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
P0C0W9 UniProt NPD GO	RL11A_YEAST	60S ribosomal protein L11-A (L16) (YL16) (39A) (RP39)	0.29	+	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]		1S1I	173
Q3E757 UniProt NPD GO	RL11B_YEAST	60S ribosomal protein L11-B (L16) (YL16) (39B) (RP39)	0.29	+	cyt	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			173
Q8MUR4 UniProt NPD GO	RL13A_CHOPR	60S ribosomal protein L13A	0.29	-	cyt	0					204
Q4R5I3 UniProt NPD GO	RL22_MACFA	60S ribosomal protein L22	0.29	-	nuc	0					127
P67984 UniProt NPD GO	RL22_MOUSE	60S ribosomal protein L22 (Heparin-binding protein HBp15)	0.29	-	nuc	0					127
P67985 UniProt NPD GO	RL22_PIG	60S ribosomal protein L22 (Heparin-binding protein HBp15)	0.29	-	nuc	0					127
P53221 UniProt NPD GO	RL26B_YEAST	60S ribosomal protein L26-B (YL33)	0.29	-	nuc	0		cytosolic large ribosomal subunit (sensu Eu... [TAS]			126
Q27021 UniProt NPD GO	RL27A_TENMO	60S ribosomal protein L27a	0.29	+	nuc	0					148
P32323 UniProt NPD GO	AGA1_YEAST	A-agglutinin attachment subunit precursor	0.29	-	exc	0	Cell membrane; lipid-anchor; GPI-anchor. Attached to the membrane by a GPI-anchor and/or by carbohyd ...	cell wall (sensu Fungi) [IDA]			725
P28907 UniProt NPD GO	CD38_HUMAN	ADP-ribosyl cyclase 1 (EC 3.2.2.5) (Cyclic ADP-ribose hydrolase 1) (cADPr hydrolase 1) (Lymphocyte d ...	0.29	-	nuc	1 *	Membrane; single-pass type II membrane protein	membrane fraction [TAS] plasma membrane [TAS]	107270	1ZVM	300
Q5YD48 UniProt NPD GO	ACF_MOUSE	APOBEC1 complementation factor (APOBEC1-stimulating protein)	0.29	-	nuc	0	Nucleus (By similarity). Predominantly nuclear where it localizes to heterochromatin. Endoplasmic re ...	apolipoprotein B mRNA editing enzyme complex [ISS] cytoplasm [ISS]			595
P06290 UniProt NPD GO	ATPF_TOBAC	ATP synthase B chain (EC 3.6.3.14) (ATPase subunit I)	0.29	-	nuc	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				184
P31853 UniProt NPD GO	ATPX_SPIOL	ATP synthase B' chain, chloroplast precursor (EC 3.6.3.14) (Subunit II)	0.29	-	nuc	0	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein				222
Q41075 UniProt NPD GO	ATPG_PHATR	ATP synthase gamma chain, chloroplast precursor (EC 3.6.3.14)	0.29	-	exc	0	Plastid; chloroplast; chloroplast thylakoid membrane				370
P38077 UniProt NPD GO	ATPG_YEAST	ATP synthase gamma chain, mitochondrial precursor (EC 3.6.3.14)	0.29	-	mit	0	Mitochondrion	proton-transporting ATP synthase, central s... [IMP]			311
Q3BAQ7 UniProt NPD GO	ATPA_PHAAO	ATP synthase subunit alpha (EC 3.6.3.14) (ATPase subunit alpha) (ATP synthase F1 sector subunit alph ...	0.29	-	cyt	0	Plastid; chloroplast; chloroplast thylakoid membrane; peripheral membrane protein (By similarity)				507
Q6C4D4 UniProt NPD GO	DBP2_YARLI	ATP-dependent RNA helicase DBP2 (EC 3.6.1.-)	0.29	+	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				552
Q8TFK8 UniProt NPD GO	DED1_CANGA	ATP-dependent RNA helicase DED1 (EC 3.6.1.-)	0.29	-	cyt	0	Cytoplasm (By similarity)				617
Q5AVM1 UniProt NPD GO	DBP5_EMENI	ATP-dependent RNA helicase dbp5 (EC 3.6.1.-)	0.29	-	nuc	0	Cytoplasm. Nucleus; nuclear envelope; nuclear pore complex; cytoplasmic side. Nuclear pore complex c ...				477
Q02785 UniProt NPD GO	PDR12_YEAST	ATP-dependent permease PDR12	0.29	-	end	11	Membrane; multi-pass membrane protein (Potential)	plasma membrane [IDA]			1511
O88932 UniProt NPD GO	IRK15_MOUSE	ATP-sensitive inward rectifier potassium channel 15 (Potassium channel, inwardly rectifying subfamil ...	0.29	-	mit	2	Membrane; multi-pass membrane protein				375
Q9M2A0 UniProt NPD GO	PMA8_ARATH	ATPase 8, plasma membrane-type (EC 3.6.3.6) (Proton pump 8)	0.29	-	end	9	Membrane; multi-pass membrane protein				948
O35143 UniProt NPD GO	ATIF1_MOUSE	ATPase inhibitor, mitochondrial precursor	0.29	-	nuc	0	Mitochondrion	mitochondrion [IDA]			106
Q03344 UniProt NPD GO	ATIF1_RAT	ATPase inhibitor, mitochondrial precursor	0.29	-	nuc	0	Mitochondrion	mitochondrion [IDA]			107
