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
O08859 UniProt NPD GO	TSG6_MOUSE	Tumor necrosis factor-inducible protein TSG-6 precursor (TNF-stimulated gene 6 protein)	0.01	-	end	0					275
P98065 UniProt NPD GO	TSG6_RABIT	Tumor necrosis factor-inducible protein TSG-6 precursor (TNF-stimulated gene 6 protein) (Hyaluronate ...	0.01	-	cyt	0					276
P98066 UniProt NPD GO	TSG6_HUMAN	Tumor necrosis factor-inducible protein TSG-6 precursor (TNF-stimulated gene 6 protein) (Hyaluronate ...	0.01	-	end	0			600410	1O7C	277
Q5EBF8 UniProt NPD GO	ATRAP_XENTR	Type-1 angiotensin II receptor-associated protein-like	0.01	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				163
P35373 UniProt NPD GO	AGTRM_XENLA	Type-1-like angiotensin II receptor 2 (AT1)	0.01	-	end	7 *	Membrane; multi-pass membrane protein				363
P46960 UniProt NPD GO	PTB1_SCHPO	Type-2 proteins geranylgeranyltransferase subunit beta (EC 2.5.1.60) (Type II proteins geranylgerany ...	0.01	-	cyt	0					311
Q06086 UniProt NPD GO	TYDC2_PETCR	Tyrosine decarboxylase 2 (EC 4.1.1.25)	0.01	-	cyt	0					514
Q06087 UniProt NPD GO	TYDC3_PETCR	Tyrosine decarboxylase 3 (EC 4.1.1.25)	0.01	-	cyt	0					516
Q06088 UniProt NPD GO	TYDC4_PETCR	Tyrosine decarboxylase 4 (EC 4.1.1.25)	0.01	-	cyt	0					508
P41239 UniProt NPD GO	CSK_CHICK	Tyrosine-protein kinase CSK (EC 2.7.10.2) (C-SRC kinase)	0.01	-	cyt	0	Cytoplasm (Probable)				450
P32577 UniProt NPD GO	CSK_RAT	Tyrosine-protein kinase CSK (EC 2.7.10.2) (C-SRC kinase)	0.01	-	cyt	0	Cytoplasm (By similarity). Mainly. Cell membrane (By similarity). Also present in lipid rafts (By si ...			1K9A	450
P41240 UniProt NPD GO	CSK_HUMAN	Tyrosine-protein kinase CSK (EC 2.7.10.2) (C-SRC kinase) (Protein-tyrosine kinase CYL)	0.01	-	cyt	0	Cytoplasm (By similarity). Mainly. Cell membrane (By similarity). Also present in lipid rafts (By si ...	cytoplasm [TAS] plasma membrane [IPI]	124095	1CSK	450
P41241 UniProt NPD GO	CSK_MOUSE	Tyrosine-protein kinase CSK (EC 2.7.10.2) (C-SRC kinase) (Protein-tyrosine kinase MPK-2) (p50CSK)	0.01	-	cyt	0	Cytoplasm. Mainly. Cell membrane. Also present in lipid rafts	intercellular junction [IDA] plasma membrane [TAS]		1JEG	450
Q9UUI1 UniProt NPD GO	LSM6_SCHPO	U6 snRNA-associated Sm-like protein LSm6	0.01	-	cyt	0	Nucleus (By similarity)				75
Q3ZCE0 UniProt NPD GO	LSM8_BOVIN	U6 snRNA-associated Sm-like protein LSm8	0.01	-	cyt	0	Nucleus (Potential)				95
O95777 UniProt NPD GO	LSM8_HUMAN	U6 snRNA-associated Sm-like protein LSm8	0.01	-	cyt	0	Nucleus (Potential)	nucleus [NAS]	607288		95
Q6ZWM4 UniProt NPD GO	LSM8_MOUSE	U6 snRNA-associated Sm-like protein LSm8	0.01	-	cyt	0					95
Q5RCP3 UniProt NPD GO	LSM8_PONPY	U6 snRNA-associated Sm-like protein LSm8	0.01	-	cyt	0	Nucleus (Potential)				95
O74483 UniProt NPD GO	LSM8_SCHPO	U6 snRNA-associated Sm-like protein LSm8	0.01	-	cyt	0	Nucleus (By similarity)				94
Q6FV75 UniProt NPD GO	ALG14_CANGA	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.01	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				242
Q6CJG3 UniProt NPD GO	ALG14_KLULA	UDP-N-acetylglucosamine transferase subunit ALG14 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.01	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				236
Q4WQN1 UniProt NPD GO	ALG13_ASPFU	UDP-N-acetylglucosamine transferase subunit alg13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.01	-	cyt	0	Endoplasmic reticulum (By similarity)				152
O14190 UniProt NPD GO	ALG13_SCHPO	UDP-N-acetylglucosamine transferase subunit alg13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.01	-	cyt	0	Endoplasmic reticulum (By similarity)				162
O77592 UniProt NPD GO	S35A3_CANFA	UDP-N-acetylglucosamine transporter (Golgi UDP-GlcNAc transporter) (Solute carrier family 35 member ...	0.01	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein				326
Q9Y2D2 UniProt NPD GO	S35A3_HUMAN	UDP-N-acetylglucosamine transporter (Golgi UDP-GlcNAc transporter) (Solute carrier family 35 member ...	0.01	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	Golgi apparatus [TAS]	605632		325
