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
Q10066 UniProt NPD GO	ARGI2_SCHPO	Arginase (EC 3.5.3.1)	0.06	-	cyt	0					323
Q74ZW4 UniProt NPD GO	ARGI_ASHGO	Arginase (EC 3.5.3.1)	0.06	-	mit	0	Cytoplasm (By similarity)				399
Q91553 UniProt NPD GO	ARGN1_XENLA	Arginase, non-hepatic 1 (EC 3.5.3.1)	0.06	-	mit	0					360
Q91554 UniProt NPD GO	ARGN2_XENLA	Arginase, non-hepatic 2 (EC 3.5.3.1)	0.06	-	mit	0					360
Q91555 UniProt NPD GO	ARGN3_XENLA	Arginase, non-hepatic 3 (EC 3.5.3.1)	0.06	-	mit	0					360
Q5KP51 UniProt NPD GO	RMT2_CRYNE	Arginine N-methyltransferase 2 (EC 2.1.1.-)	0.06	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				363
Q96412 UniProt NPD GO	SPE1_DIACA	Arginine decarboxylase (EC 4.1.1.19) (ARGDC) (ADC)	0.06	-	cyt	0					725
P14568 UniProt NPD GO	ASSY_BOVIN	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.06	-	cyt	0					412
P09034 UniProt NPD GO	ASSY_RAT	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.06	-	cyt	0					412
O94354 UniProt NPD GO	ASSY_SCHPO	Argininosuccinate synthase (EC 6.3.4.5) (Citrulline--aspartate ligase)	0.06	-	cyt	0					410
P15289 UniProt NPD GO	ARSA_HUMAN	Arylsulfatase A precursor (EC 3.1.6.8) (ASA) (Cerebroside-sulfatase) [Contains: Arylsulfatase A comp ...	0.06	-	exc	0	Lysosome	lysosome [TAS]	250100	2AIK	507
P54793 UniProt NPD GO	ARSF_HUMAN	Arylsulfatase F precursor (EC 3.1.6.-) (ASF)	0.06	-	end	2	Secreted protein (Potential)		300003		590
P81990 UniProt NPD GO	CRVP_ASPSC	Ascarin (Fragment)	0.06	-	cyt	0	Secreted protein				30
P49078 UniProt NPD GO	ASNS_ARATH	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.06	-	mit	0					583
O24661 UniProt NPD GO	ASNS_TRIVS	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.06	-	mit	0					585
P00504 UniProt NPD GO	AATC_CHICK	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.06	-	cyt	0	Cytoplasm			2CST	411
P13221 UniProt NPD GO	AATC_RAT	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.06	-	cyt	0	Cytoplasm	cytosol [TAS]			412
P12344 UniProt NPD GO	AATM_BOVIN	Aspartate aminotransferase, mitochondrial precursor (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloac ...	0.06	-	nuc	0	Mitochondrion; mitochondrial matrix				430
P18144 UniProt NPD GO	ANF_ANGJA	Atrial natriuretic factor (ANF) (Atrial natriuretic peptide) (ANP)	0.06	-	nuc	0	Secreted protein				27
Q10142 UniProt NPD GO	AUR1_SCHPO	Aureobasidin A resistance protein homolog	0.06	-	end	6 *	Membrane; multi-pass membrane protein (Potential)				422
Q5A6K2 UniProt NPD GO	ATG22_CANAL	Autophagy-related protein 22	0.06	-	end	9	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				500
Q6CD56 UniProt NPD GO	ATG22_YARLI	Autophagy-related protein 22	0.06	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				589
Q5AW93 UniProt NPD GO	AT221_EMENI	Autophagy-related protein 22-1	0.06	-	end	11	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				580
Q9CPX6 UniProt NPD GO	ATG3_MOUSE	Autophagy-related protein 3 (APG3-like)	0.06	-	nuc	0	Cytoplasm (By similarity)				314
Q6GQE7 UniProt NPD GO	ATG3_XENLA	Autophagy-related protein 3 (APG3-like)	0.06	-	nuc	0	Cytoplasm (By similarity)				313
Q5I0S6 UniProt NPD GO	ATG3_XENTR	Autophagy-related protein 3 (APG3-like)	0.06	-	nuc	0	Cytoplasm (By similarity)				312
Q6AZ50 UniProt NPD GO	ATG3_RAT	Autophagy-related protein 3 (APG3-like) (Preconditioning-inducible gene 1 protein)	0.06	-	nuc	0	Cytoplasm (By similarity)				314
