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
O93505 UniProt NPD GO	TYRP2_CHICK	L-dopachrome tautomerase precursor (EC 5.3.3.12) (DT) (DCT) (L-dopachrome delta-isomerase) (Tyrosina ...	0.32	-	cyt	1	Melanosome; melanosomal membrane; single-pass type I membrane protein (By similarity)				521
P29812 UniProt NPD GO	TYRP2_MOUSE	L-dopachrome tautomerase precursor (EC 5.3.3.12) (DT) (DCT) (L-dopachrome delta-isomerase) (Tyrosina ...	0.32	-	end	1	Melanosome; melanosomal membrane; single-pass type I membrane protein	cytosol [IDA] melanosome [IDA] microsome [IDA]			517
P81447 UniProt NPD GO	LCTN_CAPHI	Lactophorin precursor (28 kDa milk glycoprotein PP3) (Proteose-peptone component 3) (Glycosylation-d ...	0.32	-	exc	0	Membrane; peripheral membrane protein	membrane [IEP]			154
Q67BJ4 UniProt NPD GO	A4GAT_MOUSE	Lactosylceramide 4-alpha-galactosyltransferase (EC 2.4.1.228) (Alpha-1,4-galactosyltransferase) (UDP ...	0.32	-	cyt	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				359
Q9NS86 UniProt NPD GO	LANC2_HUMAN	LanC-like protein 2 (Testis-specific adriamycin sensitivity protein)	0.32	-	cyt	0	Nucleus. Cytoplasm. Cell membrane	cytosol [IDA] nucleus [IDA] plasma membrane [IDA]			450
Q9JJK2 UniProt NPD GO	LANC2_MOUSE	LanC-like protein 2 (Testis-specific adriamycin sensitivity protein)	0.32	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Cell membrane (By similarity)	cytosol [ISS] nucleus [ISS] plasma membrane [ISS]			450
Q02400 UniProt NPD GO	LE193_HORVU	Late embryogenesis abundant protein B19.3 (LEA B19.3)	0.32	-	nuc	0					133
Q05191 UniProt NPD GO	LE194_HORVU	Late embryogenesis abundant protein B19.4	0.32	-	nuc	0					153
P09441 UniProt NPD GO	LEA13_GOSHI	Late embryogenesis abundant protein D-113 (LEA D-113)	0.32	-	nuc	0					165
P05047 UniProt NPD GO	LECA_SARPE	Lectin subunit alpha precursor	0.32	-	nuc	1 *					283
P57785 UniProt NPD GO	LEFTB_MOUSE	Left-right determination factor B precursor (Lefty-2 protein)	0.32	-	exc	0	Secreted protein				368
O02720 UniProt NPD GO	LEP_CANFA	Leptin precursor (Obesity factor)	0.32	-	exc	0	Secreted protein (Probable)				167
P41160 UniProt NPD GO	LEP_MOUSE	Leptin precursor (Obesity factor)	0.32	-	exc	0	Secreted protein (Probable)	extracellular space [IDA]			167
Q6FUI5 UniProt NPD GO	LCMT1_CANGA	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.32	-	mit	0					318
Q6BQD2 UniProt NPD GO	LCMT1_DEBHA	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.32	-	nuc	0					369
Q9LYN8 UniProt NPD GO	EXS_ARATH	Leucine-rich repeat receptor protein kinase EXS precursor (EC 2.7.11.1) (Extra sporogenous cells pro ...	0.32	-	end	1	Cell membrane; single-pass type I membrane protein				1192
P59035 UniProt NPD GO	LRRC3_RAT	Leucine-rich repeat-containing protein 3 precursor	0.32	-	exc	1					257
Q9HBW1 UniProt NPD GO	LRRC4_HUMAN	Leucine-rich repeat-containing protein 4 precursor (Brain tumor-associated protein LRRC4) (NAG14)	0.32	-	end	2 *	Membrane; single-pass type I membrane protein (Potential)				653
Q95666 UniProt NPD GO	CHLB_PINST	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.32	-	cyt	0	Plastid; chloroplast				511
Q00864 UniProt NPD GO	CHLB_PINTH	Light-independent protochlorophyllide reductase subunit B (EC 1.18.-.-) (LI-POR subunit B) (DPOR sub ...	0.32	-	cyt	0	Plastid; chloroplast				510
P26180 UniProt NPD GO	CHLN_PINCO	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.32	-	cyt	0	Plastid; chloroplast				459
O99019 UniProt NPD GO	LIPC_SOLDE	Light-induced protein, chloroplast precursor (C40.4)	0.32	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane	thylakoid membrane (sensu Viridiplantae) [ISS]			326
Q8WVP7 UniProt NPD GO	LMBR1_HUMAN	Limb region 1 protein homolog (Differentiation-related gene 14 protein)	0.32	-	end	9 *	Membrane; multi-pass membrane protein (By similarity)		605522		490
P10881 UniProt NPD GO	LA_BOVIN	Lupus La protein homolog (La ribonucleoprotein) (La autoantigen homolog)	0.32	-	nuc	0	Nucleus (Probable)				404
Q9D7Z7 UniProt NPD GO	LYPD5_MOUSE	Ly6/PLAUR domain-containing protein 5 precursor	0.32	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (Potential)				256
