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
Q6FQY4 UniProt NPD GO	ENO2_CANGA	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2)	0.08	-	cyt	0	Cytoplasm (By similarity)				437
Q6BI20 UniProt NPD GO	ENO2_DEBHA	Enolase 2 (EC 4.2.1.11) (2-phosphoglycerate dehydratase 2) (2-phospho-D-glycerate hydro-lyase 2)	0.08	-	cyt	0	Cytoplasm (By similarity)				439
P17561 UniProt NPD GO	EPD_BRARE	Ependymin precursor (EPD)	0.08	-	exc	0	Secreted protein				217
P32187 UniProt NPD GO	EPD_CLUHA	Ependymin precursor (EPD)	0.08	-	end	0	Secreted protein				212
O08542 UniProt NPD GO	EFNA4_MOUSE	Ephrin-A4 precursor (EPH-related receptor tyrosine kinase ligand 4) (LERK-4)	0.08	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor (By similarity)				206
O08543 UniProt NPD GO	EFNA5_MOUSE	Ephrin-A5 precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (AL-1)	0.08	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Compartmentalized in discrete caveolae-like membrane microd ...			1SHX	228
P97605 UniProt NPD GO	EFNA5_RAT	Ephrin-A5 precursor (EPH-related receptor tyrosine kinase ligand 7) (LERK-7) (AL-1)	0.08	-	end	0	Cell membrane; lipid-anchor; GPI-anchor. Compartmentalized in discrete caveolae-like membrane microd ...				228
Q924X1 UniProt NPD GO	EPGN_MOUSE	Epigen precursor (Epithelial mitogen) (EPG)	0.08	-	end	1	Membrane; single-pass type I membrane protein (Probable)				152
P07099 UniProt NPD GO	HYEP_HUMAN	Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase)	0.08	-	cyt	0	Microsome; microsomal membrane; single-pass membrane protein		607748		455
P07687 UniProt NPD GO	HYEP_RAT	Epoxide hydrolase 1 (EC 3.3.2.3) (Microsomal epoxide hydrolase) (Epoxide hydratase)	0.08	-	mit	0	Microsome; microsomal membrane; single-pass membrane protein	microsome [TAS]			455
P07865 UniProt NPD GO	EPO_MACFA	Erythropoietin precursor	0.08	-	mit	1 *	Secreted protein				192
Q9H0W9 UniProt NPD GO	CK054_HUMAN	Ester hydrolase C11orf54 (EC 3.1.-.-)	0.08	-	cyt	0	Nucleus			1XCR	315
P25725 UniProt NPD GO	EST5C_DROPS	Esterase-5C precursor (EC 3.1.1.1) (Est-5C) (Carboxylic-ester hydrolase 5C) (Carboxylesterase-5C)	0.08	-	end	0	Secreted protein				545
O54939 UniProt NPD GO	DHB3_RAT	Estradiol 17-beta-dehydrogenase 3 (EC 1.1.1.62) (17-beta-HSD 3) (Testicular 17-beta-hydroxysteroid d ...	0.08	-	nuc	0					306
O49187 UniProt NPD GO	ETR2_LYCES	Ethylene receptor 2 (EC 2.7.13.3) (LeETR2)	0.08	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				736
Q9BMX0 UniProt NPD GO	ERF1_DICDI	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm				441
Q8BWY3 UniProt NPD GO	ERF1_MOUSE	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm (By similarity)				436
Q5R4C7 UniProt NPD GO	ERF1_PONPY	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm (By similarity)				436
P62497 UniProt NPD GO	ERF1_RABIT	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm				436
Q5U2Q7 UniProt NPD GO	ERF1_RAT	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm (By similarity)				436
P62498 UniProt NPD GO	ERF1_XENTR	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1)	0.08	-	cyt	0	Cytoplasm (By similarity)				437
P62496 UniProt NPD GO	ERF1_MESAU	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1) (Cl1 protein) ...	0.08	-	cyt	0	Cytoplasm				436
P62495 UniProt NPD GO	ERF1_HUMAN	Eukaryotic peptide chain release factor subunit 1 (eRF1) (Eukaryotic release factor 1) (TB3-1) (Cl1 ...	0.08	-	cyt	0	Cytoplasm		600285	1DT9	436
Q24208 UniProt NPD GO	IF2G_DROME	Eukaryotic translation initiation factor 2 subunit gamma (eIF-2-gamma) (Protein suppressor of varieg ...	0.08	-	cyt	0					475
O74743 UniProt NPD GO	IF4E2_SCHPO	Eukaryotic translation initiation factor 4E-2 (eIF4E-2) (eIF-4E-2) (mRNA cap-binding protein 2) (eIF ...	0.08	-	cyt	0		eukaryotic translation initiation factor 4F... [TAS]			243
P19211 UniProt NPD GO	IF5A1_YEAST	Eukaryotic translation initiation factor 5A-1 (eIF-5A-1) (eIF-4D) (Hypusine-containing protein HP1)	0.08	-	cyt	0		ribosome [TAS]			156
