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
Q75W84 UniProt NPD GO	ANR_EISFO	Annetocin receptor	0.14	-	end	7	Membrane; multi-pass membrane protein	integral to membrane [IC]			420
P70075 UniProt NPD GO	ANXA5_CYNPY	Annexin A5 (Annexin V)	0.14	-	cyt	0					323
P22465 UniProt NPD GO	ANX10_DROME	Annexin-B10 (Annexin-10) (Annexin X)	0.14	-	cyt	0					320
O23918 UniProt NPD GO	HCBT3_DIACA	Anthranilate N-benzoyltransferase protein 3 (EC 2.3.1.144) (Anthranilate N-hydroxycinnamoyl/benzoylt ...	0.14	-	cyt	0					445
P83140 UniProt NPD GO	AFP1S_MALPA	Antifungal protein 1 small subunit (CW-1) (Fragment)	0.14	-		0					16
Q00746 UniProt NPD GO	ANG1_EMENI	Antigen 1 precursor (ASPND1)	0.14	-	exc	0					277
Q16981 UniProt NPD GO	APLC_APLCA	Aplycalcin	0.14	-	cyt	0					190
Q95AG0 UniProt NPD GO	CYF_CHLSU	Apocytochrome f precursor	0.14	-	nuc	2 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				317
P16013 UniProt NPD GO	CYF_SPIOL	Apocytochrome f precursor	0.14	-	nuc	1	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				320
P83704 UniProt NPD GO	APOA2_HORSE	Apolipoprotein A-II (Apo-AII) (ApoA-II)	0.14	-	cyt	0	Secreted protein				76
Q9BG58 UniProt NPD GO	APOC2_TUPGL	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.14	-	exc	0	Secreted protein				101
O95445 UniProt NPD GO	APOM_HUMAN	Apolipoprotein M (Apo-M) (ApoM) (Protein G3a)	0.14	-	cyt	0	Secreted protein. Present in high density lipoprotein (HDL) and to a lesser extent in triglyceride-r ...	integral to plasma membrane [TAS]	606907		188
Q9BWW8 UniProt NPD GO	APOL6_HUMAN	Apolipoprotein-L6 (Apolipoprotein L-VI) (ApoL-VI)	0.14	-	mit	3	Cytoplasm (Probable)	cytoplasm [NAS]	607256		343
P59692 UniProt NPD GO	SIVA_RAT	Apoptosis regulatory protein Siva (CD27-binding protein) (CD27BP)	0.14	-	mit	0	Cytoplasm (By similarity)				177
Q9UBU3 UniProt NPD GO	GHRL_HUMAN	Appetite-regulating hormone precursor (Growth hormone secretagogue) (Growth hormone-releasing peptid ...	0.14	-	exc	1 *	Secreted protein	extracellular space [ISS]	605353	1P7X	117
P50635 UniProt NPD GO	APY_AEDAE	Apyrase precursor (EC 3.6.1.5) (ATP-diphosphatase) (Adenosine diphosphatase) (ADPase) (ATP-diphospho ...	0.14	-	cyt	1 *	Secreted protein				562
Q6BNS9 UniProt NPD GO	RMT2_DEBHA	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.14	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				434
Q03471 UniProt NPD GO	ARIS_PENRO	Aristolochene synthase (EC 4.2.3.9) (Sesquiterpene cyclase) (AS)	0.14	-	cyt	0	Cytoplasm			1F1P	342
P20711 UniProt NPD GO	DDC_HUMAN	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.14	-	nuc	0			608643		480
P80041 UniProt NPD GO	DDC_PIG	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.14	-	cyt	0				1JS6	486
P37200 UniProt NPD GO	ARRE_RAT	Arrestin-E (Fragment)	0.14	-	nuc	0					72
Q10723 UniProt NPD GO	ARS_VOLCA	Arylsulfatase precursor (EC 3.1.6.1) (AS) (Aryl-sulfate sulphohydrolase)	0.14	-	exc	1 *	Periplasm				649
P33097 UniProt NPD GO	AATC_BOVIN	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.14	-	cyt	0	Cytoplasm				412
Q99MQ4 UniProt NPD GO	ASPN_MOUSE	Asporin precursor	0.14	+	nuc	0	Secreted protein; extracellular space; extracellular matrix (By similarity)	extracellular matrix (sensu Metazoa) [IDA]			373
P24259 UniProt NPD GO	ANF_PIG	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin) [ ...	0.14	-	exc	0	Secreted protein				150
P10730 UniProt NPD GO	ANPRC_BOVIN	Atrial natriuretic peptide clearance receptor precursor (ANP-C) (ANPRC) (NPR-C) (Atrial natriuretic ...	0.14	-	end	1	Membrane; single-pass type I membrane protein				537
Q6FWS7 UniProt NPD GO	ATG10_CANGA	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.14	-	cyt	0	Cytoplasm (By similarity)				159
