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
Q9Y4K0 UniProt NPD GO	LOXL2_HUMAN	Lysyl oxidase homolog 2 precursor (EC 1.4.3.-) (Lysyl oxidase-like protein 2) (Lysyl oxidase-related ...	0.42	-	exc	0	Secreted protein; extracellular space (Potential)	extracellular space [TAS]	606663		774
Q9QYH1 UniProt NPD GO	MPP4_RAT	MAGUK p55 subfamily member 4 (Discs large homolog 6) (rDLG6)	0.42	-	nuc	0	Cytoplasm. Localized at photoreceptor synaptic terminals in retina (By similarity)				441
Q9NZW5 UniProt NPD GO	MPP6_HUMAN	MAGUK p55 subfamily member 6 (Veli-associated MAGUK 1) (VAM-1)	0.42	-	cyt	0	Membrane; peripheral membrane protein (By similarity)	membrane [NAS]	606959		540
Q9Y884 UniProt NPD GO	SKH1_SCHPO	MAP kinase kinase skh1/pek1 (EC 2.7.12.2)	0.42	-	nuc	0		cell septum [IDA] cytoplasm [IDA]			363
O23693 UniProt NPD GO	MLO4_ARATH	MLO-like protein 4 (AtMlo4)	0.42	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				573
Q96T76 UniProt NPD GO	MMS19_HUMAN	MMS19-like protein (hMMS19) (MET18 homolog)	0.42	-	cyt	0	Nucleus				1030
O97432 UniProt NPD GO	MRJP5_APIME	Major royal jelly protein 5 precursor (MRJP-5) (Bee-milk protein)	0.42	-	exc	0	Secreted protein				598
Q06815 UniProt NPD GO	MRL1_YEAST	Mannose 6-phosphate receptor-like protein 1 precursor	0.42	-	mit	2 *	Golgi apparatus; trans-Golgi network; trans-Golgi network membrane; single-pass type I membrane prot ...	cytoplasm [IDA] late endosome [IDA]			381
Q7TN38 UniProt NPD GO	MRGRH_RAT	Mas-related G-protein coupled receptor member H	0.42	-	end	7 *	Membrane; multi-pass membrane protein				321
P12174 UniProt NPD GO	MATK_MARPO	Maturase K (Intron maturase)	0.42	-	mit	0	Plastid; chloroplast				370
Q14703 UniProt NPD GO	MBTP1_HUMAN	Membrane-bound transcription factor site 1 protease precursor (EC 3.4.21.-) (S1P endopeptidase) (Sit ...	0.42	+	end	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein. Golgi ap ...	endoplasmic reticulum lumen [TAS]	603355		1052
Q15726 UniProt NPD GO	KISS1_HUMAN	Metastasis-suppressor KiSS-1 precursor (Kisspeptin-1) [Contains: Metastin (Kisspeptin-54); Kisspepti ...	0.42	-	exc	0	Secreted protein		603286		145
P51398 UniProt NPD GO	RT29_HUMAN	Mitochondrial 28S ribosomal protein S29 (S29mt) (MRP-S29) (Death-associated protein 3) (DAP-3) (Ioni ...	0.42	-	mit	0	Mitochondrion		602074		398
P82930 UniProt NPD GO	RT34_HUMAN	Mitochondrial 28S ribosomal protein S34 (S34mt) (MRP-S34)	0.42	-	mit	0	Mitochondrion				218
O21281 UniProt NPD GO	RM32_RECAM	Mitochondrial 60S ribosomal protein L32	0.42	-	nuc	0	Mitochondrion				62
Q8VCF0 UniProt NPD GO	MAVS_MOUSE	Mitochondrial antiviral signaling protein (Interferon-beta promoter stimulator protein 1) (IPS-1) (V ...	0.42	-	nuc	1	Mitochondrion; mitochondrial outer membrane (By similarity)				503
Q9CYG7 UniProt NPD GO	OM34_MOUSE	Mitochondrial import receptor subunit TOM34 (Translocase of outer membrane 34 kDa subunit)	0.42	-	nuc	0	Cytoplasm (By similarity). Mitochondrion; mitochondrial outer membrane; peripheral membrane protein; ...				309
