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
P21570 UniProt NPD GO	ANG1_MOUSE	Angiogenin-1 precursor (EC 3.1.27.-) (Ribonuclease 5) (RNase 5)	0.33	-	exc	1 *	Secreted protein	basal lamina [ISS] extracellular space [ISS] nucleolus [ISS] nucleus [ISS]		2BWL	145
Q56H28 UniProt NPD GO	ACE2_FELCA	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.33	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				805
Q56NL1 UniProt NPD GO	ACE2_PAGLA	Angiotensin-converting enzyme 2 precursor (EC 3.4.17.-) (ACE-related carboxypeptidase)	0.33	-	end	1	Cell membrane; single-pass type I membrane protein (By similarity). Processed form: Secreted protein ...				805
Q8WXJ9 UniProt NPD GO	ASB17_HUMAN	Ankyrin repeat and SOCS box protein 17 (ASB-17)	0.33	-	mit	0					295
Q8WWH4 UniProt NPD GO	ASZ1_HUMAN	Ankyrin repeat, SAM and basic leucine zipper domain-containing protein 1 (Germ cell-specific ankyrin ...	0.33	-	nuc	0	Cytoplasm (By similarity)	cytoplasm [ISS]			475
P79134 UniProt NPD GO	ANXA6_BOVIN	Annexin A6 (Annexin VI) (Lipocortin VI) (P68) (P70) (Protein III) (Chromobindin-20) (67 kDa calelect ...	0.33	-	cyt	0	Stress fibers (By similarity)			1AVC	618
Q92125 UniProt NPD GO	ANXA7_XENLA	Annexin A7 (Annexin VII) (Synexin)	0.33	-	nuc	0					512
P00899 UniProt NPD GO	TRPE_YEAST	Anthranilate synthase component 1 (EC 4.1.3.27) (Anthranilate synthase component I)	0.33	-	cyt	0		anthranilate synthase complex [IPI] cytoplasm [IDA]			506
P35581 UniProt NPD GO	APD22_APIME	Apidaecins type 22 precursor [Contains: Apidaecin-1B (Apidaecin IB); Apidaecin-1A (Apidaecin IA)]	0.33	-	nuc	1 *	Secreted protein				144
P68292 UniProt NPD GO	APOA1_MACFA	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.33	-	exc	0	Secreted protein				267
P68293 UniProt NPD GO	APOA1_PAPHA	Apolipoprotein A-I precursor (Apo-AI) (ApoA-I)	0.33	-	exc	0	Secreted protein				267
O46409 UniProt NPD GO	APOA4_PIG	Apolipoprotein A-IV precursor (Apo-AIV) (ApoA-IV)	0.33	-	exc	0	Secreted protein				382
P48999 UniProt NPD GO	LOX5_MOUSE	Arachidonate 5-lipoxygenase (EC 1.13.11.34) (5-lipoxygenase) (5-LO)	0.33	-	cyt	0	Cytoplasm	cytoplasm [IDA] nucleus [IDA]			673
Q43629 UniProt NPD GO	ARC4_PHAVU	Arcelin-4 precursor	0.33	-	exc	0					266
Q95V58 UniProt NPD GO	KARG_ARTSF	Arginine kinase (EC 2.7.3.3) (AK)	0.33	-	cyt	0					356
P33110 UniProt NPD GO	ARLY_ANSAN	Argininosuccinate lyase (EC 4.3.2.1) (Arginosuccinase) (ASAL) (Delta crystallin)	0.33	-	nuc	0				1XWO	466
Q9H6L4 UniProt NPD GO	ARMC7_HUMAN	Armadillo repeat-containing protein 7	0.33	-	nuc	0					198
Q9QZH8 UniProt NPD GO	AAAD_RAT	Arylacetamide deacetylase (EC 3.1.1.-) (AADAC)	0.33	-	mit	2 *	Endoplasmic reticulum; endoplasmic reticulum membrane; single-pass type II membrane protein (By simi ...	endoplasmic reticulum membrane [ISS] microsome [ISS]			397
