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
Q9VC99 UniProt NPD GO	UCK_DROME	Probable uridine-cytidine kinase (EC 2.7.1.48) (UCK) (Uridine monophosphokinase) (Cytidine monophosp ...	0.05	-	nuc	0					260
Q9YGI1 UniProt NPD GO	TXW3_NAJAT	Probable weak neurotoxin NNAM3 precursor	0.05	-	mit	1 *	Secreted protein				86
Q9FIS2 UniProt NPD GO	ZIP12_ARATH	Probable zinc transporter 12 precursor (ZRT/IRT-like protein 12)	0.05	-	end	9 *	Cell membrane; multi-pass membrane protein (Potential)				355
Q9R0B9 UniProt NPD GO	PLOD2_MOUSE	Procollagen-lysine,2-oxoglutarate 5-dioxygenase 2 precursor (EC 1.14.11.4) (Lysyl hydroxylase 2) (LH ...	0.05	-	mit	0	Endoplasmic reticulum; rough endoplasmic reticulum; rough endoplasmic reticulum cisterna; peripheral ...				737
P67857 UniProt NPD GO	PRCT_CARMA	Proctolin	0.05	-		0	Secreted protein				5
P67858 UniProt NPD GO	PRCT_LIMPO	Proctolin	0.05	-		0	Secreted protein				5
P67859 UniProt NPD GO	PRCT_PERAM	Proctolin	0.05	-		0	Secreted protein				5
P49230 UniProt NPD GO	PROF_ENTHI	Profilin	0.05	-	cyt	0					130
Q32PB1 UniProt NPD GO	PROF3_BOVIN	Profilin-3	0.05	-	cyt	0					137
Q6TCG8 UniProt NPD GO	PAQR3_MOUSE	Progestin and adipoQ receptor family member 3 (Progestin and adipoQ receptor family member III)	0.05	-	end	7	Membrane; multi-pass membrane protein (Potential)				311
Q9IA10 UniProt NPD GO	GON1_DICLA	Progonadoliberin-1 precursor (Progonadoliberin I) [Contains: Gonadoliberin-1 (Gonadoliberin I) (Lute ...	0.05	-	exc	0	Secreted protein				99
P14676 UniProt NPD GO	PRL_CHICK	Prolactin precursor (PRL)	0.05	-	end	0	Secreted protein				229
O82134 UniProt NPD GO	PCNA_PEA	Proliferating cell nuclear antigen	0.05	-	mit	0	Nucleus				266
Q9PTP1 UniProt NPD GO	PCNA_BRARE	Proliferating cell nuclear antigen (PCNA)	0.05	-	cyt	0	Nucleus (By similarity)	nucleus [IDA]			260
O02115 UniProt NPD GO	PCNA_CAEEL	Proliferating cell nuclear antigen (PCNA)	0.05	-	cyt	0	Nucleus				229
O94903 UniProt NPD GO	PROSC_HUMAN	Proline synthetase co-transcribed bacterial homolog protein	0.05	-	cyt	0		cytoplasm [TAS]	604436		275
Q9QUR6 UniProt NPD GO	PPCE_MOUSE	Prolyl endopeptidase (EC 3.4.21.26) (Post-proline cleaving enzyme) (PE)	0.05	-	nuc	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			710
O14684 UniProt NPD GO	PTGES_HUMAN	Prostaglandin E synthase (EC 5.3.99.3) (Microsomal glutathione S-transferase 1-like 1) (MGST1-L1) (p ...	0.05	-	nuc	2 *	Membrane; multi-pass membrane protein (Potential)	membrane fraction [TAS]	605172		152
Q9ESD1 UniProt NPD GO	PRSS8_MOUSE	Prostasin precursor (EC 3.4.21.-) (Channel-activating protease 1) [Contains: Prostasin light chain; ...	0.05	-	exc	0	Prostasin: Cell membrane; single-pass membrane protein (By similarity). Prostasin light chain, prost ...				342
Q16651 UniProt NPD GO	PRSS8_HUMAN	Prostasin precursor (EC 3.4.21.-) [Contains: Prostasin light chain; Prostasin heavy chain]	0.05	-	exc	0	Prostasin: Cell membrane; single-pass membrane protein. Prostasin light chain, prostasin heavy chain ...	extracellular region [TAS] extracellular space [TAS] plasma membrane [TAS]	600823		343
P01094 UniProt NPD GO	IPA3_YEAST	Protease A inhibitor 3 (Proteinase inhibitor I(A)3) (Saccharopepsin inhibitor) (Proteinase yscA-inhi ...	0.05	-	nuc	0		cytoplasm [TAS]		1G0V	68
Q9LU10 UniProt NPD GO	DEGP8_ARATH	Protease Do-like 8, chloroplast precursor (EC 3.4.21.-)	0.05	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid lumen (Probable)				448
P82968 UniProt NPD GO	MCPI_MELCP	Protease inhibitor (McaPI)	0.05	-	nuc	0					197
Q9BSG0 UniProt NPD GO	PAP21_HUMAN	Protease-associated domain-containing protein of 21 kDa precursor (hPAP21)	0.05	-	exc	1 *	Secreted protein	extracellular region [IDA]			188
