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
Q9WVK0 UniProt NPD GO	ATRAP_MOUSE	Type-1 angiotensin II receptor-associated protein (AT1 receptor-associated protein)	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...	cell cortex [IDA] plasma membrane [IDA]			161
Q5RER2 UniProt NPD GO	ATRAP_PONPY	Type-1 angiotensin II receptor-associated protein (AT1 receptor-associated protein)	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				152
Q642A2 UniProt NPD GO	ATRAP_RAT	Type-1 angiotensin II receptor-associated protein (AT1 receptor-associated protein)	0.00	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity). ...				160
Q28929 UniProt NPD GO	AGTR2_SHEEP	Type-2 angiotensin II receptor (AT2) (Fragment)	0.00	-	end	7 *	Membrane; multi-pass membrane protein				260
Q01758 UniProt NPD GO	ISP2_OSMMO	Type-2 ice-structuring protein precursor (Type II antifreeze protein) (AFP)	0.00	-	exc	0	Secreted protein				175
P20133 UniProt NPD GO	BET2_YEAST	Type-2 proteins geranylgeranyltransferase subunit beta (EC 2.5.1.60) (Type II proteins geranylgerany ...	0.00	-	cyt	0		Rab-protein geranylgeranyltransferase complex [IDA]			325
Q05806 UniProt NPD GO	THN5_WHEAT	Type-5 thionin precursor [Contains: Type-5 thionin (Type V thionin); Acidic protein]	0.00	-	cyt	0	Secreted protein (Potential)				131
P80969 UniProt NPD GO	THT10_TOBAC	Tyramine N-feruloyltransferase 10/30 (EC 2.3.1.110) (Hydroxycinnamoyl-CoA: tyramine N-hydroxycinnamo ...	0.00	-	cyt	0	Cytoplasm (Potential)				226
Q9SMB8 UniProt NPD GO	THT11_TOBAC	Tyramine N-feruloyltransferase 4/11 (EC 2.3.1.110) (Hydroxycinnamoyl-CoA: tyramine N-hydroxycinnamoy ...	0.00	-	cyt	0	Cytoplasm (Potential)				226
P33447 UniProt NPD GO	ATTY_TRYCR	Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)	0.00	-	cyt	0	Cytoplasm. Mainly. Mitochondrion. Present to a small extent in the mitochondrial fraction			1BW0	416
P11681 UniProt NPD GO	ABL_CALVI	Tyrosine-protein kinase ABL (EC 2.7.10.2) (Fragment)	0.00	-	cyt	0	Cytoplasm				74
Q2HJH0 UniProt NPD GO	LSM5_BOVIN	U6 snRNA-associated Sm-like protein LSm5	0.00	-	cyt	0	Nucleus (By similarity)				90
Q9Y4Y9 UniProt NPD GO	LSM5_HUMAN	U6 snRNA-associated Sm-like protein LSm5	0.00	-	cyt	0	Nucleus (By similarity)	nucleus [TAS]	607285		90
P62322 UniProt NPD GO	LSM5_MOUSE	U6 snRNA-associated Sm-like protein LSm5	0.00	-	cyt	0	Nucleus (By similarity)				90
Q5R628 UniProt NPD GO	LSM5_PONPY	U6 snRNA-associated Sm-like protein LSm5	0.00	-	cyt	0	Nucleus (By similarity)				90
P40089 UniProt NPD GO	LSM5_YEAST	U6 snRNA-associated Sm-like protein LSm5	0.00	-	cyt	0	Nucleus	nucleolus [IDA] small nucleolar ribonucleoprotein complex [IPI] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			93
Q6YC49 UniProt NPD GO	S35A3_BOVIN	UDP-N-acetylglucosamine transporter (Golgi UDP-GlcNAc transporter) (Solute carrier family 35 member ...	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				326
Q8R1T4 UniProt NPD GO	S35A3_MOUSE	UDP-N-acetylglucosamine transporter (Golgi UDP-GlcNAc transporter) (Solute carrier family 35 member ...	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				326
Q6AXR5 UniProt NPD GO	S35A3_RAT	UDP-N-acetylglucosamine transporter (Golgi UDP-GlcNAc transporter) (Solute carrier family 35 member ...	0.00	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)				326
P24140 UniProt NPD GO	GPT_CRIGR	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				408
P23338 UniProt NPD GO	GPT_CRILO	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein				408
