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
P22357 UniProt NPD GO	ASF1_HELAN	Anther-specific protein SF18 precursor (Fragment)	0.07	-	nuc	0					161
P20302 UniProt NPD GO	APRP_ENTHI	Antigenic protein P1 (Pathogenic protein 1) (Fragment)	0.07	-	cyt	0					639
P81572 UniProt NPD GO	DEFD1_SPIOL	Antimicrobial peptide D1 (So-D1) (Defensin D1) (Fragment)	0.07	-	nuc	0					22
P32262 UniProt NPD GO	ANT3_SHEEP	Antithrombin-III precursor (ATIII)	0.07	-	mit	0	Secreted protein; extracellular space				465
P56316 UniProt NPD GO	CYF_CHLVU	Apocytochrome f precursor	0.07	-	end	1 *	Plastid; chloroplast; chloroplast thylakoid membrane; single-pass membrane protein (By similarity)				315
P18656 UniProt NPD GO	APOA2_MACFA	Apolipoprotein A-II precursor (Apo-AII) (ApoA-II)	0.07	-	exc	0	Secreted protein				100
P02655 UniProt NPD GO	APOC2_HUMAN	Apolipoprotein C-II precursor (Apo-CII) (ApoC-II)	0.07	-	exc	0	Secreted protein	extracellular region [NAS]	207750	1SOH	101
Q07813 UniProt NPD GO	BAXA_MOUSE	Apoptosis regulator BAX, membrane isoform alpha	0.07	-	end	1	Membrane; single-pass membrane protein	cytosol [IDA] mitochondrial outer membrane [IDA]			192
Q8W037 UniProt NPD GO	NIP21_ARATH	Aquaporin NIP2.1 (NOD26-like intrinsic protein 2.1) (Nodulin-26-like major intrinsic protein 4) (AtN ...	0.07	-	end	5 *	Membrane; multi-pass membrane protein (Probable)				288
P55087 UniProt NPD GO	AQP4_HUMAN	Aquaporin-4 (AQP-4) (WCH4) (Mercurial-insensitive water channel) (MIWC)	0.07	-	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	600308		323
Q41116 UniProt NPD GO	AR5B_PHAVU	Arcelin-5B precursor	0.07	-	vac	0					261
P40906 UniProt NPD GO	ARGI_COCIM	Arginase (EC 3.5.3.1)	0.07	-	cyt	0					322
O08691 UniProt NPD GO	ARGI2_MOUSE	Arginase-2, mitochondrial precursor (EC 3.5.3.1) (Arginase II) (Non-hepatic arginase) (Kidney-type a ...	0.07	-	mit	0	Mitochondrion				354
Q4X1R1 UniProt NPD GO	RMT2_ASPFU	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				424
Q4IQK7 UniProt NPD GO	RMT2_GIBZE	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.07	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)				425
Q9XY07 UniProt NPD GO	KARG_STIJA	Arginine kinase (EC 2.7.3.3) (AK)	0.07	-	nuc	0					370
P17770 UniProt NPD GO	DDC_CATRO	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (Tryptophan decarboxyl ...	0.07	-	cyt	0					500
Q06597 UniProt NPD GO	ACR2_YEAST	Arsenical-resistance protein ACR2	0.07	-	nuc	0					130
P14296 UniProt NPD GO	ARYA_MANSE	Arylphorin subunit alpha precursor	0.07	-	exc	0	Secreted protein; extracellular space				702
P51689 UniProt NPD GO	ARSD_HUMAN	Arylsulfatase D precursor (EC 3.1.6.-) (ASD)	0.07	-	mit	3	Lysosome (Potential)		300002		593
P19252 UniProt NPD GO	ASNS2_PEA	Asparagine synthetase, root [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine syn ...	0.07	-	mit	0					582
P10723 UniProt NPD GO	SYNC_BRUMA	Asparaginyl-tRNA synthetase, cytoplasmic (EC 6.1.1.22) (Asparagine--tRNA ligase) (AsnRS) (Potentiall ...	0.07	-	cyt	0	Cytoplasm (Probable)				548
P46644 UniProt NPD GO	AAT3_ARATH	Aspartate aminotransferase, chloroplast precursor (EC 2.6.1.1) (Transaminase A)	0.07	-	nuc	0	Plastid; chloroplast (Potential)				449
P26563 UniProt NPD GO	AATM_LUPAN	Aspartate aminotransferase-P2, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Fragment)	0.07	-	cyt	0	Mitochondrion; mitochondrial matrix				454
Q43645 UniProt NPD GO	API4_SOLTU	Aspartic protease inhibitor 4 precursor (API-13) (PI13)	0.07	-	exc	0	Vacuole (By similarity)				220
