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
P49902 UniProt NPD GO	5NTC_HUMAN	Cytosolic purine 5'-nucleotidase (EC 3.1.3.5) (5'-nucleotidase cytosolic II)	0.33	-	cyt	0	Cytoplasm		600417		561
Q6CKH5 UniProt NPD GO	DAD3_KLULA	DASH complex subunit DAD3 (Outer kinetochore protein DAD3)	0.33	-	nuc	0	Nucleus (By similarity). Associates with the mitotic spindle and the kinetochore (By similarity)				85
Q7YR25 UniProt NPD GO	ABC3G_CERAE	DNA dC->dU-editing enzyme APOBEC-3G (EC 3.5.4.-) (Fragment)	0.33	-	cyt	0	Cytoplasm (By similarity). Mainly. Nucleus (By similarity). Small amount are found in the nucleus (B ...				377
P48581 UniProt NPD GO	RAD17_YEAST	DNA damage checkpoint control protein RAD17 (EC 3.1.11.2) (DNA repair exonuclease RAD17)	0.33	-	nuc	0	Nucleus (Potential)	nucleus [IPI]			401
Q5YLB4 UniProt NPD GO	GYRB_NICBE	DNA gyrase subunit B, chloroplast/mitochondrial precursor (EC 5.99.1.3)	0.33	-	mit	0	Plastid; chloroplast. Mitochondrion				731
Q3MHE4 UniProt NPD GO	MSH2_BOVIN	DNA mismatch repair protein Msh2 (MutS protein homolog 2)	0.33	-	nuc	0	Nucleus (Potential)				934
Q10315 UniProt NPD GO	DPB3_SCHPO	DNA polymerase epsilon subunit C (EC 2.7.7.7) (DNA polymerase II subunit C)	0.33	-	nuc	0	Nucleus	epsilon DNA polymerase complex [IPI] nucleus [IDA]			199
P22193 UniProt NPD GO	RAD1_SCHPO	DNA repair exonuclease rad1 (EC 3.1.11.2)	0.33	-	cyt	0	Nucleus (Potential)	checkpoint clamp complex [IDA]			323
Q9FL33 UniProt NPD GO	MCM3_ARATH	DNA replication licensing factor MCM3 homolog (Minichromosome maintenance protein 3 homolog)	0.33	-	cyt	0	Nucleus (Probable)				776
P22134 UniProt NPD GO	MAG_YEAST	DNA-3-methyladenine glycosylase (EC 3.2.2.21) (3-methyladenine DNA glycosidase) (3MEA DNA glycosylas ...	0.33	-	cyt	0	Nucleus	nucleus [IC]			296
Q3ZC46 UniProt NPD GO	ID2_BOVIN	DNA-binding protein inhibitor ID-2 (Inhibitor of DNA binding 2)	0.33	-	nuc	0	Nucleus (By similarity)				134
Q6BI69 UniProt NPD GO	RPC1_DEBHA	DNA-directed RNA polymerase III largest subunit (EC 2.7.7.6)	0.33	+	cyt	0	Nucleus				1457
Q2MI69 UniProt NPD GO	RPOA_LYCES	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.33	-	mit	0	Plastid; chloroplast				337
Q3C1M3 UniProt NPD GO	RPOA_NICSY	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.33	-	mit	0	Plastid; chloroplast				337
P06269 UniProt NPD GO	RPOA_TOBAC	DNA-directed RNA polymerase alpha chain (EC 2.7.7.6) (PEP) (Plastid-encoded RNA polymerase subunit a ...	0.33	-	mit	0	Plastid; chloroplast				337
Q5U2R1 UniProt NPD GO	DLP1_RAT	Decaprenyl-diphosphate synthase subunit 2 (EC 2.5.1.-) (Decaprenyl pyrophosphate synthetase subunit ...	0.33	-	mit	0					401
P84758 UniProt NPD GO	DEF3_PAPHA	Defensin-3 (PhD3)	0.33	-	mit	0	Secreted protein				32
P42759 UniProt NPD GO	ERD10_ARATH	Dehydrin ERD10 (Low-temperature-induced protein LTI45)	0.33	+	nuc	0					260
Q9UGM3 UniProt NPD GO	DMBT1_HUMAN	Deleted in malignant brain tumors 1 protein precursor (Glycoprotein 340) (Gp-340) (Surfactant pulmon ...	0.33	-	nuc	0	Secreted protein (By similarity). Some isoforms may be membrane-bound. Localized to the lumenal aspe ...	cytoplasm [ISS] extracellular region [ISS] phagocytic vesicle membrane [ISS]	601969		2413
Q61483 UniProt NPD GO	DLL1_MOUSE	Delta-like protein 1 precursor (Drosophila Delta homolog 1) (Delta1)	0.33	-	end	1 *	Membrane; single-pass type I membrane protein	cytoplasmic vesicle [IDA] extracellular region [ISS] integral to plasma membrane [ISS] plasma membrane [IDA]			722
O04847 UniProt NPD GO	DV4H_CATRO	Desacetoxyvindoline 4-hydroxylase (EC 1.14.11.20)	0.33	-	nuc	0	Cytoplasm				401
P55292 UniProt NPD GO	DSC2_MOUSE	Desmocollin-2 precursor (Epithelial type 2 desmocollin)	0.33	-	end	1	Membrane; single-pass type I membrane protein				902
Q86SJ6 UniProt NPD GO	DSG4_HUMAN	Desmoglein-4 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein (By similarity)		607903		1040
Q5RBH2 UniProt NPD GO	DBLOH_PONPY	Diablo homolog, mitochondrial precursor	0.33	-	mit	0	Mitochondrion (By similarity). But released into the cytosol when cells undergo apoptosis (By simila ...				239
