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
Q90ZK5 UniProt NPD GO	DRG2_PHYBI	Dermaseptin DRG2 precursor (Dermaseptin-2)	0.04	-	exc	0	Secreted protein (Probable)				77
O93451 UniProt NPD GO	DMS1_PACDA	Dermaseptin PD-1-5 precursor	0.04	-	exc	0	Secreted protein				77
O93452 UniProt NPD GO	DMS2_PACDA	Dermaseptin PD-2-2 precursor	0.04	-	exc	0	Secreted protein				75
Q01612 UniProt NPD GO	SAT1_MESAU	Diamine acetyltransferase 1 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 1) (SSAT) (SSA ...	0.04	-	cyt	0	Cytoplasm				171
Q96F10 UniProt NPD GO	SAT2_HUMAN	Diamine acetyltransferase 2 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 2) (Polyamine ...	0.04	-	cyt	0	Intracellular organelles			2BEI	170
Q6P8J2 UniProt NPD GO	SAT2_MOUSE	Diamine acetyltransferase 2 (EC 2.3.1.57) (Spermidine/spermine N(1)-acetyltransferase 2) (Polyamine ...	0.04	-	cyt	0	Intracellular organelles (By similarity)				170
P14721 UniProt NPD GO	DFRA_ANTMA	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase)	0.04	-	nuc	0					446
P51102 UniProt NPD GO	DFRA_ARATH	Dihydroflavonol-4-reductase (EC 1.1.1.219) (DFR) (Dihydrokaempferol 4-reductase) (TRANSPARENT TESTA ...	0.04	-	cyt	0					382
Q9U8B8 UniProt NPD GO	DYR_HELVI	Dihydrofolate reductase (EC 1.5.1.3)	0.04	-	cyt	0					185
Q04933 UniProt NPD GO	DLDH_TRYBB	Dihydrolipoyl dehydrogenase (EC 1.8.1.4) (Dihydrolipoamide dehydrogenase)	0.04	-	nuc	0					479
P08461 UniProt NPD GO	ODP2_RAT	Dihydrolipoyllysine-residue acetyltransferase component of pyruvate dehydrogenase complex (EC 2.3.1. ...	0.04	-	cyt	0	Mitochondrion; mitochondrial matrix	pyruvate dehydrogenase complex [TAS]			555
Q7Z892 UniProt NPD GO	PYRD1_SACKL	Dihydroorotate dehydrogenase (EC 1.3.3.1) (Dihydroorotate oxidase) (DHOdehase) (DHODase) (DHOD)	0.04	-	cyt	0	Cytoplasm (By similarity)				314
Q9EQF5 UniProt NPD GO	DPYS_MOUSE	Dihydropyrimidinase (EC 3.5.2.2) (DHPase) (Hydantoinase) (DHP)	0.04	-	nuc	0					519
Q63150 UniProt NPD GO	DPYS_RAT	Dihydropyrimidinase (EC 3.5.2.2) (DHPase) (Hydantoinase) (DHP)	0.04	-	nuc	0					519
O13022 UniProt NPD GO	DPYL3_XENLA	Dihydropyrimidinase-related protein 3 (DRP-3) (Neural-specific protein 1)	0.04	-	cyt	0					571
O13902 UniProt NPD GO	DAK1_SCHPO	Dihydroxyacetone kinase 1 (EC 2.7.1.29) (Glycerone kinase 1) (DHA kinase 1)	0.04	-	cyt	0		cytoplasm [IDA]			580
P54838 UniProt NPD GO	DAK1_YEAST	Dihydroxyacetone kinase 1 (EC 2.7.1.29) (Glycerone kinase 1) (DHA kinase 1)	0.04	-	cyt	0		cytoplasm [IDA]			584
Q9UW98 UniProt NPD GO	DPP5_TRIRU	Dipeptidyl-peptidase 5 precursor (EC 3.4.14.-) (Dipeptidyl-peptidase V) (DPP V) (DppV) (Allergen Tri ...	0.04	-	exc	0	Secreted protein				726
P32461 UniProt NPD GO	DPH2_YEAST	Diphthamide biosynthesis protein 2 (Diphtheria toxin resistance protein 2)	0.04	-	cyt	0	Cytoplasm	cytoplasm [IDA]			534
Q4WPF7 UniProt NPD GO	DPH4_ASPFU	Diphthamide biosynthesis protein 4	0.04	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				199
Q6BN80 UniProt NPD GO	DPH5_DEBHA	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.04	-	cyt	0	Cytoplasm (By similarity)				300
Q6C1E0 UniProt NPD GO	DPH5_YARLI	Diphthine synthase (EC 2.1.1.98) (Diphthamide biosynthesis methyltransferase)	0.04	-	cyt	0	Cytoplasm (By similarity)				300
P82015 UniProt NPD GO	DIUH2_HYLLI	Diuretic hormone 2 (DH-2) (Diuretic peptide 2) (DP-2) (DH(30))	0.04	-	nuc	0	Secreted protein				30
P52872 UniProt NPD GO	DAD1_CAEEL	Dolichyl-diphosphooligosaccharide--protein glycosyltransferase subunit dad-1 (EC 2.4.1.119) (Oligosa ...	0.04	-	end	3 *	Membrane; multi-pass membrane protein (Potential)				113
