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
Q9V3C0 UniProt NPD GO	ABS_DROME	ATP-dependent RNA helicase abstrakt (EC 3.6.1.-) (DEAD box protein abstrakt)	0.43	-	nuc	0	Nucleus (Potential)				619
Q8X0X2 UniProt NPD GO	DBP5_NEUCR	ATP-dependent RNA helicase dbp-5 (EC 3.6.1.-)	0.43	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				483
Q4WH83 UniProt NPD GO	DBP3_ASPFU	ATP-dependent RNA helicase dbp3 (EC 3.6.1.-)	0.43	-	nuc	0	Nucleus; nucleolus (By similarity)				503
Q10202 UniProt NPD GO	DBP3_SCHPO	ATP-dependent RNA helicase dbp3 (EC 3.6.1.-)	0.43	+	nuc	0	Nucleus; nucleolus (By similarity)				578
Q4WEB4 UniProt NPD GO	FAL1_ASPFU	ATP-dependent RNA helicase fal1 (EC 3.6.1.-)	0.43	-	cyt	0	Nucleus; nucleolus (By similarity)				398
P01098 UniProt NPD GO	STF1_YEAST	ATPase-stabilizing factor 9 kDa, mitochondrial precursor	0.43	-	mit	0	Mitochondrion	proton-transporting ATP synthase complex (s... [TAS]			86
P10083 UniProt NPD GO	AST5_DROME	Achaete-scute complex protein T5 (Achaete)	0.43	-	nuc	0					201
P97822 UniProt NPD GO	AN32E_MOUSE	Acidic leucine-rich nuclear phosphoprotein 32 family member E (LANP-like protein) (LANP-L) (Cerebell ...	0.43	-	nuc	0	Cytoplasm. Nucleus	cytoplasm [IDA] cytoplasmic membrane-bound vesicle [IDA] nucleus [IDA]			260
P38479 UniProt NPD GO	ABP1_SACEX	Actin-binding protein	0.43	-	nuc	0	Cytoskeleton. Cortical cytoskeleton				617
Q9GZX7 UniProt NPD GO	AICDA_HUMAN	Activation-induced cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.43	-	mit	0			605258		198
Q9DBK0 UniProt NPD GO	ACO12_MOUSE	Acyl-coenzyme A thioesterase 12 (EC 3.1.2.1) (Acyl-CoA thioesterase 12) (Acyl-CoA thioester hydrolas ...	0.43	-	cyt	0	Cytoplasm (By similarity)	cytosol [TAS]			556
O60266 UniProt NPD GO	ADCY3_HUMAN	Adenylate cyclase type 3 (EC 4.6.1.1) (Adenylate cyclase type III) (Adenylate cyclase, olfactive typ ...	0.43	-	end	12	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	600291		1144
P40144 UniProt NPD GO	ADCY5_RABIT	Adenylate cyclase type 5 (EC 4.6.1.1) (Adenylate cyclase type V) (ATP pyrophosphate-lyase 5) (Adenyl ...	0.43	-	end	9	Membrane; multi-pass membrane protein				1264
Q9WTP6 UniProt NPD GO	KAD2_MOUSE	Adenylate kinase isoenzyme 2, mitochondrial (EC 2.7.4.3) (ATP-AMP transphosphorylase)	0.43	-	nuc	0	Mitochondrion; mitochondrial intermembrane space (By similarity)	mitochondrial inner membrane [IDA] mitochondrion [IDA]			231
Q13686 UniProt NPD GO	ALKB1_HUMAN	Alkylated DNA repair protein alkB homolog 1	0.43	-	cyt	0			605345		389
O70200 UniProt NPD GO	AIF1_MOUSE	Allograft inflammatory factor 1 (AIF-1) (Ionized calcium-binding adapter molecule 1)	0.43	-	nuc	0		actin filament [IDA] cytoplasm [IDA] phagocytic cup [IDA] ruffle [IDA]		1WY9	147
Q60476 UniProt NPD GO	ADA2C_CAVPO	Alpha-2C adrenergic receptor (Alpha-2C adrenoceptor) (Alpha-2C adrenoreceptor)	0.43	+	end	7 *	Membrane; multi-pass membrane protein				455
