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
Q6BMB8 UniProt NPD GO	TPIS_DEBHA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0					248
Q6CJG5 UniProt NPD GO	TPIS_KLULA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0					248
Q27775 UniProt NPD GO	TPIS_SCHJA	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	mit	0					252
P55275 UniProt NPD GO	TPIS_HELVI	Triosephosphate isomerase (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase) (Fragment)	0.03	-	nuc	0					215
Q9M4S8 UniProt NPD GO	TPIC_FRAAN	Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	mit	0	Plastid; chloroplast (By similarity)				314
P46225 UniProt NPD GO	TPIC_SECCE	Triosephosphate isomerase, chloroplast precursor (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	mit	0	Plastid; chloroplast				298
P34937 UniProt NPD GO	TPIS_HORVU	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0	Cytoplasm				252
P48494 UniProt NPD GO	TPIS_ORYSA	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0	Cytoplasm (Probable)				252
P46226 UniProt NPD GO	TPIS_SECCE	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	cyt	0	Cytoplasm (Probable)				252
P48497 UniProt NPD GO	TPIS_STELP	Triosephosphate isomerase, cytosolic (EC 5.3.1.1) (TIM) (Triose-phosphate isomerase)	0.03	-	mit	0	Cytoplasm (Probable)				257
P13438 UniProt NPD GO	TSP_MOUSE	Trophoblast-specific protein alpha precursor	0.03	-	exc	0	Secreted protein; extracellular space (Probable)				124
P35622 UniProt NPD GO	TNNC_PATYE	Troponin C (TN-C)	0.03	-	cyt	0					152
Q9BLG0 UniProt NPD GO	TNNC_TODPA	Troponin C (TN-C)	0.03	-	cyt	0					147
P13110 UniProt NPD GO	TYTR_TRYCO	Trypanothione reductase (EC 1.8.1.12) (TR) (N(1),N(8)-bis(glutathionyl)spermidine reductase)	0.03	-	cyt	0	Cytoplasm				492
O60993 UniProt NPD GO	TRYS_CRIFA	Trypanothione synthetase (EC 6.3.1.9) (Cf-TS)	0.03	-	cyt	0					652
Q26327 UniProt NPD GO	DAFT_TRYCR	Trypomastigote decay-accelerating factor (T-DAF) (Fragment)	0.03	-	cyt	0					95
P32822 UniProt NPD GO	TRYB_RAT	Trypsin V-B precursor (EC 3.4.21.4)	0.03	-	exc	0	Secreted protein; extracellular space				246
P25849 UniProt NPD GO	ITR1_LUFCY	Trypsin inhibitor 1 (Trypsin inhibitor I) (LCTI-I)	0.03	-	nuc	0	Secreted protein				29
Q4GWU5 UniProt NPD GO	SFTI1_HELAN	Trypsin inhibitor 1 precursor (SFTI-1)	0.03	-	mit	1 *				2AB9	56
P09407 UniProt NPD GO	ITI3_MOMCH	Trypsin inhibitor MCI-3	0.03	-	cyt	0					62
P35037 UniProt NPD GO	TRY3_ANOGA	Trypsin-3 precursor (EC 3.4.21.4)	0.03	-	exc	0	Secreted protein				275
P80211 UniProt NPD GO	ATSI_AMACA	Trypsin/subtilisin inhibitor (ATSI)	0.03	-	cyt	0	Secreted protein				69
Q9NRR2 UniProt NPD GO	TRYG1_HUMAN	Tryptase gamma precursor (EC 3.4.21.-) (Transmembrane tryptase) [Contains: Tryptase gamma light chai ...	0.03	-	end	1	Membrane; single-pass membrane protein (Potential)	integral to plasma membrane [TAS]	609341		321
Q02844 UniProt NPD GO	TRYB1_MOUSE	Tryptase precursor (EC 3.4.21.59) (Mast cell protease 7) (MMCP-7) (Tryptase alpha/beta-1)	0.03	-	exc	0					273
P27435 UniProt NPD GO	TRYB1_RAT	Tryptase precursor (EC 3.4.21.59) (Mast cell protease 7) (MMCP-7) (Tryptase alpha/beta-1) (Tryptase, ...	0.03	-	exc	0	Released from the secretory granules upon mast cell activation				273
P24920 UniProt NPD GO	TRPC_PHYPR	Tryptophan biosynthesis protein TRP1 [Includes: Indole-3-glycerol phosphate synthase (EC 4.1.1.48) ( ...	0.03	-	cyt	0					531
P34793 UniProt NPD GO	TRPA2_CYACA	Tryptophan synthase alpha chain (EC 4.2.1.20)	0.03	-	cyt	0	Plastid; chloroplast				242
