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
P07510 UniProt NPD GO	ACHG_HUMAN	Acetylcholine receptor protein subunit gamma precursor	0.15	-	end	4	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	100730		517
P05376 UniProt NPD GO	ACHG_XENLA	Acetylcholine receptor protein subunit gamma precursor	0.15	-	end	4	Membrane; multi-pass membrane protein				510
Q75AW1 UniProt NPD GO	ARGD_ASHGO	Acetylornithine aminotransferase, mitochondrial precursor (EC 2.6.1.11) (ACOAT)	0.15	-	mit	0	Mitochondrion; mitochondrial matrix (By similarity)				423
P17513 UniProt NPD GO	CHIP_TOBAC	Acidic endochitinase P precursor (EC 3.2.1.14) (Pathogenesis-related protein P) (PR-P)	0.15	-	mit	1 *	Secreted protein. Extracellular fluid from leaves				253
P28575 UniProt NPD GO	IPP_MOUSE	Actin-binding protein IPP (MIPP protein) (Murine IAP-promoted placenta-expressed protein)	0.15	-	nuc	0					584
Q41764 UniProt NPD GO	ADF3_MAIZE	Actin-depolymerizing factor 3 (ADF 3) (ZmABP3) (ZmADF3)	0.15	-	cyt	0	Cytoplasm. As root hairs emerges and the microfilament bundles redirect to the outgrowth ADF3 concen ...				139
Q04549 UniProt NPD GO	ARP10_YEAST	Actin-like protein ARP10	0.15	-	cyt	0		cytoplasm [IDA] dynactin complex [IPI]			284
Q6BML9 UniProt NPD GO	ARP6_DEBHA	Actin-like protein ARP6	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				409
Q6CJF4 UniProt NPD GO	ARP6_KLULA	Actin-like protein ARP6	0.15	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				415
P59998 UniProt NPD GO	ARPC4_HUMAN	Actin-related protein 2/3 complex subunit 4 (ARP2/3 complex 20 kDa subunit) (p20-ARC)	0.15	-	mit	0		Arp2/3 protein complex [TAS]	604226		167
P59999 UniProt NPD GO	ARPC4_MOUSE	Actin-related protein 2/3 complex subunit 4 (ARP2/3 complex 20 kDa subunit) (p20-ARC)	0.15	-	mit	0		Arp2/3 protein complex [TAS]			167
O65201 UniProt NPD GO	ACOX2_ARATH	Acyl-coenzyme A oxidase 2, peroxisomal precursor (EC 1.3.3.6) (AOX 2) (Long-chain acyl-CoA oxidase) ...	0.15	-	cyt	0	Peroxisome (Probable)				692
O74936 UniProt NPD GO	ACOX3_YARLI	Acyl-coenzyme A oxidase 3 (EC 1.3.3.6) (Acyl-CoA oxidase 3)	0.15	-	cyt	0	Peroxisome				700
Q7L5N7 UniProt NPD GO	AYTL1_HUMAN	Acyltransferase-like 1 (EC 2.3.1.-)	0.15	-	nuc	1	Membrane; single-pass type II membrane protein (Potential)				544
Q8W420 UniProt NPD GO	ADO2_ARATH	Adagio protein 2 (LOV kelch protein 2) (Flavin-binding kelch repeat F-box protein 1-like protein 1) ...	0.15	-	cyt	0	Nucleus				611
Q64427 UniProt NPD GO	APT_MASHI	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.15	-	cyt	0	Cytoplasm				180
P47956 UniProt NPD GO	APT_MUSPA	Adenine phosphoribosyltransferase (EC 2.4.2.7) (APRT)	0.15	-	nuc	0	Cytoplasm				180
Q9VEI3 UniProt NPD GO	S35B2_DROME	Adenosine 3'-phospho 5'-phosphosulfate transporter 1 (PAPS transporter 1) (Protein slalom)	0.15	-	end	10 *	Golgi apparatus; Golgi membrane; multi-pass membrane protein (By similarity)	Golgi apparatus [IDA] integral to membrane [NAS]			465
