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
P17505 UniProt NPD GO	MDHM_YEAST	Malate dehydrogenase, mitochondrial precursor (EC 1.1.1.37)	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [TAS]			334
Q13296 UniProt NPD GO	SG2A2_HUMAN	Mammaglobin-A precursor (Mammaglobin-1) (Secretoglobin family 2A member 2)	0.04	-	vac	0			605562		93
Q6FLP9 UniProt NPD GO	DCW1_CANGA	Mannan endo-1,6-alpha-mannosidase DCW1 precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-mannanase DCW1) ( ...	0.04	-	end	1	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				446
Q05031 UniProt NPD GO	DFG5_YEAST	Mannan endo-1,6-alpha-mannosidase DFG5 precursor (EC 3.2.1.101) (Endo-alpha-1->6-D-mannanase DFG5)	0.04	-	end	1	Cell membrane; lipid-anchor; GPI-anchor	anchored to plasma membrane [IDA]			458
Q7RVR8 UniProt NPD GO	MPG1_NEUCR	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.04	-	mit	0	Cytoplasm (By similarity)				364
P29951 UniProt NPD GO	MANA_EMENI	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.04	-	cyt	0	Cytoplasm (Probable)				461
Q8J093 UniProt NPD GO	MANA_PICAN	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.04	-	cyt	0	Cytoplasm (By similarity)				426
Q66S61 UniProt NPD GO	MBL2_CALJA	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.04	-	exc	0					248
Q66S45 UniProt NPD GO	MBL2_PRECR	Mannose-binding protein C precursor (MBP-C) (MBP1) (Mannan-binding protein) (Mannose-binding lectin) ...	0.04	-	exc	0					248
P08661 UniProt NPD GO	MBL2_RAT	Mannose-binding protein C precursor (MBP-C) (Mannan-binding protein) (RA-reactive factor P28A subuni ...	0.04	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum membrane; peripheral ...			1RDO	244
O02773 UniProt NPD GO	MA1A1_PIG	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IA (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.04	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				659
P31723 UniProt NPD GO	MAN12_PENCI	Mannosyl-oligosaccharide alpha-1,2-mannosidase precursor (EC 3.2.1.113) (Man(9)-alpha-mannosidase)	0.04	-	exc	0	Secreted protein			1KRF	511
Q4R5H6 UniProt NPD GO	SPG21_MACFA	Maspardin (Spastic paraplegia 21 autosomal recessive Mast syndrome protein homolog)	0.04	-	mit	0	Cytoplasm (By similarity)	cytosol [ISS] trans-Golgi network transport vesicle [ISS]			308
P15119 UniProt NPD GO	MCPT2_MOUSE	Mast cell protease 2 precursor (EC 3.4.21.-) (MMCP-2)	0.04	-	end	0					244
O35164 UniProt NPD GO	MCPT9_MOUSE	Mast cell protease 9 precursor (EC 3.4.21.-) (MMCP-9)	0.04	-	exc	0					246
P83235 UniProt NPD GO	MEN2_EUPNO	Mating pheromone En-2	0.04	-	nuc	0	Secreted protein	extracellular region [NAS]			60
P41983 UniProt NPD GO	MC5R_SHEEP	Melanocortin receptor 5 (MC5-R)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				325
Q864I1 UniProt NPD GO	MSHR_LEOCY	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.04	-	end	6 *	Membrane; multi-pass membrane protein				310
Q864H4 UniProt NPD GO	MSHR_SAGFU	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.04	-	end	7 *	Membrane; multi-pass membrane protein				316
P49285 UniProt NPD GO	MTR1A_CHICK	Melatonin receptor type 1A (MEL-1A-R) (CKA)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				353
P49217 UniProt NPD GO	MTR1A_PHOSU	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor)	0.04	-	end	7 *	Membrane; multi-pass membrane protein				353
P51052 UniProt NPD GO	MTR1C_BRARE	Melatonin receptor type 1C Z2.3 (MEL-1C-R) (Fragment)	0.04	-	mit	3 *	Membrane; multi-pass membrane protein				151
Q9HDY3 UniProt NPD GO	YK17_SCHPO	Membrane protein PB1A10.07c	0.04	-	end	10 *	Membrane; multi-pass membrane protein				441
Q9XFM6 UniProt NPD GO	MSBP1_ARATH	Membrane steroid-binding protein 1 (AtMP1)	0.04	-	mit	1 *	Cell membrane				220
