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
Q8TCD5 UniProt NPD GO	NT5C_HUMAN	5'(3')-deoxyribonucleotidase, cytosolic type (EC 3.1.3.-) (Cytosolic 5',3'-pyrimidine nucleotidase) ...	0.42	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]	191720		201
P80405 UniProt NPD GO	MTHFS_RABIT	5-formyltetrahydrofolate cyclo-ligase (EC 6.3.3.2) (5,10-methenyl-tetrahydrofolate synthetase) (Meth ...	0.42	-	nuc	0	Cytoplasm				201
O42384 UniProt NPD GO	5HT1B_FUGRU	5-hydroxytryptamine 1A-beta receptor (5-HT-1A-beta) (Serotonin receptor 1A-beta) (5-HT1A-beta) (F1B) ...	0.42	-	end	7 *	Membrane; multi-pass membrane protein				416
P69090 UniProt NPD GO	RL18_OREMO	60S ribosomal protein L18	0.42	-	nuc	0	Cytoplasm				187
P69091 UniProt NPD GO	RL18_ORENI	60S ribosomal protein L18	0.42	-	nuc	0	Cytoplasm				187
Q3T003 UniProt NPD GO	RL18A_BOVIN	60S ribosomal protein L18a	0.42	-	mit	0					176
Q9ATF5 UniProt NPD GO	RL18A_CASSA	60S ribosomal protein L18a	0.42	-	nuc	0					178
Q02543 UniProt NPD GO	RL18A_HUMAN	60S ribosomal protein L18a	0.42	-	mit	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]	604178		176
Q8WQI7 UniProt NPD GO	RL18A_SPOFR	60S ribosomal protein L18a	0.42	-	nuc	0					177
Q9FJX2 UniProt NPD GO	RL262_ARATH	60S ribosomal protein L26-2	0.42	-	nuc	0					146
Q95281 UniProt NPD GO	RL29_PIG	60S ribosomal protein L29	0.42	-	nuc	0					159
P14117 UniProt NPD GO	RL4_XENTR	60S ribosomal protein L4 (L1) (Fragment)	0.42	-	nuc	0					96
P14795 UniProt NPD GO	RL40_TRYCR	60S ribosomal protein L40 (CEP52)	0.42	+	nuc	0					52
P17937 UniProt NPD GO	RL7A_SCHPO	60S ribosomal protein L7-A	0.42	+	cyt	0					249
Q2TBQ5 UniProt NPD GO	RL7A_BOVIN	60S ribosomal protein L7a	0.42	-	nuc	0					265
Q9UKF2 UniProt NPD GO	ADA30_HUMAN	ADAM 30 precursor (EC 3.4.24.-) (A disintegrin and metalloproteinase domain 30)	0.42	-	end	1	Membrane; single-pass type I membrane protein	integral to membrane [TAS]	604779		790
O43005 UniProt NPD GO	AP2B_SCHPO	AP-2 complex subunit beta (Beta-adaptin) (Clathrin assembly protein large beta chain) (Clathrin asse ...	0.42	-	nuc	0	Component of the coat surrounding the cytoplasmic face of coated vesicles in the plasma membrane (By ...				677
Q9TM28 UniProt NPD GO	ATPF_CYACA	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.42	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane				175
P30393 UniProt NPD GO	ATPF_EUGGR	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.42	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				183
P55096 UniProt NPD GO	ABCD3_MOUSE	ATP-binding cassette sub-family D member 3 (70 kDa peroxisomal membrane protein) (PMP70) (PMP68)	0.42	-	mit	3 *	Peroxisome; peroxisomal membrane; multi-pass membrane protein	mitochondrial inner membrane [IDA] mitochondrion [IDA] peroxisomal membrane [IDA]			659
Q09429 UniProt NPD GO	ABCC8_RAT	ATP-binding cassette transporter sub-family C member 8 (Sulfonylurea receptor 1)	0.42	-	end	14 *	Membrane; multi-pass membrane protein	ATP-sensitive potassium channel complex [IMP] synaptic vesicle membrane [IMP]			1581
Q6BRE4 UniProt NPD GO	DBP5_DEBHA	ATP-dependent RNA helicase DBP5 (EC 3.6.1.-)	0.42	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				493
Q7S5D9 UniProt NPD GO	DHH1_NEUCR	ATP-dependent RNA helicase dhh-1 (EC 3.6.1.-)	0.42	-	nuc	0	Cytoplasm. Is concentrated in several cytoplasmic foci called P bodies (or cytoplasmic processing bo ...				569
P40550 UniProt NPD GO	PDR11_YEAST	ATP-dependent permease PDR11	0.42	-	end	12	Membrane; multi-pass membrane protein (Potential)				1410
P18823 UniProt NPD GO	ACCD_PEA	Acetyl-coenzyme A carboxylase carboxyl transferase subunit beta (EC 6.4.1.2) (ACCase beta chain)	0.42	-	nuc	0	Plastid; chloroplast				590
P21932 UniProt NPD GO	ADCY3_RAT	Adenylate cyclase type 3 (EC 4.6.1.1) (Adenylate cyclase type III) (Adenylate cyclase, olfactive typ ...	0.42	-	end	12	Membrane; multi-pass membrane protein				1144
P54819 UniProt NPD GO	KAD2_HUMAN	Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.42	-	nuc	0	Mitochondrion; mitochondrial intermembrane space		103020	2C9Y	238