P42867 UniProt NPD GO	GPT_MOUSE	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.00	-	end	10 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [TAS]			410
P07286 UniProt NPD GO	GPT_YEAST	UDP-N-acetylglucosamine--dolichyl-phosphate N-acetylglucosaminephosphotransferase (EC 2.7.8.15) (GPT ...	0.00	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum [IC]			448
P81436 UniProt NPD GO	OGT1_RABIT	UDP-N-acetylglucosamine--peptide N-acetylglucosaminyltransferase 110 kDa subunit (EC 2.4.1.-) (O-Glc ...	0.00	-	cyt	0	Nucleus (Potential)				37
Q14376 UniProt NPD GO	GALE_HUMAN	UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.00	-	cyt	0			230350	1I3N	348
Q8R059 UniProt NPD GO	GALE_MOUSE	UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.00	-	cyt	0					347
O65780 UniProt NPD GO	GALE1_CYATE	UDP-glucose 4-epimerase GEPI42 (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.00	-	cyt	0					354
O65781 UniProt NPD GO	GALE2_CYATE	UDP-glucose 4-epimerase GEPI48 (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.00	-	cyt	0					350
O01578 UniProt NPD GO	YXX3_CAEEL	UPF0041 protein F53F10.3	0.00	-	cyt	0					133
Q21828 UniProt NPD GO	YNFD_CAEEL	UPF0041 protein R07E5.13	0.00	-	mit	2 *					160
P53311 UniProt NPD GO	YG56_YEAST	UPF0041 protein YGR243W	0.00	-	mit	0		mitochondrion [IDA]			146
P35195 UniProt NPD GO	ECM15_YEAST	UPF0045 protein ECM15 (Extracellular matrix protein 15)	0.00	-	cyt	0	Cytoplasm. Nucleus	cytoplasm [IDA] nucleus [IDA]		1LXJ	104
P36088 UniProt NPD GO	YKG9_YEAST	UPF0067 protein YKL069W	0.00	-	cyt	0		cytoplasm [IDA] nucleus [IDA]		1F5M	180
P61165 UniProt NPD GO	CK010_HUMAN	UPF0197 protein C11orf10	0.00	-	end	2 *					79
Q32P84 UniProt NPD GO	CK010_BOVIN	UPF0197 protein C11orf10 homolog	0.00	-	end	2 *					79
Q6PBS6 UniProt NPD GO	CK010_BRARE	UPF0197 protein C11orf10 homolog	0.00	-	end	2 *					79
P61166 UniProt NPD GO	CK010_MOUSE	UPF0197 protein C11orf10 homolog	0.00	-	end	2 *					79
Q6GP81 UniProt NPD GO	CK010_XENLA	UPF0197 protein C11orf10 homolog	0.00	-	end	2 *					79
Q6DDB3 UniProt NPD GO	CK010_XENTR	UPF0197 protein C11orf10 homolog	0.00	-	end	2 *					79
Q60WL8 UniProt NPD GO	U197_CAEBR	UPF0197 protein CBG19073	0.00	-	end	2 *					79
Q965T1 UniProt NPD GO	U197_CAEEL	UPF0197 protein Y57E12AM.1	0.00	-	end	2 *					79
Q9P0R6 UniProt NPD GO	CN129_HUMAN	UPF0279 protein C14orf129	0.00	-	cyt	0				1SGO	139
Q8BGR8 UniProt NPD GO	CN129_MOUSE	UPF0279 protein C14orf129 homolog	0.00	-	cyt	0					139
O13748 UniProt NPD GO	YDRE_SCHPO	UPF0351 protein C16E8.14c	0.00	-	cyt	0					219
Q9LKG7 UniProt NPD GO	UGPA_ASTME	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.00	-	cyt	0	Cytoplasm (By similarity)				471
Q43772 UniProt NPD GO	UGPA_HORVU	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.00	-	cyt	0	Cytoplasm				473
P19595 UniProt NPD GO	UGPA_SOLTU	UTP--glucose-1-phosphate uridylyltransferase (EC 2.7.7.9) (UDP-glucose pyrophosphorylase) (UDPGP) (U ...	0.00	-	cyt	0	Cytoplasm				476
P57751 UniProt NPD GO	UGPA1_ARATH	UTP--glucose-1-phosphate uridylyltransferase 1 (EC 2.7.7.9) (UDP-glucose pyrophosphorylase 1) (UDPGP ...	0.00	-	cyt	0	Cytoplasm (By similarity)				470
Q9V3R8 UniProt NPD GO	UBIA1_DROME	UbiA prenyltransferase domain-containing protein 1 homolog (Protein heix)	0.00	-	end	8	Membrane; multi-pass membrane protein (Potential)				359
O14957 UniProt NPD GO	UCR11_HUMAN	Ubiquinol-cytochrome c reductase complex 6.4 kDa protein (EC 1.10.2.2) (Complex III subunit XI)	0.00	-	mit	1 *	Mitochondrion; mitochondrial inner membrane		609711		56

You are viewing entries 98451 to 98500 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.