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
Q92203 UniProt NPD GO	KAPS_EMENI	Adenylyl-sulfate kinase (EC 2.7.1.25) (APS kinase) (Adenosine-5'phosphosulfate kinase) (ATP adenosin ...	0.16	-	cyt	0					206
Q12184 UniProt NPD GO	ADRX_YEAST	Adrenodoxin homolog, mitochondrial precursor (Mitochondrial ferredoxin)	0.16	-	mit	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			172
O88398 UniProt NPD GO	AVIL_MOUSE	Advillin (p92) (Actin-binding protein DOC6)	0.16	-	mit	0					819
Q9UW18 UniProt NPD GO	TOXG_COCCA	Alanine racemase TOXG (EC 5.1.1.1)	0.16	-	cyt	0					389
Q9TLW4 UniProt NPD GO	PHAC_CYACA	Allophycocyanin alpha-B chain (Allophycocyanin gamma chain)	0.16	-	nuc	0	Plastid; chloroplast				163
O19896 UniProt NPD GO	PHAF_CYACA	Allophycocyanin beta 18 chain	0.16	-	nuc	0	Plastid; chloroplast				170
P40387 UniProt NPD GO	TPS1_SCHPO	Alpha,alpha-trehalose-phosphate synthase [UDP-forming] (EC 2.4.1.15) (Trehalose-6-phosphate synthase ...	0.16	-	cyt	0					513
Q8HZR2 UniProt NPD GO	FUT9_BOVIN	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.16	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
P27598 UniProt NPD GO	PHSL_IPOBA	Alpha-1,4 glucan phosphorylase L isozyme, chloroplast precursor (EC 2.4.1.1) (Starch phosphorylase L ...	0.16	-	nuc	0	Plastid; chloroplast. Plastid; amyloplast				955
P18130 UniProt NPD GO	ADA1A_BOVIN	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.16	-	end	7 *	Membrane; multi-pass membrane protein				466
O97944 UniProt NPD GO	CAS2_CAMDR	Alpha-S2-casein precursor	0.16	-	exc	0	Secreted protein				193
O77016 UniProt NPD GO	AMYR_DROSI	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.16	-	cyt	0	Secreted protein (Probable)				493
P35696 UniProt NPD GO	ELIA_PHYDR	Alpha-elicitin DRE-alpha	0.16	-	exc	0	Secreted protein				98
Q99172 UniProt NPD GO	MEL_ZYGCI	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase)	0.16	-	end	0					469
Q11129 UniProt NPD GO	MEL_SACMI	Alpha-galactosidase precursor (EC 3.2.1.22) (Melibiase) (Alpha-D-galactoside galactohydrolase) (MELj ...	0.16	-	vac	0					471
Q9NZD4 UniProt NPD GO	AHSP_HUMAN	Alpha-hemoglobin-stabilizing protein (Erythroid-associated factor) (Erythroid differentiation-relate ...	0.16	-	nuc	0	Cytoplasm	hemoglobin complex [NAS]	605821	1Z8U	102
P12065 UniProt NPD GO	LALBA_PAPCY	Alpha-lactalbumin (Lactose synthase B protein)	0.16	-	nuc	0	Secreted protein			1ALC	123
Q7T1N4 UniProt NPD GO	ACCN2_OPSTA	Amiloride-sensitive cation channel 2, neuronal (Acid-sensing ion channel 1)	0.16	-	mit	1 *	Cell membrane; multi-pass membrane protein (By similarity)				522
P78348 UniProt NPD GO	ACCN2_HUMAN	Amiloride-sensitive cation channel 2, neuronal (Acid-sensing ion channel 1) (ASIC1) (Brain sodium ch ...	0.16	-	mit	0	Cell membrane; multi-pass membrane protein (By similarity). Localizes in synaptosomes at dendritic s ...	integral to plasma membrane [TAS]	602866		528
Q6NXK8 UniProt NPD GO	ACCN2_MOUSE	Amiloride-sensitive cation channel 2, neuronal (Acid-sensing ion channel) (Acid-sensing ion channel ...	0.16	-	mit	0	Cell membrane; multi-pass membrane protein (By similarity). Localizes in synaptosomes at dendritic s ...	integral to plasma membrane [IDA] synaptosome [IDA]			526
P49252 UniProt NPD GO	AMO_LENCU	Amine oxidase [copper-containing] precursor (EC 1.4.3.6) (Fragment)	0.16	-	exc	0					667
O46640 UniProt NPD GO	ST3A1_RABIT	Amine sulfotransferase (EC 2.8.2.3) (Sulfotransferase 3A1) (AST-RB1)	0.16	-	cyt	0	Cytoplasm				301
O94688 UniProt NPD GO	APC15_SCHPO	Anaphase-promoting complex subunit 15 (20S cyclosome/APC complex protein apc15)	0.16	-	cyt	0					136