P43283 UniProt NPD GO	TRPB1_MAIZE	Tryptophan synthase beta chain 1 (EC 4.2.1.20) (Orange pericarp 1) (Fragment)	0.03	-	cyt	0	Plastid; chloroplast (Probable)				389
Q5R6K7 UniProt NPD GO	WRB_PONPY	Tryptophan-rich protein	0.03	-	end	3 *	Nucleus (By similarity)				174
Q6P6S5 UniProt NPD GO	WRB_RAT	Tryptophan-rich protein	0.03	-	end	3 *	Nucleus (By similarity)				174
O00258 UniProt NPD GO	WRB_HUMAN	Tryptophan-rich protein (Congenital heart disease 5 protein)	0.03	-	end	3 *	Nucleus	nucleus [TAS]	602915		174
Q9HFQ3 UniProt NPD GO	TBB_MELLI	Tubulin beta chain (Beta tubulin)	0.03	-	cyt	0					448
Q8WZE0 UniProt NPD GO	TBB_USTVI	Tubulin beta chain (Beta tubulin)	0.03	-	cyt	0					444
P06804 UniProt NPD GO	TNFA_MOUSE	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.03	-	mit	1 *	Cell membrane; single-pass type II membrane protein. Processed form: Secreted protein. Also exists a ...	extracellular space [IDA] integral to plasma membrane [TAS] plasma membrane [IDA] secretory granule [TAS]		2TNF	235
P23563 UniProt NPD GO	TNFA_PIG	Tumor necrosis factor precursor (TNF-alpha) (Tumor necrosis factor ligand superfamily member 2) (TNF ...	0.03	-	mit	1 *	Cell membrane; single-pass type II membrane protein (By similarity). Processed form: Secreted protei ...				232
Q9WV26 UniProt NPD GO	AGTR1_CAVPO	Type-1 angiotensin II receptor (AT1)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				359
O35210 UniProt NPD GO	AGTR1_MERUN	Type-1 angiotensin II receptor (AT1) (GKAT1)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				359
P29089 UniProt NPD GO	AGTRB_RAT	Type-1B angiotensin II receptor (AT1B) (AT3)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				359
P35374 UniProt NPD GO	AGTR2_MOUSE	Type-2 angiotensin II receptor (AT2)	0.03	-	end	7 *	Membrane; multi-pass membrane protein				363
P19614 UniProt NPD GO	ANPC_MACAM	Type-3 ice-structuring protein HPLC 12 (ISP type III HPLC 12) (Antifreeze protein QAE(HPLC 12))	0.03	-	cyt	0				9MSI	66
Q58CZ9 UniProt NPD GO	ATTY_BOVIN	Tyrosine aminotransferase (EC 2.6.1.5) (L-tyrosine:2-oxoglutarate aminotransferase) (TAT)	0.03	-	cyt	0					447
Q7XHL3 UniProt NPD GO	TYDC1_ORYSA	Tyrosine decarboxylase 1 (EC 4.1.1.25)	0.03	-	cyt	0					497
P28217 UniProt NPD GO	PTP25_STYPL	Tyrosine-protein phosphatase 25 (EC 3.1.3.48) (Fragment)	0.03	-	cyt	0					117
P28200 UniProt NPD GO	PTP8_STYPL	Tyrosine-protein phosphatase 8 (EC 3.1.3.48) (Fragment)	0.03	-	nuc	0					112
P47093 UniProt NPD GO	LSM8_YEAST	U6 snRNA-associated Sm-like protein LSm8	0.03	-	nuc	0	Nucleus. Cytoplasm	nucleus [IDA] snRNP U6 [IDA] U4/U6 x U5 tri-snRNP complex [IDA]			128
Q6FVR6 UniProt NPD GO	ALG13_CANGA	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.03	-	cyt	0	Endoplasmic reticulum (By similarity)				198
Q6CXY0 UniProt NPD GO	ALG13_KLULA	UDP-N-acetylglucosamine transferase subunit ALG13 (EC 2.4.1.-) (Asparagine linked glycosylation prot ...	0.03	-	cyt	0	Endoplasmic reticulum (By similarity)				197
Q755H7 UniProt NPD GO	HUT1_ASHGO	UDP-galactose transporter homolog 1	0.03	-	end	8 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				324
Q93890 UniProt NPD GO	SRF3_CAEEL	UDP-galactose/UDP-N-acetylglucosamine transporter srf-3 (Surface antigenicity abnormal 3)	0.03	-	end	8 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein	integral to Golgi membrane [IDA]			328
Q42605 UniProt NPD GO	GALE1_ARATH	UDP-glucose 4-epimerase (EC 5.1.3.2) (Galactowaldenase) (UDP-galactose 4-epimerase)	0.03	-	cyt	0					351

You are viewing entries 81901 to 81950 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.