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
Q8VC90 UniProt NPD GO	ZDH12_MOUSE	Probable palmitoyltransferase ZDHHC12 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 12) ( ...	0.15	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				267
Q5FVR1 UniProt NPD GO	ZDHC4_RAT	Probable palmitoyltransferase ZDHHC4 (EC 2.3.1.-) (Zinc finger DHHC domain-containing protein 4) (DH ...	0.15	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				343
Q19951 UniProt NPD GO	PEX13_CAEEL	Probable peroxisomal membrane protein PEX13 (Peroxin-13)	0.15	-	cyt	0	Peroxisome; peroxisomal membrane; multi-pass membrane protein (By similarity)				330
Q9VTZ6 UniProt NPD GO	PMM_DROME	Probable phosphomannomutase (EC 5.4.2.8) (PMM)	0.15	-	cyt	0	Cytoplasm (By similarity)				254
Q5ZC87 UniProt NPD GO	HAK3_ORYSA	Probable potassium transporter 3 (OsHAK3)	0.15	-	end	12	Membrane; multi-pass membrane protein (By similarity)				808
P57742 UniProt NPD GO	PFD5_ARATH	Probable prefoldin subunit 5	0.15	-	cyt	0					151
Q9VHI4 UniProt NPD GO	SF3B5_DROME	Probable splicing factor 3B subunit 5 (SF3b5) (Pre-mRNA-splicing factor SF3b 10 kDa subunit)	0.15	-	nuc	0	Nucleus (By similarity)				85
Q7S4Z6 UniProt NPD GO	FDFT_NEUCR	Probable squalene synthetase (EC 2.5.1.21) (SQS) (SS) (Farnesyl-diphosphate farnesyltransferase) (FP ...	0.15	-	nuc	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				481
P47052 UniProt NPD GO	DHSX_YEAST	Probable succinate dehydrogenase [ubiquinone] flavoprotein subunit 2, mitochondrial precursor (EC 1. ...	0.15	-	mit	0	Mitochondrion; mitochondrial inner membrane	mitochondrion [IDA]			634
Q8GZ45 UniProt NPD GO	SYTC_ARATH	Probable threonyl-tRNA synthetase, cytoplasmic (EC 6.1.1.3) (Threonine--tRNA ligase) (ThrRS)	0.15	-	cyt	0	Cytoplasm (By similarity)				458
O75005 UniProt NPD GO	SYV_SCHPO	Probable valyl-tRNA synthetase, mitochondrial precursor (EC 6.1.1.9) (Valine--tRNA ligase) (ValRS)	0.15	-	cyt	0	Mitochondrion (Probable)				980
Q5QM84 UniProt NPD GO	TPC1_ORYSA	Probable voltage-dependent calcium channel protein TPC1 (Probable voltage-gated calcium channel) (Tw ...	0.15	-	end	11	Membrane; multi-pass membrane protein				757
Q38909 UniProt NPD GO	XTH28_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 28 precursor (EC 2.4.1.207) (At-XTH28) (X ...	0.15	-	exc	0	Secreted protein; extracellular space; apoplast (Probable)				332
Q9XIW1 UniProt NPD GO	XTH5_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 5 precursor (EC 2.4.1.207) (At-XTH5) (XTH ...	0.15	-	end	0	Secreted protein; extracellular space; apoplast (Probable)				293
Q9R0E2 UniProt NPD GO	PLOD1_MOUSE	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.15	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				728
P45656 UniProt NPD GO	GON1_XENLA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.15	-	end	0	Secreted protein				89
Q02242 UniProt NPD GO	PDCD1_MOUSE	Programmed cell death protein 1 precursor (Protein PD-1) (mPD-1)	0.15	-	mit	1	Membrane; single-pass type I membrane protein			1NPU	288
P33091 UniProt NPD GO	PRL_PROAT	Prolactin (PRL)	0.15	-	cyt	0	Secreted protein				200
P18690 UniProt NPD GO	PRO3_DACGL	Prolamin alpha-3 (Fragment)	0.15	-	cyt	0					23
O01377 UniProt NPD GO	PCNA_BOMMO	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.15	-	mit	0	Nucleus				260
Q29095 UniProt NPD GO	PTGDS_PIG	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.15	-	mit	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [ISS] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			189
P30657 UniProt NPD GO	PSB4_YEAST	Proteasome component PRE4 (EC 3.4.25.1) (Macropain subunit PRE4) (Proteinase YSCE subunit PRE4) (Mul ...	0.15	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	266