Q96DX5 UniProt NPD GO	ASB9_HUMAN	Ankyrin repeat and SOCS box protein 9 (ASB-9)	0.16	-	cyt	0					294
Q9SAR5 UniProt NPD GO	AKR2_ARATH	Ankyrin repeat domain-containing protein 2 (AtAKR2)	0.16	-	nuc	0					342
O15084 UniProt NPD GO	ANR28_HUMAN	Ankyrin repeat domain-containing protein 28	0.16	-	cyt	0					1086
Q9BQI6 UniProt NPD GO	ANR32_HUMAN	Ankyrin repeat domain-containing protein 32	0.16	-	mit	0					422
P81287 UniProt NPD GO	ANXA5_BOVIN	Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagula ...	0.16	-	cyt	0					320
P48036 UniProt NPD GO	ANXA5_MOUSE	Annexin A5 (Annexin V) (Lipocortin V) (Endonexin II) (Calphobindin I) (CBP-I) (Placental anticoagula ...	0.16	-	cyt	0					319
P22464 UniProt NPD GO	ANX9_DROME	Annexin-B9 (Annexin-9) (Annexin IX)	0.16	-	cyt	0					324
P25170 UniProt NPD GO	TRPG_PHACH	Anthranilate synthase component 2 (EC 4.1.3.27) (Anthranilate synthase component II) [Includes: Glut ...	0.16	-	mit	0					788
Q90ZN1 UniProt NPD GO	NR13_CHICK	Anti-apoptotic protein NR13 (Apoptosis regulator Nr-13)	0.16	-	end	2	Cell membrane; multi-pass membrane protein				177
P82964 UniProt NPD GO	AP65_CARMA	Antibacterial 6.5 kDa protein (Fragment)	0.16	-	nuc	0					30
P36372 UniProt NPD GO	TAP2_RAT	Antigen peptide transporter 2 (APT2)	0.16	-	end	5 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein. The transmembran ...				703
P83653 UniProt NPD GO	ALO3_ACRLO	Antimicrobial peptide Alo-3	0.16	-	nuc	0	Secreted protein			1Q3J	36
P81573 UniProt NPD GO	DEFD7_SPIOL	Antimicrobial peptide D7 (So-D7) (Defensin D7) (Fragment)	0.16	-	nuc	0	Cell wall				38
Q70XZ0 UniProt NPD GO	CYF_AMBTC	Apocytochrome f precursor	0.16	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P49161 UniProt NPD GO	CYF_SOYBN	Apocytochrome f precursor	0.16	-	cyt	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P27916 UniProt NPD GO	APOC2_CAVPO	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.16	-	end	1 *	Secreted protein				100
Q91V80 UniProt NPD GO	APOF_MOUSE	Apolipoprotein F precursor (Apo-F) (Leukemia virus-inactivating factor) (LVIF)	0.16	-	end	0	Secreted protein (By similarity)				315
Q9BQE5 UniProt NPD GO	APOL2_HUMAN	Apolipoprotein-L2 (Apolipoprotein L-II) (ApoL-II)	0.16	-	end	3	Cytoplasm (Probable)	intracellular [TAS]	607252		337
Q9BPW4 UniProt NPD GO	APOL4_HUMAN	Apolipoprotein-L4 precursor (Apolipoprotein L-IV) (ApoL-IV)	0.16	-	mit	0			607254		351
Q40577 UniProt NPD GO	5EAS_TOBAC	Aristolochene synthase (EC 4.2.3.9) (5-epi-aristolochene synthase) (EAS)	0.16	-	cyt	0	Cytoplasm			5EAU	548
Q5H9R4 UniProt NPD GO	ARMX4_HUMAN	Armadillo repeat-containing X-linked protein 4	0.16	-	cyt	0					360
Q8TBH0 UniProt NPD GO	ARRD2_HUMAN	Arrestin domain-containing protein 2	0.16	-	mit	0					407
Q9JLG9 UniProt NPD GO	AIPL1_RAT	Aryl-hydrocarbon-interacting protein-like 1	0.16	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				328
P22760 UniProt NPD GO	AAAD_HUMAN	Arylacetamide deacetylase (EC 3.1.1.-) (AADAC)	0.16	-	mit	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum membrane [IDA] microsome [TAS]	600338		398
P50294 UniProt NPD GO	ARY1_MOUSE	Arylamine N-acetyltransferase 1 (EC 2.3.1.5) (Arylamide acetylase 1) (N-acetyltransferase type 1) (N ...	0.16	-	cyt	0	Cytoplasm				290
Q5ZJU3 UniProt NPD GO	ASNS_CHICK	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.16	-	cyt	0					560
Q9SW95 UniProt NPD GO	SYNC2_ARATH	Asparaginyl-tRNA synthetase, cytoplasmic 2 (EC 6.1.1.22) (Asparagine--tRNA ligase 2) (AsnRS 2)	0.16	-	cyt	0	Cytoplasm (Probable)				638

You are viewing entries 55301 to 55350 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.