Q42456 UniProt NPD GO	ASPR1_ORYSA	Aspartic proteinase oryzasin-1 precursor (EC 3.4.23.-)	0.07	-	end	1 *					509
P81992 UniProt NPD GO	CRVP2_AUSSU	Asurin-2 (Fragment)	0.07	-	nuc	0	Secreted protein				28
P45884 UniProt NPD GO	ATTA_DROME	Attacin-A precursor	0.07	-	vac	1 *	Secreted protein				224
Q6CBC3 UniProt NPD GO	ATG7_YARLI	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7)	0.07	-	cyt	0	Cytoplasm (By similarity)				598
P33079 UniProt NPD GO	A10A5_SOYBN	Auxin-induced protein 10A5	0.07	-	mit	0					93
P0C132 UniProt NPD GO	IAA30_ORYSA	Auxin-responsive protein IAA30 (Indoleacetic acid-induced protein 30)	0.07	-	cyt	0	Nucleus (By similarity)				277
O70526 UniProt NPD GO	BKRB2_CAVPO	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				372
O15155 UniProt NPD GO	BET1_HUMAN	BET1 homolog (Golgi vesicular membrane-trafficking protein p18) (hBET1)	0.07	-	cyt	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)	Golgi membrane [TAS]	605456		118
Q9XWB9 UniProt NPD GO	BAT36_CAEEL	BTB and MATH domain-containing protein 36	0.07	-	cyt	0					320
Q6J1J1 UniProt NPD GO	BIRC5_BOVIN	Baculoviral IAP repeat-containing protein 5 (Apoptosis inhibitor survivin)	0.07	-	nuc	0	Cytoplasm. Nucleus. Localizes on chromosome arms and inner centromeres from prophase through metapha ...				142
Q16611 UniProt NPD GO	BAK_HUMAN	Bcl-2 homologous antagonist/killer (Apoptosis regulator BAK) (Bcl-2-like 7 protein)	0.07	-	cyt	1	Membrane; single-pass membrane protein (Potential)		600516	1BXL	211
Q9I8I2 UniProt NPD GO	BOK_CHICK	Bcl-2-related ovarian killer protein	0.07	-	nuc	0					213
Q792S6 UniProt NPD GO	BOK_RAT	Bcl-2-related ovarian killer protein	0.07	-	mit	0					213
Q9UMX3 UniProt NPD GO	BOK_HUMAN	Bcl-2-related ovarian killer protein (Hbok)	0.07	-	mit	0			605404		212
O35425 UniProt NPD GO	BOK_MOUSE	Bcl-2-related ovarian killer protein (Matador protein) (Apoptosis activator Mtd)	0.07	-	mit	0					213
P53673 UniProt NPD GO	CRBA4_HUMAN	Beta crystallin A4 (Beta-A4-crystallin)	0.07	-	cyt	0			123631		195
P07318 UniProt NPD GO	CRBB1_BOVIN	Beta crystallin B1	0.07	-	cyt	0					252
P53674 UniProt NPD GO	CRBB1_HUMAN	Beta crystallin B1	0.07	-	cyt	0			600929	1OKI	251
P10112 UniProt NPD GO	CRBS_CYPCA	Beta crystallin S (Gamma crystallin S)	0.07	-	cyt	0					173
O75752 UniProt NPD GO	B3GT3_HUMAN	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.07	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein		603094		331
Q6AY39 UniProt NPD GO	B3GT3_RAT	Beta-1,3-galactosyltransferase 3 (EC 2.4.1.79) (Beta-1,3-GalTase 3) (Beta3Gal-T3) (b3Gal-T3) (Galact ...	0.07	-	nuc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				331
Q66HH1 UniProt NPD GO	B4GT4_RAT	Beta-1,4-galactosyltransferase 4 (EC 2.4.1.-) (Beta-1,4-GalTase 4) (Beta4Gal-T4) (b4Gal-T4) (UDP-gal ...	0.07	-	nuc	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				344
P07550 UniProt NPD GO	ADRB2_HUMAN	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein	endosome [TAS] integral to plasma membrane [TAS] lysosome [TAS] plasma membrane [TAS]	109690		413
Q28509 UniProt NPD GO	ADRB2_MACMU	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				415
P04274 UniProt NPD GO	ADRB2_MESAU	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor)	0.07	-	end	7 *	Membrane; multi-pass membrane protein				418

You are viewing entries 69551 to 69600 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.