Q5REI7 UniProt NPD GO	KAD2_PONPY	Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.42	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)				238
P13608 UniProt NPD GO	PGCA_BOVIN	Aggrecan core protein precursor (Cartilage-specific proteoglycan core protein) (CSPCP)	0.42	-	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)				2364
Q2M2S8 UniProt NPD GO	ALKB7_BOVIN	Alkylated repair protein alkB homolog 7 precursor	0.42	-	cyt	0					221
Q9BT30 UniProt NPD GO	ALKB7_HUMAN	Alkylated repair protein alkB homolog 7 precursor (Spermatogenesis-associated protein 11) (Spermatog ...	0.42	-	mit	0					221
P39673 UniProt NPD GO	MAG_DERFA	Allergen Mag (Fragment)	0.42	-	nuc	0					341
Q9VLC1 UniProt NPD GO	FUCTB_DROME	Alpha-(1,3)-fucosyltransferase B (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase)	0.42	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				444
P30533 UniProt NPD GO	AMRP_HUMAN	Alpha-2-macroglobulin receptor-associated protein precursor (Alpha-2-MRAP) (Low density lipoprotein ...	0.42	-	exc	1 *	Endoplasmic reticulum. Cytoplasm. Cell surface. Intracellular and associated with cell surface recep ...	integral to membrane [TAS] plasma membrane [TAS]	104225	2FTU	357
Q64687 UniProt NPD GO	SIA8A_MOUSE	Alpha-N-acetylneuraminide alpha-2,8-sialyltransferase (EC 2.4.99.8) (Ganglioside GD3 synthase) (Gang ...	0.42	-	gol	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				355
P04721 UniProt NPD GO	GDA1_WHEAT	Alpha/beta-gliadin A-I precursor (Prolamin)	0.42	-	exc	0					262
P51168 UniProt NPD GO	SCNNB_HUMAN	Amiloride-sensitive sodium channel subunit beta (Epithelial Na+ channel subunit beta) (Beta ENaC) (N ...	0.42	-	end	1 *	Cell membrane; apical cell membrane; multi-pass membrane protein. Apical membrane of epithelial cell ...		600760		640
P63002 UniProt NPD GO	AES_MOUSE	Amino-terminal enhancer of split (Amino enhancer of split) (GRG protein) (Protein ESP1) (Grg-5)	0.42	-	nuc	0	Nucleus (By similarity)	nucleus [IDA]			197
P63003 UniProt NPD GO	AES_RAT	Amino-terminal enhancer of split (Amino enhancer of split) (GRG protein) (Protein ESP1) (R-esp1)	0.42	-	nuc	0	Nucleus (By similarity)				197
P34514 UniProt NPD GO	ANC2_CAEEL	Anaphase-promoting complex subunit 2 (APC2) (Cyclosome subunit 2)	0.42	-	cyt	0					728
O77802 UniProt NPD GO	ANGP2_BOVIN	Angiopoietin-2 (ANG-2) (Fragment)	0.42	-	nuc	0	Secreted protein				375
P09470 UniProt NPD GO	ACE_MOUSE	Angiotensin-converting enzyme, somatic isoform precursor (EC 3.4.15.1) (Dipeptidyl carboxypeptidase ...	0.42	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				1312
Q8VHP9 UniProt NPD GO	ASB17_MOUSE	Ankyrin repeat and SOCS box protein 17 (ASB-17)	0.42	-	mit	0					295
Q6ZTN6 UniProt NPD GO	AN13D_HUMAN	Ankyrin repeat domain-containing protein 13D	0.42	-	nuc	0					518
P97384 UniProt NPD GO	ANX11_MOUSE	Annexin A11 (Annexin XI) (Calcyclin-associated annexin 50) (CAP-50)	0.42	-	nuc	0	Nucleus; nucleoplasm (By similarity). Found throughout the nucleoplasm at interphase and at the mito ...	nuclear envelope [ISS] nucleoplasm [ISS]			503
O76027 UniProt NPD GO	ANXA9_HUMAN	Annexin A9 (Annexin-31) (Annexin XXXI) (Pemphaxin)	0.42	-	mit	0		cell surface [IDA] cytosol [IDA]	603319		345
P49913 UniProt NPD GO	FAL39_HUMAN	Antibacterial protein FALL-39 precursor (FALL-39 peptide antibiotic) (Cationic antimicrobial protein ...	0.42	-	nuc	1 *	Secreted protein		600474		170
Q71SN9 UniProt NPD GO	FAL39_MACMU	Antibacterial protein FALL-39 precursor (FALL-39 peptide antibiotic) (Cationic antimicrobial protein ...	0.42	-	nuc	1 *	Secreted protein				170
Q9R0R3 UniProt NPD GO	APEL_RAT	Apelin precursor (APJ endogenous ligand) [Contains: Apelin-36; Apelin-31; Apelin-28; Apelin-13]	0.42	+	exc	1 *	Secreted protein				77
P22622 UniProt NPD GO	AMA1_PLAFR	Apical membrane antigen 1 precursor (Merozoite surface antigen)	0.42	-	cyt	1	Membrane; single-pass type I membrane protein				562

You are viewing entries 30151 to 30200 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.