O21263 UniProt NPD GO	RT04_RECAM	Mitochondrial ribosomal protein S4	0.42	-	nuc	0	Mitochondrion				249
Q8TD08 UniProt NPD GO	MK15_HUMAN	Mitogen-activated protein kinase 15 (EC 2.7.11.24) (Extracellular signal-regulated kinase 8)	0.42	-	nuc	0		extracellular region [NAS] intracellular [NAS]			544
Q8NK05 UniProt NPD GO	CPK1_CRYNE	Mitogen-activated protein kinase CPK1 (EC 2.7.11.24) (Stress-activated protein kinase CPK1)	0.42	-	cyt	0					366
Q9UTI4 UniProt NPD GO	MOA1_SCHPO	Monopolar attachment protein 1	0.42	-	nuc	0	Nucleus. Localizes to the centromere. Does not require rec8 for centromeric localization but instead ...	inner kinetochore of condensed chromosome [IDA]			172
Q5NVP9 UniProt NPD GO	MO4L1_PONPY	Mortality factor 4-like protein 1	0.42	-	cyt	0	Nucleus (By similarity)				323
Q1W668 UniProt NPD GO	SMAD2_BOVIN	Mothers against decapentaplegic homolog 2 (SMAD 2)	0.42	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...				467
P08640 UniProt NPD GO	MUC1_YEAST	Mucin-like protein 1 precursor	0.42	-	exc	1 *	Cell membrane; lipid-anchor; GPI-anchor (Potential)	plasma membrane [IDA]			1367
P43071 UniProt NPD GO	CDR1_CANAL	Multidrug resistance protein CDR1	0.42	-	end	12	Membrane; multi-pass membrane protein (Potential)				1501
Q9LK62 UniProt NPD GO	MRP7_ARATH	Multidrug resistance-associated protein 7 (EC 3.6.3.44) (Glutathione S-conjugate-transporting ATPase ...	0.42	-	end	15 *	Membrane; multi-pass membrane protein (Potential)				1493
Q61006 UniProt NPD GO	MUSK_MOUSE	Muscle, skeletal receptor tyrosine protein kinase precursor (EC 2.7.10.1) (Muscle-specific kinase re ...	0.42	-	end	2	Membrane; single-pass type I membrane protein (Potential)	integral to plasma membrane [TAS] plasma membrane [IDA]			868
O00499 UniProt NPD GO	BIN1_HUMAN	Myc box-dependent-interacting protein 1 (Bridging integrator 1) (Amphiphysin-like protein) (Amphiphy ...	0.42	-	nuc	0	Isoform BIN1: Nucleus. Isoform IIa: Cytoplasm	actin cytoskeleton [TAS]	601248	1MV3	593
P25188 UniProt NPD GO	MBP_CAVPO	Myelin basic protein (MBP)	0.42	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				167
P81558 UniProt NPD GO	MBP_PIG	Myelin basic protein (MBP)	0.42	-	nuc	0	Myelin membrane; peripheral membrane protein; cytoplasmic side. Cytoplasmic side of myelin				171
Q9ZNU2 UniProt NPD GO	NAC18_ARATH	NAC domain-containing protein 18 (ANAC018) (Protein NO APICAL MERISTEM) (AtNAM)	0.42	-	nuc	0	Nucleus (Probable)				320
Q84TE6 UniProt NPD GO	NAC22_ARATH	NAC domain-containing protein 21/22 (ANAC021) (ANAC022)	0.42	-	nuc	0	Nucleus				324
Q6EVZ6 UniProt NPD GO	NUIC_NYMAL	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.42	-	mit	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				179
