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
P56620 UniProt NPD GO	MGP_GALGA	Matrix Gla-protein (MGP)	0.57	-	nuc	0	Secreted protein				102
Q6Q7X3 UniProt NPD GO	MATK_AMBCE	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				508
Q9TNA5 UniProt NPD GO	MATK_ASPEL	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				520
Q4H1A1 UniProt NPD GO	MATK_BELCH	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				522
Q95EF8 UniProt NPD GO	MATK_GOSGO	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				504
Q7HTB5 UniProt NPD GO	MATK_GOSSC	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				504
Q646P3 UniProt NPD GO	MATK_KOEPA	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				512
Q8MEX8 UniProt NPD GO	MATK_LEPPR	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				514
Q4H192 UniProt NPD GO	MATK_MICJU	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				522
Q9TN87 UniProt NPD GO	MATK_RUSAC	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				520
Q8WHM7 UniProt NPD GO	MATK_SPIIN	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				510
Q8WHM6 UniProt NPD GO	MATK_SPIPO	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				510
Q9MSS3 UniProt NPD GO	MATK_THUOC	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				509
Q95BX6 UniProt NPD GO	MATK_ULMPA	Maturase K (Intron maturase)	0.57	-	cyt	0	Plastid; chloroplast				505
O14323 UniProt NPD GO	MCP4_SCHPO	Meiotic coiled-coil protein 4	0.57	+	nuc	0					355
Q9P6S4 UniProt NPD GO	MEU25_SCHPO	Meiotic expression up-regulated protein 25	0.57	-	nuc	0					622
O15479 UniProt NPD GO	MAGB2_HUMAN	Melanoma-associated antigen B2 (MAGE-B2 antigen) (DSS-AHC critical interval MAGE superfamily 6) (DAM ...	0.57	-	nuc	0			300098		319
Q16820 UniProt NPD GO	MEP1B_HUMAN	Meprin A subunit beta precursor (EC 3.4.24.18) (Endopeptidase-2) (N-benzoyl-L-tyrosyl-P-amino-benzoi ...	0.57	-	end	1	Membrane; single-pass type I membrane protein	extracellular space [TAS] integral to plasma membrane [TAS] plasma membrane [TAS]	600389		701
P47743 UniProt NPD GO	MGR8_MOUSE	Metabotropic glutamate receptor 8 precursor (mGluR8)	0.57	-	end	7	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]			908
Q9UBB5 UniProt NPD GO	MBD2_HUMAN	Methyl-CpG-binding domain protein 2 (Methyl-CpG-binding protein MBD2) (Demethylase) (DMTase)	0.57	+	nuc	0	Nucleus. Nuclear, in discrete foci. Detected at replication foci in late S phase	nucleus [NAS]	603547		411
P46151 UniProt NPD GO	MTHR1_YEAST	Methylenetetrahydrofolate reductase 1 (EC 1.5.1.20)	0.57	+	mit	0		cytoplasm [IDA]			657
Q5R4I6 UniProt NPD GO	MARE2_PONPY	Microtubule-associated protein RP/EB family member 2	0.57	-	nuc	0	Cytoplasm (By similarity). Associated with the microtubule network. Accumulates at the plus end of m ...				327
Q9URY0 UniProt NPD GO	YTM1_SCHPO	Microtubule-associated protein ytm1	0.57	+	nuc	0					440
P58059 UniProt NPD GO	RT21_MOUSE	Mitochondrial 28S ribosomal protein S21 (S21mt) (MRP-S21)	0.57	-	nuc	0	Mitochondrion	mitochondrial inner membrane [IDA] mitochondrion [IDA]			87
P47950 UniProt NPD GO	CYT4_NEUCR	Mitochondrial protein cyt-4	0.57	-	mit	0	Mitochondrion				1117
P60099 UniProt NPD GO	RT12_MAIZE	Mitochondrial ribosomal protein S12	0.57	-	nuc	0	Mitochondrion				125
P60098 UniProt NPD GO	RT12_WHEAT	Mitochondrial ribosomal protein S12	0.57	-	nuc	0	Mitochondrion				125
P87159 UniProt NPD GO	NIF1_SCHPO	Mitosis inhibitor nif1 (Nim1-interacting factor 1)	0.57	-	nuc	0	Cytoplasm (Potential)				681
O74309 UniProt NPD GO	SLM9_SCHPO	Mitotic control protein slm9	0.57	-	nuc	0	Nucleus	nucleus [IDA]			807
