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
P35409 UniProt NPD GO	GLHR_ANTEL	Probable glycoprotein hormone G-protein coupled receptor precursor	0.37	-	end	8 *	Membrane; multi-pass membrane protein				925
P83296 UniProt NPD GO	GR64E_DROME	Probable gustatory receptor 64e	0.37	-	end	7	Membrane; multi-pass membrane protein (Potential)	integral to membrane [NAS]			451
Q8H016 UniProt NPD GO	LOX6_ORYSA	Probable lipoxygenase 6 (EC 1.13.11.12)	0.37	-	cyt	0					918
Q9VHD2 UniProt NPD GO	MAAI2_DROME	Probable maleylacetoacetate isomerase 2 (EC 5.2.1.2) (MAAI 2)	0.37	-	nuc	0	Cytoplasm (By similarity)				227
P98200 UniProt NPD GO	AT8A2_MOUSE	Probable phospholipid-transporting ATPase IB (EC 3.6.3.1) (ATPase class I type 8A member 2)	0.37	-	end	8	Membrane; multi-pass membrane protein				1148
Q61SU8 UniProt NPD GO	PFD1_CAEBR	Probable prefoldin subunit 1	0.37	-	nuc	0					117
Q9P6Y2 UniProt NPD GO	SEN2_NEUCR	Probable tRNA-splicing endonuclease subunit sen-2 (EC 3.1.27.9) (tRNA-intron endonuclease sen-2)	0.37	-	nuc	0					633
P35172 UniProt NPD GO	TREB_YEAST	Probable trehalase (EC 3.2.1.28) (Alpha,alpha-trehalase) (Alpha,alpha-trehalose glucohydrolase)	0.37	-	cyt	0		cytoplasm [IDA] mitochondrion [IDA]			780
Q5U367 UniProt NPD GO	PLOD3_RAT	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 3 precursor (EC 1.14.11.4) (Lysyl hydroxylase 3) (LH ...	0.37	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				741
P50175 UniProt NPD GO	PENK_MESAU	Proenkephalin A precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); Met ...	0.37	-	exc	0	Secreted protein				268
P07194 UniProt NPD GO	PENKB_XENLA	Proenkephalin A-B precursor [Contains: Synenkephalin; Met-enkephalin (Opioid growth factor) (OGF); M ...	0.37	-	nuc	0	Secreted protein				216
P43306 UniProt NPD GO	GON2_CLAGA	Progonadoliberin-2 precursor (Progonadoliberin II) [Contains: Gonadoliberin-2 (Gonadoliberin II) (Lu ...	0.37	-	exc	0	Secreted protein				86
P29235 UniProt NPD GO	PRL_HYPNO	Prolactin precursor (PRL)	0.37	-	nuc	1 *	Secreted protein				210
P35395 UniProt NPD GO	PRL_HYPMO	Prolactin precursor (PRL) (Fragment)	0.37	-	mit	1 *	Secreted protein				207
P92983 UniProt NPD GO	PROD_ARATH	Proline oxidase, mitochondrial precursor (EC 1.5.3.-) (Osmotic stress-induced proline dehydrogenase) ...	0.37	-	mit	0	Mitochondrion; mitochondrial matrix				499
Q4KLM6 UniProt NPD GO	P3H2_RAT	Prolyl 3-hydroxylase 2 precursor (EC 1.14.11.7) (Leprecan-like protein 1)	0.37	-	end	0	Endoplasmic reticulum. Golgi apparatus (By similarity)				703
P41539 UniProt NPD GO	TKN1_MOUSE	Protachykinin 1 precursor (PPT) [Contains: Substance P; Neurokinin A (NKA) (Substance K) (Neuromedin ...	0.37	-	exc	0	Secreted protein	cell soma [IDA] extracellular region [IDA]			130
P40303 UniProt NPD GO	PSA7_YEAST	Proteasome component PRE6 (EC 3.4.25.1) (Macropain subunit PRE6) (Proteinase YSCE subunit PRE6) (Mul ...	0.37	-	nuc	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	254
O95870 UniProt NPD GO	BAT5_HUMAN	Protein BAT5 (HLA-B-associated transcript 5) (Protein G5)	0.37	-	mit	2	Membrane; multi-pass membrane protein (Potential)		142620		557
Q9D3D0 UniProt NPD GO	CT121_MOUSE	Protein C20orf121 homolog	0.37	-	cyt	0					343
Q8BGD0 UniProt NPD GO	CC014_MOUSE	Protein C3orf014 homolog	0.37	-	nuc	0					127
Q9HD34 UniProt NPD GO	CF149_HUMAN	Protein C6orf149	0.37	-	nuc	0					91
Q8WU49 UniProt NPD GO	CG033_HUMAN	Protein C7orf33	0.37	-	nuc	0					177
Q5RD79 UniProt NPD GO	CQ10B_PONPY	Protein COQ10 B, mitochondrial precursor	0.37	-	mit	0	Mitochondrion (Potential)				238
P53344 UniProt NPD GO	COS6_YEAST	Protein COS6	0.37	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	vacuole (sensu Fungi) [IDA]			381
Q07788 UniProt NPD GO	COS7_YEAST	Protein COS7	0.37	-	end	4 *	Membrane; multi-pass membrane protein (Potential)	mitochondrion [IDA]			383
