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
Q641X6 UniProt NPD GO	MORN1_RAT	MORN repeat-containing protein 1	0.11	-	nuc	0					483
Q05585 UniProt NPD GO	MSRE_RABIT	Macrophage scavenger receptor types I and II (Macrophage acetylated LDL receptor I and II)	0.11	-	mit	1	Membrane; single-pass type II membrane protein				454
Q39516 UniProt NPD GO	CHLI_GUITH	Magnesium-chelatase subunit chlI (EC 6.6.1.1) (Mg-protoporphyrin IX chelatase)	0.11	-	cyt	0	Plastid; chloroplast				353
P51780 UniProt NPD GO	PRIO_TRIVU	Major prion protein precursor (PrP) (PrP27-30) (PrP33-35C) (CD230 antigen)	0.11	-	nuc	3 *	Cell membrane; lipid-anchor; GPI-anchor				259
P53022 UniProt NPD GO	MSP2_GLORO	Major sperm protein 2	0.11	-	cyt	0					125
P21849 UniProt NPD GO	TSA4_GIALA	Major surface-labeled trophozoite antigen 417 precursor	0.11	-	exc	1	Cell membrane; single-pass type I membrane protein				713
P28344 UniProt NPD GO	MASY_EMENI	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.11	-	pox	0	Glyoxysome				528
Q43827 UniProt NPD GO	MASY_RAPSA	Malate synthase, glyoxysomal (EC 2.3.3.9)	0.11	-	cyt	0	Glyoxysome (By similarity)				566
Q16626 UniProt NPD GO	MEA1_HUMAN	Male-enhanced antigen 1 (Mea-1)	0.11	-	cyt	0			143170		172
Q38707 UniProt NPD GO	MTDH_APIGR	Mannitol dehydrogenase (EC 1.1.1.255) (NAD-dependent mannitol dehydrogenase)	0.11	-	cyt	0	Cytoplasm				365
Q870Y1 UniProt NPD GO	MANA_NEUCR	Mannose-6-phosphate isomerase (EC 5.3.1.8) (Phosphomannose isomerase) (PMI) (Phosphohexomutase)	0.11	-	cyt	0	Cytoplasm (By similarity)				459
O60476 UniProt NPD GO	MA1A2_HUMAN	Mannosyl-oligosaccharide 1,2-alpha-mannosidase IB (EC 3.2.1.113) (Processing alpha-1,2-mannosidase I ...	0.11	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	integral to membrane [TAS] membrane fraction [TAS]	604345		641
O15823 UniProt NPD GO	MER1_EUPOC	Mating pheromone 1 precursor	0.11	-	exc	0	Secreted protein				150
P26886 UniProt NPD GO	MER2_EUPRA	Mating pheromone Er-2/Er-9 precursor (Euplomone R2/R9)	0.11	-	exc	1 *	Secreted protein			1ERD	75
P09237 UniProt NPD GO	MMP7_HUMAN	Matrilysin precursor (EC 3.4.24.23) (Pump-1 protease) (Uterine metalloproteinase) (Matrix metallopro ...	0.11	-	exc	0		extracellular space [TAS]	178990	1MMR	267
P50280 UniProt NPD GO	MMP7_RAT	Matrilysin precursor (EC 3.4.24.23) (Pump-1 protease) (Uterine metalloproteinase) (Matrix metallopro ...	0.11	-	end	0					267
Q9NRE1 UniProt NPD GO	MMP26_HUMAN	Matrix metalloproteinase-26 precursor (EC 3.4.24.-) (MMP-26) (Matrilysin-2) (Endometase)	0.11	-	vac	0	Secreted protein	extracellular matrix (sensu Metazoa) [NAS]	605470		261
Q58T45 UniProt NPD GO	M10H3_BOMMX	Maximins 10/H3 precursor [Contains: Maximin-10; Maximin-H3]	0.11	-	end	0	Secreted protein				144
Q58T49 UniProt NPD GO	M2H81_BOMMX	Maximins 2/H8 type 1 precursor [Contains: Maximin-2; Maximin-H8]	0.11	-	end	0	Secreted protein				144
Q58T86 UniProt NPD GO	M2H82_BOMMX	Maximins 2/H8 type 2 precursor [Contains: Maximin-2; Maximin-H8]	0.11	-	end	0	Secreted protein				144
Q58T44 UniProt NPD GO	M4H35_BOMMX	Maximins 4/H3 type 5 precursor [Contains: Maximin-4; Maximin-H3]	0.11	-	end	0	Secreted protein				139
Q58T90 UniProt NPD GO	MZHV_BOMMX	Maximins z/Hv precursor [Contains: Maximin-z; Maximin-Hv]	0.11	-	end	0	Secreted protein				144