P70277 UniProt NPD GO	SIA7B_MOUSE	Alpha-N-acetylgalactosaminide alpha-2,6-sialyltransferase 2 (EC 2.4.99.-) (GalNAc alpha-2,6-sialyltr ...	0.43	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				373
P02661 UniProt NPD GO	CAS1_RAT	Alpha-S1-casein precursor	0.43	-	exc	0	Secreted protein				284
P33049 UniProt NPD GO	CAS2_CAPHI	Alpha-S2-casein precursor (Alpha-S2-CN)	0.43	-	exc	0	Secreted protein				223
Q9STV0 UniProt NPD GO	GWD2_ARATH	Alpha-glucan water dikinase 2 precursor (EC 2.7.9.4)	0.43	-	cyt	0					1278
Q25390 UniProt NPD GO	SCRA_LIMPO	Alpha-scruin	0.43	-	mit	0					918
P51167 UniProt NPD GO	SCNNA_XENLA	Amiloride-sensitive sodium channel subunit alpha (Epithelial Na+ channel subunit alpha) (Alpha ENaC) ...	0.43	-	end	2 *	Cell membrane; apical cell membrane; multi-pass membrane protein (By similarity). Apical membrane of ...				632
Q08117 UniProt NPD GO	AES_HUMAN	Amino-terminal enhancer of split (Amino enhancer of split) (GRG protein) (Protein ESP1) (Gp130-assoc ...	0.43	-	nuc	0	Nucleus (By similarity)		600188		197
Q96P71 UniProt NPD GO	AB2BP_HUMAN	Amyloid beta A4 protein-binding family A member 2-binding protein (Neuronal calcium-binding protein ...	0.43	-	nuc	0	Cytoplasm; perinuclear region. Localized predominantly around the nucleus	cytoplasm [IDA] endoplasmic reticulum membrane [IDA] Golgi cis cisterna [IDA] nucleus [NAS]			396
P16522 UniProt NPD GO	CDC23_YEAST	Anaphase-promoting complex subunit CDC23 (Cell division control protein 23)	0.43	-	cyt	0	Nucleus. Associated with the kinetochore	anaphase-promoting complex [TAS]			626
O13916 UniProt NPD GO	HCN1_SCHPO	Anaphase-promoting complex subunit hcn1 (20S cyclosome/APC complex protein hcn1) (Chaperone-like pro ...	0.43	-	nuc	0					80
Q4KL97 UniProt NPD GO	ANKR1_XENLA	Ankyrin repeat domain-containing protein 1	0.43	+	nuc	0	Nucleus (By similarity)				318
Q8NB46 UniProt NPD GO	ANR52_HUMAN	Ankyrin repeat domain-containing protein 52	0.43	-	cyt	0					1076
Q9H6X2 UniProt NPD GO	ANTR1_HUMAN	Anthrax toxin receptor 1 precursor (Tumor endothelial marker 8)	0.43	-	exc	1	Membrane; single-pass type I membrane protein (Probable)		606410		564
Q9R0R4 UniProt NPD GO	APEL_MOUSE	Apelin precursor (APJ endogenous ligand) [Contains: Apelin-36; Apelin-31; Apelin-28; Apelin-13]	0.43	+	exc	1 *					77
Q9U943 UniProt NPD GO	APLP_LOCMI	Apolipophorins precursor [Contains: Apolipophorin-2 (Apolipophorin II) (apoLp-2); Apolipophorin-1 (A ...	0.43	-	end	0	Secreted protein				3380
P27007 UniProt NPD GO	APOA1_SALSA	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.43	-	exc	0	Secreted protein				258
P14417 UniProt NPD GO	APOA_MACMU	Apolipoprotein(a) (EC 3.4.21.-) (Apo(a)) (Lp(a)) (Fragment)	0.43	-	nuc	0					1420
