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
Q9Z250 UniProt NPD GO	LIN7A_RAT	LIN-7 homolog A (LIN-7A) (Mammalian LIN-seven protein 1) (MALS-1) (Vertebrate LIN 7 homolog 1) (Veli ...	0.53	-	cyt	0	Cell membrane; peripheral membrane protein. Mainly basolateral in renal epithelial cells (By similar ...	synapse [IDA]			232
O14910 UniProt NPD GO	LIN7A_HUMAN	LIN-7 homolog A (LIN-7A) (hLin-7) (Mammalian LIN-seven protein 1) (MALS-1) (Vertebrate LIN 7 homolog ...	0.53	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...		603380		233
Q8JZS0 UniProt NPD GO	LIN7A_MOUSE	LIN-7 homolog A (LIN-7A) (mLin-7) (Mammalian LIN-seven protein 1) (MALS-1) (Vertebrate LIN 7 homolog ...	0.53	-	cyt	0	Cell membrane; peripheral membrane protein. Cell membrane; cell-cell junction; peripheral membrane p ...	basolateral plasma membrane [IDA]			233
Q5A387 UniProt NPD GO	LCMT1_CANAL	Leucine carboxyl methyltransferase 1 (EC 2.1.1.-) (Protein phosphatase methyltransferase 1)	0.53	-	nuc	0					367
Q80X72 UniProt NPD GO	LRC15_MOUSE	Leucine-rich repeat-containing protein 15 precursor	0.53	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				579
Q8N456 UniProt NPD GO	LRC18_HUMAN	Leucine-rich repeat-containing protein 18	0.53	-	nuc	0	Cytoplasm (By similarity)				261
Q32Q07 UniProt NPD GO	LRRN1_RAT	Leucine-rich repeats neuronal protein 1 precursor (Neuronal leucine-rich repeat protein 1) (NLRR-1)	0.53	-	exc	1	Membrane; single-pass type I membrane protein (Potential)				716
Q85A72 UniProt NPD GO	CHLN_ANTFO	Light-independent protochlorophyllide reductase subunit N (EC 1.18.-.-) (LI-POR subunit N) (DPOR sub ...	0.53	+	cyt	0	Plastid; chloroplast				471
Q86X29 UniProt NPD GO	LSR_HUMAN	Lipolysis-stimulated lipoprotein receptor	0.53	-	nuc	1	Cell membrane; single-pass membrane protein (Potential)	plasma membrane [ISS]			649
Q9WU74 UniProt NPD GO	LSR_RAT	Lipolysis-stimulated lipoprotein receptor precursor (Lipolysis-stimulated remnant receptor)	0.53	-	exc	1 *	Cell membrane; single-pass type I membrane protein (Potential)				593
Q60767 UniProt NPD GO	LY75_MOUSE	Lymphocyte antigen 75 precursor (DEC-205) (CD205 antigen)	0.53	-	end	1	Membrane; single-pass type I membrane protein				1723
P34098 UniProt NPD GO	MANA_DICDI	Lysosomal alpha-mannosidase precursor (EC 3.2.1.24) (Alpha-D-mannoside mannohydrolase) (Laman) [Cont ...	0.53	-	mit	0	Alpha-mannosidase 60 kDa subunit: Lysosome. Alpha-mannosidase 58 kDa subunit: Lysosome. A few precur ...				1005
Q9LLA7 UniProt NPD GO	AP32_ASAEU	MADS-box protein AeAP3-2 (APETALA3-2) (Fragment)	0.53	-	nuc	0	Nucleus (By similarity)				210
P07141 UniProt NPD GO	CSF1_MOUSE	Macrophage colony-stimulating factor 1 precursor (CSF-1) (MCSF)	0.53	-	exc	1	Cell membrane; single-pass membrane protein (By similarity). Processed form: Secreted protein; extra ...				552
P31996 UniProt NPD GO	CD68_MOUSE	Macrosialin precursor (CD68 antigen)	0.53	-	exc	1	Isoform Long: Endosome; endosomal membrane; single-pass type I membrane protein. Isoform Long: Lysos ...				326
P19615 UniProt NPD GO	MYP_STRPU	Major yolk protein precursor (MYP) (Vitellogenin)	0.53	-	exc	0	Secreted protein				1357
Q9ERV1 UniProt NPD GO	MKRN2_MOUSE	Makorin-2	0.53	-	nuc	0		intracellular [ISS]			416
Q6WRX9 UniProt NPD GO	MATPC_SCHKA	Mating-type P-specific polypeptide Pc	0.53	-	nuc	0	Nucleus (Potential)				118
Q6WRX8 UniProt NPD GO	MATPI_SCHKA	Mating-type P-specific polypeptide Pi	0.53	-	nuc	0	Nucleus (Potential)				159
P10842 UniProt NPD GO	MATPI_SCHPO	Mating-type P-specific polypeptide Pi	0.53	-	nuc	0	Nucleus (Potential)				159
P17718 UniProt NPD GO	2SS_MATST	Matteuccin light and heavy chains (Fragments)	0.53	-	nuc	0	Protein body				67
Q56B59 UniProt NPD GO	MATK_AESPA	Maturase K (Intron maturase)	0.53	-	nuc	0	Plastid; chloroplast				519
Q4H1B9 UniProt NPD GO	MATK_ARIGL	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				522
Q5GF60 UniProt NPD GO	MATK_IRISA	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				522