P09568 UniProt NPD GO	LY6C_MOUSE	Lymphocyte antigen Ly-6C precursor	0.32	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor	external side of plasma membrane [IDA]			131
Q9UBY5 UniProt NPD GO	EDG7_HUMAN	Lysophosphatidic acid receptor Edg-7 (LPA receptor 3) (LPA-3)	0.32	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605106		353
Q8MJJ2 UniProt NPD GO	LAMP3_MACMU	Lysosome-associated membrane glycoprotein 3 precursor (LAMP-3) (Lysosomal-associated membrane protei ...	0.32	-	end	1	Lysosome; lysosomal membrane; single-pass type I membrane protein (By similarity)				416
Q9UQV4 UniProt NPD GO	LAMP3_HUMAN	Lysosome-associated membrane glycoprotein 3 precursor (LAMP-3) (Lysosomal-associated membrane protei ...	0.32	-	nuc	1	Lysosome; lysosomal membrane; single-pass type I membrane protein		605883		416
Q10747 UniProt NPD GO	MIP2B_RAT	Macrophage inflammatory protein 2-beta precursor (MIP2-beta) (CINC-2-beta)	0.32	-	exc	0	Secreted protein				100
Q17060 UniProt NPD GO	MRJP3_APIME	Major royal jelly protein 3 precursor (MRJP-3) (Bee-milk protein) (Royal jelly protein RJP57-1)	0.32	-	exc	0	Secreted protein				544
Q9UHC7 UniProt NPD GO	MKRN1_HUMAN	Makorin-1 (RING finger protein 61)	0.32	-	nuc	0			607754		482
Q13064 UniProt NPD GO	MKRN3_HUMAN	Makorin-3 (Zinc finger protein 127) (RING finger protein 63)	0.32	-	cyt	0		ribonucleoprotein complex [TAS]	603856		507
O88941 UniProt NPD GO	GCS1_RAT	Mannosyl-oligosaccharide glucosidase (EC 3.2.1.106) (Glycoprotein-processing glucosidase I)	0.32	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein				834
O13595 UniProt NPD GO	MTA1_SOREQ	Mating type protein mtA-1	0.32	-	nuc	0	Nucleus (Potential)				294
P36981 UniProt NPD GO	MATB_NEUCR	Mating- type protein a-1 (Mt a-1)	0.32	-	cyt	0	Nucleus (Potential)				382
O94160 UniProt NPD GO	MAT1_ALTAL	Mating-type protein MAT-1	0.32	-	mit	0	Nucleus (Potential)				389
P60254 UniProt NPD GO	SCXC_SCOMA	Maurocalcin (MCa) (Maurocalcine)	0.32	-	nuc	0	Secreted protein			1C6W	33
P83082 UniProt NPD GO	M3H2_BOMMX	Maximins 3/H2 precursor [Contains: Maximin-3; Maximin-H2]	0.32	-	end	0	Secreted protein				144
Q5GH61 UniProt NPD GO	XK_RAT	Membrane transport protein XK (XK-related protein 1) (XK homolog)	0.32	-	end	9 *	Membrane; multi-pass membrane protein (Potential)	integral to membrane [ISS]			445
Q90252 UniProt NPD GO	MTR_BUFMA	Mesotocin receptor (MTR)	0.32	-	end	7 *	Membrane; multi-pass membrane protein				389
P39109 UniProt NPD GO	YCFI_YEAST	Metal resistance protein YCF1 (Yeast cadmium factor 1)	0.32	-	end	14 *	Membrane; multi-pass membrane protein (Potential)	vacuolar membrane [IDA]			1515
Q2T9L8 UniProt NPD GO	SYM_BOVIN	Methionyl-tRNA synthetase (EC 6.1.1.10) (Methionine--tRNA ligase) (MetRS)	0.32	-	end	0	Cytoplasm (Probable)				898
Q5MFW3 UniProt NPD GO	MMAA_RABIT	Methylmalonic aciduria type A homolog, mitochondrial precursor	0.32	-	cyt	0	Mitochondrion (By similarity)				413
P55002 UniProt NPD GO	MFAP2_MOUSE	Microfibrillar-associated protein 2 precursor (MFAP-2) (Microfibril-associated glycoprotein) (MAGP) ...	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix				183
Q8MJF1 UniProt NPD GO	MIME_RABIT	Mimecan precursor (Osteoglycin)	0.32	-	exc	0	Secreted protein; extracellular space; extracellular matrix				298
Q59J78 UniProt NPD GO	MIMIT_MOUSE	Mimitin, mitochondrial precursor (Myc-induced mitochondrial protein) (MMTN)	0.32	-	mit	0	Mitochondrion (By similarity)				168
Q12031 UniProt NPD GO	ACEB_YEAST	Mitochondrial 2-methylisocitrate lyase (EC 4.1.3.30) (Methylisocitrate lyase)	0.32	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			575
Q9ER88 UniProt NPD GO	RT29_MOUSE	Mitochondrial 28S ribosomal protein S29 (S29mt) (MRP-S29) (Death-associated protein 3) (DAP-3)	0.32	-	mit	0	Mitochondrion (By similarity)	mitochondrial matrix [IDA]			391
P15767 UniProt NPD GO	RM14_PARTE	Mitochondrial 60S ribosomal protein L14	0.32	+	nuc	0	Mitochondrion				119

You are viewing entries 38651 to 38700 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.