P00570 UniProt NPD GO	KAD1_BOVIN	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.15	-	cyt	0	Cytoplasm				194
P00568 UniProt NPD GO	KAD1_HUMAN	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.15	-	cyt	0	Cytoplasm		103000		194
P00571 UniProt NPD GO	KAD1_PIG	Adenylate kinase isoenzyme 1 (EC 2.7.4.3) (ATP-AMP transphosphorylase) (AK1) (Myokinase)	0.15	-	cyt	0	Cytoplasm			3ADK	194
P40122 UniProt NPD GO	CAP_CHLVR	Adenylyl cyclase-associated protein (CAP)	0.15	-	nuc	0	Cell membrane (By similarity)				481
Q8CG45 UniProt NPD GO	ARK72_RAT	Aflatoxin B1 aldehyde reductase member 2 (EC 1.-.-.-) (rAFAR2)	0.15	-	mit	0	Golgi apparatus; Golgi stack. Its association with the Golgi stack may facilitate secretion of GHB	Golgi apparatus [IDA]			367
Q39528 UniProt NPD GO	LEC1_CLALU	Agglutinin-1 precursor (Agglutinin I) (ClAI) (LecClAI) [Contains: Agglutinin-1 subunit A; Agglutinin ...	0.15	-	nuc	0					293
Q9BSE5 UniProt NPD GO	SPEB_HUMAN	Agmatinase, mitochondrial precursor (EC 3.5.3.11) (Agmatine ureohydrolase) (AUH)	0.15	-	mit	0	Mitochondrion				352
Q94AL9 UniProt NPD GO	AGT22_ARATH	Alanine--glyoxylate aminotransferase 2 homolog 2, mitochondrial precursor (EC 2.6.1.44) (Beta-alanin ...	0.15	-	mit	0	Mitochondrion (Potential)				477
P10127 UniProt NPD GO	ADH4_YEAST	Alcohol dehydrogenase 4 (EC 1.1.1.1) (Alcohol dehydrogenase IV)	0.15	-	nuc	0		mitochondrion [IDA]			465
Q8TDN7 UniProt NPD GO	ASAH3_HUMAN	Alkaline ceramidase 1 (EC 3.5.1.23) (Alkaline CDase-1) (AlkCDase 1) (Acylsphingosine deacylase 3) (N ...	0.15	-	end	7 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				264
Q8VHE9 UniProt NPD GO	RETST_RAT	All-trans-retinol 13,14-reductase precursor (EC 1.3.99.23) (All-trans-13,14-dihydroretinol saturase) ...	0.15	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum membrane; peripheral membrane protein (By similarity)	endoplasmic reticulum membrane [ISS] nuclear outer membrane [ISS]			609
Q9LS02 UniProt NPD GO	AOC2_ARATH	Allene oxide cyclase 2, chloroplast precursor (EC 5.3.99.6)	0.15	-	mit	0	Plastid; chloroplast	thylakoid membrane (sensu Viridiplantae) [IDA]		1Z8K	253
P61409 UniProt NPD GO	AF2_GRASP	Alpha mechanotoxin (Peptide GsAF II)	0.15	-	cyt	0	Secreted protein				31
Q9JIG1 UniProt NPD GO	FUT9_CRIGR	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.15	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
O88819 UniProt NPD GO	FUT9_MOUSE	Alpha-(1,3)-fucosyltransferase (EC 2.4.1.-) (Galactoside 3-L-fucosyltransferase) (Fucosyltransferase ...	0.15	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				359
P50076 UniProt NPD GO	ALG10_YEAST	Alpha-1,2 glucosyltransferase ALG10 (EC 2.4.1.-) (Alpha-2-glucosyltransferase ALG10) (Dolichyl-phosp ...	0.15	-	end	11 *	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	endoplasmic reticulum membrane [IMP]			525
