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
P48261 UniProt NPD GO	TRPG_CYAPA	Anthranilate synthase component II (EC 4.1.3.27) (Glutamine amido-transferase)	0.22	-	cyt	0	Plastid; cyanelle				190
P84529 UniProt NPD GO	2SS1_BRARC	Antibacterial napin (Fragments)	0.22	-		0					20
P54229 UniProt NPD GO	BMA28_BOVIN	Antibacterial peptide BMAP-28 precursor (Myeloid antibacterial peptide 28)	0.22	-	nuc	1 *	Secreted protein				159
P83596 UniProt NPD GO	EAP1_EUCUL	Antifungal peptide 1 (EAFP1)	0.22	-	nuc	0					41
P04639 UniProt NPD GO	APOA1_RAT	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.22	-	exc	0	Secreted protein				259
P14630 UniProt NPD GO	APOM_RAT	Apolipoprotein M precursor (Apo-M) (ApoM) (Protein Px)	0.22	-	cyt	0	Secreted protein. Associated with HDL				190
P49270 UniProt NPD GO	TXP6_APTSC	Aptotoxin-6 (Aptotoxin VI) (Paralytic peptide VI) (PP VI)	0.22	-	nuc	0	Secreted protein				76
O96507 UniProt NPD GO	KARG_TRYCR	Arginine kinase (EC 2.7.3.3) (AK)	0.22	-	cyt	0					357
P05083 UniProt NPD GO	ARLY2_CHICK	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL) (Delta-2 crystallin) (Delta crystallin ...	0.22	-	nuc	0					466
Q8BHS6 UniProt NPD GO	ARMX3_MOUSE	Armadillo repeat-containing X-linked protein 3	0.22	+	mit	1 *					379
Q8BNU0 UniProt NPD GO	ARMC6_MOUSE	Armadillo repeat-containing protein 6	0.22	-	mit	0					468
Q5RD03 UniProt NPD GO	ARMC6_PONPY	Armadillo repeat-containing protein 6	0.22	-	mit	0					501
Q5R5L7 UniProt NPD GO	ARRD3_PONPY	Arrestin domain-containing protein 3	0.22	-	nuc	0					414
P51484 UniProt NPD GO	ARRH_LIMPO	Arrestin, lateral eye	0.22	-	nuc	0					400
P51467 UniProt NPD GO	ARR2_ONCMY	Arrestin, red cell isoform 2 (CARR)	0.22	-	mit	0					405
Q95MP1 UniProt NPD GO	AIPL1_BOVIN	Aryl-hydrocarbon-interacting protein-like 1	0.22	-	cyt	0	Cytoplasm (By similarity). Nucleus (By similarity)	nucleus [NAS]			328
Q99PG0 UniProt NPD GO	AAAD_MOUSE	Arylacetamide deacetylase (EC 3.1.1.-) (AADAC)	0.22	-	mit	0	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum membrane [ISS] microsome [ISS]			397
P49090 UniProt NPD GO	ASNS2_YEAST	Asparagine synthetase [glutamine-hydrolyzing] 2 (EC 6.3.5.4) (Glutamine-dependent asparagine synthet ...	0.22	-	cyt	0		cytoplasm [IDA]			571
P59704 UniProt NPD GO	API_TRICO	Aspartyl protease inhibitor precursor (Tco-API-1)	0.22	-	end	0	Secreted protein (Potential)				228
P07500 UniProt NPD GO	ANF_RABIT	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin)	0.22	-	nuc	0	Secreted protein				153
Q7M459 UniProt NPD GO	ATT_APLFA	Attractin	0.22	-	nuc	0	Secreted protein (By similarity)				58
Q6CQ13 UniProt NPD GO	ATG10_KLULA	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.22	-	nuc	0	Cytoplasm (By similarity)				155
P38862 UniProt NPD GO	ATG7_YEAST	Autophagy-related protein 7 (Autophagy-related E1-like-activating enzyme ATG7) (Cytoplasm to vacuole ...	0.22	-	cyt	0	Cytoplasm	cytoplasm [IDA] cytosol [IDA] membrane [IDA] mitochondrion [IDA]			630
P20160 UniProt NPD GO	CAP7_HUMAN	Azurocidin precursor (Cationic antimicrobial protein CAP37) (Heparin-binding protein) (HBP)	0.22	-	exc	0	Cytoplasmic granule. Cytoplasmic granules of neutrophils	azurophil granule [IDA] extracellular region [NAS]	162815	1FY3	251
P97583 UniProt NPD GO	BKRB1_RAT	B1 bradykinin receptor (BK-1 receptor) (B1R) (Kinin B1 receptor) (KB1)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				337
Q8WVF5 UniProt NPD GO	KCTD4_HUMAN	BTB/POZ domain-containing protein KCTD4	0.22	-	nuc	0					259
Q8R2H3 UniProt NPD GO	BSND_RAT	Barttin	0.22	-	exc	2 *	Cell membrane; multi-pass membrane protein (By similarity). Staining in membranes of the renal tubul ...	basolateral plasma membrane [ISS] integral to plasma membrane [ISS] protein complex [ISS]			308
Q04589 UniProt NPD GO	FGFR1_RAT	Basic fibroblast growth factor receptor 1 precursor (EC 2.7.10.1) (FGFR-1) (bFGF-R) (MFR)	0.22	-	exc	1	Membrane; single-pass type I membrane protein				822
