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
P19456 UniProt NPD GO	PMA2_ARATH	ATPase 2, plasma membrane-type (EC 3.6.3.6) (Proton pump 2)	0.28	-	end	9	Cell membrane; multi-pass membrane protein (Probable)				947
P09114 UniProt NPD GO	ILV2_TOBAC	Acetolactate synthase 2, chloroplast precursor (EC 2.2.1.6) (Acetolactate synthase II) (Acetohydroxy ...	0.28	-	mit	0	Plastid; chloroplast				664
Q6YSF3 UniProt NPD GO	AN32_ORYSA	Acidic leucine-rich nuclear phosphoprotein 32-related protein (ANP32/acidic nuclear phosphoprotein-l ...	0.28	-	cyt	0					476
Q8ILI6 UniProt NPD GO	AN32_PLAF7	Acidic leucine-rich nuclear phosphoprotein 32-related protein (ANP32/acidic nuclear phosphoprotein-l ...	0.28	-	nuc	0					281
Q25381 UniProt NPD GO	ACTM_LYTPI	Actin, muscle (LPM) (Fragment)	0.28	-	nuc	0	Cytoplasm				172
Q8SAG3 UniProt NPD GO	ADF_VITVI	Actin-depolymerizing factor (ADF)	0.28	-	cyt	0					143
Q3T035 UniProt NPD GO	ARPC3_BOVIN	Actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC)	0.28	-	nuc	0					177
O15145 UniProt NPD GO	ARPC3_HUMAN	Actin-related protein 2/3 complex subunit 3 (ARP2/3 complex 21 kDa subunit) (p21-ARC)	0.28	-	nuc	0		Arp2/3 protein complex [TAS]	604225		177
Q5RC19 UniProt NPD GO	ACOX1_PONPY	Acyl-coenzyme A oxidase 1, peroxisomal (EC 1.3.3.6) (Palmitoyl-CoA oxidase) (AOX)	0.28	-	pox	0	Peroxisome (By similarity)				660
Q9EPL9 UniProt NPD GO	ACOX3_MOUSE	Acyl-coenzyme A oxidase 3, peroxisomal (EC 1.3.3.6) (Pristanoyl-CoA oxidase) (Branched-chain acyl-Co ...	0.28	-	mit	0	Peroxisome (Potential)	peroxisomal matrix [TAS]			700
O88444 UniProt NPD GO	ADCY1_MOUSE	Adenylate cyclase type 1 (EC 4.6.1.1) (Adenylate cyclase type I) (ATP pyrophosphate-lyase 1) (Ca(2+) ...	0.28	-	end	9	Membrane; multi-pass membrane protein	plasma membrane [TAS]			1118
Q80TL1 UniProt NPD GO	ADCY2_MOUSE	Adenylate cyclase type 2 (EC 4.6.1.1) (Adenylate cyclase type II) (ATP pyrophosphate-lyase 2) (Adeny ...	0.28	-	end	12 *	Membrane; multi-pass membrane protein	dendrite [IDA] plasma membrane [TAS]			1090
P26769 UniProt NPD GO	ADCY2_RAT	Adenylate cyclase type 2 (EC 4.6.1.1) (Adenylate cyclase type II) (ATP pyrophosphate-lyase 2) (Adeny ...	0.28	-	end	12 *	Membrane; multi-pass membrane protein			1U0H	1090
Q9JJ22 UniProt NPD GO	ARTS1_RAT	Adipocyte-derived leucine aminopeptidase precursor (EC 3.4.11.-) (A-LAP) (ARTS-1) (Aminopeptidase PI ...	0.28	-	cyt	0	Secreted protein (By similarity)	cytosol [ISS] endoplasmic reticulum [ISS] extracellular region [ISS] integral to membrane [ISS] microsome [IDA]			930
Q9NZ08 UniProt NPD GO	ARTS1_HUMAN	Adipocyte-derived leucine aminopeptidase precursor (EC 3.4.11.-) (A-LAP) (ARTS-1) (Aminopeptidase PI ...	0.28	-	cyt	0	Secreted protein	cytosol [NAS] endoplasmic reticulum [NAS] endoplasmic reticulum lumen [TAS] extracellular region [IDA] integral to membrane [NAS]	606832		929