P38723 UniProt NPD GO	COS8_YEAST	Protein COS8	0.37	-	end	3 *	Membrane; multi-pass membrane protein (Potential)	nuclear envelope [IDA]			381
Q12396 UniProt NPD GO	EMP46_YEAST	Protein EMP46 precursor (46 kDa endomembrane protein)	0.37	-	nuc	2 *	Golgi apparatus; Golgi apparatus membrane; single-pass type I membrane protein. Endoplasmic reticulu ...	ER to Golgi transport vesicle [IPI] Golgi membrane [IDA]		2A6X	444
Q9H0Q0 UniProt NPD GO	FA49A_HUMAN	Protein FAM49A	0.37	-	nuc	0					323
Q8BHZ0 UniProt NPD GO	FA49A_MOUSE	Protein FAM49A	0.37	-	nuc	0					323
P60924 UniProt NPD GO	K0141_RAT	Protein KIAA0141 homolog	0.37	-	mit	0					509
Q9HB07 UniProt NPD GO	MYG1_HUMAN	Protein MYG1	0.37	-	mit	0					376
Q9HAS0 UniProt NPD GO	NJMU_HUMAN	Protein Njmu-R1	0.37	-	nuc	0					366
Q811G0 UniProt NPD GO	PTHB1_MOUSE	Protein PTHB1 (Parathyroid hormone-responsive B1 gene protein homolog)	0.37	-	cyt	0					885
P31725 UniProt NPD GO	S10A9_MOUSE	Protein S100-A9 (S100 calcium-binding protein A9) (Calgranulin-B) (Migration inhibitory factor-relat ...	0.37	-	nuc	0					112
Q9UBK9 UniProt NPD GO	UXT_HUMAN	Protein UXT (Ubiquitously expressed transcript protein)	0.37	-	cyt	0			300234		157
P87387 UniProt NPD GO	WNT2B_XENLA	Protein Wnt-2b precursor (XWnt-2b)	0.37	+	exc	0	Secreted protein; extracellular space; extracellular matrix				351
P29702 UniProt NPD GO	PFTA_BOVIN	Protein farnesyltransferase/geranylgeranyltransferase type I alpha subunit (EC 2.5.1.58) (EC 2.5.1.5 ...	0.37	-	nuc	0					375
Q9JM05 UniProt NPD GO	PIAS4_MOUSE	Protein inhibitor of activated STAT protein 4 (Protein inhibitor of activated STAT protein gamma) (P ...	0.37	-	nuc	0	Nucleus; nucleoplasm; nuclear speckle. Colocalizes with promyelocytic leukemia nuclear bodies (PML N ...	nuclear matrix [IDA] nucleus [IDA]			507
P38768 UniProt NPD GO	PIH1_YEAST	Protein interacting with Hsp90 1 (Nucleolar protein 17)	0.37	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA] small nucleolar ribonucleoprotein complex [IPI]			344
P46573 UniProt NPD GO	APK1B_ARATH	Protein kinase APK1B, chloroplast precursor (EC 2.7.11.1)	0.37	+	cyt	0	Plastid; chloroplast (Potential)				412
Q01793 UniProt NPD GO	KRUP_TRICA	Protein krueppel (Fragment)	0.37	-	nuc	0	Nucleus (Probable)				74
Q5M848 UniProt NPD GO	ORAI1_RAT	Protein orai-1	0.37	-	nuc	3	Cell membrane; multi-pass membrane protein (By similarity)				304
O42334 UniProt NPD GO	PTC2_CYNPY	Protein patched homolog 2 (PTC2) (Fragment)	0.37	-	end	2	Membrane; multi-pass membrane protein				255
Q9VWV9 UniProt NPD GO	PORCN_DROME	Protein-cysteine N-palmitoyltransferase porcupine (EC 2.3.1.-)	0.37	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IDA] integral to endoplasmic reticulum membrane [NAS]			525
P04628 UniProt NPD GO	WNT1_HUMAN	Proto-oncogene protein Wnt-1 precursor	0.37	-	exc	1 *	Secreted protein; extracellular space; extracellular matrix		164820		370
P42683 UniProt NPD GO	LCK_CHICK	Proto-oncogene tyrosine-protein kinase LCK (EC 2.7.10.2) (Protein-tyrosine kinase C-TKL) (p56tk1)	0.37	-	cyt	0		lipid raft [ISS] pericentriolar material [ISS] plasma membrane [ISS]			507
Q5DRB2 UniProt NPD GO	PCDG8_PANTR	Protocadherin gamma A8 precursor (PCDH-gamma-A8)	0.37	-	nuc	1	Membrane; single-pass type I membrane protein (By similarity)				932
Q9Y5G3 UniProt NPD GO	PCDGD_HUMAN	Protocadherin gamma B1 precursor (PCDH-gamma-B1)	0.37	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		606299		927
O60245 UniProt NPD GO	PCDH7_HUMAN	Protocadherin-7 precursor (Brain-heart protocadherin) (BH-Pcdh)	0.37	-	end	2 *	Membrane; single-pass type I membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	602988		1069

You are viewing entries 34451 to 34500 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.