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
Q03044 UniProt NPD GO	A1AT_DIDMA	Alpha-1-antiproteinase precursor (Alpha-1-antitrypsin) (Alpha-1-proteinase inhibitor)	0.20	-	end	0	Secreted protein				410
P02765 UniProt NPD GO	FETUA_HUMAN	Alpha-2-HS-glycoprotein precursor (Fetuin-A) (Alpha-2-Z-globulin) (Ba-alpha-2-glycoprotein) [Contain ...	0.20	-	exc	0	Secreted protein	extracellular region [NAS] extracellular space [NAS]	138680		367
P48441 UniProt NPD GO	IDUA_MOUSE	Alpha-L-iduronidase precursor (EC 3.2.1.76)	0.20	-	exc	0	Lysosome				634
P50418 UniProt NPD GO	CAS2_RABIT	Alpha-S2A-casein precursor	0.20	-	exc	0	Secreted protein				180
P83490 UniProt NPD GO	NXAC_COERA	Alpha-colubritoxin	0.20	-	nuc	0	Secreted protein				77
O48818 UniProt NPD GO	EXPA4_ARATH	Alpha-expansin 4 precursor (AtEXPA4) (At-EXP4) (AtEx4) (Ath-ExpAlpha-1.6)	0.20	-	exc	0	Cell wall; peripheral membrane protein				257
Q9S7Y7 UniProt NPD GO	XYL1_ARATH	Alpha-xylosidase precursor (EC 3.2.1.-)	0.20	-	vac	0	Cell wall. Secreted protein; extracellular space; apoplast	cell wall (sensu Magnoliophyta) [IDA]			915
Q8JZQ5 UniProt NPD GO	ABP1_MOUSE	Amiloride-sensitive amine oxidase [copper-containing] precursor (EC 1.4.3.6) (Diamine oxidase) (DAO) ...	0.20	-	vac	0	Secreted protein; extracellular space (By similarity)				751
P93256 UniProt NPD GO	GCST_MESCR	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.20	-	cyt	0	Mitochondrion				408
P49364 UniProt NPD GO	GCST_PEA	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.20	-	mit	0	Mitochondrion				408
P54260 UniProt NPD GO	GCST_SOLTU	Aminomethyltransferase, mitochondrial precursor (EC 2.1.2.10) (Glycine cleavage system T protein) (G ...	0.20	-	mit	0	Mitochondrion				406
Q86WK7 UniProt NPD GO	AMGO3_HUMAN	Amphoterin-induced protein 3 precursor (AMIGO-3) (Alivin-3)	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS]			504
Q8C2S7 UniProt NPD GO	AMGO3_MOUSE	Amphoterin-induced protein 3 precursor (AMIGO-3) (Alivin-3)	0.20	-	end	1	Membrane; single-pass type I membrane protein (Potential)	integral to membrane [ISS]			508
Q499M5 UniProt NPD GO	ANR16_RAT	Ankyrin repeat domain-containing protein 16	0.20	-	cyt	0					370
Q8WMX8 UniProt NPD GO	ASZ1_BOVIN	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.20	-	nuc	1	Cytoplasm (By similarity)				475
Q2QLG0 UniProt NPD GO	ASZ1_CALJA	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.20	-	nuc	0	Cytoplasm (By similarity)				477
P51662 UniProt NPD GO	ANXA1_RABIT	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin II) (Chromobindin-9) (p35) (Phospholipase A2 inhibi ...	0.20	-	cyt	0					346
P24551 UniProt NPD GO	ANXA1_RODSP	Annexin A1 (Annexin I) (Lipocortin I) (Calpactin)	0.20	-	cyt	0					345
P30205 UniProt NPD GO	WC11_BOVIN	Antigen WC1.1 precursor	0.20	-	end	1	Secreted protein				1436
P80389 UniProt NPD GO	AMP1_CHICK	Antimicrobial peptide CHP1 (Chicken heterophil peptide 1)	0.20	-	mit	0					39
Q3SYR5 UniProt NPD GO	APOC4_BOVIN	Apolipoprotein C-IV precursor (Apo-CIV) (ApoC-IV)	0.20	-	exc	0	Secreted protein (By similarity)				127
P55057 UniProt NPD GO	APOC4_RABIT	Apolipoprotein C-IV precursor (Apo-CIV) (ApoC-IV) (PARP)	0.20	-	gol	0	Secreted protein				124
Q5M889 UniProt NPD GO	APOF_RAT	Apolipoprotein F precursor (Apo-F) (Liver regeneration-related protein LRRG151)	0.20	-	cyt	0	Secreted protein (By similarity)				308
Q9HAU6 UniProt NPD GO	FKSG2_HUMAN	Apoptosis inhibitor FKSG2	0.20	-	cyt	0					173
Q5R819 UniProt NPD GO	AQP1_PONPY	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.20	+	end	6 *	Membrane; multi-pass membrane protein				268
P29972 UniProt NPD GO	AQP1_HUMAN	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.20	+	end	6 *	Membrane; multi-pass membrane protein	integral to plasma membrane [TAS]	107776	1IH5	268
P47865 UniProt NPD GO	AQP1_BOVIN	Aquaporin-1 (AQP-1) (Aquaporin-CHIP) (Water channel protein for red blood cells and kidney proximal ...	0.20	+	end	6 *	Membrane; multi-pass membrane protein			1J4N	270