O13368 UniProt NPD GO	ALA1_CANAL	Agglutinin-like protein ALA1 precursor (Agglutinin-like adhesin)	0.28	-	nuc	0					1419
P42330 UniProt NPD GO	AK1C3_HUMAN	Aldo-keto reductase family 1 member C3 (EC 1.-.-.-) (Trans-1,2-dihydrobenzene-1,2-diol dehydrogenase ...	0.28	-	cyt	0	Cytoplasm		603966	1XF0	323
Q6DGA6 UniProt NPD GO	ALLC_BRARE	Allantoicase (EC 3.5.3.4) (Allantoate amidinohydrolase)	0.28	-	pox	0					395
Q9LS03 UniProt NPD GO	AOC1_ARATH	Allene oxide cyclase 1, chloroplast precursor (EC 5.3.99.6) (Early-responsive to dehydration 12 prot ...	0.28	-	mit	0	Plastid; chloroplast			1ZVC	254
O93591 UniProt NPD GO	CRYAA_ASTFA	Alpha crystallin A chain	0.28	-	nuc	0					173
P68405 UniProt NPD GO	CRYAA_MERUN	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.28	-	cyt	0					173
P68406 UniProt NPD GO	CRYAA_TUPGL	Alpha crystallin A chain [Contains: Alpha crystallin A chain, short form]	0.28	-	cyt	0					173
Q5R9K0 UniProt NPD GO	CRYAB_PONPY	Alpha crystallin B chain (Alpha(B)-crystallin)	0.28	-	mit	0					175
P02511 UniProt NPD GO	CRYAB_HUMAN	Alpha crystallin B chain (Alpha(B)-crystallin) (Rosenthal fiber component) (Heat-shock protein beta- ...	0.28	-	mit	0			608810		175
P40549 UniProt NPD GO	MNT3_YEAST	Alpha-1,3-mannosyltransferase MNT3 (EC 2.4.1.-)	0.28	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				630
P07758 UniProt NPD GO	A1AT1_MOUSE	Alpha-1-antitrypsin 1-1 precursor (Serine protease inhibitor 1-1) (Alpha-1 protease inhibitor 1) (Al ...	0.28	-	end	0	Secreted protein				413
O77713 UniProt NPD GO	ADA2B_DUGDU	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.28	-	end	6 *	Membrane; multi-pass membrane protein (By similarity)				390
O77721 UniProt NPD GO	ADA2B_HORSE	Alpha-2B adrenergic receptor (Alpha-2B adrenoceptor) (Alpha-2B adrenoreceptor) (Fragment)	0.28	-	end	6 *	Membrane; multi-pass membrane protein				389
Q8NKE2 UniProt NPD GO	AOX_CRYNV	Alternative oxidase, mitochondrial precursor (EC 1.-.-.-)	0.28	-	mit	0	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein; matrix side (By similarity ...				401
P15144 UniProt NPD GO	AMPN_HUMAN	Aminopeptidase N (EC 3.4.11.2) (hAPN) (Alanyl aminopeptidase) (Microsomal aminopeptidase) (Aminopept ...	0.28	-	exc	1 *	Cell membrane; single-pass type II membrane protein. Cytoplasm; cytosol (Potential). A soluble form ...	ER-Golgi intermediate compartment [IDA] integral to plasma membrane [TAS]	151530		966
Q5R7M3 UniProt NPD GO	AMGO2_PONPY	Amphoterin-induced protein 2 precursor (AMIGO-2)	0.28	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Nucleus (By similarity). Associa ...	integral to plasma membrane [ISS]			522
O95704 UniProt NPD GO	APBB3_HUMAN	Amyloid beta A4 precursor protein-binding family B member 3 (Fe65-like protein 2) (Fe65L2)	0.28	-	cyt	0		cytoplasm [TAS]	602711		486
