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
O47170 UniProt NPD GO	MATK_RHOHI	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				506
Q8MFF0 UniProt NPD GO	MATK_RHOSC	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				506
Q8WJN2 UniProt NPD GO	MATK_SPICA	Maturase K (Intron maturase)	0.67	-	nuc	0	Plastid; chloroplast				502
Q8MEX5 UniProt NPD GO	MATK_STAER	Maturase K (Intron maturase)	0.67	-	mit	0	Plastid; chloroplast				503
P36436 UniProt NPD GO	MATK_SULSU	Maturase K (Intron maturase)	0.67	-	cyt	0	Plastid; chloroplast				506
Q9UTR7 UniProt NPD GO	MCP3_SCHPO	Meiotic coiled-coil protein 3	0.67	-	nuc	0					952
P55163 UniProt NPD GO	GEX3_CAEEL	Membrane-associated protein gex-3	0.67	-	vac	0					1141
O60783 UniProt NPD GO	RT14_HUMAN	Mitochondrial 28S ribosomal protein S14 (S14mt) (MRP-S14)	0.67	+	nuc	0	Mitochondrion	mitochondrial ribosome [NAS]			128
Q9CZW5 UniProt NPD GO	TOM70_MOUSE	Mitochondrial precursor proteins import receptor (Translocase of outer membrane TOM70)	0.67	+	nuc	0	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)	mitochondrion [IDA]			611
P15758 UniProt NPD GO	RT13_OENBE	Mitochondrial ribosomal protein S13	0.67	-	nuc	0	Mitochondrion				114
P26868 UniProt NPD GO	RT08_MARPO	Mitochondrial ribosomal protein S8	0.67	-	mit	0	Mitochondrion				152
Q9LM33 UniProt NPD GO	MPK8_ARATH	Mitogen-activated protein kinase 8 (EC 2.7.11.24) (MAP kinase 8) (AtMPK8)	0.67	-	nuc	0					589
O22042 UniProt NPD GO	M3K3_ARATH	Mitogen-activated protein kinase kinase kinase 3 (EC 2.7.11.25) (Arabidopsis NPK1-related protein ki ...	0.67	-	nuc	0					651
Q9H8L6 UniProt NPD GO	MMRN2_HUMAN	Multimerin-2 precursor (EMILIN-3) (Elastin microfibril interface located protein 3) (Elastin microfi ...	0.67	-	cyt	0	Secreted protein; extracellular space; extracellular matrix		608925		949
Q920H4 UniProt NPD GO	ACM5_MOUSE	Muscarinic acetylcholine receptor M5	0.67	-	end	7 *	Membrane; multi-pass membrane protein				532
P40965 UniProt NPD GO	MSH4_YEAST	MutS protein homolog 4	0.67	-	nuc	0		nuclear chromosome [IDA]			878
O55087 UniProt NPD GO	MEF2B_MOUSE	Myocyte-specific enhancer factor 2B	0.67	-	nuc	0	Nucleus (By similarity)	nucleus [IC]			349
Q5RGJ8 UniProt NPD GO	GNPTA_BRARE	N-acetylglucosamine-1-phosphotransferase subunits alpha/beta precursor (EC 2.7.8.17) (GlcNAc-1-phosp ...	0.67	-	end	2 *	Subunit alpha: Golgi apparatus; Golgi membrane; single-pass type I membrane protein (By similarity). ...				1219
Q56YN3 UniProt NPD GO	NADK1_ARATH	NAD(H) kinase 1 (EC 2.7.1.23) (EC 2.7.1.86) (AtNADK-1)	0.67	-	nuc	0					524
P17568 UniProt NPD GO	NDUB7_HUMAN	NADH dehydrogenase [ubiquinone] 1 beta subcomplex subunit 7 (EC 1.6.5.3) (EC 1.6.99.3) (NADH-ubiquin ...	0.67	+	nuc	0	Mitochondrion; mitochondrial inner membrane; matrix side		603842		136
Q8C7U1 UniProt NPD GO	N4BP3_MOUSE	NEDD4-binding protein 3 (N4BP3)	0.67	-	nuc	0	Cytoplasmic vesicle; cytoplasmic vesicle membrane; peripheral membrane protein (By similarity)				537
P08551 UniProt NPD GO	NFL_MOUSE	Neurofilament triplet L protein (68 kDa neurofilament protein) (Neurofilament light polypeptide) (NF ...	0.67	-	nuc	0					542
P35616 UniProt NPD GO	NFL_XENLA	Neurofilament triplet L protein (Neurofilament light polypeptide) (NF-L)	0.67	-	nuc	0					543
P23645 UniProt NPD GO	BIB_DROME	Neurogenic protein big brain	0.67	-	nuc	6	Membrane; multi-pass membrane protein				696
O62699 UniProt NPD GO	NOS2_CANFA	Nitric oxide synthase, inducible (EC 1.14.13.39) (NOS type II) (Inducible NO synthase) (Inducible NO ...	0.67	-	nuc	0					1154
Q8L4H4 UniProt NPD GO	NORK_MEDTR	Nodulation receptor kinase precursor (EC 2.7.11.1) (Does not make infections protein 2) (Symbiosis r ...	0.67	-	end	2 *					925
Q9NA51 UniProt NPD GO	NHR5_CAEEL	Nuclear hormone receptor family member nhr-5	0.67	-	nuc	0	Nucleus (By similarity)				703