Q94CG2 UniProt NPD GO	BET12_ARATH	Bet1-like SNARE 1-2 (AtBET12) (Bet1/Sft1-like SNARE 14b) (AtBS14b)	0.22	-	nuc	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein (By similarity)				130
Q9JJU9 UniProt NPD GO	CRBB3_MOUSE	Beta crystallin B3 (Beta-B3-crystallin)	0.22	-	cyt	0					210
Q10468 UniProt NPD GO	B4GN1_RAT	Beta-1,4 N-acetylgalactosaminyltransferase 1 (EC 2.4.1.92) ((N-acetylneuraminyl)-galactosylglucosylc ...	0.22	-	exc	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein	plasma membrane [IDA]			533
P32120 UniProt NPD GO	ARRB2_BOVIN	Beta-arrestin-2 (Arrestin, beta 2) (Arrestin-3)	0.22	-	mit	0	Cytoplasm (By similarity). Nucleus (By similarity)				420
O89117 UniProt NPD GO	BD01_RAT	Beta-defensin 1 precursor (BD-1) (RBD-1)	0.22	-	nuc	1 *	Secreted protein (By similarity)				69
P81534 UniProt NPD GO	D103A_HUMAN	Beta-defensin 103A precursor (Beta-defensin 3) (DEFB-3) (BD-3) (hBD-3) (HBD3) (Defensin-like protein ...	0.22	-	cyt	1 *	Secreted protein	extracellular region [NAS]	606611	1KJ6	67
Q30KQ7 UniProt NPD GO	DB113_HUMAN	Beta-defensin 113 precursor (Defensin, beta 113) (Beta-defensin 13) (DEFB-13)	0.22	-	exc	0	Secreted protein (By similarity)				82
Q5J602 UniProt NPD GO	DB119_MACMU	Beta-defensin 119 precursor (Defensin, beta 119)	0.22	-	nuc	0	Secreted protein (Potential)				84
Q70KL2 UniProt NPD GO	BD40_MOUSE	Beta-defensin 40 precursor (Defensin, beta 40) (BD-40) (mBD-40)	0.22	-	vac	0	Secreted protein (By similarity)				73
Q56UD4 UniProt NPD GO	INV2_ORYSA	Beta-fructofuranosidase, insoluble isoenzyme 2 precursor (EC 3.2.1.26) (Sucrose hydrolase 2) (Invert ...	0.22	+	exc	0	Secreted protein; extracellular space; apoplast (Probable). Cell wall (Probable). Associated to the ...				598
P33686 UniProt NPD GO	LACB2_CANFA	Beta-lactoglobulin-2 (Beta-LG-2) (Beta-lactoglobulin-2)	0.22	-	cyt	0	Secreted protein				161
Q9SA18 UniProt NPD GO	AKH1_ARATH	Bifunctional aspartokinase/homoserine dehydrogenase 1, chloroplast precursor (AK-HD 1) (AK-HSDH 1) ( ...	0.22	-	cyt	0	Plastid; chloroplast				911
Q27783 UniProt NPD GO	DRTS_TRYBB	Bifunctional dihydrofolate reductase-thymidylate synthase (DHFR-TS) [Includes: Dihydrofolate reducta ...	0.22	-	mit	0					527
P20772 UniProt NPD GO	PUR2_SCHPO	Bifunctional purine biosynthetic protein ADE1 [Includes: Phosphoribosylamine--glycine ligase (EC 6.3 ...	0.22	-	cyt	0					788
O95342 UniProt NPD GO	ABCBB_HUMAN	Bile salt export pump (ATP-binding cassette sub-family B member 11)	0.22	-	end	10	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS] membrane fraction [TAS]	603201		1321
Q9QY30 UniProt NPD GO	ABCBB_MOUSE	Bile salt export pump (ATP-binding cassette sub-family B member 11) (Sister of P-glycoprotein)	0.22	-	end	9	Membrane; multi-pass membrane protein	intercellular canaliculus [IDA]			1321
Q4R7C8 UniProt NPD GO	BL1S2_MACFA	Biogenesis of lysosome-related organelles complex-1 subunit 2	0.22	-	nuc	0	Centrosome. Localizes to the centrosomes in a microtubule-dependent manner (By similarity)				142
P35371 UniProt NPD GO	BRS3_CAVPO	Bombesin receptor subtype-3 (BRS-3)	0.22	-	end	7 *	Membrane; multi-pass membrane protein				399
P08955 UniProt NPD GO	PYR1_MESAU	CAD protein [Includes: Glutamine-dependent carbamoyl-phosphate synthase (EC 6.3.5.5); Aspartate carb ...	0.22	-	nuc	0	Cytoplasm				2225
Q13740 UniProt NPD GO	CD166_HUMAN	CD166 antigen precursor (Activated leukocyte-cell adhesion molecule) (ALCAM)	0.22	-	end	1 *	Membrane; single-pass type I membrane protein		601662	1KJC	583
Q9VCY3 UniProt NPD GO	CSN6_DROME	COP9 signalosome complex subunit 6 (Signalosome subunit 6) (Dch6)	0.22	-	cyt	0	Cytoplasm (Probable). Nucleus (Probable)	signalosome complex [IMP]			341
Q99627 UniProt NPD GO	CSN8_HUMAN	COP9 signalosome complex subunit 8 (Signalosome subunit 8) (SGN8) (JAB1-containing signalosome subun ...	0.22	-	cyt	0	Cytoplasm. Nucleus	nucleus [TAS]			209

You are viewing entries 48151 to 48200 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.