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
Q9V773 UniProt NPD GO	C6A20_DROME	Probable cytochrome P450 6a20 (EC 1.14.-.-) (CYPVIA20)	0.17	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (Potential)				501
Q9LMP6 UniProt NPD GO	DRL3_ARATH	Probable disease resistance protein At1g15890	0.17	-	mit	0					921
Q09226 UniProt NPD GO	ALG6_CAEEL	Probable dolichyl pyrophosphate Man9GlcNAc2 alpha-1,3-glucosyltransferase (EC 2.4.1.-) (Dolichyl-P-G ...	0.17	-	end	11	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (Potential)				503
Q9VH78 UniProt NPD GO	ALG12_DROME	Probable dolichyl-P-Man:Man(7)GlcNAc(2)-PP-dolichyl-alpha-1,6-mannosyltransferase (EC 2.4.1.-) (Mann ...	0.17	-	end	9	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)	endoplasmic reticulum [ISS]			678
O60087 UniProt NPD GO	AMYG_SCHPO	Probable glucoamylase precursor (EC 3.2.1.3) (Glucan 1,4-alpha-glucosidase) (1,4-alpha-D-glucan gluc ...	0.17	-	end	0					450
O13810 UniProt NPD GO	PROB_SCHPO	Probable glutamate 5-kinase (EC 2.7.2.11) (Gamma-glutamyl kinase) (GK)	0.17	-	cyt	0	Cytoplasm (By similarity)				402
P90795 UniProt NPD GO	GPDM_CAEEL	Probable glycerol-3-phosphate dehydrogenase, mitochondrial precursor (EC 1.1.99.5) (GPD-M) (GPDH-M)	0.17	-	vac	0	Mitochondrion (By similarity)				722
P32623 UniProt NPD GO	CRH2_YEAST	Probable glycosidase CRH2 precursor (EC 3.2.-.-) (Congo red hypersensitive protein 2) (Unknown trans ...	0.17	-	nuc	0	Cell wall; lipid-anchor; GPI-anchor. GPI-anchored cell wall protein (GPI-CWP). Localized at the cell ...	cell wall (sensu Fungi) [IDA] septin ring (sensu Saccharomyces) [IDA]			467
Q05790 UniProt NPD GO	CRR1_YEAST	Probable glycosidase CRR1 precursor (EC 3.2.-.-) (CRH-related protein 1)	0.17	-	mit	0	Spore wall envelope	spore wall (sensu Fungi) [IDA]			422
Q5SPH9 UniProt NPD GO	RT10_BRARE	Probable mitochondrial ribosomal protein S10	0.17	-	mit	0	Mitochondrion (By similarity)				187
P83220 UniProt NPD GO	MIH_JASLA	Probable molt-inhibiting hormone (MIH)	0.17	-	cyt	0	Secreted protein				74
P91660 UniProt NPD GO	L259_DROME	Probable multidrug resistance-associated protein lethal(2)03659 (Wunen region A protein)	0.17	-	end	11	Membrane; multi-pass membrane protein	integral to membrane [NAS]			1290
P98197 UniProt NPD GO	AT11A_MOUSE	Probable phospholipid-transporting ATPase IH (EC 3.6.3.1) (ATPase class I type 11A) (ATPase IS)	0.17	-	end	7	Membrane; multi-pass membrane protein				1187
Q7Q3N5 UniProt NPD GO	PORCN_ANOGA	Probable protein-cysteine N-palmitoyltransferase porcupine (EC 2.3.1.-)	0.17	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				495
Q6AY30 UniProt NPD GO	SCPDH_RAT	Probable saccharopine dehydrogenase (EC 1.5.1.9)	0.17	-	nuc	1					429
Q22018 UniProt NPD GO	DTYMK_CAEEL	Probable thymidylate kinase (EC 2.7.4.9) (dTMP kinase)	0.17	-	cyt	0					218
Q38907 UniProt NPD GO	XTH25_ARATH	Probable xyloglucan endotransglucosylase/hydrolase protein 25 precursor (EC 2.4.1.207) (At-XTH25) (X ...	0.17	-	exc	1 *	Secreted protein; extracellular space; apoplast (Probable)				284
Q63321 UniProt NPD GO	PLOD1_RAT	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 1 precursor (EC 1.14.11.4) (Lysyl hydroxylase 1) (LH ...	0.17	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				728
O75340 UniProt NPD GO	PDCD6_HUMAN	Programmed cell death protein 6 (Probable calcium-binding protein ALG-2)	0.17	-	cyt	0			601057		191
P12815 UniProt NPD GO	PDCD6_MOUSE	Programmed cell death protein 6 (Probable calcium-binding protein ALG-2) (PMP41) (ALG-257)	0.17	-	cyt	0		microsome [IDA] soluble fraction [IDA]		1HQV	191
P15873 UniProt NPD GO	PCNA_YEAST	Proliferating cell nuclear antigen (PCNA)	0.17	-	cyt	0	Nucleus	nucleus [IDA] PCNA complex [TAS] replication fork [TAS]		1SXJ	258