Q20765 UniProt NPD GO	NHR7_CAEEL	Nuclear hormone receptor family member nhr-7	0.67	-	nuc	0	Nucleus (Potential)				536
Q8WUM0 UniProt NPD GO	NU133_HUMAN	Nuclear pore complex protein Nup133 (Nucleoporin Nup133) (133 kDa nucleoporin)	0.67	-	mit	0	Nucleus; nuclear envelope; nuclear pore complex. Located on both the cytoplasmic and nuclear sides o ...	nuclear pore [IDA]	607613	1XKS	1156
Q9LVJ7 UniProt NPD GO	NFYA6_ARATH	Nuclear transcription factor Y subunit A-6 (AtNF-YA-6)	0.67	-	nuc	0	Nucleus (Probable)				308
P81117 UniProt NPD GO	NUCB2_MOUSE	Nucleobindin-2 precursor (DNA-binding protein NEFA)	0.67	-	exc	0	In dendrites and perikarya of brain neurons. Abundant in the ER cisternae and nuclear envelope, but ...	cytoplasm [IDA] endoplasmic reticulum [IDA] nuclear outer membrane [IDA] nucleus [IDA]			420
Q8SVJ8 UniProt NPD GO	NOG1_ENCCU	Nucleolar GTP-binding protein 1	0.67	-	mit	0	Nucleus; nucleolus (By similarity)				528
P52891 UniProt NPD GO	NUP84_YEAST	Nucleoporin NUP84 (Nuclear pore protein NUP84)	0.67	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side; nucleoplasmic side. Symmetric dis ...	nuclear pore [IDA]			726
Q7KRY6 UniProt NPD GO	NHK1_DROME	Nucleosomal histone kinase 1 (EC 2.7.11.1) (Protein baellchen)	0.67	+	nuc	0	Cytoplasm. Nucleus. Chromatin-associated during mitosis	chromatin [IDA] nucleus [IDA]			599
Q9WUQ3 UniProt NPD GO	OLIG1_RAT	Oligodendrocyte transcription factor 1 (Oligo1) (Olg-1 bHLH protein)	0.67	-	nuc	0	Nucleus (By similarity)				261
Q9JKN5 UniProt NPD GO	OLIG1_MOUSE	Oligodendrocyte transcription factor 1 (Oligo1) (Oligodendrocyte-specific bHLH transcription factor ...	0.67	-	nuc	0	Nucleus (By similarity)				260
Q15406 UniProt NPD GO	NR6A1_HUMAN	Orphan nuclear receptor NR6A1 (Germ cell nuclear factor) (GCNF) (Retinoid receptor-related testis-sp ...	0.67	-	nuc	0	Nucleus (Probable)		602778		480
P16258 UniProt NPD GO	OSBP1_RABIT	Oxysterol-binding protein 1	0.67	-	nuc	0	Cytoplasm (By similarity). Golgi apparatus; Golgi membrane; peripheral membrane protein (By similari ...				809
Q9BWX1 UniProt NPD GO	PHF7_HUMAN	PHD finger protein 7 (Protein NYD-SP6)	0.67	-	nuc	0	Nucleus				381
P54279 UniProt NPD GO	PMS2_MOUSE	PMS1 protein homolog 2 (DNA mismatch repair protein PMS2)	0.67	-	nuc	0		nucleus [ISS]			859
O95522 UniProt NPD GO	PRA12_HUMAN	PRAME family member DJ1198H6.2	0.67	-	cyt	0					483
P32114 UniProt NPD GO	PAX2_MOUSE	Paired box protein Pax-2	0.67	-	nuc	0	Nucleus	transcription factor complex [TAS]			415
O60045 UniProt NPD GO	SSP1_NEUCR	Peptidyl-prolyl cis-trans isomerase ssp-1 (EC 5.2.1.8) (PPIase ssp1)	0.67	-	nuc	0					186
Q9D787 UniProt NPD GO	PPIL2_MOUSE	Peptidyl-prolyl cis-trans isomerase-like 2 (EC 5.2.1.8) (PPIase) (Rotamase) (Cyclophilin-60) (Cyclop ...	0.67	-	nuc	0	Nucleus (By similarity)				521
Q7SGP2 UniProt NPD GO	PEX6_NEUCR	Peroxisomal biogenesis factor 6 (Peroxin-6)	0.67	-	mit	0					1381
P80667 UniProt NPD GO	PEX13_YEAST	Peroxisomal membrane protein PAS20 (Peroxin-13)	0.67	-	nuc	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein			1NM7	386
P54676 UniProt NPD GO	PI3K4_DICDI	Phosphatidylinositol 3-kinase VPS34-like (EC 2.7.1.137) (PI3-kinase) (PtdIns-3-kinase) (PI3K)	0.67	-	nuc	0					816
O00329 UniProt NPD GO	PK3CD_HUMAN	Phosphatidylinositol-4,5-bisphosphate 3-kinase catalytic subunit delta isoform (EC 2.7.1.153) (PI3-k ...	0.67	-	cyt	0		phosphoinositide 3-kinase complex [NAS]	602839		1044
P51062 UniProt NPD GO	CAPP_PEA	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.67	-	cyt	0	Cytoplasm (By similarity)				967
P29196 UniProt NPD GO	CAPP_SOLTU	Phosphoenolpyruvate carboxylase (EC 4.1.1.31) (PEPCase) (PEPC)	0.67	-	nuc	0	Cytoplasm				965

You are viewing entries 15351 to 15400 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.