P12244 UniProt NPD GO	GSBP_CHICK	Dolichyl-diphosphooligosaccharide--protein glycotransferase precursor (EC 2.4.1.119) (Glycosylation ...	0.04	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum lumen				508
O14972 UniProt NPD GO	DSCR3_HUMAN	Down syndrome critical region protein 3 (Down syndrome critical region protein A)	0.04	-	cyt	0			605298		297
Q5RF33 UniProt NPD GO	DSCR3_PONPY	Down syndrome critical region protein 3 homolog	0.04	-	cyt	0					297
O35075 UniProt NPD GO	DSCR3_MOUSE	Down syndrome critical region protein 3 homolog (Down syndrome critical region protein A homolog)	0.04	-	cyt	0					297
Q8K4T5 UniProt NPD GO	DUS19_MOUSE	Dual specificity protein phosphatase 19 (EC 3.1.3.48) (EC 3.1.3.16) (Stress-activated protein kinase ...	0.04	-	nuc	0		cytoplasm [IDA]			220
Q95LF2 UniProt NPD GO	DUFFY_MACMU	Duffy antigen/chemokine receptor (CD234 antigen)	0.04	-	vac	7	Membrane; multi-pass membrane protein				335
Q95LG5 UniProt NPD GO	DUFFY_PAPHA	Duffy antigen/chemokine receptor (CD234 antigen)	0.04	-	end	7	Membrane; multi-pass membrane protein				336
Q5R7D8 UniProt NPD GO	DCTN6_PONPY	Dynactin subunit 6 (Dynactin subunit p27)	0.04	-	nuc	0					190
Q9WUB4 UniProt NPD GO	DCTN6_MOUSE	Dynactin subunit 6 (Dynactin subunit p27) (WS-3 protein)	0.04	-	nuc	0		dynactin complex [IDA] mitochondrion [NAS]			190
Q39579 UniProt NPD GO	DYL2_CHLRE	Dynein 11 kDa light chain, flagellar outer arm	0.04	-	cyt	0					120
Q39591 UniProt NPD GO	DYL4_CHLRE	Dynein 14 kDa light chain, flagellar outer arm	0.04	-	cyt	0					129
Q39584 UniProt NPD GO	DYL3_CHLRE	Dynein 18 kDa light chain, flagellar outer arm	0.04	-	cyt	0					159
O94111 UniProt NPD GO	DYL1_EMENI	Dynein light chain, cytoplasmic (8 kDa cytoplasmic dynein light chain)	0.04	-	cyt	0	Cytoplasm				94
O44017 UniProt NPD GO	ERD2_ENTHI	ER lumen protein retaining receptor	0.04	-	end	6 *	Membrane; multi-pass membrane protein				215
Q02920 UniProt NPD GO	NO70_SOYBN	Early nodulin 70	0.04	-	end	9	Membrane; multi-pass membrane protein (Potential)				485
O95834 UniProt NPD GO	EMAL2_HUMAN	Echinoderm microtubule-associated protein-like 2 (EMAP-2) (HuEMAP-2)	0.04	-	mit	1		microtubule associated complex [TAS]			649
Q6UWV6 UniProt NPD GO	ENPP7_HUMAN	Ectonucleotide pyrophosphatase/phosphodiesterase 7 precursor (EC 3.1.4.12) (E-NPP7) (NPP-7) (Alkalin ...	0.04	-	exc	0	Membrane; single-pass type I membrane protein (Potential). Localized at the surface of the microvill ...	Golgi apparatus [IDA] membrane [NAS] microvillus [IDA]			458
Q01382 UniProt NPD GO	ELYS_HALKA	Egg-lysin precursor (Sperm-lysin)	0.04	-	end	0					154
P01051 UniProt NPD GO	ICIC_HIRME	Eglin C	0.04	-	cyt	0	Secreted protein			3TEC	70
O46644 UniProt NPD GO	ELA1_MACFA	Elastase-1 precursor (EC 3.4.21.36)	0.04	-	vac	0	Secreted protein				266
P08217 UniProt NPD GO	ELA2A_HUMAN	Elastase-2A precursor (EC 3.4.21.71)	0.04	-	exc	0	Secreted protein		609443		269
P11547 UniProt NPD GO	ELN_SHEEP	Elastin (Tropoelastin) (Fragment)	0.04	-	cyt	1 *	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers				100
P04985 UniProt NPD GO	ELN_BOVIN	Elastin precursor (Tropoelastin)	0.04	-	mit	1 *	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers				747
P54320 UniProt NPD GO	ELN_MOUSE	Elastin precursor (Tropoelastin)	0.04	-	cyt	0	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers				860
Q99372 UniProt NPD GO	ELN_RAT	Elastin precursor (Tropoelastin)	0.04	-	cyt	0	Secreted protein; extracellular space; extracellular matrix. Extracellular matrix of elastic fibers	extracellular matrix (sensu Metazoa) [TAS]			870
P40911 UniProt NPD GO	EF1A_AJECA	Elongation factor 1-alpha (EF-1-alpha)	0.04	-	cyt	0	Cytoplasm				460

You are viewing entries 76851 to 76900 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.