonuclease subunit Sen15 (tRNA-intron endonuclease Sen15) (HsSen15)	0.01	-	cyt	0	Nucleus (Probable). Nucleus; nucleolus (Probable). May be transiently localized in the nucleolus (Pr ...		608756		171
P41277 UniProt NPD GO	GPP1_YEAST	(DL)-glycerol-3-phosphatase 1 (EC 3.1.3.-)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			249
P40106 UniProt NPD GO	GPP2_YEAST	(DL)-glycerol-3-phosphatase 2 (EC 3.1.3.-)	0.00	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			250
P52704 UniProt NPD GO	HNL_HEVBR	(S)-acetone-cyanohydrin lyase (EC 4.1.2.39) ((S)-hydroxynitrile lyase) ((S)-hydroxynitrilase) (Oxyni ...	0.00	-	cyt	0				7YAS	257
Q8W108 UniProt NPD GO	ARD3_ARATH	1,2-dihydroxy-3-keto-5-methylthiopentene dioxygenase 3 (EC 1.13.-.-) (Aci-reductone dioxygenase 3)	0.00	-	cyt	0					199
P82125 UniProt NPD GO	AFR_PIG	1,5-anhydro-D-fructose reductase (EC 1.1.1.263) (AF reductase) (Fragments)	0.00	-	cyt	0					206
P83011 UniProt NPD GO	13KDA_SCYCA	13.2 kDa protein (Fragment)	0.00	-		0	Microsome	microsome [IDA]			14
P80796 UniProt NPD GO	CWP19_TOBAC	14 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				11
Q9DAK9 UniProt NPD GO	PHP14_MOUSE	14 kDa phosphohistidine phosphatase (EC 3.1.3.-) (Phosphohistidine phosphatase 1)	0.00	-	cyt	0	Cytoplasm (By similarity)	cytosol [ISS]			124
P59083 UniProt NPD GO	PHP14_PIG	14 kDa phosphohistidine phosphatase (EC 3.1.3.-) (Phosphohistidine phosphatase 1) (Fragments)	0.00	-	cyt	0	Cytoplasm				53
Q9NRX4 UniProt NPD GO	PHP14_HUMAN	14 kDa phosphohistidine phosphatase (EC 3.1.3.-) (Phosphohistidine phosphatase 1) (Protein janus-A h ...	0.00	-	cyt	0	Cytoplasm (By similarity)	cytoplasm [TAS] cytosol [NAS]			125
Q91499 UniProt NPD GO	I14K_TORMA	14 kDa transmembrane protein	0.00	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)				107
P80795 UniProt NPD GO	CWP18_TOBAC	15 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				15
Q3T0C2 UniProt NPD GO	PGDH_BOVIN	15-hydroxyprostaglandin dehydrogenase [NAD+] (EC 1.1.1.141) (PGDH) (Prostaglandin dehydrogenase 1)	0.00	-	cyt	0	Cytoplasm (By similarity)				266
P23668 UniProt NPD GO	LEG6_CHICK	16 kDa beta-galactoside-binding lectin (C-16) (Galectin CG-16)	0.00	-	cyt	0				1QMJ	134
Q9ZT47 UniProt NPD GO	PP16A_CUCMA	16 kDa phloem protein 1	0.00	-	cyt	0					149
Q96468 UniProt NPD GO	BAS1_HORVU	2-cys peroxiredoxin BAS1, chloroplast precursor (EC 1.11.1.15) (Thiol-specific antioxidant protein) ...	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				210
P80602 UniProt NPD GO	BAS1_WHEAT	2-cys peroxiredoxin BAS1, chloroplast precursor (EC 1.11.1.15) (Thiol-specific antioxidant protein) ...	0.00	-	cyt	0	Plastid; chloroplast				210
P38774 UniProt NPD GO	DOG1_YEAST	2-deoxyglucose-6-phosphate phosphatase 1 (EC 3.1.3.68) (2-DOG-6-P 1) (2-deoxyglucose-6-phosphatase 1 ...	0.00	-	cyt	0					246
Q16880 UniProt NPD GO	CGT_HUMAN	2-hydroxyacylsphingosine 1-beta-galactosyltransferase precursor (EC 2.4.1.45) (UDP-galactose-ceramid ...	0.00	-	end	2 *			601291		541
P80822 UniProt NPD GO	CWP26_LYCES	20 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				10
P84579 UniProt NPD GO	CH10C_POPEU	20 kDa chaperonin (Protein Cpn21) (Chloroplast protein Cpn10) (Chloroplast chaperonin 10) (Ch-CPN10) ...	0.00	-	cyt	0	Plastid; chloroplast (By similarity)				53