Q2KMM4 UniProt NPD GO	LX12B_RAT	Arachidonate 12-lipoxygenase, 12R type (EC 1.13.11.-) (Epidermis-type lipoxygenase 12) (12R-lipoxyge ...	0.43	-	cyt	0					701
Q8K4F2 UniProt NPD GO	LX15B_RAT	Arachidonate 15-lipoxygenase type II (EC 1.13.11.33) (15-LOX-2)	0.43	-	cyt	0	Cytoplasm (By similarity)	intracellular [ISS]			677
Q8K221 UniProt NPD GO	ARFP2_MOUSE	Arfaptin-2 (ADP-ribosylation factor-interacting protein 2)	0.43	-	cyt	0					341
Q6AY65 UniProt NPD GO	ARFP2_RAT	Arfaptin-2 (ADP-ribosylation factor-interacting protein 2)	0.43	-	cyt	0					341
P53365 UniProt NPD GO	ARFP2_HUMAN	Arfaptin-2 (ADP-ribosylation factor-interacting protein 2) (Partner of RAC1) (Protein POR1)	0.43	-	cyt	0		cell cortex [IDA] cytoplasm [TAS] plasma membrane [TAS] ruffle [IMP]	601638	1I4T	341
P14868 UniProt NPD GO	SYD_HUMAN	Aspartyl-tRNA synthetase (EC 6.1.1.12) (Aspartate--tRNA ligase) (AspRS)	0.43	-	nuc	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	603084		501
Q9Y5Q5 UniProt NPD GO	CORIN_HUMAN	Atrial natriuteric peptide-converting enzyme (EC 3.4.21.-) (pro-ANP-converting enzyme) (Corin) (Hear ...	0.43	-	nuc	1 *	Membrane; single-pass type II membrane protein	integral to plasma membrane [TAS] plasma membrane [TAS]	605236		1042
O88282 UniProt NPD GO	BCL6B_MOUSE	B-cell CLL/lymphoma 6 member B protein (Bcl6-associated zinc finger protein)	0.43	-	nuc	0	Nucleus	nucleus [IDA]			474
Q9UHQ4 UniProt NPD GO	BAP29_HUMAN	B-cell receptor-associated protein 29 (BCR-associated protein Bap29)	0.43	-	end	3 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				241
Q8HZP3 UniProt NPD GO	BKRB1_CERPY	B1 bradykinin receptor (BK-1 receptor) (B1R)	0.43	+	end	7 *	Membrane; multi-pass membrane protein				352
Q04118 UniProt NPD GO	PRB3_HUMAN	Basic salivary proline-rich protein 3 precursor (Parotid salivary glycoprotein G1) (Proline-rich pro ...	0.43	-	exc	0			168840		309
Q96LW7 UniProt NPD GO	BINCA_HUMAN	Bcl10-interacting CARD protein (BinCARD)	0.43	-	nuc	0	Nucleus. Co-expression with BCL10 induced translocation from nucleus to cytosol	cytosol [NAS] nucleus [NAS]			228
Q6QNF3 UniProt NPD GO	PGFRB_CANFA	Beta platelet-derived growth factor receptor precursor (EC 2.7.10.1) (PDGF-R-beta)	0.43	-	end	1	Membrane; single-pass type I membrane protein				1103
Q02527 UniProt NPD GO	MGAT3_RAT	Beta-1,4-mannosyl-glycoprotein 4-beta-N-acetylglucosaminyltransferase (EC 2.4.1.144) (N-glycosyl-oli ...	0.43	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein				538
Q8N687 UniProt NPD GO	DB125_HUMAN	Beta-defensin 125 precursor (Defensin, beta 125) (Beta-defensin 25) (DEFB-25)	0.43	-	nuc	0	Secreted protein (Potential)				152
Q85FR6 UniProt NPD GO	RPOC_CYAME	Bifunctional DNA-directed RNA polymerase beta' and beta'' chain (EC 2.7.7.6) (PEP) [Includes: DNA-di ...	0.43	-	cyt	0	Plastid; chloroplast				1676

You are viewing entries 29451 to 29500 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.