O19043 UniProt NPD GO	LOX12_RABIT	Arachidonate 12-lipoxygenase, 12S-type (EC 1.13.11.31) (12-LOX)	0.20	-	cyt	0	Cytoplasm				662
P12530 UniProt NPD GO	LOX15_RABIT	Arachidonate 15-lipoxygenase (EC 1.13.11.33) (Omega-6 lipoxygenase) (Erythroid cell-specific 15-lipo ...	0.20	-	cyt	0	Cytoplasm			1LOX	662
O61367 UniProt NPD GO	KARG_APIME	Arginine kinase (EC 2.7.3.3) (AK)	0.20	-	cyt	0					355
Q01592 UniProt NPD GO	ARLY_COLLI	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL) (Delta crystallin)	0.20	-	nuc	0					466
Q5R9J3 UniProt NPD GO	ARMX3_PONPY	Armadillo repeat-containing X-linked protein 3	0.20	+	mit	1 *					379
Q9UH62 UniProt NPD GO	ARMX3_HUMAN	Armadillo repeat-containing X-linked protein 3 (Protein ALEX3) (ARM protein lost in epithelial cance ...	0.20	+	mit	1 *			300364		379
P14173 UniProt NPD GO	DDC_RAT	Aromatic-L-amino-acid decarboxylase (EC 4.1.1.28) (AADC) (DOPA decarboxylase) (DDC)	0.20	-	cyt	0		intracellular [TAS]			480
Q6TXF1 UniProt NPD GO	ARRD3_RAT	Arrestin domain-containing protein 3 (Liver regeneration-related protein LRRG00048)	0.20	-	nuc	0					414
P50428 UniProt NPD GO	ARSA_MOUSE	Arylsulfatase A precursor (EC 3.1.6.8) (ASA) (Cerebroside-sulfatase)	0.20	-	exc	0	Lysosome	integral to membrane of membrane fraction [IDA] plasma membrane [IDA]			506
Q58D72 UniProt NPD GO	SPG3A_BOVIN	Atlastin (GTP-binding protein 3) (Guanine nucleotide-binding protein 3)	0.20	-	end	2					558
P05125 UniProt NPD GO	ANF_MOUSE	Atrial natriuretic factor precursor (ANF) (Atrial natriuretic peptide) (ANP) (Prepronatriodilatin) [ ...	0.20	-	exc	1 *	Secreted protein	cytoplasm [IDA]			152
Q6C4Y4 UniProt NPD GO	ATG16_YARLI	Autophagy protein 16	0.20	-	nuc	0	Vacuole (By similarity). Cytoplasmic vesicle (By similarity). Vesicular and vacuolar. Found in punct ...				94
Q5AEI2 UniProt NPD GO	ATG10_CANAL	Autophagy-related protein 10 (Autophagy-related E2-like-conjugating enzyme ATG10)	0.20	-	cyt	0	Cytoplasm (By similarity)				177
Q6FQJ2 UniProt NPD GO	ATG3_CANGA	Autophagy-related protein 3 (Autophagy-related E2-like conjugation enzyme ATG3)	0.20	-	mit	0	Cytoplasm (By similarity)				309
Q5ZKY2 UniProt NPD GO	ATG7_CHICK	Autophagy-related protein 7 (APG7-like) (Ubiquitin-activating enzyme E1-like protein)	0.20	-	nuc	0	Cytoplasm (Probable)				709
Q641Y5 UniProt NPD GO	ATG7_RAT	Autophagy-related protein 7 (APG7-like) (Ubiquitin-activating enzyme E1-like protein)	0.20	-	nuc	0	Cytoplasm (Probable)				698
Q9C966 UniProt NPD GO	IAA15_ARATH	Auxin-responsive protein IAA15 (Indoleacetic acid-induced protein 15)	0.20	-	cyt	0	Nucleus (By similarity)				179
Q75GB1 UniProt NPD GO	IAA17_ORYSA	Auxin-responsive protein IAA17 (Indoleacetic acid-induced protein 17)	0.20	-	nuc	0	Nucleus (By similarity)				257
Q6AT33 UniProt NPD GO	IAA19_ORYSA	Auxin-responsive protein IAA19 (Indoleacetic acid-induced protein 19)	0.20	-	nuc	0	Nucleus (By similarity)				281
Q38826 UniProt NPD GO	IAA8_ARATH	Auxin-responsive protein IAA8 (Indoleacetic acid-induced protein 8)	0.20	-	nuc	0	Nucleus (By similarity)				321
Q09095 UniProt NPD GO	AVEA_AVESA	Avenin-A (Gamma-4 avenin) (Prolamin) (Celiac immunoreactive protein 1) (CIP-1) (Fragment)	0.20	-	nuc	0	Protein body (By similarity). Protein bodies inside vacuoles (By similarity)				36
O35152 UniProt NPD GO	BET1L_RAT	BET1-like protein (Vesicle transport protein GOS15) (Golgi SNARE with a size of 15 kDa) (GS15) (GOS- ...	0.20	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type IV membrane protein	Golgi membrane [IDA] integral to Golgi membrane [IDA]			111
Q8WZ55 UniProt NPD GO	BSND_HUMAN	Barttin	0.20	-	mit	2 *	Cell membrane; multi-pass membrane protein (By similarity). Cytoplasm (By similarity). A significant ...	basolateral plasma membrane [ISS] integral to plasma membrane [ISS] protein complex [ISS]	606412		320

You are viewing entries 50351 to 50400 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.