Q02073 UniProt NPD GO	CH10C_SPIOL	20 kDa chaperonin, chloroplast precursor (Protein Cpn21) (Chloroplast protein Cpn10) (Chloroplast ch ...	0.00	-	cyt	0	Plastid; chloroplast				255
O65282 UniProt NPD GO	CH10C_ARATH	20 kDa chaperonin, chloroplast precursor (Protein Cpn21) (Chloroplast protein Cpn10) (Chloroplast ch ...	0.00	-	mit	0	Plastid; chloroplast				253
P35430 UniProt NPD GO	AHD2_TETPY	20-alpha-hydroxysteroid dehydrogenase (EC 1.1.1.149) (20-alpha-HSD) (Fragment)	0.00	-		0					18
P80802 UniProt NPD GO	CWP05_LYCES	22 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				15
P80821 UniProt NPD GO	CWP25_LYCES	23 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				20
Q26499 UniProt NPD GO	IM23_SCHHA	23 kDa integral membrane protein (Sh23)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				218
P27591 UniProt NPD GO	IM23_SCHJA	23 kDa integral membrane protein (Sj23)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				218
P19331 UniProt NPD GO	IM23_SCHMA	23 kDa integral membrane protein (Sm23)	0.00	-	end	4 *	Membrane; multi-pass membrane protein				218
P32024 UniProt NPD GO	JI23_HORVU	23 kDa jasmonate-induced protein	0.00	-	cyt	0					210
P14592 UniProt NPD GO	24KD_PLACH	24 kDa antigen (Fragment)	0.00	-	cyt	0					37
Q39227 UniProt NPD GO	SMT2_ARATH	24-methylenesterol C-methyltransferase 2 (EC 2.1.1.143) (24-sterol C-methyltransferase 2) (Sterol-C- ...	0.00	-	nuc	1 *					361
P13829 UniProt NPD GO	OS25_PLAFO	25 kDa ookinete surface antigen precursor (Pfs25)	0.00	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				217
P19455 UniProt NPD GO	OS25_PLARE	25 kDa ookinete surface antigen precursor (Prs25)	0.00	-	nuc	1	Cell membrane; lipid-anchor; GPI-anchor (Potential)				217
P82437 UniProt NPD GO	CWP29_TOBAC	26 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				12
P81925 UniProt NPD GO	AB27_CYPCA	27 kDa antibacterial protein (Fragment)	0.00	-		0					19
P80809 UniProt NPD GO	CWP12_LYCES	27 kDa cell wall protein (Fragment)	0.00	-		0	Cell wall				13
P33405 UniProt NPD GO	28KD_TRIFO	28 kDa protein (Fragment)	0.00	-	cyt	0					29
Q9Y3B2 UniProt NPD GO	EXOS1_HUMAN	3'-5' exoribonuclease CSL4 homolog (EC 3.1.13.-) (Exosome component 1)	0.00	-	cyt	0	Nucleus; nucleolus	exosome (RNase complex) [NAS] nucleolus [IDA]	606493		195
Q9DAA6 UniProt NPD GO	EXOS1_MOUSE	3'-5' exoribonuclease CSL4 homolog (EC 3.1.13.-) (Exosome component 1)	0.00	-	cyt	0	Nucleus; nucleolus (By similarity)	exosome (RNase complex) [ISS] nucleolus [ISS]			195
Q60490 UniProt NPD GO	EBP_CAVPO	3-beta-hydroxysteroid-delta(8),delta(7)-isomerase (EC 5.3.3.5) (Cholestenol delta-isomerase) (Delta8 ...	0.00	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				228
Q01987 UniProt NPD GO	LEU3_CANBO	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				365
Q12545 UniProt NPD GO	LEU3_CEPAC	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				380
Q9HDQ1 UniProt NPD GO	LEU3_HANAN	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				364
P23390 UniProt NPD GO	LEU3_KLULA	3-isopropylmalate dehydrogenase (EC 1.1.1.85) (Beta-IPM dehydrogenase) (IMDH) (3-IPM-DH)	0.00	-	cyt	0	Cytoplasm				362

You are viewing entries 92151 to 92200 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.