P50296 UniProt NPD GO	ARY3_MOUSE	Arylamine N-acetyltransferase 3 (EC 2.3.1.5) (Arylamide acetylase 3) (N-acetyltransferase type 3) (N ...	0.33	-	cyt	0	Cytoplasm	plasma membrane [IDA]			290
P53379 UniProt NPD GO	MKC7_YEAST	Aspartic proteinase MKC7 precursor (EC 3.4.23.41) (Yapsin-2)	0.33	-	nuc	0	Cell membrane; lipid-anchor; GPI-anchor	cell wall (sensu Fungi) [IDA]			596
Q5B2Q6 UniProt NPD GO	ATG5_EMENI	Autophagy protein 5	0.33	-	nuc	0	Cytoplasm (By similarity). Membrane; peripheral membrane protein (By similarity)				482
Q6FM63 UniProt NPD GO	ATG18_CANGA	Autophagy-related protein 18	0.33	-	nuc	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				505
Q9HDZ7 UniProt NPD GO	ATG18_SCHPO	Autophagy-related protein 18	0.33	-	mit	0	Membrane-associated. Peripheral membrane protein of pre-autophagosomal structure (PAS) and vacuole ( ...				373
Q9XFM0 UniProt NPD GO	IAA28_ARATH	Auxin-responsive protein IAA28 (Indoleacetic acid-induced protein 28)	0.33	-	nuc	0	Nucleus (By similarity)				175
P33078 UniProt NPD GO	IAA5_ARATH	Auxin-responsive protein IAA5 (Indoleacetic acid-induced protein 5) (Auxin-induced protein AUX2-27)	0.33	-	nuc	0	Nucleus (By similarity)				163
Q8GW46 UniProt NPD GO	YAB5_ARATH	Axial regulator YABBY5	0.33	-	nuc	0	Nucleus (By similarity)				164
P55957 UniProt NPD GO	BID_HUMAN	BH3-interacting domain death agonist (BID) (p22 BID) [Contains: BH3-interacting domain death agonist ...	0.33	-	nuc	0	Cytoplasm. When uncleaved, it is predominantly cytoplasmic. Mitochodrion; mitochondrial membrane. p1 ...	cytosol [TAS] membrane fraction [TAS] mitochondrion [TAS]	601997	2BID	195
P13752 UniProt NPD GO	HA1A_BOVIN	BOLA class I histocompatibility antigen, alpha chain BL3-6 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein				360
Q8R4G8 UniProt NPD GO	KCTD1_RAT	BTB/POZ domain-containing protein KCTD1 (Vitamin A-deficient testicular protein 6)	0.33	-	mit	0					257
Q63073 UniProt NPD GO	BTG1_RAT	BTG1 protein (Anti-proliferative factor)	0.33	-	nuc	0		cytoplasm [ISS] nucleus [ISS]			171
Q8VIM4 UniProt NPD GO	BSND_MOUSE	Barttin	0.33	-	exc	2 *	Cell membrane; basolateral cell membrane; multi-pass membrane protein. Staining in membranes of the ...	basolateral plasma membrane [IDA] integral to plasma membrane [IDA] protein complex [IDA]			307
Q05538 UniProt NPD GO	CHIC_LYCES	Basic 30 kDa endochitinase precursor (EC 3.2.1.14)	0.33	-	exc	0	Vacuole. Cell wall. Vacuolar, protoplast and cell wall				322
Q8K589 UniProt NPD GO	BMF_RAT	Bcl-2-modifying factor	0.33	-	nuc	0					185
Q58D91 UniProt NPD GO	BINCA_BOVIN	Bcl10-interacting CARD protein (BinCARD)	0.33	-	nuc	0	Nucleus (By similarity). Co-expression with BCL10 induced translocation from nucleus to cytosol (By ...				183
Q91318 UniProt NPD GO	CRBB2_RANCA	Beta crystallin B2 (Beta-crystallin Bp)	0.33	-	nuc	0					204
