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
P51613 UniProt NPD GO	CHIB_VITVI	Basic endochitinase precursor (EC 3.2.1.14)	0.20	-	end	0					314
Q8BGM5 UniProt NPD GO	VMDL1_MOUSE	Bestrophin-2 (Vitelliform macular dystrophy 2-like protein 1)	0.20	-	nuc	5 *	Cell membrane; multi-pass membrane protein				508
O35486 UniProt NPD GO	CRBS_MOUSE	Beta crystallin S (Gamma crystallin S)	0.20	-	nuc	0				2A5M	177
O09010 UniProt NPD GO	LFNG_MOUSE	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.20	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				378
P79948 UniProt NPD GO	LFNG_XENLA	Beta-1,3-N-acetylglucosaminyltransferase lunatic fringe (EC 2.4.1.222) (O-fucosylpeptide 3-beta-N-ac ...	0.20	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				375
Q9N295 UniProt NPD GO	B3GT5_PANTR	Beta-1,3-galactosyltransferase 5 (EC 2.4.1.-) (Beta-1,3-GalTase 5) (Beta3Gal-T5) (b3Gal-T5) (UDP-gal ...	0.20	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (Potential)				297
O02662 UniProt NPD GO	ADRB3_CANFA	Beta-3 adrenergic receptor (Beta-3 adrenoceptor) (Beta-3 adrenoreceptor)	0.20	-	end	7 *	Membrane; multi-pass membrane protein				405
Q8IZN7 UniProt NPD GO	D107A_HUMAN	Beta-defensin 107A precursor (Defensin, beta 107A) (Defensin, beta 107) (Beta-defensin 7) (DEFB-7) ( ...	0.20	-	mit	1 *	Secreted protein				66
Q91VD6 UniProt NPD GO	BD06_MOUSE	Beta-defensin 6 precursor (Defensin, beta 6) (BD-6) (mBD-6)	0.20	-	nuc	1 *	Secreted protein				63
P46166 UniProt NPD GO	BD08_BOVIN	Beta-defensin 8 (BNDB-8) (BNBD-8)	0.20	-	mit	0	Secreted protein				38
O18815 UniProt NPD GO	BDC7_BOVIN	Beta-defensin C7 precursor (BBD(C7)) (Fragment)	0.20	-	mit	0	Secreted protein				53
P02758 UniProt NPD GO	LACB1_HORSE	Beta-lactoglobulin-1 precursor (Beta-LG-1) (Beta-lactoglobulin I) (BLGI)	0.20	-	end	0	Secreted protein				180
O00462 UniProt NPD GO	MANBA_HUMAN	Beta-mannosidase precursor (EC 3.2.1.25) (Lysosomal beta A mannosidase) (Mannanase) (Mannase)	0.20	-	exc	0	Lysosome		609489		879
Q5PQN2 UniProt NPD GO	BFAR_RAT	Bifunctional apoptosis regulator	0.20	-	end	2	Endoplasmic reticulum; endoplasmic reticulum membrane; multi-pass membrane protein (By similarity)				450
P19835 UniProt NPD GO	CEL_HUMAN	Bile salt-activated lipase precursor (EC 3.1.1.3) (EC 3.1.1.13) (BAL) (Bile salt-stimulated lipase) ...	0.20	-	exc	0		cytoplasm [ISS]	114840	1JMY	742
P84213 UniProt NPD GO	BOMB_BOMVA	Bombesin precursor	0.20	-	exc	0	Secreted protein	extracellular region [IDA]			107
P36895 UniProt NPD GO	BMR1A_MOUSE	Bone morphogenetic protein receptor type IA precursor (EC 2.7.11.30) (Serine/threonine-protein kinas ...	0.20	-	end	1	Membrane; single-pass type I membrane protein				532
P01057 UniProt NPD GO	IBB3_DOLAX	Bowman-Birk type proteinase inhibitor DE-3	0.20	-	nuc	0					76
P83283 UniProt NPD GO	IBB2_AMBCE	Bowman-birk type proteinase inhibitor 2 (TcTI2)	0.20	-	nuc	0					63
Q9P290 UniProt NPD GO	BOCT_RAT	Brain-type organic cation transporter (Solute carrier family 22 member 17)	0.20	-	end	11	Membrane; multi-pass membrane protein (Potential)				516
P56498 UniProt NPD GO	CXCR4_FELCA	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (SDF-1 receptor) (Stromal cell-derived factor 1 re ...	0.20	-	end	7 *	Membrane; multi-pass membrane protein				353
O08565 UniProt NPD GO	CXCR4_RAT	C-X-C chemokine receptor type 4 (CXC-R4) (CXCR-4) (Stromal cell-derived factor 1 receptor) (SDF-1 re ...	0.20	-	end	7 *	Membrane; multi-pass membrane protein				349
P34997 UniProt NPD GO	CXCR5_RAT	C-X-C chemokine receptor type 5 (CXC-R5) (CXCR-5) (Burkitt lymphoma receptor 1 homolog) (Neurolympha ...	0.20	+	end	7	Membrane; multi-pass membrane protein				374
P56546 UniProt NPD GO	CTBP2_MOUSE	C-terminal-binding protein 2 (CtBP2)	0.20	+	nuc	0	Nucleus (Potential)	nucleus [IDA]			445
P18104 UniProt NPD GO	ANFC_PIG	C-type natriuretic peptide precursor [Contains: CNP-22; CNP-29; CNP-53]	0.20	-	exc	0	Secreted protein				126
Q9NRP2 UniProt NPD GO	CP061_HUMAN	C16orf61 protein	0.20	+	nuc	0					79