Q864K3 UniProt NPD GO	MSHR_ERYPA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864F4 UniProt NPD GO	MSHR_LEMCA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein				317
Q864J1 UniProt NPD GO	MSHR_MANSP	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864J3 UniProt NPD GO	MSHR_PAPAN	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	4 *	Membrane; multi-pass membrane protein				317
Q864J2 UniProt NPD GO	MSHR_PAPHA	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	4 *	Membrane; multi-pass membrane protein				317
O19037 UniProt NPD GO	MSHR_SHEEP	Melanocyte-stimulating hormone receptor (MSH-R) (Melanotropin receptor) (Melanocortin receptor 1) (M ...	0.11	-	end	7 *	Membrane; multi-pass membrane protein				317
Q9UBF1 UniProt NPD GO	MAGC2_HUMAN	Melanoma-associated antigen C2 (MAGE-C2 antigen) (MAGE-E1 antigen) (Hepatocellular carcinoma-associa ...	0.11	-	nuc	0	Cytoplasm. Nucleus. Nuclear in germ cells. Cytoplasmic in well-differentiated hepatocellular carcino ...	cytoplasm [IDA] nucleus [IDA]	300468		373
Q9GZW8 UniProt NPD GO	MS4A7_HUMAN	Membrane-spanning 4-domains subfamily A member 7 (CD20/FC-epsilon-RI-beta family member 4) (Four-spa ...	0.11	-	end	4 *	Membrane; multi-pass membrane protein		606502		240
Q14832 UniProt NPD GO	MGR3_HUMAN	Metabotropic glutamate receptor 3 precursor (mGluR3)	0.11	-	end	6	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	601115	1S8M	879
Q5RAL3 UniProt NPD GO	MGR3_PONPY	Metabotropic glutamate receptor 3 precursor (mGluR3)	0.11	-	end	6	Membrane; multi-pass membrane protein				879
Q9JHB3 UniProt NPD GO	TIMP4_MOUSE	Metalloproteinase inhibitor 4 precursor (TIMP-4) (Tissue inhibitor of metalloproteinases 4)	0.11	-	exc	0	Secreted protein				224
P81556 UniProt NPD GO	TIMP4_RAT	Metalloproteinase inhibitor 4 precursor (TIMP-4) (Tissue inhibitor of metalloproteinases 4)	0.11	-	exc	0	Secreted protein				224
P55951 UniProt NPD GO	MT_ASTFL	Metallothionein (MT)	0.11	-	nuc	0					58
P52723 UniProt NPD GO	MT_CARAU	Metallothionein (MT)	0.11	-	nuc	0					60
P55948 UniProt NPD GO	MT_CARMA	Metallothionein (MT)	0.11	-	nuc	0					58
P51902 UniProt NPD GO	MT_GADMO	Metallothionein (MT)	0.11	-	nuc	0					60
O93571 UniProt NPD GO	MT_ICTPU	Metallothionein (MT)	0.11	-	nuc	0					60
P52725 UniProt NPD GO	MT_PERFL	Metallothionein (MT)	0.11	-	nuc	0					60
Q708T3 UniProt NPD GO	MT_PODSI	Metallothionein (MT)	0.11	-	nuc	0					63
P80593 UniProt NPD GO	MT_RUTRU	Metallothionein (MT)	0.11	-	nuc	0					60
P52727 UniProt NPD GO	MTA_SPAAU	Metallothionein A (MT A)	0.11	-	nuc	0					60
Q8AWG2 UniProt NPD GO	MTA_CARCW	Metallothionein A (MT-A)	0.11	-	nuc	0					60
P62338 UniProt NPD GO	MTA_CHIRA	Metallothionein A (MT-A)	0.11	-	nuc	0					60
P68506 UniProt NPD GO	MTA_CHIHA	Metallothionein A (MT-A) (MT-I)	0.11	-	nuc	0					60
P68507 UniProt NPD GO	MTA_GYMAC	Metallothionein A (MT-A) (MT-I)	0.11	-	nuc	0					60
P68508 UniProt NPD GO	MTA_PAGBO	Metallothionein A (MT-A) (MT-I)	0.11	-	nuc	0					60
P62339 UniProt NPD GO	MTA_NOTCO	Metallothionein A (MT-A) (MT_nc)	0.11	-	nuc	0				1M0J	60
P52720 UniProt NPD GO	MTB_SALSA	Metallothionein B (MT-B)	0.11	-	nuc	0					60

You are viewing entries 63001 to 63050 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.