P23638 UniProt NPD GO	PSA4_YEAST	Proteasome component Y13 (EC 3.4.25.1) (Macropain subunit Y13) (Proteinase YSCE subunit 13) (Multica ...	0.15	-	mit	0	Cytoplasm. Nucleus	proteasome core complex, alpha-subunit comp... [IPI]		2FNY	258
O44156 UniProt NPD GO	PSA1_CAEEL	Proteasome subunit alpha type 1 (EC 3.4.25.1) (Proteasome subunit alpha 6)	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				260
P0C1G8 UniProt NPD GO	PSA4A_ORYSA	Proteasome subunit alpha type 4-1 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome sub ...	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
Q5VRG3 UniProt NPD GO	PSA4B_ORYSA	Proteasome subunit alpha type 4-2 (EC 3.4.25.1) (20S proteasome alpha subunit C) (20S proteasome sub ...	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
Q9U794 UniProt NPD GO	PSB1_TRYBB	Proteasome subunit beta type 1 (EC 3.4.25.1) (20S proteasome beta 6 subunit)	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				258
P34286 UniProt NPD GO	PSB1_CAEEL	Proteasome subunit beta type 1 (EC 3.4.25.1) (Proteasome subunit beta 6)	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				258
P99026 UniProt NPD GO	PSB4_MOUSE	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain ...	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				264
P34067 UniProt NPD GO	PSB4_RAT	Proteasome subunit beta type 4 precursor (EC 3.4.25.1) (Proteasome beta chain) (Macropain beta chain ...	0.15	-	cyt	0	Cytoplasm. Nucleus				263
Q6FXM4 UniProt NPD GO	AF9_CANGA	Protein AF-9 homolog	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				221
Q4I7S1 UniProt NPD GO	AF9_GIBZE	Protein AF-9 homolog	0.15	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				268
Q9LW64 UniProt NPD GO	SF3BA_ARATH	Protein At3g23325	0.15	-	nuc	0					87
P58728 UniProt NPD GO	SF3BB_ARATH	Protein At4g14342	0.15	-	nuc	0					87
P41506 UniProt NPD GO	BP4C_BRANA	Protein BP4C	0.15	-	nuc	1 *					73
Q8N6V4 UniProt NPD GO	CJ053_HUMAN	Protein C10orf53	0.15	-	cyt	0					157
Q8NDC0 UniProt NPD GO	CN032_HUMAN	Protein C14orf32	0.15	-	nuc	0					244
Q5E9L3 UniProt NPD GO	CN032_BOVIN	Protein C14orf32 homolog	0.15	-	nuc	0					239
Q4R837 UniProt NPD GO	CN032_MACFA	Protein C14orf32 homolog	0.15	-	nuc	0					244
Q5R623 UniProt NPD GO	CN032_PONPY	Protein C14orf32 homolog	0.15	-	nuc	0					244
Q9H246 UniProt NPD GO	CA021_HUMAN	Protein C1orf21 (Proliferation-inducing gene 13 protein 13)	0.15	-	nuc	0					121
Q3TT38 UniProt NPD GO	CF106_MOUSE	Protein C6orf106 homolog	0.15	-	nuc	0					291
Q66HC3 UniProt NPD GO	CI072_RAT	Protein C9orf72 homolog	0.15	-	cyt	0					481
P47818 UniProt NPD GO	CCC1_YEAST	Protein CCC1	0.15	-	end	3	Vacuole; vacuolar membrane; multi-pass membrane protein (Potential)	Golgi apparatus [IDA] vacuolar membrane (sensu Fungi) [IDA]			322
Q9QUK3 UniProt NPD GO	CLN8_MOUSE	Protein CLN8	0.15	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				288
P53053 UniProt NPD GO	COS12_YEAST	Protein COS12	0.15	-	end	2	Membrane; multi-pass membrane protein (Potential)				380
P38819 UniProt NPD GO	ERP5_YEAST	Protein ERP5 precursor	0.15	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type I membrane protein (By simil ...				212
P58499 UniProt NPD GO	FAM3B_HUMAN	Protein FAM3B precursor (Cytokine-like protein 2-21)	0.15	-	mit	1 *	Secreted. Localized in discrete vesicular and perinuclear structure. Seems not to localize with micr ...	extracellular region [NAS]	608617		235
Q5XI89 UniProt NPD GO	FA55D_RAT	Protein FAM55D precursor	0.15	-	mit	1 *	Secreted protein (Potential)				542
Q9DCV4 UniProt NPD GO	FA82B_MOUSE	Protein FAM82B	0.15	-	mit	0					305

You are viewing entries 57451 to 57500 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.