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
P28514 UniProt NPD GO	ARY2_CALVI	Arylphorin subunit C223 precursor	0.03	-	vac	0	Secreted protein; extracellular space				759
P51690 UniProt NPD GO	ARSE_HUMAN	Arylsulfatase E precursor (EC 3.1.6.-) (ASE)	0.03	-	end	3	Golgi apparatus; Golgi stack		302950		589
Q60HH5 UniProt NPD GO	ARSE_MACFA	Arylsulfatase E precursor (EC 3.1.6.-) (ASE)	0.03	-	end	4 *	Golgi apparatus; Golgi stack (By similarity)				588
P50473 UniProt NPD GO	ARS_STRPU	Arylsulfatase precursor (EC 3.1.6.1) (AS) (Aryl-sulfate sulphohydrolase) (ARS)	0.03	-	exc	0	Secreted protein				567
P63115 UniProt NPD GO	AAA1_MOUSE	Asc-type amino acid transporter 1 (Asc-1) (D-serine transporter)	0.03	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [NAS]			530
P63116 UniProt NPD GO	AAA1_RAT	Asc-type amino acid transporter 1 (Asc-1) (D-serine transporter)	0.03	-	end	12 *	Membrane; multi-pass membrane protein (Probable)	integral to plasma membrane [ISS]			530
P49094 UniProt NPD GO	ASNS_MAIZE	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.03	-	mit	0					585
P49088 UniProt NPD GO	ASNS_RAT	Asparagine synthetase [glutamine-hydrolyzing] (EC 6.3.5.4) (Glutamine-dependent asparagine synthetas ...	0.03	-	cyt	0					560
Q9SSK1 UniProt NPD GO	SYNC3_ARATH	Asparaginyl-tRNA synthetase, cytoplasmic 3 (EC 6.1.1.22) (Asparagine--tRNA ligase 3) (AsnRS 3)	0.03	-	cyt	0	Cytoplasm (Probable)				571
P12343 UniProt NPD GO	AATC_RABIT	Aspartate aminotransferase, cytoplasmic (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate transa ...	0.03	-	cyt	0	Cytoplasm				30
P12345 UniProt NPD GO	AATM_RABIT	Aspartate aminotransferase, mitochondrial (EC 2.6.1.1) (Transaminase A) (Glutamate oxaloacetate tran ...	0.03	-	nuc	0	Mitochondrion; mitochondrial matrix	mitochondrial matrix [IDA]			30
Q41480 UniProt NPD GO	API1_SOLTU	Aspartic protease inhibitor 1 precursor (pA1) (gCDI-A1) (STPIA) (STPID)	0.03	-	vac	1 *	Vacuole (By similarity)				221
Q41448 UniProt NPD GO	API7_SOLTU	Aspartic protease inhibitor 7 precursor (Cathepsin D inhibitor p749)	0.03	-	exc	0	Vacuole (By similarity)				221
Q60HH2 UniProt NPD GO	ACY2_MACFA	Aspartoacylase (EC 3.5.1.15) (Aminoacylase-2) (ACY-2)	0.03	-	cyt	0					313
P41748 UniProt NPD GO	PEPF_ASPFU	Aspergillopepsin F precursor (EC 3.4.23.18) (Aspergillopepsin I)	0.03	-	nuc	1 *	Secreted protein				395
Q12380 UniProt NPD GO	ATG5_YEAST	Autophagy protein 5	0.03	-	cyt	0	Cytoplasm. Membrane; peripheral membrane protein. Found in pre-autophagosomal structure and other pu ...	autophagic vacuole [IDA] cytosol [IDA]			294
Q55S70 UniProt NPD GO	ATG12_CRYNE	Autophagy-related protein 12 (Autophagy-related ubiquitin-like modifier ATG12)	0.03	-	cyt	0	Cytoplasm (Probable)				105
Q6FX92 UniProt NPD GO	ATG22_CANGA	Autophagy-related protein 22	0.03	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				541
P25568 UniProt NPD GO	ATG22_YEAST	Autophagy-related protein 22	0.03	-	end	10	Vacuole; vacuolar membrane; multi-pass membrane protein. Vacuole and punctate structures	vacuolar membrane [IDA]			528
Q4WZY1 UniProt NPD GO	AT222_ASPFU	Autophagy-related protein 22-2	0.03	-	end	12 *	Vacuole; vacuolar membrane; multi-pass membrane protein (By similarity). Vacuole and punctate struct ...				613
Q9FEL8 UniProt NPD GO	LAX1_MEDTR	Auxin transporter-like protein 1 (AUX1-like protein 1) (MtLAX1)	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				479
Q9S836 UniProt NPD GO	LAX2_ARATH	Auxin transporter-like protein 2 (AUX1-like protein 2)	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				483
Q8L883 UniProt NPD GO	LAX5_MEDTR	Auxin transporter-like protein 5 (AUX1-like protein 5) (MtLAX5)	0.03	-	end	10	Cell membrane; multi-pass membrane protein (By similarity)				490
P33491 UniProt NPD GO	ABP2_TOBAC	Auxin-binding protein T92 precursor (ABP)	0.03	-	end	0	Endoplasmic reticulum; endoplasmic reticulum lumen				187