P27810 UniProt NPD GO	KTR1_YEAST	Alpha-1,2 mannosyltransferase KTR1 (EC 2.4.1.131)	0.15	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	Golgi apparatus [IDA]			393
Q8VDI9 UniProt NPD GO	ALG9_MOUSE	Alpha-1,2-mannosyltransferase ALG9 (EC 2.4.1.-) (Asparagine-linked glycosylation protein 9 homolog) ...	0.15	-	end	8	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				611
P02764 UniProt NPD GO	A1AG_RAT	Alpha-1-acid glycoprotein precursor (Orosomucoid) (OMD)	0.15	-	mit	0					205
O54759 UniProt NPD GO	ALST_TAMSI	Alpha-1-antitrypsin-like protein CM55-ST precursor	0.15	-	end	0					413
Q9WU25 UniProt NPD GO	ADA1A_CAVPO	Alpha-1A adrenergic receptor (Alpha 1A-adrenoceptor) (Alpha 1A-adrenoreceptor) (Alpha-1C adrenergic ...	0.15	-	end	7 *	Membrane; multi-pass membrane protein				466
P19269 UniProt NPD GO	AMY1_DEBOC	Alpha-amylase 1 precursor (EC 3.2.1.1) (1,4-alpha-D-glucan glucanohydrolase 1)	0.15	-	exc	0					512
O77015 UniProt NPD GO	AMYR_DROOR	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.15	-	cyt	0	Secreted protein (Probable)				493
O76261 UniProt NPD GO	AMYR_DROSE	Alpha-amylase-related protein precursor (EC 3.2.1.1)	0.15	-	cyt	0	Secreted protein (Probable)				493
P11643 UniProt NPD GO	IAAD_HORVU	Alpha-amylase/trypsin inhibitor CMd precursor (Chloroform/methanol-soluble protein CMd)	0.15	-	exc	1 *	Secreted protein				171
P35698 UniProt NPD GO	ELIA_PHYME	Alpha-elicitin MGM-alpha	0.15	-	nuc	0	Secreted protein				98
Q38865 UniProt NPD GO	EXPA6_ARATH	Alpha-expansin 6 precursor (AtEXPA6) (At-EXP6) (AtEx6) (Ath-ExpAlpha-1.8)	0.15	-	exc	0	Cell wall; peripheral membrane protein				257
O09174 UniProt NPD GO	AMACR_MOUSE	Alpha-methylacyl-CoA racemase (EC 5.1.99.4) (2-methylacyl-CoA racemase)	0.15	-	nuc	0	Peroxisome. Mitochondrion	mitochondrion [IDA]			380
Q56X52 UniProt NPD GO	AOX4_ARATH	Alternative oxidase 4, chloroplast precursor (EC 1.-.-.-) (Protein IMMUTANS) (Plastid terminal oxida ...	0.15	-	mit	2	Plastid; chloroplast; chloroplast thylakoid membrane; multi-pass membrane protein. Plastid; chromopl ...				351
Q6Q2J0 UniProt NPD GO	AOFA_PIG	Amine oxidase [flavin-containing] A (EC 1.4.3.4) (Monoamine oxidase type A) (MAO-A)	0.15	+	cyt	1	Mitochondrion; mitochondrial outer membrane (By similarity)				527
Q8VCT3 UniProt NPD GO	AMPB_MOUSE	Aminopeptidase B (EC 3.4.11.6) (Ap-B) (Arginyl aminopeptidase) (Arginine aminopeptidase) (Cytosol am ...	0.15	-	cyt	0	Secreted protein	extracellular region [ISS] Golgi apparatus [ISS] plasma membrane [ISS]			650
P53390 UniProt NPD GO	MEP3_YEAST	Ammonium transporter MEP3	0.15	-	end	11 *	Membrane; multi-pass membrane protein	plasma membrane [IMP]			489

You are viewing entries 56601 to 56650 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.