Q9W7E7 UniProt NPD GO	SMAD5_BRARE	Mothers against decapentaplegic homolog 5 (SMAD 5) (Mothers against DPP homolog 5) (Smad5) (Somitabu ...	0.57	-	nuc	0	Cytoplasm (By similarity). In the cytoplasm in the absence of ligand. Nucleus (By similarity). Migra ...	integral to membrane [ISS] intracellular [ISS] nucleus [ISS]			464
P11229 UniProt NPD GO	ACM1_HUMAN	Muscarinic acetylcholine receptor M1	0.57	-	end	7 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS] plasma membrane [TAS]	118510		460
P56489 UniProt NPD GO	ACM1_MACMU	Muscarinic acetylcholine receptor M1	0.57	-	end	7 *	Membrane; multi-pass membrane protein				460
Q5R949 UniProt NPD GO	ACM1_PONPY	Muscarinic acetylcholine receptor M1	0.57	-	end	7 *	Membrane; multi-pass membrane protein				460
O01761 UniProt NPD GO	UNC89_CAEEL	Muscle M-line assembly protein unc-89 (Uncoordinated protein 89)	0.57	+	nuc	0				1FHO	8081
Q63994 UniProt NPD GO	CD33_MOUSE	Myeloid cell surface antigen CD33 precursor (Siglec-3)	0.57	-	end	1	Membrane; single-pass type I membrane protein				403
Q594P2 UniProt NPD GO	MYOC_FELCA	Myocilin precursor	0.57	-	nuc	0	Located preferentially in the ciliary rootlet and basal body of the connecting cilium of photorecept ...				490
O70249 UniProt NPD GO	OGG1_RAT	N-glycosylase/DNA lyase [Includes: 8-oxoguanine DNA glycosylase (EC 3.2.2.-); DNA-(apurinic or apyri ...	0.57	-	mit	0	Nucleus (By similarity)	mitochondrion [IDA] nucleus [IDA]			345
P41833 UniProt NPD GO	IME4_YEAST	N6-adenosine-methyltransferase IME4 (EC 2.1.1.62)	0.57	-	nuc	0	Nucleus (Probable)				600
P06670 UniProt NPD GO	NUKC_MAIZE	NAD(P)H-quinone oxidoreductase chain K, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase, chain K) (N ...	0.57	-	nuc	0	Plastid; chloroplast				248
O98692 UniProt NPD GO	NUIC_HORVU	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.57	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
P46722 UniProt NPD GO	NUIC_MAIZE	NAD(P)H-quinone oxidoreductase subunit I, chloroplast (EC 1.6.5.-) (NAD(P)H dehydrogenase subunit I) ...	0.57	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				180
Q5M8S7 UniProt NPD GO	NIPA_XENTR	NIPA-like protein (Zinc finger C3HC-type protein 1-like)	0.57	-	nuc	0	Nucleus (By similarity)				478
P26715 UniProt NPD GO	NKG2A_HUMAN	NKG2-A/NKG2-B type II integral membrane protein (NKG2-A/B-activating NK receptor) (NK cell receptor ...	0.57	-	nuc	1	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS]	161555		233
Q8SQG9 UniProt NPD GO	NHRF2_RABIT	Na(+)/H(+) exchange regulatory cofactor NHE-RF2 (PDZ domain-containing protein NHERF-2) (Solute carr ...	0.57	-	nuc	0	Intracytoplasmic membrane; peripheral membrane protein (By similarity). Nucleus (By similarity). Nuc ...				316
Q92859 UniProt NPD GO	NEO1_HUMAN	Neogenin precursor	0.57	-	exc	1	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [NAS]	601907	1X5K	1461
P97798 UniProt NPD GO	NEO1_MOUSE	Neogenin precursor	0.57	-	end	1	Membrane; single-pass type I membrane protein				1493
Q95TU8 UniProt NPD GO	UNC5_DROME	Netrin receptor unc-5 precursor (Unc5 netrin receptor)	0.57	-	mit	1 *	Membrane; single-pass type I membrane protein (By similarity)				1072
O77788 UniProt NPD GO	NFM_BOVIN	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.57	-	nuc	0					925
P16053 UniProt NPD GO	NFM_CHICK	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.57	-	nuc	0					857
P08552 UniProt NPD GO	NFM_PIG	Neurofilament triplet M protein (160 kDa neurofilament protein) (Neurofilament medium polypeptide) ( ...	0.57	-	nuc	0					454

You are viewing entries 20851 to 20900 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.