P33081 UniProt NPD GO	AX15A_SOYBN	Auxin-induced protein 15A	0.03	-	cyt	0					82
Q6J163 UniProt NPD GO	5NG4_PINTA	Auxin-induced protein 5NG4	0.03	-	end	10 *	Membrane; multi-pass membrane protein (Potential). Detected in the periphery of cells and punctate s ...	cell cortex [IDA] cytoplasm [IDA] integral to plasma membrane [NAS]			410
P56733 UniProt NPD GO	AVR3_CHICK	Avidin-related protein 3 precursor	0.03	-	exc	0					150
Q8BXV2 UniProt NPD GO	BRI3B_MOUSE	BRI3-binding protein (I3-binding protein)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (Potential)				253
P14663 UniProt NPD GO	CEC3_MANSE	Bactericidin B-3 (Cecropin-like peptide B-3)	0.03	-	nuc	0	Secreted protein				37
P14664 UniProt NPD GO	CEC4_MANSE	Bactericidin B-4 (Cecropin-like peptide B-4)	0.03	-	nuc	0	Secreted protein				37
Q9R1T1 UniProt NPD GO	BAF_RAT	Barrier-to-autointegration factor (LAP2-binding protein 1)	0.03	-	cyt	0	Nucleus (By similarity). Cytoplasm (By similarity). Significantly enriched at the nuclear inner memb ...				89
Q9W6I0 UniProt NPD GO	BZFB_XENLA	Basic FGF-repressed Zic-binding protein homolog (Zic3-binding protein)	0.03	-	cyt	0					200
P29137 UniProt NPD GO	CHI1_CASSA	Basic endochitinase CH1 (EC 3.2.1.14) (Fragment)	0.03	-	cyt	0					35
Q9NL89 UniProt NPD GO	BGBP_BOMMO	Beta-1,3-glucan-binding protein precursor (BGBP) (Beta-1,3-glucan recognition protein) (BetaGRP)	0.03	-	cyt	0	Secreted protein (By similarity)	extracellular region [IDA]			495
O70431 UniProt NPD GO	ADRB2_MERUN	Beta-2 adrenergic receptor (Beta-2 adrenoceptor) (Beta-2 adrenoreceptor) (Fragment)	0.03	-	end	4 *	Membrane; multi-pass membrane protein (By similarity)				251
Q95LB0 UniProt NPD GO	APOH_PANTR	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.03	-	exc	0	Secreted protein (By similarity)				345
P02749 UniProt NPD GO	APOH_HUMAN	Beta-2-glycoprotein 1 precursor (Beta-2-glycoprotein I) (Apolipoprotein H) (Apo-H) (B2GPI) (Beta(2)G ...	0.03	-	exc	0	Secreted protein	extracellular region [NAS]	138700	1QUB	345
P55076 UniProt NPD GO	B2MG_BARIN	Beta-2-microglobulin precursor	0.03	-	mit	0	Secreted protein				116
Q8AYH8 UniProt NPD GO	B2MG_PAROL	Beta-2-microglobulin precursor	0.03	-	mit	0	Secreted protein				115
Q8CIQ3 UniProt NPD GO	B2MG_SIGHI	Beta-2-microglobulin precursor	0.03	-	exc	0	Secreted protein				119
Q864T6 UniProt NPD GO	B2MG_TACAC	Beta-2-microglobulin precursor	0.03	-	exc	0	Secreted protein				118
O64407 UniProt NPD GO	AMYB_VIGUN	Beta-amylase (EC 3.2.1.2) (1,4-alpha-D-glucan maltohydrolase)	0.03	-	cyt	0					496
Q95M66 UniProt NPD GO	BD01_SAGOE	Beta-defensin 1 precursor (BD-1) (Defensin, beta 1)	0.03	-	exc	0	Secreted protein				68
Q8N104 UniProt NPD GO	D106A_HUMAN	Beta-defensin 106A precursor (Beta-defensin 6) (DEFB-6) (BD-6)	0.03	-	end	0	Secreted protein	extracellular region [NAS]			65
Q5IAB3 UniProt NPD GO	D106A_PANTR	Beta-defensin 106A precursor (Defensin, beta 106A) (Defensin, beta 106) (Beta-defensin 6) (DEFB-6) ( ...	0.03	-	end	0	Secreted protein (By similarity)				65
Q8R2I7 UniProt NPD GO	BD11_MOUSE	Beta-defensin 11 precursor (Defensin, beta 11) (BD-11) (mBD-11)	0.03	-	exc	0	Secreted protein (By similarity)				77
Q30KR0 UniProt NPD GO	DB110_HUMAN	Beta-defensin 110 precursor (Defensin, beta 110) (Beta-defensin 10) (DEFB-10)	0.03	-	mit	0	Secreted protein (By similarity)				62
Q30KJ9 UniProt NPD GO	DB130_PANTR	Beta-defensin 130 precursor (Defensin, beta 130)	0.03	-	nuc	0	Secreted protein (Potential)				79
Q30KQ2 UniProt NPD GO	DB130_HUMAN	Beta-defensin 130 precursor (Defensin, beta 130) (Beta-defensin 30) (DEFB-30)	0.03	-	nuc	0	Secreted protein (Potential)				79
Q9BDS9 UniProt NPD GO	BD02_MACMU	Beta-defensin 2 precursor (BD-2) (RhBD-2) (Defensin, beta 2)	0.03	-	end	1 *	Secreted protein (By similarity)				64

You are viewing entries 79201 to 79250 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.