Q58DA6 UniProt NPD GO	S35A2_BOVIN	UDP-galactose translocator (UDP-galactose transporter) (UGT) (UDP-Gal-Tr) (Solute carrier family 35 ...	0.01	-	end	8 *	Membrane; multi-pass membrane protein (By similarity)				393
P78381 UniProt NPD GO	S35A2_HUMAN	UDP-galactose translocator (UDP-galactose transporter) (UGT) (UDP-Gal-Tr) (Solute carrier family 35 ...	0.01	-	end	8 *	Membrane; multi-pass membrane protein		314375		396
Q6CR04 UniProt NPD GO	HUT1_KLULA	UDP-galactose transporter homolog 1	0.01	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				339
P18645 UniProt NPD GO	GALE_RAT	UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.01	-	cyt	0					347
Q28612 UniProt NPD GO	UD14_RABIT	UDP-glucuronosyltransferase 1-4 precursor (EC 2.4.1.17) (UDPGT) (UGT1*4) (UGT1-04) (UGT1.4) (UGT1A4) ...	0.01	-	end	1	Microsome				532
P08542 UniProt NPD GO	UDB3_RAT	UDP-glucuronosyltransferase 2B3 precursor (EC 2.4.1.17) (UDPGT) (Testosterone, dihydrotestosterone, ...	0.01	-	end	1	Microsome				530
Q6K1J1 UniProt NPD GO	UDB31_CANFA	UDP-glucuronosyltransferase 2B31 precursor (EC 2.4.1.17) (UDPGT)	0.01	-	nuc	1	Microsome				530
Q10320 UniProt NPD GO	YD68_SCHPO	UPF0016 protein C17G8.08c	0.01	-	end	7 *	Membrane; multi-pass membrane protein (Potential)				287
O94725 UniProt NPD GO	YCFD_SCHPO	UPF0364 protein C1393.13	0.01	-	cyt	0					442
Q9UT55 UniProt NPD GO	YI94_SCHPO	UPF0364 protein C806.04c	0.01	-	cyt	0					440
Q5BJC2 UniProt NPD GO	U373_BRARE	UPF0373 protein precursor	0.01	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				72
Q5ZII6 UniProt NPD GO	U373_CHICK	UPF0373 protein precursor	0.01	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				72
Q28FL7 UniProt NPD GO	U373_XENTR	UPF0373 protein precursor	0.01	-	exc	2 *	Membrane; single-pass type I membrane protein (Potential)				72
Q9SDX3 UniProt NPD GO	UGPA_MUSAC	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.01	-	cyt	0	Cytoplasm (By similarity)				467
Q5ZKS8 UniProt NPD GO	UBIA1_CHICK	UbiA prenyltransferase domain-containing protein 1	0.01	-	end	7	Membrane; multi-pass membrane protein (Potential)				333
Q9DC60 UniProt NPD GO	UBIA1_MOUSE	UbiA prenyltransferase domain-containing protein 1	0.01	-	end	7	Membrane; multi-pass membrane protein. Cytoplasm. Nucleus (By similarity)				336
Q28HR4 UniProt NPD GO	UBIA1_XENTR	UbiA prenyltransferase domain-containing protein 1	0.01	-	end	7	Membrane; multi-pass membrane protein (Potential)				345
Q9Y5Z9 UniProt NPD GO	UBIA1_HUMAN	UbiA prenyltransferase domain-containing protein 1 (Transitional epithelial response protein 1)	0.01	-	end	7	Membrane; multi-pass membrane protein. Cytoplasm. Nucleus				338
P07552 UniProt NPD GO	UCR11_BOVIN	Ubiquinol-cytochrome c reductase complex 6.4 kDa protein (EC 1.10.2.2) (Complex III subunit XI)	0.01	-	mit	1 *	Mitochondrion; mitochondrial inner membrane			1SQX	56
P46269 UniProt NPD GO	UCRQ_SOLTU	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (EC 1.10.2.2) (Ubiquinol-cy ...	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane				71
P08525 UniProt NPD GO	UCRQ_YEAST	Ubiquinol-cytochrome c reductase complex ubiquinone-binding protein QP-C (Ubiquinol-cytochrome c red ...	0.01	-	cyt	1	Mitochondrion; mitochondrial inner membrane	respiratory chain complex III (sensu Eukary... [IDA]		1P84	94
P08067 UniProt NPD GO	UCRI_YEAST	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Complex ...	0.01	-	mit	0		respiratory chain complex III (sensu Eukary... [IDA]		1P84	215
Q69BK1 UniProt NPD GO	UCRI_CERAE	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane (By similarity)				274
P07056 UniProt NPD GO	UCRI_NEUCR	Ubiquinol-cytochrome c reductase iron-sulfur subunit, mitochondrial precursor (EC 1.10.2.2) (Rieske ...	0.01	-	mit	0	Mitochondrion; mitochondrial inner membrane				231
P35122 UniProt NPD GO	UCHL_DROME	Ubiquitin carboxyl-terminal hydrolase (EC 3.4.19.12) (Ubiquitin thioesterase)	0.01	-	cyt	0					227

You are viewing entries 91901 to 91950 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.