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
P10887 UniProt NPD GO	MDH_NITAL	Malate dehydrogenase (EC 1.1.1.37) (Fragment)	0.01	-	cyt	0					32
Q3T145 UniProt NPD GO	MDHC_BOVIN	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm (By similarity)				333
Q5ZME2 UniProt NPD GO	MDHC_CHICK	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	cyt	0	Cytoplasm (By similarity)				334
Q7YRU4 UniProt NPD GO	MDHC_FELCA	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm (By similarity)				333
P40925 UniProt NPD GO	MDHC_HUMAN	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm	cytosol [TAS]	154200		333
P14152 UniProt NPD GO	MDHC_MOUSE	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm				333
P11708 UniProt NPD GO	MDHC_PIG	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm	cytosol [IDA]		5MDH	333
O88989 UniProt NPD GO	MDHC_RAT	Malate dehydrogenase, cytoplasmic (EC 1.1.1.37) (Cytosolic malate dehydrogenase)	0.01	-	mit	0	Cytoplasm (By similarity)				333
P84209 UniProt NPD GO	MDHM_IMPCY	Malate dehydrogenase, mitochondrial (EC 1.1.1.37) (Fragments)	0.01	-	cyt	0	Mitochondrion; mitochondrial matrix (By similarity)				31
Q01642 UniProt NPD GO	MS84A_DROME	Male-specific sperm protein Mst84Da	0.01	-	nuc	0					63
P57113 UniProt NPD GO	MAAI_RAT	Maleylacetoacetate isomerase (EC 5.2.1.2) (MAAI) (Glutathione S-transferase zeta 1) (EC 2.5.1.18) (G ...	0.01	-	nuc	0	Cytoplasm				28
P50537 UniProt NPD GO	MAE1_SCHPO	Malic acid transport protein (Malate permease)	0.01	-	end	10 *	Membrane; multi-pass membrane protein				438
P55296 UniProt NPD GO	MANA_PIRSP	Mannan endo-1,4-beta-mannosidase A precursor (EC 3.2.1.78) (Beta-mannanase A) (1,4-beta-D-mannan man ...	0.01	-	vac	0					606
P42754 UniProt NPD GO	MTDH_PETCR	Mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase) (Fragment)	0.01	-	cyt	0					337
Q9Y725 UniProt NPD GO	MPG1_CANGA	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (ATP-mannose-1-phosphate guanylyltransferase) (G ...	0.01	-	cyt	0	Cytoplasm (By similarity)				361
O93827 UniProt NPD GO	MPG1_CANAL	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (ATP-mannose-1-phosphate guanylyltransferase) (G ...	0.01	-	mit	0	Cytoplasm (By similarity)				362
Q752H4 UniProt NPD GO	MPG1_ASHGO	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.01	-	cyt	0	Cytoplasm (By similarity)				361
Q5KKH2 UniProt NPD GO	MPG1_CRYNE	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.01	-	cyt	0	Cytoplasm (By similarity)				364
O74624 UniProt NPD GO	MPG1_TRIRE	Mannose-1-phosphate guanyltransferase (EC 2.7.7.13) (GTP-mannose-1-phosphate guanylyltransferase) (G ...	0.01	-	cyt	0	Cytoplasm (By similarity)				364
Q9LTI3 UniProt NPD GO	MPU1_ARATH	Mannose-P-dolichol utilization defect 1 protein homolog	0.01	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				239
P19999 UniProt NPD GO	MBL1_RAT	Mannose-binding protein A precursor (MBP-A) (Mannan-binding protein)	0.01	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum membrane; peripheral ...			4KMB	238
P39039 UniProt NPD GO	MBL1_MOUSE	Mannose-binding protein A precursor (MBP-A) (Mannan-binding protein) (Ra-reactive factor polysacchar ...	0.01	-	nuc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum membrane; peripheral ...				239
P41317 UniProt NPD GO	MBL2_MOUSE	Mannose-binding protein C precursor (MBP-C) (Mannan-binding protein) (RA-reactive factor P28A subuni ...	0.01	-	vac	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum membrane; peripheral ...				244