Q9NT62 UniProt NPD GO	ATG3_HUMAN	Autophagy-related protein 3 (APG3-like) (hApg3) (Protein PC3-96)	0.06	-	nuc	0	Cytoplasm	cytoplasmic ubiquitin ligase complex [IPI] cytosol [IDA]	609606		314
Q5SMQ9 UniProt NPD GO	PIN1_ORYSA	Auxin efflux carrier component 1 (OsPIN1) (Ethylene insensitive root 1 homolog)	0.06	-	end	10 *	Membrane; multi-pass membrane protein (Potential)				595
Q9LFB2 UniProt NPD GO	LAX1_ARATH	Auxin transporter-like protein 1 (AUX1-like protein 1)	0.06	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				488
Q7XGU4 UniProt NPD GO	LAX3_ORYSA	Auxin transporter-like protein 3	0.06	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				547
P40691 UniProt NPD GO	A115_TOBAC	Auxin-induced protein PCNT115	0.06	-	cyt	0					307
Q652A1 UniProt NPD GO	IAA26_ORYSA	Auxin-responsive protein IAA26 (Indoleacetic acid-induced protein 26)	0.06	-	mit	0	Nucleus (By similarity)				140
P33077 UniProt NPD GO	IAA4_ARATH	Auxin-responsive protein IAA4 (Indoleacetic acid-induced protein 4) (Auxin-induced protein AUX2-11)	0.06	-	cyt	0	Nucleus				186
P25023 UniProt NPD GO	BKRB2_RAT	B2 bradykinin receptor (BK-2 receptor) (B2R)	0.06	-	end	8 *	Membrane; multi-pass membrane protein				396
P28814 UniProt NPD GO	BARW_HORVU	Barwin	0.06	-	cyt	0				1BW4	125
P22585 UniProt NPD GO	LECB2_PSOSC	Basic lectin B2 (Fragment)	0.06	-		0					15
P56374 UniProt NPD GO	CRBA4_RAT	Beta crystallin A4 (Beta-A4-crystallin)	0.06	-	cyt	0					195
P02523 UniProt NPD GO	CRBB1_RAT	Beta crystallin B1 [Contains: Beta crystallin B1B]	0.06	-	cyt	0					249
O70430 UniProt NPD GO	ADRB1_MERUN	Beta-1 adrenergic receptor (Beta-1 adrenoceptor) (Beta-1 adrenoreceptor) (Fragment)	0.06	-	nuc	1 *	Cell membrane; multi-pass membrane protein (By similarity). Localized at the plasma membrane. Found ...				73
Q8MU95 UniProt NPD GO	BGBP_PLOIN	Beta-1,3-glucan-binding protein precursor (BGBP) (Beta-1,3-glucan recognition protein) (BetaGRP)	0.06	-	exc	0	Secreted protein	extracellular region [IDA]			488
Q80WN7 UniProt NPD GO	B4GT4_CRIGR	Beta-1,4-galactosyltransferase 4 (EC 2.4.1.-) (Beta-1,4-GalTase 4) (Beta4Gal-T4) (b4Gal-T4) (UDP-gal ...	0.06	-	cyt	1 *	Golgi apparatus; Golgi stack; Golgi stack membrane; single-pass type II membrane protein (By similar ...				344
Q9GKM2 UniProt NPD GO	B2MG_TRIVU	Beta-2-microglobulin precursor	0.06	-	exc	0	Secreted protein				122
Q8R5C5 UniProt NPD GO	ACTY_MOUSE	Beta-centractin (Actin-related protein 1B) (ARP1B)	0.06	-	cyt	0					376
Q8K4N3 UniProt NPD GO	BD12_MOUSE	Beta-defensin 12 precursor (Defensin, beta 12) (BD-12) (mBD-12)	0.06	-	cyt	1 *	Secreted protein (By similarity)				85
Q91V82 UniProt NPD GO	BD08_MOUSE	Beta-defensin 8 precursor (Defensin, beta 8) (BD-8) (mBD-8) (Defensin-related peptide) (Defr1)	0.06	-	end	0	Secreted protein (By similarity)			1E4R	60
Q8R2I6 UniProt NPD GO	BD09_MOUSE	Beta-defensin 9 precursor (Defensin, beta 9) (BD-9) (mBD-9)	0.06	-	exc	1 *	Secreted protein (By similarity)				67
P07322 UniProt NPD GO	ENOB_CHICK	Beta-enolase (EC 4.2.1.11) (2-phospho-D-glycerate hydro-lyase) (Phosphopyruvate hydratase)	0.06	-	cyt	0	Cytoplasm				433
P49175 UniProt NPD GO	INV1_MAIZE	Beta-fructofuranosidase 1 precursor (EC 3.2.1.26) (Sucrose 1) (Invertase 1)	0.06	-	gol	1 *	Vacuole				670
Q9TRY9 UniProt NPD GO	BGAL_CANFA	Beta-galactosidase precursor (EC 3.2.1.23) (Lactase) (Acid beta-galactosidase)	0.06	-	exc	0	Lysosome				668

You are viewing entries 71601 to 71650 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.