Q20751 UniProt NPD GO	IF5A2_CAEEL	Eukaryotic translation initiation factor 5A-2 (eIF-5A-2) (Initiation factor five protein 2)	0.08	-	cyt	0					161
P43005 UniProt NPD GO	EAA3_HUMAN	Excitatory amino acid transporter 3 (Sodium-dependent glutamate/aspartate transporter 3) (Excitatory ...	0.08	-	end	8 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	133550		524
Q755Y4 UniProt NPD GO	YFAS1_ASHGO	FAS1 domain-containing protein AER383W precursor	0.08	-	exc	0	Vacuole (By similarity)				250
Q38936 UniProt NPD GO	FKB22_ARATH	FK506-binding protein 2-2 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rot ...	0.08	-	exc	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (Potential)				163
O95302 UniProt NPD GO	FKBP9_HUMAN	FK506-binding protein 9 precursor (EC 5.2.1.8) (Peptidyl-prolyl cis-trans isomerase) (PPIase) (Rotam ...	0.08	-	end	0	Endoplasmic reticulum (By similarity)	endoplasmic reticulum [ISS]			570
Q56JX9 UniProt NPD GO	FABPI_BOVIN	Fatty acid-binding protein, intestinal (I-FABP) (FABPI)	0.08	-	cyt	0	Cytoplasm (By similarity)				131
P82188 UniProt NPD GO	FABPL_LAMJA	Fatty acid-binding protein, liver (L-FABP) (Fragment)	0.08	-	cyt	0	Cytoplasm				114
P30839 UniProt NPD GO	AL3A2_RAT	Fatty aldehyde dehydrogenase (EC 1.2.1.3) (Aldehyde dehydrogenase, microsomal) (Aldehyde dehydrogena ...	0.08	-	gol	1	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass membrane protein; cytoplasmic sid ...	cytosol [IDA] extrinsic to endoplasmic reticulum membrane [IDA] microsome [NAS] nucleus [IDA]			484
Q98U05 UniProt NPD GO	KRFB_MYCAM	Feather beta keratin (F-ker)	0.08	-	nuc	0					97
P04458 UniProt NPD GO	KRFB_CHICK	Feather keratin II (Keratin gene B protein) (F-ker)	0.08	-	nuc	0					97
P41346 UniProt NPD GO	FENR_VICFA	Ferredoxin--NADP reductase, chloroplast precursor (EC 1.18.1.2) (FNR)	0.08	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...				363
P10933 UniProt NPD GO	FENR1_PEA	Ferredoxin--NADP reductase, leaf isozyme, chloroplast precursor (EC 1.18.1.2) (FNR)	0.08	-	mit	0	Plastid; chloroplast; chloroplast stroma. Stromal side of the thylakoid membrane in the vicinity of ...			1QGA	360
P94044 UniProt NPD GO	FER6_MAIZE	Ferredoxin-6, chloroplast precursor (Ferredoxin VI) (Fd VI)	0.08	-	mit	0	Plastid; chloroplast				155
O49856 UniProt NPD GO	FTRC_SOYBN	Ferredoxin-thioredoxin reductase catalytic chain, chloroplast precursor (EC 1.18.-.-) (FTR-C)	0.08	-	mit	0	Plastid; chloroplast				144
P36033 UniProt NPD GO	FRE2_YEAST	Ferric reductase transmembrane component 2 precursor (EC 1.16.1.7) (Ferric-chelate reductase 2)	0.08	-	end	7	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			711
Q96540 UniProt NPD GO	FRI1_BRANA	Ferritin-1, chloroplast precursor (EC 1.16.3.1)	0.08	-	nuc	0	Plastid; chloroplast (By similarity)				254
P42045 UniProt NPD GO	HEMH_HORVU	Ferrochelatase-2, chloroplast precursor (EC 4.99.1.1) (Ferrochelatase II) (Protoheme ferro-lyase 2) ...	0.08	-	cyt	1	Plastid; chloroplast				484
P14467 UniProt NPD GO	FIBB_BUBBU	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.08	-	nuc	0	Secreted protein				21
P19344 UniProt NPD GO	FIBB_PAPAN	Fibrinogen beta chain [Contains: Fibrinopeptide B] (Fragment)	0.08	-		0	Secreted protein				9
P81802 UniProt NPD GO	FIBR_EISFO	Fibrinolytic enzyme large subunit (EC 3.4.-.-) (Fragment)	0.08	-	nuc	0					25
Q61851 UniProt NPD GO	FGFR3_MOUSE	Fibroblast growth factor receptor 3 precursor (EC 2.7.10.1) (FGFR-3) (Heparin-binding growth factor ...	0.08	-	end	2	Membrane; single-pass type I membrane protein	internal side of plasma membrane [IDA] lysosome [IDA] perinuclear region [IDA]			801
P32599 UniProt NPD GO	FIMB_YEAST	Fimbrin (ABP67)	0.08	-	cyt	0		actin cable [IDA] actin cortical patch [IDA]			642
P48418 UniProt NPD GO	C75A1_PETHY	Flavonoid 3',5'-hydroxylase 1 (EC 1.14.13.88) (F3'5'H) (Cytochrome P450 75A1) (CYPLXXVA1)	0.08	-	nuc	3 *	Microsome (Potential)				506
Q9DEB5 UniProt NPD GO	FZ10A_XENLA	Frizzled-10-A precursor (Fz-10A) (Xfz10A)	0.08	-	end	7 *	Membrane; multi-pass membrane protein				586

You are viewing entries 68001 to 68050 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.