Q8IZ96 UniProt NPD GO	CKLF1_HUMAN	CKLF-like MARVEL transmembrane domain-containing protein 1 (Chemokine-like factor superfamily member ...	0.20	-	end	4 *	Membrane; multi-pass membrane protein		607884		169
O94454 UniProt NPD GO	CSN5_SCHPO	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.20	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)	signalosome complex [IDA]			299
Q6C703 UniProt NPD GO	CSN5_YARLI	COP9 signalosome complex subunit 5 (EC 3.4.-.-)	0.20	-	nuc	0	Cytoplasm (By similarity). Nucleus (By similarity)				354
Q5RF54 UniProt NPD GO	CSN8_PONPY	COP9 signalosome complex subunit 8 (Signalosome subunit 8)	0.20	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				209
Q751L7 UniProt NPD GO	PYRG_ASHGO	CTP synthase (EC 6.3.4.2) (UTP--ammonia ligase) (CTP synthetase)	0.20	-	nuc	0					576
P55281 UniProt NPD GO	CAD17_RAT	Cadherin-17 precursor (Liver-intestine-cadherin) (LI-cadherin)	0.20	-	end	1	Membrane; single-pass type I membrane protein	basolateral plasma membrane [IDA]			827
Q60755 UniProt NPD GO	CALCR_MOUSE	Calcitonin receptor precursor (CT-R)	0.20	-	end	7	Membrane; multi-pass membrane protein				515
Q9JLK7 UniProt NPD GO	CABP1_MOUSE	Calcium-binding protein 1 (CaBP1)	0.20	-	nuc	0					226
P37397 UniProt NPD GO	CNN3_RAT	Calponin-3 (Calponin, acidic isoform) (Calponin, non-muscle isoform)	0.20	-	nuc	0		actin filament [TAS] microtubule [TAS]			330
Q40401 UniProt NPD GO	CALR_NICPL	Calreticulin precursor	0.20	-	end	1 *	Endoplasmic reticulum; endoplasmic reticulum lumen (By similarity)				416
O15438 UniProt NPD GO	MRP3_HUMAN	Canalicular multispecific organic anion transporter 2 (Multidrug resistance-associated protein 3) (M ...	0.20	-	end	14 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	604323		1527
P78358 UniProt NPD GO	CTG1B_HUMAN	Cancer/testis antigen 1B (L antigen family member 2) (LAGE-2 protein) (Autoimmunogenic cancer/testis ...	0.20	-	nuc	0			300156	2BNR	180
O75828 UniProt NPD GO	DHC3_HUMAN	Carbonyl reductase [NADPH] 3 (EC 1.1.1.184) (NADPH-dependent carbonyl reductase 3)	0.20	-	mit	0	Cytoplasm (Potential)		603608		276
Q9JHH6 UniProt NPD GO	CBPB2_MOUSE	Carboxypeptidase B2 precursor (EC 3.4.17.20) (Carboxypeptidase U) (Thrombin-activable fibrinolysis i ...	0.20	-	cyt	0	Secreted protein				422
P61012 UniProt NPD GO	PPLA_CANFA	Cardiac phospholamban (PLB)	0.20	-	mit	1 *	Membrane				52
P61013 UniProt NPD GO	PPLA_PIG	Cardiac phospholamban (PLB)	0.20	-	mit	1 *	Membrane (By similarity)			1FJP	52
Q07560 UniProt NPD GO	CRD1_YEAST	Cardiolipin synthetase (EC 2.7.8.-) (Cardiolipin synthase) (CLS)	0.20	-	mit	3	Mitochondrion; mitochondrial inner membrane; multi-pass membrane protein	mitochondrial envelope [IDA]			283
Q60753 UniProt NPD GO	CTF1_MOUSE	Cardiotrophin-1 (CT-1)	0.20	-	cyt	0	Secreted protein				203
Q68Y62 UniProt NPD GO	CPT1A_HORSE	Carnitine O-palmitoyltransferase I, liver isoform (EC 2.3.1.21) (CPT I) (CPTI-L) (Carnitine palmitoy ...	0.20	-	nuc	2	Mitochondrion; mitochondrial outer membrane; multi-pass membrane protein (By similarity)				776
Q8TG11 UniProt NPD GO	CSK2C_NEUCR	Casein kinase II subunit beta-2 (CK II beta-2)	0.20	+	cyt	0					285
Q9BXQ7 UniProt NPD GO	CECR4_HUMAN	Cat eye syndrome critical region protein 4 (Fragment)	0.20	-	nuc	0					124
P56202 UniProt NPD GO	CATW_HUMAN	Cathepsin W precursor (EC 3.4.22.-) (Lymphopain)	0.20	-	exc	0			602364		376
P54209 UniProt NPD GO	ATC1_DUNBI	Cation-transporting ATPase CA1 (EC 3.6.3.-)	0.20	-	end	8	Membrane; multi-pass membrane protein				1037
P06704 UniProt NPD GO	CDC31_YEAST	Cell division control protein 31 (Nucleoporin CDC31) (Nuclear pore protein CDC31)	0.20	-	cyt	0	Nucleus; nuclear envelope; nuclear pore complex. Spindle pole body, SPB half-bridge	half bridge of spindle pole body [TAS] nuclear pore [TAS]		2GV5	161

You are viewing entries 50401 to 50450 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.)

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