Q30KQ8 UniProt NPD GO	DB112_HUMAN	Beta-defensin 112 precursor (Defensin, beta 112) (Beta-defensin 12) (DEFB-12)	0.33	-	nuc	0	Secreted protein (By similarity)				113
Q30KK0 UniProt NPD GO	DB129_PANTR	Beta-defensin 129 precursor (Defensin, beta 129)	0.33	-	nuc	0	Secreted protein (Potential)				183
Q9H1M3 UniProt NPD GO	DB129_HUMAN	Beta-defensin 129 precursor (Defensin, beta 129) (Beta-defensin 29) (DEFB-29)	0.33	-	nuc	0	Secreted protein (Potential)				183
P82683 UniProt NPD GO	MLA3_VISAL	Beta-galactoside-specific lectin III A chain, isoform 1 (EC 3.2.2.22) (MLA-3A, isoform 1) (ML-III A, ...	0.33	-	mit	0					254
Q9ES46 UniProt NPD GO	PARVB_MOUSE	Beta-parvin	0.33	-	mit	0	Cell membrane; cell-matrix junction; focal adhesion; cytoplasmic side (By similarity). Constituent o ...				365
Q05928 UniProt NPD GO	BTC_MOUSE	Betacellulin precursor (BTC)	0.33	+	end	2 *	Precursor form: Cell membrane; single-pass type I membrane protein. Mature form: Secreted protein; e ...				177
O88428 UniProt NPD GO	PAPS2_MOUSE	Bifunctional 3'-phosphoadenosine 5'-phosphosulfate synthetase 2 (PAPS synthetase 2) (PAPSS 2) (Sulfu ...	0.33	-	cyt	0		intracellular [ISS]			621
Q8CGC7 UniProt NPD GO	SYEP_MOUSE	Bifunctional aminoacyl-tRNA synthetase [Includes: Glutamyl-tRNA synthetase (EC 6.1.1.17) (Glutamate- ...	0.33	-	cyt	0					1512
Q9V3L1 UniProt NPD GO	NDST_DROME	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase (EC 2.8.2.8) (Glucosaminyl N-deacetyla ...	0.33	-	mit	1	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				1048
O97583 UniProt NPD GO	NDST2_BOVIN	Bifunctional heparan sulfate N-deacetylase/N-sulfotransferase 2 (EC 2.8.2.8) (Glucosaminyl N-deacety ...	0.33	-	mit	1 *	Golgi apparatus; Golgi membrane; single-pass type II membrane protein (By similarity)				884
P31936 UniProt NPD GO	SIAL_PIG	Bone sialoprotein-2 (Bone sialoprotein II) (BSP II) (Cell-binding sialoprotein) (Integrin-binding si ...	0.33	-	nuc	0	Secreted protein				300
P25431 UniProt NPD GO	BDNF_VIPLE	Brain-derived neurotrophic factor (BDNF) (Fragment)	0.33	-	nuc	0	Secreted protein				43
Q96KV6 UniProt NPD GO	BT2A3_HUMAN	Butyrophilin subfamily 2 member A3 precursor	0.33	-	end	2 *	Membrane; single-pass type I membrane protein (By similarity)				567
Q7TST0 UniProt NPD GO	BTNL1_MOUSE	Butyrophilin-like protein 1 precursor	0.33	-	end	1	Membrane; single-pass type I membrane protein (By similarity)				341
Q92478 UniProt NPD GO	CLC2B_HUMAN	C-type lectin domain family 2 member B (C-type lectin superfamily member 2) (Activation-induced C-ty ...	0.33	-	mit	1 *	Membrane; single-pass type II membrane protein (Probable)	integral to plasma membrane [TAS]	603242		149

You are viewing entries 37351 to 37400 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.