O42971 UniProt NPD GO	APC10_SCHPO	Anaphase-promoting complex subunit 10 (20S cyclosome/APC complex protein apc10)	0.28	-	cyt	0					189
Q9V831 UniProt NPD GO	APC10_DROME	Anaphase-promoting complex subunit 10 (APC10) (Cyclosome subunit 10)	0.28	-	cyt	0					195
Q861Y4 UniProt NPD GO	ANGI_TRAFR	Angiogenin precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.28	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]			146
Q06807 UniProt NPD GO	TIE2_BOVIN	Angiopoietin-1 receptor precursor (EC 2.7.10.1) (Tyrosine-protein kinase receptor TIE-2) (CD202b ant ...	0.28	-	end	1	Membrane; single-pass type I membrane protein				1125
Q8K4V2 UniProt NPD GO	B3A4_RAT	Anion exchange protein 4 (Anion exchanger 4) (Solute carrier family 4 member 9)	0.28	-	end	11	Cell membrane; basolateral cell membrane; multi-pass membrane protein. In contrast to the rabbit ort ...	basolateral plasma membrane [IDA]			953
Q96Q91 UniProt NPD GO	B3A4_HUMAN	Anion exchange protein 4 (Anion exchanger 4) (Solute carrier family 4 member 9) (Sodium bicarbonate ...	0.28	-	end	11	Membrane; multi-pass membrane protein				983
Q2IBE3 UniProt NPD GO	ASZ1_PONPY	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.28	-	nuc	0	Cytoplasm (By similarity)				475
Q99JG3 UniProt NPD GO	ANX13_MOUSE	Annexin A13 (Annexin XIII)	0.28	-	cyt	0	Cell membrane (By similarity). Associated with the plasma membrane of undifferentiated, proliferatin ...				316
P54228 UniProt NPD GO	BMA27_BOVIN	Antibacterial peptide BMAP-27 precursor (Myeloid antibacterial peptide 27)	0.28	+	nuc	1 *	Secreted protein				158
P83138 UniProt NPD GO	AFP4_MALPA	Antifungal protein 4 (CW-4) (Fragment)	0.28	-	nuc	0	Secreted protein				37
O18759 UniProt NPD GO	APOA1_TUPGB	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.28	-	exc	0	Secreted protein				265
Q400C7 UniProt NPD GO	AMZ2_RAT	Archaemetzincin-2 (EC 3.-.-.-) (Archeobacterial metalloproteinase-like protein 2)	0.28	-	cyt	0					359
Q60HH3 UniProt NPD GO	ARLY_MACFA	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL)	0.28	-	cyt	0					464
Q3UJZ3 UniProt NPD GO	ARMC7_MOUSE	Armadillo repeat-containing protein 7	0.28	-	nuc	0					198
Q7QHW5 UniProt NPD GO	ARM_ANOGA	Armadillo segment polarity protein	0.28	-	nuc	0	Cytoplasm (By similarity). Cell membrane; peripheral membrane protein; cytoplasmic side (By similari ...				830
P12275 UniProt NPD GO	ARYL_CHICK	Arylamine N-acetyltransferase, liver isozyme (EC 2.3.1.5) (Arylamine acetylase)	0.28	-	nuc	0					287
O43776 UniProt NPD GO	SYNC_HUMAN	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS)	0.28	-	cyt	0	Cytoplasm	cytoplasm [TAS] soluble fraction [TAS]	108410		548
P00508 UniProt NPD GO	AATM_CHICK	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.28	-	nuc	0	Mitochondrion; mitochondrial matrix			9AAT	423

You are viewing entries 42001 to 42050 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.