P09342 UniProt NPD GO	ILV1_TOBAC	Acetolactate synthase 1, chloroplast precursor (EC 2.2.1.6) (Acetolactate synthase I) (Acetohydroxy- ...	0.29	-	mit	0	Plastid; chloroplast				667
P17644 UniProt NPD GO	ACH2_DROME	Acetylcholine receptor protein subunit alpha-like 2 precursor	0.29	-	end	4	Membrane; multi-pass membrane protein				576
Q75W64 UniProt NPD GO	AICDA_CANFA	Activation-induced cytidine deaminase (EC 3.5.4.5) (Cytidine aminohydrolase)	0.29	-	cyt	0					198
O24428 UniProt NPD GO	STAD_ELAGV	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.29	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				393
Q40731 UniProt NPD GO	STAD_ORYSA	Acyl-[acyl-carrier-protein] desaturase, chloroplast precursor (EC 1.14.19.2) (Stearoyl-ACP desaturas ...	0.29	-	mit	0	Plastid; chloroplast (By similarity). In green tissue, found in chloroplasts. Plastid (By similarity ...				390
Q00468 UniProt NPD GO	ACOX2_CANMA	Acyl-coenzyme A oxidase 2 (EC 1.3.3.6) (Acyl-CoA oxidase 2) (AOX 2)	0.29	-	nuc	0	Peroxisome				724
Q9XYM0 UniProt NPD GO	CRK_DROME	Adapter molecule Crk	0.29	+	cyt	0					271
O95622 UniProt NPD GO	ADCY5_HUMAN	Adenylate cyclase type 5 (EC 4.6.1.1) (Adenylate cyclase type V) (ATP pyrophosphate-lyase 5) (Adenyl ...	0.29	-	end	6	Membrane; multi-pass membrane protein		600293		894
O61069 UniProt NPD GO	KAD_TRYBR	Adenylate kinase (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK)	0.29	-	nuc	0					209
P56473 UniProt NPD GO	AGRP_MOUSE	Agouti-related protein precursor	0.29	-	exc	0	Secreted protein				131
Q8QZR5 UniProt NPD GO	ALAT1_MOUSE	Alanine aminotransferase 1 (EC 2.6.1.2) (ALT1) (Glutamic--pyruvic transaminase 1) (GPT 1) (Glutamic- ...	0.29	-	cyt	0	Cytoplasm (By similarity)				495
Q75DC2 UniProt NPD GO	ASR1_ASHGO	Alcohol-sensitive RING finger protein 1	0.29	-	nuc	0	Cytoplasm (By similarity). Predominantly. Nucleus (By similarity). Accumulates in the nucleus specif ...				328
Q7G191 UniProt NPD GO	ALDO4_ARATH	Aldehyde oxidase 4 (EC 1.2.3.1) (AO-4) (AtAO-4) (AtAO2)	0.29	-	cyt	0					1337
P31757 UniProt NPD GO	ALLN_ALLCE	Alliin lyase precursor (EC 4.4.1.4) (Alliinase) (Cysteine sulphoxide lyase)	0.29	-	end	0	Vacuole				479
P55008 UniProt NPD GO	AIF1_HUMAN	Allograft inflammatory factor 1 (AIF-1) (Ionized calcium-binding adapter molecule 1) (Protein G1)	0.29	-	nuc	0		nucleus [TAS]	601833	2G2B	147
P68284 UniProt NPD GO	CRYAA_GIRCA	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.29	-	mit	0					173
P68285 UniProt NPD GO	CRYAA_HIPAM	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.29	-	mit	0					173
P82531 UniProt NPD GO	CRYAA_PTEPO	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.29	-	cyt	0					173
O12987 UniProt NPD GO	CRYAB_COLLI	Alpha crystallin B chain (Alpha(B)-crystallin) (Fragment)	0.29	-	exc	0					52
Q8HYJ7 UniProt NPD GO	FUT5_GORGO	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.29	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				374
Q8HYJ4 UniProt NPD GO	FUT5_PONPY	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.65) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferas ...	0.29	-	mit	0	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				374
Q9N0W2 UniProt NPD GO	FUT8_BOVIN	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.29	+	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				575
Q9WTS2 UniProt NPD GO	FUT8_MOUSE	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.29	+	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				575
P79282 UniProt NPD GO	FUT8_PIG	Alpha-(1,6)-fucosyltransferase (EC 2.4.1.68) (Glycoprotein 6-alpha-L-fucosyltransferase) (GDP-fucose ...	0.29	+	exc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				575
Q921V5 UniProt NPD GO	MGAT2_MOUSE	Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) (Mannoside ace ...	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				442
O19071 UniProt NPD GO	MGAT2_PIG	Alpha-1,6-mannosyl-glycoprotein 2-beta-N-acetylglucosaminyltransferase (EC 2.4.1.143) (Mannoside ace ...	0.29	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				446

You are viewing entries 40951 to 41000 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.