P61074 UniProt NPD GO	PCNA_PLAF7	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.17	-	mit	0	Nucleus (By similarity)				274
P31008 UniProt NPD GO	PCNA_PLAFK	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.17	-	mit	0	Nucleus				274
P53358 UniProt NPD GO	PCNA_STYCL	Proliferating cell nuclear antigen (PCNA) (Cyclin)	0.17	-	mit	0	Nucleus				264
Q00265 UniProt NPD GO	PCNA2_DAUCA	Proliferating cell nuclear antigen large form (PCNA) (Cyclin)	0.17	-	cyt	0	Nucleus				365
P04095 UniProt NPD GO	PLF1_MOUSE	Proliferin-1 precursor (Mitogen-regulated protein 1)	0.17	-	mit	0	Secreted protein				224
P06600 UniProt NPD GO	PRP33_DAUCA	Proline-rich 33 kDa extensin-related protein precursor (Fragment)	0.17	-	nuc	0					211
Q19842 UniProt NPD GO	PCCA_CAEEL	Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit alpha) ( ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				724
Q91ZA3 UniProt NPD GO	PCCA_MOUSE	Propionyl-CoA carboxylase alpha chain, mitochondrial precursor (EC 6.4.1.3) (PCCase subunit alpha) ( ...	0.17	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)	mitochondrion [IDA]			724
Q90955 UniProt NPD GO	TEBP_CHICK	Prostaglandin E synthase 3 (EC 5.3.99.3) (Cytosolic prostaglandin E2 synthase) (cPGES) (Telomerase-b ...	0.17	-	nuc	0	Cytoplasm (By similarity)	chromosome, telomeric region [ISS] soluble fraction [IDA] telomerase holoenzyme complex [ISS]			146
Q9XSM0 UniProt NPD GO	PTGDS_SHEEP	Prostaglandin-H2 D-isomerase precursor (EC 5.3.99.2) (Lipocalin-type prostaglandin-D synthase) (Glut ...	0.17	-	exc	0	Endoplasmic reticulum; rough endoplasmic reticulum (By similarity). Detected on rough endoplasmic re ...	extracellular region [IDA] Golgi apparatus [ISS] nuclear envelope [ISS] rough endoplasmic reticulum [ISS]			191
P57096 UniProt NPD GO	PSCA_MOUSE	Prostate stem cell antigen precursor	0.17	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				123
Q9SEL7 UniProt NPD GO	DEGP5_ARATH	Protease Do-like 5, chloroplast precursor (EC 3.4.21.-)	0.17	-	mit	0	Plastid; chloroplast; chloroplast thylakoid lumen				323
Q8RY22 UniProt NPD GO	DEGP7_ARATH	Protease Do-like 7 (EC 3.4.21.-)	0.17	-	cyt	0	Cytoplasm (Potential)				1097
O16811 UniProt NPD GO	PSA71_DROVI	Proteasome subunit alpha type 7-1 (EC 3.4.25.1) (Proteasome 28 kDa subunit 1)	0.17	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				247
Q9N9W8 UniProt NPD GO	PSB3_GIALA	Proteasome subunit beta type 3 (EC 3.4.25.1)	0.17	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				207
Q66HF0 UniProt NPD GO	ARMX6_RAT	Protein ARMCX6	0.17	-	end	0					301
Q8CDT7 UniProt NPD GO	CJ107_MOUSE	Protein C10orf107 homolog	0.17	-	mit	0					208
Q9D882 UniProt NPD GO	CJ035_MOUSE	Protein C10orf35 homolog	0.17	-	nuc	1					120
Q9USW4 UniProt NPD GO	YHZ9_SCHPO	Protein C21B10.09 in chromosome II	0.17	-	end	10	Membrane; multi-pass membrane protein				519
Q96HZ7 UniProt NPD GO	CU119_HUMAN	Protein C21orf119	0.17	-	mit	0					61
Q68US6 UniProt NPD GO	CU119_PANTR	Protein C21orf119 homolog	0.17	-	cyt	0					61
P59052 UniProt NPD GO	CU088_HUMAN	Protein C21orf88	0.17	-	mit	0					145
Q01832 UniProt NPD GO	C4_GIALA	Protein C4	0.17	-	nuc	0					198
Q96KF7 UniProt NPD GO	CF162_HUMAN	Protein C6orf162	0.17	-	nuc	1 *					97
Q9CQQ0 UniProt NPD GO	CF162_MOUSE	Protein C6orf162 homolog	0.17	-	nuc	1 *					97
Q5REX0 UniProt NPD GO	CF162_PONPY	Protein C6orf162 homolog	0.17	-	nuc	1 *					97
Q96LT7 UniProt NPD GO	CI072_HUMAN	Protein C9orf72	0.17	-	cyt	0					481
Q8IYS8 UniProt NPD GO	FA44C_HUMAN	Protein FAM44C	0.17	-	nuc	0					184
Q96KN4 UniProt NPD GO	FA84A_HUMAN	Protein FAM84A (Protein NSE1)	0.17	-	cyt	0					292

You are viewing entries 54751 to 54800 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.