Q9GIG3 UniProt NPD GO	MATK_LILTS	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				512
Q95DQ8 UniProt NPD GO	MATK_NICRU	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				509
Q9XR19 UniProt NPD GO	MATK_PARTT	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				517
Q9XPP4 UniProt NPD GO	MATK_TRIPU	Maturase K (Intron maturase)	0.53	-	cyt	0	Plastid; chloroplast				515
Q6PP79 UniProt NPD GO	MATK_VIGSU	Maturase K (Intron maturase)	0.53	-	nuc	0	Plastid; chloroplast				504
P34764 UniProt NPD GO	MEC3_CAEBR	Mechanosensory protein 3	0.53	+	nuc	0	Nucleus				318
Q96LZ2 UniProt NPD GO	MAGBA_HUMAN	Melanoma-associated antigen B10 (MAGE-B10 antigen)	0.53	-	nuc	0					347
Q9Y5V3 UniProt NPD GO	MAGD1_HUMAN	Melanoma-associated antigen D1 (MAGE-D1 antigen) (Neurotrophin receptor-interacting MAGE homolog) (M ...	0.53	-	nuc	0	Cytoplasm. Cell membrane; peripheral membrane protein. Expression shifts from the cytoplasm to the p ...		300224		778
P28826 UniProt NPD GO	MEP1B_RAT	Meprin A subunit beta precursor (EC 3.4.24.18) (Endopeptidase-2)	0.53	-	end	1 *	Membrane; single-pass type I membrane protein				704
P21303 UniProt NPD GO	PK66_PLAKU	Merozoite receptor PK66 precursor (66 kDa protective minor surface antigen)	0.53	+	nuc	1	Membrane; single-pass type I membrane protein. Concentrated at the apical end prior to rupture, foll ...				563
Q9H1K6 UniProt NPD GO	MESD1_HUMAN	Mesoderm development candidate 1	0.53	-	nuc	0					362
Q9ERE8 UniProt NPD GO	MESD1_MOUSE	Mesoderm development candidate 1	0.53	-	nuc	0					362
O45503 UniProt NPD GO	MTX1_CAEEL	Metaxin-1 homolog	0.53	-	cyt	0	Mitochondrion; mitochondrial outer membrane (By similarity)				312
Q9Z2E1 UniProt NPD GO	MBD2_MOUSE	Methyl-CpG-binding domain protein 2 (Methyl-CpG-binding protein MBD2)	0.53	+	nuc	0	Nucleus (By similarity). Nuclear, in discrete foci. Detected at replication foci in late S phase (By ...	heterochromatin [IDA] nucleus [IDA]			414
Q08457 UniProt NPD GO	YO060_YEAST	Mitochondrial morphogenesis protein YOR060C	0.53	-	mit	0	Nucleus. Spindle pole	cytoplasm [IDA] endoplasmic reticulum [IDA] nuclear envelope [IDA] nucleus [IDA]			257
P92557 UniProt NPD GO	RT07_ARATH	Mitochondrial ribosomal protein S7	0.53	-	cyt	0	Mitochondrion				148
Q3T0N5 UniProt NPD GO	MK13_BOVIN	Mitogen-activated protein kinase 13 (EC 2.7.11.24)	0.53	-	cyt	0					366
P39205 UniProt NPD GO	CIN_DROME	Molybdenum cofactor synthesis protein cinnamon	0.53	-	nuc	0					674
Q9JIW5 UniProt NPD GO	SMAD9_MOUSE	Mothers against decapentaplegic homolog 9 (SMAD 9) (Mothers against DPP homolog 9) (Smad9) (Smad8)	0.53	-	nuc	0	Cytoplasm. In the cytoplasm in the absence of ligand. Nucleus. Migration to the nucleus when complex ...				430
P12657 UniProt NPD GO	ACM1_MOUSE	Muscarinic acetylcholine receptor M1	0.53	-	end	6 *	Membrane; multi-pass membrane protein				460
Q5R6I2 UniProt NPD GO	MYOZ2_PONPY	Myozenin-2 (Calsarcin-1)	0.53	-	nuc	0	Colocalizes with ACTN1 and PPP3CA at the Z-line of heart and skeletal muscle (By similarity)				264
P19787 UniProt NPD GO	ACVS1_PENCH	N-(5-amino-5-carboxypentanoyl)-L-cysteinyl-D-valine synthase (EC 6.3.2.26) (Delta-(L-alpha-aminoadip ...	0.53	-	end	0					3746
Q12387 UniProt NPD GO	MDM20_YEAST	N-terminal acetyltransferase B complex subunit MDM20 (NatB complex subunit MDM20) (Mitochondrial dis ...	0.53	-	nuc	0	Cytoplasm	NatB complex [IDA]			796
Q37787 UniProt NPD GO	NUGM_BETVU	NADH-ubiquinone oxidoreductase 27 kDa subunit (EC 1.6.5.3) (EC 1.6.99.3) (Complex I-27KD) (CI-27KD) ...	0.53	-	cyt	0	Mitochondrion; mitochondrial inner membrane; peripheral membrane protein; matrix side				192
P34129 UniProt NPD GO	NGF_XIPMA	Nerve growth factor precursor (NGF)	0.53	-	exc	1 *	Secreted protein				194
O09118 UniProt NPD GO	NET1_MOUSE	Netrin-1 precursor	0.53	-	nuc	1 *	Secreted protein; extracellular space				604

You are viewing entries 23201 to 23250 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.