Q871U2 UniProt NPD GO	ATG7_NEUCR	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme atg-7)	0.14	-	nuc	0	Cytoplasm (By similarity)				699
Q9C6B8 UniProt NPD GO	PINI_ARATH	Auxin efflux carrier component 1 (Protein PIN-FORMED) (AtPIN1)	0.14	-	end	9 *	Membrane; multi-pass membrane protein (Potential)	cytoplasm [IDA]			622
P0C133 UniProt NPD GO	IAA31_ORYSA	Auxin-responsive protein IAA31 (Indoleacetic acid-induced protein 31)	0.14	-	cyt	0	Nucleus (By similarity)				197
P40293 UniProt NPD GO	CD79A_BOVIN	B-cell antigen receptor complex-associated protein alpha-chain precursor (IG-alpha) (MB-1 membrane g ...	0.14	-	nuc	2 *	Membrane; single-pass type I membrane protein				223
Q9H0C5 UniProt NPD GO	BTBD1_HUMAN	BTB/POZ domain-containing protein 1 (Hepatitis C virus NS5A-transactivated protein 8) (NS5ATP8)	0.14	-	nuc	0	Cytoplasm. Cytoplasmic bodies		608530		482
Q8K2J9 UniProt NPD GO	BTBD6_MOUSE	BTB/POZ domain-containing protein 6	0.14	-	cyt	0					410
P38971 UniProt NPD GO	ALP1_YEAST	Basic amino-acid permease	0.14	+	end	12	Membrane; multi-pass membrane protein				573
Q66RM2 UniProt NPD GO	BI1_PIG	Bax inhibitor 1 (BI-1) (Testis-enhanced gene transcript)	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				237
Q5R7R1 UniProt NPD GO	BI1_PONPY	Bax inhibitor 1 (BI-1) (Testis-enhanced gene transcript)	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				237
P55061 UniProt NPD GO	BI1_HUMAN	Bax inhibitor 1 (BI-1) (Testis-enhanced gene transcript) (Transmembrane BAX inhibitor motif-containi ...	0.14	-	end	6 *	Membrane; multi-pass membrane protein (Potential)	endoplasmic reticulum [TAS] insoluble fraction [TAS] integral to plasma membrane [TAS] nucleus [TAS]	600748		237
Q03562 UniProt NPD GO	BRE3_CAEEL	Beta 1,4-mannosyltransferase bre-3 (EC 2.4.1.-) (Bt toxin-resistant protein 3)	0.14	-	end	5 *	Cytoplasm. In punctate structures throughout the cell	cytoplasm [IEP]			455
P00987 UniProt NPD GO	IVB1_BUNMU	Beta bungarotoxin B1 chain, major component precursor	0.14	-	exc	0	Secreted protein				85
Q91314 UniProt NPD GO	CRB12_RANCA	Beta crystallin A1-2	0.14	-	cyt	0					198
P11842 UniProt NPD GO	CRBA4_BOVIN	Beta crystallin A4 (Beta-A4-crystallin)	0.14	-	cyt	0					209
Q9WVK5 UniProt NPD GO	B4GT6_MOUSE	Beta-1,4-galactosyltransferase 6 (EC 2.4.1.-) (Beta-1,4-GalTase 6) (Beta4Gal-T6) (b4Gal-T6) (UDP-gal ...	0.14	-	mit	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				382
Q9XT57 UniProt NPD GO	ADRB3_CAPHI	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.14	-	end	6 *	Membrane; multi-pass membrane protein				405
P83943 UniProt NPD GO	BD01_CHILA	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1) (cBD-1)	0.14	-	exc	1 *	Secreted protein				67
Q8NG35 UniProt NPD GO	D105A_HUMAN	Beta-defensin 105A precursor (Beta-defensin 5) (DEFB-5) (BD-5)	0.14	-	exc	1 *	Secreted protein				78
P46167 UniProt NPD GO	BD09_BOVIN	Beta-defensin 9 precursor (BNDB-9) (BNBD-9) (Fragment)	0.14	-	mit	0	Secreted protein				55
Q5JJV0 UniProt NPD GO	INV4_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 4 precursor (EC 3.2.1.26) (Sucrose hydrolase 4) (Invert ...	0.14	-	exc	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				590
P49614 UniProt NPD GO	HEXB_FELCA	Beta-hexosaminidase beta chain precursor (EC 3.2.1.52) (N-acetyl-beta-glucosaminidase) (Beta-N-acety ...	0.14	-	mit	0	Lysosome				531
P25142 UniProt NPD GO	MSMB_MACMU	Beta-microseminoprotein precursor (Prostate secreted seminal plasma protein) (Prostate secretory pro ...	0.14	-	exc	1 *	Secreted protein. Sperm surface (By similarity)				114
Q9NZS9 UniProt NPD GO	BFAR_HUMAN	Bifunctional apoptosis regulator (RING finger protein 47)	0.14	-	end	3	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [IDA]			450

You are viewing entries 58001 to 58050 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.