Q99N03 UniProt NPD GO	M4A10_MOUSE	Membrane-spanning 4-domains subfamily A member 10	0.04	-	cyt	4	Membrane; multi-pass membrane protein				267
Q9NXJ0 UniProt NPD GO	M4A12_HUMAN	Membrane-spanning 4-domains subfamily A member 12	0.04	-	end	4	Membrane; multi-pass membrane protein		606550		267
Q9S9N8 UniProt NPD GO	NRAM6_ARATH	Metal transporter Nramp6 (AtNramp6)	0.04	-	end	12 *	Membrane; multi-pass membrane protein (Probable)				527
P01076 UniProt NPD GO	MCPI_LYCES	Metallocarboxypeptidase inhibitor precursor (MCPI) (Carboxypeptidase inhibitor)	0.04	-	vac	1 *					77
P04358 UniProt NPD GO	MT_AGABI	Metallothionein (MT)	0.04	-	nuc	0					25
P23038 UniProt NPD GO	MT_CRAVI	Metallothionein (MT)	0.04	-	nuc	0					74
P02807 UniProt NPD GO	MT_NEUCR	Metallothionein (MT)	0.04	-	nuc	0				1T2Y	25
P15786 UniProt NPD GO	MT1_COLLI	Metallothionein-1 (MT-1) (Metallothionein-I) (MT-I)	0.04	-	nuc	0					63
P11956 UniProt NPD GO	MT2_DROME	Metallothionein-2 (MT-2) (Metallothionein B)	0.04	-	nuc	0					43
P30571 UniProt NPD GO	MT1_MAIZE	Metallothionein-like protein 1 (MT-1)	0.04	-	nuc	0					76
Q40158 UniProt NPD GO	MT2B_LYCES	Metallothionein-like protein type 2 B	0.04	-	nuc	0					82
P43390 UniProt NPD GO	MT2_ACTCH	Metallothionein-like protein type 2 PKIWI504	0.04	-	nuc	0					78
Q9FV52 UniProt NPD GO	AMP1B_ARATH	Methionine aminopeptidase 1B, chloroplast precursor (EC 3.4.11.18) (MetAP 1B) (MAP 1B) (Peptidase M ...	0.04	-	vac	0	Plastid; chloroplast				369
Q8SR45 UniProt NPD GO	AMPM2_ENCCU	Methionine aminopeptidase 2 (EC 3.4.11.18) (MetAP 2) (Peptidase M 2) (MetAP2) (MAP-2)	0.04	-	cyt	0					358
Q9JLC3 UniProt NPD GO	MSRX_MOUSE	Methionine-R-sulfoxide reductase (EC 1.8.4.-) (Selenoprotein X 1) (Selenoprotein R)	0.04	-	nuc	0		cytoplasm [IDA] nucleus [IDA]			116
Q6TDU1 UniProt NPD GO	MGMT_CANFA	Methylated-DNA--protein-cysteine methyltransferase (EC 2.1.1.63) (6-O-methylguanine-DNA methyltransf ...	0.04	-	cyt	0	Nucleus (Probable)				216
Q13825 UniProt NPD GO	AUMH_HUMAN	Methylglutaconyl-CoA hydratase, mitochondrial precursor (EC 4.2.1.18) (AU-specific RNA-binding enoyl ...	0.04	-	mit	0	Mitochondrion (By similarity)		250950	1HZD	339
Q28678 UniProt NPD GO	ICLN_RABIT	Methylosome subunit pICln (Chloride conductance regulatory protein ICln) (I(Cln)) (Chloride channel, ...	0.04	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity). A small fraction is also associated with the cyt ...				236
P84346 UniProt NPD GO	MEX1_JACME	Mexicain (EC 3.4.22.-)	0.04	-	cyt	0	Secreted protein				214
P55918 UniProt NPD GO	MFAP4_BOVIN	Microfibril-associated glycoprotein 4 precursor (36 kDa microfibril-associated glycoprotein) (36 kDa ...	0.04	-	cyt	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				255
Q26539 UniProt NPD GO	MIA1_SARMU	Microneme antigen precursor	0.04	-	mit	1 *	Microneme				241
Q64L89 UniProt NPD GO	MGST1_BOVIN	Microsomal glutathione S-transferase 1 (EC 2.5.1.18) (Microsomal GST-1)	0.04	-	cyt	3 *	Microsome (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral membrane protein ...				155
Q91VS7 UniProt NPD GO	MGST1_MOUSE	Microsomal glutathione S-transferase 1 (EC 2.5.1.18) (Microsomal GST-1) (Microsomal GST-I)	0.04	-	cyt	3 *	Microsome (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral membrane protein ...	microsome [IDA] mitochondrial inner membrane [IDA] mitochondrion [IDA]			154
Q2KJG4 UniProt NPD GO	MGST2_BOVIN	Microsomal glutathione S-transferase 2 (EC 2.5.1.18) (Microsomal GST-2)	0.04	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				146
O97370 UniProt NPD GO	EURM3_EURMA	Mite allergen Eur m 3 precursor (EC 3.4.21.-)	0.04	-	end	0	Secreted protein				261
O21252 UniProt NPD GO	RM05_RECAM	Mitochondrial 60S ribosomal protein L5	0.04	-	cyt	0	Mitochondrion				182

You are viewing entries 77501 to 77550 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.