Q9UL46 UniProt NPD GO	PSME2_HUMAN	Proteasome activator complex subunit 2 (Proteasome activator 28-subunit beta) (PA28beta) (PA28b) (Ac ...	0.05	-	cyt	0		proteasome complex (sensu Eukaryota) [TAS]	602161		238
P23724 UniProt NPD GO	PSB1_YEAST	Proteasome component C5 (EC 3.4.25.1) (Multicatalytic endopeptidase complex subunit C5)	0.05	-	cyt	0	Cytoplasm. Nucleus	proteasome core complex, beta-subunit compl... [IPI]		2FNY	241
P34066 UniProt NPD GO	PSA1A_ARATH	Proteasome subunit alpha type 1-A (EC 3.4.25.1) (Proteasome subunit alpha type 6) (20S proteasome al ...	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				278
O81148 UniProt NPD GO	PSA4_ARATH	Proteasome subunit alpha type 4 (EC 3.4.25.1) (Proteasome subunit alpha type 3) (20S proteasome alph ...	0.05	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				250
Q9XZJ4 UniProt NPD GO	PSA6_DROME	Proteasome subunit alpha type 6 (EC 3.4.25.1) (20S proteasome subunit alpha-1)	0.05	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				244
O24030 UniProt NPD GO	PSA7_LYCES	Proteasome subunit alpha type 7 (EC 3.4.25.1) (20S proteasome alpha subunit D) (20S proteasome subun ...	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				259
Q9IB84 UniProt NPD GO	PSB11_CARAU	Proteasome subunit beta type 1-A (EC 3.4.25.1) (20S proteasome beta 6 subunit A) (B6-A)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				238
Q9IB83 UniProt NPD GO	PSB12_CARAU	Proteasome subunit beta type 1-B (EC 3.4.25.1) (20S proteasome beta 6 subunit B) (B6-B)	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				237
O24361 UniProt NPD GO	PSB5_SPIOL	Proteasome subunit beta type 5 precursor (EC 3.4.25.1) (20S proteasome subunit E) (Proteasome epsilo ...	0.05	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				272
P15649 UniProt NPD GO	7E_DICDI	Protein 7E	0.05	-	nuc	0					97
Q13015 UniProt NPD GO	AF1Q_HUMAN	Protein AF1q	0.05	-	cyt	0			604684		90
Q8LAW2 UniProt NPD GO	AFR_ARATH	Protein AFR (Protein ATTENUATED FAR-RED RESPONSE)	0.05	-	cyt	0					372
P54121 UniProt NPD GO	AIG2_ARATH	Protein AIG2	0.05	-	cyt	0					170
P39945 UniProt NPD GO	AST2_YEAST	Protein AST2	0.05	-	cyt	0		cytoplasm [IDA]			430
Q6P8Z1 UniProt NPD GO	MYCB_MOUSE	Protein B-Myc	0.05	-	nuc	0	Nucleus	spindle [IDA]			170
Q5SWW7 UniProt NPD GO	CJ055_HUMAN	Protein C10orf55	0.05	-	nuc	0					151
Q568T4 UniProt NPD GO	CK073_BRARE	Protein C11orf73 homolog	0.05	-	cyt	0	Cytoplasm (By similarity)				197
Q9UUI8 UniProt NPD GO	YIY4_SCHPO	Protein C22F8.04 in chromosome I	0.05	-	end	10	Membrane; multi-pass membrane protein				383
Q9GKT6 UniProt NPD GO	CB032_MACFA	Protein C2orf32 homolog	0.05	-	cyt	0					164
Q969F1 UniProt NPD GO	CF051_HUMAN	Protein C6orf51	0.05	-	cyt	0					213
Q96GE9 UniProt NPD GO	CI123_HUMAN	Protein C9orf123	0.05	-	cyt	2 *	Membrane; multi-pass membrane protein (Potential)				116
Q5W0N0 UniProt NPD GO	CI057_HUMAN	Protein C9orf57	0.05	-	cyt	1 *	Membrane; single-pass membrane protein (Potential)				161
Q8N6L7 UniProt NPD GO	CI071_HUMAN	Protein C9orf71	0.05	-	end	2 *	Membrane; multi-pass membrane protein (Potential)				170
Q90773 UniProt NPD GO	CEPU1_CHICK	Protein CEPU-1 precursor	0.05	-	cyt	1 *	Cell membrane; lipid-anchor; GPI-anchor				353
P40526 UniProt NPD GO	DFG10_YEAST	Protein DFG10	0.05	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				253
P32601 UniProt NPD GO	DSS4_YEAST	Protein DSS4	0.05	-	nuc	0		membrane fraction [IDA] soluble fraction [IDA]			143

You are viewing entries 75351 to 75400 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.