P30617 UniProt NPD GO	LEC_GALNI	Mannose-specific lectin precursor (Agglutinin) (LecGNA 2)	0.01	-	exc	0	Secreted protein (By similarity)			1NIV	157
Q91WW4 UniProt NPD GO	MRGA2_MOUSE	Mas-related G-protein coupled receptor member A2	0.01	-	end	7 *	Membrane; multi-pass membrane protein				305
Q5U9D7 UniProt NPD GO	MRGRE_MACFA	Mas-related G-protein coupled receptor member E	0.01	-	end	7 *	Membrane; multi-pass membrane protein				311
Q86SM8 UniProt NPD GO	MRGRE_HUMAN	Mas-related G-protein coupled receptor member E (G-protein coupled receptor 167) (Fragment)	0.01	-	end	4 *	Membrane; multi-pass membrane protein		607232		145
Q7TN39 UniProt NPD GO	MRGRG_RAT	Mas-related G-protein coupled receptor member G	0.01	-	end	6 *	Membrane; multi-pass membrane protein				289
P50340 UniProt NPD GO	MCPT1_MERUN	Mast cell protease 1 precursor (EC 3.4.21.-)	0.01	-	exc	0					246
P21843 UniProt NPD GO	MCPT3_MOUSE	Mast cell protease 3 (EC 3.4.21.-) (MMCP-3) (Fragment)	0.01	-	nuc	0					21
P42716 UniProt NPD GO	MAST_PARID	Mastoparan (MP)	0.01	-		0	Secreted protein				14
P0C1Q5 UniProt NPD GO	MASTP_PROSY	Mastoparan (Protonectarina-MP)	0.01	-		0	Secreted protein				14
P0C1Q4 UniProt NPD GO	MASTI_POLPI	Mastoparan-1 (Mastoparan I) (MPI)	0.01	-		0	Secreted protein				14
P69035 UniProt NPD GO	MAST2_PROEX	Mastoparan-2 (Mastoparan II) (MP-II)	0.01	-		0	Secreted protein				14
P0C1Q6 UniProt NPD GO	MASTA_VESAN	Mastoparan-A	0.01	-		0	Secreted protein				14
P0C1Q8 UniProt NPD GO	MAST1_VESVU	Mastoparan-V1	0.01	-		0	Secreted protein				15
P01515 UniProt NPD GO	MAST_VESXA	Mastoparan-X (MP-X)	0.01	-		0	Secreted protein			1A13	14
P0C1M4 UniProt NPD GO	MASTA_VESMG	Mastoparan-like peptide 12a	0.01	-		0	Secreted protein				14
P0C1M5 UniProt NPD GO	MASTB_VESMG	Mastoparan-like peptide 12b	0.01	-		0	Secreted protein				13
P26887 UniProt NPD GO	MER11_EUPRA	Mating pheromone Er-11 (Euplomone R11)	0.01	-	nuc	0	Secreted protein			1ERY	39
P83347 UniProt NPD GO	MGP_PRIGL	Matrix Gla-protein (MGP) (Fragment)	0.01	-	nuc	0	Secreted protein	extracellular matrix [TAS]			30
P32244 UniProt NPD GO	MC3R_RAT	Melanocortin receptor 3 (MC3-R)	0.01	-	vac	7 *	Membrane; multi-pass membrane protein				323
P70596 UniProt NPD GO	MC4R_RAT	Melanocortin receptor 4 (MC4-R)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				332
Q864H9 UniProt NPD GO	MSHR_CALAR	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				344
Q864I0 UniProt NPD GO	MSHR_CEBPY	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				344
Q9TU05 UniProt NPD GO	MSHR_PIG	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.01	-	end	7 *	Membrane; multi-pass membrane protein				320
P43357 UniProt NPD GO	MAGA3_HUMAN	Melanoma-associated antigen 3 (MAGE-3 antigen) (Antigen MZ2-D)	0.01	-	cyt	0			300174		314
Q16674 UniProt NPD GO	MIA_HUMAN	Melanoma-derived growth regulatory protein precursor (Melanoma inhibitory activity)	0.01	-	end	1 *	Secreted protein	extracellular space [TAS]	601340	1K0X	131
P01207 UniProt NPD GO	MLB_SQUAC	Melanotropin beta	0.01	-		0					16
P48039 UniProt NPD GO	MTR1A_HUMAN	Melatonin receptor type 1A (Mel-1A-R) (Mel1a melatonin receptor)	0.01	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600665		350

You are viewing entries 89501 to 89550 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.