Q9GMF1 UniProt NPD GO	DGAT1_CERAE	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase)	0.33	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				491
Q9ERM3 UniProt NPD GO	DGAT1_RAT	Diacylglycerol O-acyltransferase 1 (EC 2.3.1.20) (Diglyceride acyltransferase)	0.33	-	end	6	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				498
Q8VEJ3 UniProt NPD GO	DKK4_MOUSE	Dickkopf-related protein 4 precursor (Dkk-4) (Dickkopf-4)	0.33	-	exc	0	Secreted protein (By similarity)				221
Q4R7M2 UniProt NPD GO	DPEP3_MACFA	Dipeptidase 3 precursor (EC 3.4.13.19)	0.33	-	mit	0	Membrane; lipid-anchor; GPI-anchor (By similarity)				488
Q80YA7 UniProt NPD GO	DPP8_MOUSE	Dipeptidyl peptidase 8 (EC 3.4.14.5) (Dipeptidyl peptidase VIII) (DP8)	0.33	-	cyt	0	Cytoplasm (By similarity)				892
Q6CUQ9 UniProt NPD GO	DPH4_KLULA	Diphthamide biosynthesis protein 4	0.33	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				162
Q9QYI5 UniProt NPD GO	DNJBA_MOUSE	DnaJ homolog subfamily B member 10 (mDJ8)	0.33	-	nuc	0					259
Q5RA30 UniProt NPD GO	DOK4_PONPY	Docking protein 4 (Downstream of tyrosine kinase 4)	0.33	-	nuc	0					339
Q64623 UniProt NPD GO	DUS1_RAT	Dual specificity protein phosphatase 1 (EC 3.1.3.48) (EC 3.1.3.16) (MAP kinase phosphatase 1) (MKP-1 ...	0.33	-	cyt	0					367
Q9D9T8 UniProt NPD GO	EFHC1_MOUSE	EF-hand domain-containing protein 1	0.33	-	nuc	0		axoneme [IDA] cell soma [IDA] cilium [IDA] flagellum [IDA]			648
Q7YQD7 UniProt NPD GO	FBLN3_MACFA	EGF-containing fibulin-like extracellular matrix protein 1 precursor (Fibulin-3) (FIBL-3)	0.33	-	exc	0	Secreted protein				493
Q12805 UniProt NPD GO	FBLN3_HUMAN	EGF-containing fibulin-like extracellular matrix protein 1 precursor (Fibulin-3) (FIBL-3) (Fibrillin ...	0.33	-	exc	0	Secreted protein	extracellular matrix (sensu Metazoa) [TAS]	601548		493
Q61701 UniProt NPD GO	ELAV4_MOUSE	ELAV-like protein 4 (Paraneoplastic encephalomyelitis antigen HuD) (Hu-antigen D)	0.33	-	nuc	0					385
P20934 UniProt NPD GO	EVI2A_MOUSE	EVI2A protein precursor (Ecotropic viral integration site 2A protein)	0.33	-	end	1	Membrane; single-pass type I membrane protein				223
P26633 UniProt NPD GO	EGR2_CRIGR	Early growth response protein 2 (EGR-2) (Krox-20 protein) (Fragment)	0.33	-	nuc	0	Nucleus				62
Q40357 UniProt NPD GO	NO10_MEDSA	Early nodulin 10 precursor	0.33	-	exc	1 *					122
Q9VUI3 UniProt NPD GO	EMAL_DROME	Echinoderm microtubule-associated protein-like CG13466	0.33	-	cyt	0					819
Q9R1E6 UniProt NPD GO	ENPP2_MOUSE	Ectonucleotide pyrophosphatase/phosphodiesterase 2 (E-NPP 2) (Phosphodiesterase I/nucleotide pyropho ...	0.33	-	mit	1 *	Membrane; single-pass type II membrane protein				862
P14400 UniProt NPD GO	ENP1_TORCA	Electromotor neuron-associated protein 1 (Fragment)	0.33	+	nuc	0	Membrane; peripheral membrane protein. Associated with membranes of intracellular organelles				721
Q29387 UniProt NPD GO	EF1G_PIG	Elongation factor 1-gamma (EF-1-gamma) (eEF-1B gamma) (Fragment)	0.33	-	cyt	0					432
P21226 UniProt NPD GO	CHI2_PEA	Endochitinase A2 precursor (EC 3.2.1.14)	0.33	-	exc	0					324
P13096 UniProt NPD GO	ESM5_DROME	Enhancer of split m5 protein (E(spl)m5)	0.33	-	nuc	0	Nucleus (Probable)	nucleus [IDA]			178
Q07291 UniProt NPD GO	ESM8_DROHY	Enhancer of split m8 protein (E(spl)m8)	0.33	-	nuc	0	Nucleus (Probable)				183
O04408 UniProt NPD GO	KSA_PEA	Ent-kaurene synthase A, chloroplast precursor (EC 5.5.1.13) (Ent-copalyl diphosphate synthase) (KSA) ...	0.33	-	cyt	0	Plastid; chloroplast				801
Q07497 UniProt NPD GO	EPHB5_CHICK	Ephrin type-B receptor 5 precursor (EC 2.7.10.1) (Tyrosine-protein kinase CEK9)	0.33	-	nuc	1	Membrane; single-pass type I membrane protein				1002
P52795 UniProt NPD GO	EFNB1_MOUSE	Ephrin-B1 precursor (EPH-related receptor tyrosine kinase ligand 2) (LERK-2) (ELK ligand) (ELK-L) (S ...	0.33	-	mit	1	Membrane; single-pass type I membrane protein	lipid raft [IDA]			345

You are viewing entries 37501 to 37550 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.