Q4R834 UniProt NPD GO	SIRT2_MACFA	NAD-dependent deacetylase sirtuin-2 (EC 3.5.1.-) (SIR2-like protein 2)	0.42	-	nuc	0	Cytoplasm. Colocalizes with microtubules (By similarity)				389
Q8R216 UniProt NPD GO	SIRT4_MOUSE	NAD-dependent deacetylase sirtuin-4 (EC 3.5.1.-) (SIR2-like protein 4)	0.42	-	nuc	0					333
Q757M7 UniProt NPD GO	SIR2_ASHGO	NAD-dependent histone deacetylase SIR2 (EC 3.5.1.-) (Regulatory protein SIR2) (Silent information re ...	0.42	-	nuc	0	Nucleus (By similarity)				559
Q9Z1P6 UniProt NPD GO	NDUA7_MOUSE	NADH dehydrogenase [ubiquinone] 1 alpha subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiqui ...	0.42	-	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrion [IDA]			112
Q9CQC7 UniProt NPD GO	NDUB4_MOUSE	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 4 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.42	-	nuc	1	Mitochondrion; mitochondrial inner membrane; matrix side	mitochondrial inner membrane [IDA]			128
Q03017 UniProt NPD GO	CACT_DROME	NF-kappa-B inhibitor cactus	0.42	-	nuc	0	Cytoplasm	cytoplasm [IDA]			500
O54910 UniProt NPD GO	IKBE_MOUSE	NF-kappa-B inhibitor epsilon (NF-kappa-BIE) (I-kappa-B-epsilon) (IkappaBepsilon) (IKB-epsilon) (IKB- ...	0.42	-	nuc	0	Cytoplasm				364
Q8K1S4 UniProt NPD GO	UNC5A_MOUSE	Netrin receptor UNC5A precursor (Unc-5 homolog A) (Unc-5 homolog 1)	0.42	-	end	2	Cell membrane; single-pass type I membrane protein (By similarity). The interaction with PRKCABP reg ...				898
Q8IZJ1 UniProt NPD GO	UNC5B_HUMAN	Netrin receptor UNC5B precursor (Unc-5 homolog B) (Unc-5 homolog 2) (p53-regulated receptor for deat ...	0.42	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		607870		945
Q7T2Z5 UniProt NPD GO	UNC5C_CHICK	Netrin receptor UNC5C precursor (Unc-5 homolog C) (Unc-5 homolog 3) (cUNC-5H3)	0.42	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				931
Q9P2S2 UniProt NPD GO	NRX2A_HUMAN	Neurexin-2-alpha precursor (Neurexin II-alpha)	0.42	-	end	1	Membrane; single-pass type I membrane protein (Potential)		600566		1712
Q9HDB5 UniProt NPD GO	NRX3B_HUMAN	Neurexin-3-beta precursor (Neurexin III-beta)	0.42	-	nuc	1 *	Membrane; single-pass type I membrane protein (Potential)		600567		536
P12284 UniProt NPD GO	AGNX_APLSP	Neuroactive polyprotein R15-1 precursor [Contains: R15 alpha-2 peptide; R15 beta peptide; R15 gamma ...	0.42	-	nuc	1 *	Secreted protein				142
Q8BVW0 UniProt NPD GO	GANC_MOUSE	Neutral alpha-glucosidase C (EC 3.2.1.-)	0.42	+	cyt	0					898
Q9HAN9 UniProt NPD GO	NMNA1_HUMAN	Nicotinamide mononucleotide adenylyltransferase 1 (EC 2.7.7.1) (NMN adenylyltransferase 1)	0.42	+	nuc	0	Nucleus	nucleus [IDA]	608700	1KR2	279
Q9R117 UniProt NPD GO	TYK2_MOUSE	Non-receptor tyrosine-protein kinase TYK2 (EC 2.7.10.2)	0.42	-	mit	0					1180
Q4IQX3 UniProt NPD GO	NHP6_GIBZE	Nonhistone chromosomal protein 6	0.42	-	nuc	0	Nucleus (By similarity)				101

You are viewing entries 30501 to 30550 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.